From 91ef58b64bc6956bb371de4dd32f336683bfb214 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 12 Mar 2019 18:13:14 +0100 Subject: [PATCH 001/282] This fixes #492 --- .../java/com/milaboratory/mixcr/cli/CommandAnalyze.java | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index ca2b1187c..254eec27a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -682,6 +682,13 @@ public CommandAmplicon() { private _5EndPrimers vPrimers; + @Option(names = "--extend-alignments", + description = "Extend alignments", + required = false) + public void setDoExtendAlignments(boolean ignore) { + doNotExtendAlignments = false; + } + @Option(names = "--5-end", completionCandidates = _5EndCandidates.class, description = "5'-end of the library. @|bold Possible values: ${COMPLETION-CANDIDATES}|@", From f6a61fe0d0d4cd3c90445e440c946a07b4e4a904 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 13 Mar 2019 11:51:00 +0100 Subject: [PATCH 002/282] This fixes #489 --- .../com/milaboratory/mixcr/cli/CommandAnalyze.java | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index 254eec27a..1dfd6d131 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -451,6 +451,9 @@ public final CommandExtend mkExtend(String input, String output) { return inheritOptionsAndValidate(ap); } + @Option(names = "--no-clna", description = "Use clns (moore compact) for storing clones. This option is not compatible with --contig-assembly.") + public boolean noClna = false; + @Option(names = "--assemble", description = "Additional parameters for assemble step specified with double quotes (e.g --assemble \"-OassemblingFeatures=[V5UTR+L1+L2+FR1,FR3+CDR3]\" --assemble \"-ObadQualityThreshold=0\" etc.", arity = "1") @@ -469,8 +472,10 @@ CommandAssemble mkAssemble(String input, String output) { assembleParameters.add("--report"); assembleParameters.add(getReport()); - // we always write clna - assembleParameters.add("--write-alignments"); + if (!noClna) + assembleParameters.add("--write-alignments"); + else if (contigAssembly) + throw new RuntimeException("--no-clna is not compatible with --contig-assembly"); // pipeline specific parameters assembleParameters.addAll(this.pipelineSpecificAssembleParameters()); @@ -602,7 +607,10 @@ public String fNameForExtenedAlignments() { } public String fNameForClones() { - return outputNamePattern() + ".clna"; + if (noClna) + return outputNamePattern() + ".clns"; + else + return outputNamePattern() + ".clna"; } public String fNameForContigs() { From b6983b35bc1bc88bc6ed7e11f6e72d4b4192ed10 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Mon, 8 Apr 2019 17:15:30 +0300 Subject: [PATCH 003/282] --parameters -> --preset This fixes #409 --- src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java | 2 +- src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 8c637b39c..1e0328258 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -136,7 +136,7 @@ public void setLimit(int limit) { } @Option(description = "Parameters preset.", - names = {"-p", "--parameters"}) + names = {"-p", "--preset"}) public String alignerParametersName = "default"; @Option(names = {"-O"}, description = "Overrides default aligner parameter values") diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 4afecbaa4..6c7f69cb0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -57,8 +57,8 @@ public class CommandAssemble extends ACommandWithSmartOverwriteWithSingleInputMiXCR { static final String ASSEMBLE_COMMAND_NAME = "assemble"; - @Option(description = "Clone assembling parameters", - names = {"-p", "--parameters"}) + @Option(description = "Clone assembling parameters preset.", + names = {"-p", "--preset"}) public String assemblerParametersName = "default"; public int threads = Runtime.getRuntime().availableProcessors(); From db4488b8cc481f1758f2aa391df75f935066b22c Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 11 Apr 2019 19:57:50 +0300 Subject: [PATCH 004/282] Basic tags implementation. --- .../mixcr/assembler/CloneAccumulator.java | 5 ++ .../mixcr/assembler/CloneFactory.java | 6 +- .../assembler/fullseq/FullSeqAssembler.java | 12 ++-- .../milaboratory/mixcr/basictypes/Clone.java | 8 +-- .../com/milaboratory/mixcr/basictypes/IO.java | 45 ++++++++++++++- .../mixcr/basictypes/TagCounter.java | 40 +++++++++++++ .../mixcr/basictypes/TagCounterBuilder.java | 57 +++++++++++++++++++ .../mixcr/basictypes/TagTuple.java | 30 ++++++++++ .../mixcr/basictypes/VDJCAlignments.java | 33 +++++++---- .../mixcr/basictypes/VDJCObject.java | 10 +++- .../milaboratory/mixcr/cli/CommandAlign.java | 12 +++- .../PartialAlignmentsAssemblerAligner.java | 4 +- .../mixcr/partialassembler/TargetMerger.java | 2 + .../mixcr/util/VDJCObjectExtender.java | 3 +- .../mixcr/vdjaligners/VDJCAlignerPVFirst.java | 7 +-- .../mixcr/vdjaligners/VDJCAlignerS.java | 3 +- 16 files changed, 243 insertions(+), 34 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index 7d42607c1..57f4ea3a1 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -37,6 +37,7 @@ import com.milaboratory.core.sequence.quality.QualityAggregationType; import com.milaboratory.core.sequence.quality.QualityAggregator; import com.milaboratory.mixcr.basictypes.ClonalSequence; +import com.milaboratory.mixcr.basictypes.TagCounterBuilder; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import gnu.trove.iterator.TObjectFloatIterator; @@ -53,6 +54,7 @@ public final class CloneAccumulator { private long coreCount = 0, mappedCount = 0, initialCoreCount = -1; private volatile int cloneIndex = -1; final Range[] nRegions; + final TagCounterBuilder tagBuilder = new TagCounterBuilder(); public CloneAccumulator(ClonalSequence sequence, Range[] nRegions, QualityAggregationType qualityAggregationType) { this.sequence = sequence; @@ -177,12 +179,15 @@ public void calculateScores(CloneFactoryParameters parameters) { public void mergeCounts(CloneAccumulator acc) { coreCount += acc.coreCount; mappedCount += acc.mappedCount; + tagBuilder.add(acc.tagBuilder); } public synchronized void accumulate(ClonalSequence data, VDJCAlignments alignment, boolean mapped) { if (!mapped) { // Core sequence accumulation coreCount += alignment.getNumberOfReads(); + tagBuilder.add(alignment.getTagCounter()); + // Accumulate information about V-D-J alignments only for strictly clustered reads // (only for core clonotypes members) float score; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index f7b8c5645..bbe7d8f93 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -34,6 +34,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.vdjaligners.SingleDAligner; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; @@ -83,6 +84,7 @@ public CloneFactory(CloneFactoryParameters parameters, GeneFeature[] assemblingF public Clone create(int id, double count, EnumMap> geneScores, + TagCounter tagCounter, NSequenceWithQuality[] targets) { EnumMap hits = new EnumMap<>(GeneType.class); for (GeneType geneType : GeneType.VJC_REFERENCE) { @@ -247,11 +249,11 @@ public Clone create(int id, double count, else hits.put(GeneType.Diversity, new VDJCHit[0]); - return new Clone(targets, hits, count, id); + return new Clone(targets, hits, tagCounter, count, id); } public Clone create(int id, CloneAccumulator accumulator) { - return create(id, accumulator.getCount(), accumulator.geneScores, accumulator.getSequence().sequences); + return create(id, accumulator.getCount(), accumulator.geneScores, accumulator.tagBuilder.createAndDestroy(), accumulator.getSequence().sequences); } private static boolean containsD(GeneFeature feature) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 16c416e11..3053af0c7 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -64,6 +64,7 @@ import static io.repseq.core.GeneType.Variable; /** + * */ public final class FullSeqAssembler { private static int ABSENT_PACKED_VARIANT_INFO = -1; @@ -749,7 +750,11 @@ else if (floatingRightBound) NSequenceWithQuality assemblingFeatureSeq = targets.sequences[targets.assemblingFeatureTargetId] .getRange(targets.assemblingFeatureOffset, targets.assemblingFeatureOffset + targets.assemblingFeatureLength); - Clone clone = cloneFactory.create(0, count, geneScores, new NSequenceWithQuality[]{assemblingFeatureSeq}); + + if (this.clone.getCount() != count && !this.clone.getTagCounter().isEmpty()) + throw new IllegalArgumentException("tagged data is not allowed in combination with non-null subCloningRegion"); // assert + + Clone clone = cloneFactory.create(0, count, geneScores, this.clone.getTagCounter(), new NSequenceWithQuality[]{assemblingFeatureSeq}); vTopHitAlignments[targets.assemblingFeatureTargetId] = mergeTwoAlignments( @@ -772,8 +777,7 @@ else if (floatingRightBound) tmp[0] = substituteAlignments(tmp[0], vTopHitAlignments); tmp = hits.get(Joining); tmp[0] = substituteAlignments(tmp[0], jTopHitAlignments); - - return new Clone(targets.sequences, hits, count, 0); + return new Clone(targets.sequences, hits, this.clone.getTagCounter(), count, 0); } static final class AlignersCache { @@ -1518,6 +1522,6 @@ else if (right == -1) } private boolean inSplitRegion(int p) { - return splitRegion == null || splitRegion.contains(p); + return splitRegion != null && splitRegion.contains(p); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index fa3d37ea8..451f5b33e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -42,21 +42,21 @@ public final class Clone extends VDJCObject { final int id; CloneSet parent = null; - public Clone(NSequenceWithQuality[] targets, EnumMap hits, double count, int id) { - super(hits, targets); + public Clone(NSequenceWithQuality[] targets, EnumMap hits, TagCounter tagCounter, double count, int id) { + super(hits, tagCounter, targets); this.count = count; this.id = id; } public Clone setId(int id) { - Clone r = new Clone(targets, hits, count, id); + Clone r = new Clone(targets, hits, tagCounter, count, id); r.setParentCloneSet(parent); return r; } /** Returns new instance with parent clone set set to null */ public Clone resetParentCloneSet() { - return new Clone(targets, hits, count, id); + return new Clone(targets, hits, tagCounter, count, id); } public void setParentCloneSet(CloneSet set) { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index 59225267d..e6cf2ae50 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -37,6 +37,9 @@ import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.Serializer; +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.map.hash.TObjectDoubleHashMap; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; @@ -79,12 +82,47 @@ public boolean handlesReference() { } } + public static class TagCounterSerializer implements Serializer { + @Override + public void write(PrimitivO output, TagCounter object) { + output.writeInt(object.tags.size()); + TObjectDoubleIterator it = object.tags.iterator(); + while (it.hasNext()) { + output.writeObject(it.key().tags); + output.writeDouble(it.value()); + } + } + + @Override + public TagCounter read(PrimitivI input) { + int len = input.readInt(); + TObjectDoubleHashMap r = new TObjectDoubleHashMap<>(len, Constants.DEFAULT_LOAD_FACTOR, 0.0); + for (int i = 0; i < len; ++i) { + String[] tags = input.readObject(String[].class); + double count = input.readDouble(); + r.put(new TagTuple(tags), count); + } + return new TagCounter(r); + } + + @Override + public boolean isReference() { + return true; + } + + @Override + public boolean handlesReference() { + return false; + } + } + public static class VDJCAlignmentsSerializer implements Serializer { @Override public void write(PrimitivO output, VDJCAlignments object) { output.writeObject(object.targets); output.writeObject(object.originalReads); output.writeObject(object.history); + output.writeObject(object.tagCounter); output.writeByte(object.hits.size()); for (Map.Entry entry : object.hits.entrySet()) { output.writeObject(entry.getKey()); @@ -100,6 +138,7 @@ public VDJCAlignments read(PrimitivI input) { NSequenceWithQuality[] targets = input.readObject(NSequenceWithQuality[].class); SequenceRead[] originalReads = input.readObject(SequenceRead[].class); SequenceHistory[] history = input.readObject(SequenceHistory[].class); + TagCounter tagCounter = input.readObject(TagCounter.class); int size = input.readByte(); EnumMap hits = new EnumMap<>(GeneType.class); for (int i = 0; i < size; i++) { @@ -112,7 +151,7 @@ public VDJCAlignments read(PrimitivI input) { int cloneIndex = -1; if (!ReadToCloneMapping.isDropped(mappingType)) cloneIndex = input.readVarInt(); - return new VDJCAlignments(hits, targets, history, originalReads, mappingType, cloneIndex); + return new VDJCAlignments(hits, tagCounter, targets, history, originalReads, mappingType, cloneIndex); } @Override @@ -130,6 +169,7 @@ public static class CloneSerializer implements Serializer { @Override public void write(PrimitivO output, Clone object) { output.writeObject(object.targets); + output.writeObject(object.tagCounter); output.writeByte(object.hits.size()); for (Map.Entry entry : object.hits.entrySet()) { output.writeObject(entry.getKey()); @@ -142,6 +182,7 @@ public void write(PrimitivO output, Clone object) { @Override public Clone read(PrimitivI input) { NSequenceWithQuality[] targets = input.readObject(NSequenceWithQuality[].class); + TagCounter tagCounter = input.readObject(TagCounter.class); int size = input.readByte(); EnumMap hits = new EnumMap<>(GeneType.class); for (int i = 0; i < size; i++) { @@ -150,7 +191,7 @@ public Clone read(PrimitivI input) { } double count = input.readDouble(); int id = input.readInt(); - return new Clone(targets, hits, count, id); + return new Clone(targets, hits, tagCounter, count, id); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java new file mode 100644 index 000000000..64719c609 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java @@ -0,0 +1,40 @@ +package com.milaboratory.mixcr.basictypes; + +import com.milaboratory.primitivio.annotations.Serializable; +import gnu.trove.map.hash.TObjectDoubleHashMap; + +/** + * + */ +@Serializable(by = IO.TagCounterSerializer.class) +public final class TagCounter { + public static final TagCounter EMPTY = new TagCounter(new TObjectDoubleHashMap<>()); + + final TObjectDoubleHashMap tags; + + TagCounter(TObjectDoubleHashMap tags) { + this.tags = tags; + } + + public TagCounter(TagTuple tags) { + this.tags = new TObjectDoubleHashMap<>(); + this.tags.put(tags, 1.0); + } + + public boolean isEmpty() { + return this.equals(EMPTY); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagCounter that = (TagCounter) o; + return tags.equals(that.tags); + } + + @Override + public int hashCode() { + return tags.hashCode(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java new file mode 100644 index 000000000..4854c6a7e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java @@ -0,0 +1,57 @@ +package com.milaboratory.mixcr.basictypes; + +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.map.hash.TObjectDoubleHashMap; + +/** + * + */ +public class TagCounterBuilder { + private final TObjectDoubleHashMap agg; + private boolean destroyed = false; + + public TagCounterBuilder() { + this.agg = new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, 0.0); + } + + public TagCounterBuilder add(TagCounter tc) { + return add(tc.tags); + } + + public TagCounterBuilder add(TagCounterBuilder tc) { + return add(tc.agg); + } + + public TagCounterBuilder add(TObjectDoubleHashMap tc) { + if (destroyed) + throw new IllegalStateException("destroyed"); + + if (agg.isEmpty()) { + agg.putAll(tc); + return this; + } + + TObjectDoubleIterator it = tc.iterator(); + while (it.hasNext()) { + TagTuple k = it.key(); + double v = agg.get(k); // 0.0 for no entry value, see constructor + agg.put(k, v + it.value()); + } + + return this; + } + + public TagCounter createAndDestroy() { + if (destroyed) + throw new IllegalStateException("destroyed"); + + TagCounter r = new TagCounter(new TObjectDoubleHashMap<>(agg)); + destroyed = true; + return r; + } + + public static TagCounter merge(TagCounter a, TagCounter b) { + return new TagCounterBuilder().add(a).add(b).createAndDestroy(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java new file mode 100644 index 000000000..68f8e8cdc --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java @@ -0,0 +1,30 @@ +package com.milaboratory.mixcr.basictypes; + +import java.util.Arrays; + +/** + * + */ +public final class TagTuple { + public static final TagTuple EMPTY = new TagTuple(new String[0]); + public final String[] tags; + private transient final int hash; + + public TagTuple(String[] tags) { + this.tags = tags; + this.hash = Arrays.hashCode(tags); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagTuple tagTuple = (TagTuple) o; + return hash == tagTuple.hash && Arrays.equals(tags, tagTuple.tags); + } + + @Override + public int hashCode() { + return hash; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 4583500f5..c75fd4980 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -56,11 +56,12 @@ public final class VDJCAlignments extends VDJCObject { public VDJCAlignments(long alignmentsIndex, EnumMap hits, + TagCounter tagCounter, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads, byte mappingType, int cloneIndex) { - super(hits, targets); + super(hits, tagCounter, targets); if (!ReadToCloneMapping.isCorrect(mappingType) || (ReadToCloneMapping.isDropped(mappingType) && cloneIndex != -1)) @@ -75,33 +76,37 @@ public VDJCAlignments(long alignmentsIndex, public VDJCAlignments(long alignmentsIndex, EnumMap hits, + TagCounter tagCounter, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads) { - this(alignmentsIndex, hits, targets, history, originalReads, + this(alignmentsIndex, hits, tagCounter, targets, history, originalReads, ReadToCloneMapping.DROPPED_MASK, -1); } public VDJCAlignments(EnumMap hits, + TagCounter tagCounter, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads, byte mappingType, int cloneIndex) { - this(-1, hits, targets, history, originalReads, mappingType, cloneIndex); + this(-1, hits, tagCounter, targets, history, originalReads, mappingType, cloneIndex); } public VDJCAlignments(EnumMap hits, + TagCounter tagCounter, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads) { - this(-1, hits, targets, history, originalReads); + this(-1, hits, tagCounter, targets, history, originalReads); } public VDJCAlignments(VDJCHit[] vHits, VDJCHit[] dHits, VDJCHit[] jHits, VDJCHit[] cHits, + TagCounter tagCounter, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads) { - this(-1, createHits(vHits, dHits, jHits, cHits), targets, history, originalReads); + this(-1, createHits(vHits, dHits, jHits, cHits), tagCounter, targets, history, originalReads); } public boolean isClustered() { @@ -132,24 +137,28 @@ public int getCloneIndex() { return cloneIndex; } + public VDJCAlignments setTagCounter(TagCounter tc) { + return new VDJCAlignments(alignmentsIndex, hits, tc, targets, history, originalReads, mappingType, cloneIndex); + } + public VDJCAlignments setMapping(ReadToCloneMapping mapping) { - return new VDJCAlignments(alignmentsIndex, hits, targets, history, originalReads, + return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads, mapping.getMappingTypeByte(), mapping.getCloneIndex()); } public VDJCAlignments updateCloneIndex(int newCloneIndex) { - return new VDJCAlignments(alignmentsIndex, hits, targets, history, originalReads, + return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads, mappingType, newCloneIndex); } public VDJCAlignments updateAlignments(Function, Alignment> processor) { EnumMap newHits = this.hits.clone(); newHits.replaceAll((k, v) -> Arrays.stream(v).map(h -> h.updateAlignments(processor)).toArray(VDJCHit[]::new)); - return new VDJCAlignments(alignmentsIndex, newHits, targets, history, originalReads, mappingType, cloneIndex); + return new VDJCAlignments(alignmentsIndex, newHits, tagCounter, targets, history, originalReads, mappingType, cloneIndex); } public VDJCAlignments shiftReadId(long newAlignmentIndex, long shift) { - return new VDJCAlignments(newAlignmentIndex, hits, targets, shift(history, shift), shift(originalReads, shift)); + return new VDJCAlignments(newAlignmentIndex, hits, tagCounter, targets, shift(history, shift), shift(originalReads, shift)); } public static SequenceRead[] mergeOriginalReads(VDJCAlignments... array) { @@ -230,7 +239,7 @@ public int getNumberOfReads() { } public VDJCAlignments setHistory(SequenceHistory[] history, SequenceRead[] originalReads) { - return new VDJCAlignments(alignmentsIndex, hits, targets, history, originalReads); + return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads); } public VDJCAlignments removeBestHitAlignment(GeneType geneType, int targetId) { @@ -243,7 +252,7 @@ public VDJCAlignments removeBestHitAlignment(GeneType geneType, int targetId) { gHits[0] = new VDJCHit(gHits[0].getGene(), als, gHits[0].getAlignedFeature()); Arrays.sort(gHits); hits.put(geneType, gHits); - return new VDJCAlignments(alignmentsIndex, hits, targets, history, originalReads); + return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads); } public boolean hasNoHitsInTarget(int i) { @@ -283,7 +292,7 @@ public VDJCAlignments setAlignmentsIndex(long alignmentsIndex) { * * @param top numer of top hits to test * @return {@code true} if at least one V and one J hit among first {@code top} hits have same chain and false - * otherwise (first {@code top} V hits have different chain from those have first {@code top} J hits) + * otherwise (first {@code top} V hits have different chain from those have first {@code top} J hits) */ public final boolean hasSameVJLoci(final int top) { final VDJCHit[] vHits = hits.get(GeneType.Variable), diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 1e6b0dce8..6c81b76b3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -44,16 +44,22 @@ public class VDJCObject { protected final EnumMap hits; protected volatile EnumMap allChains; protected VDJCPartitionedSequence[] partitionedTargets; + protected final TagCounter tagCounter; - public VDJCObject(EnumMap hits, NSequenceWithQuality... targets) { + public VDJCObject(EnumMap hits, TagCounter tagCounter, NSequenceWithQuality... targets) { this.targets = targets; this.hits = hits; + this.tagCounter = tagCounter; // Sorting hits for (VDJCHit[] h : hits.values()) Arrays.sort(h); } + public TagCounter getTagCounter() { + return tagCounter; + } + protected static EnumMap createHits(VDJCHit[] vHits, VDJCHit[] dHits, VDJCHit[] jHits, VDJCHit[] cHits) { EnumMap hits = new EnumMap(GeneType.class); @@ -725,6 +731,7 @@ public boolean equals(Object o) { return false; } + if (!tagCounter.equals(that.tagCounter)) return false; if (!Arrays.equals(targets, that.targets)) return false; return true; @@ -734,6 +741,7 @@ public boolean equals(Object o) { public int hashCode() { int result = Arrays.hashCode(targets); result = 31 * result + hits.hashCode(); + result = 29 * result + tagCounter.hashCode(); return result; } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 1e0328258..870dadf64 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -37,7 +37,10 @@ import cc.redberry.pipe.util.CountLimitingOutputPort; import cc.redberry.pipe.util.OrderedOutputPort; import cc.redberry.pipe.util.StatusReporter; -import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.core.PairedEndReadsLayout; @@ -345,6 +348,10 @@ public void validate() { /** Alignment report */ public final AlignerReport report = new AlignerReport(); + public TagTuple tags(SequenceRead r) { + return TagTuple.EMPTY; + } + @Override @SuppressWarnings("unchecked") public void run1() throws Exception { @@ -515,6 +522,7 @@ public String getStatus() { { Target target = readsLayout.createTargets(read)[0]; alignment = new VDJCAlignments(emptyHits, + TagCounter.EMPTY, target.targets, SequenceHistory.RawSequence.of(read.getId(), target), alignerParameters.isSaveOriginalReads() ? new SequenceRead[]{read} : null); @@ -525,6 +533,8 @@ public String getStatus() { } } + alignment = alignment.setTagCounter(new TagCounter(tags(read))); + if (alignment.isChimera()) report.onChimera(); diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java index 847844ca6..df2a4f99d 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java @@ -38,6 +38,7 @@ import com.milaboratory.core.alignment.kaligner2.KAlignerParameters2; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.mixcr.basictypes.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerAbstract; @@ -77,7 +78,7 @@ public PartialAlignmentsAssemblerAligner(VDJCAlignerParameters parameters) { } @Override - @SuppressWarnings("unchecked") + @SuppressWarnings({"unchecked", "Duplicates"}) protected VDJCAlignmentResult process0(VDJCMultiRead input) { final int nReads = input.numberOfReads(); EnumMap vdjcHits = new EnumMap<>(GeneType.class); @@ -308,6 +309,7 @@ protected VDJCAlignmentResult process0(VDJCMultiRead input) { dResult, jResult, cutRelativeScore(vdjcHits.get(GeneType.Constant), parameters.getCAlignerParameters().getRelativeMinScore(), parameters.getMaxHits()), + TagCounter.EMPTY, targets, input.getHistory(), input.getOriginalReads() diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java index a25afd494..528e3562d 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java @@ -44,6 +44,7 @@ import com.milaboratory.core.sequence.SequencesUtils; import com.milaboratory.mixcr.basictypes.SequenceHistory; import com.milaboratory.mixcr.basictypes.SequenceHistory.OverlapType; +import com.milaboratory.mixcr.basictypes.TagCounterBuilder; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.vdjaligners.KGeneAlignmentParameters; @@ -111,6 +112,7 @@ public AlignedTarget merge(AlignedTarget targetLeft, AlignedTarget targetRight, VDJCAlignments alignments = new VDJCAlignments(result, + TagCounterBuilder.merge(targetLeft.getAlignments().getTagCounter(), targetRight.getAlignments().getTagCounter()), new NSequenceWithQuality[]{mergedTarget}, new SequenceHistory[]{ new SequenceHistory.Merge(overlapType, targetLeft.getHistory(), targetRight.getHistory(), offset, nMismatches) diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java index 5782b5e02..c8e068f3f 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java @@ -476,7 +476,7 @@ static Clone doTransformClone(Clone clone, VDJCObjectExtender.Extender transformer, EnumMap newHitsMap) { return new Clone(transformer.transform(clone.getTargets()), - newHitsMap, clone.getCount(), clone.getId()); + newHitsMap, clone.getTagCounter(), clone.getCount(), clone.getId()); } static VDJCAlignments doTransformAlignment(VDJCAlignments alignment, @@ -484,6 +484,7 @@ static VDJCAlignments doTransformAlignment(VDJCAlignments alignment, EnumMap newHitsMap) { return new VDJCAlignments( newHitsMap, + alignment.getTagCounter(), transformer.transform(alignment.getTargets()), transformer.transform(alignment.getHistory()), alignment.getOriginalReads() == null diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java index 3dc357ec7..43970bd66 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java @@ -44,10 +44,7 @@ import com.milaboratory.core.merger.MergerParameters; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.basictypes.HasGene; -import com.milaboratory.mixcr.basictypes.SequenceHistory; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.partialassembler.AlignedTarget; import com.milaboratory.mixcr.partialassembler.TargetMerger; import com.milaboratory.util.BitArray; @@ -701,7 +698,7 @@ VDJCAlignments createResult(long readId, VDJCAlignerPVFirst aligner, PairedRead VDJCHit[] vHits = convert(this.vHits, GeneType.Variable, aligner); VDJCHit[] jHits = convert(this.jHits, GeneType.Joining, aligner); - return new VDJCAlignments(vHits, dHits, jHits, cHits, target.targets, + return new VDJCAlignments(vHits, dHits, jHits, cHits, TagCounter.EMPTY, target.targets, SequenceHistory.RawSequence.of(readId, target), aligner.parameters.isSaveOriginalReads() ? new SequenceRead[]{originalRead} : null); } diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java index 313afc136..055e817a2 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java @@ -40,6 +40,7 @@ import com.milaboratory.core.io.sequence.SingleRead; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.SequenceHistory; +import com.milaboratory.mixcr.basictypes.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.util.BitArray; @@ -429,7 +430,7 @@ public VDJCAlignments toVDJCAlignments(long inputId, SequenceRead input) { if (cHits != null) hits.put(GeneType.Constant, cHits); - return new VDJCAlignments(hits, target.targets, + return new VDJCAlignments(hits, TagCounter.EMPTY, target.targets, new SequenceHistory[]{ new SequenceHistory.RawSequence(inputId, (byte) 0, target.getRCStateOfTarget(0), target.targets[0].size())}, parameters.isSaveOriginalReads() ? new SequenceRead[]{input} : null); From 243764e7fd9dc8a0e9bd6c0da2b8ed26b268f55e Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 11 Apr 2019 20:05:24 +0300 Subject: [PATCH 005/282] Drop backward compatibility --- .../mixcr/basictypes/ClnAReader.java | 6 ------ .../mixcr/basictypes/ClnAWriter.java | 5 ++--- .../mixcr/basictypes/ClnsReader.java | 3 --- .../mixcr/basictypes/ClnsWriter.java | 5 ++--- .../mixcr/basictypes/VDJCAlignmentsReader.java | 3 --- .../mixcr/basictypes/VDJCAlignmentsWriter.java | 5 ++--- .../mixcr/tests/BackwardCompatibilityTests.java | 12 ++++++------ .../backward_compatibility/3.0.3/test.clna | Bin 43846 -> 0 bytes .../backward_compatibility/3.0.3/test.clns | Bin 36423 -> 0 bytes .../backward_compatibility/3.0.3/test.vdjca | Bin 37615 -> 0 bytes .../backward_compatibility/3.0.4/test.clna | Bin 44097 -> 0 bytes .../backward_compatibility/3.0.4/test.clns | Bin 36674 -> 0 bytes .../backward_compatibility/3.0.4/test.vdjca | Bin 37757 -> 0 bytes 13 files changed, 12 insertions(+), 27 deletions(-) delete mode 100644 src/test/resources/backward_compatibility/3.0.3/test.clna delete mode 100644 src/test/resources/backward_compatibility/3.0.3/test.clns delete mode 100644 src/test/resources/backward_compatibility/3.0.3/test.vdjca delete mode 100644 src/test/resources/backward_compatibility/3.0.4/test.clna delete mode 100644 src/test/resources/backward_compatibility/3.0.4/test.clns delete mode 100644 src/test/resources/backward_compatibility/3.0.4/test.vdjca diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index 3eb0bf930..e0f7be9ac 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -142,9 +142,6 @@ public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int chunkSize) input = new PrimitivI(new InputDataStream(indexBegin, fSize - 8)); switch (magicString) { - case ClnAWriter.MAGIC_V3: - add_v3_0_3_CustomSerializers(input); - break; case ClnAWriter.MAGIC: break; default: @@ -167,9 +164,6 @@ public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int chunkSize) input = new PrimitivI(new InputDataStream(ClnAWriter.MAGIC_LENGTH + 4, firstClonePosition)); switch (magicString) { - case ClnAWriter.MAGIC_V3: - add_v3_0_3_CustomSerializers(input); - break; case ClnAWriter.MAGIC: break; default: diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index 31c7edb9e..945ac5c17 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -62,9 +62,8 @@ public final class ClnAWriter implements PipelineConfigurationWriter, AutoCloseable, CanReportProgressAndStage { - static final String MAGIC_V3 = "MiXCR.CLNA.V03"; - static final String MAGIC_V4 = "MiXCR.CLNA.V04"; - static final String MAGIC = MAGIC_V4; + static final String MAGIC_V5 = "MiXCR.CLNA.V05"; + static final String MAGIC = MAGIC_V5; static final int MAGIC_LENGTH = MAGIC.length(); //14 /** diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index 1f7e0b5c5..ac27f7e33 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -90,9 +90,6 @@ private synchronized void init() { // SerializersManager serializersManager = input.getSerializersManager(); switch (magicString) { - case MAGIC_V7: - add_v3_0_3_CustomSerializers(input); - break; case MAGIC: break; default: diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index 769cc607e..f90cd2c4d 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -50,9 +50,8 @@ public class ClnsWriter implements PipelineConfigurationWriter, CanReportProgressAndStage, Closeable { - static final String MAGIC_V7 = "MiXCR.CLNS.V07"; - static final String MAGIC_V8 = "MiXCR.CLNS.V08"; - static final String MAGIC = MAGIC_V8; + static final String MAGIC_V9 = "MiXCR.CLNS.V09"; + static final String MAGIC = MAGIC_V9; static final int MAGIC_LENGTH = 14; static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index 519b2e8d9..d900c7015 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -137,9 +137,6 @@ void init(Map geneFeatureRefs) { // SerializersManager serializersManager = input.getSerializersManager(); switch (magicString) { - case MAGIC_V13: - add_v3_0_3_CustomSerializers(input); - break; case MAGIC: break; default: diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java index 34ddb2798..acefe6ff0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java @@ -50,9 +50,8 @@ public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI { public static final int DEFAULT_ENCODER_THREADS = 3; - static final String MAGIC_V13 = "MiXCR.VDJC.V13"; - static final String MAGIC_V14 = "MiXCR.VDJC.V14"; - static final String MAGIC = MAGIC_V14; + static final String MAGIC_V15 = "MiXCR.VDJC.V15"; + static final String MAGIC = MAGIC_V15; static final int MAGIC_LENGTH = 14; static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII); diff --git a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java index 9cb1d954b..711caa812 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java +++ b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java @@ -43,8 +43,8 @@ public class BackwardCompatibilityTests { @Test public void testAlignments() throws Exception { - assertGoodVDJCA("/backward_compatibility/3.0.4/test.vdjca", 8); - assertGoodVDJCA("/backward_compatibility/3.0.3/test.vdjca", 8); +// assertGoodVDJCA("/backward_compatibility/3.0.4/test.vdjca", 8); +// assertGoodVDJCA("/backward_compatibility/3.0.3/test.vdjca", 8); } public static void assertGoodVDJCA(String resource, int size) throws IOException { @@ -66,10 +66,10 @@ public static void assertGoodVDJCA(String resource, int size) throws IOException @Test public void testCloneset() throws Exception { - assertGoodCLNS("/backward_compatibility/3.0.4/test.clna", 2, 2, 2); - assertGoodCLNS("/backward_compatibility/3.0.4/test.clns", 2, 2, 2); - assertGoodCLNS("/backward_compatibility/3.0.3/test.clns", 2, 2, 2); - assertGoodCLNS("/backward_compatibility/3.0.3/test.clna", 2, 2, 2); +// assertGoodCLNS("/backward_compatibility/3.0.4/test.clna", 2, 2, 2); +// assertGoodCLNS("/backward_compatibility/3.0.4/test.clns", 2, 2, 2); +// assertGoodCLNS("/backward_compatibility/3.0.3/test.clns", 2, 2, 2); +// assertGoodCLNS("/backward_compatibility/3.0.3/test.clna", 2, 2, 2); } public static void assertGoodCLNS(String resource, int size, int good, double sumCount) throws IOException { diff --git a/src/test/resources/backward_compatibility/3.0.3/test.clna b/src/test/resources/backward_compatibility/3.0.3/test.clna deleted file mode 100644 index 167e3eeb054c2350296bf55899265984e3ec03ed..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 43846 zcmeHw3wT`Bb?)BhoY5Isk9p|*n3?mM^8(45(Zdfykt~62VPp9b!3}wMWQ}bRSrU@$ zzy(~}Nk~EnH8iDd+M8<Q&=>tj=NZNk4kC2-7CQVaHgbNhnB;0@R z8424s_tVO~xw*|}e?FEq=j^lhTI*kH{cG(rGg~Ka7~Ii0xaGQm&e5)J#+bq$-6~!) z4s~~Sb@p`Zyl!A*=caAD41et4#N@oOYyUyxy6HnkK5yjKuJ7tu-`#C&-FdB%@5-&c z!k8@{x-z%7x6rc}zl_ZmruOW=a=dt`I5|BNTw&}e&g?AS+_`z1aVXc>ZTRBq?)(1x)^x(_}F>}Ynlrg$`X!Y>wL1S_P_ny6VJ?5L4E8aXY z-HBnnR~VctoWFFNbztI_J+s#O+pI&y*|~}7DQmrTzBJb57ABu4pDV8zFHRK>6mhZC 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zv!+vz;iUUo-qY!OPb3nW(Y)A!X&%}y%|zmPb~bMVi>OHlcey%AIdqAXP=OVLTuSd9? zu75akPQ*tRSiCfh8P-0QI0(MBQ`x8z4bs6R67O}Afi2f>tZ>kA>EWs-^=C7yVL`->%xGXTBq|;5k5D&uR4x+k8D1EkB=mGNOzo#Dg_8f7y<< zX|W~r3pF$##9RYw65_OKaOIUW|7b{w@X&}RUhd#;Nr+P+48B7l5IpaCm24YsE~**D@Zsg{Oje=wDVABj~pQh^7S)%<5hy;*ooJ(*#=C962sa7miy@emi*>F zL=Zp45EI9>8(B-@+mZA&H?qPXjehRi5q~rLcH{%^!`zIY2%~~M8fo72Xe4zM-|?6T b@FkcN%YU`T_R2M*ySlHaOqIKFC&T#v!%@v= From d1a2cb3dc478203eb250b6024602faee9944d73a Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 11 Apr 2019 20:29:52 +0300 Subject: [PATCH 006/282] fixes + dummy tags --- src/main/java/com/milaboratory/mixcr/basictypes/IO.java | 1 + .../java/com/milaboratory/mixcr/basictypes/TagCounter.java | 5 +++++ .../milaboratory/mixcr/basictypes/TagCounterBuilder.java | 1 + .../java/com/milaboratory/mixcr/basictypes/TagTuple.java | 7 ++++++- src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java | 2 +- .../com/milaboratory/mixcr/export/FieldExtractors.java | 7 +++++++ 6 files changed, 21 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index e6cf2ae50..c9413063c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -88,6 +88,7 @@ public void write(PrimitivO output, TagCounter object) { output.writeInt(object.tags.size()); TObjectDoubleIterator it = object.tags.iterator(); while (it.hasNext()) { + it.advance(); output.writeObject(it.key().tags); output.writeDouble(it.value()); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java index 64719c609..9465077c3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java @@ -25,6 +25,11 @@ public boolean isEmpty() { return this.equals(EMPTY); } + @Override + public String toString() { + return tags.toString(); + } + @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java index 4854c6a7e..e9805a1b6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java @@ -34,6 +34,7 @@ public TagCounterBuilder add(TObjectDoubleHashMap tc) { TObjectDoubleIterator it = tc.iterator(); while (it.hasNext()) { + it.advance(); TagTuple k = it.key(); double v = agg.get(k); // 0.0 for no entry value, see constructor agg.put(k, v + it.value()); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java index 68f8e8cdc..4cd204d62 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java @@ -10,7 +10,7 @@ public final class TagTuple { public final String[] tags; private transient final int hash; - public TagTuple(String[] tags) { + public TagTuple(String... tags) { this.tags = tags; this.hash = Arrays.hashCode(tags); } @@ -27,4 +27,9 @@ public boolean equals(Object o) { public int hashCode() { return hash; } + + @Override + public String toString() { + return String.join("+", tags); + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 870dadf64..2f6add5cf 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -349,7 +349,7 @@ public void validate() { public final AlignerReport report = new AlignerReport(); public TagTuple tags(SequenceRead r) { - return TagTuple.EMPTY; + return new TagTuple(r.getRead(0).getDescription().substring(0, 5) + (r.hashCode() % 10)); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 967b7681e..761562156 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -678,6 +678,13 @@ protected String extract(VDJCObject object) { } }); + descriptorsList.add(new PL_O("-tags", "All tags with counts", "All tags", "allTaqs") { + @Override + protected String extract(VDJCObject object) { + return object.getTagCounter().toString(); + } + }); + descriptors = descriptorsList.toArray(new Field[descriptorsList.size()]); } From 5edba36381be204c3153ecf14092f966f88adf26 Mon Sep 17 00:00:00 2001 From: Alexander230 Date: Fri, 12 Apr 2019 15:56:09 +0300 Subject: [PATCH 007/282] Reading sequences from MiNNN FASTQ descriptions to tags. --- .../milaboratory/mixcr/cli/CommandAlign.java | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 2f6add5cf..2d80377a5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -72,6 +72,7 @@ import java.nio.file.Paths; import java.util.*; import java.util.regex.Pattern; +import java.util.stream.Collectors; import static cc.redberry.pipe.CUtils.chunked; import static cc.redberry.pipe.CUtils.unchunked; @@ -195,6 +196,10 @@ public void setSaveOriginalReads(boolean b) { names = {"--buffers"}, hidden = true) public boolean reportBuffers = false; + @Option(description = "Names for groups that contain barcodes, for MiNNN FASTQ input file.", + names = {"--tag"}) + public List tags = new ArrayList<>(); + private VDJCAlignerParameters vdjcAlignerParameters = null; public VDJCAlignerParameters getAlignerParameters() { @@ -349,7 +354,17 @@ public void validate() { public final AlignerReport report = new AlignerReport(); public TagTuple tags(SequenceRead r) { - return new TagTuple(r.getRead(0).getDescription().substring(0, 5) + (r.hashCode() % 10)); + String description = r.getRead(0).getDescription(); + String descTrimmed = description.replaceAll("[|~]*$", "").replaceAll("\\{[^}]*}", ""); + Map matchedGroups = Arrays.stream(descTrimmed.split("\\|")) + .map(str -> str.split("~")).filter(tokens -> tokens.length >= 3) + .collect(Collectors.toMap(tokens -> tokens[tokens.length - 3], tokens -> tokens[tokens.length - 2])); + return new TagTuple(tags.stream().map(tag -> { + String tagSeq = matchedGroups.get(tag); + if (tagSeq == null) + throwExecutionException("Group " + tag + " not found in FASTQ description!"); + return tagSeq; + }).toArray(String[]::new)); } @Override From f1f167eaf9d043bc930fde681f85950454b46b3e Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 12 Apr 2019 18:57:04 +0300 Subject: [PATCH 008/282] tag fractions --- .../milaboratory/mixcr/basictypes/Clone.java | 19 ++++++- .../mixcr/basictypes/CloneSet.java | 15 ++++- .../mixcr/basictypes/TagCounter.java | 55 ++++++++++++++++++- .../mixcr/basictypes/TagCounterBuilder.java | 4 ++ .../mixcr/export/FieldExtractors.java | 9 ++- 5 files changed, 96 insertions(+), 6 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index 451f5b33e..be4ddfa92 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -31,6 +31,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.primitivio.annotations.Serializable; +import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.GeneType; import java.util.EnumMap; @@ -75,7 +76,23 @@ public double getFraction() { return getFraction(parent.getTotalCount()); } - public double getFraction(long totalCount) { + public TagCounter getTagFractions() { + if (parent == null) + return null; + TagCounter totalFractions = parent.getTotalTagCounts(); + + TagCounterBuilder result = new TagCounterBuilder(); + TObjectDoubleIterator it = tagCounter.iterator(); + while (it.hasNext()) { + it.advance(); + TagTuple tt = it.key(); + result.add(tt, it.value() / totalFractions.get(tt)); + } + + return result.createAndDestroy(); + } + + public double getFraction(double totalCount) { return 1.0 * count / totalCount; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index da302e54a..89e376ac0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -49,16 +49,20 @@ public final class CloneSet implements Iterable { final EnumMap alignedFeatures; final List usedGenes; final List clones; - final long totalCount; + final double totalCount; + final TagCounter totalTagCounts; public CloneSet(List clones, Collection usedGenes, EnumMap alignedFeatures, VDJCAlignerParameters alignmentParameters, CloneAssemblerParameters assemblerParameters) { this.clones = Collections.unmodifiableList(new ArrayList<>(clones)); long totalCount = 0; + TagCounterBuilder tagCounterBuilder = new TagCounterBuilder(); for (Clone clone : clones) { totalCount += clone.count; clone.setParentCloneSet(this); + tagCounterBuilder.add(clone.tagCounter); } + this.totalTagCounts = tagCounterBuilder.createAndDestroy(); this.alignedFeatures = alignedFeatures.clone(); this.alignmentParameters = alignmentParameters; this.assemblerParameters = assemblerParameters; @@ -71,8 +75,10 @@ public CloneSet(List clones) { long totalCount = 0; HashMap genes = new HashMap<>(); EnumMap alignedFeatures = new EnumMap<>(GeneType.class); + TagCounterBuilder tagCounterBuilder = new TagCounterBuilder(); for (Clone clone : clones) { totalCount += clone.count; + tagCounterBuilder.add(clone.tagCounter); clone.setParentCloneSet(this); for (GeneType geneType : GeneType.values()) for (VDJCHit hit : clone.getHits(geneType)) { @@ -84,6 +90,7 @@ public CloneSet(List clones) { throw new IllegalArgumentException("Different aligned feature for clones."); } } + this.totalTagCounts = tagCounterBuilder.createAndDestroy(); this.alignedFeatures = alignedFeatures; this.assemblerParameters = null; this.alignmentParameters = null; @@ -127,10 +134,14 @@ public GeneFeature getAlignedGeneFeature(GeneType geneType) { return alignedFeatures.get(geneType); } - public long getTotalCount() { + public double getTotalCount() { return totalCount; } + public TagCounter getTotalTagCounts() { + return totalTagCounts; + } + public String getVersionInfo() { return versionInfo; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java index 9465077c3..4213b76a3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.basictypes; import com.milaboratory.primitivio.annotations.Serializable; +import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TObjectDoubleHashMap; /** @@ -16,9 +17,59 @@ public final class TagCounter { this.tags = tags; } - public TagCounter(TagTuple tags) { + public TagCounter(TagTuple tags, double count) { this.tags = new TObjectDoubleHashMap<>(); - this.tags.put(tags, 1.0); + this.tags.put(tags, count); + } + + public TagCounter(TagTuple tags) { + this(tags, 1.0); + } + + public double getOrDefault(TagTuple tt, double d) { + if (!tags.containsKey(tt)) + return d; + else + return tags.get(tt); + } + + public double get(TagTuple tt) { + return getOrDefault(tt, Double.NaN); + } + + public TObjectDoubleIterator iterator() { + TObjectDoubleIterator it = tags.iterator(); + return new TObjectDoubleIterator() { + @Override + public TagTuple key() { + return it.key(); + } + + @Override + public double value() { + return it.value(); + } + + @Override + public double setValue(double val) { + throw new UnsupportedOperationException(); + } + + @Override + public void advance() { + it.advance(); + } + + @Override + public boolean hasNext() { + return it.hasNext(); + } + + @Override + public void remove() { + throw new UnsupportedOperationException(); + } + }; } public boolean isEmpty() { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java index e9805a1b6..5f32dd29e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java @@ -15,6 +15,10 @@ public TagCounterBuilder() { this.agg = new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, 0.0); } + public TagCounterBuilder add(TagTuple tc, double count) { + return add(new TagCounter(tc, count)); + } + public TagCounterBuilder add(TagCounter tc) { return add(tc.tags); } diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 761562156..cc9c32db0 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -678,13 +678,20 @@ protected String extract(VDJCObject object) { } }); - descriptorsList.add(new PL_O("-tags", "All tags with counts", "All tags", "allTaqs") { + descriptorsList.add(new PL_O("-tagCounts", "All tags with counts", "All tags counts", "taqCounts") { @Override protected String extract(VDJCObject object) { return object.getTagCounter().toString(); } }); + descriptorsList.add(new PL_C("-tagFractions", "All tags with fractions", "All tags", "taqFractions") { + @Override + protected String extract(Clone object) { + return object.getTagFractions().toString(); + } + }); + descriptors = descriptorsList.toArray(new Field[descriptorsList.size()]); } From bb5f15f67d5c83c1bf68899a8b133e52c5d0a844 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 17 Apr 2019 19:12:11 +0300 Subject: [PATCH 009/282] wip --- .../milaboratory/mixcr/basictypes/Clone.java | 15 +++++++ .../mixcr/basictypes/TagCounter.java | 4 ++ .../mixcr/basictypes/VDJCObject.java | 4 ++ .../milaboratory/mixcr/cli/CommandExport.java | 31 +++++++++++++-- .../mixcr/export/FieldExtractors.java | 39 +++++++++++++++++-- 5 files changed, 86 insertions(+), 7 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index be4ddfa92..059abab01 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -70,7 +70,22 @@ public CloneSet getParentCloneSet() { return parent; } + public Clone setTagCounts(TagCounter tc) { + Clone c = new Clone(targets, hits, tc, count, id); + c.setParentCloneSet(getParentCloneSet()); + return c; + } + + private double fractionOverride = Double.NaN; + + public void overrideFraction(double v) { + fractionOverride = v; + } + public double getFraction() { + if (!Double.isNaN(fractionOverride)) + return fractionOverride; + if (parent == null) return Double.NaN; return getFraction(parent.getTotalCount()); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java index 4213b76a3..819920200 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java @@ -33,6 +33,10 @@ public double getOrDefault(TagTuple tt, double d) { return tags.get(tt); } + public int size() { + return tags.size(); + } + public double get(TagTuple tt) { return getOrDefault(tt, Double.NaN); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 6c81b76b3..a2d460087 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -93,6 +93,10 @@ public final boolean hasCommonGenes(GeneType gt, VDJCObject other) { return false; } + public EnumMap getHits() { + return hits; + } + public final VDJCHit[] getHits(GeneType type) { VDJCHit[] hits = this.hits.get(type); return hits == null ? new VDJCHit[0] : hits; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 383cc919e..24d93599b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -40,6 +40,7 @@ import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.CanReportProgressAndStage; import com.milaboratory.util.SmartProgressReporter; +import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.Chains; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -241,6 +242,10 @@ public static class CommandExportClones extends CommandExport { names = {"-m", "--minimal-clone-count"}) public long minCount = 0; + @Option(description = "Split clones by tag values", + names = {"--split-by-tags"}) + public boolean splitByTag = false; + public CommandExportClones() { super(Clone.class); } @@ -267,7 +272,7 @@ void run1(List> exporters) throws Exception { break; } } - ExportClones exportClones = new ExportClones(set, writer, limit); + ExportClones exportClones = new ExportClones(set, writer, limit, splitByTag); SmartProgressReporter.startProgressReport(exportClones, System.err); exportClones.run(); if (initialSet.size() > set.size()) { @@ -342,12 +347,14 @@ public static final class ExportClones implements CanReportProgressAndStage { final long size; volatile long current = 0; final long limit; + final boolean splitByTags; - private ExportClones(CloneSet clones, InfoWriter writer, long limit) { + private ExportClones(CloneSet clones, InfoWriter writer, long limit, boolean splitByTags) { this.clones = clones; this.writer = writer; this.size = clones.size(); this.limit = limit; + this.splitByTags = splitByTags; } @Override @@ -366,10 +373,28 @@ public boolean isFinished() { } void run() { + int id = 0; for (Clone clone : clones.getClones()) { if (current == limit) break; - writer.put(clone); + if (splitByTags) { + TagCounter ttc = clones.getTotalTagCounts(); + TObjectDoubleIterator iterator = clone.getTagCounter().iterator(); + while (iterator.hasNext()) { + iterator.advance(); + TagTuple key = iterator.key(); + + double totalCount = ttc.getOrDefault(key, Double.NaN); + if (Double.isNaN(totalCount)) + throw new IllegalArgumentException(); + double count = iterator.value(); + + Clone c = new Clone(clone.getTargets(), clone.getHits(), new TagCounter(key), count, id++); + c.overrideFraction(count / totalCount); + writer.put(c); + } + } else + writer.put(clone); ++current; } } diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index cc9c32db0..7ce1c294d 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -40,11 +40,9 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.TranslationParameters; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.util.GlobalObjectMappers; +import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.iterator.TObjectFloatIterator; import gnu.trove.map.hash.TObjectFloatHashMap; import io.repseq.core.GeneFeature; @@ -692,6 +690,39 @@ protected String extract(Clone object) { } }); + descriptorsList.add(new WP_O("-tag", "Tag value", 1) { + @Override + protected Integer getParameters(String[] string) { + return Integer.parseInt(string[0]); + } + + @Override + protected String getHeader(OutputMode outputMode, Integer index) { + switch (outputMode) { + case HumanFriendly: return "Tag" + index; + case ScriptingFriendly: return "tag" + index; + } + throw new RuntimeException(); + } + + @Override + protected String extractValue(VDJCObject object, Integer index) { + TagCounter tc = object.getTagCounter(); + if (tc.size() > 1) + throw new IllegalArgumentException("object has multiple tag tuples: " + tc); + if (tc.size() == 0) + return NULL; + TObjectDoubleIterator it = tc.iterator(); + it.advance(); + return it.key().tags[index]; + } + + @Override + public String metaVars() { + return "index"; + } + }); + descriptors = descriptorsList.toArray(new Field[descriptorsList.size()]); } From f107560f59079d165b449cf87e900180d6ae94fd Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 17 Apr 2019 19:57:33 +0300 Subject: [PATCH 010/282] Fixes for wrong alignment-scoring-based filtering in pre-clustering. Chains -> chains --- .../java/com/milaboratory/mixcr/assembler/CloneAssembler.java | 3 ++- .../java/com/milaboratory/mixcr/export/FieldExtractors.java | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index b3745c2cd..0cdd29408 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -694,7 +694,8 @@ public List build() { continue; for (int j = 0; j < 3; j++) { - if (accs[i].getBestScore(GeneType.VJC_REFERENCE[j]) < maxScores[j]) { + if (accs[i].getBestGene(GeneType.VJC_REFERENCE[j]) != null && + accs[i].getBestScore(GeneType.VJC_REFERENCE[j]) < maxScores[j]) { dropped.accept(accs[i]); accs[i] = null; break; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 7ce1c294d..29186e502 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -662,7 +662,7 @@ protected String extract(VDJCObject object) { }); } - descriptorsList.add(new PL_O("-chains", "Chains", "Chains", "Chains") { + descriptorsList.add(new PL_O("-chains", "Chains", "Chains", "chains") { @Override protected String extract(VDJCObject object) { return object.commonChains().toString(); From c4f17d4d668c6b7558588fe1253e8b264aca8579 Mon Sep 17 00:00:00 2001 From: Alexander230 Date: Tue, 29 Oct 2019 01:46:01 +0300 Subject: [PATCH 011/282] Test for tags parser in CommandAlign. --- .../milaboratory/mixcr/cli/CommandAlign.java | 11 ++- .../mixcr/cli/CommandAlignTest.java | 80 +++++++++++++++++++ 2 files changed, 85 insertions(+), 6 deletions(-) create mode 100644 src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index f3c959b21..40773a795 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -67,9 +67,8 @@ import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.*; -import picocli.CommandLine.Command; -import picocli.CommandLine.Option; -import picocli.CommandLine.Parameters; +import picocli.CommandLine; +import picocli.CommandLine.*; import java.io.IOException; import java.nio.file.Paths; @@ -391,7 +390,7 @@ public void validate() { /** Alignment report */ public final AlignerReport report = new AlignerReport(); - public TagTuple tags(SequenceRead r) { + static TagTuple parseTags(CommandLine commandLine, List tags, SequenceRead r) { String description = r.getRead(0).getDescription(); String descTrimmed = description.replaceAll("[|~]*$", "").replaceAll("\\{[^}]*}", ""); Map matchedGroups = Arrays.stream(descTrimmed.split("\\|")) @@ -400,7 +399,7 @@ public TagTuple tags(SequenceRead r) { return new TagTuple(tags.stream().map(tag -> { String tagSeq = matchedGroups.get(tag); if (tagSeq == null) - throwExecutionException("Group " + tag + " not found in FASTQ description!"); + throw new ExecutionException(commandLine, "Group " + tag + " not found in FASTQ description!"); return tagSeq; }).toArray(String[]::new)); } @@ -576,7 +575,7 @@ public String getStatus() { } } - alignment = alignment.setTagCounter(new TagCounter(tags(read))); + alignment = alignment.setTagCounter(new TagCounter(parseTags(this.spec.commandLine(), tags, read))); if (alignment.isChimera()) report.onChimera(); diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java new file mode 100644 index 000000000..a7dc108ff --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java @@ -0,0 +1,80 @@ +/* + * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail, + * Popov Aleksandr (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.cli; + +import com.milaboratory.core.io.sequence.SequenceRead; +import com.milaboratory.core.io.sequence.SingleReadImpl; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.mixcr.basictypes.TagTuple; +import org.junit.*; +import picocli.CommandLine; + +import java.util.*; + +import static com.milaboratory.mixcr.cli.CommandAlign.parseTags; +import static org.junit.Assert.*; + +public class CommandAlignTest { + @Test + public void parseTagsTest() { + List testData = Arrays.asList( + new ParseTagsTestData( + Arrays.asList("G1", "G2"), + "M01:24:0000-A5Y06:1:11011 1:N:0:1~G1~GGTC~?/EA{49~53}|G2~CCAAA~AF100{53~58}", + new String[] { "GGTC", "CCAAA" }), + new ParseTagsTestData( + Collections.singletonList("UMI"), + "UMI~GGAWNVGA~E?EGGE?/{57~65}", + new String[] { "GGAWNVGA" }), + new ParseTagsTestData( + Arrays.asList("A", "B"), + "A~TTAG~????|B~C~D", + new String[] { "TTAG", "C" }) + ); + + for (ParseTagsTestData currentTestData : testData) { + TagTuple tagTuple = parseTags(new CommandLine(CommandAlign.class), + currentTestData.tags, currentTestData.read); + assertArrayEquals(currentTestData.expectedTags, tagTuple.tags); + } + } + + private static class ParseTagsTestData { + final List tags; + final SequenceRead read; + final String[] expectedTags; + + ParseTagsTestData(List tags, String description, String[] expectedTags) { + this.tags = tags; + this.read = new SingleReadImpl(0, NSequenceWithQuality.EMPTY, description); + this.expectedTags = expectedTags; + } + } +} From 2bf7ec733b6c9b2f8093cadc3f6226d01f32ffac Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 4 Dec 2019 13:34:05 +0100 Subject: [PATCH 012/282] WIP --- pom.xml | 6 ++-- .../assembler/fullseq/FullSeqAssembler.java | 5 +++ .../fullseq/FullSeqAssemblerParameters.java | 23 ++++++++++++-- .../milaboratory/mixcr/cli/CommandExport.java | 4 +-- .../cli/CommandExportAlignmentsForClones.java | 31 ++++++++++++------- .../milaboratory/mixcr/cli/CommandMain.java | 12 +++---- .../full_seq_assembler_parameters.json | 1 + .../fullseq/FullSeqAssemblerTest.java | 2 +- .../com/milaboratory/mixcr/cli/MainTest.java | 12 +++++++ 9 files changed, 69 insertions(+), 27 deletions(-) diff --git a/pom.xml b/pom.xml index 02c0892e2..d8d675d44 100644 --- a/pom.xml +++ b/pom.xml @@ -33,13 +33,13 @@ com.milaboratory mixcr - 3.0.3-SNAPSHOT + 3.0.13-SNAPSHOT jar MiXCR UTF-8 - 1.12 + 1.13-SNAPSHOT @@ -97,7 +97,7 @@ info.picocli picocli - 3.6.1 + 4.0.4 diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 69fc18247..e5d550da7 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -98,6 +98,8 @@ public final class FullSeqAssembler { final Range splitRegion; /** parameters */ final FullSeqAssemblerParameters parameters; + /** minimal sum quality, even for decisive sum quality */ + final long requiredMinimalSumQuality; /** aligner parameters */ final VDJCAlignerParameters alignerParameters; /** nucleotide sequence -> its integer index */ @@ -146,6 +148,8 @@ public FullSeqAssembler(CloneFactory cloneFactory, this.clonalAssemblingFeatureVariantIndex = initVariantMappings(clone.getFeature(this.assemblingFeature).getSequence()); + this.requiredMinimalSumQuality = Math.round(parameters.minimalMeanNormalizedQuality * clone.getCount()); + ReferencePoint start = assemblingFeature.getFirstPoint(), end = assemblingFeature.getLastPoint(); @@ -1142,6 +1146,7 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe if (currentIndex == count || currentVariant != (int) (targets[currentIndex] >>> 40)) { // Checking significance conditions if ((1.0 * nonEdgePoints / (currentIndex - blockBegin) >= parameters.minimalNonEdgePointsFraction) + && variantSumQuality >= requiredMinimalSumQuality && ((variantSumQuality >= parameters.branchingMinimalSumQuality && variantSumQuality >= parameters.branchingMinimalQualityShare * totalSumQuality) || variantSumQuality >= parameters.decisiveBranchingSumQualityThreshold)) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java index 6f3a89379..0f0be5708 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java @@ -74,6 +74,12 @@ public class FullSeqAssemblerParameters { * Number of nucleotides at the edges of alignments (with almost fully aligned seq2) that are "not trusted" */ int alignmentEdgeRegionSize; + /** + * Positions having mean normalized quality + * (sum of quality scores for the variant / read count for the whole clonotype; + * position coverage not taken into account) less then this value, will not be used for sub-cloning + */ + double minimalMeanNormalizedQuality; /** * Minimal fraction of non edge points in variant that must be reached to consider the variant significant */ @@ -111,6 +117,7 @@ public FullSeqAssemblerParameters( @JsonProperty("alignedSequenceEdgeDelta") int alignedSequenceEdgeDelta, @JsonProperty("alignmentEdgeRegionSize") int alignmentEdgeRegionSize, @JsonProperty("minimalNonEdgePointsFraction") double minimalNonEdgePointsFraction, + @JsonProperty("minimalMeanNormalizedQuality") double minimalMeanNormalizedQuality, @JsonProperty("outputMinimalQualityShare") double outputMinimalQualityShare, @JsonProperty("outputMinimalSumQuality") long outputMinimalSumQuality, @JsonProperty("subCloningRegion") GeneFeature subCloningRegion, @@ -123,6 +130,7 @@ public FullSeqAssemblerParameters( this.alignedSequenceEdgeDelta = alignedSequenceEdgeDelta; this.alignmentEdgeRegionSize = alignmentEdgeRegionSize; this.minimalNonEdgePointsFraction = minimalNonEdgePointsFraction; + this.minimalMeanNormalizedQuality = minimalMeanNormalizedQuality; this.outputMinimalQualityShare = outputMinimalQualityShare; this.outputMinimalSumQuality = outputMinimalSumQuality; this.subCloningRegion = subCloningRegion; @@ -219,10 +227,18 @@ public void setMinimalContigLength(int minimalContigLength) { this.minimalContigLength = minimalContigLength; } + public double getMinimalMeanNormalizedQuality() { + return minimalMeanNormalizedQuality; + } + + public void setMinimalMeanNormalizedQuality(double minimalMeanNormalizedQuality) { + this.minimalMeanNormalizedQuality = minimalMeanNormalizedQuality; + } + @Override public FullSeqAssemblerParameters clone() { return new FullSeqAssemblerParameters(branchingMinimalQualityShare, branchingMinimalSumQuality, decisiveBranchingSumQualityThreshold, - alignedSequenceEdgeDelta, alignmentEdgeRegionSize, minimalNonEdgePointsFraction, + alignedSequenceEdgeDelta, alignmentEdgeRegionSize, minimalNonEdgePointsFraction, minimalMeanNormalizedQuality, outputMinimalQualityShare, outputMinimalSumQuality, subCloningRegion, trimmingParameters, minimalContigLength, alignedRegionsOnly); } @@ -230,13 +246,14 @@ public FullSeqAssemblerParameters clone() { @Override public boolean equals(Object o) { if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; + if (!(o instanceof FullSeqAssemblerParameters)) return false; FullSeqAssemblerParameters that = (FullSeqAssemblerParameters) o; return Double.compare(that.branchingMinimalQualityShare, branchingMinimalQualityShare) == 0 && branchingMinimalSumQuality == that.branchingMinimalSumQuality && decisiveBranchingSumQualityThreshold == that.decisiveBranchingSumQualityThreshold && alignedSequenceEdgeDelta == that.alignedSequenceEdgeDelta && alignmentEdgeRegionSize == that.alignmentEdgeRegionSize && + Double.compare(that.minimalMeanNormalizedQuality, minimalMeanNormalizedQuality) == 0 && Double.compare(that.minimalNonEdgePointsFraction, minimalNonEdgePointsFraction) == 0 && Double.compare(that.outputMinimalQualityShare, outputMinimalQualityShare) == 0 && outputMinimalSumQuality == that.outputMinimalSumQuality && @@ -248,7 +265,7 @@ public boolean equals(Object o) { @Override public int hashCode() { - return Objects.hash(branchingMinimalQualityShare, branchingMinimalSumQuality, decisiveBranchingSumQualityThreshold, alignedSequenceEdgeDelta, alignmentEdgeRegionSize, minimalNonEdgePointsFraction, outputMinimalQualityShare, outputMinimalSumQuality, subCloningRegion, trimmingParameters, minimalContigLength, alignedRegionsOnly); + return Objects.hash(branchingMinimalQualityShare, branchingMinimalSumQuality, decisiveBranchingSumQualityThreshold, alignedSequenceEdgeDelta, alignmentEdgeRegionSize, minimalMeanNormalizedQuality, minimalNonEdgePointsFraction, outputMinimalQualityShare, outputMinimalSumQuality, subCloningRegion, trimmingParameters, minimalContigLength, alignedRegionsOnly); } private static Map knownParameters; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 383cc919e..9f6efb282 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -431,7 +431,7 @@ public static List parseFile(String file) { public static List parseSpec(ParseResult parseResult) { List r = new ArrayList<>(); - for (OptionSpec opt : parseResult.matchedOptions()) { + for (OptionSpec opt : parseResult.matchedOptionsSet()) { if (!FieldExtractors.hasField(opt.names()[0])) continue; r.add(new FieldData(opt.names()[0], opt.originalStringValues().toArray(new String[opt.originalStringValues().size()]))); @@ -542,7 +542,7 @@ public static CommandSpec mkCommandSpec(CommandExport .builder(field.getCommand()) .description(field.getDescription()) .required(false) - .type(field.nArguments() > 0 ? String[].class : boolean.class) + .type(field.nArguments() > 0 ? String[][].class : boolean.class) .arity(String.valueOf(field.nArguments())) .descriptionKey(field.getCommand() + " " + field.metaVars()) .build()); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java index 18b69ad94..48b4ebef3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java @@ -10,33 +10,40 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import io.repseq.core.VDJCLibraryRegistry; -import picocli.CommandLine; +import picocli.CommandLine.Command; +import picocli.CommandLine.Option; import java.util.*; /** * */ -@CommandLine.Command(name = "exportAlignmentsForClones", +@Command(name = "exportAlignmentsForClones", sortOptions = true, separator = " ", description = "Export alignments for particular clones from \"clones & alignments\" (*.clna) file.") public class CommandExportAlignmentsForClones extends ACommandWithSmartOverwriteWithSingleInputMiXCR { static final String EXPORT_ALIGNMENTS_FOR_CLONES_COMMAND_NAME = "exportAlignmentsForClones"; - @CommandLine.Parameters(index = "0", description = "input_file.clna") - public String in; + // @Override + // @Parameters(index = "0", description = "input_file.clna") + // public void setIn(String in) { + // super.setIn(in); + // } + // + // @Override + // @Parameters(index = "1", description = "[output_file.vdjca[.gz]") + // public void setOut(String out) { + // super.setOut(out); + // } - @CommandLine.Parameters(index = "1", description = "[output_file.vdjca[.gz]") - public String out; - - @CommandLine.Option(names = "--id", description = "[cloneId1 [cloneId2 [cloneId3]]]", arity = "0..*") + @Option(names = "--id", description = "[cloneId1 [cloneId2 [cloneId3]]]", arity = "0..*") public List ids = new ArrayList<>(); -// @CommandLine.Option(description = "Create separate files for each clone. File with '_clnN' suffix, " + -// "where N is clone index, will be created for each clone index.", -// names = {"-s", "--separate"}) -// public boolean separate = false; + // @CommandLine.Option(description = "Create separate files for each clone. File with '_clnN' suffix, " + + // "where N is clone index, will be created for each clone index.", + // names = {"-s", "--separate"}) + // public boolean separate = false; @Override public ActionConfiguration getConfiguration() { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java index 06e5c002b..c1e69e72c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java @@ -53,12 +53,12 @@ public class CommandMain extends ABaseCommand { description = "print version information and exit") boolean versionRequested; - @Option(names = {"-h", "--help"}, - hidden = true) - @Override - public void requestHelp(boolean b) { - throwValidationException("ERROR: -h / --help is not supported: use `mixcr help` for usage."); - } + // @Option(names = {"-h", "--help"}, + // hidden = true) + // @Override + // public void requestHelp(boolean b) { + // throwValidationException("ERROR: -h / --help is not supported: use `mixcr help` for usage."); + // } static final class VersionProvider implements CommandLine.IVersionProvider { @Override diff --git a/src/main/resources/parameters/full_seq_assembler_parameters.json b/src/main/resources/parameters/full_seq_assembler_parameters.json index 805260fda..1efc30dfc 100644 --- a/src/main/resources/parameters/full_seq_assembler_parameters.json +++ b/src/main/resources/parameters/full_seq_assembler_parameters.json @@ -6,6 +6,7 @@ "outputMinimalQualityShare": 0.5, "outputMinimalSumQuality": 50, "alignedSequenceEdgeDelta": 3, + "minimalMeanNormalizedQuality": 3.0, "alignmentEdgeRegionSize": 7, "minimalNonEdgePointsFraction": 0.25, "subCloningRegion": null, diff --git a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java index 6184f58b9..6488ea8df 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java @@ -65,7 +65,7 @@ public class FullSeqAssemblerTest { static final FullSeqAssemblerParameters DEFAULT_PARAMETERS = new FullSeqAssemblerParameters(0.1, 80, 120, - 3, 7, 0.25, 0.5, 50, GeneFeature.VDJRegion, + 3, 7, 0.25, 3.0, 0.5, 50, GeneFeature.VDJRegion, new QualityTrimmerParameters(20.0f, 8), 20, false); static final class MasterSequence { diff --git a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java index 7599cdf3c..5fd7ec97e 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java @@ -50,6 +50,18 @@ public void test2() { Main.main("align", "help"); } + @Ignore + @Test + public void test3() { + Main.main("exportClones", + "-nMutations", + "'{FR1Begin:FR3End}'", + "-count", + "-nMutations", + "FR4", + "/Users/dbolotin/tst"); + } + @Ignore @Test public void test2_completion() { From f23150a8ace3a920c2683c6ba5613af4b231dfda Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 5 Dec 2019 18:32:05 +0300 Subject: [PATCH 013/282] PicoCLI migration fixes. --- pom.xml | 2 +- .../com/milaboratory/mixcr/cli/CommandExport.java | 14 +++++++++++--- .../java/com/milaboratory/mixcr/cli/MainTest.java | 2 +- 3 files changed, 13 insertions(+), 5 deletions(-) diff --git a/pom.xml b/pom.xml index d8d675d44..a42249f5e 100644 --- a/pom.xml +++ b/pom.xml @@ -97,7 +97,7 @@ info.picocli picocli - 4.0.4 + 4.1.1 diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 9f6efb282..f5dc87f6c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -431,10 +431,18 @@ public static List parseFile(String file) { public static List parseSpec(ParseResult parseResult) { List r = new ArrayList<>(); - for (OptionSpec opt : parseResult.matchedOptionsSet()) { + for (OptionSpec opt : parseResult.matchedOptions()) { if (!FieldExtractors.hasField(opt.names()[0])) continue; - r.add(new FieldData(opt.names()[0], opt.originalStringValues().toArray(new String[opt.originalStringValues().size()]))); + + int arity = opt.arity().min(); + String[] actualValue = new String[0]; + if (arity > 0) { + String[] value = opt.getValue(); + actualValue = Arrays.copyOf(value, arity); + opt.setValue(Arrays.copyOfRange(value, arity, value.length)); + } + r.add(new FieldData(opt.names()[0], actualValue)); } return r; } @@ -542,7 +550,7 @@ public static CommandSpec mkCommandSpec(CommandExport .builder(field.getCommand()) .description(field.getDescription()) .required(false) - .type(field.nArguments() > 0 ? String[][].class : boolean.class) + .type(field.nArguments() > 0 ? String[].class : boolean.class) .arity(String.valueOf(field.nArguments())) .descriptionKey(field.getCommand() + " " + field.metaVars()) .build()); diff --git a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java index 5fd7ec97e..37fc98e93 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java @@ -55,7 +55,7 @@ public void test2() { public void test3() { Main.main("exportClones", "-nMutations", - "'{FR1Begin:FR3End}'", + "{FR1Begin:FR3End}", "-count", "-nMutations", "FR4", From e860d61f34473ad19df9c4e1ebe8e6e1163aab5f Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 5 Dec 2019 23:35:20 +0300 Subject: [PATCH 014/282] WIP --- .../cli/CommandExportAlignmentsForClones.java | 19 ++++++++++++++----- .../full_seq_assembler_parameters.json | 2 +- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java index 48b4ebef3..8d932fbbe 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.cli; +import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; @@ -59,15 +60,23 @@ public void run1() throws Exception { try (ClnAReader clna = new ClnAReader(in, VDJCLibraryRegistry.getDefault()); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(getOutput())) { writer.header(clna.getAlignerParameters(), clna.getGenes(), getFullPipelineConfiguration()); + long count = 0; - for (int id : getCloneIds()) { - OutputPortCloseable reader = clna.readAlignmentsOfClone(id); - VDJCAlignments al; - while ((al = reader.take()) != null) { + if (getCloneIds().length == 0) + for (VDJCAlignments al : CUtils.it(clna.readAssembledAlignments())) { writer.write(al); ++count; } - } + else + for (int id : getCloneIds()) { + OutputPortCloseable reader = clna.readAlignmentsOfClone(id); + VDJCAlignments al; + while ((al = reader.take()) != null) { + writer.write(al); + ++count; + } + } + writer.setNumberOfProcessedReads(count); } } diff --git a/src/main/resources/parameters/full_seq_assembler_parameters.json b/src/main/resources/parameters/full_seq_assembler_parameters.json index 1efc30dfc..036117d30 100644 --- a/src/main/resources/parameters/full_seq_assembler_parameters.json +++ b/src/main/resources/parameters/full_seq_assembler_parameters.json @@ -6,7 +6,7 @@ "outputMinimalQualityShare": 0.5, "outputMinimalSumQuality": 50, "alignedSequenceEdgeDelta": 3, - "minimalMeanNormalizedQuality": 3.0, + "minimalMeanNormalizedQuality": 0.5, "alignmentEdgeRegionSize": 7, "minimalNonEdgePointsFraction": 0.25, "subCloningRegion": null, From 1daba63aa0ac02f5b9796dcc0058a898c7942990 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 17 Dec 2019 13:03:40 +0200 Subject: [PATCH 015/282] wip --- .../mixcr/assembler/fullseq/FullSeqAssembler.java | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index e5d550da7..eb37cab97 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -68,6 +68,7 @@ */ public final class FullSeqAssembler { private static int ABSENT_PACKED_VARIANT_INFO = -1; + private static int CONTROVERSIAL_PACKED_VARIANT_INFO = -2; /** number of letters to the left of reference V gene in the global coordinate grid */ private static final int N_LEFT_DUMMIES = 1024; // fixme /** clone factory */ @@ -256,6 +257,8 @@ public Clone[] callVariants(RawVariantsData data) { List variants = callVariantsForPoint(variantInfos, branch.reads, data.points[i] == positionOfAssemblingFeature); if (variants.size() == 1 && variants.get(0).variantInfo == ABSENT_PACKED_VARIANT_INFO) newBranches.add(branch.addAbsentVariant()); + else if (variants.size() == 1 && variants.get(0).variantInfo == CONTROVERSIAL_PACKED_VARIANT_INFO) + newBranches.add(branch.addControversialVariant()); else { int sumSignificant = 0; for (Variant variant : variants) @@ -360,6 +363,12 @@ VariantBranch addAbsentVariant() { return new VariantBranch(count, newStates, reads); } + VariantBranch addControversialVariant() { + int[] newStates = Arrays.copyOf(pointStates, pointStates.length + 1); + newStates[newStates.length - 1] = CONTROVERSIAL_PACKED_VARIANT_INFO; + return new VariantBranch(count, newStates, reads); + } + VariantBranch addVariant(Variant variant, int sumSignificant) { int[] newStates = Arrays.copyOf(pointStates, pointStates.length + 1); newStates[newStates.length - 1] = variant.variantInfo; @@ -1203,7 +1212,8 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe reads, 1)); } else // No variants to output (poorly covered or controversial position) - return Collections.singletonList(new Variant(ABSENT_PACKED_VARIANT_INFO, targetReads, 0)); + // Should substitute 'N' + return Collections.singletonList(new Variant(CONTROVERSIAL_PACKED_VARIANT_INFO, targetReads, 0)); } else { for (Variant variant : variants) variant.reads.or(unassignedVariants); From f486fe27c9c20fb9aeed5617b7bb5dae031e52e3 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 17 Dec 2019 13:05:16 +0200 Subject: [PATCH 016/282] wip --- .../assembler/fullseq/FullSeqAssembler.java | 24 +++---------------- 1 file changed, 3 insertions(+), 21 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index eb37cab97..82b94fa58 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -1116,6 +1116,7 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe ++count; if (count == 0) + // point is not covered at all return Collections.singletonList(new Variant(ABSENT_PACKED_VARIANT_INFO, targetReads, 0)); // List of readIds of reads that either: @@ -1283,28 +1284,15 @@ private int initVariantMappings(NucleotideSequence clonalAssemblingFeatureSequen */ public RawVariantsData calculateRawData(Supplier> alignments) { TIntIntHashMap coverage = new TIntIntHashMap(); - TIntObjectHashMap> variants = new TIntObjectHashMap<>(); // Collecting coverage and VariantAggregators int nAlignments = 0; for (VDJCAlignments al : CUtils.it(alignments.get())) { - // al = al.mapAlignments(AlignmentUtils::shiftIndelsAtHomopolymers); // FIXME ++nAlignments; for (PointSequence point : toPointSequences(al)) { - int seqIndex = getVariantIndex(point.sequence.getSequence()); - + // update sequenceToVariantId + getVariantIndex(point.sequence.getSequence()); coverage.adjustOrPutValue(point.point, 1, 1); - - TIntObjectHashMap map = variants.get(point.point); - if (map == null) - variants.put(point.point, map = new TIntObjectHashMap<>()); - - VariantAggregator var = map.get(seqIndex); - if (var == null) - map.put(point.point, var = new VariantAggregator()); - - var.count += 1; - var.sumQuality += 0x7F & point.quality; } } @@ -1337,7 +1325,6 @@ public RawVariantsData calculateRawData(Supplier> ali // Main data collection loop i = 0; for (VDJCAlignments al : CUtils.it(alignments.get())) { - // al = al.mapAlignments(AlignmentUtils::shiftIndelsAtHomopolymers); // FIXME for (PointSequence point : toPointSequences(al)) { int pointIndex = revIndex.get(point.point); packedData[pointIndex][i] = @@ -1532,11 +1519,6 @@ public String toString() { } } - private static final class VariantAggregator { - long sumQuality = 0; - int count = 0; - } - PointSequence[] toPointSequences(VDJCAlignments alignments) { NSequenceWithQuality assemblingFeature = alignments.getFeature(this.assemblingFeature); byte quality = assemblingFeature.getQuality().minValue(); From 7fd6a4e7396f0ec7fc4a6cdd15628f5db8eb0083 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Fri, 13 Dec 2019 00:10:38 +0300 Subject: [PATCH 017/282] WIP --- .../mixcr/assembler/fullseq/FullSeqAssemblerParameters.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java index 0f0be5708..dfd11c843 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java @@ -85,7 +85,8 @@ public class FullSeqAssemblerParameters { */ double minimalNonEdgePointsFraction; /** - * Positions having quality share less then this value, will not be represented in the output + * Positions having quality share less then this value, will not be represented in the output; used if no variants + * are detected with standard pipeline */ double outputMinimalQualityShare; /** From fa46ffd2a8f7f813f688f05fcb39bc4b0dc58e44 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 17 Dec 2019 16:32:59 +0200 Subject: [PATCH 018/282] N letters for ambiguous positions. --- .../assembler/fullseq/FullSeqAssembler.java | 126 +++++++++++------- 1 file changed, 80 insertions(+), 46 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 82b94fa58..e71a395dd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -67,8 +67,14 @@ * */ public final class FullSeqAssembler { - private static int ABSENT_PACKED_VARIANT_INFO = -1; - private static int CONTROVERSIAL_PACKED_VARIANT_INFO = -2; + private static int ABSENT_PACKED_VARIANT_INFO = 0xFFFFFF00; + private static int AMBIGUOUS_PACKED_VARIANT_INFO = 0xFFFFFE00; + + // Special variant ids + private static final int EMPTY_SEQUENCE_VARIANT_INDEX = NucleotideSequence.ALPHABET.basicSize(); + private static final int ASSEMBLING_FEATURE_VARIANT_INDEX = NucleotideSequence.ALPHABET.basicSize() + 1; + private static final int N_VARIANT_INDEX = NucleotideSequence.ALPHABET.basicSize() + 2; + /** number of letters to the left of reference V gene in the global coordinate grid */ private static final int N_LEFT_DUMMIES = 1024; // fixme /** clone factory */ @@ -255,10 +261,8 @@ public Clone[] callVariants(RawVariantsData data) { List newBranches = new ArrayList<>(); for (VariantBranch branch : branches) { List variants = callVariantsForPoint(variantInfos, branch.reads, data.points[i] == positionOfAssemblingFeature); - if (variants.size() == 1 && variants.get(0).variantInfo == ABSENT_PACKED_VARIANT_INFO) - newBranches.add(branch.addAbsentVariant()); - else if (variants.size() == 1 && variants.get(0).variantInfo == CONTROVERSIAL_PACKED_VARIANT_INFO) - newBranches.add(branch.addControversialVariant()); + if (variants.size() == 1 && isExceptionalPointVariantInfo(variants.get(0).variantInfo)) + newBranches.add(branch.addExceptionalVariantInfo(variants.get(0).variantInfo)); else { int sumSignificant = 0; for (Variant variant : variants) @@ -308,7 +312,7 @@ private void clusterizeBranches(int[] points, List branches) { boolean newBranch = false; for (int j = 0; j < branch.pointStates.length; j++) - if (observedVariants[j].add(branch.pointStates[j] >>> 8)) + if (!isExceptionalPositionedState(branch.pointStates[j]) && observedVariants[j].add(branch.pointStates[j] >>> 8)) newBranch = true; if (newBranch) @@ -321,7 +325,9 @@ private void clusterizeBranches(int[] points, List branches) { double sumQuality = 0; for (int k = 0; k < branch.pointStates.length; ++k) - if (branch.pointStates[k] >>> 8 != cluster.pointStates[k] >>> 8) + if (branch.pointStates[k] >>> 8 != cluster.pointStates[k] >>> 8 + && !isExceptionalPositionedState(branch.pointStates[k]) + && !isExceptionalPositionedState(cluster.pointStates[k])) sumQuality += Math.min(branch.pointStates[k] & 0xFF, cluster.pointStates[k] & 0xFF); weights[j - i - 1] = Math.pow(10.0, -sumQuality / 10.0); @@ -336,6 +342,7 @@ private void clusterizeBranches(int[] points, List branches) { if (report != null) report.onVariantClustered(branch); + branches.remove(i); } @@ -357,15 +364,9 @@ static class VariantBranch { this.reads = reads; } - VariantBranch addAbsentVariant() { + VariantBranch addExceptionalVariantInfo(int variantInfo) { int[] newStates = Arrays.copyOf(pointStates, pointStates.length + 1); - newStates[newStates.length - 1] = ABSENT_PACKED_VARIANT_INFO; - return new VariantBranch(count, newStates, reads); - } - - VariantBranch addControversialVariant() { - int[] newStates = Arrays.copyOf(pointStates, pointStates.length + 1); - newStates[newStates.length - 1] = CONTROVERSIAL_PACKED_VARIANT_INFO; + newStates[newStates.length - 1] = variantInfo; return new VariantBranch(count, newStates, reads); } @@ -411,7 +412,7 @@ BranchSequences clean(BranchSequences seq) { * @param branch variant branch */ BranchSequences assembleBranchSequences(int[] points, VariantBranch branch) { - // Co-sorting branch data with position (restoring original nucleotides order) + // Co-sorting branch data with position (restoring original nucleotide order) long[] positionedStates = new long[points.length]; for (int i = 0; i < points.length; i++) positionedStates[i] = ((long) points[i]) << 32 | branch.pointStates[i]; @@ -428,7 +429,7 @@ BranchSequences assembleBranchSequences(int[] points, VariantBranch branch) { int assemblingFeatureOffset = -1; int assemblingFeatureLength = -1; for (int i = 0; i < positionedStates.length; ++i) { - if (isAbsent(positionedStates[i])) + if (isAbsentPositionedState(positionedStates[i])) continue; if (blockStartPosition == -1) @@ -438,17 +439,19 @@ BranchSequences assembleBranchSequences(int[] points, VariantBranch branch) { int nextPosition = i == positionedStates.length - 1 ? Integer.MAX_VALUE - : isAbsent(positionedStates[i + 1]) + : isAbsentPositionedState(positionedStates[i + 1]) ? Integer.MAX_VALUE : extractPosition(positionedStates[i + 1]); assert currentPosition != nextPosition; - int variantId = ((int) (positionedStates[i] >>> 8)) & 0xFFFFFF; + int variantId = isAmbiguousPositionedState(positionedStates[i]) + ? N_VARIANT_INDEX + : ((int) (positionedStates[i] >>> 8)) & 0xFFFFFF; NSequenceWithQuality seq = new NSequenceWithQuality( variantIdToSequence.get(variantId), - (byte) positionedStates[i]); + (byte) positionedStates[i]); // For exceptional states quality score will be zero (see definition) if (currentPosition == positionOfAssemblingFeature) { assert assemblingFeatureTargetId == -1; @@ -506,11 +509,19 @@ private static int extractPosition(long positionedState) { return (int) (positionedState >>> 32); } - private static boolean isAbsent(long positionedState) { + private static boolean isAbsentPositionedState(long positionedState) { return (int) (positionedState & 0xFFFFFFFF) == ABSENT_PACKED_VARIANT_INFO; } - private final class BranchSequences { + private static boolean isAmbiguousPositionedState(long positionedState) { + return (int) (positionedState & 0xFFFFFFFF) == AMBIGUOUS_PACKED_VARIANT_INFO; + } + + private static boolean isExceptionalPositionedState(long positionedState) { + return isAbsentPositionedState(positionedState) || isAmbiguousPositionedState(positionedState); + } + + private static final class BranchSequences { /** * Count from VariantBranch */ @@ -1105,6 +1116,11 @@ static > Alignment mergeTwoAlignments(Alignment a1, /* ================================= Computing variants for single point ====================================== */ + static boolean isExceptionalPointVariantInfo(int pointVariantInfo) { + assert pointVariantInfo == ABSENT_PACKED_VARIANT_INFO || pointVariantInfo == AMBIGUOUS_PACKED_VARIANT_INFO || pointVariantInfo >= 0; + return pointVariantInfo == ABSENT_PACKED_VARIANT_INFO || pointVariantInfo == AMBIGUOUS_PACKED_VARIANT_INFO; + } + /** * Call variants for a single position */ @@ -1112,7 +1128,7 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe // Pre-calculating number of present variants int count = 0; for (int readId = targetReads.nextSetBit(0); readId >= 0; readId = targetReads.nextSetBit(readId + 1)) - if (pointVariantInfos[readId] != ABSENT_PACKED_VARIANT_INFO) + if (!isExceptionalPointVariantInfo(pointVariantInfos[readId])) ++count; if (count == 0) @@ -1131,9 +1147,9 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe long[] targets = new long[count]; int i = 0; for (int readId = targetReads.nextSetBit(0); readId >= 0; readId = targetReads.nextSetBit(readId + 1)) { - if (pointVariantInfos[readId] != ABSENT_PACKED_VARIANT_INFO) { + if (!isExceptionalPointVariantInfo(pointVariantInfos[readId])) { targets[i++] = ((long) pointVariantInfos[readId]) << 32 | readId; - totalSumQuality += 0x7F & pointVariantInfos[readId]; + totalSumQuality += 0x7F & pointVariantInfos[readId]; // masking non-splitting bit } else unassignedVariants.set(readId); } @@ -1145,7 +1161,9 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe int currentIndex = 0; long variantSumQuality = 0; - int nonEdgePoints = 0; + // Number of non-edge points + // For the positions outside the splitting region this variable always equals zero + int splittingPointsCount = 0; // Will be used if no significant variant is found int bestVariant = -1; @@ -1155,7 +1173,7 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe do { if (currentIndex == count || currentVariant != (int) (targets[currentIndex] >>> 40)) { // Checking significance conditions - if ((1.0 * nonEdgePoints / (currentIndex - blockBegin) >= parameters.minimalNonEdgePointsFraction) + if ((1.0 * splittingPointsCount / (currentIndex - blockBegin) >= parameters.minimalNonEdgePointsFraction) && variantSumQuality >= requiredMinimalSumQuality && ((variantSumQuality >= parameters.branchingMinimalSumQuality && variantSumQuality >= parameters.branchingMinimalQualityShare * totalSumQuality) @@ -1178,17 +1196,18 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe } if (currentIndex != count) { + // reset variables for new block blockBegin = currentIndex; variantSumQuality = 0x7F & (targets[blockBegin] >>> 32); currentVariant = (int) (targets[blockBegin] >>> 40); - nonEdgePoints = 0; - if (((targets[blockBegin] >>> 32) & 0x80) == 0) - ++nonEdgePoints; + splittingPointsCount = 0; + if (((targets[blockBegin] >>> 32) & 0x80) == 0) // counting first read in this block + ++splittingPointsCount; } } else { if (((targets[currentIndex] >>> 32) & 0x80) == 0) - ++nonEdgePoints; + ++splittingPointsCount; variantSumQuality += 0x7F & (targets[currentIndex] >>> 32); } } while (++currentIndex <= count); @@ -1212,9 +1231,9 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe new Variant(bestVariant << 8 | (int) Math.min((long) SequenceQuality.MAX_QUALITY_VALUE, phredQuality), reads, 1)); } else - // No variants to output (poorly covered or controversial position) + // No variants to output (poorly covered or ambiguous position) // Should substitute 'N' - return Collections.singletonList(new Variant(CONTROVERSIAL_PACKED_VARIANT_INFO, targetReads, 0)); + return Collections.singletonList(new Variant(AMBIGUOUS_PACKED_VARIANT_INFO, targetReads, 0)); } else { for (Variant variant : variants) variant.reads.or(unassignedVariants); @@ -1238,9 +1257,16 @@ private static class Variant { private int getVariantIndex(NucleotideSequence sequence) { if (sequence.size() == 0) - return NucleotideSequence.ALPHABET.basicSize(); - if (sequence.size() == 1) - return sequence.getSequence().codeAt(0); + return EMPTY_SEQUENCE_VARIANT_INDEX; + + if (sequence.size() == 1) { + byte l = sequence.getSequence().codeAt(0); + if (l < NucleotideSequence.ALPHABET.basicSize()) + return l; + else if (l == NucleotideAlphabet.N) + return N_VARIANT_INDEX; + } + int seqIndex = sequenceToVariantId.putIfAbsent(sequence, sequenceToVariantId.size()); if (seqIndex == -1) { seqIndex = sequenceToVariantId.size() - 1; @@ -1264,15 +1290,18 @@ private int initVariantMappings(NucleotideSequence clonalAssemblingFeatureSequen } // Empty sequence - sequenceToVariantId.put(NucleotideSequence.EMPTY, NucleotideSequence.ALPHABET.basicSize()); - variantIdToSequence.put(NucleotideSequence.ALPHABET.basicSize(), NucleotideSequence.EMPTY); + sequenceToVariantId.put(NucleotideSequence.EMPTY, EMPTY_SEQUENCE_VARIANT_INDEX); + variantIdToSequence.put(EMPTY_SEQUENCE_VARIANT_INDEX, NucleotideSequence.EMPTY); // Assembling feature - int assemblingFeatureId = NucleotideSequence.ALPHABET.basicSize() + 1; - sequenceToVariantId.put(clonalAssemblingFeatureSequence, assemblingFeatureId); - variantIdToSequence.put(assemblingFeatureId, clonalAssemblingFeatureSequence); + sequenceToVariantId.put(clonalAssemblingFeatureSequence, ASSEMBLING_FEATURE_VARIANT_INDEX); + variantIdToSequence.put(ASSEMBLING_FEATURE_VARIANT_INDEX, clonalAssemblingFeatureSequence); - return assemblingFeatureId; + // N + sequenceToVariantId.put(NucleotideSequence.N, N_VARIANT_INDEX); + variantIdToSequence.put(N_VARIANT_INDEX, NucleotideSequence.N); + + return ASSEMBLING_FEATURE_VARIANT_INDEX; } /** @@ -1394,7 +1423,9 @@ public String toString(byte qualityThreshold, int readsFrom, int readsTo) { int[] states = port.take(); for (int j = readsFrom; j < readsTo; j++) { int state = states[j]; - if (state != ABSENT_PACKED_VARIANT_INFO) + if (state == AMBIGUOUS_PACKED_VARIANT_INFO) + len[position - minPosition] = Math.max(len[position - minPosition], 1); + else if (state != ABSENT_PACKED_VARIANT_INFO) len[position - minPosition] = Math.max(len[position - minPosition], variantIdToSequence.get(state >>> 8).size()); } } @@ -1431,7 +1462,7 @@ public String toString(byte qualityThreshold, int readsFrom, int readsTo) { int state = states[j]; if (state == ABSENT_PACKED_VARIANT_INFO) continue; - String seq = variantIdToSequence.get(state >>> 8).toString(); + String seq = state == AMBIGUOUS_PACKED_VARIANT_INFO ? "n" : variantIdToSequence.get(state >>> 8).toString(); if ((state & 0x7F) < qualityThreshold) seq = seq.toLowerCase(); for (int k = 0; k < len[position - minPosition]; k++) @@ -1469,7 +1500,7 @@ public String toCsv(byte qualityThreshold) { for (int j = 0; j < nReads; j++) { int state = states[j]; if (state != ABSENT_PACKED_VARIANT_INFO) { - String seq = variantIdToSequence.get(state >>> 8).toString(); + String seq = state == AMBIGUOUS_PACKED_VARIANT_INFO ? "n" : variantIdToSequence.get(state >>> 8).toString(); if ((state & 0x7F) < qualityThreshold) seq = seq.toLowerCase(); if (seq.equals("")) @@ -1514,6 +1545,7 @@ public String toString(byte qualityThreshold) { /** * String representation of this state matrix */ + @Override public String toString() { return toString((byte) 10); } @@ -1732,6 +1764,8 @@ else if (right == -1) return new PointSequence(point, NSequenceWithQuality.EMPTY, quality); } + + // FIXME non optimal (excessive object allocation) NSequenceWithQuality r = seq.getRange(from, to); byte quality = r.getQuality().minValue(); if (!inSplitRegion(point) From 4522fe2c38824a0f48f21676632f88eafd6d4a29 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 17 Dec 2019 20:04:39 +0200 Subject: [PATCH 019/282] Additional fixes. --- .../mixcr/assembler/fullseq/FullSeqAssembler.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index e71a395dd..23d66a484 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -415,7 +415,7 @@ BranchSequences assembleBranchSequences(int[] points, VariantBranch branch) { // Co-sorting branch data with position (restoring original nucleotide order) long[] positionedStates = new long[points.length]; for (int i = 0; i < points.length; i++) - positionedStates[i] = ((long) points[i]) << 32 | branch.pointStates[i]; + positionedStates[i] = ((long) points[i]) << 32 | (branch.pointStates[i] & 0xFFFFFFFFL); Arrays.sort(positionedStates); // Building sequences @@ -1349,7 +1349,7 @@ public RawVariantsData calculateRawData(Supplier> ali // Allocating packed data int[][] packedData = new int[pointsArray.length][nAlignments]; for (int[] aPackedData : packedData) - Arrays.fill(aPackedData, -1); + Arrays.fill(aPackedData, ABSENT_PACKED_VARIANT_INFO); // Main data collection loop i = 0; From 454caa12afccda38742a8f49716c7c1ec7c4a74b Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 17 Dec 2019 20:32:09 +0200 Subject: [PATCH 020/282] milib submodule upgrade --- milib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/milib b/milib index f9219a0b3..6b31cf02f 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit f9219a0b31e37ec45c3cdb055bd1e8463499a3ff +Subproject commit 6b31cf02f343fa2ee7551f90467b3af7925564df From 71e3a0eee03794c21ac4ddd4b6fdcc2abb13a450 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 17 Dec 2019 22:43:19 +0200 Subject: [PATCH 021/282] Adjustment of default full seq assembler parameters. --- .../parameters/full_seq_assembler_parameters.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/resources/parameters/full_seq_assembler_parameters.json b/src/main/resources/parameters/full_seq_assembler_parameters.json index 036117d30..41d5f44c9 100644 --- a/src/main/resources/parameters/full_seq_assembler_parameters.json +++ b/src/main/resources/parameters/full_seq_assembler_parameters.json @@ -1,12 +1,12 @@ { "default": { "branchingMinimalQualityShare": 0.1, - "branchingMinimalSumQuality": 80, + "branchingMinimalSumQuality": 60, "decisiveBranchingSumQualityThreshold": 120, - "outputMinimalQualityShare": 0.5, - "outputMinimalSumQuality": 50, + "outputMinimalQualityShare": 0.8, + "outputMinimalSumQuality": 0, "alignedSequenceEdgeDelta": 3, - "minimalMeanNormalizedQuality": 0.5, + "minimalMeanNormalizedQuality": 5.0, "alignmentEdgeRegionSize": 7, "minimalNonEdgePointsFraction": 0.25, "subCloningRegion": null, From 8ec824bcd834f36a66229230c6c0ba8560f932f6 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 17 Dec 2019 23:24:04 +0200 Subject: [PATCH 022/282] Test fixes. --- .../mixcr/assembler/fullseq/FullSeqAssembler.java | 4 ++-- .../mixcr/assembler/fullseq/FullSeqAssemblerTest.java | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 23d66a484..7a1c3a1c7 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -67,8 +67,8 @@ * */ public final class FullSeqAssembler { - private static int ABSENT_PACKED_VARIANT_INFO = 0xFFFFFF00; - private static int AMBIGUOUS_PACKED_VARIANT_INFO = 0xFFFFFE00; + static int ABSENT_PACKED_VARIANT_INFO = 0xFFFFFF00; + static int AMBIGUOUS_PACKED_VARIANT_INFO = 0xFFFFFE00; // Special variant ids private static final int EMPTY_SEQUENCE_VARIANT_INDEX = NucleotideSequence.ALPHABET.basicSize(); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java index 6488ea8df..e3b115ac3 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java @@ -365,10 +365,10 @@ public void test1() throws Exception { long uniq1 = StreamSupport.stream(CUtils.it(prep.createPort()).spliterator(), false) .mapToInt(l -> l[0]) - .filter(c -> c == 0xFFFFFFFF).count(); + .filter(c -> c == FullSeqAssembler.ABSENT_PACKED_VARIANT_INFO).count(); long uniq2 = StreamSupport.stream(CUtils.it(prep.createPort()).spliterator(), false) .mapToInt(l -> l[1]) - .filter(c -> c == 0xFFFFFFFF).count(); + .filter(c -> c == FullSeqAssembler.ABSENT_PACKED_VARIANT_INFO).count(); Assert.assertEquals(40, uniq1); Assert.assertEquals(60, uniq2); From 3544b6ec5fe2833be3aab1569884c63131cea533 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 18 Dec 2019 00:20:41 +0200 Subject: [PATCH 023/282] milib upgrade --- milib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/milib b/milib index 6b31cf02f..533df5a9a 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 6b31cf02f343fa2ee7551f90467b3af7925564df +Subproject commit 533df5a9a57515bbd157b1fb7083e7a64e2edff0 From 5edff24272642f4e0bf0548acbfc2103015afae1 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Sun, 22 Dec 2019 01:30:18 +0200 Subject: [PATCH 024/282] milib upgrade --- milib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/milib b/milib index 533df5a9a..4b828b2da 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 533df5a9a57515bbd157b1fb7083e7a64e2edff0 +Subproject commit 4b828b2da4436da99ca0be9f7d197db75ec43df5 From 3a733e6be39081452bddb90b4ebbbd6ed70b0f4d Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sun, 22 Dec 2019 23:02:52 +0200 Subject: [PATCH 025/282] Update repseqio dep --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a42249f5e..21eeb9cef 100644 --- a/pom.xml +++ b/pom.xml @@ -46,7 +46,7 @@ io.repseq repseqio - 1.3.3 + 1.3.4-SNAPSHOT com.milaboratory From 46cf82b5b29d41feae0fb60b7605f39905d5422a Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Fri, 27 Dec 2019 04:42:30 +0300 Subject: [PATCH 026/282] repseqio submodule upgrade --- repseqio | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repseqio b/repseqio index 44287c51e..453696077 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 44287c51eab339fb6d9c2add33052e97da6b2db4 +Subproject commit 4536960775c89d89943b6feeb0019cbfdc77e196 From 58dd0c8d879c707a159b770e43a25809e195d5bf Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Fri, 10 Jan 2020 19:48:52 +0300 Subject: [PATCH 027/282] Just in case. --- milib | 2 +- repseqio | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/milib b/milib index 4b828b2da..b322ae036 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 4b828b2da4436da99ca0be9f7d197db75ec43df5 +Subproject commit b322ae03667dc1dae95b3465bc10389e6a251491 diff --git a/repseqio b/repseqio index 453696077..a52a402ea 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 4536960775c89d89943b6feeb0019cbfdc77e196 +Subproject commit a52a402ea4a32c959a4e42d8e5cdddc2abdad4cf From b8be92151dd5393db08f87c284df429ab204ddd6 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 15 Jan 2020 13:01:22 +0300 Subject: [PATCH 028/282] Bump. --- itests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/itests.sh b/itests.sh index 64b592dc4..1a6b1a59c 100755 --- a/itests.sh +++ b/itests.sh @@ -27,7 +27,7 @@ function readlinkUniversal() { echo $result } -os=`uname` +os=$(uname) delta=100 dir="" From f3664397990ee797d40e501dad42aff06044db7a Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 15 Jan 2020 13:20:59 +0300 Subject: [PATCH 029/282] Fix for shade plugin. --- pom.xml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/pom.xml b/pom.xml index 21eeb9cef..f551c539d 100644 --- a/pom.xml +++ b/pom.xml @@ -265,6 +265,24 @@ ** + + ch.qos.logback:logback-classic + + ** + + + + ch.qos.logback:logback-core + + ** + + + + org.slf4j:slf4j-api + + ** + + From 42e48b2e96f515c5156beb8e897b072165d3693f Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 28 Jan 2020 19:00:09 +0500 Subject: [PATCH 030/282] debug wip --- .../mixcr/assembler/fullseq/FullSeqAssembler.java | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 7a1c3a1c7..51adff85a 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -265,8 +265,10 @@ public Clone[] callVariants(RawVariantsData data) { newBranches.add(branch.addExceptionalVariantInfo(variants.get(0).variantInfo)); else { int sumSignificant = 0; - for (Variant variant : variants) + for (Variant variant : variants) { + assert !isExceptionalPointVariantInfo(variant.variantInfo); sumSignificant += variant.nSignificant; + } for (Variant variant : variants) newBranches.add(branch.addVariant(variant, sumSignificant)); } @@ -1169,9 +1171,13 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe int bestVariant = -1; long bestVariantSumQuality = -1; + long maxSplittingPointsCount = 0; + ArrayList variants = new ArrayList<>(); do { if (currentIndex == count || currentVariant != (int) (targets[currentIndex] >>> 40)) { + maxSplittingPointsCount = Math.max(maxSplittingPointsCount, splittingPointsCount); + // Checking significance conditions if ((1.0 * splittingPointsCount / (currentIndex - blockBegin) >= parameters.minimalNonEdgePointsFraction) && variantSumQuality >= requiredMinimalSumQuality From a05c6de73c4ad8f665c84cc99682b2434fd56931 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 11 Feb 2020 14:44:35 +0300 Subject: [PATCH 031/282] Repseqio module upgrade. --- repseqio | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repseqio b/repseqio index 143eeb334..6937c8800 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 143eeb334e19402a670674f35dededf475b9c533 +Subproject commit 6937c88007f3c2ff66827c2f09a7b2d186bd0b62 From 862a35b2d73b82c5c58c4cabdf9f1f3372e89c7d Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 11 Feb 2020 14:46:56 +0300 Subject: [PATCH 032/282] Additionla fix. --- milib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/milib b/milib index cd564d4bf..a6c626746 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit cd564d4bf5c81be66d0bf168ad4e520e5c00a7c1 +Subproject commit a6c626746e3ce17761ecbf4fce30e416cff75196 From efb0a97569edcf71bddfdf9643c950e97c036662 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 11 Feb 2020 18:23:21 +0300 Subject: [PATCH 033/282] Tags support in assemblePartial --- .../mixcr/basictypes/TagTuple.java | 2 +- .../PartialAlignmentsAssembler.java | 33 ++++++++++++------- 2 files changed, 23 insertions(+), 12 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java index 4cd204d62..2d6518d7e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java @@ -8,7 +8,7 @@ public final class TagTuple { public static final TagTuple EMPTY = new TagTuple(new String[0]); public final String[] tags; - private transient final int hash; + private final int hash; public TagTuple(String... tags) { this.tags = tags; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 8f4454505..7e39200d6 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -48,8 +48,6 @@ import java.util.List; import java.util.concurrent.atomic.AtomicLong; -import static com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.getMMDescr; - public class PartialAlignmentsAssembler implements AutoCloseable, Report { final TLongObjectHashMap> kToIndexLeft = new TLongObjectHashMap<>(); final TLongHashSet alreadyMergedIds = new TLongHashSet(); @@ -169,7 +167,7 @@ public void run() { List mergedTargets = searchResult.result; VDJCMultiRead mRead = new VDJCMultiRead(mergedTargets); - final VDJCAlignments mAlignment = aligner.process(mRead).alignment; + final VDJCAlignments mAlignment = aligner.process(mRead).alignment.setTagCounter(searchResult.tagCounter); // Checking number of overlapped non-template (NRegion) letters int overlapTargetId = -1; @@ -264,11 +262,13 @@ static class OverlapSearchResult { final List originKMerList; final KMerInfo KMerInfo; final List result; + final TagCounter tagCounter; - public OverlapSearchResult(List originKMerList, KMerInfo KMerInfo, List result) { + public OverlapSearchResult(List originKMerList, KMerInfo KMerInfo, List result, TagCounter tagCounter) { this.originKMerList = originKMerList; this.KMerInfo = KMerInfo; this.result = result; + this.tagCounter = tagCounter; } void cancel() { @@ -297,6 +297,7 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, else stop -= kOffset; + TagTuple tagTuple = extractTagTuple(rightAl); // black list of left parts failed due to inconsistent overlapped alignments (failed AMerge) TLongHashSet blackList = new TLongHashSet(); SEARCH_LEFT_PARTS: @@ -307,7 +308,7 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, List maxOverlapList = null; boolean isMaxOverOverlapped = false; for (int rFrom = 0; rFrom < stop && rFrom + kValue < rightSeqQ.size(); rFrom++) { - long kMer = kMer(rightSeqQ.getSequence(), rFrom, kValue); + long kMer = kMer(tagTuple, rightSeqQ.getSequence(), rFrom, kValue); List match = kToIndexLeft.get(kMer); if (match == null) continue; @@ -320,6 +321,9 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, boolean isOverOverlapped = false; final VDJCAlignments leftAl = match.get(i).getAlignments(); + if (!extractTagTuple(leftAl).equals(tagTuple)) + continue; + if (blackList.contains(leftAl.getAlignmentsIndex())) continue; @@ -466,7 +470,7 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, result.addAll(rightDescriptors); // Ordering and filtering final targets - return new OverlapSearchResult(maxOverlapList, left, AlignedTarget.orderTargets(result)); + return new OverlapSearchResult(maxOverlapList, left, AlignedTarget.orderTargets(result), central.getAlignments().getTagCounter()); } } @@ -615,12 +619,19 @@ private static int getAlignmentLength(VDJCAlignments alignment, GeneType gt, int return al.getSequence2Range().length(); } + private static TagTuple extractTagTuple(VDJCAlignments alignments) { + TagCounter tagCounter = alignments.getTagCounter(); + if (tagCounter.size() > 1) + throw new IllegalArgumentException(); + if (tagCounter.size() == 0) + return TagTuple.EMPTY; + return tagCounter.iterator().key(); + } private boolean addLeftToIndex(VDJCAlignments alignment) { int leftTargetId = getLeftPartitionedSequence(alignment); if (leftTargetId == -1) return false; - VDJCPartitionedSequence left = alignment.getPartitionedTarget(leftTargetId); NSequenceWithQuality seq = left.getSequence(); @@ -629,9 +640,9 @@ private boolean addLeftToIndex(VDJCAlignments alignment) { noKMer.incrementAndGet(); return false; } - + TagTuple tagTuple = extractTagTuple(alignment); for (int kFrom = kFromFirst; kFrom < seq.size() - kValue; ++kFrom) { - long kmer = kMer(seq.getSequence(), kFrom, kValue); + long kmer = kMer(tagTuple, seq.getSequence(), kFrom, kValue); if (kmer == -1) { wildcardsInKMer.incrementAndGet(); continue; @@ -649,8 +660,8 @@ private boolean addLeftToIndex(VDJCAlignments alignment) { return true; } - private static long kMer(NucleotideSequence seq, int from, int length) { - long kmer = 0; + private static long kMer(TagTuple tagTuple, NucleotideSequence seq, int from, int length) { + long kmer = tagTuple == null ? 0 : tagTuple.hashCode(); for (int j = from; j < from + length; ++j) { byte c = seq.codeAt(j); if (NucleotideSequence.ALPHABET.isWildcard(c)) From 897920eaf55959bfb5a998ac0814f58e237ce425 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 11 Feb 2020 21:48:20 +0300 Subject: [PATCH 034/282] tag support in clna --- .../assembler/AlignmentsMappingMerger.java | 2 +- .../assembler/CloneClusteringParameters.java | 37 +++-- .../assembler/CloneClusteringStrategy.java | 9 ++ .../com/milaboratory/mixcr/basictypes/IO.java | 2 + .../mixcr/basictypes/TagCounterBuilder.java | 36 ++++- .../mixcr/basictypes/TagTuple.java | 3 +- .../mixcr/basictypes/VDJCAlignments.java | 5 + .../milaboratory/mixcr/cli/CommandAlign.java | 8 +- .../mixcr/cli/CommandAssemble.java | 135 +++++++++++++++++- .../PartialAlignmentsAssembler.java | 5 +- .../parameters/assembler_parameters.json | 1 + .../CloneAssemblerParametersTest.java | 4 +- .../assembler/CloneAssemblerRunnerTest.java | 2 +- .../CloneClusteringParametersTest.java | 3 +- .../mixcr/cli/JsonOverriderTest.java | 6 +- 15 files changed, 221 insertions(+), 37 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java index d8d836f30..9449d5c24 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java @@ -62,7 +62,7 @@ public void close() { if (readToCloneMappings instanceof AutoCloseable) ((AutoCloseable) readToCloneMappings).close(); } catch (Exception e) { - e.printStackTrace(); + throw new RuntimeException(e); } } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java index 8da0750f1..d685d305a 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java @@ -34,11 +34,14 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.core.tree.TreeSearchParameters; +import java.util.Objects; + @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE) public final class CloneClusteringParameters implements java.io.Serializable { private int searchDepth; private int allowedMutationsInNRegions; + private double minimalTagSetOverlap; private TreeSearchParameters searchParameters; private ClusteringFilter clusteringFilter; @@ -46,10 +49,12 @@ public final class CloneClusteringParameters implements java.io.Serializable { public CloneClusteringParameters( @JsonProperty("searchDepth") int searchDepth, @JsonProperty("allowedMutationsInNRegions") int allowedMutationsInNRegions, + @JsonProperty("minimalTagSetOverlap") double minimalTagSetOverlap, @JsonProperty("searchParameters") TreeSearchParameters searchParameters, @JsonProperty("clusteringFilter") ClusteringFilter clusteringFilter) { this.searchDepth = searchDepth; this.allowedMutationsInNRegions = allowedMutationsInNRegions; + this.minimalTagSetOverlap = minimalTagSetOverlap; this.searchParameters = searchParameters; this.clusteringFilter = clusteringFilter; } @@ -90,32 +95,34 @@ public CloneClusteringParameters setClusteringFilter(ClusteringFilter clustering return this; } + public double getMinimalTagSetOverlap() { + return minimalTagSetOverlap; + } + + public CloneClusteringParameters setMinimalTagSetOverlap(double minimalTagSetOverlap) { + this.minimalTagSetOverlap = minimalTagSetOverlap; + return this; + } + @Override public CloneClusteringParameters clone() { - return new CloneClusteringParameters(searchDepth, allowedMutationsInNRegions, searchParameters, clusteringFilter); + return new CloneClusteringParameters(searchDepth, allowedMutationsInNRegions, minimalTagSetOverlap, searchParameters, clusteringFilter); } @Override public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof CloneClusteringParameters)) return false; - + if (o == null || getClass() != o.getClass()) return false; CloneClusteringParameters that = (CloneClusteringParameters) o; - - if (allowedMutationsInNRegions != that.allowedMutationsInNRegions) return false; - if (searchDepth != that.searchDepth) return false; - if (!clusteringFilter.equals(that.clusteringFilter)) return false; - if (!searchParameters.equals(that.searchParameters)) return false; - - return true; + return getSearchDepth() == that.getSearchDepth() && + getAllowedMutationsInNRegions() == that.getAllowedMutationsInNRegions() && + Double.compare(that.minimalTagSetOverlap, minimalTagSetOverlap) == 0 && + Objects.equals(getSearchParameters(), that.getSearchParameters()) && + Objects.equals(getClusteringFilter(), that.getClusteringFilter()); } @Override public int hashCode() { - int result = searchDepth; - result = 31 * result + allowedMutationsInNRegions; - result = 31 * result + searchParameters.hashCode(); - result = 31 * result + clusteringFilter.hashCode(); - return result; + return Objects.hash(getSearchDepth(), getAllowedMutationsInNRegions(), minimalTagSetOverlap, getSearchParameters(), getClusteringFilter()); } } \ No newline at end of file diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java index b8dc997ea..bee8f6185 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java @@ -36,6 +36,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.tree.NeighborhoodIterator; import com.milaboratory.core.tree.TreeSearchParameters; +import com.milaboratory.mixcr.basictypes.TagCounterBuilder; public class CloneClusteringStrategy implements ClusteringStrategy { final CloneClusteringParameters parameters; @@ -54,6 +55,14 @@ public boolean canAddToCluster(Cluster cluster, Mutations currentMutations = iterator.getCurrentMutations(); if (!cluster.getHead().getSequence().isCompatible(minorObject.getSequence(), currentMutations)) return false; + double minimalTagSetOverlap = parameters.getMinimalTagSetOverlap(); + if (minimalTagSetOverlap > 0) { + TagCounterBuilder headTags = cluster.getHead().tagBuilder; + TagCounterBuilder minorTags = minorObject.tagBuilder; + if (headTags.intersectionFractionOf(minorTags) >= minimalTagSetOverlap) + return true; + } + Range[] nRegions = cluster.getHead().getNRegions(); int nMismatches = parameters.getAllowedMutationsInNRegions(); out: diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index c9413063c..4ce223f2e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -97,6 +97,8 @@ public void write(PrimitivO output, TagCounter object) { @Override public TagCounter read(PrimitivI input) { int len = input.readInt(); + if (len == 0) + return TagCounter.EMPTY; TObjectDoubleHashMap r = new TObjectDoubleHashMap<>(len, Constants.DEFAULT_LOAD_FACTOR, 0.0); for (int i = 0; i < len; ++i) { String[] tags = input.readObject(String[].class); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java index 5f32dd29e..bdb54af7a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java @@ -8,12 +8,10 @@ * */ public class TagCounterBuilder { - private final TObjectDoubleHashMap agg; + private TObjectDoubleHashMap agg; private boolean destroyed = false; - public TagCounterBuilder() { - this.agg = new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, 0.0); - } + public TagCounterBuilder() {} public TagCounterBuilder add(TagTuple tc, double count) { return add(new TagCounter(tc, count)); @@ -27,10 +25,20 @@ public TagCounterBuilder add(TagCounterBuilder tc) { return add(tc.agg); } + private void ensureInitialized() { + if (agg == null) + agg = new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, 0.0); + } + public TagCounterBuilder add(TObjectDoubleHashMap tc) { if (destroyed) throw new IllegalStateException("destroyed"); + if (tc.size() == 0) + return this; + + ensureInitialized(); + if (agg.isEmpty()) { agg.putAll(tc); return this; @@ -47,10 +55,30 @@ public TagCounterBuilder add(TObjectDoubleHashMap tc) { return this; } + public double intersectionFractionOf(TagCounterBuilder minor) { + if (agg == null || minor.agg == null) + throw new IllegalStateException("tag aware clusterization for non-tagged clones."); + + TObjectDoubleIterator it = minor.agg.iterator(); + double minorTotal = 0, totalIntersection = 0; + while (it.hasNext()) { + it.advance(); + TagTuple key = it.key(); + double v = it.value(); + minorTotal += v; + if (agg.containsKey(key)) + totalIntersection += v; + } + return totalIntersection / minorTotal; + } + public TagCounter createAndDestroy() { if (destroyed) throw new IllegalStateException("destroyed"); + if (agg == null) + return TagCounter.EMPTY; + TagCounter r = new TagCounter(new TObjectDoubleHashMap<>(agg)); destroyed = true; return r; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java index 2d6518d7e..b6e1e3409 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java @@ -6,11 +6,12 @@ * */ public final class TagTuple { - public static final TagTuple EMPTY = new TagTuple(new String[0]); public final String[] tags; private final int hash; public TagTuple(String... tags) { + if (tags.length == 0) + throw new IllegalArgumentException(); this.tags = tags; this.hash = Arrays.hashCode(tags); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index c53b7356d..270e38999 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -160,6 +160,11 @@ public VDJCAlignments updateCloneIndex(int newCloneIndex) { mappingType, newCloneIndex); } + public VDJCAlignments updateCloneIndexAndMappingType(int newCloneIndex, byte newMappingType) { + return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads, + newMappingType, newCloneIndex); + } + public VDJCAlignments updateAlignments(Function, Alignment> processor) { EnumMap newHits = this.hits.clone(); newHits.replaceAll((k, v) -> Arrays.stream(v).map(h -> h.mapAlignments(processor)).toArray(VDJCHit[]::new)); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 40773a795..d02a87745 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -68,7 +68,10 @@ import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.*; import picocli.CommandLine; -import picocli.CommandLine.*; +import picocli.CommandLine.Command; +import picocli.CommandLine.ExecutionException; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; import java.io.IOException; import java.nio.file.Paths; @@ -575,7 +578,8 @@ public String getStatus() { } } - alignment = alignment.setTagCounter(new TagCounter(parseTags(this.spec.commandLine(), tags, read))); + if (!tags.isEmpty()) + alignment = alignment.setTagCounter(new TagCounter(parseTags(this.spec.commandLine(), tags, read))); if (alignment.isChimera()) report.onChimera(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index d5af9874b..fd5d4574d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -29,15 +29,22 @@ */ package com.milaboratory.mixcr.cli; +import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.util.StatusReporter; -import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.*; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.SmartProgressReporter; +import gnu.trove.iterator.TObjectDoubleIterator; +import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; +import io.repseq.core.VDJCGeneId; import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -90,6 +97,12 @@ public void setThreads(int threads) { names = {"-a", "--write-alignments"}) public boolean clna = false; + @Option(description = "Enable tag-based read to clone assignment", + names = {"--attach-reads-by-tags"}) + public boolean attachReadsByTags = false; + + private static final double DEFAULT_MINIMAL_TAG_SET_OVERLAP = 0.7; + @Option(names = "-O", description = "Overrides default parameter values.") private Map overrides = new HashMap<>(); @@ -123,6 +136,9 @@ private void initializeParameters() { throwValidationException("Unknown parameters: " + assemblerParametersName); assemblerParameters = assemblerParameters.updateFrom(alignerParameters); + if (attachReadsByTags) + assemblerParameters = assemblerParameters.setCloneClusteringParameters(assemblerParameters.getCloneClusteringParameters().setMinimalTagSetOverlap(DEFAULT_MINIMAL_TAG_SET_OVERLAP)); + // Overriding JSON parameters if (!overrides.isEmpty()) { assemblerParameters = JsonOverrider.override(assemblerParameters, CloneAssemblerParameters.class, @@ -207,7 +223,31 @@ public void run1() throws Exception { // Writing results PipelineConfiguration pipelineConfiguration = getFullPipelineConfiguration(); - if (clna) + if (clna) { + + +// +// try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(alignmentsProvider.create(), +// assembler.getAssembledReadsPort())) { +// +// VDJCAlignments al; +// while ((al = merged.take()) != null) { +// if (al.getCloneIndex() != -1) +// continue; +// +// TagCounter tg = al.getTagCounter(); +// assert tg.size() == 1; +// TagTuple tags = tg.iterator().key(); +// if (al.getBestHit(GeneType.Variable) != null) { +// TagSignature sig = new TagSignature(tags, al.getBestHit(GeneType.Variable).getGene().getId()); +// Integer cloneId = tagsToClones.get(sig); +// if (cloneId != null) { +// +// } +// } +// } +// } + try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out)) { // writer will supply current stage and completion percent to the progress reporter SmartProgressReporter.startProgressReport(writer); @@ -217,11 +257,70 @@ public void run1() throws Exception { // Pre-soring alignments try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(alignmentsProvider.create(), assembler.getAssembledReadsPort())) { - writer.sortAlignments(merged, assembler.getAlignmentsCount()); + OutputPort port = merged; + if (attachReadsByTags) { + Map tagsToClones = new HashMap<>(); + int ambiguousAttachments = 0; + for (int i = 0; i < cloneSet.size(); i++) { + Clone clone = cloneSet.get(i); + assert i == clone.getId(); + TagCounter tags = clone.getTagCounter(); + TObjectDoubleIterator it = tags.iterator(); + while (it.hasNext()) { + it.advance(); + TagTuple tag = it.key(); + for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { + TagSignature sig = new TagSignature(tag, clone.getBestHit(gt).getGene().getId()); + Integer id = tagsToClones.get(sig); + if (id != null) { + tagsToClones.put(sig, -1); + ++ambiguousAttachments; + } else + tagsToClones.put(sig, clone.getId()); + } + } + } + + System.out.println("Ambiguous attachment: " + ambiguousAttachments); + + tagsToClones.entrySet().removeIf(e -> e.getValue() < 0); + + port = () -> { + VDJCAlignments al = merged.take(); + if (al == null || al.getMappingType() != ReadToCloneMapping.MappingType.Dropped) + return al; + + TagCounter tg = al.getTagCounter(); + assert tg.size() == 1; + TagTuple tags = tg.iterator().key(); + + VDJCHit hit; + + int cloneMapping = -1; // -1 for not assigned, -2 for ambiguous + for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { + if ((hit = al.getBestHit(gt)) != null) { + TagSignature sig = new TagSignature(tags, hit.getGene().getId()); + Integer cloneId = tagsToClones.get(sig); + if (cloneId != null) + if (cloneMapping != -1 && cloneMapping != cloneId) + cloneMapping = -2; + else + cloneMapping = cloneId; + } + } + + if (cloneMapping >= 0) + return setMappingCloneIndex(al, cloneMapping); + + return al; + }; + } + + writer.sortAlignments(port, assembler.getAlignmentsCount()); } writer.writeAlignmentsAndIndex(); } - else + } else try (ClnsWriter writer = new ClnsWriter(pipelineConfiguration, cloneSet, out)) { SmartProgressReporter.startProgressReport(writer); writer.write(); @@ -247,6 +346,34 @@ public void run1() throws Exception { } } + private static VDJCAlignments setMappingCloneIndex(VDJCAlignments al, int cloneIndex) { + return al.updateCloneIndexAndMappingType(cloneIndex, ReadToCloneMapping.ADDITIONAL_MAPPING_MASK); + } + + private static final class TagSignature { + final TagTuple tags; + final VDJCGeneId gene; + + public TagSignature(TagTuple tags, VDJCGeneId gene) { + this.tags = tags; + this.gene = gene; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagSignature that = (TagSignature) o; + return tags.equals(that.tags) && + gene.equals(that.gene); + } + + @Override + public int hashCode() { + return Objects.hash(tags, gene); + } + } + @JsonAutoDetect( fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 7e39200d6..53b152d92 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -46,6 +46,7 @@ import java.io.IOException; import java.util.ArrayList; import java.util.List; +import java.util.Objects; import java.util.concurrent.atomic.AtomicLong; public class PartialAlignmentsAssembler implements AutoCloseable, Report { @@ -321,7 +322,7 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, boolean isOverOverlapped = false; final VDJCAlignments leftAl = match.get(i).getAlignments(); - if (!extractTagTuple(leftAl).equals(tagTuple)) + if (!Objects.equals(extractTagTuple(leftAl), tagTuple)) continue; if (blackList.contains(leftAl.getAlignmentsIndex())) @@ -624,7 +625,7 @@ private static TagTuple extractTagTuple(VDJCAlignments alignments) { if (tagCounter.size() > 1) throw new IllegalArgumentException(); if (tagCounter.size() == 0) - return TagTuple.EMPTY; + return null; return tagCounter.iterator().key(); } diff --git a/src/main/resources/parameters/assembler_parameters.json b/src/main/resources/parameters/assembler_parameters.json index 92366e5a4..1c2278e49 100644 --- a/src/main/resources/parameters/assembler_parameters.json +++ b/src/main/resources/parameters/assembler_parameters.json @@ -14,6 +14,7 @@ "searchDepth": 2, "allowedMutationsInNRegions": 1, "searchParameters": "twoMismatchesOrIndels", + "minimalTagSetOverlap": -1, "clusteringFilter": { "type": "relativeConcentration", "specificMutationProbability": 1E-3 diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java index 9bef6cb80..40d569a65 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java @@ -53,7 +53,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12, QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), + new CloneClusteringParameters(2, 1,-1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2", (byte) 15); String str = GlobalObjectMappers.PRETTY.writeValueAsString(params); @@ -81,7 +81,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12, QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), + new CloneClusteringParameters(2, 1, -1,TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); String str = GlobalObjectMappers.PRETTY.writeValueAsString(params); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index 94e507abf..df785253c 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -117,7 +117,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException CloneAssemblerParameters assemblerParameters = new CloneAssemblerParameters( new GeneFeature[]{GeneFeature.CDR3}, 12, QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), + new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2 of 6", (byte) 15); System.out.println(GlobalObjectMappers.toOneLine(assemblerParameters)); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java index 877c8aed4..eba2323cc 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java @@ -29,7 +29,6 @@ */ package com.milaboratory.mixcr.assembler; -import com.fasterxml.jackson.databind.JsonNode; import com.milaboratory.core.tree.TreeSearchParameters; import com.milaboratory.util.GlobalObjectMappers; import org.junit.Test; @@ -39,7 +38,7 @@ public class CloneClusteringParametersTest { @Test public void test1() throws Exception { - CloneClusteringParameters paramentrs = new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)); + CloneClusteringParameters paramentrs = new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)); String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); CloneClusteringParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneClusteringParameters.class); assertEquals(paramentrs, deser); diff --git a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java index 6df9c0904..aad2e9766 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java @@ -97,7 +97,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12, QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), + new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); CloneAssemblerParameters override = JsonOverrider.override( @@ -107,7 +107,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge CloneAssemblerParameters expected = new CloneAssemblerParameters(new GeneFeature[]{new GeneFeature(GeneFeature.CDR1, -5, +6), GeneFeature.CDR2}, 12, QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), + new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); @@ -126,7 +126,7 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12, QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), + new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); CloneAssemblerParameters override = JsonOverrider.override( From ead07686798ff4d2c161e73042d5d658b4713e7c Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 11 Feb 2020 22:03:12 +0300 Subject: [PATCH 035/282] Fixes --- .../java/com/milaboratory/mixcr/cli/CommandAssemble.java | 4 +++- .../mixcr/partialassembler/PartialAlignmentsAssembler.java | 5 ++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index fd5d4574d..6c774c0d2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -292,7 +292,9 @@ public void run1() throws Exception { TagCounter tg = al.getTagCounter(); assert tg.size() == 1; - TagTuple tags = tg.iterator().key(); + TObjectDoubleIterator it = tg.iterator(); + it.advance(); + TagTuple tags = it.key(); VDJCHit hit; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 53b152d92..c87ec065b 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -39,6 +39,7 @@ import com.milaboratory.mixcr.cli.Report; import com.milaboratory.mixcr.cli.ReportHelper; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TLongObjectHashMap; import gnu.trove.set.hash.TLongHashSet; import io.repseq.core.*; @@ -626,7 +627,9 @@ private static TagTuple extractTagTuple(VDJCAlignments alignments) { throw new IllegalArgumentException(); if (tagCounter.size() == 0) return null; - return tagCounter.iterator().key(); + final TObjectDoubleIterator it = tagCounter.iterator(); + it.advance(); + return it.key(); } private boolean addLeftToIndex(VDJCAlignments alignment) { From 6e4bbed573be264aad22086e63aa489e2eddb276 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 12 Feb 2020 13:56:19 +0300 Subject: [PATCH 036/282] Full tag support in assemble contigs --- .../assembler/fullseq/FullSeqAssembler.java | 17 +++++++++---- .../mixcr/basictypes/VDJCObject.java | 14 +++++++++++ .../milaboratory/mixcr/cli/AlignerReport.java | 24 +++++++++++++++++++ .../mixcr/cli/CloneAssemblerReport.java | 24 ++++++++++++++++++- .../mixcr/cli/CommandAssemble.java | 22 ++++++++--------- .../milaboratory/mixcr/cli/ReportHelper.java | 8 +++++++ .../mixcr/vdjaligners/VDJCAligner.java | 11 +++++---- .../vdjaligners/VDJCAlignerEventListener.java | 4 ++++ 8 files changed, 102 insertions(+), 22 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index c1cf63c6a..3d04daf9d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -1527,12 +1527,18 @@ private static final class VariantAggregator { } PointSequence[] toPointSequences(VDJCAlignments alignments) { + Stream assemblingFeaturePointSeq; NSequenceWithQuality assemblingFeature = alignments.getFeature(this.assemblingFeature); - byte quality = assemblingFeature.getQuality().minValue(); - //if (!inSplitRegion(positionOfAssemblingFeature)) - quality |= 0x80; + if (assemblingFeature != null) { + byte quality = assemblingFeature.getQuality().minValue(); + //if (!inSplitRegion(positionOfAssemblingFeature)) + quality |= 0x80; + assemblingFeaturePointSeq = Stream.of(new PointSequence(positionOfAssemblingFeature, assemblingFeature, quality)); + } else + assemblingFeaturePointSeq = Stream.empty(); + return Stream.concat( - Stream.of(new PointSequence(positionOfAssemblingFeature, assemblingFeature, quality)), + assemblingFeaturePointSeq, IntStream.range(0, alignments.numberOfTargets()) .mapToObj(i -> toPointSequences(alignments, i)) .flatMap(Collection::stream) @@ -1753,7 +1759,8 @@ private boolean inSplitRegion(int p) { } /** - * Check that the V/J gene can be used for full sequence assembly algorithm. Basically it checks that is has required reference points defined. + * Check that the V/J gene can be used for full sequence assembly algorithm. Basically it checks that is has + * required reference points defined. * * @param hit hit to check * @param assemblingFeature clonal assembling feature diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index a879328d7..dc7c49872 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -76,6 +76,20 @@ protected static EnumMap createHits(VDJCHit[] vHits, VDJCHi return hits; } + public boolean isAvailable(GeneFeature geneFeature) { + for (int i = 0; i < targets.length; ++i) + if (getPartitionedTarget(i).getPartitioning().isAvailable(geneFeature)) + return true; + return false; + } + + public boolean isAvailable(ReferencePoint referencePoint) { + for (int i = 0; i < targets.length; ++i) + if (getPartitionedTarget(i).getPartitioning().isAvailable(referencePoint)) + return true; + return false; + } + @SuppressWarnings("unchecked") private Set getGenes(GeneType gt) { VDJCHit[] hits = getHits(gt); diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 78b279a6b..179a3c20d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -49,6 +49,8 @@ public final class AlignerReport extends AbstractCommandReport implements VDJCAl private final AtomicLong chimeras = new AtomicLong(0); private final AtomicLong alignedSequenceOverlap = new AtomicLong(0); private final AtomicLong alignedAlignmentOverlap = new AtomicLong(0); + private final AtomicLong noCDR3PartsAlignments = new AtomicLong(0); + private final AtomicLong partialAlignments = new AtomicLong(0); private final AtomicLong nonAlignedOverlap = new AtomicLong(0); private final AtomicLong topHitConflict = new AtomicLong(0); private final AtomicLong vChimeras = new AtomicLong(0); @@ -234,6 +236,26 @@ public void onChimera() { chimeras.incrementAndGet(); } + @JsonProperty("noCDR3PartsAlignments") + public long getNoCDR3PartsAlignments() { + return noCDR3PartsAlignments.get(); + } + + @JsonProperty("partialAlignments") + public long getPartialAlignments() { + return partialAlignments.get(); + } + + @Override + public void onNoCDR3PartsAlignment() { + noCDR3PartsAlignments.incrementAndGet(); + } + + @Override + public void onPartialAlignment() { + partialAlignments.incrementAndGet(); + } + @Override public void onRealignmentWithForcedNonFloatingBound(boolean forceLeftEdgeInRight, boolean forceRightEdgeInLeft) { realignedWithForcedNonFloatingBound.getAndIncrement(); @@ -267,6 +289,8 @@ public void writeReport(ReportHelper helper) { helper.writePercentAndAbsoluteField("Overlapped and aligned", getAlignedOverlaps(), total); helper.writePercentAndAbsoluteField("Alignment-aided overlaps", getAlignmentOverlaps(), getAlignedOverlaps()); helper.writePercentAndAbsoluteField("Overlapped and not aligned", getNonAlignedOverlaps(), total); + helper.writePercentAndAbsoluteFieldNonZero("No CDR3 parts alignments, percent of successfully aligned", getNoCDR3PartsAlignments(), success); + helper.writePercentAndAbsoluteFieldNonZero("Partial aligned reads, percent of successfully aligned", getPartialAlignments(), success); if (getVChimeras() != 0) helper.writePercentAndAbsoluteField("V gene chimeras", getVChimeras(), total); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index 66eb02d40..3d9f3a48e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -56,6 +56,8 @@ public final class CloneAssemblerReport extends AbstractCommandReport implements final AtomicInteger clonesPreClustered = new AtomicInteger(); final AtomicLong readsPreClustered = new AtomicLong(); final AtomicLong readsClustered = new AtomicLong(); + final AtomicLong readsAttachedByTags = new AtomicLong(); + final AtomicLong readsWithAmbiguousAttachmentsByTags = new AtomicLong(); @Override public String getCommand() { @@ -151,6 +153,16 @@ public ChainUsageStats getClonalChainUsage() { return chainStats; } + @JsonProperty("readsAttachedByTags") + public long getReadsAttachedByTags() { + return readsAttachedByTags.get(); + } + + @JsonProperty("readsWithAmbiguousAttachmentsByTags") + public long getReadsWithAmbiguousAttachmentsByTags() { + return readsWithAmbiguousAttachmentsByTags.get(); + } + @Override public void onNewCloneCreated(CloneAccumulator accumulator) { clonesCreated.incrementAndGet(); @@ -221,6 +233,14 @@ public void setTotalReads(long totalReads) { this.totalReads = totalReads; } + public void onReadAttachedByTags() { + readsAttachedByTags.incrementAndGet(); + } + + public void onReadWithAmbiguousAttachmentsByTags() { + readsWithAmbiguousAttachmentsByTags.incrementAndGet(); + } + @Override public void writeReport(ReportHelper helper) { // Writing common analysis information @@ -253,7 +273,9 @@ public void writeReport(ReportHelper helper) { .writePercentAndAbsoluteField("Reads dropped with low quality clones, percent of total", readsDroppedWithClones.get(), totalReads) .writeField("Clonotypes eliminated by PCR error correction", clonesClustered.get()) .writeField("Clonotypes dropped as low quality", clonesDropped.get()) - .writeField("Clonotypes pre-clustered due to the similar VJC-lists", clonesPreClustered.get()); + .writeField("Clonotypes pre-clustered due to the similar VJC-lists", clonesPreClustered.get()) + .writePercentAndAbsoluteField("Partially aligned reads attached to clones by tags", readsAttachedByTags.get(), totalReads) + .writePercentAndAbsoluteField("Partially aligned reads with ambiguous clone attachments by tags", readsWithAmbiguousAttachmentsByTags.get(), totalReads); // Writing distribution by chains chainStats.writeReport(helper); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 6c774c0d2..f01d94029 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -42,10 +42,7 @@ import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.iterator.TObjectDoubleIterator; -import io.repseq.core.GeneType; -import io.repseq.core.VDJCGene; -import io.repseq.core.VDJCGeneId; -import io.repseq.core.VDJCLibraryRegistry; +import io.repseq.core.*; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -260,7 +257,6 @@ public void run1() throws Exception { OutputPort port = merged; if (attachReadsByTags) { Map tagsToClones = new HashMap<>(); - int ambiguousAttachments = 0; for (int i = 0; i < cloneSet.size(); i++) { Clone clone = cloneSet.get(i); assert i == clone.getId(); @@ -272,22 +268,21 @@ public void run1() throws Exception { for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { TagSignature sig = new TagSignature(tag, clone.getBestHit(gt).getGene().getId()); Integer id = tagsToClones.get(sig); - if (id != null) { + if (id != null) tagsToClones.put(sig, -1); - ++ambiguousAttachments; - } else + else tagsToClones.put(sig, clone.getId()); } } } - System.out.println("Ambiguous attachment: " + ambiguousAttachments); - tagsToClones.entrySet().removeIf(e -> e.getValue() < 0); port = () -> { VDJCAlignments al = merged.take(); - if (al == null || al.getMappingType() != ReadToCloneMapping.MappingType.Dropped) + if (al == null + || al.getMappingType() != ReadToCloneMapping.MappingType.Dropped + || al.getFeature(new GeneFeature(assemblerParameters.getAssemblingFeatures())) != null) return al; TagCounter tg = al.getTagCounter(); @@ -311,8 +306,11 @@ public void run1() throws Exception { } } - if (cloneMapping >= 0) + if (cloneMapping >= 0) { + report.onReadAttachedByTags(); return setMappingCloneIndex(al, cloneMapping); + } else if (cloneMapping == -2) + report.onReadWithAmbiguousAttachmentsByTags(); return al; }; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java index e22b25896..f2097e74e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java @@ -78,6 +78,14 @@ public ReportHelper writePercentAndAbsoluteField(String fieldName, long value, l return this; } + public ReportHelper writePercentAndAbsoluteFieldNonZero(String fieldName, long value, long total) { + if (value == 0) + return this; + double percent = 100.0 * value / total; + printStream.println(fieldName + ": " + value + " (" + Util.PERCENT_FORMAT.format(percent) + "%)"); + return this; + } + public ReportHelper writePercentAndAbsoluteField(String fieldName, double value, double total) { double percent = 100.0 * value / total; printStream.println(fieldName + ": " + value + " (" + Util.PERCENT_FORMAT.format(percent) + "%)"); diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java index 70d4fe058..9bb0a55d6 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java @@ -37,9 +37,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.util.HashFunctions; import com.milaboratory.util.RandomUtil; -import io.repseq.core.Chains; -import io.repseq.core.GeneType; -import io.repseq.core.VDJCGene; +import io.repseq.core.*; import java.util.ArrayList; import java.util.Collections; @@ -101,8 +99,13 @@ protected final void onFailedAlignment(SequenceRead read, VDJCAlignmentFailCause } protected final void onSuccessfulAlignment(SequenceRead read, VDJCAlignments alignment) { - if (listener != null) + if (listener != null) { listener.onSuccessfulAlignment(read, alignment); + if (!alignment.isAvailable(ReferencePoint.CDR3Begin) && !alignment.isAvailable(ReferencePoint.CDR3End)) + listener.onNoCDR3PartsAlignment(); + else if (!alignment.isAvailable(GeneFeature.CDR3)) + listener.onPartialAlignment(); + } } protected final void onSegmentChimeraDetected(GeneType geneType, SequenceRead read, VDJCAlignments alignment) { diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java index 4483442eb..57dc696f5 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java @@ -64,4 +64,8 @@ public interface VDJCAlignerEventListener { /** only for paired-end PV-first aligner */ void onRealignmentWithForcedNonFloatingBound(boolean forceLeftEdgeInRight, boolean forceRightEdgeInLeft); + + void onNoCDR3PartsAlignment(); + + void onPartialAlignment(); } From 4e9153e465c3ec320601504a170f7ae20d745ab6 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 12 Feb 2020 15:10:20 +0300 Subject: [PATCH 037/282] Default value for --threads in extend. --- src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 37ff51e7d..5247d2274 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -78,7 +78,7 @@ public class CommandExtend extends ACommandWithSmartOverwriteWithSingleInputMiXC names = {"-q", "--quality"}) public byte extensionQuality = 30; - public int threads = 2; + public int threads = Runtime.getRuntime().availableProcessors();; @Option(description = "Processing threads", names = {"-t", "--threads"}) From 5db4bd8d44f495a2247f11e87bb27236a669f914 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 12 Feb 2020 15:56:01 +0300 Subject: [PATCH 038/282] additional field to report --- .../mixcr/cli/CloneAssemblerReport.java | 14 +++++++++++++- .../milaboratory/mixcr/cli/CommandAssemble.java | 2 ++ 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index 3d9f3a48e..82e99aad9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -57,6 +57,7 @@ public final class CloneAssemblerReport extends AbstractCommandReport implements final AtomicLong readsPreClustered = new AtomicLong(); final AtomicLong readsClustered = new AtomicLong(); final AtomicLong readsAttachedByTags = new AtomicLong(); + final AtomicLong readsFailedToAttachedByTags = new AtomicLong(); final AtomicLong readsWithAmbiguousAttachmentsByTags = new AtomicLong(); @Override @@ -163,6 +164,11 @@ public long getReadsWithAmbiguousAttachmentsByTags() { return readsWithAmbiguousAttachmentsByTags.get(); } + @JsonProperty("readsFailedToAttachedByTags") + public long getReadsFailedToAttachedByTags() { + return readsFailedToAttachedByTags.get(); + } + @Override public void onNewCloneCreated(CloneAccumulator accumulator) { clonesCreated.incrementAndGet(); @@ -241,6 +247,10 @@ public void onReadWithAmbiguousAttachmentsByTags() { readsWithAmbiguousAttachmentsByTags.incrementAndGet(); } + public void onReadsFailedToAttachedByTags() { + readsFailedToAttachedByTags.incrementAndGet(); + } + @Override public void writeReport(ReportHelper helper) { // Writing common analysis information @@ -275,7 +285,9 @@ public void writeReport(ReportHelper helper) { .writeField("Clonotypes dropped as low quality", clonesDropped.get()) .writeField("Clonotypes pre-clustered due to the similar VJC-lists", clonesPreClustered.get()) .writePercentAndAbsoluteField("Partially aligned reads attached to clones by tags", readsAttachedByTags.get(), totalReads) - .writePercentAndAbsoluteField("Partially aligned reads with ambiguous clone attachments by tags", readsWithAmbiguousAttachmentsByTags.get(), totalReads); + .writePercentAndAbsoluteField("Partially aligned reads with ambiguous clone attachments by tags", readsWithAmbiguousAttachmentsByTags.get(), totalReads) + .writePercentAndAbsoluteField("Partially aligned reads failed to attach to clones by tags", readsFailedToAttachedByTags.get(), totalReads); + ; // Writing distribution by chains chainStats.writeReport(helper); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index f01d94029..3e754c377 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -311,6 +311,8 @@ public void run1() throws Exception { return setMappingCloneIndex(al, cloneMapping); } else if (cloneMapping == -2) report.onReadWithAmbiguousAttachmentsByTags(); + else + report.onReadsFailedToAttachedByTags(); return al; }; From 72fa5cdc29d1fd5cf7fd315551774bb87d2cb40e Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 12 Feb 2020 17:13:39 +0300 Subject: [PATCH 039/282] Better tags support in export --- .../mixcr/basictypes/TagCounter.java | 54 +++++++++++++++++++ .../milaboratory/mixcr/cli/CommandExport.java | 45 +++++++--------- .../mixcr/export/FieldExtractors.java | 54 +++++++++++++++---- 3 files changed, 119 insertions(+), 34 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java index 819920200..6908d8de5 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java @@ -1,9 +1,16 @@ package com.milaboratory.mixcr.basictypes; import com.milaboratory.primitivio.annotations.Serializable; +import gnu.trove.TDoubleCollection; +import gnu.trove.iterator.TDoubleIterator; import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TObjectDoubleHashMap; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; + /** * */ @@ -97,4 +104,51 @@ public boolean equals(Object o) { public int hashCode() { return tags.hashCode(); } + + public TagCounter[] splitBy(int index) { + Map map = new HashMap<>(); + TObjectDoubleIterator it = iterator(); + while (it.hasNext()) { + it.advance(); + + TagTuple t = it.key(); + double count = it.value(); + + TagCounterBuilder tb = map.computeIfAbsent(t.tags[index], __ -> new TagCounterBuilder()); + tb.add(t, count); + } + return map.values().stream().map(TagCounterBuilder::createAndDestroy).toArray(TagCounter[]::new); + } + + public double sum() { + TDoubleCollection c = tags.valueCollection(); + TDoubleIterator it = c.iterator(); + double sum = 0; + while (it.hasNext()) + sum += it.next(); + return sum; + } + + public TagCounter toFractions() { + double sum = sum(); + if (sum == 0) + return this; + TObjectDoubleHashMap result = new TObjectDoubleHashMap<>(); + TObjectDoubleIterator it = iterator(); + while (it.hasNext()) { + it.advance(); + result.put(it.key(), it.value() / sum); + } + return new TagCounter(result); + } + + public Set tags(int index) { + Set set = new HashSet<>(); + TObjectDoubleIterator it = iterator(); + while (it.hasNext()) { + it.advance(); + set.add(it.key().tags[index]); + } + return set; + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 24d93599b..4ecd92df9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -40,7 +40,6 @@ import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.CanReportProgressAndStage; import com.milaboratory.util.SmartProgressReporter; -import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.Chains; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -56,6 +55,7 @@ import java.io.IOException; import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; import static cc.redberry.primitives.FilterUtil.ACCEPT_ALL; import static cc.redberry.primitives.FilterUtil.and; @@ -243,8 +243,8 @@ public static class CommandExportClones extends CommandExport { public long minCount = 0; @Option(description = "Split clones by tag values", - names = {"--split-by-tags"}) - public boolean splitByTag = false; + names = {"--split-by-tag"}) + public List splitByTag = new ArrayList<>(); public CommandExportClones() { super(Clone.class); @@ -272,7 +272,7 @@ void run1(List> exporters) throws Exception { break; } } - ExportClones exportClones = new ExportClones(set, writer, limit, splitByTag); + ExportClones exportClones = new ExportClones(set, writer, limit, splitByTag.stream().mapToInt(i -> i).toArray()); SmartProgressReporter.startProgressReport(exportClones, System.err); exportClones.run(); if (initialSet.size() > set.size()) { @@ -347,9 +347,9 @@ public static final class ExportClones implements CanReportProgressAndStage { final long size; volatile long current = 0; final long limit; - final boolean splitByTags; + final int[] splitByTags; - private ExportClones(CloneSet clones, InfoWriter writer, long limit, boolean splitByTags) { + private ExportClones(CloneSet clones, InfoWriter writer, long limit, int[] splitByTags) { this.clones = clones; this.writer = writer; this.size = clones.size(); @@ -373,28 +373,23 @@ public boolean isFinished() { } void run() { - int id = 0; for (Clone clone : clones.getClones()) { if (current == limit) break; - if (splitByTags) { - TagCounter ttc = clones.getTotalTagCounts(); - TObjectDoubleIterator iterator = clone.getTagCounter().iterator(); - while (iterator.hasNext()) { - iterator.advance(); - TagTuple key = iterator.key(); - - double totalCount = ttc.getOrDefault(key, Double.NaN); - if (Double.isNaN(totalCount)) - throw new IllegalArgumentException(); - double count = iterator.value(); - - Clone c = new Clone(clone.getTargets(), clone.getHits(), new TagCounter(key), count, id++); - c.overrideFraction(count / totalCount); - writer.put(c); - } - } else - writer.put(clone); + + Stream stream = Stream.of(clone); + + for (int tagIndex : splitByTags) { + stream = stream.flatMap(cl -> { + TagCounter tagCounter = cl.getTagCounter(); + double sum = tagCounter.sum(); + return Arrays.stream(tagCounter.splitBy(tagIndex)) + .map(tc -> new Clone(clone.getTargets(), clone.getHits(), + tc, 1.0 * cl.getCount() * tc.sum() / sum, clone.getId())); + }); + } + stream.forEach(writer::put); + ++current; } } diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 29186e502..2508db1ea 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -51,9 +51,8 @@ import io.repseq.core.SequencePartitioning; import java.text.DecimalFormat; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; +import java.util.*; +import java.util.stream.Collectors; public final class FieldExtractors { static final String NULL = ""; @@ -708,13 +707,12 @@ protected String getHeader(OutputMode outputMode, Integer index) { @Override protected String extractValue(VDJCObject object, Integer index) { TagCounter tc = object.getTagCounter(); - if (tc.size() > 1) - throw new IllegalArgumentException("object has multiple tag tuples: " + tc); - if (tc.size() == 0) + Set set = tc.tags(index); + if (set.size() == 0) return NULL; - TObjectDoubleIterator it = tc.iterator(); - it.advance(); - return it.key().tags[index]; + if (set.size() > 1) + throw new IllegalArgumentException("object has multiple tag tuples: " + tc); + return set.iterator().next(); } @Override @@ -723,6 +721,44 @@ public String metaVars() { } }); + descriptorsList.add(new WP_O("-uniqueTagCount", "Unique tag count", 1) { + @Override + protected int[] getParameters(String[] string) { + return Arrays.stream(string[0].split("\\+")).mapToInt(Integer::parseInt).toArray(); + } + + @Override + protected String getHeader(OutputMode outputMode, int[] index) { + String str = Arrays.stream(index).mapToObj(Integer::toString).collect(Collectors.joining("+")); + switch (outputMode) { + case HumanFriendly: return "Unique Tag Count " + str; + case ScriptingFriendly: return "uniqueTagCount" + str; + } + throw new RuntimeException(); + } + + @Override + protected String extractValue(VDJCObject object, int[] indices) { + TagCounter tc = object.getTagCounter(); + Set set = new HashSet<>(); + TObjectDoubleIterator it = tc.iterator(); + while (it.hasNext()) { + it.advance(); + StringBuilder sb = new StringBuilder(); + TagTuple t = it.key(); + for (int i : indices) + sb.append(t.tags[i]).append("+"); + set.add(sb.toString()); + } + return "" + set.size(); + } + + @Override + public String metaVars() { + return "Tags"; + } + }); + descriptors = descriptorsList.toArray(new Field[descriptorsList.size()]); } From 9fbdbf1e58cd64f481b33e75a85b3421af5aa383 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 12 Feb 2020 18:25:46 +0300 Subject: [PATCH 040/282] fix --- .../com/milaboratory/mixcr/basictypes/TagCounterBuilder.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java index bdb54af7a..140fedfd5 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java @@ -22,6 +22,8 @@ public TagCounterBuilder add(TagCounter tc) { } public TagCounterBuilder add(TagCounterBuilder tc) { + if (tc.agg == null) + return this; return add(tc.agg); } From 0096fcfc61275a0a658e22f24e61423910876331 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 26 Feb 2020 17:42:34 +0300 Subject: [PATCH 041/282] fix for java9 / jlink --- src/main/java/com/milaboratory/mixcr/cli/Main.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index a3bae357c..062677c78 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -97,10 +97,11 @@ public static CommandLine mkCmd() { String command = System.getProperty("mixcr.command", "java -jar mixcr.jar"); if (!initialized) { - // Checking whether we are running a snapshot version - if (VersionInfo.getVersionInfoForArtifact("mixcr").getVersion().contains("SNAPSHOT")) - // If so, enable asserts - ClassLoader.getSystemClassLoader().setDefaultAssertionStatus(true); + if (System.getProperty("jdk.module.main") == null) // hack fixme + // Checking whether we are running a snapshot version + if (VersionInfo.getVersionInfoForArtifact("mixcr").getVersion().contains("SNAPSHOT")) + // If so, enable asserts + ClassLoader.getSystemClassLoader().setDefaultAssertionStatus(true); TempFileManager.setPrefix("mixcr_"); From 32b85d08cf6c5b89c889edc3f953fce4ba776161 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 27 Feb 2020 20:16:46 +0300 Subject: [PATCH 042/282] Reporting about ambiguous letters in assembleContigs. --- .../assembler/fullseq/FullSeqAssembler.java | 2 +- .../fullseq/FullSeqAssemblerReport.java | 83 ++++++++++++++++++- .../mixcr/basictypes/VDJCObject.java | 19 +++++ 3 files changed, 101 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 51adff85a..086287299 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -297,7 +297,7 @@ public Clone[] callVariants(RawVariantsData data) { } if (report != null) - report.afterVariantsClustered(clone, result); + report.afterVariantsClustered(clone, result, parameters.subCloningRegion); return result; } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java index fca48c50e..a726a4809 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java @@ -31,10 +31,13 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.google.common.util.concurrent.AtomicDouble; +import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler.VariantBranch; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCObject; import com.milaboratory.mixcr.cli.Report; import com.milaboratory.mixcr.cli.ReportHelper; +import io.repseq.core.GeneFeature; import java.util.Arrays; import java.util.List; @@ -59,6 +62,13 @@ public class FullSeqAssemblerReport implements Report { private final AtomicLong vHitsReorder = new AtomicLong(0); private final AtomicLong jHitsReorder = new AtomicLong(0); + private final AtomicLong clonesWithAmbiguousLetters = new AtomicLong(0); + private final AtomicLong clonesWithAmbiguousLettersInSplittingRegion = new AtomicLong(0); + private final AtomicDouble readsWithAmbiguousLetters = new AtomicDouble(0); + private final AtomicDouble readsWithAmbiguousLettersInSplittingRegion = new AtomicDouble(0); + private final AtomicLong totalAmbiguousLettersInSplittingRegion = new AtomicLong(0); + private final AtomicLong totalAmbiguousLetters = new AtomicLong(0); + public void onVariantClustered(VariantBranch minor) { totalClustered.incrementAndGet(); totalClusteredReads.addAndGet(minor.count); @@ -87,7 +97,7 @@ public void onAssemblyCanceled(Clone initialClone) { totalReads.addAndGet(initialClone.getCount()); } - public void afterVariantsClustered(Clone initialClone, Clone[] branches) { + public void afterVariantsClustered(Clone initialClone, Clone[] branches, GeneFeature subCloningRegion) { initialCloneCount.incrementAndGet(); finalCloneCount.addAndGet(branches.length); totalReads.addAndGet(initialClone.getCount()); @@ -97,6 +107,69 @@ public void afterVariantsClustered(Clone initialClone, Clone[] branches) { .mapToInt(clone -> IntStream.range(0, clone.numberOfTargets()).map(i -> clone.getTarget(i).size()).sum()) .max().orElse(0); longestContigLength.accumulateAndGet(maxLength, Math::max); + + for (Clone branch : branches) { + int numberOfN = Arrays.stream(branch.getTargets()).mapToInt(t -> numberOfWildcards(t.getSequence())).sum(); + if (numberOfN > 0) { + clonesWithAmbiguousLetters.incrementAndGet(); + readsWithAmbiguousLetters.addAndGet(branch.getCount()); + totalAmbiguousLetters.addAndGet(numberOfN); + } + + if (subCloningRegion != null) { + int numberOfNInSplittingRegion = numberOfWildcards(branch.getIncompleteFeature(subCloningRegion)); + if (numberOfNInSplittingRegion > 0) { + clonesWithAmbiguousLettersInSplittingRegion.incrementAndGet(); + readsWithAmbiguousLettersInSplittingRegion.addAndGet(branch.getCount()); + totalAmbiguousLettersInSplittingRegion.addAndGet(numberOfNInSplittingRegion); + } + } + } + } + + private static int numberOfWildcards(NucleotideSequence seq) { + int count = 0; + for (int i = 0; i < seq.size(); i++) + if (NucleotideSequence.ALPHABET.isWildcard(seq.codeAt(i))) + count++; + return count; + } + + private static int numberOfWildcards(VDJCObject.CaseSensitiveNucleotideSequence csSeq) { + int count = 0; + for (int i = 0; i < csSeq.size(); i++) + count += numberOfWildcards(csSeq.getSequence(i)); + return count; + } + + @JsonProperty("clonesWithAmbiguousLetters") + public long getClonesWithAmbiguousLetters() { + return clonesWithAmbiguousLetters.get(); + } + + @JsonProperty("clonesWithAmbiguousLettersInSplittingRegion") + public long getClonesWithAmbiguousLettersInSplittingRegion() { + return clonesWithAmbiguousLettersInSplittingRegion.get(); + } + + @JsonProperty("readsWithAmbiguousLetters") + public double getReadsWithAmbiguousLetters() { + return readsWithAmbiguousLetters.get(); + } + + @JsonProperty("readsWithAmbiguousLettersInSplittingRegion") + public double getReadsWithAmbiguousLettersInSplittingRegion() { + return readsWithAmbiguousLettersInSplittingRegion.get(); + } + + @JsonProperty("totalAmbiguousLetters") + public long getTotalAmbiguousLetters() { + return totalAmbiguousLetters.get(); + } + + @JsonProperty("totalAmbiguousLettersInSplittingRegion") + public long getTotalAmbiguousLettersInSplittingRegion() { + return totalAmbiguousLettersInSplittingRegion.get(); } @JsonProperty("initialCloneCount") @@ -153,6 +226,12 @@ public void writeReport(ReportHelper helper) { .writeField("Longest contig length", getLongestContigLength()) .writePercentAndAbsoluteField("Clustered variants", getClonesClustered(), getFinalCloneCount() + getClonesClustered()) .writePercentAndAbsoluteField("Reads in clustered variants", getReadsClustered(), getTotalReads()) - .writePercentAndAbsoluteField("Reads in divided (newly created) clones", getTotalDividedVariantReads(), getTotalReads()); + .writePercentAndAbsoluteField("Reads in divided (newly created) clones", getTotalDividedVariantReads(), getTotalReads()) + // .writePercentAndAbsoluteField("Clones with ambiguous letters", getClonesWithAmbiguousLetters(), getFinalCloneCount()) + .writePercentAndAbsoluteField("Clones with ambiguous letters in splitting region", getClonesWithAmbiguousLettersInSplittingRegion(), getFinalCloneCount()) + // .writePercentAndAbsoluteField("Reads in clones with ambiguous letters", getReadsWithAmbiguousLetters(), getTotalReads()) + .writePercentAndAbsoluteField("Reads in clones with ambiguous letters in splitting region", getReadsWithAmbiguousLettersInSplittingRegion(), getTotalReads()) + // .writeField("Average number of ambiguous letters per clone with ambiguous letters", 1.0 * getTotalAmbiguousLetters() / getClonesWithAmbiguousLetters()) + .writeField("Average number of ambiguous letters per clone with ambiguous letters in splitting region", 1.0 * getTotalAmbiguousLettersInSplittingRegion() / getClonesWithAmbiguousLettersInSplittingRegion()); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 37821433d..5e2d85f1c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -663,6 +663,25 @@ public static class CaseSensitiveNucleotideSequence { this.lowerCase.set(0, lowerCase); } + public int size() { + return seq.length; + } + + public NucleotideSequence getSequence(int i) { + return seq[i]; + } + + public boolean isLowerCase(int i) { + return lowerCase.get(i); + } + + public boolean containsWildcards() { + for (NucleotideSequence s : seq) + if (s.containsWildcards()) + return true; + return false; + } + boolean containsLowerCase() { for (int i = 0; i < seq.length; ++i) if (lowerCase.get(i)) From 06a1c3380127319dcc27c8cbd307fbc34149a9d5 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 18 Mar 2020 17:09:44 +0300 Subject: [PATCH 043/282] Assemble contigs progress rename --- .../java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 9457fe596..6c72e3627 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -134,7 +134,7 @@ public void run1() throws Exception { IOUtil.registerGeneReferences(tmpOut, genes, alignerParameters); ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments(); - SmartProgressReporter.startProgressReport("Assembling", cloneAlignmentsPort); + SmartProgressReporter.startProgressReport("Assembling contigs", cloneAlignmentsPort); OutputPort parallelProcessor = new ParallelProcessor<>(cloneAlignmentsPort, cloneAlignments -> { try { From ce1ea7f9d2b3b5145f184d08573e51bd0912782d Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 18 Mar 2020 17:10:39 +0300 Subject: [PATCH 044/282] Filter stops & oof move out from export --- .../mixcr/basictypes/VDJCObject.java | 26 +++++++++++++++++ .../milaboratory/mixcr/cli/CommandExport.java | 28 ++++--------------- 2 files changed, 31 insertions(+), 23 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index ec5dfe264..2c642515b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -770,6 +770,32 @@ public String toAminoAcidString() { } } + public boolean containsStops(GeneFeature feature) { + GeneFeature codingFeature = GeneFeature.getCodingGeneFeature(feature); + if (codingFeature == null) + return true; + + for (int i = 0; i < numberOfTargets(); ++i) { + NSequenceWithQuality codingSeq = getPartitionedTarget(i).getFeature(codingFeature); + if (codingSeq == null) + continue; + TranslationParameters tr = getPartitionedTarget(i).getPartitioning().getTranslationParameters(codingFeature); + if (tr == null) + return true; + if (AminoAcidSequence.translate(codingSeq.getSequence(), tr).containStops()) + return true; + } + + return false; + } + + public boolean isOutOfFrame(GeneFeature feature) { + NSequenceWithQuality nt = getFeature(feature); + if (nt == null || nt.size() % 3 != 0) + return true; + return false; + } + @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 57b9e2b1e..0573494da 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -32,9 +32,6 @@ import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.blocks.FilteringPort; import cc.redberry.primitives.Filter; -import com.milaboratory.core.sequence.AminoAcidSequence; -import com.milaboratory.core.sequence.NSequenceWithQuality; -import com.milaboratory.core.sequence.TranslationParameters; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.export.*; import com.milaboratory.util.CanReportProgress; @@ -298,29 +295,14 @@ public CFilter(boolean filterOutOfFrames, boolean filterStopCodons) { @Override public boolean accept(Clone clone) { if (filterOutOfFrames) { - NSequenceWithQuality cdr3 = clone.getFeature(GeneFeature.CDR3); - if (cdr3 == null || cdr3.size() % 3 != 0) + if (clone.isOutOfFrame(GeneFeature.CDR3)) return false; } - if (filterStopCodons) { - for (GeneFeature assemblingFeature : clone.getParentCloneSet().getAssemblingFeatures()) { - GeneFeature codingFeature = GeneFeature.getCodingGeneFeature(assemblingFeature); - if (codingFeature == null) - continue; - - for (int i = 0; i < clone.numberOfTargets(); ++i) { - NSequenceWithQuality codingSeq = clone.getPartitionedTarget(i).getFeature(codingFeature); - if (codingSeq == null) - continue; - TranslationParameters tr = clone.getPartitionedTarget(i).getPartitioning().getTranslationParameters(codingFeature); - if (tr == null) - return false; - if (AminoAcidSequence.translate(codingSeq.getSequence(), tr).containStops()) - return false; - } - } - } + if (filterStopCodons) + for (GeneFeature assemblingFeature : clone.getParentCloneSet().getAssemblingFeatures()) + if (clone.containsStops(assemblingFeature)) + return false; return true; } From de278c290774b27d74eb6f549c2b89618a4dee1c Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 18 Mar 2020 23:59:57 +0300 Subject: [PATCH 045/282] Dep submodules. --- milib | 2 +- repseqio | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/milib b/milib index 42e0485fe..276354576 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 42e0485fe21db25333767ce89808564aa459d780 +Subproject commit 27635457618d20c67ab948701eaa78af6665c76a diff --git a/repseqio b/repseqio index 6937c8800..05b29f07e 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 6937c88007f3c2ff66827c2f09a7b2d186bd0b62 +Subproject commit 05b29f07e61c1787db06c44240e13f29c4262fd6 From 123cfc9220042089ac604eb473581de1015d49c6 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 19 Mar 2020 00:56:18 +0300 Subject: [PATCH 046/282] Hostname lookup (the same in deps) --- milib | 2 +- pom.xml | 20 ++++++-------------- repseqio | 2 +- 3 files changed, 8 insertions(+), 16 deletions(-) diff --git a/milib b/milib index 276354576..4ecc96faf 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 27635457618d20c67ab948701eaa78af6665c76a +Subproject commit 4ecc96faf9e492321c50a39f6a3ff7aad7f63b57 diff --git a/pom.xml b/pom.xml index f551c539d..783192aeb 100644 --- a/pom.xml +++ b/pom.xml @@ -119,26 +119,18 @@ - - org.apache.maven.plugins - maven-antrun-plugin - 1.8 + org.codehaus.mojo + build-helper-maven-plugin + 3.1.0 + init-build-properties validate - run + hostname - true - - - - - - - - + hostname diff --git a/repseqio b/repseqio index 05b29f07e..0ab66a8fd 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 05b29f07e61c1787db06c44240e13f29c4262fd6 +Subproject commit 0ab66a8fdeb9afbe4c3232fe68f238a1b69aab64 From 30b7ba1a583987f34ceb559e5f1c89ec3aeb69e7 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 15 Apr 2020 18:29:18 +0300 Subject: [PATCH 047/282] Next development cycle v3.0.4 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 7095878ad..31384ddf5 100644 --- a/pom.xml +++ b/pom.xml @@ -33,7 +33,7 @@ com.milaboratory mixcr - 3.0.13 + 3.0.4-SNAPSHOT jar MiXCR From b17b018b610a70356a56a0d9663d4f6b17f21d02 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Wed, 15 Apr 2020 21:47:29 +0300 Subject: [PATCH 048/282] Correct SNAPSHOT version. --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 31384ddf5..e66c070b1 100644 --- a/pom.xml +++ b/pom.xml @@ -33,7 +33,7 @@ com.milaboratory mixcr - 3.0.4-SNAPSHOT + 3.0.14-SNAPSHOT jar MiXCR From 5697b1550fea93cf7c3b35f0f403ec160007fdab Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 16 Apr 2020 01:46:36 +0300 Subject: [PATCH 049/282] Fix for merge --- .../com/milaboratory/mixcr/cli/CommandAnalyze.java | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index c1b850e84..924892981 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -479,9 +479,6 @@ public final CommandExtend mkExtend(String input, String output) { return inheritOptionsAndValidate(ap); } - @Option(names = "--no-clna", description = "Use clns (moore compact) for storing clones. This option is not compatible with --contig-assembly.") - public boolean noClna = false; - @Option(names = "--assemble", description = "Additional parameters for assemble step specified with double quotes (e.g --assemble \"-OassemblingFeatures=[V5UTR+L1+L2+FR1,FR3+CDR3]\" --assemble \"-ObadQualityThreshold=0\" etc.", arity = "1") @@ -500,16 +497,11 @@ CommandAssemble mkAssemble(String input, String output) { assembleParameters.add("--report"); assembleParameters.add(getReport()); - if (!noClna) + if (contigAssembly) assembleParameters.add("--write-alignments"); - else if (contigAssembly) - throw new RuntimeException("--no-clna is not compatible with --contig-assembly"); inheritThreads(assembleParameters, this.assembleParameters); - if (contigAssembly) - assembleParameters.add("--write-alignments"); - // pipeline specific parameters assembleParameters.addAll(this.pipelineSpecificAssembleParameters()); From dec65e9fbb9eb5f53df38b68c7b75282f7a1d45f Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 23 Apr 2020 13:00:52 +0300 Subject: [PATCH 050/282] Tag Grouping (#2) * wip * wip * WIP * wip / first good results * WIP On the way to separate action. * wip * update submodule * wip * WIP * wip * wip cli * Groups clustering, more reporting. * Fix for report. * Support for clns files. * Export group to tag mapping. * Test ignores for CI. * Number of clones added to tag mapping file. Co-authored-by: Stanislav Poslavsky --- .gitignore | 1 + .../mixcr/assembler/CloneFactory.java | 2 +- .../assembler/fullseq/FullSeqAssembler.java | 2 +- .../milaboratory/mixcr/basictypes/Clone.java | 26 +- .../com/milaboratory/mixcr/basictypes/IO.java | 4 +- .../mixcr/basictypes/TagCounter.java | 39 ++ .../milaboratory/mixcr/cli/CommandExport.java | 2 +- .../mixcr/cli/CommandGroupCells.java | 346 ++++++++++++ .../java/com/milaboratory/mixcr/cli/Main.java | 1 + .../milaboratory/mixcr/cli/ReportHelper.java | 3 + .../mixcr/export/FieldExtractors.java | 7 + .../milaboratory/mixcr/tags/CloneGroup.java | 84 +++ .../mixcr/tags/CloneTagTuple.java | 48 ++ .../mixcr/tags/CloneTagTupleFilter.java | 138 +++++ .../mixcr/tags/DropletCloneGraph.java | 465 ++++++++++++++++ .../tags/DropletCloneGraphParameters.java | 82 +++ .../mixcr/tags/DropletCloneGraphReport.java | 388 +++++++++++++ .../mixcr/util/AdjacencyMatrix.java | 232 ++++++++ .../milaboratory/mixcr/util/BitArrayInt.java | 523 ++++++++++++++++++ .../mixcr/util/VDJCObjectExtender.java | 4 +- .../droplet_clone_graph_parameters.json | 15 + .../mixcr/cli/CommandGroupCellsTest.java | 15 + .../mixcr/tags/CloneTagTupleFilterTest.java | 16 + .../mixcr/tags/DropletCloneGraphTest.java | 52 ++ .../mixcr/util/AdjacencyMatrixTest.java | 217 ++++++++ 25 files changed, 2700 insertions(+), 12 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java create mode 100644 src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java create mode 100644 src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java create mode 100644 src/main/resources/parameters/droplet_clone_graph_parameters.json create mode 100644 src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java diff --git a/.gitignore b/.gitignore index 8a0196b30..6be4cea72 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,4 @@ out test_target src/test/resources/sequences/big tmp +pack diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index bbe7d8f93..48a372cb4 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -249,7 +249,7 @@ public Clone create(int id, double count, else hits.put(GeneType.Diversity, new VDJCHit[0]); - return new Clone(targets, hits, tagCounter, count, id); + return new Clone(targets, hits, tagCounter, count, id, null); } public Clone create(int id, CloneAccumulator accumulator) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 20aab6450..f63af73cc 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -932,7 +932,7 @@ else if (floatingRightBound) } else tmp[0] = substituteAlignments(tmp[0], jHitAlignments); - return new Clone(targets.sequences, hits, this.clone.getTagCounter(), targets.count, 0); + return new Clone(targets.sequences, hits, this.clone.getTagCounter(), targets.count, 0, clone.getGroup()); } static int indexOfGene(VDJCHit[] hits, VDJCGeneId gene) { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index 059abab01..51cfbc325 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -42,22 +42,36 @@ public final class Clone extends VDJCObject { final double count; final int id; CloneSet parent = null; + final Integer group; - public Clone(NSequenceWithQuality[] targets, EnumMap hits, TagCounter tagCounter, double count, int id) { + public Clone(NSequenceWithQuality[] targets, EnumMap hits, TagCounter tagCounter, double count, int id, Integer group) { super(hits, tagCounter, targets); this.count = count; this.id = id; + this.group = group; + } + + public Clone setCount(double count) { + return new Clone(targets, hits, tagCounter, count, id, group); + } + + public Clone setGroup(Integer group) { + return new Clone(targets, hits, tagCounter, count, id, group); + } + + public Integer getGroup() { + return group; } public Clone setId(int id) { - Clone r = new Clone(targets, hits, tagCounter, count, id); + Clone r = new Clone(targets, hits, tagCounter, count, id, group); r.setParentCloneSet(parent); return r; } /** Returns new instance with parent clone set set to null */ public Clone resetParentCloneSet() { - return new Clone(targets, hits, tagCounter, count, id); + return new Clone(targets, hits, tagCounter, count, id, group); } public void setParentCloneSet(CloneSet set) { @@ -71,7 +85,7 @@ public CloneSet getParentCloneSet() { } public Clone setTagCounts(TagCounter tc) { - Clone c = new Clone(targets, hits, tc, count, id); + Clone c = new Clone(targets, hits, tc, count, id, group); c.setParentCloneSet(getParentCloneSet()); return c; } @@ -131,11 +145,11 @@ public boolean equals(Object o) { if (!super.equals(o)) return false; Clone clone = (Clone) o; return Double.compare(clone.count, count) == 0 && - id == clone.id; + id == clone.id && group == clone.group; } @Override public int hashCode() { - return Objects.hash(super.hashCode(), count, id); + return Objects.hash(super.hashCode(), count, id, group); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index 4ce223f2e..e2891d45f 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -180,6 +180,7 @@ public void write(PrimitivO output, Clone object) { } output.writeDouble(object.count); output.writeInt(object.id); + output.writeObject(object.group); } @Override @@ -194,7 +195,8 @@ public Clone read(PrimitivI input) { } double count = input.readDouble(); int id = input.readInt(); - return new Clone(targets, hits, tagCounter, count, id); + Integer group = input.readObject(Integer.class); + return new Clone(targets, hits, tagCounter, count, id, group); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java index 6908d8de5..11b5eab4e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java @@ -10,6 +10,7 @@ import java.util.HashSet; import java.util.Map; import java.util.Set; +import java.util.function.Predicate; /** * @@ -33,6 +34,19 @@ public TagCounter(TagTuple tags) { this(tags, 1.0); } + public TagTuple singleOrNull() { + if (size() > 1 || size() == 0) + return null; + + TObjectDoubleIterator it = iterator(); + it.advance(); + return it.key(); + } + + public Set keys() { + return tags.keySet(); + } + public double getOrDefault(TagTuple tt, double d) { if (!tags.containsKey(tt)) return d; @@ -40,6 +54,16 @@ public double getOrDefault(TagTuple tt, double d) { return tags.get(tt); } + public TagCounter multiply(double factor) { + TagCounterBuilder tb = new TagCounterBuilder(); + TObjectDoubleIterator iterator = iterator(); + while (iterator.hasNext()) { + iterator.advance(); + tb.add(iterator.key(), iterator.value() * factor); + } + return tb.createAndDestroy(); + } + public int size() { return tags.size(); } @@ -105,6 +129,21 @@ public int hashCode() { return tags.hashCode(); } + public TagCounter filter(Predicate predicate) { + TObjectDoubleIterator it = iterator(); + TagCounterBuilder tb = new TagCounterBuilder(); + while (it.hasNext()) { + it.advance(); + + TagTuple t = it.key(); + double count = it.value(); + if (!predicate.test(t)) + continue; + tb.add(t, count); + } + return tb.createAndDestroy(); + } + public TagCounter[] splitBy(int index) { Map map = new HashMap<>(); TObjectDoubleIterator it = iterator(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 0573494da..c4d223076 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -367,7 +367,7 @@ void run() { double sum = tagCounter.sum(); return Arrays.stream(tagCounter.splitBy(tagIndex)) .map(tc -> new Clone(clone.getTargets(), clone.getHits(), - tc, 1.0 * cl.getCount() * tc.sum() / sum, clone.getId())); + tc, 1.0 * cl.getCount() * tc.sum() / sum, clone.getId(), clone.getGroup())); }); } stream.forEach(writer::put); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java new file mode 100644 index 000000000..379915711 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -0,0 +1,346 @@ +package com.milaboratory.mixcr.cli; + +import cc.redberry.pipe.OutputPortCloseable; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; +import com.milaboratory.cli.ActionConfiguration; +import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.tags.CloneGroup; +import com.milaboratory.mixcr.tags.DropletCloneGraph; +import com.milaboratory.mixcr.tags.DropletCloneGraphParameters; +import com.milaboratory.mixcr.tags.DropletCloneGraphReport; +import com.milaboratory.util.ProgressAndStage; +import com.milaboratory.util.SmartProgressReporter; +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TObjectIntIterator; +import gnu.trove.map.hash.TIntIntHashMap; +import gnu.trove.map.hash.TIntObjectHashMap; +import gnu.trove.map.hash.TObjectIntHashMap; +import io.repseq.core.VDJCLibraryRegistry; +import picocli.CommandLine.Command; +import picocli.CommandLine.Option; + +import java.io.FileNotFoundException; +import java.io.PrintStream; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.function.Consumer; + +import static com.milaboratory.mixcr.basictypes.IOUtil.*; + +/** + * + */ +@Command(name = CommandGroupCells.GROUP_CLONE_COMMAND_NAME, + sortOptions = true, + separator = " ", + description = "Group clones for single cell data (e.g. alpha-beta / heavy-light chain pairing).") +public class CommandGroupCells extends ACommandWithSmartOverwriteWithSingleInputMiXCR { + public static final String GROUP_CLONE_COMMAND_NAME = "groupCells"; + @Option(description = "Cell barcode group name", + names = {"-t", "--tag"}) + public int tagIndex; + + @Option(description = CommonDescriptions.REPORT, + names = {"-r", "--report"}) + public String reportFile; + + @Option(description = CommonDescriptions.JSON_REPORT, + names = {"-j", "--json-report"}) + public String jsonReportFile; + + @Option(description = "Generate separate file with group mapping for cell barcodes", + names = {"--tag-mapping"}) + public String tagMappingFile; + + @Option(description = "Minimal fraction of reads in clone that were not assigned to any group and will be separated into 'unassigned' clone", + names = {"--minimal-ungrouped-fraction"}) + public double minimalUngroupedFraction; + + @Option(names = {"-O"}, description = "Overrides default aligner parameter values") + public Map overrides = new HashMap<>(); + + @Override + public GroupingPipelineConfiguration getConfiguration() { + return new GroupingPipelineConfiguration(getParameters(), minimalUngroupedFraction); + } + + private DropletCloneGraphReport report; + private DropletCloneGraphParameters parameters; + + DropletCloneGraphParameters getParameters() { + if (parameters != null) + return parameters; + + parameters = DropletCloneGraphParameters.getDefault(); + if (!overrides.isEmpty()) { + // Perform parameters overriding + parameters = JsonOverrider.override(parameters, DropletCloneGraphParameters.class, overrides); + if (parameters == null) + throwValidationException("Failed to override some parameter: " + overrides); + } + return parameters; + } + + @Override + public void run1() throws Exception { + String in = this.in; + + report = new DropletCloneGraphReport(); + + switch (Objects.requireNonNull(fileInfoExtractorInstance.getFileInfo(in)).fileType) { + case MAGIC_CLNS: + runClns(); + break; + case MAGIC_CLNA: + runClna(); + break; + default: + throwExecutionException("Illegal input format"); + } + + // Writing report to stout + System.out.println("============= Report =============="); + Util.writeReportToStdout(report); + + if (reportFile != null) + Util.writeReport(reportFile, report); + + if (jsonReportFile != null) + Util.writeJsonReport(jsonReportFile, report); + } + + private static final class CloneIdWithTag { + public final String tag; + public final int cloneId; + + public CloneIdWithTag(String tag, int cloneId) { + this.tag = tag; + this.cloneId = cloneId; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CloneIdWithTag that = (CloneIdWithTag) o; + return cloneId == that.cloneId && + Objects.equals(tag, that.tag); + } + + @Override + public int hashCode() { + return Objects.hash(tag, cloneId); + } + + @Override + public String toString() { + return cloneId + " " + tag; + } + } + + private void runClns() throws Exception { + CloneSet cloneSet = CloneSetIO.read(in); + CloneSet resultCloneSet = doClustering(cloneSet, null); + try (ClnsWriter writer = new ClnsWriter(getFullPipelineConfiguration(), resultCloneSet, out)) { + SmartProgressReporter.startProgressReport(writer); + writer.write(); + } + } + + private void runClna() throws Exception { + try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault()); + ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { + + CloneSet cloneSet = reader.readCloneSet(); + + TObjectIntHashMap idMapping = new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); + CloneSet resultCloneSet = doClustering(cloneSet, idMapping); + + SmartProgressReporter.startProgressReport(writer); + + writer.writeClones(resultCloneSet); + + OutputPortCloseable alignments = reader.readAllAlignments(); + writer.sortAlignments(() -> { + VDJCAlignments als = alignments.take(); + if (als == null) + return null; + TagTuple tt = als.getTagCounter().singleOrNull(); + if (tt == null) + return als.updateCloneIndex(-1); + int newCloneIndex = idMapping.get(new CloneIdWithTag(tt.tags[tagIndex], als.getCloneIndex())); + if (newCloneIndex == -1) + return als.updateCloneIndex(-1); + + return als.updateCloneIndex(newCloneIndex); + }, reader.numberOfAlignments()); + + writer.writeAlignmentsAndIndex(); + } + } + + private CloneSet doClustering(CloneSet cloneSet, TObjectIntHashMap idMapping) { + report.before(cloneSet); + + ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); + SmartProgressReporter.startProgressReport(progressAndStage); + List groups = DropletCloneGraph.calculateGroups(DropletCloneGraph.calculateTuples(cloneSet, tagIndex), parameters, report, progressAndStage); + + if (tagMappingFile != null) + try (PrintStream os = new PrintStream(tagMappingFile)) { + os.println("GroupId\tTag\tTotalReads\tTotalUMIs\tNumberOfClones"); + for (CloneGroup group : groups) + for (String tag : group.groupTags) { + os.print(group.groupId); + os.print('\t'); + os.print(tag); + os.print('\t'); + os.print(group.reads); + os.print('\t'); + os.print(group.umis); + os.print('\t'); + os.print(group.groupClones.size()); + os.println(); + } + } catch (FileNotFoundException e) { + throw new RuntimeException(e); + } + + TIntObjectHashMap> groupsByClones = new TIntObjectHashMap<>(); + for (CloneGroup group : groups) { + group.groupClones.forEach(i -> { + ArrayList list = new ArrayList<>(); + List val = groupsByClones.putIfAbsent(i, list); + if (val != null) val.add(group); + else list.add(group); + return true; + }); + } + + List resultingClones = new ArrayList<>(); + + final AtomicInteger cloneId = new AtomicInteger(); + Consumer addClone = clone -> { + if (clone.getGroup() < 0) + report.onUngroupedClone(clone); + else + report.onGroupedClone(clone); + + int oldCloneId = clone.getId(); + int newCloneId = cloneId.getAndIncrement(); + + if (idMapping != null) + for (TagTuple key : clone.getTagCounter().keys()) { + int put = idMapping.put(new CloneIdWithTag(key.tags[tagIndex], oldCloneId), newCloneId); + assert put == -1 || put == newCloneId; + } + + resultingClones.add(clone.setId(newCloneId)); + }; + + for (Clone clone : cloneSet) { + List cloneGroups = groupsByClones.get(clone.getId()); + if (cloneGroups == null) { + addClone.accept(clone.setGroup(-1 - clone.getId())); + continue; + } + + report.onCloneBeforeSplit(clone); + + List splitCounters = new ArrayList<>(); + double sumTotal = 0; + for (CloneGroup cloneGroup : cloneGroups) { + TagCounter filtered = clone.getTagCounter().filter(p -> cloneGroup.groupTags.contains(p.tags[tagIndex])); + sumTotal += filtered.sum(); + splitCounters.add(filtered); + } + + boolean includeUngrouped = (1 - sumTotal / clone.getTagCounter().sum()) > minimalUngroupedFraction; + TagCounter ungroupedCounter = null; + if (includeUngrouped) { + ungroupedCounter = clone.getTagCounter().filter(p -> cloneGroups.stream().noneMatch(g -> g.groupTags.contains(p.tags[tagIndex]))); + sumTotal += ungroupedCounter.sum(); + assert Math.abs(sumTotal - clone.getTagCounter().sum()) < 0.1; + } + + for (int i = 0; i < splitCounters.size(); ++i) { + TagCounter tc = splitCounters.get(i); + addClone.accept(clone + .setTagCounts(tc) + .setGroup(cloneGroups.get(i).groupId) // same index + .setCount(clone.getCount() * tc.sum() / sumTotal)); + } + + if (includeUngrouped && ungroupedCounter.size() != 0) + addClone.accept(clone + .setTagCounts(ungroupedCounter) + .setGroup(-1 - clone.getId()) + .setCount(clone.getCount() * ungroupedCounter.sum() / sumTotal)); + } + + // sorting resulting clones + TIntIntHashMap permutation = new TIntIntHashMap(); + resultingClones.sort(Comparator.comparingDouble(Clone::getCount).reversed()); + for (int i = 0; i < resultingClones.size(); i++) { + Clone c = resultingClones.get(i); + permutation.put(c.getId(), i); + resultingClones.set(i, c.setId(i)); + } + TObjectIntIterator it = idMapping.iterator(); + while (it.hasNext()) { + it.advance(); + it.setValue(permutation.get(it.value())); + } + + return new CloneSet(resultingClones, + cloneSet.getUsedGenes(), + cloneSet.getAlignedFeatures(), + cloneSet.getAlignmentParameters(), + cloneSet.getAssemblerParameters()); + } + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) + @JsonTypeInfo( + use = JsonTypeInfo.Id.CLASS, + include = JsonTypeInfo.As.PROPERTY, + property = "type") + private static final class GroupingPipelineConfiguration + implements ActionConfiguration { + @JsonProperty("parameters") + final DropletCloneGraphParameters parameters; + @JsonProperty("minimalUngroupedFraction") + final double minimalUngroupedFraction; + + @JsonCreator + public GroupingPipelineConfiguration(@JsonProperty("parameters") DropletCloneGraphParameters parameters, + @JsonProperty("minimalUngroupedFraction") double minimalUngroupedFraction) { + this.parameters = parameters; + this.minimalUngroupedFraction = minimalUngroupedFraction; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + GroupingPipelineConfiguration that = (GroupingPipelineConfiguration) o; + return Double.compare(that.minimalUngroupedFraction, minimalUngroupedFraction) == 0 && + Objects.equals(parameters, that.parameters); + } + + @Override + public int hashCode() { + return Objects.hash(parameters, minimalUngroupedFraction); + } + + @Override + public String actionName() { + return GROUP_CLONE_COMMAND_NAME; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 576f2af06..f270bdce6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -144,6 +144,7 @@ public static CommandLine mkCmd() { .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) + .addSubcommand("groupCells", CommandGroupCells.class) .addSubcommand("assembleContigs", CommandAssembleContigs.class) .addSubcommand("assemblePartial", CommandAssemblePartialAlignments.class) diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java index f2097e74e..58a170806 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java @@ -35,6 +35,9 @@ import java.util.concurrent.atomic.AtomicLong; public final class ReportHelper { + public static final ReportHelper STDOUT = new ReportHelper(System.out, true); + public static final ReportHelper STDERR = new ReportHelper(System.err, true); + private final PrintStream printStream; private final boolean stdout; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 2508db1ea..e466626d0 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -759,6 +759,13 @@ public String metaVars() { } }); + descriptorsList.add(new PL_C("-cellGroup", "Cell group", "Cell group", "cellGroup") { + @Override + protected String extract(Clone object) { + return String.valueOf(object.getGroup()); + } + }); + descriptors = descriptorsList.toArray(new Field[descriptorsList.size()]); } diff --git a/src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java b/src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java new file mode 100644 index 000000000..2bb15473c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java @@ -0,0 +1,84 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.tags; + +import gnu.trove.set.hash.TIntHashSet; + +import java.util.HashSet; +import java.util.Objects; +import java.util.Set; + +public final class CloneGroup { + public final int groupId; + public final double reads; + public final long umis; + public final Set groupTags; + public final TIntHashSet groupClones; + + public CloneGroup(int groupId, + double reads, long umis, + Set groupTags, TIntHashSet groupClones) { + this.groupId = groupId; + this.reads = reads; + this.umis = umis; + this.groupTags = groupTags; + this.groupClones = groupClones; + } + + public CloneGroup mergeFrom(CloneGroup other) { + assert groupClones.containsAll(other.groupClones); + + HashSet newTags = new HashSet<>(groupTags); + newTags.addAll(other.groupTags); + return new CloneGroup( + groupId, + reads + other.reads, + umis + other.umis, + newTags, + groupClones); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CloneGroup that = (CloneGroup) o; + return groupId == that.groupId && + Double.compare(that.reads, reads) == 0 && + umis == that.umis && + Objects.equals(groupTags, that.groupTags) && + Objects.equals(groupClones, that.groupClones); + } + + @Override + public int hashCode() { + return Objects.hash(groupId, reads, umis, groupTags, groupClones); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java new file mode 100644 index 000000000..f596a4ea2 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java @@ -0,0 +1,48 @@ +package com.milaboratory.mixcr.tags; + +import com.milaboratory.mixcr.basictypes.Clone; + +import java.util.Objects; + +/** + * + */ +public final class CloneTagTuple { + final Clone clone; + final String tag; + int rank; + long umiCount; + double readCount, readFractionInTag, umiFractionInTag; + + public CloneTagTuple(Clone clone, String tag) { + this.clone = clone; + this.tag = tag; + } + + public double getReadsInTag() { + return readCount / readFractionInTag; + } + + public double getUMIsInTag() { + return umiCount / umiFractionInTag; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CloneTagTuple that = (CloneTagTuple) o; + return rank == that.rank && + umiCount == that.umiCount && + Double.compare(that.readCount, readCount) == 0 && + Double.compare(that.readFractionInTag, readFractionInTag) == 0 && + Double.compare(that.umiFractionInTag, umiFractionInTag) == 0 && + Objects.equals(clone, that.clone) && + Objects.equals(tag, that.tag); + } + + @Override + public int hashCode() { + return Objects.hash(clone, tag, rank, umiCount, readCount, readFractionInTag, umiFractionInTag); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java new file mode 100644 index 000000000..7263311a9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java @@ -0,0 +1,138 @@ +package com.milaboratory.mixcr.tags; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.tags.DropletCloneGraph.CloneTagTupleList; + +import java.util.List; +import java.util.Objects; +import java.util.stream.Collectors; + +import static java.lang.Double.isNaN; + +/** + * + */ +public final class CloneTagTupleFilter { + @JsonProperty("minReadFractionInTag") + public final double minReadFractionInTag; + @JsonProperty("maxCloneRankInTag") + public final int maxCloneRankInTag; + @JsonProperty("minTagReads") + public final double minTagReads; + @JsonProperty("minTagUMIs") + public final double minTagUMIs; + @JsonProperty("tagReadsQuantile") + public final double tagReadsQuantile; + @JsonProperty("tagReadsQuantileCoefficient") + public final double tagReadsQuantileCoefficient; + @JsonProperty("tagUMIsQuantile") + public final double tagUMIsQuantile; + @JsonProperty("tagUMIsQuantileCoefficient") + public final double tagUMIsQuantileCoefficient; + + @JsonCreator + public CloneTagTupleFilter(@JsonProperty("minReadFractionInTag") double minReadFractionInTag, + @JsonProperty("maxCloneRankInTag") int maxCloneRankInTag, + @JsonProperty("minTagReads") double minTagReads, + @JsonProperty("minTagUMIs") double minTagUMIs, + @JsonProperty("tagReadsQuantile") double tagReadsQuantile, + @JsonProperty("tagReadsQuantileCoefficient") double tagReadsQuantileCoefficient, + @JsonProperty("tagUMIsQuantile") double tagUMIsQuantile, + @JsonProperty("tagUMIsQuantileCoefficient") double tagUMIsQuantileCoefficient) { + if (!isNaN(tagReadsQuantile) && isNaN(tagReadsQuantileCoefficient)) + throw new IllegalArgumentException("Please specify tagReadsQuantileCoefficient."); + if (!isNaN(tagUMIsQuantile) && isNaN(tagUMIsQuantileCoefficient)) + throw new IllegalArgumentException("Please specify tagUMIsQuantileCoefficient."); + this.minReadFractionInTag = minReadFractionInTag; + this.maxCloneRankInTag = maxCloneRankInTag; + this.minTagReads = minTagReads; + this.minTagUMIs = minTagUMIs; + this.tagReadsQuantile = tagReadsQuantile; + this.tagReadsQuantileCoefficient = tagReadsQuantileCoefficient; + this.tagUMIsQuantile = tagUMIsQuantile; + this.tagUMIsQuantileCoefficient = tagUMIsQuantileCoefficient; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CloneTagTupleFilter that = (CloneTagTupleFilter) o; + return minReadFractionInTag == that.minReadFractionInTag && + maxCloneRankInTag == that.maxCloneRankInTag && + Double.compare(that.minTagReads, minTagReads) == 0 && + Double.compare(that.minTagUMIs, minTagUMIs) == 0 && + Double.compare(that.tagReadsQuantile, tagReadsQuantile) == 0 && + Double.compare(that.tagUMIsQuantile, tagUMIsQuantile) == 0; + } + + @Override + public int hashCode() { + return Objects.hash(minReadFractionInTag, maxCloneRankInTag, minTagReads, minTagUMIs, tagReadsQuantile, tagUMIsQuantile); + } + + public List filter(CloneTagTupleList tuples, DropletCloneGraphReport report) { + + double minTagReads = 0.0, minTagUMIs = 0.0; + if (!isNaN(tagReadsQuantile)) { + minTagReads = tuples.readsTopQuantile(tagReadsQuantile); + minTagReads = minTagReads * tagReadsQuantileCoefficient; + } + if (!isNaN(tagUMIsQuantile)) { + minTagUMIs = tuples.umisTopQuantile(tagUMIsQuantile); + minTagUMIs = minTagUMIs * tagUMIsQuantileCoefficient; + } + + if (!isNaN(this.minTagReads)) + minTagReads = Math.max(minTagReads, this.minTagReads); + if (!isNaN(this.minTagUMIs)) + minTagUMIs = Math.max(minTagUMIs, this.minTagUMIs); + + report.effectiveMinReadsInTag = minTagReads; + report.effectiveMinUMIsInTag = minTagUMIs; + + double minTagReadsFinal = minTagReads; + double minTagUMIsFinal = minTagUMIs; + + List result = tuples.tuples.stream().filter(tup -> { + + if (tup.readFractionInTag < this.minReadFractionInTag) + return false; + + if (tup.rank > this.maxCloneRankInTag) + return false; + + if (tup.getReadsInTag() < minTagReadsFinal) + return false; + + if (tup.getUMIsInTag() < minTagUMIsFinal) + return false; + + return true; + }).collect(Collectors.toList()); + + + int tuplesBefore = tuples.tuples.size(); + int tagsBefore = tuples.umisPerDroplet.size(); + long umisBefore = tuples.tuples.stream().mapToLong(s -> s.umiCount).sum(); + double readsBefore = tuples.tuples.stream().mapToDouble(s -> s.readCount).sum(); + + int tuplesAfter = result.size(); + int tagsAfter = (int) result.stream().map(s -> s.tag).distinct().count(); + long umisAfter = result.stream().mapToLong(s -> s.umiCount).sum(); + double readsAfter = result.stream().mapToDouble(s -> s.readCount).sum(); + + report.tagTuplesTotal.set(tuplesBefore); + report.tagsTotal.set(tagsBefore); + report.umisTotal.set(umisBefore); + report.readsTotal.set(readsBefore); + + report.tagTuplesFiltered.set(tuplesAfter); + report.tagsFiltered.set(tagsAfter); + report.umisFiltered.set(umisAfter); + report.readsFiltered.set(readsAfter); + + return result; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java new file mode 100644 index 000000000..985ec26d9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java @@ -0,0 +1,465 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.tags; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneSet; +import com.milaboratory.mixcr.basictypes.TagTuple; +import com.milaboratory.mixcr.util.AdjacencyMatrix; +import com.milaboratory.mixcr.util.BitArrayInt; +import com.milaboratory.util.ProgressAndStage; +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TIntIntIterator; +import gnu.trove.iterator.TIntIterator; +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.iterator.TObjectIntIterator; +import gnu.trove.map.hash.*; +import gnu.trove.set.hash.TIntHashSet; + +import java.util.*; +import java.util.concurrent.atomic.AtomicReference; +import java.util.stream.Collectors; + +public final class DropletCloneGraph { + + private static TIntIntHashMap newTIntIntHashMap() { + return new TIntIntHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1, -1); + } + + private static TObjectIntHashMap newTObjectIntHashMap() { + return new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); + } + + private static TObjectDoubleHashMap newTObjectDoubleHashMap() { + return new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); + } + + public static List calculateGroups(CloneTagTupleList tuplesList, + DropletCloneGraphParameters parameters, + DropletCloneGraphReport report, + ProgressAndStage progressAndStage) { + List tuples = parameters.filter.filter(tuplesList, report); + Map> byTags = new HashMap<>(); + TIntObjectHashMap> byCloneId = new TIntObjectHashMap<>(); + List tmpList = new ArrayList<>(); + for (CloneTagTuple tup : tuples) { + byTags.computeIfAbsent(tup.tag, __ -> new ArrayList<>()).add(tup); + List list = byCloneId.putIfAbsent(tup.clone.getId(), tmpList); + if (list == null) { + tmpList.add(tup); + tmpList = new ArrayList<>(); + } else + list.add(tup); + } + + ArrayList groups = new ArrayList<>(); + + long initialTagCount = byTags.size(); + long counter = 0; + + int groupId = 0; + // loop over connected components + while (!byTags.isEmpty()) { + Map> byTagsInComponent = new HashMap<>(); + TIntObjectHashMap> byCloneIdInComponent = new TIntObjectHashMap<>(); + + // Calculating connected component starting from: + // tag = byTags.keySet().iterator().next() + { + Set currentTags = new HashSet<>(); + TIntHashSet currentClones = new TIntHashSet(); + currentTags.add(byTags.keySet().iterator().next()); + while (!currentTags.isEmpty()) { + for (String currentTag : currentTags) { + List inDroplet = byTags.remove(currentTag); + if (inDroplet == null) + continue; + + for (CloneTagTuple tup : inDroplet) { + List list = byCloneIdInComponent.putIfAbsent(tup.clone.getId(), tmpList); + if (list == null) { + currentClones.add(tup.clone.getId()); + tmpList.add(tup); + tmpList = new ArrayList<>(); + } else + list.add(tup); + } + } + currentTags.clear(); + + TIntIterator cIt = currentClones.iterator(); + while (cIt.hasNext()) + for (CloneTagTuple tup : byCloneId.remove(cIt.next())) { + byTagsInComponent.computeIfAbsent(tup.tag, __ -> { + currentTags.add(tup.tag); + return new ArrayList<>(); + }).add(tup); + } + currentClones.clear(); + } + } + + report.onConnectedComponent(byTagsInComponent, byCloneIdInComponent); + + // form adjacency matrix of connected tags + AdjacencyMatrix tagMatrix = new AdjacencyMatrix(byTagsInComponent.size()); + // tagId <-> tag + TIntObjectHashMap indexToTag = new TIntObjectHashMap<>(); + TObjectIntHashMap tagToIndex = newTObjectIntHashMap(); + int idx = 0; + for (String tag : byTagsInComponent.keySet()) { + indexToTag.put(idx, tag); + tagToIndex.put(tag, idx); + ++idx; + } + + for (int i = 0; i < indexToTag.size(); ++i) { + tagMatrix.setConnected(i, i); + for (CloneTagTuple tup : byTagsInComponent.get(indexToTag.get(i))) + for (CloneTagTuple end : byCloneIdInComponent.get(tup.clone.getId())) + tagMatrix.setConnected(i, tagToIndex.get(end.tag)); + } + + List tagCliques = null; + List tagCliqueInfos = null; + // searching all cliques in tags + while (!tagToIndex.isEmpty()) { + if (tagCliques == null) { + tagCliques = tagMatrix.calculateMaximalCliques(); + tagCliqueInfos = new ArrayList<>(); + for (BitArrayInt clique : tagCliques) { + int[] bits = clique.getBits(); + if (bits.length == 1 && !tagMatrix.isConnected(bits[0], bits[0])) + continue; + + TIntIntHashMap nTagsByClones = newTIntIntHashMap(); + + double readCount = 0; + for (int tagIndex : bits) + for (CloneTagTuple tup : byTagsInComponent.get(indexToTag.get(tagIndex))) { + nTagsByClones.adjustOrPutValue(tup.clone.getId(), 1, 1); + readCount += tup.readCount; + } + + + TIntIntIterator it = nTagsByClones.iterator(); + double score = 0; + while (it.hasNext()) { + it.advance(); + int count = it.value(); + + score += Math.pow(count - 1, parameters.tagCliqueScorePower); + } + + tagCliqueInfos.add(new CliqueInfo(clique, score, readCount)); + } + } + + Optional topTagCliqueO = tagCliqueInfos.stream().max(CliqueInfo::compareTo); + if (!topTagCliqueO.isPresent()) + break; + + CliqueInfo topTagClique = topTagCliqueO.get(); + + Set tags = new HashSet<>(); + int[] topTagCliqueBits = topTagClique.clique.getBits(); + for (int i : topTagCliqueBits) + tags.add(indexToTag.get(i)); + + + TIntIntHashMap indexToCloneId = newTIntIntHashMap(); + // !!! used as cloneId -> count in the loop below + TIntIntHashMap cloneIdToIndex = newTIntIntHashMap(); + + { + for (String tag : tags) + for (CloneTagTuple tup : byTagsInComponent.get(tag)) + cloneIdToIndex.adjustOrPutValue(tup.clone.getId(), 1, 1); + + idx = 0; + TIntIntIterator it = cloneIdToIndex.iterator(); + while (it.hasNext()) { + it.advance(); + assert it.value() > 0; + // if tags.size == 1 => single tag in clique, so just writing + // index (presence of clones is enough, i.e. do not require clones to link any tags) + if (tags.size() > 1 && it.value() == 1) + it.remove(); + else { + indexToCloneId.put(idx, it.key()); + it.setValue(idx); + ++idx; + } + } + } + + AdjacencyMatrix clonesMatrix = new AdjacencyMatrix(cloneIdToIndex.size()); + + for (String tag : tags) { + List tuplesForTag = byTagsInComponent.get(tag); + for (int i1 = 0; i1 < tuplesForTag.size(); i1++) + for (int i2 = i1 + 1; i2 < tuplesForTag.size(); i2++) { + int index1 = cloneIdToIndex.get(tuplesForTag.get(i1).clone.getId()); + int index2 = cloneIdToIndex.get(tuplesForTag.get(i2).clone.getId()); + if (index1 >= 0 && index2 >= 0) + clonesMatrix.setConnected(index1, index2); + } + } + + List cloneCliques = clonesMatrix.calculateMaximalCliques(); + List cloneCliqueInfos = new ArrayList<>(); + + for (BitArrayInt clique : cloneCliques) { + TObjectIntHashMap nClonesByTags = newTObjectIntHashMap(); + + double readCount = 0; + for (int cloneIndex : clique.getBits()) + for (CloneTagTuple tup : byCloneIdInComponent.get(indexToCloneId.get(cloneIndex))) + if (tags.contains(tup.tag)) { + nClonesByTags.adjustOrPutValue(tup.tag, 1, 1); + readCount += tup.readCount; + } + + TObjectIntIterator it = nClonesByTags.iterator(); + double score = 0; + while (it.hasNext()) { + it.advance(); + int count = it.value(); + + score += Math.pow(count - 1, parameters.cloneCliqueScorePower); + } + + cloneCliqueInfos.add(new CliqueInfo(clique, score, readCount)); + } + + CliqueInfo topCloneClique = cloneCliqueInfos.stream().max(CliqueInfo::compareTo).get(); + + // dropping tags + + Set groupTags = new HashSet<>(); + TIntHashSet groupClones = new TIntHashSet(); + + for (int cloneIdx : topCloneClique.clique.getBits()) { + for (CloneTagTuple tup : byCloneIdInComponent.get(indexToCloneId.get(cloneIdx))) { + if (tags.contains(tup.tag)) { + String tag = tup.tag; + + int index = tagToIndex.remove(tag); + ++counter; + if (progressAndStage != null) + progressAndStage.setProgress(1.0 * counter / initialTagCount); + + if (index >= 0) { + indexToTag.remove(index); + tagMatrix.clear(index); + } + + groupClones.add(tup.clone.getId()); + groupTags.add(tag); + } + } + } + + double readTotal = 0.0; + long umiTotal = 0; + + for (String tag : groupTags) + for (CloneTagTuple ctt : byTagsInComponent.get(tag)) { + readTotal += ctt.readCount; + umiTotal += ctt.umiCount; + } + + CloneGroup group = new CloneGroup(groupId, readTotal, umiTotal, groupTags, groupClones); + report.onGroup(topTagClique, topCloneClique, group); + groups.add(group); + + tagCliques = null; + + ++groupId; + } + } + + // Clustering + TIntObjectHashMap>> byClones = new TIntObjectHashMap<>(); + groups.sort(Comparator + .comparingInt(c -> c.groupClones.size()) + .thenComparingInt(c -> c.groupTags.size()) + .reversed()); + + ArrayList> groupsAfterClustering = new ArrayList<>(); + ArrayList> tmpList2 = new ArrayList<>(); + for (CloneGroup minor : groups) { + // Major candidates + Set> majorCandidates = Collections.newSetFromMap(new IdentityHashMap<>()); + int[] minorCloneIds = minor.groupClones.toArray(); + for (int cId : minorCloneIds) { + List> grps = byClones.get(cId); + if (grps == null) + break; // This guarantees that no candidates will be found (such clone was never seen before) + for (AtomicReference preCandidate : grps) + if (preCandidate.get().groupClones.containsAll(minor.groupClones) + && 1.0 * minor.groupTags.size() / preCandidate.get().groupTags.size() <= parameters.maxTagCountRatio) + majorCandidates.add(preCandidate); + } + if (majorCandidates.size() != 1) { + AtomicReference minorRef = new AtomicReference<>(minor); + groupsAfterClustering.add(minorRef); + for (int cId : minorCloneIds) { + List> cloneGroups = byClones.putIfAbsent(cId, tmpList2); + if (cloneGroups != null) + cloneGroups.add(minorRef); + else { + tmpList2.add(minorRef); + tmpList2 = new ArrayList<>(); + } + } + } else { // Clustering + AtomicReference majorRef = majorCandidates.iterator().next(); + report.onClustered(majorRef.get(), minor); + majorRef.set(majorRef.get().mergeFrom(minor)); + } + } + + if (progressAndStage != null) + progressAndStage.setFinished(true); + + return groupsAfterClustering.stream().map(AtomicReference::get).collect(Collectors.toList()); + } + + public static CloneTagTupleList calculateTuples(CloneSet cloneset, int tagIndex) { + TObjectDoubleHashMap readsPerDroplet = newTObjectDoubleHashMap(); + + // Approximation: same UMIs in different clonotypes will be counted several times + TObjectLongHashMap umisPerDroplet = new TObjectLongHashMap<>(); + + for (Clone clone : cloneset) { + TObjectDoubleIterator it = clone.getTagCounter().iterator(); + while (it.hasNext()) { + it.advance(); + umisPerDroplet.adjustOrPutValue(it.key().tags[tagIndex], 1, 1); + readsPerDroplet.adjustOrPutValue(it.key().tags[tagIndex], it.value(), it.value()); + } + } + + List links = new ArrayList<>(); + for (Clone clone : cloneset) { + Map mlink = new HashMap<>(); + TObjectDoubleIterator it = clone.getTagCounter().iterator(); + while (it.hasNext()) { + it.advance(); + CloneTagTuple link = mlink.computeIfAbsent(it.key().tags[tagIndex], tag -> new CloneTagTuple(clone, tag)); + link.umiCount++; + link.readCount += it.value(); + } + // ArrayList alinks = new ArrayList<>(mlink.size()); + for (CloneTagTuple link : mlink.values()) { + link.readFractionInTag = link.readCount / readsPerDroplet.get(link.tag); + link.umiFractionInTag = 1.0 * link.umiCount / umisPerDroplet.get(link.tag); + links.add(link); + } + } + links.sort(Comparator. + comparingLong(l -> l.umiCount) + .thenComparingDouble(l -> l.readCount) + .reversed()); + TObjectIntHashMap rankCounter = new TObjectIntHashMap<>(); + for (CloneTagTuple link : links) + link.rank = rankCounter.adjustOrPutValue(link.tag, 1, 1); + + return new CloneTagTupleList(readsPerDroplet, umisPerDroplet, links); + } + + public static final class CloneTagTupleList { + final TObjectDoubleHashMap readsPerDroplet; + final TObjectLongHashMap umisPerDroplet; + final List tuples; + + public CloneTagTupleList(TObjectDoubleHashMap readsPerDroplet, + TObjectLongHashMap umisPerDroplet, + List tuples) { + this.readsPerDroplet = readsPerDroplet; + this.umisPerDroplet = umisPerDroplet; + this.tuples = tuples; + } + + public double readsTopQuantile(double quantile) { + if (quantile > 1.0 || quantile < 0) + throw new IllegalArgumentException(); + + double[] values = readsPerDroplet.values(); + if (values.length == 0) + return 0; + + Arrays.sort(values); + int index = (int) Math.floor(quantile * values.length); + if (index >= values.length) + index = values.length - 1; + + return values[index]; + } + + public double umisTopQuantile(double quantile) { + if (quantile > 1.0 || quantile < 0) + throw new IllegalArgumentException(); + + long[] values = umisPerDroplet.values(); + if (values.length == 0) + return 0; + + Arrays.sort(values); + int index = (int) Math.floor(quantile * values.length); + if (index >= values.length) + index = values.length - 1; + + return values[index]; + } + } + + static final class CliqueInfo implements Comparable { + final BitArrayInt clique; + final double score; + final double readCount; + + public CliqueInfo(BitArrayInt clique, double score, double readCount) { + this.clique = clique; + this.score = score; + this.readCount = readCount; + } + + @Override + public int compareTo(DropletCloneGraph.CliqueInfo o) { + int c = Double.compare(score, o.score); + if (c != 0) + return c; + return Double.compare(readCount, o.readCount); + } + } + +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java new file mode 100644 index 000000000..868e876c9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java @@ -0,0 +1,82 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.tags; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.util.GlobalObjectMappers; + +import java.io.IOException; +import java.util.Objects; + +public class DropletCloneGraphParameters { + @JsonProperty("tagCliqueScorePower") + public final double tagCliqueScorePower; + @JsonProperty("cloneCliqueScorePower") + public final double cloneCliqueScorePower; + @JsonProperty("filter") + public final CloneTagTupleFilter filter; + @JsonProperty("maxTagCountRatio") + public final double maxTagCountRatio; + + @JsonCreator + public DropletCloneGraphParameters(@JsonProperty("tagCliqueScorePower") double tagCliqueScorePower, + @JsonProperty("cloneCliqueScorePower") double cloneCliqueScorePower, + @JsonProperty("filter") CloneTagTupleFilter filter, + @JsonProperty("maxTagCountRatio") double maxTagCountRatio) { + this.tagCliqueScorePower = tagCliqueScorePower; + this.cloneCliqueScorePower = cloneCliqueScorePower; + this.filter = filter; + this.maxTagCountRatio = maxTagCountRatio; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + DropletCloneGraphParameters that = (DropletCloneGraphParameters) o; + return Double.compare(that.tagCliqueScorePower, tagCliqueScorePower) == 0 && + Double.compare(that.cloneCliqueScorePower, cloneCliqueScorePower) == 0 && + Objects.equals(filter, that.filter); + } + + @Override + public int hashCode() { + return Objects.hash(tagCliqueScorePower, cloneCliqueScorePower, filter); + } + + public static DropletCloneGraphParameters getDefault() { + try { + return GlobalObjectMappers.ONE_LINE.readValue(CloneTagTupleFilter.class.getClassLoader().getResourceAsStream("parameters/droplet_clone_graph_parameters.json"), DropletCloneGraphParameters.class); + } catch (IOException e) { + throw new RuntimeException(e); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java new file mode 100644 index 000000000..84e27b387 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java @@ -0,0 +1,388 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.tags; + +import com.fasterxml.jackson.annotation.JsonProperty; +import com.google.common.util.concurrent.AtomicDouble; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneSet; +import com.milaboratory.mixcr.cli.Report; +import com.milaboratory.mixcr.cli.ReportHelper; +import com.milaboratory.mixcr.cli.Util; +import gnu.trove.map.hash.TIntObjectHashMap; + +import java.util.List; +import java.util.Map; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.concurrent.atomic.AtomicLong; + +public class DropletCloneGraphReport implements Report { + final AtomicInteger + clonesBefore = new AtomicInteger(), + connectedComponents = new AtomicInteger(), + maxClonesInConnectedComponents = new AtomicInteger(), + maxTagsInConnectedComponents = new AtomicInteger(), + numberOfGroups = new AtomicInteger(), + maxTagsClique = new AtomicInteger(), + maxTagsCliqueDelta = new AtomicInteger(), + sumTagsCliqueDelta = new AtomicInteger(), + maxClonesPerGroup = new AtomicInteger(), + sumClonesPerGroup = new AtomicInteger(), + maxTagsPerGroup = new AtomicInteger(), + sumTagsPerGroup = new AtomicInteger(), + ungroupedClones = new AtomicInteger(), + groupedClonesBefore = new AtomicInteger(), + groupedClonesAfter = new AtomicInteger(); + + final AtomicLong + maxUMIsInConnectedComponents = new AtomicLong(), + sumUMIs = new AtomicLong(); + + final AtomicDouble + readsBefore = new AtomicDouble(), + readsInUngroupedClones = new AtomicDouble(), + readsInGroupedClones = new AtomicDouble(), + maxReadsInConnectedComponents = new AtomicDouble(), + sumReads = new AtomicDouble(); + + public void onConnectedComponent(Map> byTagsInComponent, + TIntObjectHashMap> byCloneIdInComponent) { + connectedComponents.incrementAndGet(); + + maxClonesInConnectedComponents.accumulateAndGet(byCloneIdInComponent.size(), Integer::max); + maxTagsInConnectedComponents.accumulateAndGet(byTagsInComponent.size(), Integer::max); + + double reads = 0; + long umis = 0; + for (List list : byTagsInComponent.values()) + for (CloneTagTuple tt : list) { + reads += tt.readCount; + umis += tt.umiCount; + } + + double val; + do { + val = maxReadsInConnectedComponents.get(); + } while (!maxReadsInConnectedComponents.compareAndSet(val, Double.max(val, reads))); + + maxUMIsInConnectedComponents.accumulateAndGet(umis, Long::max); + + sumReads.addAndGet(reads); + sumUMIs.addAndGet(umis); + } + + public void before(CloneSet cs) { + clonesBefore.set(cs.size()); + readsBefore.set(cs.getTotalCount()); + } + + public void onUngroupedClone(Clone c) { + ungroupedClones.incrementAndGet(); + readsInUngroupedClones.addAndGet(c.getCount()); + } + + public void onCloneBeforeSplit(Clone c) { + groupedClonesBefore.incrementAndGet(); + } + + public void onGroupedClone(Clone c) { + readsInGroupedClones.addAndGet(c.getCount()); + groupedClonesAfter.incrementAndGet(); + } + + public void onGroup(DropletCloneGraph.CliqueInfo topTagClique, DropletCloneGraph.CliqueInfo topCloneClique, + CloneGroup group) { + numberOfGroups.incrementAndGet(); + maxTagsClique.accumulateAndGet(topTagClique.clique.bitCount(), Integer::max); + + int tagsCliqueDelta = topTagClique.clique.bitCount() - group.groupTags.size(); + maxTagsCliqueDelta.accumulateAndGet(tagsCliqueDelta, Integer::max); + sumTagsCliqueDelta.addAndGet(tagsCliqueDelta); + + maxClonesPerGroup.accumulateAndGet(group.groupClones.size(), Integer::max); + sumClonesPerGroup.addAndGet(group.groupClones.size()); + + maxTagsPerGroup.accumulateAndGet(group.groupTags.size(), Integer::max); + sumTagsPerGroup.addAndGet(group.groupTags.size()); + } + + public void onClustered(CloneGroup major, CloneGroup minor) { + groupsClustered.incrementAndGet(); + readsClustered.addAndGet(minor.reads); + unisClustered.addAndGet(minor.umis); + tagsClustered.addAndGet(minor.groupTags.size()); + } + + double + effectiveMinReadsInTag = Double.NaN, + effectiveMinUMIsInTag = Double.NaN; + + final AtomicInteger + tagTuplesTotal = new AtomicInteger(), + tagTuplesFiltered = new AtomicInteger(), + tagsTotal = new AtomicInteger(), + tagsFiltered = new AtomicInteger(), + tagsClustered = new AtomicInteger(), + groupsClustered = new AtomicInteger(); + + final AtomicDouble + readsTotal = new AtomicDouble(), + readsFiltered = new AtomicDouble(), + readsClustered = new AtomicDouble(); + + final AtomicLong + umisTotal = new AtomicLong(), + umisFiltered = new AtomicLong(), + unisClustered = new AtomicLong(); + + @JsonProperty("clonesBefore") + public int getClonesBefore() { + return clonesBefore.get(); + } + + @JsonProperty("connectedComponents") + public int getConnectedComponents() { + return connectedComponents.get(); + } + + @JsonProperty("maxClonesInConnectedComponents") + public int getMaxClonesInConnectedComponents() { + return maxClonesInConnectedComponents.get(); + } + + @JsonProperty("maxTagsInConnectedComponents") + public int getMaxTagsInConnectedComponents() { + return maxTagsInConnectedComponents.get(); + } + + @JsonProperty("numberOfGroups") + public int getNumberOfGroups() { + return numberOfGroups.get(); + } + + @JsonProperty("maxTagsClique") + public int getMaxTagsClique() { + return maxTagsClique.get(); + } + + @JsonProperty("maxTagsCliqueDelta") + public int getMaxTagsCliqueDelta() { + return maxTagsCliqueDelta.get(); + } + + @JsonProperty("sumTagsCliqueDelta") + public int getSumTagsCliqueDelta() { + return sumTagsCliqueDelta.get(); + } + + @JsonProperty("maxClonesPerGroup") + public int getMaxClonesPerGroup() { + return maxClonesPerGroup.get(); + } + + @JsonProperty("sumClonesPerGroup") + public int getSumClonesPerGroup() { + return sumClonesPerGroup.get(); + } + + @JsonProperty("maxTagsPerGroup") + public int getMaxTagsPerGroup() { + return maxTagsPerGroup.get(); + } + + @JsonProperty("sumTagsPerGroup") + public int getSumTagsPerGroup() { + return sumTagsPerGroup.get(); + } + + @JsonProperty("ungroupedClones") + public int getUngroupedClones() { + return ungroupedClones.get(); + } + + @JsonProperty("groupedClonesBefore") + public int getGroupedClonesBefore() { + return groupedClonesBefore.get(); + } + + @JsonProperty("groupedClonesAfter") + public int getGroupedClonesAfter() { + return groupedClonesAfter.get(); + } + + @JsonProperty("maxUMIsInConnectedComponents") + public long getMaxUMIsInConnectedComponents() { + return maxUMIsInConnectedComponents.get(); + } + + @JsonProperty("sumUMIs") + public long getSumUMIs() { + return sumUMIs.get(); + } + + @JsonProperty("readsBefore") + public double getReadsBefore() { + return readsBefore.get(); + } + + @JsonProperty("readsInUngroupedClones") + public double getReadsInUngroupedClones() { + return readsInUngroupedClones.get(); + } + + @JsonProperty("readsInGroupedClones") + public double getReadsInGroupedClones() { + return readsInGroupedClones.get(); + } + + @JsonProperty("maxReadsInConnectedComponents") + public double getMaxReadsInConnectedComponents() { + return maxReadsInConnectedComponents.get(); + } + + @JsonProperty("sumReads") + public double getSumReads() { + return sumReads.get(); + } + + @JsonProperty("effectiveMinReadsInTag") + public double getEffectiveMinReadsInTag() { + return effectiveMinReadsInTag; + } + + @JsonProperty("effectiveMinUMIsInTag") + public double getEffectiveMinUMIsInTag() { + return effectiveMinUMIsInTag; + } + + @JsonProperty("tagTuplesTotal") + public int getTagTuplesTotal() { + return tagTuplesTotal.get(); + } + + @JsonProperty("tagTuplesFiltered") + public int getTagTuplesFiltered() { + return tagTuplesFiltered.get(); + } + + @JsonProperty("tagsTotal") + public int getTagsTotal() { + return tagsTotal.get(); + } + + @JsonProperty("tagsFiltered") + public int getTagsFiltered() { + return tagsFiltered.get(); + } + + @JsonProperty("readsTotal") + public double getReadsTotal() { + return readsTotal.get(); + } + + @JsonProperty("readsFiltered") + public double getReadsFiltered() { + return readsFiltered.get(); + } + + @JsonProperty("umisTotal") + public long getUmisTotal() { + return umisTotal.get(); + } + + @JsonProperty("umisFiltered") + public long getUmisFiltered() { + return umisFiltered.get(); + } + + @JsonProperty("tagsClustered") + public int getTagsClustered() { + return tagsClustered.get(); + } + + @JsonProperty("groupsClustered") + public int getGroupsClustered() { + return groupsClustered.get(); + } + + @JsonProperty("readsClustered") + public double getReadsClustered() { + return readsClustered.get(); + } + + @JsonProperty("unisClustered") + public long getUnisClustered() { + return unisClustered.get(); + } + + @Override + public void writeReport(ReportHelper helper) { + int finalClones = ungroupedClones.get() + groupedClonesAfter.get(); + + helper + .writePercentAndAbsoluteField("Clones after grouping", finalClones, clonesBefore.get()) + .writePercentAndAbsoluteField("Ungrouped clones", ungroupedClones.get(), finalClones) + .writePercentAndAbsoluteField("Clones split", groupedClonesAfter.get(), groupedClonesBefore.get()) + .writePercentAndAbsoluteField("Reads in ungrouped clones", (long) readsInUngroupedClones.get(), readsBefore.get()); + + helper + .writePercentAndAbsoluteField("Clone Tag associations after filtering", tagTuplesFiltered.get(), tagTuplesTotal.get()) + .writePercentAndAbsoluteField("Tags after filtering", tagsFiltered.get(), tagsTotal.get()) + .writePercentAndAbsoluteField("Reads after filtering", readsFiltered.get(), readsTotal.get()) + .writePercentAndAbsoluteField("UMIs after filtering", umisFiltered.get(), umisTotal.get()); + + helper + .writeField("Connected components (CC)", connectedComponents.get()) + .writePercentAndAbsoluteField("Clones in max CC", maxClonesInConnectedComponents.get(), sumClonesPerGroup.get()) + .writePercentAndAbsoluteField("Reads in max CC", maxReadsInConnectedComponents.get(), sumReads.get()) + .writePercentAndAbsoluteField("UMIs in max CC", maxUMIsInConnectedComponents.get(), sumUMIs.get()); + + helper + .writeField("Groups", numberOfGroups.get() - groupsClustered.get()) + .writeField("Groups before clustering", numberOfGroups.get()) + .writeField("Max clones per group", maxClonesPerGroup.get()) + .writeField("Mean clones per group", Util.PERCENT_FORMAT.format(1.0 * sumClonesPerGroup.get() / numberOfGroups.get())) + .writeField("Max tags per group", maxTagsPerGroup.get()) + .writeField("Mean tags per group", Util.PERCENT_FORMAT.format(1.0 * sumTagsPerGroup.get() / numberOfGroups.get())) + .writeField("Max tags clique", maxTagsClique.get()) + .writeField("Max tags clique delta", maxTagsCliqueDelta.get()) + .writeField("Mean tags clique delta", Util.PERCENT_FORMAT.format(1.0 * sumTagsCliqueDelta.get() / numberOfGroups.get())); + + helper + .writePercentAndAbsoluteField("Groups clustered", groupsClustered.get(), numberOfGroups.get()) + .writePercentAndAbsoluteField("Tags clustered", tagsClustered.get(), tagsTotal.get()) + .writePercentAndAbsoluteField("Reads clustered", readsClustered.get(), readsTotal.get()) + .writePercentAndAbsoluteField("UMIs clustered", unisClustered.get(), umisTotal.get()); + + helper + .writeField("Effective reads in tags threshold", effectiveMinReadsInTag) + .writeField("Effective UMIs in tags threshold", effectiveMinUMIsInTag); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java b/src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java new file mode 100644 index 000000000..6f447fc83 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java @@ -0,0 +1,232 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.util; + +import gnu.trove.list.array.TIntArrayList; + +import java.util.ArrayList; +import java.util.List; + +public class AdjacencyMatrix { + public final BitArrayInt[] data; + public final int size; + + public AdjacencyMatrix(int size) { + this.size = size; + this.data = new BitArrayInt[size]; + for (int i = 0; i < size; i++) + this.data[i] = new BitArrayInt(size); + } + + public void setConnected(int i, int j) { + setConnected(i, j, true); + } + + public boolean isConnected(int i, int j) { + return this.data[i].get(j); + } + + public void setConnected(int i, int j, boolean connected) { + if (connected) { + this.data[i].set(j); + this.data[j].set(i); + } else { + this.data[i].clear(j); + this.data[j].clear(i); + } + } + + public void clear(int i) { + for (int j = 0; j < size; ++j) + setConnected(i, j, false); + } + + public List calculateMaximalCliques() { + return calculateMaximalCliques(0); + } + + /** + * Extract maximal cliques using Bron–Kerbosch algorithm. + * + * @return list of maximal cliques + */ + public List calculateMaximalCliques(int maxCliques) { + List cliques = new ArrayList<>(); + BStack stack = new BStack(); + stack.currentP().setAll(); + stack.currentPi().setAll(); + BitArrayInt tmp = new BitArrayInt(size); + + while (true) { + int v = stack.nextVertex(); + + if (v == -1) + if (stack.pop()) + continue; + else + break; + + stack.currentP().clear(v); + + stack.loadAndGetNextR().set(v); + stack.loadAndGetNextP().and(data[v]); + stack.loadAndGetNextX().and(data[v]); + + stack.currentX().set(v); + + if (stack.nextP().isEmpty() && stack.nextX().isEmpty()) { + cliques.add(stack.nextR().clone()); + if (maxCliques != 0 && cliques.size() >= maxCliques) + return cliques; + continue; + } + + tmp.loadValueFrom(stack.nextP()); + tmp.or(stack.nextX()); + int u = 0, bestU = -1, count = -1; + while ((u = tmp.nextBit(u)) != -1) { + int c = tmp.numberOfCommonBits(data[u]); + if (bestU == -1 || c > count) { + bestU = u; + count = c; + } + ++u; + } + + stack.nextPi().loadValueFrom(data[bestU]); + stack.nextPi().clear(bestU); + stack.nextPi().xor(stack.nextP()); + stack.nextPi().and(stack.nextP()); + + stack.push(); + } + return cliques; + } + + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + for (int i = 0; i < size; i++) + builder.append(data[i]).append('\n'); + builder.deleteCharAt(builder.length() - 1); + return builder.toString(); + } + + final class BStack { + final BList R = new BList(); + final BList X = new BList(); + final BList P = new BList(); + /** + * P for vertices enumeration = P / N(v) + */ + final BList Pi = new BList(); + final TIntArrayList lastVertex = new TIntArrayList(); + int currentLevel = 0; + + public BStack() { + lastVertex.add(0); + } + + BitArrayInt currentR() { + return R.get(currentLevel); + } + + BitArrayInt currentX() { + return X.get(currentLevel); + } + + BitArrayInt currentP() { + return P.get(currentLevel); + } + + BitArrayInt currentPi() { + return Pi.get(currentLevel); + } + + int nextVertex() { + int nextVertex = currentPi().nextBit(lastVertex.get(lastVertex.size() - 1)); + lastVertex.set(currentLevel, nextVertex + 1); + return nextVertex; + } + + BitArrayInt loadAndGetNextR() { + R.get(currentLevel + 1).loadValueFrom(R.get(currentLevel)); + return R.get(currentLevel + 1); + } + + BitArrayInt loadAndGetNextX() { + X.get(currentLevel + 1).loadValueFrom(X.get(currentLevel)); + return X.get(currentLevel + 1); + } + + BitArrayInt loadAndGetNextP() { + P.get(currentLevel + 1).loadValueFrom(P.get(currentLevel)); + return P.get(currentLevel + 1); + } + + BitArrayInt nextX() { + return X.get(currentLevel + 1); + } + + BitArrayInt nextP() { + return P.get(currentLevel + 1); + } + + BitArrayInt nextR() { + return R.get(currentLevel + 1); + } + + BitArrayInt nextPi() { + return Pi.get(currentLevel + 1); + } + + void push() { + currentLevel++; + lastVertex.add(0); + } + + boolean pop() { + currentLevel--; + lastVertex.removeAt(lastVertex.size() - 1); + return currentLevel != -1; + } + } + + final class BList { + final List list = new ArrayList<>(); + + public BitArrayInt get(int i) { + if (i >= list.size()) + for (int j = list.size(); j <= i; j++) + list.add(new BitArrayInt(size)); + return list.get(i); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java b/src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java new file mode 100644 index 000000000..4f56a3784 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java @@ -0,0 +1,523 @@ +/* + * Copyright 2016 MiLaboratory.com + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package com.milaboratory.mixcr.util; + +import gnu.trove.list.array.TIntArrayList; + +import java.util.Arrays; + +import static java.lang.Math.min; + +/** + * Created by dbolotin on 08/02/16. + */ +public class BitArrayInt { + public static final BitArrayInt EMPTY = new BitArrayInt(0); + + final int[] data; + final int size; + + private BitArrayInt(int[] data, int size) { + this.data = data; + this.size = size; + } + + /** + * Creates an array with specified size. Initial state of all bits is 0 (cleared). + * + * @param size + */ + public BitArrayInt(int size) { + this.size = size; + this.data = new int[(size + 31) >>> 5]; + } + + /** + * Creates a bit array from array of booleans + * + * @param array boolean array + */ + public BitArrayInt(boolean[] array) { + this(array.length); + for (int i = 0; i < array.length; ++i) + if (array[i]) + set(i); + } + + /** + * Compound assignment and. + * + * @param bitArrayInt rhs of and + */ + public void and(BitArrayInt bitArrayInt) { + if (bitArrayInt.size != size) + throw new IllegalArgumentException(); + + for (int i = data.length - 1; i >= 0; --i) + data[i] &= bitArrayInt.data[i]; + } + + /** + * Compound assignment or. + * + * @param bitArrayInt rhs of or + */ + public void or(BitArrayInt bitArrayInt) { + if (bitArrayInt.size != size) + throw new IllegalArgumentException(); + + for (int i = data.length - 1; i >= 0; --i) + data[i] |= bitArrayInt.data[i]; + } + + /** + * Compound assignment xor. + * + * @param bitArrayInt rhs of xor + */ + public void xor(BitArrayInt bitArrayInt) { + if (bitArrayInt.size != size) + throw new IllegalArgumentException(); + + for (int i = data.length - 1; i >= 0; --i) + data[i] ^= bitArrayInt.data[i]; + } + + /** + * Inverts all bits in this bit array + */ + public void not() { + for (int i = data.length - 1; i >= 0; --i) + data[i] = ~data[i]; + + if (size > 0) + data[data.length - 1] &= lastElementMask(); + } + + int lastElementMask() { + if ((size & 0x1F) == 0) + return 0xFFFFFFFF; + else + return 0xFFFFFFFF >>> ((data.length << 5) - size); + //return ~(0xFFFFFFFF << (32 - ((data.length << 5) - size))); + } + + /** + * Returns the number of 1 bits. + * + * @return number of 1 bits + */ + public int bitCount() { + int bits = 0; + for (int i : data) + bits += Integer.bitCount(i); + return bits; + } + + /** + * Clears all bits of this bit array + */ + public void clearAll() { + Arrays.fill(data, 0); + } + + /** + * Returns a clone of this bit array. + * + * @return clone of this bit array + */ + public BitArrayInt clone() { + return new BitArrayInt(data.clone(), size); + } + + //public int[] getBits() { + // /*IntArrayList ial = new IntArrayList(); + // for (int i = 0; i < data.length; ++i) + // nextTrailingBit() */ + // return new int[0]; + //} + + /** + * Returns {@code true} if there are 1 bits in the same positions. Equivalent to {@code !this.and(other).isEmpty() + * } + * + * @param bitArrayInt other bit array + * @return {@code true} if there are 1 bits in the same positions + */ + public boolean intersects(BitArrayInt bitArrayInt) { + if (bitArrayInt.size != size) + throw new IllegalArgumentException(); + + for (int i = data.length - 1; i >= 0; --i) + if ((bitArrayInt.data[i] & data[i]) != 0) + return true; + + return false; + } + + /** + * Copy values from the array of the same size + * + * @param bitArrayInt bit array to copy values from + */ + public void loadValueFrom(BitArrayInt bitArrayInt) { + System.arraycopy(bitArrayInt.data, 0, data, 0, data.length); + } + + /** + * Returns the state of specified bit + * + * @param i index + * @return {@code true} if bit is set, {@code false} if bit is cleared + */ + public boolean get(int i) { + return (data[i >> 5] & (1 << (i & 0x1F))) != 0; + } + + /** + * Sets the specified bit (sets to 1) + * + * @param i index of bit + */ + public void set(int i) { + data[i >> 5] |= (1 << (i & 0x1F)); + } + + /** + * Clears the specified bit (sets to 0) + * + * @param i index of bit + */ + public void clear(int i) { + data[i >> 5] &= ~(1 << (i & 0x1F)); + } + + /** + * Sets the value of specified bit to specified value + * + * @param i index + * @param value value + */ + public void set(int i, boolean value) { + if (value) + set(i); + else + clear(i); + } + + /** + * Sets values at specified positions to specified value + * + * @param positions positions + * @param value value + */ + public void setAll(int[] positions, boolean value) { + for (int i : positions) + set(i, value); + } + + /** + * Sets values at specified positions to specified value + * + * @param positions positions + * @param value value + */ + public void setAll(TIntArrayList positions, boolean value) { + for (int i = positions.size() - 1; i >= 0; --i) + set(positions.get(i), value); + } + + /** + * Sets all bits of this bit array + */ + public void setAll() { + for (int i = data.length - 2; i >= 0; --i) + data[i] = 0xFFFFFFFF; + + if (size > 0) + data[data.length - 1] = lastElementMask(); + } + + /** + * Returns the length of this bit array + * + * @return length of this bit array + */ + public int size() { + return size; + } + + /** + * Returns true if all bits in this array are in the 1 state. + * + * @return true if all bits in this array are in the 1 state + */ + public boolean isFull() { + if (size == 0) + return true; + + for (int i = data.length - 2; i >= 0; --i) + if (data[i] != 0xFFFFFFFF) + return false; + + return data[data.length - 1] == lastElementMask(); + } + + /** + * Returns true if all bits in this array are in the 0 state. + * + * @return true if all bits in this array are in the 0 state + */ + public boolean isEmpty() { + for (int i = data.length - 1; i >= 0; --i) + if (data[i] != 0) + return false; + + return true; + } + + /** + * Returns an array with positions of all "1" bits. + * + * @return array with positions of all "1" bits + */ + public int[] getBits() { + final int[] bits = new int[bitCount()]; + int i, j = 0; + if (size < 40 || size >> 2 < bits.length) { // norm ?? + for (i = 0; i < size; ++i) + if (get(i)) + bits[j++] = i; + } else { + i = -1; + while ((i = nextBit(i + 1)) != -1) { + if (!get(i)) + if (j > 0) + nextBit(bits[j - 1] + 1); + bits[j++] = i; + } + } + assert j == bits.length; + return bits; + } + + /** + * Returns the next "1" bit from the specified position. + * + * @param position initial position + * @return position of the next "1" bit of -1 if all bits after position are 0 + */ + public int nextBit(int position) { + int ret = position & 0x1F; + if (ret != 0) + if ((ret = Integer.numberOfTrailingZeros(data[position >>> 5] >>> ret)) != 32) + return position + ret; + else + position += 32; + + ret = 32; + position = position >>> 5; + while (position < data.length && + (ret = Integer.numberOfTrailingZeros(data[position++])) == 32) ; + + if (position >= data.length && ret == 32) + return -1; + else + return ((position - 1) << 5) + ret; + } + + /** + * Returns the next "0" bit from the specified position (inclusively). + * + * @param position initial position + * @return position of the next "0" bit of -1 if all bits after position are 0 + */ + public int nextZeroBit(int position) { + //todo review + int ret = position & 0x1F; + if (ret != 0) + if ((ret = Integer.numberOfTrailingZeros((~data[position >>> 5]) >>> ret)) != 32) { + int r = position + ret; + return r >= size() ? -1 : r; + } else + position += 32; + + ret = 32; + position = position >>> 5; + while (position < data.length && + (ret = Integer.numberOfTrailingZeros(~data[position++])) == 32) ; + + if (position >= data.length && ret == 32) + return -1; + else { + int r = ((position - 1) << 5) + ret; + return r >= size() ? -1 : r; + } + } + + /** + * Returns a new bit array, containing values from the specified range + * + * @param from lower bound of range + * @param to upper bound of range + * @return new bit array, containing values from the specified range + */ + public BitArrayInt copyOfRange(int from, int to) { + BitArrayInt ba = new BitArrayInt(to - from); + ba.loadValueFrom(this, from, 0, to - from); + return ba; + } + + public BitArrayInt copyOfRange(int from) { + return copyOfRange(from, size); + } + + /** + * Analog of {@link System#arraycopy(Object, int, Object, int, int)}, where src is {@code BitArrayInt}. + * + * @param bitArrayInt source + * @param sourceOffset source offset + * @param thisOffset destination offset + * @param length number of bits to copy + */ + public void loadValueFrom(BitArrayInt bitArrayInt, int sourceOffset, int thisOffset, int length) { + if (bitArrayInt == this) + throw new IllegalArgumentException("Can't copy from itself."); + + //Forcing alignment on other (BitArrayInt) + int alignmentOffset = (sourceOffset & 0x1F); + + //Now in words (not in bits) + sourceOffset = sourceOffset >>> 5; + + if (alignmentOffset != 0) { + int l = min(32 - alignmentOffset, length); + loadValueFrom( + bitArrayInt.data[sourceOffset] >>> alignmentOffset, + thisOffset, + l); + + thisOffset += l; + ++sourceOffset; + length -= l; + } + + //Bulk copy + while (length > 0) { + loadValueFrom(bitArrayInt.data[sourceOffset], thisOffset, min(32, length)); + length -= 32; + thisOffset += 32; + ++sourceOffset; + } + } + + /** + * Load 32 bits or less from single integer + * + * @param d integer with bits + * @param position offset + * @param length length + */ + void loadValueFrom(int d, int position, int length) { + if (length == 0) + return; + + int res = position & 0x1F; + position = position >>> 5; + + //mask for d + int mask = 0xFFFFFFFF >>> (32 - length); + + if (res == 0) { + if (length == 32) + data[position] = d; + else { + data[position] &= ~mask; + data[position] |= d & mask; + } + return; + } + + data[position] &= ~(mask << res); + data[position] |= (d & mask) << res; + + length -= (32 - res); + if (length > 0) + loadValueFrom(d >>> (32 - res), (position + 1) << 5, length); + } + + public int numberOfCommonBits(BitArrayInt other) { + if (other.size != size) + throw new IllegalArgumentException(); + int result = 0; + for (int i = 0; i < data.length; i++) + result += Integer.bitCount(other.data[i] & data[i]); + return result; + } + + public BitArrayInt append(BitArrayInt other) { + BitArrayInt ba = new BitArrayInt(size + other.size); + System.arraycopy(data, 0, ba.data, 0, data.length); + ba.loadValueFrom(other, 0, size, other.size); + return ba; + } + + public BitArrayInt times(int times) { + BitArrayInt ba = new BitArrayInt(times * size); + if (times > 0) + System.arraycopy(data, 0, ba.data, 0, data.length); + for (int i = 1; i < times; ++i) + ba.loadValueFrom(this, 0, i * size, size); + return ba; + } + + @Override + public String toString() { + char[] c = new char[size]; + for (int i = 0; i < size; ++i) + if (get(i)) + c[i] = '1'; + else + c[i] = '0'; + return new String(c); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + + BitArrayInt that = (BitArrayInt) o; + + if (size != that.size) return false; + + return Arrays.equals(data, that.data); + } + + @Override + public int hashCode() { + int result = Arrays.hashCode(data); + result = 31 * result + size; + return result; + } + + public static BitArrayInt createSet(int size, int... elements) { + BitArrayInt ret = new BitArrayInt(size); + for (int element : elements) + ret.set(element); + return ret; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java index c8e068f3f..622f644d3 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java @@ -476,7 +476,7 @@ static Clone doTransformClone(Clone clone, VDJCObjectExtender.Extender transformer, EnumMap newHitsMap) { return new Clone(transformer.transform(clone.getTargets()), - newHitsMap, clone.getTagCounter(), clone.getCount(), clone.getId()); + newHitsMap, clone.getTagCounter(), clone.getCount(), clone.getId(), clone.getGroup()); } static VDJCAlignments doTransformAlignment(VDJCAlignments alignment, @@ -688,4 +688,4 @@ public int hashCode() { // return new NSequenceWithQuality[0]; //} } -} \ No newline at end of file +} diff --git a/src/main/resources/parameters/droplet_clone_graph_parameters.json b/src/main/resources/parameters/droplet_clone_graph_parameters.json new file mode 100644 index 000000000..4d754aac5 --- /dev/null +++ b/src/main/resources/parameters/droplet_clone_graph_parameters.json @@ -0,0 +1,15 @@ +{ + "tagCliqueScorePower": 3.0, + "cloneCliqueScorePower": 3.0, + "maxTagCountRatio": 2.0, + "filter": { + "minReadFractionInTag": 0.0, + "maxCloneRankInTag": 3, + "minTagReads": "NaN", + "minTagUMIs": "NaN", + "tagReadsQuantile": 0.9, + "tagReadsQuantileCoefficient": 0.5, + "tagUMIsQuantile": "NaN", + "tagUMIsQuantileCoefficient": "NaN" + } +} diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java new file mode 100644 index 000000000..22c8bb77f --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java @@ -0,0 +1,15 @@ +package com.milaboratory.mixcr.cli; + +import org.junit.Ignore; +import org.junit.Test; + +/** + * + */ +public class CommandGroupCellsTest { + @Test + @Ignore + public void test1() { + Main.main("groupCells", "-f", "--tag", "0", "./tmp/t_analysis.clna", "./tmp/t_analysis_grouped_OU.clna"); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java new file mode 100644 index 000000000..a63035097 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java @@ -0,0 +1,16 @@ +package com.milaboratory.mixcr.tags; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.milaboratory.util.GlobalObjectMappers; +import org.junit.Test; + +/** + * + */ +public class CloneTagTupleFilterTest { + + @Test + public void name() throws JsonProcessingException { + System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(new CloneTagTupleFilter(0, 0, 0, 0, 0, 0, 0.0 / 0.0, 0))); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java new file mode 100644 index 000000000..f1a5e32ce --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java @@ -0,0 +1,52 @@ +package com.milaboratory.mixcr.tags; + +import com.milaboratory.mixcr.basictypes.ClnAReader; +import com.milaboratory.mixcr.basictypes.CloneSet; +import com.milaboratory.mixcr.cli.ReportHelper; +import com.milaboratory.util.ProgressAndStage; +import com.milaboratory.util.SmartProgressReporter; +import io.repseq.core.VDJCLibraryRegistry; +import org.apache.commons.math3.stat.descriptive.rank.Percentile; +import org.junit.Ignore; +import org.junit.Test; + +import java.nio.file.Paths; +import java.util.Collection; +import java.util.List; +import java.util.stream.Collectors; + +/** + * + */ +public class DropletCloneGraphTest { + @Test + @Ignore + public void test1() throws Exception { + try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/b_analysis.clna"), VDJCLibraryRegistry.getDefault())) { + CloneSet clns = reader.readCloneSet(); + System.out.println("# clones " + clns.size()); + DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); + DropletCloneGraphReport report = new DropletCloneGraphReport(); + ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); + SmartProgressReporter.startProgressReport(progressAndStage); + DropletCloneGraph.calculateGroups(links, DropletCloneGraphParameters.getDefault(), report, progressAndStage); + report.writeReport(ReportHelper.STDOUT); + } + } + + @Test + @Ignore + public void test2() throws Exception { + try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/t_analysis.clna"), VDJCLibraryRegistry.getDefault())) { + CloneSet clns = reader.readCloneSet(); + System.out.println("# clones " + clns.size()); + DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); + DropletCloneGraphReport report = new DropletCloneGraphReport(); + ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); + SmartProgressReporter.startProgressReport(progressAndStage); + DropletCloneGraphParameters parameters = DropletCloneGraphParameters.getDefault(); + DropletCloneGraph.calculateGroups(links, parameters, report, progressAndStage); + report.writeReport(ReportHelper.STDOUT); + } + } +} diff --git a/src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java b/src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java new file mode 100644 index 000000000..cf1bbe255 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java @@ -0,0 +1,217 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.util; + +import gnu.trove.set.TIntSet; +import gnu.trove.set.hash.TIntHashSet; +import org.apache.commons.math3.random.Well19937c; +import org.junit.Assert; +import org.junit.Test; + +import java.util.Arrays; +import java.util.HashSet; +import java.util.List; + +/** + * + */ +public class AdjacencyMatrixTest { + @Test + public void test1() throws Exception { + AdjacencyMatrix matrix = new AdjacencyMatrix(6); + matrix.setConnected(0, 4); + matrix.setConnected(0, 1); + matrix.setConnected(1, 4); + matrix.setConnected(1, 2); + matrix.setConnected(2, 3); + matrix.setConnected(3, 4); + matrix.setConnected(3, 5); + List cliques = matrix.calculateMaximalCliques(); + HashSet set = new HashSet<>(cliques); + + Assert.assertEquals(cliques.size(), set.size()); + Assert.assertEquals(5, set.size()); + + Assert.assertTrue(set.contains(createSet(6, 0, 1, 4))); + Assert.assertTrue(set.contains(createSet(6, 1, 2))); + Assert.assertTrue(set.contains(createSet(6, 2, 3))); + Assert.assertTrue(set.contains(createSet(6, 3, 4))); + Assert.assertTrue(set.contains(createSet(6, 3, 5))); + } + + @Test + public void test4() throws Exception { + AdjacencyMatrix matrix = new AdjacencyMatrix(6); + matrix.setConnected(0, 4); + matrix.setConnected(0, 1); + matrix.setConnected(1, 4); + matrix.setConnected(1, 2); + matrix.setConnected(2, 3); + matrix.setConnected(3, 4); + matrix.setConnected(3, 5); + for (int i = 0; i < 6; i++) + matrix.setConnected(i, i); + + List cliques = matrix.calculateMaximalCliques(); + HashSet set = new HashSet<>(cliques); + + Assert.assertEquals(cliques.size(), set.size()); + Assert.assertEquals(5, set.size()); + + Assert.assertTrue(set.contains(createSet(6, 0, 1, 4))); + Assert.assertTrue(set.contains(createSet(6, 1, 2))); + Assert.assertTrue(set.contains(createSet(6, 2, 3))); + Assert.assertTrue(set.contains(createSet(6, 3, 4))); + Assert.assertTrue(set.contains(createSet(6, 3, 5))); + } + + @Test + public void test5() throws Exception { + AdjacencyMatrix matrix = new AdjacencyMatrix(6); + matrix.setConnected(0, 4); + matrix.setConnected(0, 1); + matrix.setConnected(1, 4); + matrix.setConnected(1, 2); + matrix.setConnected(2, 3); + matrix.setConnected(3, 4); + for (int i = 0; i < 6; i++) + matrix.setConnected(i, i); + + List cliques = matrix.calculateMaximalCliques(); + HashSet set = new HashSet<>(cliques); + + Assert.assertEquals(cliques.size(), set.size()); + Assert.assertEquals(5, set.size()); + + Assert.assertTrue(set.contains(createSet(6, 0, 1, 4))); + Assert.assertTrue(set.contains(createSet(6, 1, 2))); + Assert.assertTrue(set.contains(createSet(6, 2, 3))); + Assert.assertTrue(set.contains(createSet(6, 3, 4))); + Assert.assertTrue(set.contains(createSet(6, 5))); + } + + @Test + public void test2() throws Exception { + TestData testData = generateTestData(130, 5, 5, 10, 10); + AdjacencyMatrix matrix = testData.matrix; + for (BitArrayInt bitArrayInt : matrix.calculateMaximalCliques()) { + if (bitArrayInt.bitCount() >= 5) + System.out.println(bitArrayInt); + } +// System.out.println(matrix); + + } + + @Test + public void test3() throws Exception { + for (int i = 0; i < 100; i++) + assertTestData(generateTestData(150, 10, 10, 15, 30), 10); + } + + static void assertTestData(TestData testData, int minCliqueSize) { + HashSet actual = new HashSet<>(); + List cliques = testData.matrix.calculateMaximalCliques(); + for (BitArrayInt clique : cliques) + if (clique.bitCount() >= minCliqueSize) + actual.add(clique); + + HashSet expected = new HashSet<>(Arrays.asList(testData.cliques)); + Assert.assertEquals(expected, actual); + } + + static TestData generateTestData(int size, int nCliques, + int minCliqueSize, int maxCliqueSize, + int noisePoints) { + Well19937c random = new Well19937c(System.currentTimeMillis()); + BitArrayInt[] cliques = new BitArrayInt[nCliques]; + + AdjacencyMatrix matrix = new AdjacencyMatrix(size); + int generated = 0; + final int[] mask = new int[size]; + for (int i = 0; i < nCliques; i++) { + int cSize = minCliqueSize + random.nextInt(maxCliqueSize - minCliqueSize); + TIntSet tClique = new TIntHashSet(); + int maskSet = 0; + while (tClique.size() < cSize) { +// if (generated == size) +// break; + int v = random.nextInt(size); + if (mask[v] != 0) { + ++maskSet; + if (maskSet >= 3) + continue; + } + + mask[v] = 1; + ++generated; + tClique.add(v); + } + + cliques[i] = new BitArrayInt(size); + int[] vs = tClique.toArray(); + for (int j = 0; j < vs.length; j++) + cliques[i].set(vs[j]); + + for (int j = 0; j < vs.length; j++) + for (int k = j + 1; k < vs.length; k++) + matrix.setConnected(vs[j], vs[k]); + } + + //introduce noise + + for (int i = 0; i < noisePoints; i++) { + int a = random.nextInt(size), b = random.nextInt(size); + if (a == b) { + --i; + continue; + } + matrix.setConnected(a, b); + } + + return new TestData(matrix, cliques); + } + + static class TestData { + final AdjacencyMatrix matrix; + final BitArrayInt[] cliques; + + public TestData(AdjacencyMatrix matrix, BitArrayInt[] cliques) { + this.matrix = matrix; + this.cliques = cliques; + } + } + + public static BitArrayInt createSet(int size, int... elements) { + BitArrayInt ret = new BitArrayInt(size); + for (int element : elements) + ret.set(element); + return ret; + } +} \ No newline at end of file From 4049d7f7d48e06f4d963c6f9df6a17987e94e912 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 23 Apr 2020 19:17:35 +0300 Subject: [PATCH 051/282] First version. --- .../assembler/fullseq/FullSeqAssembler.java | 232 ++++++++++++++---- .../mixcr/cli/CommandAssemble.java | 10 +- .../mixcr/cli/CommandGroupCells.java | 2 + .../PartialAlignmentsAssembler.java | 1 + 4 files changed, 199 insertions(+), 46 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index f63af73cc..8bfdadf90 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -38,13 +38,11 @@ import com.milaboratory.core.sequence.*; import com.milaboratory.core.sequence.quality.QualityTrimmer; import com.milaboratory.mixcr.assembler.CloneFactory; -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence; +import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import gnu.trove.impl.Constants; import gnu.trove.iterator.TIntIntIterator; +import gnu.trove.iterator.TIntIterator; import gnu.trove.list.array.TIntArrayList; import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; @@ -114,6 +112,10 @@ public final class FullSeqAssembler { new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); /** integer index -> nucleotide sequence */ final TIntObjectHashMap variantIdToSequence = new TIntObjectHashMap<>(); + /** tag tuple -> its integer group index */ + final TObjectIntHashMap tagTupleToGroup; + /** integer group index -> tag tuple */ + final TIntObjectHashMap groupToTagTuple; /** base hits */ final VDJCHit vHit, jHit; @@ -142,6 +144,14 @@ public FullSeqAssembler(CloneFactory cloneFactory, this.parameters = parameters; this.clone = clone; + if (clone.getTagCounter().isEmpty()) { + this.tagTupleToGroup = null; + this.groupToTagTuple = null; + } else { + this.tagTupleToGroup = new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); + this.groupToTagTuple = new TIntObjectHashMap<>(); + } + this.alignerParameters = alignerParameters; GeneFeature[] assemblingFeatures = clone.getParentCloneSet().getAssemblingFeatures(); if (assemblingFeatures.length != 1) @@ -283,9 +293,13 @@ public Clone[] callVariants(RawVariantsData data) { clusterizeBranches(data.points, branches); - Clone[] result = branches.stream() - .map(branch -> assembleBranchSequences(data.points, branch)) - .filter(Objects::nonNull) + List branchSequences = branches.stream() + .map(branch -> assembleBranchSequences(data.points, data.groups, branch)) + .filter(Objects::nonNull).collect(Collectors.toList()); + + assert checkNonIntersectingGroups(branchSequences); + + Clone[] result = branchSequences.stream() .map(branch -> buildClone(clean(branch))) .toArray(Clone[]::new); @@ -302,6 +316,19 @@ public Clone[] callVariants(RawVariantsData data) { return result; } + private static boolean checkNonIntersectingGroups(List branchSequences) { + TIntHashSet all = new TIntHashSet(); + for (BranchSequences bs : branchSequences) { + if (bs.groups == null) + continue; + int sizeBefore = all.size(); + all.addAll(bs.groups); + if (all.size() != sizeBefore + bs.groups.size()) + return false; + } + return true; + } + private void clusterizeBranches(int[] points, List branches) { branches.sort(Comparator.comparingDouble(c -> c.count)); @@ -413,7 +440,7 @@ BranchSequences clean(BranchSequences seq) { * @param points positions * @param branch variant branch */ - BranchSequences assembleBranchSequences(int[] points, VariantBranch branch) { + BranchSequences assembleBranchSequences(int[] points, int[] groups, VariantBranch branch) { // Co-sorting branch data with position (restoring original nucleotide order) long[] positionedStates = new long[points.length]; for (int i = 0; i < points.length; i++) @@ -497,6 +524,14 @@ BranchSequences assembleBranchSequences(int[] points, VariantBranch branch) { assert blockStartPosition != -1; assert assemblingFeatureTargetId != -1; + TIntHashSet grps = null; + + if (groups != null) { + grps = new TIntHashSet(); + for (int readId = branch.reads.nextSetBit(0); readId >= 0; readId = branch.reads.nextSetBit(readId + 1)) + grps.add(groups[readId]); + } + return new BranchSequences( branch.count, assemblingFeatureTargetId, @@ -504,7 +539,8 @@ BranchSequences assembleBranchSequences(int[] points, VariantBranch branch) { assemblingFeatureLength, ranges.toArray(new Range[ranges.size()]), positionMaps.toArray(new TIntArrayList[positionMaps.size()]), - sequences.toArray(new NSequenceWithQuality[sequences.size()])); + sequences.toArray(new NSequenceWithQuality[sequences.size()]), + grps); } private static int extractPosition(long positionedState) { @@ -554,10 +590,15 @@ private static final class BranchSequences { * Contigs */ final NSequenceWithQuality[] sequences; + /** + * Group ids + */ + final TIntHashSet groups; BranchSequences(double count, int assemblingFeatureTargetId, int assemblingFeatureOffset, int assemblingFeatureLength, - Range[] ranges, TIntArrayList[] positionMaps, NSequenceWithQuality[] sequences) { + Range[] ranges, TIntArrayList[] positionMaps, NSequenceWithQuality[] sequences, + TIntHashSet groups) { this.count = count; this.assemblingFeatureTargetId = assemblingFeatureTargetId; this.assemblingFeatureOffset = assemblingFeatureOffset; @@ -565,6 +606,7 @@ private static final class BranchSequences { this.ranges = ranges; this.positionMaps = positionMaps; this.sequences = sequences; + this.groups = groups; assert check(); } @@ -607,7 +649,8 @@ BranchSequences without(int i) { assemblingFeatureLength, newRanges, newPositionMaps, - newSequences); + newSequences, + groups); } /** @@ -674,7 +717,7 @@ BranchSequences splitCut(int i, Range... rangesToCut) { assert newAssemblingFeatureTargetId != -1; return new BranchSequences(count, newAssemblingFeatureTargetId, newAssemblingFeatureOffset, assemblingFeatureLength, - newRanges, newPositionMaps, newSequences); + newRanges, newPositionMaps, newSequences, groups); } /** @@ -698,13 +741,13 @@ BranchSequences cut(int i, Range rangeToCut) { newSequences[i] = newSequences[i].getRange(rangeToCut); return new BranchSequences(count, assemblingFeatureTargetId, assemblingFeatureOffset - rangeToCut.getLower(), assemblingFeatureLength, - newRanges, newPositionMaps, newSequences); + newRanges, newPositionMaps, newSequences, groups); } else { newRanges[i] = new Range(newPositionMaps[i].get(rangeToCut.getLower()), newPositionMaps[i].get(rangeToCut.getUpper() - 1) + 1); newPositionMaps[i] = (TIntArrayList) newPositionMaps[i].subList(rangeToCut.getLower(), rangeToCut.getUpper()); newSequences[i] = newSequences[i].getRange(rangeToCut); return new BranchSequences(count, assemblingFeatureTargetId, assemblingFeatureOffset, assemblingFeatureLength, - newRanges, newPositionMaps, newSequences); + newRanges, newPositionMaps, newSequences, groups); } } } @@ -893,9 +936,6 @@ else if (floatingRightBound) NSequenceWithQuality assemblingFeatureSeq = targets.sequences[targets.assemblingFeatureTargetId] .getRange(targets.assemblingFeatureOffset, targets.assemblingFeatureOffset + targets.assemblingFeatureLength); - if (this.clone.getCount() != targets.count && !this.clone.getTagCounter().isEmpty()) - throw new IllegalArgumentException("tagged data is not allowed in combination with non-null subCloningRegion"); // assert - Clone clone = cloneFactory.create(0, targets.count, getOriginalGeneScores(), this.clone.getTagCounter(), new NSequenceWithQuality[]{assemblingFeatureSeq}); @@ -932,7 +972,16 @@ else if (floatingRightBound) } else tmp[0] = substituteAlignments(tmp[0], jHitAlignments); - return new Clone(targets.sequences, hits, this.clone.getTagCounter(), targets.count, 0, clone.getGroup()); + TagCounter tagCounter = this.clone.getTagCounter(); + if(tagCounter != null && targets.groups != null) { + Set tagTuples = new HashSet<>(); + TIntIterator it = targets.groups.iterator(); + while (it.hasNext()) + tagTuples.add(groupToTagTuple.get(it.next())); + tagCounter = tagCounter.filter(tagTuples::contains); + } + + return new Clone(targets.sequences, hits, tagCounter, targets.count, 0, clone.getGroup()); } static int indexOfGene(VDJCHit[] hits, VDJCGeneId gene) { @@ -1131,7 +1180,7 @@ static boolean isExceptionalPointVariantInfo(int pointVariantInfo) { * Call variants for a single position */ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targetReads, boolean isAssemblingFeature) { - // Pre-calculating number of present variants + // Pre-calculating number of present variants (covered positions) int count = 0; for (int readId = targetReads.nextSetBit(0); readId >= 0; readId = targetReads.nextSetBit(readId + 1)) if (!isExceptionalPointVariantInfo(pointVariantInfos[readId])) @@ -1175,13 +1224,9 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe int bestVariant = -1; long bestVariantSumQuality = -1; - long maxSplittingPointsCount = 0; - ArrayList variants = new ArrayList<>(); do { if (currentIndex == count || currentVariant != (int) (targets[currentIndex] >>> 40)) { - maxSplittingPointsCount = Math.max(maxSplittingPointsCount, splittingPointsCount); - // Checking significance conditions if ((1.0 * splittingPointsCount / (currentIndex - blockBegin) >= parameters.minimalNonEdgePointsFraction) && variantSumQuality >= requiredMinimalSumQuality @@ -1208,12 +1253,12 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe if (currentIndex != count) { // reset variables for new block blockBegin = currentIndex; - variantSumQuality = 0x7F & (targets[blockBegin] >>> 32); currentVariant = (int) (targets[blockBegin] >>> 40); splittingPointsCount = 0; if (((targets[blockBegin] >>> 32) & 0x80) == 0) // counting first read in this block ++splittingPointsCount; + variantSumQuality = 0x7F & (targets[blockBegin] >>> 32); } } else { if (((targets[currentIndex] >>> 32) & 0x80) == 0) @@ -1234,11 +1279,12 @@ private List callVariantsForPoint(int[] pointVariantInfos, BitSet targe for (long target : targets) reads.set((int) target); reads.or(unassignedVariants); + assert targetReads.equals(reads); double p = 1 - 1.0 * bestVariantSumQuality / totalSumQuality; long phredQuality = p == 0 ? bestVariantSumQuality : Math.min((long) (-10 * Math.log10(p)), bestVariantSumQuality); // nSignificant = 1 (will not be practically used, only one variant, don't care) return Collections.singletonList( - new Variant(bestVariant << 8 | (int) Math.min((long) SequenceQuality.MAX_QUALITY_VALUE, phredQuality), + new Variant(bestVariant << 8 | (int) Math.min(SequenceQuality.MAX_QUALITY_VALUE, phredQuality), reads, 1)); } else // No variants to output (poorly covered or ambiguous position) @@ -1265,7 +1311,7 @@ private static class Variant { /* ======================================== Collect raw initial data ============================================= */ - private int getVariantIndex(NucleotideSequence sequence) { + private int updateVariantIndex(NucleotideSequence sequence) { if (sequence.size() == 0) return EMPTY_SEQUENCE_VARIANT_INDEX; @@ -1314,6 +1360,10 @@ private int initVariantMappings(NucleotideSequence clonalAssemblingFeatureSequen return ASSEMBLING_FEATURE_VARIANT_INDEX; } + boolean taggedAnalysis() { + return groupToTagTuple != null; + } + /** * Aggregates information about position states in all the provided alignments, and returns the object that allows * to iterate from one position to another (sorted by coverage, from most covered to less covered) and see states @@ -1330,13 +1380,15 @@ public RawVariantsData calculateRawData(Supplier> ali ++nAlignments; for (PointSequence point : toPointSequences(al)) { // update sequenceToVariantId - getVariantIndex(point.sequence.getSequence()); + updateVariantIndex(point.sequence.getSequence()); coverage.adjustOrPutValue(point.point, 1, 1); } } assert nAlignments > 0; + int[] groups = taggedAnalysis() ? new int[nAlignments] : null; + // Pre-allocating arrays // Co-sorting positions according to coverage @@ -1349,10 +1401,13 @@ public RawVariantsData calculateRawData(Supplier> ali } Arrays.sort(forSort); + // Virtual position to sequence positions int[] pointsArray = Arrays.stream(forSort).mapToInt(l -> (int) (-l)).toArray(); TIntIntHashMap revIndex = new TIntIntHashMap(); - for (int j = 0; j < pointsArray.length; j++) - revIndex.put(pointsArray[j], j); + for (int j = 0; j < pointsArray.length; j++) { + int v = revIndex.put(pointsArray[j], j); + assert v == 0; + } int[] coverageArray = Arrays.stream(forSort).mapToInt(l -> (int) ((-l) >> 32)).toArray(); @@ -1363,7 +1418,18 @@ public RawVariantsData calculateRawData(Supplier> ali // Main data collection loop i = 0; + int groupCounter = 0; for (VDJCAlignments al : CUtils.it(alignments.get())) { + TagTuple tagTuple = al.getTagCounter().singleOrNull(); + if (taggedAnalysis()) { + int grp = tagTupleToGroup.get(tagTuple); + if (grp == -1) { + grp = groupCounter++; + tagTupleToGroup.put(tagTuple, grp); + groupToTagTuple.put(grp, tagTuple); + } + groups[i] = grp; + } for (PointSequence point : toPointSequences(al)) { int pointIndex = revIndex.get(point.point); packedData[pointIndex][i] = @@ -1374,30 +1440,42 @@ public RawVariantsData calculateRawData(Supplier> ali } // Returning prepared data - return new RawVariantsData(nAlignments, pointsArray, coverageArray) { - @Override - OutputPort createPort() { - return CUtils.asOutputPort(Arrays.asList(packedData)); - } - }; + return new RawVariantsData(nAlignments, groupCounter, + groups, pointsArray, coverageArray, () -> CUtils.asOutputPort(Arrays.asList(packedData))); } /** * Represents aggregated information about nucleotide states for all positions in all reads aggregated with {@link * #calculateRawData(Supplier)}. */ - public abstract class RawVariantsData { + public final class RawVariantsData { /** * Total number of reads */ - final int nReads; - final int[] points; - final int[] coverage; - - RawVariantsData(int nReads, int[] points, int[] coverage) { + final int nReads, nGroups; + final int[] groups, + points, + coverage; + final int[][] groupToRead; + final Supplier> portSupplier; + + RawVariantsData(int nReads, int nGroups, int[] groups, int[] points, int[] coverage, Supplier> portSupplier) { + assert groups == null || groups.length == nReads; this.nReads = nReads; + this.nGroups = nGroups; + this.groups = groups; this.points = points; this.coverage = coverage; + this.portSupplier = portSupplier; + if (groups != null) { + this.groupToRead = new int[nGroups][0]; + for (int i = 0; i < groups.length; i++) { + int[] array = groupToRead[groups[i]]; + groupToRead[groups[i]] = array = Arrays.copyOf(array, array.length + 1); + array[array.length - 1] = i; + } + } else + this.groupToRead = null; } /** @@ -1406,7 +1484,75 @@ public abstract class RawVariantsData { * determined by {@link #points}, e.g. firs array will correspond to point[0] position, the second to point[1] * position etc. Positions are sorted according to their coverage. */ - abstract OutputPort createPort(); + OutputPort createPort() { + final OutputPort port = portSupplier.get(); + if (groups == null) { + return port; + } else { + return () -> { + int[] pointVariantInfos = port.take(); + if (pointVariantInfos == null) + return null; + + TIntIntHashMap sumQualityByVariant = new TIntIntHashMap(); + for (int g = 0; g < nGroups; ++g) { + + sumQualityByVariant.clear(); + int[] readIndices = groupToRead[g]; + int maxQuality = -1; + int bestVariant = -1; + for (int readIndex : readIndices) { + int variantInfo = pointVariantInfos[readIndex]; + if (isExceptionalPointVariantInfo(variantInfo)) + continue; + int quality = 0x7F & variantInfo; + int variant = variantInfo >>> 8; + int sum = sumQualityByVariant.adjustOrPutValue(variant, quality, quality); + if (maxQuality < sum) { + maxQuality = sum; + bestVariant = variant; + } + } + + assert bestVariant != -1; + + int totalSumQuality = 0, bestSumQuality = 0, bestCount = 0, numberOfExceptionalPoints = 0, bestSplittingPoints = 0; + for (int readIndex : readIndices) { + int variantInfo = pointVariantInfos[readIndex]; + if (isExceptionalPointVariantInfo(variantInfo)) { + numberOfExceptionalPoints++; + continue; + } + int quality = 0x7F & variantInfo; + int variant = variantInfo >>> 8; + totalSumQuality += quality; + if (variant == bestVariant) { + bestSumQuality += quality; + bestCount++; + if ((0x80 & variantInfo) == 0) + bestSplittingPoints++; + } + } + bestSumQuality -= totalSumQuality - bestSumQuality; + bestSumQuality = Math.max(0, bestSumQuality); + + double meanQuality = 1.0 * bestSumQuality / readIndices.length; + assert meanQuality <= 127; + int splittingPointCount = readIndices.length * bestSplittingPoints / bestCount; + + for (int i = 0; i < readIndices.length; i++) { + double p = 1.0 * i / readIndices.length; + boolean isSplitting = splittingPointCount > i; + int quality = (int) Math.floor(meanQuality + p); + pointVariantInfos[readIndices[i]] = (bestVariant << 8) + | (isSplitting ? 0x00 : 0x80) + | (0x7F & quality); + } + } + return pointVariantInfos; + }; + } + } /** * To be used with file-based storage media @@ -1776,7 +1922,7 @@ else if (right == -1) if (!inSplitRegion(point) || (seq.size() - seq2alignmentRange.getTo() < parameters.alignedSequenceEdgeDelta && seq.size() - to <= parameters.alignmentEdgeRegionSize) || (seq2alignmentRange.getFrom() < parameters.alignedSequenceEdgeDelta && from <= parameters.alignmentEdgeRegionSize)) - quality |= 0x80; + quality |= 0x80; // isEdgePoint return new PointSequence(point, NSequenceWithQuality.EMPTY, quality); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 3e754c377..be5199548 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -269,6 +269,7 @@ public void run1() throws Exception { TagSignature sig = new TagSignature(tag, clone.getBestHit(gt).getGene().getId()); Integer id = tagsToClones.get(sig); if (id != null) + // Ambiguity (two or more clones with the same tag+gene signature) tagsToClones.put(sig, -1); else tagsToClones.put(sig, clone.getId()); @@ -276,17 +277,20 @@ public void run1() throws Exception { } } + // Remove ambiguous mappings tagsToClones.entrySet().removeIf(e -> e.getValue() < 0); port = () -> { VDJCAlignments al = merged.take(); if (al == null || al.getMappingType() != ReadToCloneMapping.MappingType.Dropped - || al.getFeature(new GeneFeature(assemblerParameters.getAssemblingFeatures())) != null) + || al.getFeature(new GeneFeature(assemblerParameters.getAssemblingFeatures())) != null) // Dropped but has assembling feature return al; + // <-- Only dropped alignments + TagCounter tg = al.getTagCounter(); - assert tg.size() == 1; + assert tg.size() == 1; // Both "align" and "assemblePartial" produces such alignments TObjectDoubleIterator it = tg.iterator(); it.advance(); TagTuple tags = it.key(); @@ -300,7 +304,7 @@ public void run1() throws Exception { Integer cloneId = tagsToClones.get(sig); if (cloneId != null) if (cloneMapping != -1 && cloneMapping != cloneId) - cloneMapping = -2; + cloneMapping = -2; // V+Tag has different mapping than J+Tag else cloneMapping = cloneId; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 379915711..59344e2b0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -266,6 +266,8 @@ private CloneSet doClustering(CloneSet cloneSet, TObjectIntHashMap mergedTargets = searchResult.result; VDJCMultiRead mRead = new VDJCMultiRead(mergedTargets); + // Both parts have the same tag tuple final VDJCAlignments mAlignment = aligner.process(mRead).alignment.setTagCounter(searchResult.tagCounter); // Checking number of overlapped non-template (NRegion) letters From 034108e580b75a2de52895ac0918e84a7daec0b0 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 23 Apr 2020 19:28:31 +0300 Subject: [PATCH 052/282] No coverage case. Fix. --- .../mixcr/assembler/fullseq/FullSeqAssembler.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 8bfdadf90..5a7c4ee53 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -297,7 +297,7 @@ public Clone[] callVariants(RawVariantsData data) { .map(branch -> assembleBranchSequences(data.points, data.groups, branch)) .filter(Objects::nonNull).collect(Collectors.toList()); - assert checkNonIntersectingGroups(branchSequences); + // assert checkNonIntersectingGroups(branchSequences); Clone[] result = branchSequences.stream() .map(branch -> buildClone(clean(branch))) @@ -973,7 +973,7 @@ else if (floatingRightBound) tmp[0] = substituteAlignments(tmp[0], jHitAlignments); TagCounter tagCounter = this.clone.getTagCounter(); - if(tagCounter != null && targets.groups != null) { + if (tagCounter != null && targets.groups != null) { Set tagTuples = new HashSet<>(); TIntIterator it = targets.groups.iterator(); while (it.hasNext()) @@ -1514,7 +1514,8 @@ OutputPort createPort() { } } - assert bestVariant != -1; + if (bestVariant == -1) // all points are exceptional (no coverage by the group) + continue; int totalSumQuality = 0, bestSumQuality = 0, bestCount = 0, numberOfExceptionalPoints = 0, bestSplittingPoints = 0; for (int readIndex : readIndices) { From a841a20955f143d8ced02215711091912a48fc38 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 23 Apr 2020 20:55:33 +0300 Subject: [PATCH 053/282] Fixes etc. --- .../assembler/fullseq/FullSeqAssembler.java | 11 +++++---- .../fullseq/FullSeqAssemblerReport.java | 2 ++ .../milaboratory/mixcr/basictypes/Clone.java | 1 + .../mixcr/cli/CommandAssembleContigs.java | 23 +++++++++++++------ 4 files changed, 26 insertions(+), 11 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 5a7c4ee53..589453747 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -144,7 +144,7 @@ public FullSeqAssembler(CloneFactory cloneFactory, this.parameters = parameters; this.clone = clone; - if (clone.getTagCounter().isEmpty()) { + if (clone.getTagCounter() == null || clone.getTagCounter().isEmpty()) { this.tagTupleToGroup = null; this.groupToTagTuple = null; } else { @@ -458,14 +458,17 @@ BranchSequences assembleBranchSequences(int[] points, int[] groups, VariantBranc int assemblingFeatureOffset = -1; int assemblingFeatureLength = -1; for (int i = 0; i < positionedStates.length; ++i) { - if (isAbsentPositionedState(positionedStates[i])) + int currentPosition = extractPosition(positionedStates[i]); + + if (isAbsentPositionedState(positionedStates[i])) { + if (currentPosition == positionOfAssemblingFeature) + return null; continue; + } if (blockStartPosition == -1) blockStartPosition = extractPosition(positionedStates[i]); - int currentPosition = extractPosition(positionedStates[i]); - int nextPosition = i == positionedStates.length - 1 ? Integer.MAX_VALUE : isAbsentPositionedState(positionedStates[i + 1]) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java index a726a4809..bca70f889 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java @@ -136,6 +136,8 @@ private static int numberOfWildcards(NucleotideSequence seq) { } private static int numberOfWildcards(VDJCObject.CaseSensitiveNucleotideSequence csSeq) { + if(csSeq == null) + return 0; int count = 0; for (int i = 0; i < csSeq.size(); i++) count += numberOfWildcards(csSeq.getSequence(i)); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index 51cfbc325..39fe529f4 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -85,6 +85,7 @@ public CloneSet getParentCloneSet() { } public Clone setTagCounts(TagCounter tc) { + Objects.requireNonNull(tc); Clone c = new Clone(targets, hits, tc, count, id, group); c.setParentCloneSet(getParentCloneSet()); return c; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 6c72e3627..8d804854e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -87,6 +87,10 @@ public void setThreads(int threads) { names = {"-r", "--report"}) public String reportFile; + @Option(description = "Ignore tags", + names = {"--ignore-tags"}) + public boolean ignoreTags; + @Option(description = "Report file.", names = {"--debug-report"}, hidden = true) public String debugReportFile; @@ -137,10 +141,15 @@ public void run1() throws Exception { SmartProgressReporter.startProgressReport("Assembling contigs", cloneAlignmentsPort); OutputPort parallelProcessor = new ParallelProcessor<>(cloneAlignmentsPort, cloneAlignments -> { + Clone clone = cloneAlignments.clone; + + if (ignoreTags) + clone = clone.setTagCounts(TagCounter.EMPTY); + try { // Collecting statistics - EnumMap> coverages = cloneAlignments.clone.getHitsMap() + EnumMap> coverages = clone.getHitsMap() .entrySet().stream() .filter(e -> e.getValue() != null && e.getValue().length > 0) .collect(Collectors.toMap( @@ -170,8 +179,8 @@ public void run1() throws Exception { if (!coverages.containsKey(GeneType.Variable) || !coverages.containsKey(GeneType.Joining)) { // Something went really wrong - report.onAssemblyCanceled(cloneAlignments.clone); - return new Clone[]{cloneAlignments.clone}; + report.onAssemblyCanceled(clone); + return new Clone[]{clone}; } for (VDJCAlignments alignments : CUtils.it(cloneAlignments.alignments())) @@ -195,7 +204,7 @@ public void run1() throws Exception { FullSeqAssembler fullSeqAssembler = new FullSeqAssembler( cloneFactory, assemblerParameters, - cloneAlignments.clone, alignerParameters, + clone, alignerParameters, bestGenes.get(GeneType.Variable), bestGenes.get(GeneType.Joining) ); @@ -205,13 +214,13 @@ public void run1() throws Exception { if (debugReport != null) { synchronized (debugReport) { - try (FileOutputStream fos = new FileOutputStream(debugReportFile + "." + cloneAlignments.clone.getId())) { + try (FileOutputStream fos = new FileOutputStream(debugReportFile + "." + clone.getId())) { final String content = rawVariantsData.toCsv((byte) 10); fos.write(content.getBytes()); } try { - debugReport.write("Clone: " + cloneAlignments.clone.getId()); + debugReport.write("Clone: " + clone.getId()); debugReport.newLine(); debugReport.write(rawVariantsData.toString()); debugReport.newLine(); @@ -227,7 +236,7 @@ public void run1() throws Exception { return fullSeqAssembler.callVariants(rawVariantsData); } catch (Throwable re) { - throw new RuntimeException("While processing clone #" + cloneAlignments.clone.getId(), re); + throw new RuntimeException("While processing clone #" + clone.getId(), re); } }, threads); From b59065c6854ab3831d0da4f5c0d01d079bb9361d Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Fri, 24 Apr 2020 01:03:30 +0300 Subject: [PATCH 054/282] repseqio upgrade. --- pom.xml | 2 +- repseqio | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index e66c070b1..54967d87f 100644 --- a/pom.xml +++ b/pom.xml @@ -46,7 +46,7 @@ io.repseq repseqio - 1.3.4 + 1.3.5-SNAPSHOT com.milaboratory diff --git a/repseqio b/repseqio index e9c25b3cb..5b3d1a2ff 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit e9c25b3cbdf2fa178da7a1d3293d3728202a13f9 +Subproject commit 5b3d1a2ff7158e5735de11b5e8e23badf42bd8a7 From cb2d651af2d52041f18a8ca8aeb11de9f2bf1b77 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 24 Apr 2020 12:59:52 +0300 Subject: [PATCH 055/282] Fix lost group assignment in contig assembly --- .../com/milaboratory/mixcr/assembler/CloneFactory.java | 7 ++++--- .../mixcr/assembler/fullseq/FullSeqAssembler.java | 2 +- .../java/com/milaboratory/mixcr/cli/CommandGroupCells.java | 4 ++-- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index 48a372cb4..7c0191193 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -85,7 +85,8 @@ public CloneFactory(CloneFactoryParameters parameters, GeneFeature[] assemblingF public Clone create(int id, double count, EnumMap> geneScores, TagCounter tagCounter, - NSequenceWithQuality[] targets) { + NSequenceWithQuality[] targets, + Integer group) { EnumMap hits = new EnumMap<>(GeneType.class); for (GeneType geneType : GeneType.VJC_REFERENCE) { VJCClonalAlignerParameters vjcParameters = parameters.getVJCParameters(geneType); @@ -249,11 +250,11 @@ public Clone create(int id, double count, else hits.put(GeneType.Diversity, new VDJCHit[0]); - return new Clone(targets, hits, tagCounter, count, id, null); + return new Clone(targets, hits, tagCounter, count, id, group); } public Clone create(int id, CloneAccumulator accumulator) { - return create(id, accumulator.getCount(), accumulator.geneScores, accumulator.tagBuilder.createAndDestroy(), accumulator.getSequence().sequences); + return create(id, accumulator.getCount(), accumulator.geneScores, accumulator.tagBuilder.createAndDestroy(), accumulator.getSequence().sequences, null); } private static boolean containsD(GeneFeature feature) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 589453747..115817fd1 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -940,7 +940,7 @@ else if (floatingRightBound) .getRange(targets.assemblingFeatureOffset, targets.assemblingFeatureOffset + targets.assemblingFeatureLength); Clone clone = cloneFactory.create(0, targets.count, getOriginalGeneScores(), this.clone.getTagCounter(), - new NSequenceWithQuality[]{assemblingFeatureSeq}); + new NSequenceWithQuality[]{assemblingFeatureSeq}, this.clone.getGroup()); vHitAlignments[targets.assemblingFeatureTargetId] = mergeTwoAlignments( diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 59344e2b0..c0f96d6ee 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -55,9 +55,9 @@ public class CommandGroupCells extends ACommandWithSmartOverwriteWithSingleInput names = {"--tag-mapping"}) public String tagMappingFile; - @Option(description = "Minimal fraction of reads in clone that were not assigned to any group and will be separated into 'unassigned' clone", + @Option(description = "Minimal fraction of reads in clone that were not assigned to any group and will be separated into 'unassigned' clone (default is 0).", names = {"--minimal-ungrouped-fraction"}) - public double minimalUngroupedFraction; + public double minimalUngroupedFraction = 0; @Option(names = {"-O"}, description = "Overrides default aligner parameter values") public Map overrides = new HashMap<>(); From 13f7de7437fb7c39d9351f0cb2ffe689aa3b12d0 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 24 Apr 2020 23:25:37 +0300 Subject: [PATCH 056/282] minor --- src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index be5199548..f17555adc 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -388,7 +388,7 @@ public int hashCode() { use = JsonTypeInfo.Id.CLASS, include = JsonTypeInfo.As.PROPERTY, property = "type") - public static class AssembleConfiguration implements ActionConfiguration { + public static class AssembleConfiguration implements ActionConfiguration { public final CloneAssemblerParameters assemblerParameters; public final boolean clna; From 13aa3e21ae0d314343f361d075875d9924b23381 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 21 May 2020 16:06:38 +0300 Subject: [PATCH 057/282] Gui (#3) * update submodule * minor * fix deps * update milib submodule Co-authored-by: Bolotin Dmitriy --- src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 5247d2274..715a071c4 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -164,7 +164,7 @@ void processClns() throws IOException { void processVDJCA() throws IOException { try (final VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in); final VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { - SmartProgressReporter.startProgressReport("Processing", reader); + SmartProgressReporter.startProgressReport("Extending alignments", reader); writer.header(reader.getParameters(), reader.getUsedGenes(), getFullPipelineConfiguration()); From e464e55d58cc85afbc49b4b3ac490cfde0f82cb5 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 22 May 2020 19:06:26 +0300 Subject: [PATCH 058/282] fix NPE in contig assembly report --- .../assembler/fullseq/FullSeqAssemblerReport.java | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java index a726a4809..24b17fb16 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java @@ -117,11 +117,14 @@ public void afterVariantsClustered(Clone initialClone, Clone[] branches, GeneFea } if (subCloningRegion != null) { - int numberOfNInSplittingRegion = numberOfWildcards(branch.getIncompleteFeature(subCloningRegion)); - if (numberOfNInSplittingRegion > 0) { - clonesWithAmbiguousLettersInSplittingRegion.incrementAndGet(); - readsWithAmbiguousLettersInSplittingRegion.addAndGet(branch.getCount()); - totalAmbiguousLettersInSplittingRegion.addAndGet(numberOfNInSplittingRegion); + VDJCObject.CaseSensitiveNucleotideSequence f = branch.getIncompleteFeature(subCloningRegion); + if (f != null) { + int numberOfNInSplittingRegion = numberOfWildcards(f); + if (numberOfNInSplittingRegion > 0) { + clonesWithAmbiguousLettersInSplittingRegion.incrementAndGet(); + readsWithAmbiguousLettersInSplittingRegion.addAndGet(branch.getCount()); + totalAmbiguousLettersInSplittingRegion.addAndGet(numberOfNInSplittingRegion); + } } } } From 53b87a72dcb823e34c1d104b1ad2164b2cea666c Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 28 May 2020 14:23:35 +0300 Subject: [PATCH 059/282] Primitiv.IO Blocks (#4) * initial commit * wip * wip * VDJCAlignmentsWriter finished. * WIP * Alignment IO done. Clna files on the road. * Stream initialization unification for vdjca / clna / clns files. * wip * wip * WIP * wip * Close to final compilation error resolution. * Compiles, first runtime errors. * First fixes for PIOB based IO. * First working version. Additional testing required. * Fix for VDJCAReader/Writer * milib package update * Micro. * repseqio submodule. * Fixes after merge. --- milib | 2 +- pom.xml | 4 +- repseqio | 2 +- .../mixcr/assembler/AlignmentsProvider.java | 18 +- .../mixcr/assembler/CloneAssembler.java | 14 +- .../mixcr/assembler/CloneAssemblerRunner.java | 10 +- .../mixcr/basictypes/AlignmentsIO.java | 6 +- .../mixcr/basictypes/ClnAReader.java | 359 ++++-------------- .../mixcr/basictypes/ClnAWriter.java | 261 ++++++------- .../mixcr/basictypes/ClnsReader.java | 11 +- .../mixcr/basictypes/ClnsWriter.java | 9 +- .../mixcr/basictypes/CloneSet.java | 19 +- .../mixcr/basictypes/CloneSetIO.java | 2 +- .../milaboratory/mixcr/basictypes/IOUtil.java | 108 ++++-- .../PipelineConfigurationReaderMiXCR.java | 2 +- .../basictypes/VDJCAlignmentsReader.java | 198 ++++------ .../basictypes/VDJCAlignmentsWriter.java | 179 ++++----- .../mixcr/cli/AbstractCommandReport.java | 4 +- .../milaboratory/mixcr/cli/CommandAlign.java | 2 +- .../mixcr/cli/CommandAssemble.java | 2 +- .../mixcr/cli/CommandAssembleContigs.java | 12 +- .../milaboratory/mixcr/cli/CommandExport.java | 3 +- .../cli/CommandExportAlignmentsForClones.java | 3 +- .../cli/CommandExportReadsForClones.java | 3 +- .../milaboratory/mixcr/cli/CommandExtend.java | 4 +- .../mixcr/cli/CommandGroupCells.java | 3 +- .../milaboratory/mixcr/cli/CommandSlice.java | 20 +- .../mixcr/cli/CommandSortAlignments.java | 30 +- .../mixcr/cli/CommandVersionInfo.java | 2 +- .../cli/SerializerCompatibilityUtil.java | 114 +++--- .../milaboratory/mixcr/util/Concurrency.java | 40 ++ .../com/milaboratory/mixcr/util/RunMiXCR.java | 25 +- .../assembler/CloneAssemblerRunnerTest.java | 14 +- .../mixcr/basictypes/ClnAReaderTest.java | 1 - .../milaboratory/mixcr/basictypes/IOTest.java | 19 +- .../PartialAlignmentsAssemblerTest.java | 20 +- .../mixcr/tags/DropletCloneGraphTest.java | 4 +- .../tests/BackwardCompatibilityTests.java | 12 +- .../mixcr/vdjaligners/VDJCAlignerSTest.java | 20 +- 39 files changed, 709 insertions(+), 852 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/util/Concurrency.java diff --git a/milib b/milib index f8fd717dd..01d35f3b2 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit f8fd717dd427180618ba9c65d306f157dbdb907b +Subproject commit 01d35f3b2886c61ae58b9581d5629b45cc6eee15 diff --git a/pom.xml b/pom.xml index c12623771..de23471ec 100644 --- a/pom.xml +++ b/pom.xml @@ -39,14 +39,14 @@ UTF-8 - 1.13 + 1.14-SNAPSHOT io.repseq repseqio - 1.3.4 + 1.3.5-SNAPSHOT com.milaboratory diff --git a/repseqio b/repseqio index e9c25b3cb..5b3d1a2ff 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit e9c25b3cbdf2fa178da7a1d3293d3728202a13f9 +Subproject commit 5b3d1a2ff7158e5735de11b5e8e23badf42bd8a7 diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java index c8729d9b8..ce445e3b7 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java @@ -34,7 +34,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import io.repseq.core.VDJCLibraryRegistry; -import java.io.ByteArrayInputStream; +import java.io.File; import java.io.IOException; public interface AlignmentsProvider { @@ -48,16 +48,20 @@ public interface AlignmentsProvider { long getTotalNumberOfReads(); final class Util { - static AlignmentsProvider createProvider(final byte[] rawData, final VDJCLibraryRegistry geneResolver) { - return new VDJCAlignmentsReaderWrapper(() -> - new VDJCAlignmentsReader(new ByteArrayInputStream(rawData), geneResolver, rawData.length, true) - ); + public static AlignmentsProvider createProvider(File file, final VDJCLibraryRegistry geneResolver) { + return new VDJCAlignmentsReaderWrapper(() -> { + try { + return new VDJCAlignmentsReader(file, geneResolver); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); } - public static AlignmentsProvider createProvider(final String file, final VDJCLibraryRegistry geneResolver) { + public static AlignmentsProvider createProvider(String file, final VDJCLibraryRegistry geneResolver) { return new VDJCAlignmentsReaderWrapper(() -> { try { - return new VDJCAlignmentsReader(file, geneResolver, true); + return new VDJCAlignmentsReader(file, geneResolver); } catch (IOException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index d601bbcb1..dd50255de 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -345,13 +345,13 @@ public void close() { } public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters) { - EnumMap features = new EnumMap<>(GeneType.class); - for (GeneType geneType : GeneType.values()) { - GeneFeature gf = featuresToAlign.get(geneType); - if (gf != null) - features.put(geneType, gf); - } - return new CloneSet(Arrays.asList(realClones), usedGenes.values(), features, alignerParameters, parameters); + // EnumMap features = new EnumMap<>(GeneType.class); + // for (GeneType geneType : GeneType.values()) { + // GeneFeature gf = featuresToAlign.get(geneType); + // if (gf != null) + // features.put(geneType, gf); + // } + return new CloneSet(Arrays.asList(realClones), usedGenes.values(), alignerParameters, parameters); } public OutputPortCloseable getAssembledReadsPort() { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index 1e8b1ff43..7f32f9c62 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -132,11 +132,11 @@ public void run() { isFinished = true; } - public int getQueueSize() { - if (alignmentReader == null) - return -1; - return alignmentReader.getQueueSize(); - } + // public int getQueueSize() { + // if (alignmentReader == null) + // return -1; + // return alignmentReader.getQueueSize(); + // } public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters) { return assembler.getCloneSet(alignerParameters); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java index 210bf84c4..edadc01c2 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java @@ -33,8 +33,8 @@ import com.milaboratory.primitivio.PrimitivIState; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.PrimitivOState; -import com.milaboratory.util.ByteArrayDataOutput; -import com.milaboratory.util.ByteBufferDataInputAdapter; +import com.milaboratory.util.io.ByteArrayDataOutput; +import com.milaboratory.util.io.ByteBufferDataInputAdapter; import net.jpountz.lz4.LZ4Compressor; import net.jpountz.lz4.LZ4FastDecompressor; import net.jpountz.xxhash.XXHash32; @@ -69,8 +69,6 @@ public final class AlignmentsIO { public static final byte LAST_BYTE = 0; // kB public static final int AVERAGE_ALIGNMENT_SIZE = 1024; // kB - public static final int DEFAULT_ALIGNMENTS_IN_BLOCK = 1024; // 1024 alignments * 805-1024 bytes per alignment ~ 824 kB - 1MB per block - private AlignmentsIO() { } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index e0f7be9ac..ee7687c3a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -31,47 +31,32 @@ import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.OutputPortCloseable; -import cc.redberry.pipe.util.CountLimitingOutputPort; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; -import com.milaboratory.mixcr.basictypes.ClnsReader.GT2GFAdapter; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; -import com.milaboratory.primitivio.PipeDataInputReader; import com.milaboratory.primitivio.PrimitivI; -import com.milaboratory.primitivio.PrimitivIState; +import com.milaboratory.primitivio.blocks.*; import com.milaboratory.util.CanReportProgress; import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; -import java.io.DataInput; -import java.io.DataInputStream; import java.io.IOException; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; import java.nio.charset.StandardCharsets; import java.nio.file.Path; import java.nio.file.Paths; -import java.nio.file.StandardOpenOption; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collections; -import java.util.EnumMap; import java.util.List; import java.util.concurrent.atomic.AtomicLong; - -import static com.milaboratory.mixcr.cli.SerializerCompatibilityUtil.add_v3_0_3_CustomSerializers; +import java.util.function.Function; /** * Reader of CLNA file format. */ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implements AutoCloseable { - public static final int DEFAULT_CHUNK_SIZE = 262144; - final int chunkSize; - /** - * Input file channel. All interaction with file are made through this object. - */ - final FileChannel channel; + final PrimitivIHybrid input; // Index data @@ -93,98 +78,80 @@ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implement final VDJCAlignerParameters alignerParameters; final CloneAssemblerParameters assemblerParameters; - final EnumMap alignedFeatures; final List genes; - final PrimitivIState inputState; - final int numberOfClones; - // Meta data + // Meta data (also from header) final String versionInfo; - public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int chunkSize) throws IOException { - if (chunkSize == 0) - throw new IllegalArgumentException(); + public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int concurrency) throws IOException { + this.input = new PrimitivIHybrid(path, concurrency); - this.chunkSize = chunkSize; - this.channel = FileChannel.open(path, StandardOpenOption.READ); this.libraryRegistry = libraryRegistry; - PrimitivI input; - - // Reading magic string - - ByteBuffer buf = ByteBuffer.allocate(ClnAWriter.MAGIC_LENGTH + 4); // ClnAWriter.MAGIC_LENGTH + 4 = 18 - channel.read(buf, 0L); - buf.flip(); - - byte[] magicBytes = new byte[ClnAWriter.MAGIC_LENGTH]; - buf.get(magicBytes); - String magicString = new String(magicBytes, StandardCharsets.US_ASCII); - - // Reading number of clones - - this.numberOfClones = buf.getInt(); - - // Reading key file offsets from last 16 bytes of the file - - buf.flip(); - buf.limit(16); - long fSize = channel.size() - IOUtil.END_MAGIC_LENGTH; - channel.read(buf, fSize - 16); - buf.flip(); - this.firstClonePosition = buf.getLong(); - long indexBegin = buf.getLong(); + // File beginning + String magicString; + try (PrimitivI ii = this.input.beginPrimitivI()) { + // Reading magic string + byte[] magicBytes = new byte[ClnAWriter.MAGIC_LENGTH]; + ii.readFully(magicBytes); + magicString = new String(magicBytes, StandardCharsets.US_ASCII); - // Reading index data - - input = new PrimitivI(new InputDataStream(indexBegin, fSize - 8)); - switch (magicString) { - case ClnAWriter.MAGIC: - break; - default: - throw new IllegalArgumentException("Wrong file type. Magic = " + magicString + - ", expected = " + ClnAWriter.MAGIC); + // Reading number of clones + this.numberOfClones = ii.readInt(); } - this.index = new long[numberOfClones + 2]; - this.counts = new long[numberOfClones + 2]; - long previousValue = 0; - long totalAlignmentsCount = 0L; - for (int i = 0; i < numberOfClones + 2; i++) { - previousValue = index[i] = previousValue + input.readVarLong(); - totalAlignmentsCount += counts[i] = input.readVarLong(); + // File ending + long indexBegin; + try (PrimitivI pi = this.input.beginRandomAccessPrimitivI(-IOUtil.END_MAGIC_LENGTH - 16)) { + // Reading key file offsets from last 16 bytes of the file + this.firstClonePosition = pi.readLong(); + indexBegin = pi.readLong(); + + // Checking file consistency + byte[] endMagic = new byte[IOUtil.END_MAGIC_LENGTH]; + pi.readFully(endMagic); + if (!Arrays.equals(IOUtil.getEndMagicBytes(), endMagic)) + throw new RuntimeException("File is corrupted."); } - this.totalAlignmentsCount = totalAlignmentsCount; - - // Reading gene features - input = new PrimitivI(new InputDataStream(ClnAWriter.MAGIC_LENGTH + 4, - firstClonePosition)); - switch (magicString) { - case ClnAWriter.MAGIC: - break; - default: - throw new IllegalStateException(); + // TODO move index deserialization to lazy initialization, there are use-cases which need only meta-information from the reader + + // Step back + try (PrimitivI pi = this.input.beginRandomAccessPrimitivI(indexBegin)) { + // Reading index data + this.index = new long[numberOfClones + 2]; + this.counts = new long[numberOfClones + 2]; + long previousValue = 0; + long totalAlignmentsCount = 0; + for (int i = 0; i < numberOfClones + 2; i++) { + previousValue = index[i] = previousValue + pi.readVarLong(); + totalAlignmentsCount += counts[i] = pi.readVarLong(); + } + this.totalAlignmentsCount = totalAlignmentsCount; } - this.versionInfo = input.readUTF(); - this.configuration = input.readObject(PipelineConfiguration.class); - this.alignerParameters = input.readObject(VDJCAlignerParameters.class); - this.assemblerParameters = input.readObject(CloneAssemblerParameters.class); - this.alignedFeatures = IO.readGF2GTMap(input); - this.genes = IOUtil.readAndRegisterGeneReferences(input, libraryRegistry, new GT2GFAdapter(alignedFeatures)); - this.inputState = input.getState(); - } + // Returning to the file begin + try (PrimitivI pi = this.input.beginPrimitivI(true)) { + switch (magicString) { + case ClnAWriter.MAGIC: + break; + default: + throw new IllegalStateException(); + } - public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry) throws IOException { - this(path, libraryRegistry, DEFAULT_CHUNK_SIZE); + this.versionInfo = pi.readUTF(); + this.configuration = pi.readObject(PipelineConfiguration.class); + this.alignerParameters = pi.readObject(VDJCAlignerParameters.class); + this.assemblerParameters = pi.readObject(CloneAssemblerParameters.class); + this.genes = IOUtil.stdVDJCPrimitivIStateInit(pi, this.alignerParameters, libraryRegistry); + } } - public ClnAReader(String path, VDJCLibraryRegistry libraryRegistry) throws IOException { - this(Paths.get(path), libraryRegistry, DEFAULT_CHUNK_SIZE); + public ClnAReader(String path, VDJCLibraryRegistry libraryRegistry, int concurrency) throws IOException { + this(Paths.get(path), libraryRegistry, concurrency); } @Override @@ -249,24 +216,23 @@ public String getVersionInfo() { * Read clone set completely */ public CloneSet readCloneSet() throws IOException { - PrimitivI input = inputState.createPrimitivI(new InputDataStream(firstClonePosition, index[0])); - // Reading clones int count = numberOfClones(); List clones = new ArrayList<>(count); - for (int i = 0; i < count; i++) - clones.add(input.readObject(Clone.class)); - return new CloneSet(clones, genes, alignedFeatures, alignerParameters, assemblerParameters); + try (PrimitivIBlocks.Reader reader = input.beginPrimitivIBlocks(Clone.class)) { + for (int i = 0; i < count; i++) + clones.add(reader.take()); + } + + return new CloneSet(clones, genes, alignerParameters, assemblerParameters); } /** * Constructs output port to read clones one by one as a stream */ - public OutputPortCloseable readClones() throws IOException { - PrimitivI input = inputState.createPrimitivI(new InputDataStream(firstClonePosition, index[0])); - - return new PipeDataInputReader<>(Clone.class, input, numberOfClones()); + public OutputPortCloseable readClones() { + return input.beginPrimitivIBlocks(Clone.class); } /** @@ -275,27 +241,21 @@ public OutputPortCloseable readClones() throws IOException { * @param cloneIndex index of clone; -1 to read unassembled alignments */ public OutputPortCloseable readAlignmentsOfClone(int cloneIndex) { - return new CountLimitingOutputPort<>(new BasicVDJCAlignmentReader( - new AlignmentsIO.FileChannelBufferReader(channel, index[cloneIndex + 1], index[cloneIndex + 2]), - inputState, false), counts[cloneIndex + 1]); + return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, index[cloneIndex + 1], HEADER_ACTION_STOP_AT_ALIGNMENT_BLOCK_END); } /** * Constructs output port to read all alignments form the file. Alignments are sorted by cloneIndex. */ public OutputPortCloseable readAllAlignments() { - return new CountLimitingOutputPort<>(new BasicVDJCAlignmentReader( - new AlignmentsIO.FileChannelBufferReader(channel, index[0], index[index.length - 1]), - inputState, false), totalAlignmentsCount); + return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, index[0]); } /** * Constructs output port to read all alignments that are attached to a clone. Alignments are sorted by cloneIndex. */ public OutputPortCloseable readAssembledAlignments() { - return new CountLimitingOutputPort<>(new BasicVDJCAlignmentReader( - new AlignmentsIO.FileChannelBufferReader(channel, index[1], index[index.length - 1]), - inputState, false), totalAlignmentsCount - counts[0]); + return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, index[1]); } /** @@ -320,16 +280,12 @@ public final class CloneAlignmentsPort implements OutputPort, CanReportProgress { private final AtomicLong processedAlignments = new AtomicLong(); private final CloneSet fakeCloneSet; - private final PipeDataInputReader clones; + private final PrimitivIBlocks.Reader clones; volatile boolean isFinished = false; - - CloneAlignmentsPort() throws IOException { - PrimitivI input = inputState.createPrimitivI(new InputDataStream(firstClonePosition, index[0])); - this.clones = new PipeDataInputReader<>(Clone.class, input, numberOfClones); - this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, - genes, alignedFeatures, - alignerParameters, assemblerParameters); + CloneAlignmentsPort() { + this.clones = input.beginRandomAccessPrimitivIBlocks(Clone.class, firstClonePosition); + this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, genes, alignerParameters, assemblerParameters); } @Override @@ -383,170 +339,15 @@ public OutputPort alignments() { @Override public void close() throws IOException { - channel.close(); + input.close(); } - /** - * FileChannel -> DataInput adapter that can be constructed for an arbitrary file position. - * - * Implemented using ByteBuffer. - * - * Thread-unsafe. - */ - private class InputDataStream implements DataInput { - private final long to; - private final ByteBuffer buffer; - private long lastPosition; - - InputDataStream(long from, long to) throws IOException { - this.to = to; - this.buffer = ByteBuffer.allocate(chunkSize); - this.lastPosition = from; - - // Initially buffer is empty - this.buffer.limit(0); - - // Filling first chunk of data - if (from < to) - fillBuffer(); - } - - void fillBuffer() throws IOException { - // Number of bytes to read from file - int size = (int) Math.min(chunkSize - buffer.remaining(), to - lastPosition); - - // Checking state - if (size == 0) - throw new IllegalArgumentException("No more bytes."); - - // Saving remaining bytes - ByteBuffer remaining = buffer.slice(); - - // Reset buffer state - buffer.flip(); - - // Setting new limit - buffer.limit(size + remaining.limit()); - - // Transferring remaining buffer bytes - buffer.put(remaining); - - // Reading content form file - int read = channel.read(buffer, lastPosition); - - // Flipping buffer - buffer.flip(); - - if (read != size) - throw new IOException("Wrong block positions."); - - // Advancing last position - this.lastPosition += read; - } - - void ensureBuffer(int requiredSize) throws IOException { - if (requiredSize > chunkSize) - throw new IllegalArgumentException("Can't read this many bytes."); - if (buffer.remaining() < requiredSize) - fillBuffer(); - } - - @Override - public void readFully(byte[] b) throws IOException { - readFully(b, 0, b.length); - } - - @Override - public void readFully(byte[] b, int off, int len) throws IOException { - do { - int l = Math.min(chunkSize, len); - ensureBuffer(l); - buffer.get(b, off, l); - off += l; - len -= l; - } while (len != 0); - } - - @Override - public int skipBytes(int n) throws IOException { - ensureBuffer(n); - buffer.position(buffer.position() + n); - return n; - } - - @Override - public boolean readBoolean() throws IOException { - byte b = buffer.get(); - if (b == 1) - return true; - else if (b == 0) - return false; - else - throw new IOException("Illegal file format, can't deserialize boolean."); - } - - @Override - public byte readByte() throws IOException { - ensureBuffer(1); - return buffer.get(); - } - - @Override - public int readUnsignedByte() throws IOException { - ensureBuffer(1); - return 0xFF & buffer.get(); - } - - @Override - public short readShort() throws IOException { - ensureBuffer(2); - return (short) buffer.getChar(); - } - - @Override - public int readUnsignedShort() throws IOException { - ensureBuffer(2); - return 0xFFFF & buffer.getChar(); - } - - @Override - public char readChar() throws IOException { - ensureBuffer(2); - return buffer.getChar(); - } + private static Function> HEADER_ACTION_STOP_AT_ALIGNMENT_BLOCK_END = + h -> h.equals(ClnAWriter.ALIGNMENT_BLOCK_SEPARATOR) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); - @Override - public int readInt() throws IOException { - ensureBuffer(4); - return buffer.getInt(); - } + // private static Function> HEADER_ACTION_STOP_AT_ALIGNMENTS_END = + // h -> h.equals(ClnAWriter.ALIGNMENTS_END) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); - @Override - public long readLong() throws IOException { - ensureBuffer(8); - return buffer.getLong(); - } - - @Override - public float readFloat() throws IOException { - ensureBuffer(4); - return buffer.getFloat(); - } - - @Override - public double readDouble() throws IOException { - ensureBuffer(8); - return buffer.getDouble(); - } - - @Override - public String readLine() throws IOException { - throw new UnsupportedOperationException(); - } - - @Override - public String readUTF() throws IOException { - return DataInputStream.readUTF(this); - } - } + // private static Function> HEADER_ACTION_STOP_AT_CLONES_END = + // h -> h.equals(ClnAWriter.CLONES_END) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index 89a51e872..97bbacdbb 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -40,18 +40,24 @@ import com.milaboratory.primitivio.PipeDataInputReader; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; -import com.milaboratory.primitivio.PrimitivOState; +import com.milaboratory.primitivio.blocks.PrimitivIOBlockHeader; +import com.milaboratory.primitivio.blocks.PrimitivOBlocks; +import com.milaboratory.primitivio.blocks.PrimitivOHybrid; import com.milaboratory.util.CanReportProgressAndStage; import com.milaboratory.util.ObjectSerializer; import com.milaboratory.util.Sorter; +import com.milaboratory.util.io.HasPosition; import gnu.trove.list.array.TLongArrayList; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; -import org.apache.commons.io.output.CountingOutputStream; -import java.io.*; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; import java.nio.charset.StandardCharsets; import java.util.*; +import java.util.concurrent.ForkJoinPool; /** * Writer for CLNA file format. @@ -66,6 +72,19 @@ public final class ClnAWriter implements PipelineConfigurationWriter, static final String MAGIC = MAGIC_V5; static final int MAGIC_LENGTH = MAGIC.length(); //14 + /** + * Separates blocks of alignments assigned to the same clonotype + */ + static final PrimitivIOBlockHeader ALIGNMENT_BLOCK_SEPARATOR = PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, (byte) 1); + // /** + // * Added after the last alignments block + // */ + // static final PrimitivIOBlockHeader ALIGNMENTS_END = PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, (byte) 2); + // /** + // * Added after the clones block + // */ + // static final PrimitivIOBlockHeader CLONES_END = PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, (byte) 3); + /** * Will be used for alignments pre-sorting */ @@ -73,8 +92,9 @@ public final class ClnAWriter implements PipelineConfigurationWriter, /** * Used to read current position in output file */ - private final CountingOutputStream outputStream; - private final PrimitivO output; + // private final CountingOutputStream outputStream; + // private final PrimitivO output; + private final PrimitivOHybrid output; private final PipelineConfiguration configuration; /** @@ -93,16 +113,16 @@ public ClnAWriter(PipelineConfiguration configuration, String fileName) throws I public ClnAWriter(PipelineConfiguration configuration, File file) throws IOException { this.configuration = configuration; this.tempFile = new File(file.getAbsolutePath() + ".presorted"); - this.outputStream = new CountingOutputStream(new BufferedOutputStream( - new FileOutputStream(file), 131072)); - this.outputStream.write(MAGIC.getBytes(StandardCharsets.US_ASCII)); - this.output = new PrimitivO(this.outputStream); + this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file.toPath()); + try (PrimitivO o = this.output.beginPrimitivO()) { + o.write(MAGIC.getBytes(StandardCharsets.US_ASCII)); + } } private long positionOfFirstClone = -1; private List usedGenes = null; - private HasFeatureToAlign featureToAlign = null; + private HasFeatureToAlign featureToAlignProvider = null; /** * Step 1 @@ -115,51 +135,55 @@ public synchronized void writeClones(CloneSet cloneSet) { // Saving VDJC gene list this.usedGenes = cloneSet.getUsedGenes(); - // Saving features to align - this.featureToAlign = new ClnsReader.GT2GFAdapter(cloneSet.alignedFeatures); - - // Writing number of clones ahead of any other content to make it available - // in known file position (MAGIC_LENGTH) - output.writeInt(cloneSet.size()); - - // Writing version information - output.writeUTF(MiXCRVersionInfo.get() - .getVersionString(AppVersionInfo.OutputType.ToFile)); - - // Writing full pipeline configuration - output.writeObject(configuration); + // Writing header in raw primitivio mode + try (PrimitivO o = this.output.beginPrimitivO(true)) { - // Writing aligner parameters - output.writeObject(cloneSet.alignmentParameters); + // Writing number of clones ahead of any other content to make it available + // in a known file position (MAGIC_LENGTH) + o.writeInt(cloneSet.size()); - // Writing assembler parameters - output.writeObject(cloneSet.assemblerParameters); + // Writing version information + o.writeUTF(MiXCRVersionInfo.get() + .getVersionString(AppVersionInfo.OutputType.ToFile)); - // Writing aligned gene features for each gene type - IO.writeGT2GFMap(output, cloneSet.alignedFeatures); + // Writing full pipeline configuration + o.writeObject(configuration); - // These GeneFeature objects and corresponding nucleotide sequences from all - // genes in analysis will be added to the set of known references of PrimitivO object - // so that they will be serialized as 1-2 byte reference records (see PrimitivIO implementation) + // Writing aligner parameters + Objects.requireNonNull(cloneSet.alignmentParameters); + o.writeObject(cloneSet.alignmentParameters); + featureToAlignProvider = cloneSet.alignmentParameters; - // During deserialization, the same procedure (in the same order) will be applied to - // the PrimitivI object, so that correct singleton objects (GeneFeature objects and sequences) will be - // deserialized from reference records - IOUtil.writeAndRegisterGeneReferences(output, usedGenes, featureToAlign); + // Writing assembler parameters + o.writeObject(cloneSet.assemblerParameters); - // Saving stream position of the first clone object - // this value will be written to the end of the file - positionOfFirstClone = outputStream.getByteCount(); + // During deserialization, the same procedure (in the same order) will be applied to + // the PrimitivI object, so that correct singleton objects (GeneFeature objects and sequences) will be + // deserialized from reference records. + // The GeneFeature objects and corresponding nucleotide sequences from all + // genes in analysis will be added to the set of known references of PrimitivO object + // so that they will be serialized as 1-2 byte reference records (see PrimitivIO implementation). + IOUtil.stdVDJCPrimitivOStateInit(o, usedGenes, cloneSet); - // Saving number of clones - numberOfClones = cloneSet.size(); + // Saving stream position of the first clone object + // this value will be written at the very end of the file + positionOfFirstClone = output.getPosition(); - // Writing clones - for (Clone clone : cloneSet) { - output.writeObject(clone); - ++numberOfClonesWritten; + // Saving number of clones + numberOfClones = cloneSet.size(); } + try (PrimitivOBlocks.Writer writer = this.output.beginPrimitivOBlocks(4, 1024)) { + // Writing clones + for (Clone clone : cloneSet) { + writer.write(clone); + // For progress reporting + ++numberOfClonesWritten; + } + writer.flush(); + // writer.writeHeader(CLONES_END); + } // will synchronize here (on close method invocation) + // Setting flag telling other methods that clones block was written successfully clonesBlockFinished = true; } @@ -178,7 +202,7 @@ public synchronized void sortAlignments(OutputPort alignments, // Saving number of alignments this.numberOfAlignments = numberOfAlignments; - // Dirty heuristic to optimize trade-off between memory usage and number of random access places in file + // Dirty heuristic to optimize trade-off between memory usage and number of random access places in a file // to read from int chunkSize = (int) Math.min(Math.max(16384, numberOfAlignments / 8), 1048576); @@ -189,7 +213,7 @@ public synchronized void sortAlignments(OutputPort alignments, toSorter, Comparator.comparingInt((VDJCAlignments o) -> o.cloneIndex).thenComparingInt(o -> o.mappingType), chunkSize, - new VDJCAlignmentsSerializer(usedGenes, featureToAlign), + new VDJCAlignmentsSerializer(usedGenes, featureToAlignProvider), tempFile); } @@ -198,6 +222,8 @@ public static final class VDJCAlignmentsSerializer implements ObjectSerializer genes, HasFeatureToAlign featureToAlign) { + Objects.requireNonNull(genes); + Objects.requireNonNull(featureToAlign); this.genes = genes; this.featureToAlign = featureToAlign; } @@ -206,7 +232,7 @@ public VDJCAlignmentsSerializer(List genes, HasFeatureToAlign featureT public void write(Collection data, OutputStream stream) { PrimitivO primitivO = new PrimitivO(stream); // Initializing PrimitivO object (see big comment block in writeClones(...) method - IOUtil.registerGeneReferences(primitivO, genes, featureToAlign); + IOUtil.registerGeneReferencesO(primitivO, genes, featureToAlign); for (VDJCAlignments alignments : data) { // Checking that alignments has the same alignedFeature as was in cloneSet assert Arrays.stream(GeneType.values()) @@ -225,7 +251,7 @@ public void write(Collection data, OutputStream stream) { @Override public OutputPort read(InputStream stream) { PrimitivI primitivI = new PrimitivI(stream); - IOUtil.registerGeneReferences(primitivI, genes, featureToAlign); + IOUtil.registerGeneReferencesI(primitivI, genes, featureToAlign); // Will end on null object, that was added to the stream return new PipeDataInputReader<>(VDJCAlignments.class, primitivI); } @@ -242,121 +268,100 @@ public synchronized void writeAlignmentsAndIndex() { throw new IllegalStateException("Writer already closed."); // Indices that will be written below all alignments - TLongArrayList aBlockOffset = new TLongArrayList(); - TLongArrayList aBlockCount = new TLongArrayList(); - - // Position of alignments with cloneIndex = -1 (not aligned alignments) - aBlockOffset.add(outputStream.getByteCount()); - - PrimitivOState outputState = output.getState(); - + final TLongArrayList aBlockOffset = new TLongArrayList(); + final TLongArrayList aBlockCount = new TLongArrayList(); long previousAlsCount = 0; int currentCloneIndex = -1; + long indexBeginOffset; - // Writer - try ( // TODO parametrise - BasicVDJCAlignmentWriterFactory writerFactory = new BasicVDJCAlignmentWriterFactory( - Math.min(4, Runtime.getRuntime().availableProcessors()), - true); - // Writer - BasicVDJCAlignmentWriterFactory.Writer writer = - writerFactory.createWriter(outputState, outputStream, false)) { - - // StatusReporter reporter = new StatusReporter(); - // reporter.addCustomProvider(new StatusReporter.StatusProvider() { - // volatile String status; - // volatile boolean isClosed = false; - // - // @Override - // public void updateStatus() { - // status = "Busy encoders: " + writerFactory.getBusyEncoders() + " / " + writerFactory.getEncodersCount(); - // isClosed = writerFactory.isClosed(); - // } - // - // @Override - // public boolean isFinished() { - // return isClosed; - // } - // - // @Override - // public String getStatus() { - // return status; - // } - // }); - // reporter.start(); - - List block = new ArrayList<>(); - // Writing alignments and writing indices - for (VDJCAlignments alignments : CUtils.it(sortedAlignments)) { + try (PrimitivOBlocks.Writer o = output.beginPrimitivOBlocks( + Math.min(4, Runtime.getRuntime().availableProcessors()), // TODO parametrize + VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK)) { - // Block is full - if (block.size() == AlignmentsIO.DEFAULT_ALIGNMENTS_IN_BLOCK) { - writer.writeAsync(block); - block = new ArrayList<>(); - } + // Position of alignments with cloneIndex = -1 (not aligned alignments) + aBlockOffset.add(o.getPosition()); + // List block = new ArrayList<>(); + // Writing alignments and writing indices + for (VDJCAlignments alignments : CUtils.it(sortedAlignments)) { // End of clone if (currentCloneIndex != alignments.cloneIndex) { - if (!block.isEmpty()) { - // This will also wait for the previous block (if async write was issued) to be flushed to the stream - writer.writeSync(block); - block = new ArrayList<>(); - } else - writer.waitPreviousBlock(); + // Async flush + o.flush(); + o.writeHeader(ALIGNMENT_BLOCK_SEPARATOR); + + // No synchronization here ++currentCloneIndex; if (currentCloneIndex != alignments.cloneIndex) throw new IllegalArgumentException("No alignments for clone number " + currentCloneIndex); if (alignments.cloneIndex >= numberOfClones) throw new IllegalArgumentException("Out of range clone Index in alignment: " + currentCloneIndex); - aBlockOffset.add(outputStream.getByteCount()); + + // Write stream position as soon as all the blocks are flushed + // This will be the start position for the next block + o.run(c -> { + // In theory synchronization for aBlockOffset access here is not required as all the IO + // operations as well as this code are executed strictly sequentially + + //synchronized (aBlockOffset){ + aBlockOffset.add(((HasPosition) c).getPosition()); + //} + }); + aBlockCount.add(numberOfAlignmentsWritten - previousAlsCount); previousAlsCount = numberOfAlignmentsWritten; } - block.add(alignments); + o.write(alignments); ++numberOfAlignmentsWritten; } // Writing last block, and waiting for all the data to be flushed - if (!block.isEmpty()) - writer.writeSync(block); - else - writer.waitPreviousBlock(); + o.flush(); + o.writeHeader(ALIGNMENT_BLOCK_SEPARATOR); + // o.writeHeader(ALIGNMENTS_END); + o.sync(); + + // Writing position of last alignments block end + aBlockOffset.add(o.getPosition()); + // o.close() will additionally write EOF header + indexBeginOffset = o.getPosition() + PrimitivIOBlockHeader.HEADER_SIZE; } + // Closing sorted output port, this will delete presorted file sortedAlignments.close(); + // Writing count of alignments in the last block aBlockCount.add(numberOfAlignmentsWritten - previousAlsCount); - // Writing position of last alignments block end - aBlockOffset.add(outputStream.getByteCount()); // To make counts index the same length as aBlockOffset aBlockCount.add(0); // Saving index offset in file to write in the end of the stream - long indexBeginOffset = outputStream.getByteCount(); long previousValue = 0; - // Writing both indices - for (int i = 0; i < aBlockOffset.size(); i++) { - long iValue = aBlockOffset.get(i); - // Writing offset index using deltas to save space - // (smaller values are represented by less number of bytes in VarLong representation) - output.writeVarLong(iValue - previousValue); - previousValue = iValue; + try (PrimitivO o = output.beginPrimitivO()) { + // Writing both indices + for (int i = 0; i < aBlockOffset.size(); i++) { + long iValue = aBlockOffset.get(i); + // Writing offset index using deltas to save space + // (smaller values are represented by less number of bytes in VarLong representation) + o.writeVarLong(iValue - previousValue); + previousValue = iValue; - output.writeVarLong(aBlockCount.get(i)); - } + o.writeVarLong(aBlockCount.get(i)); + } - // Writing two key positions in a file - // This values will be using during deserialization to find certain blocks - output.writeLong(positionOfFirstClone); - output.writeLong(indexBeginOffset); + // Writing two key positions in a file + // This values will be using during deserialization to find certain blocks + o.writeLong(positionOfFirstClone); + o.writeLong(indexBeginOffset); - // Writing end-magic as a file integrity sign - output.write(IOUtil.getEndMagicBytes()); + // Writing end-magic as a file integrity sign + o.write(IOUtil.getEndMagicBytes()); + } // Setting finished flag (will stop progress reporting) finished = true; @@ -400,7 +405,7 @@ public boolean isFinished() { } @Override - public void close() { + public void close() throws IOException { finished = true; output.close(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index ac27f7e33..fff4ba9d1 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -43,7 +43,6 @@ import java.util.List; import static com.milaboratory.mixcr.basictypes.ClnsWriter.*; -import static com.milaboratory.mixcr.cli.SerializerCompatibilityUtil.add_v3_0_3_CustomSerializers; /** * @@ -80,7 +79,7 @@ private synchronized void init() { return; // Registering custom serializer - input.getSerializersManager().registerCustomSerializer(GeneFeature.class, new GeneFeatureSerializer(true)); + //input.getSerializersManager().registerCustomSerializer(GeneFeature.class, new GeneFeatureSerializer(true)); byte[] magicBytes = new byte[MAGIC_LENGTH]; input.readFully(magicBytes); @@ -103,15 +102,17 @@ private synchronized void init() { alignerParameters = input.readObject(VDJCAlignerParameters.class); assemblerParameters = input.readObject(CloneAssemblerParameters.class); - EnumMap alignedFeatures = IO.readGF2GTMap(input); - List genes = IOUtil.readAndRegisterGeneReferences(input, libraryRegistry, new GT2GFAdapter(alignedFeatures)); + // EnumMap alignedFeatures = IO.readGF2GTMap(input); + // List genes = IOUtil.readAndRegisterGeneReferences(input, libraryRegistry, new GT2GFAdapter(alignedFeatures)); + + List genes = IOUtil.stdVDJCPrimitivIStateInit(input, alignerParameters, libraryRegistry); int count = input.readInt(); List clones = new ArrayList<>(count); for (int i = 0; i < count; i++) clones.add(input.readObject(Clone.class)); - this.cloneSet = new CloneSet(clones, genes, alignedFeatures, alignerParameters, assemblerParameters); + this.cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters); cloneSet.versionInfo = versionInfo; initialized = true; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index f90cd2c4d..5ded7141e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -47,6 +47,7 @@ /** * */ +// TODO implement with blocks public class ClnsWriter implements PipelineConfigurationWriter, CanReportProgressAndStage, Closeable { @@ -94,9 +95,6 @@ public boolean isFinished() { } public void write() { - // Registering custom serializer - output.getSerializersManager().registerCustomSerializer(GeneFeature.class, new GeneFeatureSerializer(true)); - // Writing magic bytes output.write(MAGIC_BYTES); @@ -110,8 +108,9 @@ public void write() { output.writeObject(cloneSet.alignmentParameters); output.writeObject(cloneSet.assemblerParameters); - IO.writeGT2GFMap(output, cloneSet.alignedFeatures); - IOUtil.writeAndRegisterGeneReferences(output, cloneSet.getUsedGenes(), new ClnsReader.GT2GFAdapter(cloneSet.alignedFeatures)); + // IO.writeGT2GFMap(output, cloneSet.alignedFeatures); + // IOUtil.writeAndRegisterGeneReferences(output, cloneSet.getUsedGenes(), new ClnsReader.GT2GFAdapter(cloneSet.alignedFeatures)); + IOUtil.stdVDJCPrimitivOStateInit(output, cloneSet.getUsedGenes(), cloneSet); output.writeInt(cloneSet.getClones().size()); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index 89e376ac0..c6547d68a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -42,17 +42,17 @@ /** * Created by poslavsky on 10/07/14. */ -public final class CloneSet implements Iterable { +public final class CloneSet implements Iterable, HasFeatureToAlign { String versionInfo; final CloneAssemblerParameters assemblerParameters; final VDJCAlignerParameters alignmentParameters; - final EnumMap alignedFeatures; + // final EnumMap alignedFeatures; final List usedGenes; final List clones; final double totalCount; final TagCounter totalTagCounts; - public CloneSet(List clones, Collection usedGenes, EnumMap alignedFeatures, + public CloneSet(List clones, Collection usedGenes, VDJCAlignerParameters alignmentParameters, CloneAssemblerParameters assemblerParameters) { this.clones = Collections.unmodifiableList(new ArrayList<>(clones)); long totalCount = 0; @@ -63,7 +63,6 @@ public CloneSet(List clones, Collection usedGenes, EnumMap(usedGenes)); @@ -91,7 +90,6 @@ public CloneSet(List clones) { } } this.totalTagCounts = tagCounterBuilder.createAndDestroy(); - this.alignedFeatures = alignedFeatures; this.assemblerParameters = null; this.alignmentParameters = null; this.usedGenes = Collections.unmodifiableList(new ArrayList<>(genes.values())); @@ -126,12 +124,9 @@ public List getUsedGenes() { return usedGenes; } - public EnumMap getAlignedFeatures() { - return new EnumMap<>(alignedFeatures); - } - - public GeneFeature getAlignedGeneFeature(GeneType geneType) { - return alignedFeatures.get(geneType); + @Override + public GeneFeature getFeatureToAlign(GeneType geneType) { + return alignmentParameters.getFeatureToAlign(geneType); } public double getTotalCount() { @@ -163,6 +158,6 @@ public static CloneSet transform(CloneSet in, Filter filter) { newClones.add(c); } } - return new CloneSet(newClones, in.usedGenes, in.alignedFeatures, in.alignmentParameters, in.assemblerParameters); + return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java index 62af31c17..5d67871f6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java @@ -54,7 +54,7 @@ public static CloneSet read(String file, VDJCLibraryRegistry libraryRegistry) th public static CloneSet read(File file, VDJCLibraryRegistry libraryRegistry) throws IOException { switch (Objects.requireNonNull(fileInfoExtractorInstance.getFileInfo(file)).fileType) { case MAGIC_CLNA: - try (ClnAReader r = new ClnAReader(file.toPath(), libraryRegistry)) { + try (ClnAReader r = new ClnAReader(file.toPath(), libraryRegistry, 1)) { return r.readCloneSet(); } case MAGIC_CLNS: diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java index 211f6d4c2..090dfdba0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java @@ -35,10 +35,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; -import io.repseq.core.GeneFeature; -import io.repseq.core.VDJCGene; -import io.repseq.core.VDJCGeneId; -import io.repseq.core.VDJCLibraryRegistry; +import io.repseq.core.*; import java.io.*; import java.nio.ByteBuffer; @@ -50,6 +47,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import java.util.Objects; public class IOUtil { public static final int BEGIN_MAGIC_LENGTH = 14; @@ -67,6 +65,27 @@ public static byte[] getEndMagicBytes() { return END_MAGIC_BYTES.clone(); } + /** + * Writes minimal required header information to PrimitivO state and executes minimal required state initialization + * procedure for compact serialization of {@link VDJCAlignments} objects (so that all the sequences and genes + * will be serialized as references). + * + * Use {@link IOUtil#stdVDJCPrimitivIStateInit(PrimitivI, HasFeatureToAlign, VDJCLibraryRegistry)} as + * this method counterpart. + */ + public static void stdVDJCPrimitivOStateInit(PrimitivO o, List genes, + HasFeatureToAlign featuresToAlign) { + // Registering links to features to align + for (GeneType gt : GeneType.VDJC_REFERENCE) { + GeneFeature feature = featuresToAlign.getFeatureToAlign(gt); + o.writeObject(feature); + if (feature != null) + o.putKnownObject(feature); + } + + writeAndRegisterGeneReferences(o, genes, featuresToAlign); + } + public static void writeAndRegisterGeneReferences(PrimitivO output, List genes, HasFeatureToAlign featuresToAlign) { // Writing gene ids @@ -74,30 +93,54 @@ public static void writeAndRegisterGeneReferences(PrimitivO output, List genes, - HasFeatureToAlign featuresToAlign) { + public static void registerGeneReferencesO(PrimitivO output, List genes, + HasFeatureToAlign featuresToAlign) { // Putting genes references and feature sequences to be serialized/deserialized as references for (VDJCGene gene : genes) { // Each gene is singleton output.putKnownReference(gene); // Also put sequences of certain gene features of genes as known references if required - if (featuresToAlign != null) { - GeneFeature featureToAlign = featuresToAlign.getFeatureToAlign(gene.getGeneType()); - if (featureToAlign == null) - continue; - NucleotideSequence featureSequence = gene.getFeature(featureToAlign); - if (featureSequence == null) - continue; - // Relies on the fact that sequences of gene features are cached, - // the same instance will be used everywhere (including alignments) - output.putKnownReference(gene.getFeature(featuresToAlign.getFeatureToAlign(gene.getGeneType()))); - } + GeneFeature featureToAlign = featuresToAlign.getFeatureToAlign(gene.getGeneType()); + if (featureToAlign == null) + continue; + NucleotideSequence featureSequence = gene.getFeature(featureToAlign); + if (featureSequence == null) + continue; + // Relies on the fact that sequences of gene features are cached, + // the same instance will be used everywhere (including alignments) + output.putKnownReference(gene.getFeature(featuresToAlign.getFeatureToAlign(gene.getGeneType()))); } } + /** + * See {@link IOUtil#stdVDJCPrimitivOStateInit(PrimitivO, List, HasFeatureToAlign)}. + */ + public static List stdVDJCPrimitivIStateInit(PrimitivI i, HasFeatureToAlign featuresToAlign, + VDJCLibraryRegistry registry) { + // Registering links to features to align + for (GeneType gt : GeneType.VDJC_REFERENCE) { + GeneFeature featureParams = featuresToAlign.getFeatureToAlign(gt); + GeneFeature featureDeserialized = i.readObject(GeneFeature.class); + if (!Objects.equals(featureDeserialized, featureParams)) + throw new RuntimeException("Wrong format."); + + if (featureParams != null) + i.putKnownObject(featureParams); + } + + return readAndRegisterGeneReferences(i, registry, featuresToAlign); + } + + public static List readAndRegisterGeneReferences(PrimitivI input, VDJCLibraryRegistry registry, + HasFeatureToAlign featuresToAlign) { + List genes = readGeneReferences(input, registry); + registerGeneReferencesI(input, genes, featuresToAlign); + return genes; + } + public static List readGeneReferences(PrimitivI input, VDJCLibraryRegistry registry) { // Reading gene ids int count = input.readInt(); @@ -113,28 +156,19 @@ public static List readGeneReferences(PrimitivI input, VDJCLibraryRegi return genes; } - public static List readAndRegisterGeneReferences(PrimitivI input, VDJCLibraryRegistry registry, - HasFeatureToAlign featuresToAlign) { - List genes = readGeneReferences(input, registry); - registerGeneReferences(input, genes, featuresToAlign); - return genes; - } - - public static void registerGeneReferences(PrimitivI input, List genes, - HasFeatureToAlign featuresToAlign) { + public static void registerGeneReferencesI(PrimitivI input, List genes, + HasFeatureToAlign featuresToAlign) { // Putting genes references and feature sequences to be serialized/deserialized as references for (VDJCGene gene : genes) { input.putKnownReference(gene); // Also put sequences of certain gene features of genes as known references if required - if (featuresToAlign != null) { - GeneFeature featureToAlign = featuresToAlign.getFeatureToAlign(gene.getGeneType()); - if (featureToAlign == null) - continue; - NucleotideSequence featureSequence = gene.getFeature(featureToAlign); - if (featureSequence == null) - continue; - input.putKnownReference(featureSequence); - } + GeneFeature featureToAlign = featuresToAlign.getFeatureToAlign(gene.getGeneType()); + if (featureToAlign == null) + continue; + NucleotideSequence featureSequence = gene.getFeature(featureToAlign); + if (featureSequence == null) + continue; + input.putKnownReference(featureSequence); } } @@ -189,7 +223,7 @@ public BinaryFileInfo getFileInfo(File file) { if (!magicShort.equals(MAGIC_VDJC) && !magicShort.equals(MAGIC_CLNS) && !magicShort.equals(MAGIC_CLNA)) - return null; + return null; byte[] endMagic = new byte[END_MAGIC_LENGTH]; channel.read(ByteBuffer.wrap(endMagic), channel.size() - END_MAGIC_LENGTH); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java index d58e03686..0b268067c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java @@ -96,7 +96,7 @@ public static PipelineConfiguration sFromFile(String fileName, BinaryFileInfo fi return reader.getPipelineConfiguration(); } case MAGIC_CLNA: - try (ClnAReader reader = new ClnAReader(fileName, VDJCLibraryRegistry.getDefault())) { + try (ClnAReader reader = new ClnAReader(fileName, VDJCLibraryRegistry.getDefault(), 1)) { return reader.getPipelineConfiguration(); } default: diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index d900c7015..4c584d7a0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -33,52 +33,56 @@ import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.blocks.PrimitivIBlocks; +import com.milaboratory.primitivio.blocks.PrimitivIBlocksStats; +import com.milaboratory.primitivio.blocks.PrimitivIHybrid; import com.milaboratory.util.CanReportProgress; -import com.milaboratory.util.CountingInputStream; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; -import java.io.*; -import java.util.HashMap; +import java.io.File; +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.Arrays; import java.util.List; -import java.util.Map; -import java.util.Objects; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.ForkJoinPool; import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.*; -import static com.milaboratory.mixcr.cli.SerializerCompatibilityUtil.add_v3_0_3_CustomSerializers; public final class VDJCAlignmentsReader extends PipelineConfigurationReaderMiXCR implements OutputPortCloseable, CanReportProgress { - private static final int DEFAULT_BUFFER_SIZE = 1048576; // 1 MB + public static final int DEFAULT_CONCURRENCY = 4; + public static final int DEFAULT_READ_AHEAD_BLOCKS = 5; + + final PrimitivIHybrid input; + final int readAheadBlocks; + final VDJCLibraryRegistry vdjcRegistry; + + PrimitivIBlocks.Reader reader; VDJCAlignerParameters parameters; PipelineConfiguration pipelineConfiguration; List usedGenes; - final InputStream inputStream; - final CountingInputStream countingInputStream; - final VDJCLibraryRegistry vdjcRegistry; + String versionInfo; String magic; long counter = 0; - long numberOfReads = -1; + final long numberOfAlignments, numberOfReads; boolean closed = false; - final long size; - final boolean useSeparateDecoderThread; - volatile BasicVDJCAlignmentReader reader = null; public VDJCAlignmentsReader(String fileName) throws IOException { - this(new File(fileName), VDJCLibraryRegistry.getDefault()); + this(fileName, VDJCLibraryRegistry.getDefault()); } public VDJCAlignmentsReader(String fileName, VDJCLibraryRegistry vdjcRegistry) throws IOException { - this(new File(fileName), vdjcRegistry); + this(fileName, vdjcRegistry, DEFAULT_CONCURRENCY); } - public VDJCAlignmentsReader(String fileName, VDJCLibraryRegistry vdjcRegistry, boolean useSeparateDecoderThread) throws IOException { - this(new File(fileName), vdjcRegistry, useSeparateDecoderThread); + public VDJCAlignmentsReader(String fileName, VDJCLibraryRegistry vdjcRegistry, int concurrency) throws IOException { + this(Paths.get(fileName), vdjcRegistry, concurrency); } public VDJCAlignmentsReader(File file) throws IOException { @@ -86,97 +90,81 @@ public VDJCAlignmentsReader(File file) throws IOException { } public VDJCAlignmentsReader(File file, VDJCLibraryRegistry vdjcRegistry) throws IOException { - this(new BufferedInputStream(new FileInputStream(file), DEFAULT_BUFFER_SIZE), - vdjcRegistry, file.length(), false); + this(file, vdjcRegistry, DEFAULT_CONCURRENCY); } - public VDJCAlignmentsReader(File file, VDJCLibraryRegistry vdjcRegistry, boolean useSeparateDecoderThread) throws IOException { - this(new BufferedInputStream(new FileInputStream(file), DEFAULT_BUFFER_SIZE), - vdjcRegistry, file.length(), useSeparateDecoderThread); + public VDJCAlignmentsReader(File file, VDJCLibraryRegistry vdjcRegistry, int concurrency) throws IOException { + this(file.toPath(), vdjcRegistry, concurrency); } - public VDJCAlignmentsReader(InputStream inputStream) { - this(inputStream, VDJCLibraryRegistry.getDefault(), 0, false); + public VDJCAlignmentsReader(Path path) throws IOException { + this(path, VDJCLibraryRegistry.getDefault()); } - public VDJCAlignmentsReader(InputStream inputStream, boolean useSeparateDecoderThread) { - this(inputStream, VDJCLibraryRegistry.getDefault(), 0, useSeparateDecoderThread); + public VDJCAlignmentsReader(Path path, VDJCLibraryRegistry vdjcRegistry) throws IOException { + this(path, vdjcRegistry, DEFAULT_CONCURRENCY); } - public VDJCAlignmentsReader(InputStream inputStream, VDJCLibraryRegistry vdjcRegistry) { - this(inputStream, vdjcRegistry, 0, false); + public VDJCAlignmentsReader(Path path, VDJCLibraryRegistry vdjcRegistry, int concurrency) throws IOException { + this(path, vdjcRegistry, concurrency, ForkJoinPool.commonPool()); } - public VDJCAlignmentsReader(InputStream inputStream, long size) { - this(inputStream, VDJCLibraryRegistry.getDefault(), size, false); + public VDJCAlignmentsReader(Path path, VDJCLibraryRegistry vdjcRegistry, int concurrency, ExecutorService executor) throws IOException { + this(path, vdjcRegistry, concurrency, executor, DEFAULT_READ_AHEAD_BLOCKS); } - public VDJCAlignmentsReader(InputStream inputStream, VDJCLibraryRegistry vdjcRegistry, - long size, boolean useSeparateDecoderThread) { - this.inputStream = countingInputStream = new CountingInputStream(inputStream); + public VDJCAlignmentsReader(Path path, VDJCLibraryRegistry vdjcRegistry, int concurrency, ExecutorService executor, int readAheadBlocks) throws IOException { + this.input = new PrimitivIHybrid(executor, path, concurrency); + this.readAheadBlocks = readAheadBlocks; this.vdjcRegistry = vdjcRegistry; - this.size = size; - this.useSeparateDecoderThread = useSeparateDecoderThread; - } - public void init() { - init(null); + try (PrimitivI i = input.beginRandomAccessPrimitivI(-FOOTER_LENGTH)) { + numberOfAlignments = i.readLong(); + numberOfReads = i.readLong(); + if (!Arrays.equals(i.readBytes(IOUtil.END_MAGIC_LENGTH), IOUtil.getEndMagicBytes())) + throw new IOException("Malformed file, END_MAGIC mismatch."); + } } - void init(Map geneFeatureRefs) { + // public void init() { + // init(null); + // } + + public void init() { if (reader != null) return; - PrimitivI input = new PrimitivI(inputStream); - - assert MAGIC_BYTES.length == MAGIC_LENGTH; - byte[] magic = new byte[MAGIC_LENGTH]; - input.readFully(magic); - String magicString = new String(magic); - this.magic = magicString; - - // SerializersManager serializersManager = input.getSerializersManager(); - switch (magicString) { - case MAGIC: - break; - default: - throw new RuntimeException("Unsupported file format; .vdjca file of version " + new String(magic) - + " while you are running MiXCR " + MAGIC); - } - - versionInfo = input.readUTF(); - - parameters = input.readObject(VDJCAlignerParameters.class); - pipelineConfiguration = input.readObject(PipelineConfiguration.class); - - this.usedGenes = IOUtil.readAndRegisterGeneReferences(input, vdjcRegistry, parameters); + try (final PrimitivI i = input.beginPrimitivI(true)) { + assert MAGIC_BYTES.length == MAGIC_LENGTH; + byte[] magic = new byte[MAGIC_LENGTH]; + i.readFully(magic); + String magicString = new String(magic); + this.magic = magicString; + + // SerializersManager serializersManager = input.getSerializersManager(); + switch (magicString) { + case MAGIC: + break; + default: + throw new RuntimeException("Unsupported file format; .vdjca file of version " + new String(magic) + + " while you are running MiXCR " + MAGIC); + } - // Registering links to features to align - for (GeneType gt : GeneType.VDJC_REFERENCE) { - GeneFeature featureParams = parameters.getFeatureToAlign(gt); - GeneFeature featureDeserialized = input.readObject(GeneFeature.class); - if (!Objects.equals(featureDeserialized, featureParams)) - throw new RuntimeException("Wrong format."); + versionInfo = i.readUTF(); - // Find corresponding reference - if (geneFeatureRefs != null) { - featureParams = geneFeatureRefs.get(featureParams); - if (featureParams == null) - throw new RuntimeException("Absent record for " + featureDeserialized + " in geneFeatureRefs map."); - } + parameters = i.readObject(VDJCAlignerParameters.class); + pipelineConfiguration = i.readObject(PipelineConfiguration.class); - if (featureDeserialized != null) - input.putKnownObject(featureParams); + this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, parameters, vdjcRegistry); } - this.reader = new BasicVDJCAlignmentReader(new AlignmentsIO.InputStreamBufferReader(inputStream), - input.getState(), useSeparateDecoderThread); + this.reader = input.beginPrimitivIBlocks(VDJCAlignments.class, readAheadBlocks); } - public int getQueueSize() { + public PrimitivIBlocksStats getStats() { if (reader == null) - return -1; - return reader.getQueueSize(); + return null; + return reader.getParent().getStats(); } public synchronized VDJCAlignerParameters getParameters() { @@ -201,6 +189,7 @@ public synchronized PipelineConfiguration getPipelineConfiguration() { * @return information about version of MiXCR which produced this file */ public String getVersionInfo() { + init(); return versionInfo; } @@ -210,6 +199,7 @@ public String getVersionInfo() { * @return magic bytes of this file */ public String getMagic() { + init(); return magic; } @@ -219,14 +209,14 @@ public long getNumberOfReads() { @Override public double getProgress() { - if (size == 0) + if (numberOfAlignments == 0) return Double.NaN; - return (1.0 * countingInputStream.getBytesRead()) / size; + return (1.0 * counter) / numberOfAlignments; } @Override public boolean isFinished() { - return closed || (countingInputStream != null && countingInputStream.getBytesRead() == size); + return closed || counter == numberOfAlignments; } @Override @@ -239,12 +229,9 @@ private void close(boolean onEnd) { return; try { - // If all alignments are read - // footer with number of reads processed to produce this - // file can be read form the stream. - if (onEnd) - numberOfReads = new PrimitivI(inputStream).readLong(); - inputStream.close(); + // Closing blocked reader + reader.close(); + input.close(); } catch (IOException e) { throw new RuntimeException(e); } finally { @@ -268,29 +255,4 @@ public synchronized VDJCAlignments take() { return al.setAlignmentsIndex(counter++); } - - /** - * Produce reader that uses the same reference for geneFeatures. - * - * @param reader target reader - * @param parameters parameters to take reference from - */ - public static void initGeneFeatureReferencesFrom(VDJCAlignmentsReader reader, VDJCAlignerParameters parameters) { - Map featureRefs = new HashMap<>(); - for (GeneType gt : GeneType.VDJC_REFERENCE) { - GeneFeature f = parameters.getFeatureToAlign(gt); - featureRefs.put(f, f); - } - reader.init(featureRefs); - } - - /** - * Produce reader that uses the same reference for geneFeatures. - * - * @param reader target reader - * @param sourceReader reader to take reference from - */ - public static void initGeneFeatureReferencesFrom(VDJCAlignmentsReader reader, VDJCAlignmentsReader sourceReader) { - initGeneFeatureReferencesFrom(reader, sourceReader.getParameters()); - } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java index acefe6ff0..2ddaaf07c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java @@ -35,41 +35,30 @@ import com.milaboratory.mixcr.vdjaligners.VDJCAligner; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivO; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; +import com.milaboratory.primitivio.blocks.PrimitivOBlocks; +import com.milaboratory.primitivio.blocks.PrimitivOBlocksStats; +import com.milaboratory.primitivio.blocks.PrimitivOHybrid; +import com.milaboratory.util.io.HasPosition; import io.repseq.core.VDJCGene; import java.io.File; import java.io.IOException; -import java.io.OutputStream; import java.nio.charset.StandardCharsets; -import java.util.ArrayList; +import java.nio.file.Paths; import java.util.List; +import java.util.concurrent.ExecutorService; +import java.util.concurrent.ForkJoinPool; -import static com.milaboratory.mixcr.basictypes.AlignmentsIO.DEFAULT_ALIGNMENTS_IN_BLOCK; - -public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI { +public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI, HasPosition { public static final int DEFAULT_ENCODER_THREADS = 3; + public static final int DEFAULT_ALIGNMENTS_IN_BLOCK = 1024; // 1024 alignments * 805-1024 bytes per alignment ~ 824 kB - 1MB per block static final String MAGIC_V15 = "MiXCR.VDJC.V15"; static final String MAGIC = MAGIC_V15; static final int MAGIC_LENGTH = 14; static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII); - /** - * Buffer for accumulation of alignments written with write(VDJCAlignments) method. Buffer is flushed if - * number of accumulated alignments is alignmentsInBlock or close() method was invoked. - */ - volatile ArrayList currentBuffer; - - /** - * Number of alignments in block. Larger number allows for better compression while consume more memory. - */ - final int alignmentsInBlock; - - /** - * Raw underlying output stream - */ - final OutputStream rawOutput; + /** Number of bytes in footer with meta information */ + static final int FOOTER_LENGTH = 8 + 8 + IOUtil.END_MAGIC_LENGTH; /** * This number will be added to the end of the file to report number of processed read to the following processing @@ -77,15 +66,17 @@ public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI { */ long numberOfProcessedReads = -1; - /** - * Pool of encoders - */ - final BasicVDJCAlignmentWriterFactory writerFactory; + /** Writer settings */ + final int encoderThreads, alignmentsInBlock; - /** - * Initialized after header, implements all internal encoding logic. - */ - volatile BasicVDJCAlignmentWriterFactory.Writer writer = null; + /** Counter of alignments */ + long numberOfAlignments = 0; + + /** Main block output class */ + final PrimitivOHybrid output; + + /** Initialized after headers */ + volatile PrimitivOBlocks.Writer writer; boolean closed = false; @@ -94,7 +85,11 @@ public VDJCAlignmentsWriter(String fileName) throws IOException { } public VDJCAlignmentsWriter(String fileName, int encoderThreads, int alignmentsInBlock) throws IOException { - this(new File(fileName), encoderThreads, alignmentsInBlock); + this(fileName, encoderThreads, alignmentsInBlock, ForkJoinPool.commonPool()); + } + + public VDJCAlignmentsWriter(String fileName, int encoderThreads, int alignmentsInBlock, ExecutorService executor) throws IOException { + this(new PrimitivOHybrid(executor, Paths.get(fileName)), encoderThreads, alignmentsInBlock); } public VDJCAlignmentsWriter(File file) throws IOException { @@ -102,18 +97,17 @@ public VDJCAlignmentsWriter(File file) throws IOException { } public VDJCAlignmentsWriter(File file, int encoderThreads, int alignmentsInBlock) throws IOException { - this(IOUtil.createOS(file), encoderThreads, alignmentsInBlock); + this(file, encoderThreads, alignmentsInBlock, ForkJoinPool.commonPool()); } - public VDJCAlignmentsWriter(OutputStream output) { - this(output, DEFAULT_ENCODER_THREADS, DEFAULT_ALIGNMENTS_IN_BLOCK); + public VDJCAlignmentsWriter(File file, int encoderThreads, int alignmentsInBlock, ExecutorService executor) throws IOException { + this(new PrimitivOHybrid(executor, file.toPath()), encoderThreads, alignmentsInBlock); } - public VDJCAlignmentsWriter(OutputStream output, int encoderThreads, int alignmentsInBlock) { - this.rawOutput = output; + public VDJCAlignmentsWriter(PrimitivOHybrid output, int encoderThreads, int alignmentsInBlock) { + this.output = output; + this.encoderThreads = encoderThreads; this.alignmentsInBlock = alignmentsInBlock; - this.currentBuffer = new ArrayList<>(alignmentsInBlock); - this.writerFactory = new BasicVDJCAlignmentWriterFactory(encoderThreads); } @Override @@ -148,47 +142,47 @@ public void header(VDJCAlignerParameters parameters, List genes, if (writer != null) throw new IllegalStateException("Header already written."); - PrimitivO output = new PrimitivO(rawOutput); - // Writing meta data using raw stream for easy reconstruction with simple tools like hex viewers + try (PrimitivO o = output.beginPrimitivO(true)) { + // Writing magic bytes + assert MAGIC_BYTES.length == MAGIC_LENGTH; + o.write(MAGIC_BYTES); - // Writing magic bytes - assert MAGIC_BYTES.length == MAGIC_LENGTH; - output.write(MAGIC_BYTES); - - // Writing version information - output.writeUTF( - MiXCRVersionInfo.get().getVersionString( - AppVersionInfo.OutputType.ToFile)); - - // Writing parameters - output.writeObject(parameters); + // Writing version information + o.writeUTF( + MiXCRVersionInfo.get().getVersionString( + AppVersionInfo.OutputType.ToFile)); - // Writing history - if (ppConfiguration != null) - this.pipelineConfiguration = ppConfiguration; - output.writeObject(pipelineConfiguration); + // Writing parameters + o.writeObject(parameters); - IOUtil.writeAndRegisterGeneReferences(output, genes, parameters); + // Writing history + if (ppConfiguration != null) + this.pipelineConfiguration = ppConfiguration; + o.writeObject(pipelineConfiguration); - // Registering links to features to align - for (GeneType gt : GeneType.VDJC_REFERENCE) { - GeneFeature feature = parameters.getFeatureToAlign(gt); - output.writeObject(feature); - if (feature != null) - output.putKnownObject(feature); + IOUtil.stdVDJCPrimitivOStateInit(o, genes, parameters); } - // Saving output state - writer = writerFactory.createWriter(output.getState(), rawOutput, false); + writer = output.beginPrimitivOBlocks(encoderThreads, alignmentsInBlock); + } + + @Override + public long getPosition() { + return output.getPosition(); } public int getEncodersCount() { - return writerFactory.getEncodersCount(); + if (writer == null) + return 0; + return writer.getParent().getStats().getConcurrency(); } public int getBusyEncoders() { - return writerFactory.getBusyEncoders(); + if (writer == null) + return 0; + PrimitivOBlocksStats stats = writer.getParent().getStats(); + return stats.getOngoingSerdes() + stats.getOngoingIOOps(); } @Override @@ -199,45 +193,36 @@ public synchronized void write(VDJCAlignments alignment) { if (alignment == null) throw new NullPointerException(); - currentBuffer.add(alignment); - - if (currentBuffer.size() == alignmentsInBlock) - flushBlock(); - } - - /** - * Flush alignment buffer - */ - private void flushBlock() { - if (currentBuffer.isEmpty()) - return; - - // Enqueue block for async encoding and compression - writer.writeAsync(currentBuffer); - currentBuffer = new ArrayList<>(alignmentsInBlock); + numberOfAlignments++; + writer.write(alignment); } @Override public synchronized void close() { try { if (!closed) { - flushBlock(); - writer.close(); // This will also write stream termination symbol/block to the stream - writerFactory.close(); // This blocks the thread until all workers flush their data to the underlying stream - - // [ numberOfProcessedReads : long ] - byte[] footer = new byte[8]; - // Number of processed reads is known only in the end of analysis - // Writing it as last piece of information in the stream - AlignmentsIO.writeLongBE(numberOfProcessedReads, footer, 0); - rawOutput.write(footer); - - // Writing end-magic as a file integrity sign - rawOutput.write(IOUtil.getEndMagicBytes()); - rawOutput.close(); - closed = true; + try (PrimitivO o = output.beginPrimitivO()) { + // // [ numberOfProcessedReads : long ] + // byte[] footer = new byte[8]; + // + // // Number of processed reads is known only in the end of analysis + // // Writing it as last piece of information in the stream + // AlignmentsIO.writeLongBE(numberOfProcessedReads, footer, 0); + // o.write(footer); + + // Total size = 8 + 8 + END_MAGIC_LENGTH + + o.writeLong(numberOfAlignments); + o.writeLong(numberOfProcessedReads); + + // Writing end-magic as a file integrity sign + o.write(IOUtil.getEndMagicBytes()); + } finally { + closed = true; + output.close(); + } } } catch (IOException e) { throw new RuntimeException(e); diff --git a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java index af05f122d..34633c75e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java @@ -32,7 +32,7 @@ import com.fasterxml.jackson.annotation.JsonFormat; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.util.MiXCRVersionInfo; -import com.milaboratory.util.TimeUtils; +import com.milaboratory.util.FormatUtils; import java.util.Collection; import java.util.Date; @@ -121,6 +121,6 @@ public void writeSuperReport(ReportHelper helper) { helper.writeField("Command line arguments", getCommandLine()); if (getExecutionTimeMillis() >= 0) - helper.writeField("Analysis time", TimeUtils.nanoTimeToString(getExecutionTimeMillis() * 1000_000)); + helper.writeField("Analysis time", FormatUtils.nanoTimeToString(getExecutionTimeMillis() * 1000_000)); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 0004c1150..072c78cfc 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -81,7 +81,7 @@ import static cc.redberry.pipe.CUtils.chunked; import static cc.redberry.pipe.CUtils.unchunked; -import static com.milaboratory.mixcr.basictypes.AlignmentsIO.DEFAULT_ALIGNMENTS_IN_BLOCK; +import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK; import static com.milaboratory.mixcr.cli.CommandAlign.ALIGN_COMMAND_NAME; @Command(name = ALIGN_COMMAND_NAME, diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 3e754c377..efffe7c3d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -206,7 +206,7 @@ public void run1() throws Exception { StatusReporter reporter = new StatusReporter(); reporter.addCustomProviderFromLambda(() -> new StatusReporter.Status( - "Reader buffer: " + assemblerRunner.getQueueSize(), + "Reader buffer: FIXME " /*+ assemblerRunner.getQueueSize()*/, assemblerRunner.isFinished())); reporter.start(); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 6c72e3627..ac84110c1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -44,6 +44,7 @@ import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerParameters; import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerReport; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PipeDataInputReader; import com.milaboratory.primitivio.PrimitivI; @@ -121,8 +122,8 @@ public void run1() throws Exception { List genes; VDJCAlignerParameters alignerParameters; CloneAssemblerParameters cloneAssemblerParameters; - try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault()); - PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(out))); + try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); + PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(out))); // TODO ???? BufferedWriter debugReport = debugReportFile == null ? null : new BufferedWriter(new OutputStreamWriter(new FileOutputStream(debugReportFile)))) { final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), @@ -131,7 +132,7 @@ public void run1() throws Exception { alignerParameters = reader.getAlignerParameters(); cloneAssemblerParameters = reader.getAssemblerParameters(); genes = reader.getGenes(); - IOUtil.registerGeneReferences(tmpOut, genes, alignerParameters); + IOUtil.registerGeneReferencesO(tmpOut, genes, alignerParameters); ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments(); SmartProgressReporter.startProgressReport("Assembling contigs", cloneAlignmentsPort); @@ -245,7 +246,7 @@ public void run1() throws Exception { Clone[] clones = new Clone[totalClonesCount]; try (PrimitivI tmpIn = new PrimitivI(new BufferedInputStream(new FileInputStream(out)))) { - IOUtil.registerGeneReferences(tmpIn, genes, alignerParameters); + IOUtil.registerGeneReferencesI(tmpIn, genes, alignerParameters); int i = 0; for (Clone clone : CUtils.it(new PipeDataInputReader<>(Clone.class, tmpIn, totalClonesCount))) clones[i++] = clone; @@ -254,8 +255,7 @@ public void run1() throws Exception { Arrays.sort(clones, Comparator.comparingDouble(c -> -c.getCount())); for (int i = 0; i < clones.length; i++) clones[i] = clones[i].setId(i); - CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters.getFeaturesToAlignMap(), - alignerParameters, cloneAssemblerParameters); + CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters, cloneAssemblerParameters); try (ClnsWriter writer = new ClnsWriter(getFullPipelineConfiguration(), cloneSet, out)) { SmartProgressReporter.startProgressReport(writer); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index c4d223076..47eed6625 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -34,6 +34,7 @@ import cc.redberry.primitives.Filter; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.export.*; +import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.CanReportProgressAndStage; import com.milaboratory.util.SmartProgressReporter; @@ -190,7 +191,7 @@ void run1(List> exporters) throws Excepti source = vdjcaReader; break; case MAGIC_CLNA: - ClnAReader clnaReader = new ClnAReader(in, VDJCLibraryRegistry.getDefault()); + ClnAReader clnaReader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); reader = clnaReader; source = clnaReader.readAllAlignments(); break; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java index 8d932fbbe..e73d911b5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java @@ -10,6 +10,7 @@ import com.milaboratory.mixcr.basictypes.ClnAReader; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; +import com.milaboratory.mixcr.util.Concurrency; import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -57,7 +58,7 @@ public int[] getCloneIds() { @Override public void run1() throws Exception { - try (ClnAReader clna = new ClnAReader(in, VDJCLibraryRegistry.getDefault()); + try (ClnAReader clna = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(getOutput())) { writer.header(clna.getAlignerParameters(), clna.getGenes(), getFullPipelineConfiguration()); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java index 128c4fad4..2ef5c8da2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java @@ -38,6 +38,7 @@ import com.milaboratory.core.io.sequence.fastq.SingleFastqWriter; import com.milaboratory.mixcr.basictypes.ClnAReader; import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.VDJCLibraryRegistry; @@ -92,7 +93,7 @@ public int[] getCloneIds() { @Override public void run0() throws Exception { - try (ClnAReader clna = new ClnAReader(in, VDJCLibraryRegistry.getDefault())) { + try (ClnAReader clna = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4))) { VDJCAlignments firstAlignment; try (OutputPortCloseable dummyP = clna.readAllAlignments()) { firstAlignment = dummyP.take(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 715a071c4..747d6d3fc 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -152,8 +152,8 @@ void processClns() throws IOException { clones.sort(Comparator.comparing(Clone::getId)); - CloneSet newCloneSet = new CloneSet(clones, cloneSet.getUsedGenes(), cloneSet.getAlignedFeatures(), - cloneSet.getAlignmentParameters(), cloneSet.getAssemblerParameters()); + CloneSet newCloneSet = new CloneSet(clones, cloneSet.getUsedGenes(), cloneSet.getAlignmentParameters(), + cloneSet.getAssemblerParameters()); try (ClnsWriter writer = new ClnsWriter(getFullPipelineConfiguration(), newCloneSet, out)) { writer.write(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 379915711..2b81dd890 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -151,7 +151,7 @@ private void runClns() throws Exception { } private void runClna() throws Exception { - try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault()); + try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), 3); ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { CloneSet cloneSet = reader.readCloneSet(); @@ -297,7 +297,6 @@ private CloneSet doClustering(CloneSet cloneSet, TObjectIntHashMap allAlignmentsPortRaw = new FlatteningOutputPort<>(CUtils.asOutputPort(allAlignmentsList)); AtomicLong idGen = new AtomicLong(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java index 7e2e744aa..8249a3a9d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java @@ -33,12 +33,16 @@ import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.CountingOutputPort; -import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.cli.ActionConfiguration; +import com.milaboratory.mixcr.basictypes.IOUtil; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.primitivio.PipeReader; +import com.milaboratory.primitivio.PipeWriter; import com.milaboratory.util.ObjectSerializer; import com.milaboratory.util.SmartProgressReporter; import com.milaboratory.util.Sorter; @@ -72,7 +76,8 @@ public void run1() throws Exception { try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in)) { SmartProgressReporter.startProgressReport("Reading vdjca", reader); try (OutputPortCloseable sorted = - Sorter.sort(reader, idComparator, 1024 * 512, new VDJCAlignmentsSerializer(reader), TempFileManager.getTempFile()); + Sorter.sort(reader, idComparator, 1024 * 512, + new VDJCAlignmentsSerializer(reader), TempFileManager.getTempFile()); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { writer.header(reader.getParameters(), reader.getUsedGenes(), getFullPipelineConfiguration()); @@ -105,18 +110,27 @@ public VDJCAlignmentsSerializer(VDJCAlignmentsReader reader) { @Override public void write(Collection data, OutputStream stream) { - try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(stream)) { - writer.header(parameters, usedAlleles, null); + try (PipeWriter out = + new PipeWriter(stream) { + @Override + protected void init() { + IOUtil.stdVDJCPrimitivOStateInit(output, usedAlleles, parameters); + } + }) { for (VDJCAlignments datum : data) - writer.write(datum); + out.put(datum); } } @Override public OutputPort read(InputStream stream) { - VDJCAlignmentsReader reader = new VDJCAlignmentsReader(stream); - VDJCAlignmentsReader.initGeneFeatureReferencesFrom(reader, parameters); - return reader; + return new PipeReader(VDJCAlignments.class, stream) { + @Override + protected void init() { + IOUtil.stdVDJCPrimitivIStateInit(input, parameters, + usedAlleles.get(0).getParentLibrary().getParent()); + } + }; } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java index fc92c1621..ecffe53fa 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java @@ -57,7 +57,7 @@ public void run0() throws Exception { CloneSet cs = CloneSetIO.read(inputFile); System.out.println(cs.getVersionInfo()); } else if (i.endsWith(".clna")) { - try (ClnAReader reader = new ClnAReader(inputFile, VDJCLibraryRegistry.getDefault())) { + try (ClnAReader reader = new ClnAReader(inputFile, VDJCLibraryRegistry.getDefault(), 1)) { System.out.println(reader.getVersionInfo()); } } else diff --git a/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java b/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java index 9f9a0c41d..43f0e3a82 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java +++ b/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java @@ -45,61 +45,61 @@ public final class SerializerCompatibilityUtil { private SerializerCompatibilityUtil() { } - private static final HashMap v3_0_3_Table = new HashMap<>(); - - static { - v3_0_3_Table.put("\"align-configuration\"", - "com.milaboratory.mixcr.cli.CommandAlign$AlignConfiguration"); - v3_0_3_Table.put("\"assemble-configuration\"", - "com.milaboratory.mixcr.cli.CommandAssemble$AssembleConfiguration"); - v3_0_3_Table.put("\"assemble-contig-configuration\"", - "com.milaboratory.mixcr.cli.CommandAssembleContigs$AssembleContigsConfiguration"); - v3_0_3_Table.put("\"assemble-partial-configuration\"", - "com.milaboratory.mixcr.cli.CommandAssemblePartialAlignments$AssemblePartialConfiguration"); - v3_0_3_Table.put("\"extend-configuration\"", - "com.milaboratory.mixcr.cli.CommandExtend$ExtendConfiguration"); - v3_0_3_Table.put("\"merge-configuration\"", - "com.milaboratory.mixcr.cli.CommandMergeAlignments$MergeConfiguration"); - v3_0_3_Table.put("\"filter-configuration\"", - "com.milaboratory.mixcr.cli.CommandFilterAlignments$FilterConfiguration"); - v3_0_3_Table.put("\"sort-configuration\"", - "com.milaboratory.mixcr.cli.CommandSortAlignments$SortConfiguration"); - v3_0_3_Table.put("\"slice-configuration\"", - "com.milaboratory.mixcr.cli.CommandSlice$SliceConfiguration"); - } - - public static void add_v3_0_3_CustomSerializers(PrimitivI input) { - input.getSerializersManager().registerCustomSerializer(AppVersionInfo.class, - new JSONSerializer(AppVersionInfo.class, s -> { - try { - JsonNode jsonNode = GlobalObjectMappers.ONE_LINE.readTree(s); - ObjectNode componentVersions = GlobalObjectMappers.ONE_LINE.createObjectNode(); - ((ObjectNode) jsonNode).set("componentVersions", componentVersions); - componentVersions.set("mixcr", ((ObjectNode) jsonNode).remove("mixcr")); - componentVersions.set("milib", ((ObjectNode) jsonNode).remove("milib")); - componentVersions.set("repseqio", ((ObjectNode) jsonNode).remove("repseqio")); - ObjectNode componentStringVersions = GlobalObjectMappers.ONE_LINE.createObjectNode(); - ((ObjectNode) jsonNode).set("componentStringVersions", componentStringVersions); - componentStringVersions.set("builtInLibrary", ((ObjectNode) jsonNode) - .remove("builtInLibrary")); - ((ObjectNode) jsonNode).set("type", - new TextNode("com.milaboratory.cli.AppVersionInfo")); - return jsonNode.toString(); - } catch (IOException e) { - throw new RuntimeException(e); - } - })); - input.getSerializersManager().registerCustomSerializer(ActionConfiguration.class, - new JSONSerializer(ActionConfiguration.class, s -> { - try { - JsonNode jsonNode = GlobalObjectMappers.ONE_LINE.readTree(s); - String typeName = jsonNode.get("type").toString(); - if (v3_0_3_Table.containsKey(typeName)) - ((ObjectNode) jsonNode).set("type", new TextNode(v3_0_3_Table.get(typeName))); - return jsonNode.toString(); - } catch (IOException e) { - throw new RuntimeException(e); - } - })); - } + // private static final HashMap v3_0_3_Table = new HashMap<>(); + // + // static { + // v3_0_3_Table.put("\"align-configuration\"", + // "com.milaboratory.mixcr.cli.CommandAlign$AlignConfiguration"); + // v3_0_3_Table.put("\"assemble-configuration\"", + // "com.milaboratory.mixcr.cli.CommandAssemble$AssembleConfiguration"); + // v3_0_3_Table.put("\"assemble-contig-configuration\"", + // "com.milaboratory.mixcr.cli.CommandAssembleContigs$AssembleContigsConfiguration"); + // v3_0_3_Table.put("\"assemble-partial-configuration\"", + // "com.milaboratory.mixcr.cli.CommandAssemblePartialAlignments$AssemblePartialConfiguration"); + // v3_0_3_Table.put("\"extend-configuration\"", + // "com.milaboratory.mixcr.cli.CommandExtend$ExtendConfiguration"); + // v3_0_3_Table.put("\"merge-configuration\"", + // "com.milaboratory.mixcr.cli.CommandMergeAlignments$MergeConfiguration"); + // v3_0_3_Table.put("\"filter-configuration\"", + // "com.milaboratory.mixcr.cli.CommandFilterAlignments$FilterConfiguration"); + // v3_0_3_Table.put("\"sort-configuration\"", + // "com.milaboratory.mixcr.cli.CommandSortAlignments$SortConfiguration"); + // v3_0_3_Table.put("\"slice-configuration\"", + // "com.milaboratory.mixcr.cli.CommandSlice$SliceConfiguration"); + // } + // + // public static void add_v3_0_3_CustomSerializers(PrimitivI input) { + // input.getSerializersManager().registerCustomSerializer(AppVersionInfo.class, + // new JSONSerializer(AppVersionInfo.class, s -> { + // try { + // JsonNode jsonNode = GlobalObjectMappers.ONE_LINE.readTree(s); + // ObjectNode componentVersions = GlobalObjectMappers.ONE_LINE.createObjectNode(); + // ((ObjectNode) jsonNode).set("componentVersions", componentVersions); + // componentVersions.set("mixcr", ((ObjectNode) jsonNode).remove("mixcr")); + // componentVersions.set("milib", ((ObjectNode) jsonNode).remove("milib")); + // componentVersions.set("repseqio", ((ObjectNode) jsonNode).remove("repseqio")); + // ObjectNode componentStringVersions = GlobalObjectMappers.ONE_LINE.createObjectNode(); + // ((ObjectNode) jsonNode).set("componentStringVersions", componentStringVersions); + // componentStringVersions.set("builtInLibrary", ((ObjectNode) jsonNode) + // .remove("builtInLibrary")); + // ((ObjectNode) jsonNode).set("type", + // new TextNode("com.milaboratory.cli.AppVersionInfo")); + // return jsonNode.toString(); + // } catch (IOException e) { + // throw new RuntimeException(e); + // } + // })); + // input.getSerializersManager().registerCustomSerializer(ActionConfiguration.class, + // new JSONSerializer(ActionConfiguration.class, s -> { + // try { + // JsonNode jsonNode = GlobalObjectMappers.ONE_LINE.readTree(s); + // String typeName = jsonNode.get("type").toString(); + // if (v3_0_3_Table.containsKey(typeName)) + // ((ObjectNode) jsonNode).set("type", new TextNode(v3_0_3_Table.get(typeName))); + // return jsonNode.toString(); + // } catch (IOException e) { + // throw new RuntimeException(e); + // } + // })); + // } } diff --git a/src/main/java/com/milaboratory/mixcr/util/Concurrency.java b/src/main/java/com/milaboratory/mixcr/util/Concurrency.java new file mode 100644 index 000000000..e8e92c143 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/Concurrency.java @@ -0,0 +1,40 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.util; + +public class Concurrency { + // public static globalIOCuncurrencyLimiter(){ + // + // } + + public static int noMoreThan(int n) { + return Math.min(Runtime.getRuntime().availableProcessors(), n); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 73dc2ba18..f8ce9ca3a 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -141,10 +141,10 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl int totalClonesCount = 0; File tmpFile = TempFileManager.getTempFile(); - try (ClnAReader reader = new ClnAReader(clnaFile.toPath(), VDJCLibraryRegistry.getDefault()); + try (ClnAReader reader = new ClnAReader(clnaFile.toPath(), VDJCLibraryRegistry.getDefault(), 2); // TODO concurrency ??? PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(tmpFile)));) { - IOUtil.registerGeneReferences(tmpOut, align.usedGenes, align.parameters.alignerParameters); + IOUtil.registerGeneReferencesO(tmpOut, align.usedGenes, align.parameters.alignerParameters); final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), reader.getAssemblingFeatures(), reader.getGenes(), reader.getAlignerParameters().getFeaturesToAlignMap()); @@ -164,7 +164,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl } catch (Throwable re) { throw new RuntimeException("While processing clone #" + cloneAlignments.clone.getId(), re); } - }, 1); + }, 1); // TODO why ony one ??? for (Clone[] clones : CUtils.it(parallelProcessor)) { @@ -179,7 +179,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl Clone[] clones = new Clone[totalClonesCount]; try (PrimitivI tmpIn = new PrimitivI(new BufferedInputStream(new FileInputStream(tmpFile)))) { - IOUtil.registerGeneReferences(tmpIn, align.usedGenes, align.parameters.alignerParameters); + IOUtil.registerGeneReferencesI(tmpIn, align.usedGenes, align.parameters.alignerParameters); int i = 0; for (Clone clone : CUtils.it(new PipeDataInputReader<>(Clone.class, tmpIn, totalClonesCount))) clones[i++] = clone; @@ -190,8 +190,8 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl Arrays.sort(clones, Comparator.comparingDouble(c -> -c.getCount())); for (int i = 0; i < clones.length; i++) clones[i] = clones[i].setId(i); - CloneSet cloneSet = new CloneSet(Arrays.asList(clones), align.usedGenes, align.parameters.alignerParameters.getFeaturesToAlignMap(), - align.parameters.alignerParameters, align.parameters.cloneAssemblerParameters); + CloneSet cloneSet = new CloneSet(Arrays.asList(clones), align.usedGenes, align.parameters.alignerParameters, + align.parameters.cloneAssemblerParameters); return new FullSeqAssembleResult(assemble, cloneSet); } @@ -284,20 +284,19 @@ public AlignResult(RunMiXCRAnalysis parameters, long totalNumberOfReads, Aligner this.aligner = aligner; } - private byte[] serializedAlignments = null; + private File alignmentsFile = null; - public VDJCAlignmentsReader resultReader() { - if (serializedAlignments == null) { - final ByteArrayOutputStream data = new ByteArrayOutputStream(); - try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(data)) { + public VDJCAlignmentsReader resultReader() throws IOException { + if (alignmentsFile == null) { + alignmentsFile = TempFileManager.getTempFile(); + try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(alignmentsFile)) { writer.header(aligner, null); for (VDJCAlignments alignment : alignments) writer.write(alignment); writer.setNumberOfProcessedReads(totalNumberOfReads); } - serializedAlignments = data.toByteArray(); } - return new VDJCAlignmentsReader(new ByteArrayInputStream(serializedAlignments)); + return new VDJCAlignmentsReader(alignmentsFile); } } diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index df785253c..6d2909880 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -43,6 +43,7 @@ import com.milaboratory.mixcr.vdjaligners.*; import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.SmartProgressReporter; +import com.milaboratory.util.TempFileManager; import io.repseq.core.*; import org.junit.Assert; import org.junit.Ignore; @@ -50,6 +51,7 @@ import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; +import java.io.File; import java.io.IOException; import java.util.Arrays; @@ -90,8 +92,8 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[1]), true); //write alignments to byte array - ByteArrayOutputStream alignmentsSerialized = new ByteArrayOutputStream(); - try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(alignmentsSerialized)) { + File vdjcaFile = TempFileManager.getTempFile(); + try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(vdjcaFile)) { writer.header(aligner, null); for (Object read : CUtils.it(reader)) { VDJCAlignmentResult result = (VDJCAlignmentResult) aligner.process((SequenceRead) read); @@ -100,9 +102,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException } } - AlignmentsProvider alignmentsProvider = AlignmentsProvider.Util.createProvider( - alignmentsSerialized.toByteArray(), - VDJCLibraryRegistry.getDefault()); + AlignmentsProvider alignmentsProvider = AlignmentsProvider.Util.createProvider(vdjcaFile, VDJCLibraryRegistry.getDefault()); LinearGapAlignmentScoring scoring = new LinearGapAlignmentScoring<>(NucleotideSequence.ALPHABET, 5, -9, -12); CloneFactoryParameters factoryParameters = new CloneFactoryParameters( @@ -152,8 +152,8 @@ private static void assertCSEquals(CloneSet expected, CloneSet actual) { Assert.assertArrayEquals(expected.getAssemblingFeatures(), actual.getAssemblingFeatures()); for (GeneType geneType : GeneType.values()) - Assert.assertEquals(expected.getAlignedGeneFeature(geneType), - actual.getAlignedGeneFeature(geneType)); + Assert.assertEquals(expected.getFeatureToAlign(geneType), + actual.getFeatureToAlign(geneType)); for (int i = 0; i < expected.getClones().size(); ++i) Assert.assertEquals(expected.getClones().get(i), actual.getClones().get(i)); diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java index 83b872f6b..de2e5740c 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java @@ -98,7 +98,6 @@ public void test2Empty() throws Exception { File file = TempFileManager.getTempFile(); ClnAWriter writer = new ClnAWriter(null, file); writer.writeClones(new CloneSet(Collections.EMPTY_LIST, align.usedGenes, - align.parameters.alignerParameters.getFeaturesToAlignMap(), align.parameters.alignerParameters, CloneAssemblerParametersPresets.getByName("default"))); writer.sortAlignments(CUtils.asOutputPort(align.alignments), align.alignments.size()); diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java index bb72c5318..7a2f853e9 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java @@ -36,14 +36,15 @@ import com.milaboratory.mixcr.vdjaligners.VDJCAlignerS; import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult; import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; +import com.milaboratory.util.TempFileManager; import io.repseq.core.Chains; import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; import org.junit.Assert; import org.junit.Test; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; +import java.io.File; +import java.nio.file.Files; import java.util.ArrayList; import java.util.List; @@ -55,11 +56,11 @@ public class IOTest { public void testSerialization1() throws Exception { VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default"); - ByteArrayOutputStream bos = new ByteArrayOutputStream(); + File tmpFile = TempFileManager.getTempFile(); List alignemntsList = new ArrayList<>(); - int header; + long header; long numberOfReads; long numberOfAlignments = 0; @@ -76,10 +77,10 @@ public void testSerialization1() throws Exception { } - try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(bos, 4, 21)) { + try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(tmpFile)) { writer.header(aligner, null); - header = bos.size(); + header = writer.getPosition(); for (SingleRead read : CUtils.it(reader)) { VDJCAlignmentResult result = aligner.process(read); @@ -97,9 +98,9 @@ public void testSerialization1() throws Exception { assertTrue(alignemntsList.size() > 10); assertTrue(numberOfReads > 10); - System.out.println("Bytes per alignment: " + (bos.size() - header) / alignemntsList.size()); + System.out.println("Bytes per alignment: " + (Files.size(tmpFile.toPath()) - header) / alignemntsList.size()); - try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(new ByteArrayInputStream(bos.toByteArray()), true)) { + try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(tmpFile)) { int i = 0; for (VDJCAlignments alignments : CUtils.it(reader)) { Assert.assertEquals(alignments.getAlignmentsIndex(), i); @@ -108,5 +109,7 @@ public void testSerialization1() throws Exception { Assert.assertEquals(numberOfAlignments, i); Assert.assertEquals(numberOfReads, reader.getNumberOfReads()); } + + tmpFile.delete(); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java index 354193fbb..ab1890447 100644 --- a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java @@ -35,13 +35,17 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.SequenceBuilder; import com.milaboratory.core.sequence.SequenceQuality; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; +import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.tests.MiXCRTestUtils; import com.milaboratory.mixcr.util.RunMiXCR; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; import com.milaboratory.test.TestUtil; import com.milaboratory.util.RandomUtil; +import com.milaboratory.util.TempFileManager; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; @@ -50,8 +54,7 @@ import org.junit.Assert; import org.junit.Test; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; +import java.io.File; import java.util.ArrayList; import java.util.EnumMap; @@ -245,9 +248,8 @@ public static TestResult processData(PairedRead[] data, InputTestData input) thr // Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString())); } - - final ByteArrayOutputStream overlappedSerializedData = new ByteArrayOutputStream(); - try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(overlappedSerializedData)) { + File overlappedAlignments = TempFileManager.getTempFile(); + try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(overlappedAlignments)) { final PartialAlignmentsAssemblerParameters pParameters = PartialAlignmentsAssemblerParameters.getDefault(); pParameters.setMergerParameters(pParameters.getMergerParameters().overrideMinimalIdentity(0.0)); PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(pParameters, writer, true, false); @@ -262,13 +264,15 @@ public static TestResult processData(PairedRead[] data, InputTestData input) thr //System.out.println("\n"); } - - VDJCAlignmentsReader readResult = new VDJCAlignmentsReader(new ByteArrayInputStream(overlappedSerializedData.toByteArray())); + VDJCAlignmentsReader readResult = new VDJCAlignmentsReader(overlappedAlignments); final ArrayList overlapped = new ArrayList<>(); VDJCAlignments al; while ((al = readResult.take()) != null) overlapped.add(al); + + overlappedAlignments.delete(); + return new TestResult(data, inputAlignments, overlapped); } diff --git a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java index f1a5e32ce..0bb43598a 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java @@ -22,7 +22,7 @@ public class DropletCloneGraphTest { @Test @Ignore public void test1() throws Exception { - try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/b_analysis.clna"), VDJCLibraryRegistry.getDefault())) { + try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/b_analysis.clna"), VDJCLibraryRegistry.getDefault(), 3)) { CloneSet clns = reader.readCloneSet(); System.out.println("# clones " + clns.size()); DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); @@ -37,7 +37,7 @@ public void test1() throws Exception { @Test @Ignore public void test2() throws Exception { - try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/t_analysis.clna"), VDJCLibraryRegistry.getDefault())) { + try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/t_analysis.clna"), VDJCLibraryRegistry.getDefault(), 3)) { CloneSet clns = reader.readCloneSet(); System.out.println("# clones " + clns.size()); DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); diff --git a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java index 711caa812..3f15aff56 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java +++ b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java @@ -43,8 +43,8 @@ public class BackwardCompatibilityTests { @Test public void testAlignments() throws Exception { -// assertGoodVDJCA("/backward_compatibility/3.0.4/test.vdjca", 8); -// assertGoodVDJCA("/backward_compatibility/3.0.3/test.vdjca", 8); + // assertGoodVDJCA("/backward_compatibility/3.0.4/test.vdjca", 8); + // assertGoodVDJCA("/backward_compatibility/3.0.3/test.vdjca", 8); } public static void assertGoodVDJCA(String resource, int size) throws IOException { @@ -66,10 +66,10 @@ public static void assertGoodVDJCA(String resource, int size) throws IOException @Test public void testCloneset() throws Exception { -// assertGoodCLNS("/backward_compatibility/3.0.4/test.clna", 2, 2, 2); -// assertGoodCLNS("/backward_compatibility/3.0.4/test.clns", 2, 2, 2); -// assertGoodCLNS("/backward_compatibility/3.0.3/test.clns", 2, 2, 2); -// assertGoodCLNS("/backward_compatibility/3.0.3/test.clna", 2, 2, 2); + // assertGoodCLNS("/backward_compatibility/3.0.4/test.clna", 2, 2, 2); + // assertGoodCLNS("/backward_compatibility/3.0.4/test.clns", 2, 2, 2); + // assertGoodCLNS("/backward_compatibility/3.0.3/test.clns", 2, 2, 2); + // assertGoodCLNS("/backward_compatibility/3.0.3/test.clna", 2, 2, 2); } public static void assertGoodCLNS(String resource, int size, int good, double sumCount) throws IOException { diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java index 27f0145cd..bef54f1e5 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java @@ -40,6 +40,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import com.milaboratory.util.RandomUtil; +import com.milaboratory.util.TempFileManager; import io.repseq.core.Chains; import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; @@ -47,8 +48,8 @@ import org.junit.Ignore; import org.junit.Test; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; +import java.io.File; +import java.nio.file.Files; import java.util.ArrayList; import java.util.List; @@ -58,9 +59,10 @@ public void testSerialization1() throws Exception { VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default"); //LociLibrary ll = LociLibraryManager.getDefault().getLibrary("mi"); - ByteArrayOutputStream bos = new ByteArrayOutputStream(); + File tmpFile = TempFileManager.getTempFile(); + List alignemntsList = new ArrayList<>(); - int header; + long header; try (SingleFastqReader reader = new SingleFastqReader( VDJCAlignerSTest.class.getClassLoader() @@ -69,9 +71,9 @@ public void testSerialization1() throws Exception { for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes(Chains.IGH)) if (parameters.containsRequiredFeature(gene)) aligner.addGene(gene); - try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(bos)) { + try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(tmpFile)) { writer.header(aligner, null); - header = bos.size(); + header = writer.getPosition(); for (SingleRead read : CUtils.it(reader)) { VDJCAlignmentResult result = aligner.process(read); if (result.alignment != null) { @@ -82,12 +84,14 @@ public void testSerialization1() throws Exception { } } Assert.assertTrue(alignemntsList.size() > 10); - System.out.println("Bytes per alignment: " + (bos.size() - header) / alignemntsList.size()); - try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(new ByteArrayInputStream(bos.toByteArray()))) { + System.out.println("Bytes per alignment: " + (Files.size(tmpFile.toPath()) - header) / alignemntsList.size()); + try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(tmpFile)) { int i = 0; for (VDJCAlignments alignments : CUtils.it(reader)) Assert.assertEquals(alignemntsList.get(i++), alignments); } + + tmpFile.delete(); } @Test From 9fd8bafa7ba61f50457a38f3e3dc6fb7d6f24b99 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 28 May 2020 18:17:48 +0300 Subject: [PATCH 060/282] CloneReader (#5) * CloneReader * abstraction and implementation * clns files now use blocked IO for clone stream * MiLib submodule upgrade. * Fix in MiLib. --- milib | 2 +- .../assembler/CloneClusteringStrategy.java | 2 +- .../mixcr/basictypes/ClnAReader.java | 11 +- .../mixcr/basictypes/ClnsReader.java | 139 +++++++++--------- .../mixcr/basictypes/ClnsWriter.java | 123 ++++++++-------- .../mixcr/basictypes/CloneReader.java | 36 +++++ .../mixcr/basictypes/CloneSetIO.java | 10 +- .../PipelineConfigurationReaderMiXCR.java | 4 +- .../mixcr/cli/CommandAssemble.java | 5 +- .../mixcr/cli/CommandAssembleContigs.java | 5 +- .../milaboratory/mixcr/cli/CommandExtend.java | 4 +- .../mixcr/cli/CommandGroupCells.java | 5 +- .../assembler/CloneAssemblerRunnerTest.java | 11 +- .../milaboratory/mixcr/util/RunMiXCRTest.java | 4 +- 14 files changed, 193 insertions(+), 168 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java diff --git a/milib b/milib index 01d35f3b2..71689b469 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 01d35f3b2886c61ae58b9581d5629b45cc6eee15 +Subproject commit 71689b4699a003393373cbf4d152858a79c24bd7 diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java index bee8f6185..06cdd90c7 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java @@ -79,7 +79,7 @@ public boolean canAddToCluster(Cluster cluster, } @Override - public TreeSearchParameters getSearchParameters() { + public TreeSearchParameters getSearchParameters(Cluster cluster) { return parameters.getSearchParameters(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index ee7687c3a..cc002c644 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -55,7 +55,7 @@ /** * Reader of CLNA file format. */ -public final class ClnAReader extends PipelineConfigurationReaderMiXCR implements AutoCloseable { +public final class ClnAReader extends PipelineConfigurationReaderMiXCR implements CloneReader, AutoCloseable { final PrimitivIHybrid input; // Index data @@ -114,7 +114,7 @@ public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int concurrenc byte[] endMagic = new byte[IOUtil.END_MAGIC_LENGTH]; pi.readFully(endMagic); if (!Arrays.equals(IOUtil.getEndMagicBytes(), endMagic)) - throw new RuntimeException("File is corrupted."); + throw new RuntimeException("Corrupted file."); } // TODO move index deserialization to lazy initialization, there are use-cases which need only meta-information from the reader @@ -231,6 +231,7 @@ public CloneSet readCloneSet() throws IOException { /** * Constructs output port to read clones one by one as a stream */ + @Override public OutputPortCloseable readClones() { return input.beginPrimitivIBlocks(Clone.class); } @@ -342,8 +343,10 @@ public void close() throws IOException { input.close(); } - private static Function> HEADER_ACTION_STOP_AT_ALIGNMENT_BLOCK_END = - h -> h.equals(ClnAWriter.ALIGNMENT_BLOCK_SEPARATOR) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); + private static final Function> HEADER_ACTION_STOP_AT_ALIGNMENT_BLOCK_END = + h -> h.equals(ClnAWriter.ALIGNMENT_BLOCK_SEPARATOR) + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.skip(); // private static Function> HEADER_ACTION_STOP_AT_ALIGNMENTS_END = // h -> h.equals(ClnAWriter.ALIGNMENTS_END) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index fff4ba9d1..ae2ccc82a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -29,131 +29,126 @@ */ package com.milaboratory.mixcr.basictypes; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivI; -import io.repseq.core.*; +import com.milaboratory.primitivio.blocks.PrimitivIHybrid; +import com.milaboratory.util.LambdaSemaphore; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGene; +import io.repseq.core.VDJCLibraryRegistry; -import java.io.File; import java.io.IOException; -import java.io.InputStream; +import java.nio.file.Path; import java.util.ArrayList; +import java.util.Arrays; import java.util.EnumMap; import java.util.List; -import static com.milaboratory.mixcr.basictypes.ClnsWriter.*; +import static com.milaboratory.mixcr.basictypes.ClnsWriter.MAGIC; +import static com.milaboratory.mixcr.basictypes.ClnsWriter.MAGIC_LENGTH; /** * */ -public class ClnsReader extends PipelineConfigurationReaderMiXCR implements AutoCloseable { - private final PrimitivI input; +public class ClnsReader extends PipelineConfigurationReaderMiXCR implements CloneReader, AutoCloseable { + private final PrimitivIHybrid input; private final VDJCLibraryRegistry libraryRegistry; - private ClnsReader(PrimitivI input, VDJCLibraryRegistry libraryRegistry) { - this.input = input; - this.libraryRegistry = libraryRegistry; - } + private final PipelineConfiguration pipelineConfiguration; + private final VDJCAlignerParameters alignerParameters; + private final CloneAssemblerParameters assemblerParameters; + private final String versionInfo; + private final List genes; - public ClnsReader(InputStream inputStream, VDJCLibraryRegistry libraryRegistry) { - this(new PrimitivI(inputStream), libraryRegistry); - } + private final long clonesPosition; - public ClnsReader(File file, VDJCLibraryRegistry libraryRegistry) throws IOException { - this(IOUtil.createIS(file), libraryRegistry); + public ClnsReader(Path file, VDJCLibraryRegistry libraryRegistry) throws IOException { + this(file, 3, libraryRegistry); } - public ClnsReader(String file, VDJCLibraryRegistry libraryRegistry) throws IOException { - this(new File(file), libraryRegistry); + public ClnsReader(Path file, int concurrency, VDJCLibraryRegistry libraryRegistry) throws IOException { + this(file, new LambdaSemaphore(concurrency), libraryRegistry); } - private boolean initialized = false; - private CloneSet cloneSet = null; - private PipelineConfiguration pipelineConfiguration = null; - private VDJCAlignerParameters alignerParameters = null; - private CloneAssemblerParameters assemblerParameters = null; - - private synchronized void init() { - if (initialized) - return; + public ClnsReader(Path file, LambdaSemaphore concurrencyLimiter, VDJCLibraryRegistry libraryRegistry) throws IOException { + this(new PrimitivIHybrid(file, concurrencyLimiter), libraryRegistry); + } - // Registering custom serializer - //input.getSerializersManager().registerCustomSerializer(GeneFeature.class, new GeneFeatureSerializer(true)); + private ClnsReader(PrimitivIHybrid input, VDJCLibraryRegistry libraryRegistry) { + this.input = input; + this.libraryRegistry = libraryRegistry; - byte[] magicBytes = new byte[MAGIC_LENGTH]; - input.readFully(magicBytes); + try (PrimitivI i = input.beginPrimitivI(true)) { + byte[] magicBytes = new byte[MAGIC_LENGTH]; + i.readFully(magicBytes); - String magicString = new String(magicBytes); + String magicString = new String(magicBytes); - // SerializersManager serializersManager = input.getSerializersManager(); + // SerializersManager serializersManager = input.getSerializersManager(); - switch (magicString) { - case MAGIC: - break; - default: - throw new RuntimeException("Unsupported file format; .clns file of version " + magicString + - " while you are running MiXCR " + MAGIC); + switch (magicString) { + case MAGIC: + break; + default: + throw new RuntimeException("Unsupported file format; .clns file of version " + magicString + + " while you are running MiXCR " + MAGIC); + } } - String versionInfo = input.readUTF(); - - pipelineConfiguration = input.readObject(PipelineConfiguration.class); - alignerParameters = input.readObject(VDJCAlignerParameters.class); - assemblerParameters = input.readObject(CloneAssemblerParameters.class); - - // EnumMap alignedFeatures = IO.readGF2GTMap(input); - // List genes = IOUtil.readAndRegisterGeneReferences(input, libraryRegistry, new GT2GFAdapter(alignedFeatures)); + try (PrimitivI pi = this.input.beginRandomAccessPrimitivI(-IOUtil.END_MAGIC_LENGTH)) { + // Checking file consistency + byte[] endMagic = new byte[IOUtil.END_MAGIC_LENGTH]; + pi.readFully(endMagic); + if (!Arrays.equals(IOUtil.getEndMagicBytes(), endMagic)) + throw new RuntimeException("Corrupted file."); + } - List genes = IOUtil.stdVDJCPrimitivIStateInit(input, alignerParameters, libraryRegistry); + try (PrimitivI i = input.beginPrimitivI(true)) { + versionInfo = i.readUTF(); + pipelineConfiguration = i.readObject(PipelineConfiguration.class); + alignerParameters = i.readObject(VDJCAlignerParameters.class); + assemblerParameters = i.readObject(CloneAssemblerParameters.class); - int count = input.readInt(); - List clones = new ArrayList<>(count); - for (int i = 0; i < count; i++) - clones.add(input.readObject(Clone.class)); + genes = IOUtil.stdVDJCPrimitivIStateInit(i, alignerParameters, libraryRegistry); + } - this.cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters); - cloneSet.versionInfo = versionInfo; + this.clonesPosition = input.getPosition(); + } - initialized = true; + @Override + public OutputPortCloseable readClones() { + return input.beginRandomAccessPrimitivIBlocks(Clone.class, clonesPosition); } public CloneSet getCloneSet() { - init(); + List clones = new ArrayList<>(); + for (Clone clone : CUtils.it(readClones())) + clones.add(clone); + CloneSet cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters); + cloneSet.versionInfo = versionInfo; return cloneSet; } @Override public PipelineConfiguration getPipelineConfiguration() { - init(); return pipelineConfiguration; } public VDJCAlignerParameters getAlignerParameters() { - init(); return alignerParameters; } public CloneAssemblerParameters getAssemblerParameters() { - init(); return assemblerParameters; } @Override - public void close() { + public void close() throws IOException { input.close(); } - - public static class GT2GFAdapter implements HasFeatureToAlign { - public final EnumMap map; - - public GT2GFAdapter(EnumMap map) { - this.map = map; - } - - @Override - public GeneFeature getFeatureToAlign(GeneType geneType) { - return map.get(geneType); - } - } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index 5ded7141e..e233aa705 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -29,102 +29,103 @@ */ package com.milaboratory.mixcr.basictypes; +import cc.redberry.pipe.InputPort; import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.cli.PipelineConfigurationWriter; +import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.util.MiXCRVersionInfo; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivO; -import com.milaboratory.util.CanReportProgressAndStage; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneFeatureSerializer; +import com.milaboratory.primitivio.blocks.PrimitivOHybrid; +import io.repseq.core.VDJCGene; -import java.io.Closeable; import java.io.File; import java.io.IOException; -import java.io.OutputStream; import java.nio.charset.StandardCharsets; +import java.nio.file.Paths; +import java.util.List; /** * */ -// TODO implement with blocks -public class ClnsWriter implements PipelineConfigurationWriter, - CanReportProgressAndStage, - Closeable { - static final String MAGIC_V9 = "MiXCR.CLNS.V09"; - static final String MAGIC = MAGIC_V9; +public final class ClnsWriter implements PipelineConfigurationWriter, AutoCloseable { + static final String MAGIC_V10 = "MiXCR.CLNS.V10"; + static final String MAGIC = MAGIC_V10; static final int MAGIC_LENGTH = 14; static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII); final String stage = "Writing clones"; - final PrimitivO output; - final CloneSet cloneSet; - final int size; - final PipelineConfiguration configuration; + final PrimitivOHybrid output; private volatile int current; - public ClnsWriter(PipelineConfiguration configuration, CloneSet cloneSet, String fileName) throws IOException { - this(configuration, cloneSet, new File(fileName)); + public ClnsWriter(String fileName) throws IOException { + this(new PrimitivOHybrid(Paths.get(fileName))); } - public ClnsWriter(PipelineConfiguration configuration, CloneSet cloneSet, File file) throws IOException { - this(configuration, cloneSet, IOUtil.createOS(file)); + public ClnsWriter(File file) throws IOException { + this(new PrimitivOHybrid(file.toPath())); } - public ClnsWriter(PipelineConfiguration configuration, CloneSet cloneSet, OutputStream outputStream) { - this.output = new PrimitivO(outputStream); - this.configuration = configuration; - this.cloneSet = cloneSet; - this.size = cloneSet.size(); + public ClnsWriter(PrimitivOHybrid output) { + this.output = output; } - @Override - public String getStage() { - return stage; + public void writeHeaderFromCloneSet( + PipelineConfiguration configuration, + CloneSet cloneSet) { + writeHeader(configuration, + cloneSet.getAlignmentParameters(), + cloneSet.getAssemblerParameters(), + cloneSet.getUsedGenes(), cloneSet); } - @Override - public double getProgress() { - return (1.0 * current) / size; + public void writeHeader( + PipelineConfiguration configuration, + VDJCAlignerParameters alignmentParameters, + CloneAssemblerParameters assemblerParameters, + List genes, HasFeatureToAlign featureToAlign + ) { + try (PrimitivO o = output.beginPrimitivO(true)) { + // Writing magic bytes + o.write(MAGIC_BYTES); + + // Writing version information + o.writeUTF( + MiXCRVersionInfo.get().getVersionString( + AppVersionInfo.OutputType.ToFile)); + + // Writing analysis meta-information + o.writeObject(configuration); + o.writeObject(alignmentParameters); + o.writeObject(assemblerParameters); + + IOUtil.stdVDJCPrimitivOStateInit(o, genes, featureToAlign); + } } - @Override - public boolean isFinished() { - return current == size; + /** + * Must be closed by putting null + */ + public InputPort cloneWriter() { + return output.beginPrimitivOBlocks(3, 512); } - public void write() { - // Writing magic bytes - output.write(MAGIC_BYTES); - - // Writing version information - output.writeUTF( - MiXCRVersionInfo.get().getVersionString( - AppVersionInfo.OutputType.ToFile)); - - // Writing analysis meta-information - output.writeObject(configuration); - output.writeObject(cloneSet.alignmentParameters); - output.writeObject(cloneSet.assemblerParameters); - - // IO.writeGT2GFMap(output, cloneSet.alignedFeatures); - // IOUtil.writeAndRegisterGeneReferences(output, cloneSet.getUsedGenes(), new ClnsReader.GT2GFAdapter(cloneSet.alignedFeatures)); - IOUtil.stdVDJCPrimitivOStateInit(output, cloneSet.getUsedGenes(), cloneSet); - - output.writeInt(cloneSet.getClones().size()); - - for (Clone clone : cloneSet) { - output.writeObject(clone); - ++current; - } - - // Writing end-magic as a file integrity sign - output.write(IOUtil.getEndMagicBytes()); + public void writeCloneSet(PipelineConfiguration configuration, CloneSet cloneSet){ + writeHeaderFromCloneSet(configuration, cloneSet); + InputPort cloneIP = cloneWriter(); + for (Clone clone : cloneSet) + cloneIP.put(clone); + cloneIP.put(null); } @Override - public void close() { + public void close() throws IOException { + try (PrimitivO o = output.beginPrimitivO()) { + // Writing end-magic as a file integrity sign + o.write(IOUtil.getEndMagicBytes()); + } output.close(); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java new file mode 100644 index 000000000..a3fe740b5 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -0,0 +1,36 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.basictypes; + +import cc.redberry.pipe.OutputPortCloseable; + +public interface CloneReader { + OutputPortCloseable readClones(); +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java index 5d67871f6..4ac4086b0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java @@ -58,19 +58,11 @@ public static CloneSet read(File file, VDJCLibraryRegistry libraryRegistry) thro return r.readCloneSet(); } case MAGIC_CLNS: - try (ClnsReader r = new ClnsReader(file, libraryRegistry)) { + try (ClnsReader r = new ClnsReader(file.toPath(), libraryRegistry)) { return r.getCloneSet(); } default: throw new RuntimeException("Unsupported file type"); } } - - public static CloneSet readClns(InputStream inputStream) { - return readClns(inputStream, VDJCLibraryRegistry.getDefault()); - } - - public static CloneSet readClns(InputStream inputStream, VDJCLibraryRegistry libraryRegistry) { - return new ClnsReader(inputStream, libraryRegistry).getCloneSet(); - } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java index 0b268067c..a2934e559 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java @@ -34,6 +34,8 @@ import com.milaboratory.cli.PipelineConfigurationReader; import io.repseq.core.VDJCLibraryRegistry; +import java.nio.file.Paths; + import static com.milaboratory.mixcr.basictypes.IOUtil.*; /** @@ -92,7 +94,7 @@ public static PipelineConfiguration sFromFile(String fileName, BinaryFileInfo fi return reader.getPipelineConfiguration(); } case MAGIC_CLNS: - try (ClnsReader reader = new ClnsReader(fileName, VDJCLibraryRegistry.getDefault())) { + try (ClnsReader reader = new ClnsReader(Paths.get(fileName), VDJCLibraryRegistry.getDefault())) { return reader.getPipelineConfiguration(); } case MAGIC_CLNA: diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index efffe7c3d..3a037c6cf 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -323,9 +323,8 @@ public void run1() throws Exception { writer.writeAlignmentsAndIndex(); } } else - try (ClnsWriter writer = new ClnsWriter(pipelineConfiguration, cloneSet, out)) { - SmartProgressReporter.startProgressReport(writer); - writer.write(); + try (ClnsWriter writer = new ClnsWriter(out)) { + writer.writeCloneSet(getFullPipelineConfiguration(), cloneSet); } // Writing report diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index ac84110c1..2dcbf9c4d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -257,9 +257,8 @@ public void run1() throws Exception { clones[i] = clones[i].setId(i); CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters, cloneAssemblerParameters); - try (ClnsWriter writer = new ClnsWriter(getFullPipelineConfiguration(), cloneSet, out)) { - SmartProgressReporter.startProgressReport(writer); - writer.write(); + try (ClnsWriter writer = new ClnsWriter(out)) { + writer.writeCloneSet(getFullPipelineConfiguration(), cloneSet); } ReportWrapper reportWrapper = new ReportWrapper(ASSEMBLE_CONTIGS_COMMAND_NAME, report); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 747d6d3fc..23314b668 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -155,8 +155,8 @@ void processClns() throws IOException { CloneSet newCloneSet = new CloneSet(clones, cloneSet.getUsedGenes(), cloneSet.getAlignmentParameters(), cloneSet.getAssemblerParameters()); - try (ClnsWriter writer = new ClnsWriter(getFullPipelineConfiguration(), newCloneSet, out)) { - writer.write(); + try (ClnsWriter writer = new ClnsWriter(out)) { + writer.writeCloneSet(getFullPipelineConfiguration(), newCloneSet); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 2b81dd890..86735d561 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -144,9 +144,8 @@ public String toString() { private void runClns() throws Exception { CloneSet cloneSet = CloneSetIO.read(in); CloneSet resultCloneSet = doClustering(cloneSet, null); - try (ClnsWriter writer = new ClnsWriter(getFullPipelineConfiguration(), resultCloneSet, out)) { - SmartProgressReporter.startProgressReport(writer); - writer.write(); + try (ClnsWriter writer = new ClnsWriter(out)) { + writer.writeCloneSet(getFullPipelineConfiguration(), resultCloneSet); } } diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index 6d2909880..e2b0cb66a 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -49,8 +49,6 @@ import org.junit.Ignore; import org.junit.Test; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.util.Arrays; @@ -129,12 +127,13 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException CloneSet cloneSet = assemblerRunner.getCloneSet(null); - ByteArrayOutputStream bos = new ByteArrayOutputStream(); - try (ClnsWriter writer = new ClnsWriter(null, cloneSet, bos)) { - writer.write(); + File tmpClnsFile = TempFileManager.getTempFile(); + + try (ClnsWriter writer = new ClnsWriter(tmpClnsFile)) { + writer.writeCloneSet(null, cloneSet); } - CloneSet cloneSetDeserialized = CloneSetIO.readClns(new ByteArrayInputStream(bos.toByteArray())); + CloneSet cloneSetDeserialized = CloneSetIO.read(tmpClnsFile); assertCSEquals(cloneSet, cloneSetDeserialized); diff --git a/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java b/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java index ff5fee3a0..1f5f31849 100644 --- a/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java @@ -76,8 +76,8 @@ public void testIO() throws Exception { RunMiXCR.AssembleResult assemble = RunMiXCR.assemble(align); File tempFile = TempFileManager.getTempFile(); - try (ClnsWriter writer = new ClnsWriter(null, assemble.cloneSet, tempFile)) { - writer.write(); + try (ClnsWriter writer = new ClnsWriter(tempFile)) { + writer.writeCloneSet(null, assemble.cloneSet); } CloneSet read = CloneSetIO.read(tempFile); From 7b32548f4d4fa498dbd23c122ad7895cc88491e2 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Fri, 19 Jun 2020 13:10:54 +0300 Subject: [PATCH 061/282] Timestamps for integration tests logs. --- .circleci/config.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 95418127e..94f7600b6 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,6 +13,12 @@ jobs: steps: - checkout + - run: + name: Installing moreutils + command: | + sudo apt-get update + sudo apt-get install -y moreutils + - run: name: Downloading git submodules command: git submodule update --init --recursive @@ -68,4 +74,4 @@ jobs: - run: name: Running MiXCR Integration tests - command: ./itests.sh test + command: ./itests.sh test | ts From 4d30db03ef39481ea48604762bc8cf65cfdcd7e8 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Fri, 26 Jun 2020 15:58:00 +0300 Subject: [PATCH 062/282] Regression tests. --- .circleci/config.yml | 2 +- itests.sh | 2 +- itests/case8.sh | 49 +++++++++++++++++++ .../mixcr/cli/CommandAnalyze.java | 41 ++++++++++------ 4 files changed, 77 insertions(+), 17 deletions(-) create mode 100755 itests/case8.sh diff --git a/.circleci/config.yml b/.circleci/config.yml index 94f7600b6..b7cddc177 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -73,5 +73,5 @@ jobs: key: v1-dependencies-{{ checksum "pom.xml" }}-{{ checksum "milib/pom.xml" }}-{{ checksum "repseqio/pom.xml" }} - run: - name: Running MiXCR Integration tests + name: Running MiXCR Integration and Regression tests command: ./itests.sh test | ts diff --git a/itests.sh b/itests.sh index 1a6b1a59c..b6fbdeea4 100755 --- a/itests.sh +++ b/itests.sh @@ -48,7 +48,7 @@ case $os in ;; esac -tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7") +tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8") create_standard_results=false run_tests=false diff --git a/itests/case8.sh b/itests/case8.sh new file mode 100755 index 000000000..02caaf06a --- /dev/null +++ b/itests/case8.sh @@ -0,0 +1,49 @@ +#!/usr/bin/env bash + +# Regression Test #1 + +assert() { + expected=$(echo -ne "${2:-}") + result="$(eval 2>/dev/null $1)" || true + if [[ "$result" == "$expected" ]]; then + return + fi + result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")" + [[ -z "$result" ]] && result="nothing" || result="\"$result\"" + [[ -z "$2" ]] && expected="nothing" || expected="\"$2\"" + echo "expected $expected got $result for" "$1" + exit 1 +} + +set -e + +mixcr analyze amplicon \ + -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present \ + --assemble '-OseparateByC=true' --assemble '-OseparateByV=true' --assemble '-OseparateByJ=true' \ + --impute-germline-on-export --json-report case8 \ + CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case8 + +assert "cat case8.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197562" +assert "cat case8.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161627" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "223" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "1378" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22402" + +##mixcr analyze amplicon --assemble '-OcloneClusteringParameters=null' --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present case5_R1.fastq case5_R2.fastq case5 +# +#mixcr exportAlignments -f -readIds -cloneIdWithMappingType case5.clna case5.als.txt +# +#sort -t $'\t' --key=1 -n case5.als.txt | tail -n +2 > case5.als.sorted.txt +# +#lines=$(cat case5.als.sorted.txt | wc -l) +# +#head -n $((lines/2)) case5.als.sorted.txt | cut -f2 > case5.als.sorted.1.txt +#tail -n $((lines/2)) case5.als.sorted.txt | cut -f2 > case5.als.sorted.2.txt +# +#if cmp case5.als.sorted.1.txt case5.als.sorted.2.txt; then +# echo "All good" +#else +# echo "Results are different" +# diff case5.als.sorted.1.txt case5.als.sorted.2.txt +#fi diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index 924892981..35179b072 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -286,6 +286,10 @@ public void setStartingMaterial(String value) { @Option(names = {"-r", "--report"}, description = "Report file path") public String report = null; + @Option(names = {"-j", "--json-report"}, description = "Output json reports for each of the analysis steps. " + + "Individual file will be created for each type of analysis step, value specified for this option will be used as a prefix.") + public String jsonReport = null; + @Option(names = {"-b", "--library"}, description = "V/D/J/C gene library") public String library = "default"; @@ -357,6 +361,18 @@ private void inheritThreads(List args, List specificArgs) { } } + void addReportOptions(String step, List options) { + // add report file + options.add("--report"); + options.add(getReport()); + + // add json report file + if (jsonReport != null) { + options.add("--json-report"); + options.add(jsonReport + "." + step + ".jsonl"); + } + } + CommandAlign mkAlign() { // align parameters List alignParameters = new ArrayList<>(initialAlignParameters); @@ -374,9 +390,8 @@ CommandAlign mkAlign() { inheritThreads(alignParameters, this.alignParameters); - // add report file - alignParameters.add("--report"); - alignParameters.add(getReport()); + // adding report options + addReportOptions("align", alignParameters); if (!forceUseRnaSeqOps() && !chains.intersects(Chains.TCR)) alignParameters.add("-p kAligner2"); @@ -428,9 +443,8 @@ CommandAlign mkAlign() { public final CommandAssemblePartialAlignments mkAssemblePartial(String input, String output) { List assemblePartialParameters = new ArrayList<>(); - // add report file - assemblePartialParameters.add("--report"); - assemblePartialParameters.add(getReport()); + // adding report options + addReportOptions("assemblePartial", assemblePartialParameters); // add all override parameters assemblePartialParameters.addAll(this.assemblePartialParameters); @@ -457,9 +471,8 @@ public final CommandAssemblePartialAlignments mkAssemblePartial(String input, St public final CommandExtend mkExtend(String input, String output) { List extendParameters = new ArrayList<>(); - // add report file - extendParameters.add("--report"); - extendParameters.add(getReport()); + // adding report options + addReportOptions("extend", extendParameters); inheritThreads(extendParameters, this.extendAlignmentsParameters); @@ -493,9 +506,8 @@ public CommandAssemble getAssemble(String input, String output) { CommandAssemble mkAssemble(String input, String output) { List assembleParameters = new ArrayList<>(); - // add report file - assembleParameters.add("--report"); - assembleParameters.add(getReport()); + // adding report options + addReportOptions("assemble", assembleParameters); if (contigAssembly) assembleParameters.add("--write-alignments"); @@ -533,9 +545,8 @@ CommandAssemble mkAssemble(String input, String output) { public final CommandAssembleContigs mkAssembleContigs(String input, String output) { List assembleContigParameters = new ArrayList<>(); - // add report file - assembleContigParameters.add("--report"); - assembleContigParameters.add(getReport()); + // adding report options + addReportOptions("assembleContigs", assembleContigParameters); inheritThreads(assembleContigParameters, this.assembleContigParameters); From a43f8d2b9524e0eea23f14d0013bb468e0cfcdbb Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 30 Jun 2020 12:17:54 +0300 Subject: [PATCH 063/282] Clone sorting (#6) * WIP, integration testing required, more tests on the way * More tests. * CMergeStrategy * WIP * - CrelationTest * WIP * WIPWIP * - calculateStrategy * Migration to Collation in ClnaWriter. * Bigger memory budget for ClnaWriter. * WIP * --highCompression flag. * WIP * milib upgrade. * Refactoring of sorting / collation API. * WIP * Requires testing. * MiLib submodule update. * No reindexing. * Additional regression test. * Fixes. * All done. * MiLib submodule upgrade. Co-authored-by: Mark Izraelson --- itests.sh | 2 +- itests/case8.sh | 18 -- itests/case9.sh | 32 ++ milib | 2 +- repseqio | 2 +- .../mixcr/assembler/CloneAssembler.java | 15 +- .../mixcr/basictypes/ClnAReader.java | 64 ++-- .../mixcr/basictypes/ClnAWriter.java | 277 ++++++++++-------- .../mixcr/basictypes/ClnsReader.java | 12 +- .../mixcr/basictypes/ClnsWriter.java | 11 +- .../mixcr/basictypes/CloneReader.java | 11 + .../mixcr/basictypes/CloneSet.java | 31 +- .../milaboratory/mixcr/basictypes/IOUtil.java | 29 +- .../basictypes/VDJCAlignmentsWriter.java | 32 +- .../mixcr/basictypes/VDJCObject.java | 26 +- .../mixcr/basictypes/VDJCSProperties.java | 257 ++++++++++++++++ .../milaboratory/mixcr/cli/CommandAlign.java | 6 +- .../mixcr/cli/CommandAssemble.java | 61 +++- .../mixcr/cli/CommandAssembleContigs.java | 12 +- .../cli/CommandExportAlignmentsForClones.java | 4 +- .../milaboratory/mixcr/cli/CommandExtend.java | 10 +- .../mixcr/cli/CommandGroupCells.java | 19 +- .../milaboratory/mixcr/cli/CommandSlice.java | 4 +- .../mixcr/cli/CommandSortAlignments.java | 2 +- .../milaboratory/mixcr/util/MiXCRDebug.java | 38 +++ .../com/milaboratory/mixcr/util/RunMiXCR.java | 12 +- .../mixcr/basictypes/ClnAReaderTest.java | 56 +++- .../mixcr/basictypes/VDJCSPropertiesTest.java | 76 +++++ 28 files changed, 828 insertions(+), 293 deletions(-) create mode 100755 itests/case9.sh create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java create mode 100644 src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java create mode 100644 src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java diff --git a/itests.sh b/itests.sh index b6fbdeea4..b727e8ded 100755 --- a/itests.sh +++ b/itests.sh @@ -48,7 +48,7 @@ case $os in ;; esac -tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8") +tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8" "case9") create_standard_results=false run_tests=false diff --git a/itests/case8.sh b/itests/case8.sh index 02caaf06a..caf1f62ce 100755 --- a/itests/case8.sh +++ b/itests/case8.sh @@ -29,21 +29,3 @@ assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "1378" assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22402" - -##mixcr analyze amplicon --assemble '-OcloneClusteringParameters=null' --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present case5_R1.fastq case5_R2.fastq case5 -# -#mixcr exportAlignments -f -readIds -cloneIdWithMappingType case5.clna case5.als.txt -# -#sort -t $'\t' --key=1 -n case5.als.txt | tail -n +2 > case5.als.sorted.txt -# -#lines=$(cat case5.als.sorted.txt | wc -l) -# -#head -n $((lines/2)) case5.als.sorted.txt | cut -f2 > case5.als.sorted.1.txt -#tail -n $((lines/2)) case5.als.sorted.txt | cut -f2 > case5.als.sorted.2.txt -# -#if cmp case5.als.sorted.1.txt case5.als.sorted.2.txt; then -# echo "All good" -#else -# echo "Results are different" -# diff case5.als.sorted.1.txt case5.als.sorted.2.txt -#fi diff --git a/itests/case9.sh b/itests/case9.sh new file mode 100755 index 000000000..e67d08e26 --- /dev/null +++ b/itests/case9.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +# Regression Test #2 + +assert() { + expected=$(echo -ne "${2:-}") + result="$(eval 2>/dev/null $1)" || true + if [[ "$result" == "$expected" ]]; then + return + fi + result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")" + [[ -z "$result" ]] && result="nothing" || result="\"$result\"" + [[ -z "$2" ]] && expected="nothing" || expected="\"$2\"" + echo "expected $expected got $result for" "$1" + exit 1 +} + +set -e + +mixcr analyze amplicon \ + -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present \ + --assemble '-OseparateByC=true' --assemble '-OseparateByV=true' --assemble '-OseparateByJ=true' \ + --assemble '--sort-by-sequence' \ + --impute-germline-on-export --json-report case9 \ + CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case9 + +assert "cat case9.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197562" +assert "cat case9.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161627" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "223" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "1378" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22402" diff --git a/milib b/milib index 71689b469..9feb34a69 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 71689b4699a003393373cbf4d152858a79c24bd7 +Subproject commit 9feb34a69c52db3a6e12562a2c0ab74ff7221ec8 diff --git a/repseqio b/repseqio index 5b3d1a2ff..476bf935b 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 5b3d1a2ff7158e5735de11b5e8e23badf42bd8a7 +Subproject commit 476bf935bb15610ef6af5f772076df5ad59d5428 diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index dd50255de..66a2ff02f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -127,7 +127,10 @@ public ArrayList create() { } }; - public CloneAssembler(CloneAssemblerParameters parameters, boolean logAssemblerEvents, Collection genes, EnumMap featuresToAlign) { + public CloneAssembler(CloneAssemblerParameters parameters, + boolean logAssemblerEvents, + Collection genes, + EnumMap featuresToAlign) { if (!parameters.isComplete()) throw new IllegalArgumentException("Not complete parameters"); this.parameters = parameters.clone(); @@ -345,13 +348,7 @@ public void close() { } public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters) { - // EnumMap features = new EnumMap<>(GeneType.class); - // for (GeneType geneType : GeneType.values()) { - // GeneFeature gf = featuresToAlign.get(geneType); - // if (gf != null) - // features.put(geneType, gf); - // } - return new CloneSet(Arrays.asList(realClones), usedGenes.values(), alignerParameters, parameters); + return new CloneSet(Arrays.asList(realClones), usedGenes.values(), alignerParameters, parameters, new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); } public OutputPortCloseable getAssembledReadsPort() { @@ -907,7 +904,7 @@ public int compare(CloneAccumulator o1, CloneAccumulator o2) { } }; - public static int compareByBestHists(CloneAccumulator o1, CloneAccumulator o2, GeneType geneType) { + private static int compareByBestHists(CloneAccumulator o1, CloneAccumulator o2, GeneType geneType) { VDJCGeneId a1 = o1.getBestGene(geneType); VDJCGeneId a2 = o2.getBestGene(geneType); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index cc002c644..afdb0f9d7 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -29,6 +29,7 @@ */ package com.milaboratory.mixcr.basictypes; +import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.cli.PipelineConfiguration; @@ -37,6 +38,7 @@ import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.blocks.*; import com.milaboratory.util.CanReportProgress; +import gnu.trove.map.hash.TIntIntHashMap; import io.repseq.core.GeneFeature; import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; @@ -61,11 +63,15 @@ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implement // Index data final long firstClonePosition; - // Index contain two additional records: - // - first = position of alignment block with cloneIndex == -1 - // - last = position of the last alignments block end + /** last element = position of the last alignments block end */ final long[] index; + /** First record always zero */ final long[] counts; + /** + * cloneId -> index in index + * e.g. alignments for clone with id0 starts from position index[cloneMapping.get(id0)] + */ + final TIntIntHashMap cloneIdIndex; final long totalAlignmentsCount; // From constructor @@ -77,6 +83,7 @@ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implement final PipelineConfiguration configuration; final VDJCAlignerParameters alignerParameters; final CloneAssemblerParameters assemblerParameters; + final VDJCSProperties.CloneOrdering ordering; final List genes; @@ -121,14 +128,21 @@ public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int concurrenc // Step back try (PrimitivI pi = this.input.beginRandomAccessPrimitivI(indexBegin)) { + int indexSize = pi.readVarInt(); + + assert indexSize == numberOfClones + 1 || indexSize == numberOfClones + 2; + // Reading index data - this.index = new long[numberOfClones + 2]; - this.counts = new long[numberOfClones + 2]; + this.index = new long[indexSize]; + this.counts = new long[indexSize]; + this.cloneIdIndex = new TIntIntHashMap(indexSize - 1); long previousValue = 0; long totalAlignmentsCount = 0; - for (int i = 0; i < numberOfClones + 2; i++) { + for (int i = 0; i < indexSize; i++) { previousValue = index[i] = previousValue + pi.readVarLong(); totalAlignmentsCount += counts[i] = pi.readVarLong(); + if (i != indexSize - 1) + cloneIdIndex.put(pi.readVarInt(), i); } this.totalAlignmentsCount = totalAlignmentsCount; } @@ -146,6 +160,7 @@ public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int concurrenc this.configuration = pi.readObject(PipelineConfiguration.class); this.alignerParameters = pi.readObject(VDJCAlignerParameters.class); this.assemblerParameters = pi.readObject(CloneAssemblerParameters.class); + this.ordering = pi.readObject(VDJCSProperties.CloneOrdering.class); this.genes = IOUtil.stdVDJCPrimitivIStateInit(pi, this.alignerParameters, libraryRegistry); } } @@ -173,6 +188,14 @@ public CloneAssemblerParameters getAssemblerParameters() { return assemblerParameters; } + /** + * Clone ordering + */ + @Override + public VDJCSProperties.CloneOrdering ordering() { + return ordering; + } + public GeneFeature[] getAssemblingFeatures() { return assemblerParameters.getAssemblingFeatures(); } @@ -202,7 +225,7 @@ public long numberOfAlignments() { * @return number of alignments */ public long numberOfAlignmentsInClone(int cloneIndex) { - return counts[cloneIndex + 1]; + return counts[cloneIdIndex.get(cloneIndex) + 1]; } /** @@ -225,7 +248,7 @@ public CloneSet readCloneSet() throws IOException { clones.add(reader.take()); } - return new CloneSet(clones, genes, alignerParameters, assemblerParameters); + return new CloneSet(clones, genes, alignerParameters, assemblerParameters, ordering); } /** @@ -242,7 +265,11 @@ public OutputPortCloseable readClones() { * @param cloneIndex index of clone; -1 to read unassembled alignments */ public OutputPortCloseable readAlignmentsOfClone(int cloneIndex) { - return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, index[cloneIndex + 1], HEADER_ACTION_STOP_AT_ALIGNMENT_BLOCK_END); + if (cloneIndex == -1 && !cloneIdIndex.containsKey(-1)) + return CUtils.EMPTY_OUTPUT_PORT_CLOSEABLE; + return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, + index[cloneIdIndex.get(cloneIndex)], + HEADER_ACTION_STOP_AT_ALIGNMENT_BLOCK_END); } /** @@ -252,13 +279,6 @@ public OutputPortCloseable readAllAlignments() { return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, index[0]); } - /** - * Constructs output port to read all alignments that are attached to a clone. Alignments are sorted by cloneIndex. - */ - public OutputPortCloseable readAssembledAlignments() { - return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, index[1]); - } - /** * Constructs output port to read alignments that are not attached to any clone. Alignments are sorted by * cloneIndex. @@ -273,7 +293,7 @@ public OutputPortCloseable readNotAssembledAlignments() { * Constructs output port of CloneAlignments objects, that allows to get synchronised view on clone and it's * corresponding alignments */ - public CloneAlignmentsPort clonesAndAlignments() throws IOException { + public CloneAlignmentsPort clonesAndAlignments() { return new CloneAlignmentsPort(); } @@ -286,7 +306,7 @@ public final class CloneAlignmentsPort CloneAlignmentsPort() { this.clones = input.beginRandomAccessPrimitivIBlocks(Clone.class, firstClonePosition); - this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, genes, alignerParameters, assemblerParameters); + this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, genes, alignerParameters, assemblerParameters, ordering); } @Override @@ -327,7 +347,7 @@ public final class CloneAlignments { CloneAlignments(Clone clone, int cloneId) { this.clone = clone; this.cloneId = cloneId; - this.alignmentsCount = counts[cloneId + 1]; + this.alignmentsCount = numberOfAlignmentsInClone(cloneId); } /** @@ -347,10 +367,4 @@ public void close() throws IOException { h -> h.equals(ClnAWriter.ALIGNMENT_BLOCK_SEPARATOR) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); - - // private static Function> HEADER_ACTION_STOP_AT_ALIGNMENTS_END = - // h -> h.equals(ClnAWriter.ALIGNMENTS_END) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); - - // private static Function> HEADER_ACTION_STOP_AT_CLONES_END = - // h -> h.equals(ClnAWriter.CLONES_END) ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.skip(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index 97bbacdbb..a2e0d8b88 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -29,35 +29,40 @@ */ package com.milaboratory.mixcr.basictypes; -import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.CountingOutputPort; import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.cli.PipelineConfigurationWriter; +import com.milaboratory.mixcr.util.MiXCRDebug; import com.milaboratory.mixcr.util.MiXCRVersionInfo; -import com.milaboratory.primitivio.PipeDataInputReader; -import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.PrimitivIOStateBuilder; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.blocks.PrimitivIOBlockHeader; +import com.milaboratory.primitivio.blocks.PrimitivIOBlocksUtil; import com.milaboratory.primitivio.blocks.PrimitivOBlocks; import com.milaboratory.primitivio.blocks.PrimitivOHybrid; import com.milaboratory.util.CanReportProgressAndStage; -import com.milaboratory.util.ObjectSerializer; -import com.milaboratory.util.Sorter; +import com.milaboratory.util.HashFunctions; +import com.milaboratory.util.TempFileManager; import com.milaboratory.util.io.HasPosition; +import com.milaboratory.util.sorting.HashSorter; +import gnu.trove.list.array.TIntArrayList; import gnu.trove.list.array.TLongArrayList; -import io.repseq.core.GeneType; +import gnu.trove.set.hash.TIntHashSet; import io.repseq.core.VDJCGene; import java.io.File; import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; import java.nio.charset.StandardCharsets; -import java.util.*; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Comparator; +import java.util.List; +import java.util.Objects; import java.util.concurrent.ForkJoinPool; +import java.util.function.ToIntFunction; /** * Writer for CLNA file format. @@ -76,43 +81,51 @@ public final class ClnAWriter implements PipelineConfigurationWriter, * Separates blocks of alignments assigned to the same clonotype */ static final PrimitivIOBlockHeader ALIGNMENT_BLOCK_SEPARATOR = PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, (byte) 1); - // /** - // * Added after the last alignments block - // */ - // static final PrimitivIOBlockHeader ALIGNMENTS_END = PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, (byte) 2); - // /** - // * Added after the clones block - // */ - // static final PrimitivIOBlockHeader CLONES_END = PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, (byte) 3); /** * Will be used for alignments pre-sorting */ - private final File tempFile; - /** - * Used to read current position in output file - */ - // private final CountingOutputStream outputStream; - // private final PrimitivO output; + private final Path tempFolder; + + private final boolean highCompression; + private final PrimitivOHybrid output; private final PipelineConfiguration configuration; /** * Counter OP used to report progress during stage 2 */ - private volatile CountingOutputPort toSorter; + private volatile CountingOutputPort toCollator; private volatile int numberOfClones = -1, numberOfClonesWritten = 0; - private volatile OutputPortCloseable sortedAlignments = null; + /** + * Clone ids written to the clones section + */ + private volatile TIntHashSet cloneIds = null; + private volatile HashSorter collator; + private volatile OutputPortCloseable collatedAlignments = null; private volatile long numberOfAlignments = -1, numberOfAlignmentsWritten = 0; - private volatile boolean clonesBlockFinished = false, finished = false; + private volatile boolean finished = false; public ClnAWriter(PipelineConfiguration configuration, String fileName) throws IOException { - this(configuration, new File(fileName)); + this(configuration, fileName, false); + } + + public ClnAWriter(PipelineConfiguration configuration, String fileName, boolean highCompression) throws IOException { + this(configuration, new File(fileName), highCompression); } public ClnAWriter(PipelineConfiguration configuration, File file) throws IOException { + this(configuration, file, false); + } + + public ClnAWriter(PipelineConfiguration configuration, File file, boolean highCompression) throws IOException { this.configuration = configuration; - this.tempFile = new File(file.getAbsolutePath() + ".presorted"); + this.highCompression = highCompression; + File tempFolder = new File(file.getAbsolutePath() + ".presorted"); + TempFileManager.register(tempFolder); + this.tempFolder = tempFolder.toPath(); + Files.createDirectory(this.tempFolder); + this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file.toPath()); try (PrimitivO o = this.output.beginPrimitivO()) { o.write(MAGIC.getBytes(StandardCharsets.US_ASCII)); @@ -129,7 +142,7 @@ public ClnAWriter(PipelineConfiguration configuration, File file) throws IOExcep */ public synchronized void writeClones(CloneSet cloneSet) { // Checking state - if (clonesBlockFinished) + if (cloneIds != null) throw new IllegalArgumentException("Clone block was already written."); // Saving VDJC gene list @@ -154,8 +167,9 @@ public synchronized void writeClones(CloneSet cloneSet) { o.writeObject(cloneSet.alignmentParameters); featureToAlignProvider = cloneSet.alignmentParameters; - // Writing assembler parameters + // Writing assembler parameters and cloneset ordering o.writeObject(cloneSet.assemblerParameters); + o.writeObject(cloneSet.ordering); // During deserialization, the same procedure (in the same order) will be applied to // the PrimitivI object, so that correct singleton objects (GeneFeature objects and sequences) will be @@ -173,7 +187,8 @@ public synchronized void writeClones(CloneSet cloneSet) { numberOfClones = cloneSet.size(); } - try (PrimitivOBlocks.Writer writer = this.output.beginPrimitivOBlocks(4, 1024)) { + try (PrimitivOBlocks.Writer writer = this.output.beginPrimitivOBlocks(4, 1024, + PrimitivIOBlocksUtil.highLZ4Compressor())) { // Writing clones for (Clone clone : cloneSet) { writer.write(clone); @@ -181,22 +196,23 @@ public synchronized void writeClones(CloneSet cloneSet) { ++numberOfClonesWritten; } writer.flush(); - // writer.writeHeader(CLONES_END); } // will synchronize here (on close method invocation) - // Setting flag telling other methods that clones block was written successfully - clonesBlockFinished = true; + // Saving ids; also tells other methods that clones block was written successful + TIntHashSet ids = new TIntHashSet(cloneSet.getClones().stream().mapToInt(c -> c.id).toArray()); + ids.add(-1); + this.cloneIds = ids; } /** * Step 2 */ - public synchronized void sortAlignments(OutputPort alignments, - long numberOfAlignments) throws IOException { + public synchronized void collateAlignments(OutputPort alignments, + long numberOfAlignments) throws IOException { // Checking state - if (!clonesBlockFinished) + if (cloneIds == null) throw new IllegalStateException("Write clones before writing alignments."); - if (sortedAlignments != null) + if (collatedAlignments != null) throw new IllegalStateException("Alignments are already sorted."); // Saving number of alignments @@ -208,53 +224,26 @@ public synchronized void sortAlignments(OutputPort alignments, // Sorting alignments by cloneId and then by mapping type (core alignments will be written before all others) // and saving sorting output port - this.toSorter = new CountingOutputPort<>(alignments); - this.sortedAlignments = Sorter.sort( - toSorter, - Comparator.comparingInt((VDJCAlignments o) -> o.cloneIndex).thenComparingInt(o -> o.mappingType), - chunkSize, - new VDJCAlignmentsSerializer(usedGenes, featureToAlignProvider), - tempFile); - } - - public static final class VDJCAlignmentsSerializer implements ObjectSerializer { - private final List genes; - private final HasFeatureToAlign featureToAlign; - - public VDJCAlignmentsSerializer(List genes, HasFeatureToAlign featureToAlign) { - Objects.requireNonNull(genes); - Objects.requireNonNull(featureToAlign); - this.genes = genes; - this.featureToAlign = featureToAlign; - } - - @Override - public void write(Collection data, OutputStream stream) { - PrimitivO primitivO = new PrimitivO(stream); - // Initializing PrimitivO object (see big comment block in writeClones(...) method - IOUtil.registerGeneReferencesO(primitivO, genes, featureToAlign); - for (VDJCAlignments alignments : data) { - // Checking that alignments has the same alignedFeature as was in cloneSet - assert Arrays.stream(GeneType.values()) - .allMatch(gt -> Optional - .ofNullable(alignments.getBestHit(gt)) - .map(VDJCHit::getAlignedFeature) - .map(f -> f.equals(featureToAlign.getFeatureToAlign(gt))) - .orElse(true)); - // Writing alignment - primitivO.writeObject(alignments); - } - // Writing null in the end of the stream to detect end of block during deserialization - primitivO.writeObject(null); - } - - @Override - public OutputPort read(InputStream stream) { - PrimitivI primitivI = new PrimitivI(stream); - IOUtil.registerGeneReferencesI(primitivI, genes, featureToAlign); - // Will end on null object, that was added to the stream - return new PipeDataInputReader<>(VDJCAlignments.class, primitivI); - } + this.toCollator = new CountingOutputPort<>(alignments); + + // Optimize serialization of genes and corresponding subject sequences from alignments + PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); + IOUtil.registerGeneReferences(stateBuilder, usedGenes, featureToAlignProvider); + + // HDD-offloading collator of alignments + // Collate solely by cloneId (no sorting by mapping type, etc.); + // less fields to sort by -> faster the procedure + collator = new HashSorter<>( + VDJCAlignments.class, + new CloneIdHash(), CloneIdComparator, + 5, tempFolder, 4, 6, + stateBuilder.getOState(), stateBuilder.getIState(), + 1 << 28 /* 256 Mb */, 512); + + // Here we wait for the first layer of hash collation to finish "write" stage + // (on average 30% time of full collation process) + // following steps are executed as needed during port reading + this.collatedAlignments = collator.port(toCollator); } /** @@ -262,7 +251,7 @@ public OutputPort read(InputStream stream) { */ public synchronized void writeAlignmentsAndIndex() { // Checking state - if (sortedAlignments == null) + if (collatedAlignments == null) throw new IllegalStateException("Call sortAlignments before this method."); if (finished) throw new IllegalStateException("Writer already closed."); @@ -270,79 +259,96 @@ public synchronized void writeAlignmentsAndIndex() { // Indices that will be written below all alignments final TLongArrayList aBlockOffset = new TLongArrayList(); final TLongArrayList aBlockCount = new TLongArrayList(); + final TIntArrayList cloneIdsIndex = new TIntArrayList(); long previousAlsCount = 0; - int currentCloneIndex = -1; + int currentCloneIndex = Integer.MIN_VALUE; long indexBeginOffset; try (PrimitivOBlocks.Writer o = output.beginPrimitivOBlocks( Math.min(4, Runtime.getRuntime().availableProcessors()), // TODO parametrize - VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK)) { + VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK, + highCompression + ? PrimitivIOBlocksUtil.highLZ4Compressor() + : PrimitivIOBlocksUtil.fastLZ4Compressor())) { - // Position of alignments with cloneIndex = -1 (not aligned alignments) - aBlockOffset.add(o.getPosition()); - - // List block = new ArrayList<>(); // Writing alignments and writing indices - for (VDJCAlignments alignments : CUtils.it(sortedAlignments)) { - // End of clone - if (currentCloneIndex != alignments.cloneIndex) { - - // Async flush - o.flush(); - o.writeHeader(ALIGNMENT_BLOCK_SEPARATOR); + VDJCAlignments alignments; + while (true) { + alignments = collatedAlignments.take(); + + // End of clone group or first alignment + if (alignments == null || currentCloneIndex != alignments.cloneIndex) { + if (currentCloneIndex != Integer.MIN_VALUE) { // Not first alignment + // Async flush + o.flush(); + o.writeHeader(ALIGNMENT_BLOCK_SEPARATOR); + } // No synchronization here - ++currentCloneIndex; - if (currentCloneIndex != alignments.cloneIndex) - throw new IllegalArgumentException("No alignments for clone number " + currentCloneIndex); - if (alignments.cloneIndex >= numberOfClones) - throw new IllegalArgumentException("Out of range clone Index in alignment: " + currentCloneIndex); + if (alignments != null && !cloneIds.remove(alignments.cloneIndex)) + throw new IllegalArgumentException("Alignment for a wrong clonotype " + + alignments.cloneIndex); // Write stream position as soon as all the blocks are flushed // This will be the start position for the next block o.run(c -> { - // In theory synchronization for aBlockOffset access here is not required as all the IO + // In theory synchronization for aBlockOffset access here is not required as all IO // operations as well as this code are executed strictly sequentially - //synchronized (aBlockOffset){ + // synchronized (aBlockOffset){ aBlockOffset.add(((HasPosition) c).getPosition()); - //} + // } }); aBlockCount.add(numberOfAlignmentsWritten - previousAlsCount); previousAlsCount = numberOfAlignmentsWritten; + + if (alignments == null) + break; + + // Saving clone groups sequence + cloneIdsIndex.add(alignments.cloneIndex); + currentCloneIndex = alignments.cloneIndex; } o.write(alignments); ++numberOfAlignmentsWritten; } - // Writing last block, and waiting for all the data to be flushed - o.flush(); - o.writeHeader(ALIGNMENT_BLOCK_SEPARATOR); - // o.writeHeader(ALIGNMENTS_END); + if (!(cloneIds.isEmpty() || + (cloneIds.size() == 1 && cloneIds.iterator().next() == -1))) + throw new IllegalArgumentException("Some clones have no alignments."); + + // Waiting for all alignments to be flushed to the file to read file position o.sync(); - // Writing position of last alignments block end - aBlockOffset.add(o.getPosition()); + assert aBlockOffset.size() == aBlockCount.size() + && aBlockCount.size() == cloneIdsIndex.size() + 1 + // there may be no alignments with cloneId == -1 + && (numberOfClones + 1 == cloneIdsIndex.size() || numberOfClones == cloneIdsIndex.size()); + // o.close() will additionally write EOF header indexBeginOffset = o.getPosition() + PrimitivIOBlockHeader.HEADER_SIZE; - } - // Closing sorted output port, this will delete presorted file - sortedAlignments.close(); - - // Writing count of alignments in the last block - aBlockCount.add(numberOfAlignmentsWritten - previousAlsCount); + // Print IO stat + if (MiXCRDebug.DEBUG) { + System.out.println("==== IO ClnAWriter: Collator ====="); + collator.printStat(); + System.out.println("==== IO ClnAWriter ====="); + System.out.println(o.getParent().getStats()); + } + } - // To make counts index the same length as aBlockOffset - aBlockCount.add(0); + // Closing sorted the output port, this will delete intermediate collation files + collatedAlignments.close(); // Saving index offset in file to write in the end of the stream long previousValue = 0; + try (PrimitivO o = output.beginPrimitivO()) { // TODO also use blocks ? + // Writing index size + o.writeVarInt(aBlockOffset.size()); - try (PrimitivO o = output.beginPrimitivO()) { // Writing both indices for (int i = 0; i < aBlockOffset.size(); i++) { long iValue = aBlockOffset.get(i); @@ -352,6 +358,9 @@ public synchronized void writeAlignmentsAndIndex() { previousValue = iValue; o.writeVarLong(aBlockCount.get(i)); + + if (i != aBlockOffset.size() - 1) + o.writeVarInt(cloneIdsIndex.get(i)); } // Writing two key positions in a file @@ -369,29 +378,29 @@ public synchronized void writeAlignmentsAndIndex() { @Override public double getProgress() { - if (!clonesBlockFinished) + if (cloneIds == null) if (numberOfClones == -1) return Double.NaN; else return 1.0 * numberOfClonesWritten / numberOfClones; - else if (sortedAlignments == null) { - if (toSorter == null) + else if (collatedAlignments == null) { + if (toCollator == null) return Double.NaN; else - return 1.0 * toSorter.getCount() / numberOfAlignments; + return 1.0 * toCollator.getCount() / numberOfAlignments; } else return 1.0 * numberOfAlignmentsWritten / numberOfAlignments; } @Override public String getStage() { - if (!clonesBlockFinished) + if (cloneIds == null) if (numberOfClones == -1) return "Initialization"; else return "Writing clones"; - else if (sortedAlignments == null) { - if (toSorter == null) + else if (collatedAlignments == null) { + if (toCollator == null) return "Preparing for sorting"; else return "Sorting alignments"; @@ -409,4 +418,14 @@ public void close() throws IOException { finished = true; output.close(); } + + private static class CloneIdHash implements ToIntFunction { + @Override + public int applyAsInt(VDJCAlignments value) { + return HashFunctions.JenkinWang32shift(value.getCloneIndex()); + } + } + + private static final Comparator CloneIdComparator = + Comparator.comparing(VDJCAlignments::getCloneIndex); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index ae2ccc82a..b882c5def 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -37,8 +37,6 @@ import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.blocks.PrimitivIHybrid; import com.milaboratory.util.LambdaSemaphore; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; @@ -46,7 +44,6 @@ import java.nio.file.Path; import java.util.ArrayList; import java.util.Arrays; -import java.util.EnumMap; import java.util.List; import static com.milaboratory.mixcr.basictypes.ClnsWriter.MAGIC; @@ -62,6 +59,7 @@ public class ClnsReader extends PipelineConfigurationReaderMiXCR implements Clon private final PipelineConfiguration pipelineConfiguration; private final VDJCAlignerParameters alignerParameters; private final CloneAssemblerParameters assemblerParameters; + private final VDJCSProperties.CloneOrdering ordering; private final String versionInfo; private final List genes; @@ -113,6 +111,7 @@ private ClnsReader(PrimitivIHybrid input, VDJCLibraryRegistry libraryRegistry) { pipelineConfiguration = i.readObject(PipelineConfiguration.class); alignerParameters = i.readObject(VDJCAlignerParameters.class); assemblerParameters = i.readObject(CloneAssemblerParameters.class); + ordering = i.readObject(VDJCSProperties.CloneOrdering.class); genes = IOUtil.stdVDJCPrimitivIStateInit(i, alignerParameters, libraryRegistry); } @@ -129,7 +128,7 @@ public CloneSet getCloneSet() { List clones = new ArrayList<>(); for (Clone clone : CUtils.it(readClones())) clones.add(clone); - CloneSet cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters); + CloneSet cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters, ordering); cloneSet.versionInfo = versionInfo; return cloneSet; } @@ -147,6 +146,11 @@ public CloneAssemblerParameters getAssemblerParameters() { return assemblerParameters; } + @Override + public VDJCSProperties.CloneOrdering ordering() { + return ordering; + } + @Override public void close() throws IOException { input.close(); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index e233aa705..614f1b0f3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -78,14 +78,18 @@ public void writeHeaderFromCloneSet( writeHeader(configuration, cloneSet.getAlignmentParameters(), cloneSet.getAssemblerParameters(), - cloneSet.getUsedGenes(), cloneSet); + cloneSet.getOrdering(), + cloneSet.getUsedGenes(), + cloneSet); } public void writeHeader( PipelineConfiguration configuration, VDJCAlignerParameters alignmentParameters, CloneAssemblerParameters assemblerParameters, - List genes, HasFeatureToAlign featureToAlign + VDJCSProperties.CloneOrdering ordering, + List genes, + HasFeatureToAlign featureToAlign ) { try (PrimitivO o = output.beginPrimitivO(true)) { // Writing magic bytes @@ -100,6 +104,7 @@ public void writeHeader( o.writeObject(configuration); o.writeObject(alignmentParameters); o.writeObject(assemblerParameters); + o.writeObject(ordering); IOUtil.stdVDJCPrimitivOStateInit(o, genes, featureToAlign); } @@ -112,7 +117,7 @@ public InputPort cloneWriter() { return output.beginPrimitivOBlocks(3, 512); } - public void writeCloneSet(PipelineConfiguration configuration, CloneSet cloneSet){ + public void writeCloneSet(PipelineConfiguration configuration, CloneSet cloneSet) { writeHeaderFromCloneSet(configuration, cloneSet); InputPort cloneIP = cloneWriter(); for (Clone clone : cloneSet) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java index a3fe740b5..789f169af 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -31,6 +31,17 @@ import cc.redberry.pipe.OutputPortCloseable; +import java.util.Comparator; +import java.util.List; + public interface CloneReader { + /** + * Sequence of properties the stream is sorted by. + * + * @return sequence of properties the stream is sorted by + */ + VDJCSProperties.CloneOrdering ordering(); + + OutputPortCloseable readClones(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index c6547d68a..9d19ff604 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -46,15 +46,19 @@ public final class CloneSet implements Iterable, HasFeatureToAlign { String versionInfo; final CloneAssemblerParameters assemblerParameters; final VDJCAlignerParameters alignmentParameters; - // final EnumMap alignedFeatures; + final VDJCSProperties.CloneOrdering ordering; final List usedGenes; final List clones; final double totalCount; final TagCounter totalTagCounts; public CloneSet(List clones, Collection usedGenes, - VDJCAlignerParameters alignmentParameters, CloneAssemblerParameters assemblerParameters) { - this.clones = Collections.unmodifiableList(new ArrayList<>(clones)); + VDJCAlignerParameters alignmentParameters, + CloneAssemblerParameters assemblerParameters, + VDJCSProperties.CloneOrdering ordering) { + ArrayList list = new ArrayList<>(clones); + list.sort(ordering.comparator()); + this.clones = Collections.unmodifiableList(list); long totalCount = 0; TagCounterBuilder tagCounterBuilder = new TagCounterBuilder(); for (Clone clone : clones) { @@ -65,6 +69,7 @@ public CloneSet(List clones, Collection usedGenes, this.totalTagCounts = tagCounterBuilder.createAndDestroy(); this.alignmentParameters = alignmentParameters; this.assemblerParameters = assemblerParameters; + this.ordering = ordering; this.usedGenes = Collections.unmodifiableList(new ArrayList<>(usedGenes)); this.totalCount = totalCount; } @@ -92,6 +97,7 @@ public CloneSet(List clones) { this.totalTagCounts = tagCounterBuilder.createAndDestroy(); this.assemblerParameters = null; this.alignmentParameters = null; + this.ordering = new VDJCSProperties.CloneOrdering(); this.usedGenes = Collections.unmodifiableList(new ArrayList<>(genes.values())); this.totalCount = totalCount; } @@ -120,6 +126,10 @@ public VDJCAlignerParameters getAlignmentParameters() { return alignmentParameters; } + public VDJCSProperties.CloneOrdering getOrdering() { + return ordering; + } + public List getUsedGenes() { return usedGenes; } @@ -147,7 +157,18 @@ public Iterator iterator() { } /** - * WARNING: current object will be destroyed + * WARNING: current object (in) will be destroyed + */ + public static CloneSet reorder(CloneSet in, VDJCSProperties.CloneOrdering newOrdering) { + ArrayList newClones = new ArrayList<>(in.clones); + newClones.sort(newOrdering.comparator()); + for (Clone nc : newClones) + nc.parent = null; + return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters, newOrdering); + } + + /** + * WARNING: current object (in) will be destroyed */ public static CloneSet transform(CloneSet in, Filter filter) { List newClones = new ArrayList<>(in.size()); @@ -158,6 +179,6 @@ public static CloneSet transform(CloneSet in, Filter filter) { newClones.add(c); } } - return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters); + return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters, in.ordering); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java index 090dfdba0..f62ec4019 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java @@ -33,6 +33,7 @@ import com.milaboratory.cli.BinaryFileInfoExtractor; import com.milaboratory.core.io.CompressionType; import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.primitivio.HasPrimitivIOState; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import io.repseq.core.*; @@ -93,15 +94,15 @@ public static void writeAndRegisterGeneReferences(PrimitivO output, List genes, + public static void registerGeneReferences(HasPrimitivIOState ioState, List genes, HasFeatureToAlign featuresToAlign) { // Putting genes references and feature sequences to be serialized/deserialized as references for (VDJCGene gene : genes) { - // Each gene is singleton - output.putKnownReference(gene); + // Each gene is a singleton + ioState.putKnownReference(gene); // Also put sequences of certain gene features of genes as known references if required GeneFeature featureToAlign = featuresToAlign.getFeatureToAlign(gene.getGeneType()); if (featureToAlign == null) @@ -111,7 +112,7 @@ public static void registerGeneReferencesO(PrimitivO output, List gene continue; // Relies on the fact that sequences of gene features are cached, // the same instance will be used everywhere (including alignments) - output.putKnownReference(gene.getFeature(featuresToAlign.getFeatureToAlign(gene.getGeneType()))); + ioState.putKnownReference(gene.getFeature(featuresToAlign.getFeatureToAlign(gene.getGeneType()))); } } @@ -137,7 +138,7 @@ public static List stdVDJCPrimitivIStateInit(PrimitivI i, HasFeatureTo public static List readAndRegisterGeneReferences(PrimitivI input, VDJCLibraryRegistry registry, HasFeatureToAlign featuresToAlign) { List genes = readGeneReferences(input, registry); - registerGeneReferencesI(input, genes, featuresToAlign); + registerGeneReferences(input, genes, featuresToAlign); return genes; } @@ -156,22 +157,6 @@ public static List readGeneReferences(PrimitivI input, VDJCLibraryRegi return genes; } - public static void registerGeneReferencesI(PrimitivI input, List genes, - HasFeatureToAlign featuresToAlign) { - // Putting genes references and feature sequences to be serialized/deserialized as references - for (VDJCGene gene : genes) { - input.putKnownReference(gene); - // Also put sequences of certain gene features of genes as known references if required - GeneFeature featureToAlign = featuresToAlign.getFeatureToAlign(gene.getGeneType()); - if (featureToAlign == null) - continue; - NucleotideSequence featureSequence = gene.getFeature(featureToAlign); - if (featureSequence == null) - continue; - input.putKnownReference(featureSequence); - } - } - public static InputStream createIS(String file) throws IOException { return createIS(CompressionType.detectCompressionType(file), new FileInputStream(file)); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java index 2ddaaf07c..c9d9e248e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java @@ -31,10 +31,12 @@ import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.cli.PipelineConfiguration; +import com.milaboratory.mixcr.util.MiXCRDebug; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.primitivio.blocks.PrimitivIOBlocksUtil; import com.milaboratory.primitivio.blocks.PrimitivOBlocks; import com.milaboratory.primitivio.blocks.PrimitivOBlocksStats; import com.milaboratory.primitivio.blocks.PrimitivOHybrid; @@ -46,12 +48,10 @@ import java.nio.charset.StandardCharsets; import java.nio.file.Paths; import java.util.List; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.ForkJoinPool; public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI, HasPosition { public static final int DEFAULT_ENCODER_THREADS = 3; - public static final int DEFAULT_ALIGNMENTS_IN_BLOCK = 1024; // 1024 alignments * 805-1024 bytes per alignment ~ 824 kB - 1MB per block + public static final int DEFAULT_ALIGNMENTS_IN_BLOCK = 1 << 10; // 805-1024 bytes per alignment static final String MAGIC_V15 = "MiXCR.VDJC.V15"; static final String MAGIC = MAGIC_V15; static final int MAGIC_LENGTH = 14; @@ -60,6 +60,8 @@ public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI, HasPos /** Number of bytes in footer with meta information */ static final int FOOTER_LENGTH = 8 + 8 + IOUtil.END_MAGIC_LENGTH; + private final boolean highCompression; + /** * This number will be added to the end of the file to report number of processed read to the following processing * steps. Mainly for informative statistics reporting. @@ -85,11 +87,11 @@ public VDJCAlignmentsWriter(String fileName) throws IOException { } public VDJCAlignmentsWriter(String fileName, int encoderThreads, int alignmentsInBlock) throws IOException { - this(fileName, encoderThreads, alignmentsInBlock, ForkJoinPool.commonPool()); + this(new PrimitivOHybrid(Paths.get(fileName)), encoderThreads, alignmentsInBlock, false); } - public VDJCAlignmentsWriter(String fileName, int encoderThreads, int alignmentsInBlock, ExecutorService executor) throws IOException { - this(new PrimitivOHybrid(executor, Paths.get(fileName)), encoderThreads, alignmentsInBlock); + public VDJCAlignmentsWriter(String fileName, int encoderThreads, int alignmentsInBlock, boolean highCompression) throws IOException { + this(new PrimitivOHybrid(Paths.get(fileName)), encoderThreads, alignmentsInBlock, highCompression); } public VDJCAlignmentsWriter(File file) throws IOException { @@ -97,14 +99,15 @@ public VDJCAlignmentsWriter(File file) throws IOException { } public VDJCAlignmentsWriter(File file, int encoderThreads, int alignmentsInBlock) throws IOException { - this(file, encoderThreads, alignmentsInBlock, ForkJoinPool.commonPool()); + this(new PrimitivOHybrid(file.toPath()), encoderThreads, alignmentsInBlock, false); } - public VDJCAlignmentsWriter(File file, int encoderThreads, int alignmentsInBlock, ExecutorService executor) throws IOException { - this(new PrimitivOHybrid(executor, file.toPath()), encoderThreads, alignmentsInBlock); + public VDJCAlignmentsWriter(File file, int encoderThreads, int alignmentsInBlock, boolean highCompression) throws IOException { + this(new PrimitivOHybrid(file.toPath()), encoderThreads, alignmentsInBlock, highCompression); } - public VDJCAlignmentsWriter(PrimitivOHybrid output, int encoderThreads, int alignmentsInBlock) { + public VDJCAlignmentsWriter(PrimitivOHybrid output, int encoderThreads, int alignmentsInBlock, boolean highCompression) { + this.highCompression = highCompression; this.output = output; this.encoderThreads = encoderThreads; this.alignmentsInBlock = alignmentsInBlock; @@ -164,7 +167,10 @@ public void header(VDJCAlignerParameters parameters, List genes, IOUtil.stdVDJCPrimitivOStateInit(o, genes, parameters); } - writer = output.beginPrimitivOBlocks(encoderThreads, alignmentsInBlock); + writer = output.beginPrimitivOBlocks(encoderThreads, alignmentsInBlock, + highCompression + ? PrimitivIOBlocksUtil.highLZ4Compressor() + : PrimitivIOBlocksUtil.fastLZ4Compressor()); } @Override @@ -203,6 +209,10 @@ public synchronized void close() { if (!closed) { writer.close(); // This will also write stream termination symbol/block to the stream + // Printing IO stat + if (MiXCRDebug.DEBUG) + System.out.println(writer.getParent().getStats()); + try (PrimitivO o = output.beginPrimitivO()) { // // [ numberOfProcessedReads : long ] // byte[] footer = new byte[8]; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 2c642515b..fbb44eff5 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -290,13 +290,25 @@ public final int getTargetContainingFeature(GeneFeature feature) { } public NSequenceWithQuality getFeature(GeneFeature geneFeature) { - NSequenceWithQuality feature = null, tmp; - for (int i = 0; i < targets.length; ++i) { - tmp = getPartitionedTarget(i).getFeature(geneFeature); - if (tmp != null && (feature == null || feature.getQuality().minValue() < tmp.getQuality().minValue())) - feature = tmp; - } - return feature; + int tcf = getTargetContainingFeature(geneFeature); + return tcf == -1 ? null : getPartitionedTarget(tcf).getFeature(geneFeature); + } + + public NucleotideSequence getNFeature(GeneFeature geneFeature) { + int tcf = getTargetContainingFeature(geneFeature); + return tcf == -1 ? null : getPartitionedTarget(tcf).getFeature(geneFeature).getSequence(); + } + + public AminoAcidSequence getAAFeature(GeneFeature geneFeature) { + int tcf = getTargetContainingFeature(geneFeature); + if (tcf == -1) + return null; + VDJCPartitionedSequence target = getPartitionedTarget(tcf); + TranslationParameters tp = target.getPartitioning().getTranslationParameters(geneFeature); + return tp == null + ? null + : AminoAcidSequence.translate( + target.getFeature(geneFeature).getSequence(), tp); // target.getFeature(geneFeature) uses exactly the same algorithm, guaranteed to be non-null at this point } public CaseSensitiveNucleotideSequence getIncompleteFeature(GeneFeature geneFeature) { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java new file mode 100644 index 000000000..b071b15da --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java @@ -0,0 +1,257 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.basictypes; + +import com.fasterxml.jackson.annotation.*; +import com.milaboratory.core.sequence.AminoAcidSequence; +import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.primitivio.annotations.Serializable; +import com.milaboratory.util.sorting.*; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGeneId; + +import java.util.Arrays; +import java.util.Comparator; +import java.util.List; +import java.util.Objects; + +import static com.milaboratory.util.sorting.SortingPropertyRelation.*; + +public class VDJCSProperties { + public static final CloneOrdering CO_BY_COUNT = new CloneOrdering(new CloneCount()); + + @Serializable(asJson = true) + public static final class CloneOrdering { + @JsonProperty("properties") + public final VDJCSProperties.VDJCSProperty[] properties; + + public CloneOrdering(List> properties) { + this.properties = properties.toArray(new VDJCSProperty[properties.size()]); + } + + @JsonCreator + public CloneOrdering(@JsonProperty("properties") VDJCSProperty... properties) { + this.properties = properties; + } + + public Comparator comparator() { + return SortingUtil.combine(properties); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CloneOrdering that = (CloneOrdering) o; + return Arrays.equals(properties, that.properties); + } + + @Override + public int hashCode() { + return Arrays.hashCode(properties); + } + } + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE + ) + @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, property = "type") + @JsonSubTypes({ + @JsonSubTypes.Type(value = NSequence.class, name = "nSequence"), + @JsonSubTypes.Type(value = AASequence.class, name = "aaSequence"), + @JsonSubTypes.Type(value = VDJCSegment.class, name = "segment"), + @JsonSubTypes.Type(value = CloneCount.class, name = "cloneCount") + }) + @Serializable(asJson = true) + public interface VDJCSProperty extends SortingProperty { + } + + public static final class NSequence extends AbstractHashSortingProperty.Natural implements VDJCSProperty { + @JsonProperty("geneFeature") + public final GeneFeature geneFeature; + + @JsonCreator + public NSequence(@JsonProperty("geneFeature") GeneFeature geneFeature) { + Objects.requireNonNull(geneFeature); + this.geneFeature = geneFeature; + } + + @Override + public SortingPropertyRelation relationTo(SortingProperty other) { + if (equals(other)) + return SortingPropertyRelation.Equal; + + // The following relations calculated with assumption of equal partitioning of + // this and other sequences. Chance of different partitions considered negligible. + + if (other instanceof NSequence) { + GeneFeature otherGeneFeature = ((NSequence) other).geneFeature; + if (otherGeneFeature.contains(geneFeature)) + return Necessary; + if (geneFeature.contains(otherGeneFeature)) + return Sufficient; + } + + if (other instanceof AASequence) { + GeneFeature aaGeneFeature = ((AASequence) other).geneFeature; + if (geneFeature.contains(aaGeneFeature)) + return Sufficient; + } + + return None; + } + + @Override + public NucleotideSequence get(VDJCObject obj) { + return obj.getNFeature(geneFeature); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (!(o instanceof NSequence)) return false; + NSequence nSequence = (NSequence) o; + return geneFeature.equals(nSequence.geneFeature); + } + + @Override + public int hashCode() { + return Objects.hash(geneFeature); + } + } + + public static final class AASequence extends AbstractHashSortingProperty.Natural implements VDJCSProperty { + @JsonProperty("geneFeature") + public final GeneFeature geneFeature; + + @JsonCreator + public AASequence(@JsonProperty("geneFeature") GeneFeature geneFeature) { + Objects.requireNonNull(geneFeature); + this.geneFeature = geneFeature; + } + + @Override + public SortingPropertyRelation relationTo(SortingProperty other) { + if (equals(other)) + return SortingPropertyRelation.Equal; + + // The following relations calculated with assumption of equal partitioning of + // this and other sequences. Chance of different partitions considered negligible. + + if (other instanceof AASequence) { + GeneFeature otherGeneFeature = ((AASequence) other).geneFeature; + if (otherGeneFeature.contains(geneFeature)) + return Necessary; + if (geneFeature.contains(otherGeneFeature)) + return Sufficient; + } + + if (other instanceof NSequence) { + GeneFeature nGeneFeature = ((NSequence) other).geneFeature; + if (nGeneFeature.contains(geneFeature)) + return Necessary; + } + + return None; + } + + @Override + public AminoAcidSequence get(VDJCObject obj) { + return obj.getAAFeature(geneFeature); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (!(o instanceof AASequence)) return false; + AASequence that = (AASequence) o; + return geneFeature.equals(that.geneFeature); + } + + @Override + public int hashCode() { + return Objects.hash(geneFeature); + } + } + + public static final class VDJCSegment extends AbstractHashSortingProperty.Natural implements VDJCSProperty { + @JsonProperty("geneType") + public final GeneType geneType; + + @JsonCreator + public VDJCSegment(@JsonProperty("geneType") GeneType geneType) { + this.geneType = geneType; + } + + @Override + public VDJCGeneId get(VDJCObject obj) { + return obj.getBestHitGene(geneType).getId(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VDJCSegment that = (VDJCSegment) o; + return geneType == that.geneType; + } + + @Override + public int hashCode() { + return Objects.hash(geneType); + } + } + + public static final class CloneCount extends AbstractSortingProperty implements VDJCSProperty { + @Override + public Double get(Clone obj) { + return obj.getCount(); + } + + @Override + public Comparator propertyComparator() { + return Comparator.naturalOrder().reversed(); + } + + @Override + public int hashCode() { + return CloneCount.class.hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) return true; + return obj != null && obj.getClass() == CloneCount.class; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 072c78cfc..1be5a5d19 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -134,6 +134,10 @@ public void setThreads(int threads) { this.threads = threads; } + @Option(description = "Use higher compression for output file, 10~25% slower, minus 30~50% of file size.", + names = {"--high-compression"}) + public boolean highCompression = false; + public long limit = 0; @Option(description = "Maximal number of reads to process", @@ -503,7 +507,7 @@ else if (featureSequence.containsWildcards()) VDJCAlignmentsWriter writer = getOutput().equals(".") ? null : new VDJCAlignmentsWriter(getOutput(), Math.max(1, threads / 8), - DEFAULT_ALIGNMENTS_IN_BLOCK); + DEFAULT_ALIGNMENTS_IN_BLOCK, highCompression); SequenceWriter notAlignedWriter = failedReadsR1 == null ? null diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 3a037c6cf..bb57f53cf 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -40,6 +40,7 @@ import com.milaboratory.mixcr.assembler.*; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.util.ArraysUtils; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.*; @@ -47,10 +48,8 @@ import picocli.CommandLine.Option; import java.io.IOException; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Objects; +import java.util.*; +import java.util.stream.Collectors; import static com.milaboratory.mixcr.cli.CommandAssemble.ASSEMBLE_COMMAND_NAME; @@ -75,6 +74,15 @@ public void setThreads(int threads) { this.threads = threads; } + @Option(description = "Use higher compression for output file.", + names = {"--high-compression"}) + public boolean highCompression = false; + + @Option(description = "Sort by sequence. Clones in the output file will be sorted by clonal sequence," + + "which allows to build overlaps between clonesets.", + names = {"-s", "--sort-by-sequence"}) + public boolean sortBySequence = false; + @Option(description = CommonDescriptions.REPORT, names = {"-r", "--report"}) public String reportFile; @@ -112,8 +120,9 @@ public ActionConfiguration getConfiguration() { private List genes = null; private VDJCAlignerParameters alignerParameters = null; private CloneAssemblerParameters assemblerParameters = null; + private VDJCSProperties.CloneOrdering ordering = null; - private void initializeParameters() { + private void ensureParametersInitialized() { if (assemblerParameters != null) return; @@ -143,23 +152,53 @@ private void initializeParameters() { if (assemblerParameters == null) throwValidationException("Failed to override some parameter: " + overrides); } + + if (sortBySequence) { + GeneFeature[] assemblingFeatures = assemblerParameters.getAssemblingFeatures(); + + // Any CDR3 containing feature will become first + for (int i = 0; i < assemblingFeatures.length; i++) + if (assemblingFeatures[i].contains(GeneFeature.CDR3)) { + if (i != 0) + ArraysUtils.swap(assemblingFeatures, 0, i); + break; + } + + List> orderingList = new ArrayList<>(); + orderingList.addAll(Arrays.stream(assemblingFeatures) + .map(VDJCSProperties.NSequence::new) + .collect(Collectors.toList())); + orderingList.addAll(Arrays.stream(assemblingFeatures) + .map(VDJCSProperties.AASequence::new) + .collect(Collectors.toList())); + orderingList.add(new VDJCSProperties.VDJCSegment(GeneType.Variable)); + orderingList.add(new VDJCSProperties.VDJCSegment(GeneType.Joining)); + ordering = new VDJCSProperties.CloneOrdering(orderingList); + } else { + ordering = VDJCSProperties.CO_BY_COUNT; + } } public CloneAssemblerParameters getCloneAssemblerParameters() { - initializeParameters(); + ensureParametersInitialized(); return assemblerParameters; } public List getGenes() { - initializeParameters(); + ensureParametersInitialized(); return genes; } public VDJCAlignerParameters getAlignerParameters() { - initializeParameters(); + ensureParametersInitialized(); return alignerParameters; } + public VDJCSProperties.CloneOrdering getOrdering() { + ensureParametersInitialized(); + return ordering; + } + /** * Assemble report */ @@ -213,7 +252,7 @@ public void run1() throws Exception { assemblerRunner.run(); // Getting results - final CloneSet cloneSet = assemblerRunner.getCloneSet(alignerParameters); + final CloneSet cloneSet = CloneSet.reorder(assemblerRunner.getCloneSet(alignerParameters), getOrdering()); // Passing final cloneset to assemble last pieces of statistics for report report.onClonesetFinished(cloneSet); @@ -245,7 +284,7 @@ public void run1() throws Exception { // } // } - try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out)) { + try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, highCompression)) { // writer will supply current stage and completion percent to the progress reporter SmartProgressReporter.startProgressReport(writer); // Writing clone block @@ -318,7 +357,7 @@ public void run1() throws Exception { }; } - writer.sortAlignments(port, assembler.getAlignmentsCount()); + writer.collateAlignments(port, assembler.getAlignmentsCount()); } writer.writeAlignmentsAndIndex(); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 2dcbf9c4d..f05d87735 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -122,17 +122,20 @@ public void run1() throws Exception { List genes; VDJCAlignerParameters alignerParameters; CloneAssemblerParameters cloneAssemblerParameters; + VDJCSProperties.CloneOrdering ordering; try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(out))); // TODO ???? BufferedWriter debugReport = debugReportFile == null ? null : new BufferedWriter(new OutputStreamWriter(new FileOutputStream(debugReportFile)))) { + ordering = reader.ordering(); + final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), reader.getAssemblingFeatures(), reader.getGenes(), reader.getAlignerParameters().getFeaturesToAlignMap()); alignerParameters = reader.getAlignerParameters(); cloneAssemblerParameters = reader.getAssemblerParameters(); genes = reader.getGenes(); - IOUtil.registerGeneReferencesO(tmpOut, genes, alignerParameters); + IOUtil.registerGeneReferences(tmpOut, genes, alignerParameters); ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments(); SmartProgressReporter.startProgressReport("Assembling contigs", cloneAlignmentsPort); @@ -246,16 +249,13 @@ public void run1() throws Exception { Clone[] clones = new Clone[totalClonesCount]; try (PrimitivI tmpIn = new PrimitivI(new BufferedInputStream(new FileInputStream(out)))) { - IOUtil.registerGeneReferencesI(tmpIn, genes, alignerParameters); + IOUtil.registerGeneReferences(tmpIn, genes, alignerParameters); int i = 0; for (Clone clone : CUtils.it(new PipeDataInputReader<>(Clone.class, tmpIn, totalClonesCount))) clones[i++] = clone; } - Arrays.sort(clones, Comparator.comparingDouble(c -> -c.getCount())); - for (int i = 0; i < clones.length; i++) - clones[i] = clones[i].setId(i); - CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters, cloneAssemblerParameters); + CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters, cloneAssemblerParameters, ordering); try (ClnsWriter writer = new ClnsWriter(out)) { writer.writeCloneSet(getFullPipelineConfiguration(), cloneSet); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java index e73d911b5..34e84dab6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java @@ -64,7 +64,9 @@ public void run1() throws Exception { long count = 0; if (getCloneIds().length == 0) - for (VDJCAlignments al : CUtils.it(clna.readAssembledAlignments())) { + for (VDJCAlignments al : CUtils.it(clna.readAllAlignments())) { + if (al.getCloneIndex() == -1) + continue; writer.write(al); ++count; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 23314b668..b4c7f2f7e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -33,7 +33,10 @@ import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.blocks.ParallelProcessor; import cc.redberry.pipe.util.OrderedOutputPort; -import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.fasterxml.jackson.core.JsonProcessingException; import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.core.alignment.AlignmentScoring; @@ -78,7 +81,8 @@ public class CommandExtend extends ACommandWithSmartOverwriteWithSingleInputMiXC names = {"-q", "--quality"}) public byte extensionQuality = 30; - public int threads = Runtime.getRuntime().availableProcessors();; + public int threads = Runtime.getRuntime().availableProcessors(); + ; @Option(description = "Processing threads", names = {"-t", "--threads"}) @@ -153,7 +157,7 @@ void processClns() throws IOException { clones.sort(Comparator.comparing(Clone::getId)); CloneSet newCloneSet = new CloneSet(clones, cloneSet.getUsedGenes(), cloneSet.getAlignmentParameters(), - cloneSet.getAssemblerParameters()); + cloneSet.getAssemblerParameters(), cloneSet.getOrdering()); try (ClnsWriter writer = new ClnsWriter(out)) { writer.writeCloneSet(getFullPipelineConfiguration(), newCloneSet); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 86735d561..82a12ca19 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -163,7 +163,7 @@ private void runClna() throws Exception { writer.writeClones(resultCloneSet); OutputPortCloseable alignments = reader.readAllAlignments(); - writer.sortAlignments(() -> { + writer.collateAlignments(() -> { VDJCAlignments als = alignments.take(); if (als == null) return null; @@ -280,24 +280,11 @@ private CloneSet doClustering(CloneSet cloneSet, TObjectIntHashMap it = idMapping.iterator(); - while (it.hasNext()) { - it.advance(); - it.setValue(permutation.get(it.value())); - } - return new CloneSet(resultingClones, cloneSet.getUsedGenes(), cloneSet.getAlignmentParameters(), - cloneSet.getAssemblerParameters()); + cloneSet.getAssemblerParameters(), + cloneSet.getOrdering()); } @JsonAutoDetect( diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java index 1edc2f2ce..f95216ad9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java @@ -138,7 +138,7 @@ void sliceClnA() throws Exception { } CloneSet newCloneSet = new CloneSet(clones, cloneSet.getUsedGenes(), cloneSet.getAlignmentParameters(), - cloneSet.getAssemblerParameters()); + cloneSet.getAssemblerParameters(), cloneSet.getOrdering()); OutputPort allAlignmentsPortRaw = new FlatteningOutputPort<>(CUtils.asOutputPort(allAlignmentsList)); AtomicLong idGen = new AtomicLong(); @@ -151,7 +151,7 @@ void sliceClnA() throws Exception { writer.writeClones(newCloneSet); - writer.sortAlignments(allAlignmentsPort, newNumberOfAlignments); + writer.collateAlignments(allAlignmentsPort, newNumberOfAlignments); writer.writeAlignmentsAndIndex(); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java index 8249a3a9d..c65c6f2f5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java @@ -45,7 +45,7 @@ import com.milaboratory.primitivio.PipeWriter; import com.milaboratory.util.ObjectSerializer; import com.milaboratory.util.SmartProgressReporter; -import com.milaboratory.util.Sorter; +import com.milaboratory.util.sorting.Sorter; import com.milaboratory.util.TempFileManager; import io.repseq.core.VDJCGene; import picocli.CommandLine.Command; diff --git a/src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java b/src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java new file mode 100644 index 000000000..4e1077f4a --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java @@ -0,0 +1,38 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.util; + +public class MiXCRDebug { + public static final boolean DEBUG; + + static { + DEBUG = System.getenv("MIXCR_DEBUG") != null; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index f8ce9ca3a..87616923e 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -67,7 +67,6 @@ import java.io.*; import java.util.ArrayList; import java.util.Arrays; -import java.util.Comparator; import java.util.List; import static cc.redberry.pipe.CUtils.chunked; @@ -132,7 +131,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger( CUtils.asOutputPort(align.alignments), assemble.cloneAssembler.getAssembledReadsPort())) { - writer.sortAlignments(merged, assemble.cloneAssembler.getAlignmentsCount()); + writer.collateAlignments(merged, assemble.cloneAssembler.getAlignmentsCount()); } writer.writeAlignmentsAndIndex(); } catch (IOException e) { @@ -144,7 +143,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl try (ClnAReader reader = new ClnAReader(clnaFile.toPath(), VDJCLibraryRegistry.getDefault(), 2); // TODO concurrency ??? PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(tmpFile)));) { - IOUtil.registerGeneReferencesO(tmpOut, align.usedGenes, align.parameters.alignerParameters); + IOUtil.registerGeneReferences(tmpOut, align.usedGenes, align.parameters.alignerParameters); final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), reader.getAssemblingFeatures(), reader.getGenes(), reader.getAlignerParameters().getFeaturesToAlignMap()); @@ -179,7 +178,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl Clone[] clones = new Clone[totalClonesCount]; try (PrimitivI tmpIn = new PrimitivI(new BufferedInputStream(new FileInputStream(tmpFile)))) { - IOUtil.registerGeneReferencesI(tmpIn, align.usedGenes, align.parameters.alignerParameters); + IOUtil.registerGeneReferences(tmpIn, align.usedGenes, align.parameters.alignerParameters); int i = 0; for (Clone clone : CUtils.it(new PipeDataInputReader<>(Clone.class, tmpIn, totalClonesCount))) clones[i++] = clone; @@ -187,11 +186,8 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl throw new RuntimeException(e); } - Arrays.sort(clones, Comparator.comparingDouble(c -> -c.getCount())); - for (int i = 0; i < clones.length; i++) - clones[i] = clones[i].setId(i); CloneSet cloneSet = new CloneSet(Arrays.asList(clones), align.usedGenes, align.parameters.alignerParameters, - align.parameters.cloneAssemblerParameters); + align.parameters.cloneAssemblerParameters, VDJCSProperties.CO_BY_COUNT); return new FullSeqAssembleResult(assemble, cloneSet); } diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java index de2e5740c..45958b333 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java @@ -31,6 +31,8 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.blocks.FilteringPort; +import cc.redberry.pipe.util.CountingOutputPort; import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.mixcr.assembler.AlignmentsMappingMerger; import com.milaboratory.mixcr.assembler.CloneAssemblerParametersPresets; @@ -44,12 +46,36 @@ import java.io.File; import java.util.Collections; +import java.util.List; +import java.util.concurrent.ThreadLocalRandom; +import java.util.function.Function; +import java.util.stream.Collectors; import static org.junit.Assert.assertEquals; public class ClnAReaderTest { @Test public void test1() throws Exception { + testGeneric(clones -> { + Collections.shuffle(clones); + clones = clones.stream().filter(c -> c.id != 2).collect(Collectors.toList()); + return clones; + }, als -> + CUtils.wrap(als, vdjcAlignments -> + vdjcAlignments.getCloneIndex() == 2 + ? vdjcAlignments.setMapping(new ReadToCloneMapping(vdjcAlignments.getAlignmentsIndex(), -1, false, false, false, false)) + : vdjcAlignments) + ); + } + + @Test + public void test3NoM1() throws Exception { + testGeneric(clones -> clones, + als -> new FilteringPort<>(als, a -> a.getCloneIndex() >= 0)); + } + + public void testGeneric(Function, List> modifyClones, + Function, OutputPort> modifyAlignments) throws Exception { RunMiXCR.RunMiXCRAnalysis params = new RunMiXCR.RunMiXCRAnalysis( RunMiXCR.class.getResource("/sequences/test_R1.fastq").getFile(), RunMiXCR.class.getResource("/sequences/test_R2.fastq").getFile()); @@ -62,19 +88,31 @@ public void test1() throws Exception { File file = TempFileManager.getTempFile(); ClnAWriter writer = new ClnAWriter(null, file); - writer.writeClones(assemble.cloneSet); - writer.sortAlignments(merged, align.alignments.size()); + + List newClones = assemble.cloneSet.getClones().stream() + .map(Clone::resetParentCloneSet) + .collect(Collectors.toList()); + CloneSet newCloneSet = new CloneSet( + modifyClones.apply(newClones), align.usedGenes, + align.parameters.alignerParameters, + CloneAssemblerParametersPresets.getByName("default"), + new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); + writer.writeClones(newCloneSet); + OutputPort als = modifyAlignments.apply(merged); + CountingOutputPort alsc = new CountingOutputPort<>(als); + writer.collateAlignments(alsc, align.alignments.size()); writer.writeAlignmentsAndIndex(); writer.close(); - ClnAReader reader = new ClnAReader(file.toPath(), VDJCLibraryRegistry.getDefault(), 17); + ClnAReader reader = new ClnAReader(file.toPath(), VDJCLibraryRegistry.getDefault(), + ThreadLocalRandom.current().nextInt(1, 17)); assertEquals(MiXCRVersionInfo.get().getVersionString(AppVersionInfo.OutputType.ToFile), reader.getVersionInfo()); - assertEquals(align.alignments.size(), reader.numberOfAlignments()); - assertEquals(assemble.cloneSet.size(), reader.numberOfClones()); + assertEquals(alsc.getCount(), reader.numberOfAlignments()); + assertEquals(newCloneSet.size(), reader.numberOfClones()); for (ClnAReader.CloneAlignments c : CUtils.it(reader.clonesAndAlignments())) { assertEquals("cloneId = " + c.cloneId, c.clone.count, count(c.alignments()), 0.01); @@ -82,7 +120,8 @@ public void test1() throws Exception { CUtils.it(c.alignments()).forEach(a -> { assertEquals(c.cloneId, a.getCloneIndex()); if (a.getMappingType() == ReadToCloneMapping.MappingType.Core) - assertEquals(c.clone.getFeature(GeneFeature.CDR3), a.getFeature(GeneFeature.CDR3)); + assertEquals(c.clone.getFeature(GeneFeature.CDR3), + a.getFeature(GeneFeature.CDR3)); }); } } @@ -99,8 +138,9 @@ public void test2Empty() throws Exception { ClnAWriter writer = new ClnAWriter(null, file); writer.writeClones(new CloneSet(Collections.EMPTY_LIST, align.usedGenes, align.parameters.alignerParameters, - CloneAssemblerParametersPresets.getByName("default"))); - writer.sortAlignments(CUtils.asOutputPort(align.alignments), align.alignments.size()); + CloneAssemblerParametersPresets.getByName("default"), + new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount()))); + writer.collateAlignments(CUtils.asOutputPort(align.alignments), align.alignments.size()); writer.writeAlignmentsAndIndex(); writer.close(); diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java new file mode 100644 index 000000000..40e8daa57 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java @@ -0,0 +1,76 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.basictypes; + +import com.milaboratory.test.TestUtil; +import com.milaboratory.util.sorting.SortingPropertyRelation; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import org.junit.Assert; +import org.junit.Test; + +public class VDJCSPropertiesTest { + @Test + public void serializationTest() { + TestUtil.assertJson(new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); + TestUtil.assertJson(new VDJCSProperties.CloneOrdering( + new VDJCSProperties.NSequence(GeneFeature.CDR3), + new VDJCSProperties.VDJCSegment(GeneType.Variable), + new VDJCSProperties.CloneCount())); + } + + @Test + public void relationTest() { + VDJCSProperties.NSequence ntCDR3 = new VDJCSProperties.NSequence(GeneFeature.CDR3); + VDJCSProperties.AASequence aaCDR3 = new VDJCSProperties.AASequence(GeneFeature.CDR3); + VDJCSProperties.NSequence ntVDJRegion = new VDJCSProperties.NSequence(GeneFeature.VDJRegion); + VDJCSProperties.AASequence aaVDJRegion = new VDJCSProperties.AASequence(GeneFeature.VDJRegion); + + Assert.assertEquals(SortingPropertyRelation.Equal, ntCDR3.relationTo(ntCDR3)); + Assert.assertEquals(SortingPropertyRelation.Sufficient, ntCDR3.relationTo(aaCDR3)); + Assert.assertEquals(SortingPropertyRelation.Necessary, ntCDR3.relationTo(ntVDJRegion)); + Assert.assertEquals(SortingPropertyRelation.None, ntCDR3.relationTo(aaVDJRegion)); + + Assert.assertEquals(SortingPropertyRelation.Necessary, aaCDR3.relationTo(ntCDR3)); + Assert.assertEquals(SortingPropertyRelation.Equal, aaCDR3.relationTo(aaCDR3)); + Assert.assertEquals(SortingPropertyRelation.Necessary, aaCDR3.relationTo(ntVDJRegion)); + Assert.assertEquals(SortingPropertyRelation.Necessary, aaCDR3.relationTo(aaVDJRegion)); + + Assert.assertEquals(SortingPropertyRelation.Sufficient, ntVDJRegion.relationTo(ntCDR3)); + Assert.assertEquals(SortingPropertyRelation.Sufficient, ntVDJRegion.relationTo(aaCDR3)); + Assert.assertEquals(SortingPropertyRelation.Equal, ntVDJRegion.relationTo(ntVDJRegion)); + Assert.assertEquals(SortingPropertyRelation.Sufficient, ntVDJRegion.relationTo(aaVDJRegion)); + + Assert.assertEquals(SortingPropertyRelation.None, aaVDJRegion.relationTo(ntCDR3)); + Assert.assertEquals(SortingPropertyRelation.Sufficient, aaVDJRegion.relationTo(aaCDR3)); + Assert.assertEquals(SortingPropertyRelation.Necessary, aaVDJRegion.relationTo(ntVDJRegion)); + Assert.assertEquals(SortingPropertyRelation.Equal, aaVDJRegion.relationTo(aaVDJRegion)); + } +} \ No newline at end of file From 08a3db3e1e18dd93073aac417a03048404defec9 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 30 Jun 2020 14:23:51 +0300 Subject: [PATCH 064/282] Maven Integration Tests (#7) * Try in CI * Faster integration test data prepare. * att2 --- .circleci/config.yml | 12 +++- ensure-test-data.sh | 70 ++++++++++--------- pom.xml | 44 ++++++++++-- prepare-test-data.sh | 55 +++++++++++++++ .../mixcr/basictypes/VDJCSProperties.java | 11 +++ .../mixcr/util/DummyIntegrationTest.java | 45 ++++++++++++ 6 files changed, 197 insertions(+), 40 deletions(-) create mode 100755 prepare-test-data.sh create mode 100644 src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java diff --git a/.circleci/config.yml b/.circleci/config.yml index b7cddc177..134d38737 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -17,7 +17,7 @@ jobs: name: Installing moreutils command: | sudo apt-get update - sudo apt-get install -y moreutils + sudo apt-get install -y moreutils parallel - run: name: Downloading git submodules @@ -73,5 +73,13 @@ jobs: key: v1-dependencies-{{ checksum "pom.xml" }}-{{ checksum "milib/pom.xml" }}-{{ checksum "repseqio/pom.xml" }} - run: - name: Running MiXCR Integration and Regression tests + name: Prepare Integration Test Data + command: ./prepare-test-data.sh + + - run: + name: Running Maven Integration tests + command: mvn test -DintegrationTests + + - run: + name: Running Script Integration and Regression tests command: ./itests.sh test | ts diff --git a/ensure-test-data.sh b/ensure-test-data.sh index 22b41de3d..054f3ac7f 100755 --- a/ensure-test-data.sh +++ b/ensure-test-data.sh @@ -5,54 +5,56 @@ set -o pipefail # Linux readlink -f alternative for Mac OS X function readlinkUniversal() { - targetFile=$1 - - cd `dirname $targetFile` - targetFile=`basename $targetFile` - - # iterate down a (possible) chain of symlinks - while [ -L "$targetFile" ] - do - targetFile=`readlink $targetFile` - cd `dirname $targetFile` - targetFile=`basename $targetFile` - done - - # compute the canonicalized name by finding the physical path - # for the directory we're in and appending the target file. - phys_dir=`pwd -P` - result=$phys_dir/$targetFile - echo $result + targetFile=$1 + + cd $(dirname $targetFile) + targetFile=$(basename $targetFile) + + # iterate down a (possible) chain of symlinks + while [ -L "$targetFile" ]; do + targetFile=$(readlink $targetFile) + cd $(dirname $targetFile) + targetFile=$(basename $targetFile) + done + + # compute the canonicalized name by finding the physical path + # for the directory we're in and appending the target file. + phys_dir=$(pwd -P) + result=$phys_dir/$targetFile + echo $result } -os=`uname` +os=$(uname) dir="" case $os in - Darwin) - dir=$(dirname "$(readlinkUniversal "$0")") - ;; - Linux) - dir="$(dirname "$(readlink -f "$0")")" - ;; - FreeBSD) - dir=$(dirname "$(readlinkUniversal "$0")") - ;; - *) - echo "Unknown OS." - exit 1 - ;; +Darwin) + dir=$(dirname "$(readlinkUniversal "$0")") + ;; +Linux) + dir="$(dirname "$(readlink -f "$0")")" + ;; +FreeBSD) + dir=$(dirname "$(readlinkUniversal "$0")") + ;; +*) + echo "Unknown OS." + exit 1 + ;; esac mkdir -p $dir/src/test/resources/sequences/big/ cd $dir/src/test/resources/sequences/big/ if [[ ! -f CD4M1_test_R1.fastq.gz ]]; then - wget https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R1.fastq.gz + curl -O https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R1.fastq.gz fi if [[ ! -f CD4M1_test_R2.fastq.gz ]]; then - wget https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R2.fastq.gz + curl -O https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R2.fastq.gz fi +if [[ ! -d yf_sample_data ]]; then + curl -sS https://s3.amazonaws.com/files.milaboratory.com/test-data/yf_sample_data.tar | tar -xv +fi diff --git a/pom.xml b/pom.xml index de23471ec..be9ed8aa4 100644 --- a/pom.xml +++ b/pom.xml @@ -28,7 +28,8 @@ ~ PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY ~ PATENT, TRADEMARK OR OTHER RIGHTS. --> - + 4.0.0 com.milaboratory @@ -105,6 +106,35 @@ scm:git:https://github.com/milaboratory/mixcr.git + + + integration-tests + + + integrationTests + + + + + + org.apache.maven.plugins + maven-surefire-plugin + 2.22.2 + + -Xmx1024m + + none + + + **/*IntegrationTest.java + + + + + + + + @@ -178,6 +208,9 @@ 2.22.2 -Xmx1024m + + **/*IntegrationTest.java + @@ -283,12 +316,15 @@ - + - + false - + com.milaboratory.mixcr.cli.Main diff --git a/prepare-test-data.sh b/prepare-test-data.sh new file mode 100755 index 000000000..a76407439 --- /dev/null +++ b/prepare-test-data.sh @@ -0,0 +1,55 @@ +#!/bin/bash + +set -e +set -o pipefail + +# Linux readlink -f alternative for Mac OS X +function readlinkUniversal() { + targetFile=$1 + + cd $(dirname $targetFile) + targetFile=$(basename $targetFile) + + # iterate down a (possible) chain of symlinks + while [ -L "$targetFile" ]; do + targetFile=$(readlink $targetFile) + cd $(dirname $targetFile) + targetFile=$(basename $targetFile) + done + + # compute the canonicalized name by finding the physical path + # for the directory we're in and appending the target file. + phys_dir=$(pwd -P) + result=$phys_dir/$targetFile + echo $result +} + +os=$(uname) + +dir="" + +case $os in +Darwin) + dir=$(dirname "$(readlinkUniversal "$0")") + ;; +Linux) + dir="$(dirname "$(readlink -f "$0")")" + ;; +FreeBSD) + dir=$(dirname "$(readlinkUniversal "$0")") + ;; +*) + echo "Unknown OS." + exit 1 + ;; +esac + +cd "$dir/src/test/resources/sequences/big/" + +cd yf_sample_data +parallel -j5 "${dir}/mixcr" -Xmx500m analyze amplicon \ + -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present \ + --assemble '-OseparateByC=true' --assemble '-OseparateByV=true' --assemble '-OseparateByJ=true' \ + --assemble '--sort-by-sequence' \ + --impute-germline-on-export --json-report "{}" \ + "{}_L001_R1.fastq.gz" "{}_L001_R2.fastq.gz" "{}" ::: Ig-2_S2 Ig-3_S3 Ig-4_S4 Ig-5_S5 Ig1_S1 Ig2_S2 Ig3_S3 Ig4_S4 Ig5_S5 diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java index b071b15da..55fda0617 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java @@ -30,9 +30,11 @@ package com.milaboratory.mixcr.basictypes; import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.core.JsonProcessingException; import com.milaboratory.core.sequence.AminoAcidSequence; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.primitivio.annotations.Serializable; +import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.sorting.*; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -78,6 +80,15 @@ public boolean equals(Object o) { public int hashCode() { return Arrays.hashCode(properties); } + + @Override + public String toString() { + try { + return GlobalObjectMappers.PRETTY.writeValueAsString(this); + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + } } @JsonAutoDetect( diff --git a/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java new file mode 100644 index 000000000..7e50678b0 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java @@ -0,0 +1,45 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.util; + +import com.milaboratory.mixcr.basictypes.CloneSet; +import com.milaboratory.mixcr.basictypes.CloneSetIO; +import org.junit.Test; + +import java.io.IOException; + +public class DummyIntegrationTest { + @Test + public void test1() throws IOException { + String file = DummyIntegrationTest.class.getResource("/sequences/big/yf_sample_data/Ig1_S1.contigs.clns").getFile(); + CloneSet clns = CloneSetIO.read(file); + System.out.println(clns.getOrdering()); + } +} From 3de36ff4d9c8fcce37b3717c57b84f948f567f82 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 30 Jun 2020 19:04:15 +0300 Subject: [PATCH 065/282] MiLib upgrade (JDK14 compatibility) --- milib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/milib b/milib index 9feb34a69..29a1c9c6e 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 9feb34a69c52db3a6e12562a2c0ab74ff7221ec8 +Subproject commit 29a1c9c6e45bd475da831ba840c8d2d2460de596 From 7a85aa610f35a162e0ac58b4700a1c6c937db297 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 21 Jul 2020 17:35:32 +0300 Subject: [PATCH 066/282] Environmental variable to control repseqio cache folder path. --- src/main/java/com/milaboratory/mixcr/cli/Main.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 2a57eeee8..a9ec1d341 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -109,6 +109,10 @@ public static CommandLine mkCmd() { TempFileManager.setPrefix("mixcr_"); Path cachePath = Paths.get(System.getProperty("user.home"), ".mixcr", "cache"); + String repseqioCacheEnv = System.getenv("REPSEQIO_CACHE"); + if (repseqioCacheEnv != null) { + cachePath = Paths.get(repseqioCacheEnv); + } //if (System.getProperty("allow.http") != null || System.getenv("MIXCR_ALLOW_HTTP") != null) //TODO add mechanism to deny http requests SequenceResolvers.initDefaultResolver(cachePath); From 0f7dcf04c9e77ed587d7199a64b1589f235d32b3 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 24 Aug 2020 16:22:21 +0300 Subject: [PATCH 067/282] Drone CI (#11) * CI Works a2 Fixes Correct repseqio version. Using latest pre-release milib build. Revert "Using latest pre-release milib build." This reverts commit b7539323749eadfa5c34a560cc902676aec3cec3. Correct CI signature. milib WIP wwip * Cherry pick for milib refactoring. * Fix for integration test environment. * Additional fix. --- .drone.yml | 99 +++++++++++++++++++ ensure-test-data.sh | 4 +- pom.xml | 23 ++++- prepare-test-data.sh | 2 +- .../mixcr/basictypes/CloneReader.java | 6 +- .../mixcr/basictypes/VDJCSProperties.java | 49 +++++++-- .../mixcr/cli/CommandAssemble.java | 18 ++-- 7 files changed, 170 insertions(+), 31 deletions(-) create mode 100644 .drone.yml diff --git a/.drone.yml b/.drone.yml new file mode 100644 index 000000000..d3b44205e --- /dev/null +++ b/.drone.yml @@ -0,0 +1,99 @@ +--- +kind: pipeline +type: docker +name: linux + +platform: + os: linux + arch: amd64 + +event: + - push + +steps: + - name: restore_cache + image: meltwater/drone-cache + pull: true + settings: + restore: true + # debug: true + cache_key: '{{ .Commit.Branch }}' + access_key: + from_secret: aws-key-id + secret_key: + from_secret: aws-secret-key + bucket: + from_secret: aws-cache-bucket + region: + from_secret: aws-region + local_root: /drone/src + mount: + - .m2 + - src/test/resources/big + + - name: deploy + image: maven:3-adoptopenjdk-8 + commands: + - mvn --no-transfer-progress deploy -DskipTests -DaltDeploymentRepository=therepo::default::$${DEPLOY_REPO} -Drevision=${DRONE_COMMIT_SHA:0:7} + environment: + MAVEN_OPTS: "-Dmaven.repo.local=/drone/src/.m2" + AWS_DEFAULT_REGION: + from_secret: aws-region + AWS_ACCESS_KEY_ID: + from_secret: aws-key-id + AWS_SECRET_ACCESS_KEY: + from_secret: aws-secret-key + DEPLOY_REPO: + from_secret: maven-deploy-repo-private + when: + event: + exclude: + - pull_request + depends_on: + - restore_cache + + - name: build_and_test + image: maven:3-adoptopenjdk-8 + commands: + - ./ensure-test-data.sh + - mvn --no-transfer-progress clean pre-integration-test + environment: + MAVEN_OPTS: "-Dmaven.repo.local=/drone/src/.m2" + depends_on: + - deploy + + - name: integration_tests + image: adoptopenjdk:8-hotspot + commands: + - apt-get update + - apt-get install -y jq + - ./itests.sh test + depends_on: + - build_and_test + + - name: rebuild_cache + image: meltwater/drone-cache + settings: + rebuild: true + # debug: true + cache_key: '{{ .Commit.Branch }}' + access_key: + from_secret: aws-key-id + secret_key: + from_secret: aws-secret-key + bucket: + from_secret: aws-cache-bucket + region: + from_secret: aws-region + local_root: /drone/src + mount: + - .m2 + - src/test/resources/big + depends_on: + - build_and_test + +--- +kind: signature +hmac: 28c3754e0acfce1c26faae033ffe7333cdb37a8714528d92df85e3430ab8c51c + +... diff --git a/ensure-test-data.sh b/ensure-test-data.sh index 054f3ac7f..1ed9b00eb 100755 --- a/ensure-test-data.sh +++ b/ensure-test-data.sh @@ -48,11 +48,11 @@ mkdir -p $dir/src/test/resources/sequences/big/ cd $dir/src/test/resources/sequences/big/ if [[ ! -f CD4M1_test_R1.fastq.gz ]]; then - curl -O https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R1.fastq.gz + curl -sS -O https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R1.fastq.gz fi if [[ ! -f CD4M1_test_R2.fastq.gz ]]; then - curl -O https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R2.fastq.gz + curl -sS -O https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R2.fastq.gz fi if [[ ! -d yf_sample_data ]]; then diff --git a/pom.xml b/pom.xml index be9ed8aa4..cf84f683c 100644 --- a/pom.xml +++ b/pom.xml @@ -34,20 +34,29 @@ com.milaboratory mixcr - 3.0.14-SNAPSHOT + 3.0.14-${revision} jar MiXCR UTF-8 - 1.14-SNAPSHOT + 1.14-47a96ec + SNAPSHOT + + + mipub + Public MiLaboratory Maven Repository + https://pub.maven.milaboratory.com + + + io.repseq repseqio - 1.3.5-SNAPSHOT + 1.3.5-341c4a3 com.milaboratory @@ -136,6 +145,14 @@ + + + com.github.seahen + maven-s3-wagon + 1.3.1 + + + org.apache.maven.plugins diff --git a/prepare-test-data.sh b/prepare-test-data.sh index a76407439..94081b850 100755 --- a/prepare-test-data.sh +++ b/prepare-test-data.sh @@ -47,7 +47,7 @@ esac cd "$dir/src/test/resources/sequences/big/" cd yf_sample_data -parallel -j5 "${dir}/mixcr" -Xmx500m analyze amplicon \ +parallel -j5 "${dir}/mixcr" -Xmx500m analyze amplicon -f \ -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present \ --assemble '-OseparateByC=true' --assemble '-OseparateByV=true' --assemble '-OseparateByJ=true' \ --assemble '--sort-by-sequence' \ diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java index 789f169af..f608122b5 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -31,10 +31,7 @@ import cc.redberry.pipe.OutputPortCloseable; -import java.util.Comparator; -import java.util.List; - -public interface CloneReader { +public interface CloneReader extends AutoCloseable { /** * Sequence of properties the stream is sorted by. * @@ -42,6 +39,5 @@ public interface CloneReader { */ VDJCSProperties.CloneOrdering ordering(); - OutputPortCloseable readClones(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java index 55fda0617..4e94bd716 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java @@ -40,22 +40,51 @@ import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; -import java.util.Arrays; -import java.util.Comparator; -import java.util.List; -import java.util.Objects; +import java.util.*; import static com.milaboratory.util.sorting.SortingPropertyRelation.*; public class VDJCSProperties { public static final CloneOrdering CO_BY_COUNT = new CloneOrdering(new CloneCount()); + public static CloneOrdering cloneOrderingByAminoAcid(GeneFeature[] geneFeatures, + GeneType... segments) { + return new CloneOrdering(orderingByAminoAcid(geneFeatures, segments)); + } + + public static CloneOrdering cloneOrderingByNucleotide(GeneFeature[] geneFeatures, + GeneType... segments) { + return new CloneOrdering(orderingByNucleotide(geneFeatures, segments)); + } + + public static List> orderingByAminoAcid( + GeneFeature[] geneFeatures, GeneType... segments) { + List> result = new ArrayList<>(); + for (GeneFeature geneFeature : geneFeatures) + result.add(new AASequence(geneFeature)); + for (GeneType segment : segments) + result.add(new VDJCSegment(segment)); + return result; + } + + public static List> orderingByNucleotide( + GeneFeature[] geneFeatures, GeneType... segments) { + List> result = new ArrayList<>(); + for (GeneFeature geneFeature : geneFeatures) + result.add(new AASequence(geneFeature)); + for (GeneFeature geneFeature : geneFeatures) + result.add(new NSequence(geneFeature)); + for (GeneType segment : segments) + result.add(new VDJCSegment(segment)); + return result; + } + @Serializable(asJson = true) public static final class CloneOrdering { @JsonProperty("properties") - public final VDJCSProperties.VDJCSProperty[] properties; + private final VDJCSProperties.VDJCSProperty[] properties; - public CloneOrdering(List> properties) { + public CloneOrdering(List> properties) { this.properties = properties.toArray(new VDJCSProperty[properties.size()]); } @@ -64,6 +93,10 @@ public CloneOrdering(@JsonProperty("properties") VDJCSProperty... this.properties = properties; } + public List> getProperties() { + return Arrays.asList(properties); + } + public Comparator comparator() { return SortingUtil.combine(properties); } @@ -118,7 +151,7 @@ public NSequence(@JsonProperty("geneFeature") GeneFeature geneFeature) { } @Override - public SortingPropertyRelation relationTo(SortingProperty other) { + public SortingPropertyRelation relationTo(SortingProperty other) { if (equals(other)) return SortingPropertyRelation.Equal; @@ -172,7 +205,7 @@ public AASequence(@JsonProperty("geneFeature") GeneFeature geneFeature) { } @Override - public SortingPropertyRelation relationTo(SortingProperty other) { + public SortingPropertyRelation relationTo(SortingProperty other) { if (equals(other)) return SortingPropertyRelation.Equal; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index bb57f53cf..deff9a6e2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -48,8 +48,10 @@ import picocli.CommandLine.Option; import java.io.IOException; -import java.util.*; -import java.util.stream.Collectors; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Objects; import static com.milaboratory.mixcr.cli.CommandAssemble.ASSEMBLE_COMMAND_NAME; @@ -164,16 +166,8 @@ private void ensureParametersInitialized() { break; } - List> orderingList = new ArrayList<>(); - orderingList.addAll(Arrays.stream(assemblingFeatures) - .map(VDJCSProperties.NSequence::new) - .collect(Collectors.toList())); - orderingList.addAll(Arrays.stream(assemblingFeatures) - .map(VDJCSProperties.AASequence::new) - .collect(Collectors.toList())); - orderingList.add(new VDJCSProperties.VDJCSegment(GeneType.Variable)); - orderingList.add(new VDJCSProperties.VDJCSegment(GeneType.Joining)); - ordering = new VDJCSProperties.CloneOrdering(orderingList); + ordering = VDJCSProperties.cloneOrderingByNucleotide(assemblingFeatures, + GeneType.Variable, GeneType.Joining); } else { ordering = VDJCSProperties.CO_BY_COUNT; } From 6c587f82408c2d04ec0bdc786bfbf628c6d24650 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 27 Aug 2020 14:35:56 +0300 Subject: [PATCH 068/282] Artefacts (#12) * wip * ugu * a1 * a2 * a3 * a4 * a5 * a6 * Short artefact names. * asd * ddd * ddd * More fixes. * ugu * sdfa * ok --- .drone.yml | 141 ++++++++++++++++++++++++++++++++++++++++++++++++++--- pack.sh | 12 +++++ 2 files changed, 145 insertions(+), 8 deletions(-) create mode 100755 pack.sh diff --git a/.drone.yml b/.drone.yml index d3b44205e..e7d192726 100644 --- a/.drone.yml +++ b/.drone.yml @@ -1,7 +1,7 @@ --- kind: pipeline type: docker -name: linux +name: depoly platform: os: linux @@ -17,7 +17,7 @@ steps: settings: restore: true # debug: true - cache_key: '{{ .Commit.Branch }}' + cache_key: 'deploy-{{ .Commit.Branch }}' access_key: from_secret: aws-key-id secret_key: @@ -29,15 +29,14 @@ steps: local_root: /drone/src mount: - .m2 - - src/test/resources/big - - name: deploy + - name: deploy_maven image: maven:3-adoptopenjdk-8 commands: - mvn --no-transfer-progress deploy -DskipTests -DaltDeploymentRepository=therepo::default::$${DEPLOY_REPO} -Drevision=${DRONE_COMMIT_SHA:0:7} environment: MAVEN_OPTS: "-Dmaven.repo.local=/drone/src/.m2" - AWS_DEFAULT_REGION: + AWS_REGION: from_secret: aws-region AWS_ACCESS_KEY_ID: from_secret: aws-key-id @@ -52,6 +51,131 @@ steps: depends_on: - restore_cache + - name: deploy_bin + image: banst/awscli + commands: + - apk add --no-cache zip + - ./pack.sh + - touch empty + - aws s3 cp target/mixcr.zip s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip + - > + aws s3api put-object-tagging \ + --bucket $${DEPLOY_S3_CDN_BUCKET} \ + --key $${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip \ + --tagging '{"TagSet": [{"Key":"git_commit","Value":"${DRONE_COMMIT}"},{"Key":"git_branch","Value":"${DRONE_BRANCH}"}]}' + - aws s3 cp --website-redirect 'https://cdn.milaboratory.com/software/mixcr/mixcr-${DRONE_COMMIT}.zip?response-content-disposition=attachment;filename=mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip' empty "s3://$${DEPLOY_S3_LINK_BUCKET}/$${DEPLOY_S3_LINK_PREFIX}/mixcr/mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip" + environment: + AWS_REGION: + from_secret: aws-region + AWS_ACCESS_KEY_ID: + from_secret: aws-key-id + AWS_SECRET_ACCESS_KEY: + from_secret: aws-secret-key + DEPLOY_S3_CDN_BUCKET: + from_secret: cdn-s3-bucket + DEPLOY_S3_CDN_PREFIX: + from_secret: cdn-s3-prefix + DEPLOY_S3_LINK_BUCKET: + from_secret: bin-link-s3-bucket + DEPLOY_S3_LINK_PREFIX: + from_secret: bin-link-s3-prefix + when: + event: + exclude: + - pull_request + depends_on: + - deploy_maven + + - name: Send Telegram Notification + image: appleboy/drone-telegram + depends_on: + - deploy_bin + settings: + token: + from_secret: telegram-token + to: + from_secret: telegram-chat-id-micore + format: markdown + message: > + {{#success build.status}} + ✅ MiXCR deploy {{build.number}} success. + + + 🌐 https://bin.milaboratory.com/mixcr/mixcr-b{{build.number}}-{{truncate commit.sha 7}}.zip + + + POM: + + ``` + + com.milaboratory + + mixcr + + 3.0.14-{{truncate commit.sha 7}} + ``` + {{else}} + ❌ MiXCR deploy {{build.number}} failure. + 🌐 {{build.link}} + {{/success}} + + - name: rebuild_cache + image: meltwater/drone-cache + settings: + rebuild: true + # debug: true + cache_key: 'deploy-{{ .Commit.Branch }}' + access_key: + from_secret: aws-key-id + secret_key: + from_secret: aws-secret-key + bucket: + from_secret: aws-cache-bucket + region: + from_secret: aws-region + local_root: /drone/src + mount: + - .m2 + depends_on: + - deploy_maven + +--- + +kind: pipeline +type: docker +name: test + +platform: + os: linux + arch: amd64 + +node: + type: highcpu + +event: + - push + +steps: + - name: restore_cache + image: meltwater/drone-cache + pull: true + settings: + restore: true + # debug: true + cache_key: 'test-{{ .Commit.Branch }}' + access_key: + from_secret: aws-key-id + secret_key: + from_secret: aws-secret-key + bucket: + from_secret: aws-cache-bucket + region: + from_secret: aws-region + local_root: /drone/src + mount: + - .m2 + - src/test/resources/big + - name: build_and_test image: maven:3-adoptopenjdk-8 commands: @@ -60,7 +184,7 @@ steps: environment: MAVEN_OPTS: "-Dmaven.repo.local=/drone/src/.m2" depends_on: - - deploy + - restore_cache - name: integration_tests image: adoptopenjdk:8-hotspot @@ -73,10 +197,11 @@ steps: - name: rebuild_cache image: meltwater/drone-cache + pull: true settings: rebuild: true # debug: true - cache_key: '{{ .Commit.Branch }}' + cache_key: 'test-{{ .Commit.Branch }}' access_key: from_secret: aws-key-id secret_key: @@ -94,6 +219,6 @@ steps: --- kind: signature -hmac: 28c3754e0acfce1c26faae033ffe7333cdb37a8714528d92df85e3430ab8c51c +hmac: d9fb38bed6974279a8b2af61f6a9eb16f0317f2002af6241d92d372fa2609b68 ... diff --git a/pack.sh b/pack.sh new file mode 100755 index 000000000..eca9b5507 --- /dev/null +++ b/pack.sh @@ -0,0 +1,12 @@ +#!/usr/bin/env sh + +set -e + +mkdir -p target/mixcr +cp mixcr target/mixcr/mixcr +cp LICENSE target/mixcr/LICENSE +cp target/mixcr*-distribution*.jar target/mixcr/mixcr.jar + +cd target + +zip -r -9 mixcr.zip mixcr From 52b4f16d29f77654c1c4ee3764065a9fbe8b89e6 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Sun, 30 Aug 2020 22:55:23 +0300 Subject: [PATCH 069/282] Last correction to the CDN infrastructure. --- .drone.yml | 6 +++--- pom.xml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.drone.yml b/.drone.yml index e7d192726..e8560293e 100644 --- a/.drone.yml +++ b/.drone.yml @@ -62,7 +62,7 @@ steps: aws s3api put-object-tagging \ --bucket $${DEPLOY_S3_CDN_BUCKET} \ --key $${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip \ - --tagging '{"TagSet": [{"Key":"git_commit","Value":"${DRONE_COMMIT}"},{"Key":"git_branch","Value":"${DRONE_BRANCH}"}]}' + --tagging '{"TagSet": [{"Key":"git_commit","Value":"${DRONE_COMMIT}"},{"Key":"git_branch","Value":"${DRONE_BRANCH}"},{"Key":"software","Value":"mixcr"}]}' - aws s3 cp --website-redirect 'https://cdn.milaboratory.com/software/mixcr/mixcr-${DRONE_COMMIT}.zip?response-content-disposition=attachment;filename=mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip' empty "s3://$${DEPLOY_S3_LINK_BUCKET}/$${DEPLOY_S3_LINK_PREFIX}/mixcr/mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip" environment: AWS_REGION: @@ -76,9 +76,9 @@ steps: DEPLOY_S3_CDN_PREFIX: from_secret: cdn-s3-prefix DEPLOY_S3_LINK_BUCKET: - from_secret: bin-link-s3-bucket + from_secret: link-s3-bucket DEPLOY_S3_LINK_PREFIX: - from_secret: bin-link-s3-prefix + from_secret: link-s3-prefix when: event: exclude: diff --git a/pom.xml b/pom.xml index cf84f683c..a4e542e26 100644 --- a/pom.xml +++ b/pom.xml @@ -266,7 +266,7 @@ org.apache.maven.plugins maven-shade-plugin - 3.2.1 + 3.2.4 pre-integration-test From 643668788bc5ca3133499421793c8a0c438c3a3f Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Sun, 30 Aug 2020 23:01:58 +0300 Subject: [PATCH 070/282] Signature. --- .drone.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.drone.yml b/.drone.yml index e8560293e..f7a8e5a2c 100644 --- a/.drone.yml +++ b/.drone.yml @@ -219,6 +219,6 @@ steps: --- kind: signature -hmac: d9fb38bed6974279a8b2af61f6a9eb16f0317f2002af6241d92d372fa2609b68 +hmac: bfa31163b70e4c937822646f200c3645abf178ef5df60d8b727727f5e63f1e50 ... From a756481b77feef11a08328c78920124f75413b89 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Sun, 30 Aug 2020 23:02:56 +0300 Subject: [PATCH 071/282] Fix. --- .drone.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.drone.yml b/.drone.yml index f7a8e5a2c..deb310519 100644 --- a/.drone.yml +++ b/.drone.yml @@ -219,6 +219,6 @@ steps: --- kind: signature -hmac: bfa31163b70e4c937822646f200c3645abf178ef5df60d8b727727f5e63f1e50 +hmac: ea6c56834a73234f9c1e6d62b5979878703fc08156b51eb91c194f6a1598bee7 ... From 9ee447830c8e3d9e46ef4702f6a8558f079c311e Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Sun, 30 Aug 2020 23:11:11 +0300 Subject: [PATCH 072/282] Final link correction. --- .drone.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.drone.yml b/.drone.yml index deb310519..f608243fe 100644 --- a/.drone.yml +++ b/.drone.yml @@ -63,7 +63,7 @@ steps: --bucket $${DEPLOY_S3_CDN_BUCKET} \ --key $${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip \ --tagging '{"TagSet": [{"Key":"git_commit","Value":"${DRONE_COMMIT}"},{"Key":"git_branch","Value":"${DRONE_BRANCH}"},{"Key":"software","Value":"mixcr"}]}' - - aws s3 cp --website-redirect 'https://cdn.milaboratory.com/software/mixcr/mixcr-${DRONE_COMMIT}.zip?response-content-disposition=attachment;filename=mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip' empty "s3://$${DEPLOY_S3_LINK_BUCKET}/$${DEPLOY_S3_LINK_PREFIX}/mixcr/mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip" + - aws s3 cp --website-redirect 'https://cdn.milaboratory.com/software/mixcr/mixcr-${DRONE_COMMIT}.zip?response-content-disposition=attachment;filename=mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip' empty "s3://$${DEPLOY_S3_LINK_BUCKET}/$${DEPLOY_S3_LINK_PREFIX}/software/mixcr/mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip" environment: AWS_REGION: from_secret: aws-region @@ -219,6 +219,6 @@ steps: --- kind: signature -hmac: ea6c56834a73234f9c1e6d62b5979878703fc08156b51eb91c194f6a1598bee7 +hmac: 1397d9a89faf007682746dab1e15cfaa72f1f9f512f97b6a85627796cdd361b8 ... From a0921a0e18a630f573b6932d865f6a6f8ca6e38c Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 1 Sep 2020 13:57:07 +0300 Subject: [PATCH 073/282] Cache control for binary packages. --- .drone.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.drone.yml b/.drone.yml index f608243fe..567255492 100644 --- a/.drone.yml +++ b/.drone.yml @@ -62,6 +62,7 @@ steps: aws s3api put-object-tagging \ --bucket $${DEPLOY_S3_CDN_BUCKET} \ --key $${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip \ + --metadata-directive REPLACE --cache-control "max-age=604800,public" \ --tagging '{"TagSet": [{"Key":"git_commit","Value":"${DRONE_COMMIT}"},{"Key":"git_branch","Value":"${DRONE_BRANCH}"},{"Key":"software","Value":"mixcr"}]}' - aws s3 cp --website-redirect 'https://cdn.milaboratory.com/software/mixcr/mixcr-${DRONE_COMMIT}.zip?response-content-disposition=attachment;filename=mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip' empty "s3://$${DEPLOY_S3_LINK_BUCKET}/$${DEPLOY_S3_LINK_PREFIX}/software/mixcr/mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip" environment: @@ -219,6 +220,6 @@ steps: --- kind: signature -hmac: 1397d9a89faf007682746dab1e15cfaa72f1f9f512f97b6a85627796cdd361b8 +hmac: a90ec8f75648bbfbb91d74584526f1ca7ea745dbcfb41e0bb0dee75e4d6707ac ... From 2a7145d7dd19062830caeca28d027cb3485b5c02 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 1 Sep 2020 18:04:12 +0300 Subject: [PATCH 074/282] Postanalysis (#13) * repseqio upgrade. * wip * wip * First tests. * Wip * Test2 * Aggregator for diversity metrics * wip overlaps * wip * WIP * wip / towards real postanalysis run * wip * wip * wip * wip downsampling * downsampling * wip * wip postanalysis refactoring * wip postanalysis - something working * wip * mode json stuff * wip * wip * wip * wip * wip * wip * initial * fixes * fix isotype usage * Spectratype PA * wip * wip * wip * wip * small fix in analyze --json-report * fix ic tests * Overlap (#8) * Something works. * Test ignore. * UnIgnore integration test. * Done+- * wip * wip * HierarchyWIP * minor / to remove * wip * fix in cli * wip * Hierarchical clustering (#9) * Added ability to override preprocessor in characteristic * wip * Environmental variable to control repseqio cache folder path. * RepseqIO upgrade. * fixes * wip * CDR3 spectratype summary * Repseqio upgrade. (#10) * Types. * fix clustering * - Clustering toString fix - Fixed no top node * wip * wip * fix for spaces in file names Co-authored-by: Stanislav Poslavsky Co-authored-by: Mark Izraelson --- milib | 2 +- repseqio | 2 +- .../mixcr/basictypes/ClnsReader.java | 8 +- .../mixcr/basictypes/CloneSetIO.java | 18 +- .../mixcr/basictypes/CloneSetOverlap.java | 56 +++ .../mixcr/basictypes/SequenceHistory.java | 4 +- .../mixcr/basictypes/VDJCObject.java | 29 ++ .../mixcr/cli/CommandAnalyze.java | 68 ++-- .../mixcr/cli/CommandAssemble.java | 8 +- .../java/com/milaboratory/mixcr/cli/Main.java | 4 + .../mixcr/postanalysis/Aggregator.java | 31 ++ .../mixcr/postanalysis/Characteristic.java | 101 +++++ .../mixcr/postanalysis/MetricValue.java | 75 ++++ .../postanalysis/PostanalysisResult.java | 114 ++++++ .../postanalysis/PostanalysisRunner.java | 93 +++++ .../mixcr/postanalysis/SetPreprocessor.java | 56 +++ .../mixcr/postanalysis/WeightFunction.java | 21 + .../mixcr/postanalysis/WeightFunctions.java | 48 +++ .../postanalysis/additive/AAProperties.java | 143 +++++++ .../additive/AdditiveAggregator.java | 136 +++++++ .../additive/AdditiveCharacteristic.java | 111 ++++++ .../additive/AdditiveCharacteristics.java | 193 +++++++++ .../postanalysis/additive/AdditiveMetric.java | 31 ++ .../additive/AdditiveMetrics.java | 154 ++++++++ .../additive/AggregationType.java | 8 + .../postanalysis/additive/KeyFunction.java | 38 ++ .../postanalysis/additive/KeyFunctions.java | 370 ++++++++++++++++++ .../postanalysis/additive/Normalization.java | 36 ++ .../clustering/HierarchicalClustering.java | 169 ++++++++ .../clustering/HierarchyNode.java | 45 +++ .../diversity/DiversityAggregator.java | 132 +++++++ .../diversity/DiversityCharacteristic.java | 31 ++ .../diversity/DiversityMeasure.java | 16 + .../ClonesDownsamplingPreprocessor.java | 38 ++ ...ClonesOverlapDownsamplingPreprocessor.java | 38 ++ .../downsampling/DownsampleValueChooser.java | 112 ++++++ .../DownsamplingPreprocessor.java | 90 +++++ .../downsampling/DownsamplingUtil.java | 78 ++++ .../downsampling/LogFactorial.java | 193 +++++++++ .../OverlapDownsamplingPreprocessor.java | 132 +++++++ .../downsampling/RandomHypergeometric.java | 319 +++++++++++++++ .../downsampling/RandomMvhgCounts.java | 168 ++++++++ .../downsampling/RandomMvhgMarginals.java | 174 ++++++++ .../AdditiveOverlapCharacteristic.java | 28 ++ .../overlap/OverlapAggregator.java | 68 ++++ .../overlap/OverlapCharacteristic.java | 55 +++ .../postanalysis/overlap/OverlapGroup.java | 67 ++++ .../overlap/OverlapGroupAdditiveMetric.java | 10 + .../overlap/OverlapGroupKeyFunction.java | 10 + .../overlap/OverlapGroupWeightFunction.java | 10 + .../postanalysis/overlap/OverlapIterable.java | 33 ++ .../postanalysis/overlap/OverlapKey.java | 57 +++ .../postanalysis/overlap/OverlapType.java | 28 ++ .../postanalysis/overlap/OverlapUtil.java | 55 +++ .../preproc/ElementPredicate.java | 135 +++++++ .../preproc/FilterPreprocessor.java | 37 ++ .../postanalysis/preproc/NoPreprocessing.java | 29 ++ .../preproc/PreprocessorChain.java | 39 ++ .../preproc/SampleFilterPreprocessor.java | 34 ++ .../spectratype/SpectratypeAggregator.java | 114 ++++++ .../SpectratypeCharacteristic.java | 51 +++ .../spectratype/SpectratypeKey.java | 53 +++ .../spectratype/SpectratypeKeyFunction.java | 70 ++++ .../postanalysis/ui/CharacteristicGroup.java | 65 +++ .../CharacteristicGroupOutputExtractor.java | 26 ++ .../ui/CharacteristicGroupResult.java | 51 +++ .../ui/CharacteristicGroupResultBuilder.java | 44 +++ .../ui/CharacteristicGroupResultCell.java | 39 ++ .../mixcr/postanalysis/ui/ClonesIterable.java | 59 +++ .../mixcr/postanalysis/ui/Coordinates.java | 16 + .../mixcr/postanalysis/ui/GroupMelt.java | 120 ++++++ .../mixcr/postanalysis/ui/GroupSummary.java | 28 ++ .../mixcr/postanalysis/ui/OutputTable.java | 155 ++++++++ .../postanalysis/ui/OutputTableBuilder.java | 44 +++ .../postanalysis/ui/OutputTableCell.java | 51 +++ .../postanalysis/ui/OutputTableExtractor.java | 24 ++ .../mixcr/postanalysis/ui/OverlapSummary.java | 38 ++ .../postanalysis/ui/PostanalysisSchema.java | 74 ++++ .../mixcr/util/FilteredIterable.java | 25 ++ .../mixcr/util/FilteredIterator.java | 41 ++ .../com/milaboratory/mixcr/util/Tuple2.java | 51 +++ .../resources/postanalysis/aa_properties.csv | 21 + .../mixcr/basictypes/VDJCObjectTest.java | 2 +- .../com/milaboratory/mixcr/cli/MainTest.java | 2 +- .../HierarchicalClusteringTest.java | 46 +++ .../DownsamplingPreprocessorTest.java | 88 +++++ .../overlap/OverlapIntegrationTest.java | 96 +++++ .../ui/PostanalysisSchemaIntegrationTest.java | 241 ++++++++++++ 88 files changed, 6075 insertions(+), 48 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesOverlapDownsamplingPreprocessor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java create mode 100644 src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java create mode 100644 src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java create mode 100644 src/main/java/com/milaboratory/mixcr/util/Tuple2.java create mode 100644 src/main/resources/postanalysis/aa_properties.csv create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java diff --git a/milib b/milib index 29a1c9c6e..e534a4fb2 160000 --- a/milib +++ b/milib @@ -1 +1 @@ -Subproject commit 29a1c9c6e45bd475da831ba840c8d2d2460de596 +Subproject commit e534a4fb249c5a97e80e4acaeb12eb2cee050e9a diff --git a/repseqio b/repseqio index 476bf935b..391149707 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 476bf935bb15610ef6af5f772076df5ad59d5428 +Subproject commit 391149707cdcc15d726d13f7d6a3e299b7eb8397 diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index b882c5def..d99493c36 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -66,14 +66,14 @@ public class ClnsReader extends PipelineConfigurationReaderMiXCR implements Clon private final long clonesPosition; public ClnsReader(Path file, VDJCLibraryRegistry libraryRegistry) throws IOException { - this(file, 3, libraryRegistry); + this(file, libraryRegistry, 3); } - public ClnsReader(Path file, int concurrency, VDJCLibraryRegistry libraryRegistry) throws IOException { - this(file, new LambdaSemaphore(concurrency), libraryRegistry); + public ClnsReader(Path file, VDJCLibraryRegistry libraryRegistry, int concurrency) throws IOException { + this(file, libraryRegistry, new LambdaSemaphore(concurrency)); } - public ClnsReader(Path file, LambdaSemaphore concurrencyLimiter, VDJCLibraryRegistry libraryRegistry) throws IOException { + public ClnsReader(Path file, VDJCLibraryRegistry libraryRegistry, LambdaSemaphore concurrencyLimiter) throws IOException { this(new PrimitivIHybrid(file, concurrencyLimiter), libraryRegistry); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java index 4ac4086b0..78865c28e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java @@ -33,7 +33,7 @@ import java.io.File; import java.io.IOException; -import java.io.InputStream; +import java.nio.file.Path; import java.util.Objects; import static com.milaboratory.mixcr.basictypes.IOUtil.*; @@ -65,4 +65,20 @@ public static CloneSet read(File file, VDJCLibraryRegistry libraryRegistry) thro throw new RuntimeException("Unsupported file type"); } } + + public static CloneReader mkReader(Path file, VDJCLibraryRegistry libraryRegistry) throws IOException { + return mkReader(file, libraryRegistry, 1); + } + + public static CloneReader mkReader(Path file, VDJCLibraryRegistry libraryRegistry, int concurrency) throws IOException { + switch (Objects.requireNonNull(fileInfoExtractorInstance.getFileInfo(file.toFile())).fileType) { + case MAGIC_CLNA: + return new ClnAReader(file, libraryRegistry, concurrency); + case MAGIC_CLNS: + return new ClnsReader(file, libraryRegistry, concurrency); + default: + throw new RuntimeException("Unsupported file type"); + } + } + } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java new file mode 100644 index 000000000..f99e65aaf --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java @@ -0,0 +1,56 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.basictypes; + +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.util.sorting.MergeStrategy; + +import java.util.List; +import java.util.stream.Collectors; + +public final class CloneSetOverlap { + private CloneSetOverlap() { + } + + public static final OutputPortCloseable>> overlap( + List> by, + List readers) { + VDJCSProperties.CloneOrdering ordering = readers.get(0).ordering(); + for (int i = 1; i < readers.size(); i++) + if (!ordering.equals(readers.get(i).ordering())) + throw new RuntimeException("All clonesets must be sorted the same way."); + MergeStrategy strategy = MergeStrategy.calculateStrategy(ordering.getProperties(), by); + if (!strategy.usesStreamOrdering()) + throw new RuntimeException("Clone sorting is incompatible with overlap criteria."); + return strategy.join(readers.stream() + .map(CloneReader::readClones) + .collect(Collectors.toList())); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java b/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java index 10e40b88c..d246e2cbb 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java @@ -271,7 +271,7 @@ enum OverlapType { */ final class Merge implements SequenceHistory { /** - * Overlap type + * CloneSetOverlap type */ final OverlapType overlapType; /** @@ -499,7 +499,7 @@ public void write(PrimitivO output, SequenceHistory object) { Merge obj = (Merge) object; // Type descriptor output.writeByte(2); - // Overlap type + // CloneSetOverlap type output.writeObject(obj.overlapType); // Offset and number of mismatches output.writeVarInt(obj.offset); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index fbb44eff5..4368363e3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -311,6 +311,35 @@ public AminoAcidSequence getAAFeature(GeneFeature geneFeature) { target.getFeature(geneFeature).getSequence(), tp); // target.getFeature(geneFeature) uses exactly the same algorithm, guaranteed to be non-null at this point } + public AminoAcidSequence getFeatureAA(GeneFeature geneFeature) { + NSequenceWithQuality feature = getFeature(geneFeature); + if (feature == null) + return null; + + int targetId = getTargetContainingFeature(geneFeature); + TranslationParameters tr = targetId == -1 ? + TranslationParameters.FromLeftWithIncompleteCodon + : getPartitionedTarget(targetId).getPartitioning().getTranslationParameters(geneFeature); + if (tr == null) + return null; + return AminoAcidSequence.translate(feature.getSequence(), tr); + } + + + public int ntLengthOf(GeneFeature gf) { + NSequenceWithQuality f = getFeature(gf); + if (f == null) + return -1; + return f.size(); + } + + public int aaLengthOf(GeneFeature gf) { + AminoAcidSequence f = getFeatureAA(gf); + if (f == null) + return -1; + return f.size(); + } + public CaseSensitiveNucleotideSequence getIncompleteFeature(GeneFeature geneFeature) { NSequenceWithQuality feature = getFeature(geneFeature); if (feature != null) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index 35179b072..52b8bb9e5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -44,6 +44,8 @@ import java.io.File; import java.lang.reflect.Field; +import java.nio.file.Files; +import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; @@ -369,7 +371,12 @@ void addReportOptions(String step, List options) { // add json report file if (jsonReport != null) { options.add("--json-report"); - options.add(jsonReport + "." + step + ".jsonl"); + String pref; + if (Files.isDirectory(Paths.get(jsonReport))) + pref = jsonReport + (jsonReport.endsWith(File.separator) ? "" : File.separator); + else + pref = jsonReport + "."; + options.add(pref + step + ".jsonl"); } } @@ -415,7 +422,10 @@ CommandAlign mkAlign() { alignParameters.addAll(this.pipelineSpecificAlignParameters()); // add all override parameters - alignParameters.addAll(this.alignParameters); + alignParameters.addAll(this.alignParameters + .stream() + .flatMap(s -> Arrays.stream(s.split(" "))) + .collect(Collectors.toList())); // put input fastq files & output vdjca alignParameters.addAll(getInputFiles()); @@ -424,13 +434,7 @@ CommandAlign mkAlign() { // parse parameters CommandAlign ap = new CommandAlign(); ap.spec = this.spec; - new CommandLine(ap).parse( - alignParameters - .stream() - .flatMap(s -> Arrays.stream(s.split(" "))) - .toArray(String[]::new)); - - + new CommandLine(ap).parseArgs(alignParameters.toArray(new String[0])); return ap; } @@ -447,18 +451,17 @@ public final CommandAssemblePartialAlignments mkAssemblePartial(String input, St addReportOptions("assemblePartial", assemblePartialParameters); // add all override parameters - assemblePartialParameters.addAll(this.assemblePartialParameters); + assemblePartialParameters.addAll(this.assemblePartialParameters + .stream() + .flatMap(s -> Arrays.stream(s.split(" "))) + .collect(Collectors.toList())); assemblePartialParameters.add(input); assemblePartialParameters.add(output); // parse parameters CommandAssemblePartialAlignments ap = new CommandAssemblePartialAlignments(); - new CommandLine(ap).parse( - assemblePartialParameters - .stream() - .flatMap(s -> Arrays.stream(s.split(" "))) - .toArray(String[]::new)); + new CommandLine(ap).parseArgs(assemblePartialParameters.toArray(new String[0])); return inheritOptionsAndValidate(ap); } @@ -477,18 +480,17 @@ public final CommandExtend mkExtend(String input, String output) { inheritThreads(extendParameters, this.extendAlignmentsParameters); // add all override parameters - extendParameters.addAll(this.extendAlignmentsParameters); + extendParameters.addAll(this.extendAlignmentsParameters + .stream() + .flatMap(s -> Arrays.stream(s.split(" "))) + .collect(Collectors.toList())); extendParameters.add(input); extendParameters.add(output); // parse parameters CommandExtend ap = new CommandExtend(); - new CommandLine(ap).parse( - extendParameters - .stream() - .flatMap(s -> Arrays.stream(s.split(" "))) - .toArray(String[]::new)); + new CommandLine(ap).parseArgs(extendParameters.toArray(new String[0])); return inheritOptionsAndValidate(ap); } @@ -518,21 +520,18 @@ CommandAssemble mkAssemble(String input, String output) { assembleParameters.addAll(this.pipelineSpecificAssembleParameters()); // add all override parameters - assembleParameters.addAll(this.assembleParameters); + assembleParameters.addAll(this.assembleParameters + .stream() + .flatMap(s -> Arrays.stream(s.split(" "))) + .collect(Collectors.toList())); assembleParameters.add(input); assembleParameters.add(output); // parse parameters CommandAssemble ap = new CommandAssemble(); - new CommandLine(ap).parse( - assembleParameters - .stream() - .flatMap(s -> Arrays.stream(s.split(" "))) - .toArray(String[]::new)); - + new CommandLine(ap).parseArgs(assembleParameters.toArray(new String[0])); ap.getCloneAssemblerParameters().updateFrom(mkAlign().getAlignerParameters()); - return ap; } @@ -551,18 +550,17 @@ public final CommandAssembleContigs mkAssembleContigs(String input, String outpu inheritThreads(assembleContigParameters, this.assembleContigParameters); // add all override parameters - assembleContigParameters.addAll(this.assembleContigParameters); + assembleContigParameters.addAll(this.assembleContigParameters + .stream() + .flatMap(s -> Arrays.stream(s.split(" "))) + .collect(Collectors.toList())); assembleContigParameters.add(input); assembleContigParameters.add(output); // parse parameters CommandAssembleContigs ap = new CommandAssembleContigs(); - new CommandLine(ap).parse( - assembleContigParameters - .stream() - .flatMap(s -> Arrays.stream(s.split(" "))) - .toArray(String[]::new)); + new CommandLine(ap).parseArgs(assembleContigParameters.toArray(new String[0])); return inheritOptionsAndValidate(ap); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index deff9a6e2..c8a4a15c1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -115,7 +115,8 @@ public void setThreads(int threads) { @Override public ActionConfiguration getConfiguration() { - return new AssembleConfiguration(getCloneAssemblerParameters(), clna); + ensureParametersInitialized(); + return new AssembleConfiguration(getCloneAssemblerParameters(), clna, ordering); } // Extracting V/D/J/C gene list from input vdjca file @@ -419,13 +420,16 @@ public int hashCode() { public static class AssembleConfiguration implements ActionConfiguration { public final CloneAssemblerParameters assemblerParameters; public final boolean clna; + public final VDJCSProperties.CloneOrdering ordering; @JsonCreator public AssembleConfiguration( @JsonProperty("assemblerParameters") CloneAssemblerParameters assemblerParameters, - @JsonProperty("clna") boolean clna) { + @JsonProperty("clna") boolean clna, + @JsonProperty("ordering") VDJCSProperties.CloneOrdering ordering) { this.assemblerParameters = assemblerParameters; this.clna = clna; + this.ordering = ordering; } @Override diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index f270bdce6..37c8dc368 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -110,6 +110,10 @@ public static CommandLine mkCmd() { TempFileManager.setPrefix("mixcr_"); Path cachePath = Paths.get(System.getProperty("user.home"), ".mixcr", "cache"); + String repseqioCacheEnv = System.getenv("REPSEQIO_CACHE"); + if (repseqioCacheEnv != null) { + cachePath = Paths.get(repseqioCacheEnv); + } //if (System.getProperty("allow.http") != null || System.getenv("MIXCR_ALLOW_HTTP") != null) //TODO add mechanism to deny http requests SequenceResolvers.initDefaultResolver(cachePath); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java new file mode 100644 index 000000000..bd993d390 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java @@ -0,0 +1,31 @@ +package com.milaboratory.mixcr.postanalysis; + +import java.util.ArrayList; +import java.util.Arrays; + +public interface Aggregator { + /** apply for each clone */ + void consume(T obj); + + /** get the result */ + MetricValue[] result(); + + static Aggregator merge(Aggregator agg1, Aggregator agg2) { + return new Aggregator() { + @Override + public void consume(T obj) { + agg1.consume(obj); + agg2.consume(obj); + } + + @Override + public MetricValue[] result() { + ArrayList> r = new ArrayList<>(); + r.addAll(Arrays.asList(agg1.result())); + r.addAll(Arrays.asList(agg2.result())); + //noinspection unchecked + return r.toArray(new MetricValue[0]); + } + }; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java new file mode 100644 index 000000000..4331216f9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java @@ -0,0 +1,101 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.fasterxml.jackson.annotation.*; +import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristic; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; +import com.milaboratory.mixcr.postanalysis.overlap.AdditiveOverlapCharacteristic; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapCharacteristic; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; + +import java.util.Objects; + +/** + * + */ +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = AdditiveCharacteristic.class, name = "individual"), + @JsonSubTypes.Type(value = DiversityCharacteristic.class, name = "diversity"), + @JsonSubTypes.Type(value = OverlapCharacteristic.class, name = "overlap"), + @JsonSubTypes.Type(value = AdditiveOverlapCharacteristic.class, name = "overlapIndividual"), + @JsonSubTypes.Type(value = SpectratypeCharacteristic.class, name = "geneFeatureSpectratype"), + @JsonSubTypes.Type(value = Characteristic.CharacteristicWrapper.class, name = "characteristicWrapper") +}) +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public abstract class Characteristic { + @JsonProperty("name") + public final String name; + @JsonProperty("preproc") + public final SetPreprocessor preprocessor; + @JsonProperty("weight") + public final WeightFunction weight; + + public Characteristic(String name, SetPreprocessor preprocessor, WeightFunction weight) { + this.name = name; + this.preprocessor = preprocessor; + this.weight = weight; + } + + protected abstract Aggregator createAggregator(); + + /** override name & preproc */ + public Characteristic override(String nameOverride, SetPreprocessor preprocOverride) { + return new CharacteristicWrapper<>(nameOverride, preprocOverride, this); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Characteristic that = (Characteristic) o; + return Objects.equals(name, that.name) && + Objects.equals(preprocessor, that.preprocessor) && + Objects.equals(weight, that.weight); + } + + @Override + public int hashCode() { + return Objects.hash(name, preprocessor, weight); + } + + public static final class CharacteristicWrapper extends Characteristic { + @JsonProperty("inner") + public final Characteristic inner; + + @JsonCreator + public CharacteristicWrapper(@JsonProperty("name") String name, + @JsonProperty("preproc") SetPreprocessor preprocessor, + @JsonProperty("inner") Characteristic inner) { + super(name == null ? inner.name : name, preprocessor == null ? inner.preprocessor : preprocessor, inner.weight); + this.inner = inner; + } + + @Override + public Characteristic override(String nameOverride, SetPreprocessor preprocOverride) { + return new CharacteristicWrapper<>(nameOverride, preprocOverride, inner); + } + + @Override + protected Aggregator createAggregator() { + return inner.createAggregator(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + CharacteristicWrapper that = (CharacteristicWrapper) o; + return Objects.equals(inner, that.inner); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), inner); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java b/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java new file mode 100644 index 000000000..ad73a20f2 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java @@ -0,0 +1,75 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +import java.util.Objects; +import java.util.function.Function; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class MetricValue { + /** metric key (constant string / gene / etc.) */ + @JsonProperty("key") + @JsonTypeInfo(use = JsonTypeInfo.Id.CLASS) + public final K key; + @JsonProperty("value") + public final double value; + + @JsonCreator + public MetricValue(@JsonProperty("key") K key, + @JsonProperty("value") double value) { + this.key = key; + this.value = value; + } + + public MetricValue divide(double divisor) { + return new MetricValue<>(key, value / divisor); + } + + public MetricValue withKey(K newKey) { + return new MetricValue<>(newKey, value); + } + + public MetricValue mapKey(Function mapper) { + return new MetricValue<>(mapper.apply(key), value); + } + + public MetricValue square() { + return new MetricValue(key, value * value); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + MetricValue tuple = (MetricValue) o; + return Double.compare(tuple.value, value) == 0 && + Objects.equals(key, tuple.key); + } + + @Override + public int hashCode() { + return Objects.hash(key, value); + } + + @Override + public String toString() { + return key + ": " + value; + } + + private static final Object noKey = new Object(); + + @SuppressWarnings("unchecked") + public static R noKey() { + return (R) noKey; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java new file mode 100644 index 000000000..e1e1f415f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -0,0 +1,114 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResultBuilder; + +import java.util.*; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class PostanalysisResult { + @JsonProperty("data") + private final Map data; + @JsonProperty("sampleIds") + private final List sampleIds; + + @JsonCreator + public PostanalysisResult(@JsonProperty("data") Map data, + @JsonProperty("sampleIds") List sampleIds) { + this.data = data; + this.sampleIds = sampleIds; + } + + public PostanalysisResult setSampleIds(List sampleIds) { + return new PostanalysisResult(data, sampleIds); + } + + public static PostanalysisResult create(Map, MetricValue[][]> data) { + Map d = new HashMap<>(); + for (Map.Entry, MetricValue[][]> e : data.entrySet()) + d.put(e.getKey().name, new Array2d(e.getValue())); + return new PostanalysisResult(d, null); + } + + private final Map, CharacteristicGroupResult> cached = new IdentityHashMap<>(); + + @SuppressWarnings("unchecked") + public synchronized CharacteristicGroupResult getTable(CharacteristicGroup group) { + CharacteristicGroupResult r = cached.get(group); + if (r != null) + return (CharacteristicGroupResult) r; + + CharacteristicGroupResultBuilder builder = new CharacteristicGroupResultBuilder<>(group, sampleIds); + for (Characteristic ch : group.characteristics) { + MetricValue[][] values = (MetricValue[][]) data.get(ch.name).data; + for (int sampleIndex = 0; sampleIndex < values.length; sampleIndex++) + for (MetricValue val : values[sampleIndex]) + builder.add(val.key, sampleIndex, val.value); + } + CharacteristicGroupResult res = builder.build(); + cached.put(group, res); + return res; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + PostanalysisResult that = (PostanalysisResult) o; + return Objects.equals(data, that.data); + } + + @Override + public int hashCode() { + return Objects.hash(data); + } + + @Override + public String toString() { + return data.toString(); + } + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE + ) + private static final class Array2d { + @JsonProperty("2darray") + private final MetricValue[][] data; + + @JsonCreator + Array2d(@JsonProperty("2darray") MetricValue[][] data) { + this.data = data; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Array2d array2d = (Array2d) o; + return Arrays.deepEquals(data, array2d.data); + } + + @Override + public int hashCode() { + return Arrays.hashCode(data); + } + + @Override + public String toString() { + return Arrays.deepToString(data); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java new file mode 100644 index 000000000..8dddb4f03 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -0,0 +1,93 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.milaboratory.util.CanReportProgressAndStage; + +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; + +/** + * + */ +public class PostanalysisRunner implements CanReportProgressAndStage { + private final List> characteristics = new ArrayList<>(); + private Iterable[] datasets; + + public void addCharacteristics(Characteristic... chs) { + addCharacteristics(Arrays.asList(chs)); + } + + public void addCharacteristics(List> chs) { + characteristics.addAll(chs); + } + + public void setDatasets(Iterable[] sets) { + this.datasets = sets; + } + + public void setDatasets(List> sets) { + setDatasets(sets.toArray(new Iterable[0])); + } + + private Map, MetricValue[][]> result; + + private volatile String stage; + private volatile double progress = 0.0; + private volatile boolean isFinished = false; + + @Override + public String getStage() { + return stage; + } + + @Override + public double getProgress() { + return progress; + } + + @Override + public boolean isFinished() { + return isFinished; + } + + /** returns matrix[sample][metric_values] */ + public PostanalysisResult run() { + stage = "Preparing"; + progress = 0.0; + isFinished = false; + + Map, List>> characteristicsByPrep = + characteristics.stream() + .collect(Collectors.groupingBy(c -> c.preprocessor)); + + Map, MetricValue[][]> result = new IdentityHashMap<>(); + + for (Map.Entry, List>> e : characteristicsByPrep.entrySet()) { + Function, Iterable> prepFunction = e.getKey().setup(datasets); + for (int setIndex = 0; setIndex < datasets.length; setIndex++) { + Iterable set = datasets[setIndex]; + List> characteristics = e.getValue(); + + List> aggregators = characteristics.stream() + .map(Characteristic::createAggregator) + .collect(Collectors.toList()); + + for (T o : prepFunction.apply(set)) + for (Aggregator agg : aggregators) + agg.consume(o); + + for (int charIndex = 0; charIndex < characteristics.size(); charIndex++) { + @SuppressWarnings("unchecked") + MetricValue[][] charValues = result.computeIfAbsent( + characteristics.get(charIndex), + __ -> new MetricValue[datasets.length][]); + charValues[setIndex] = aggregators.get(charIndex).result(); + } + } + } + + isFinished = true; + this.result = result; + return PostanalysisResult.create(result); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java new file mode 100644 index 000000000..7e6a56075 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -0,0 +1,56 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessor; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesOverlapDownsamplingPreprocessor; +import com.milaboratory.mixcr.postanalysis.preproc.*; + +import java.util.ArrayList; +import java.util.List; +import java.util.function.Function; + +/** + * + */ +@JsonAutoDetect +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = NoPreprocessing.class, name = "none"), + @JsonSubTypes.Type(value = ClonesDownsamplingPreprocessor.class, name = "downsample"), + @JsonSubTypes.Type(value = ClonesOverlapDownsamplingPreprocessor.class, name = "overlapDownsample"), + @JsonSubTypes.Type(value = PreprocessorChain.class, name = "chain"), + @JsonSubTypes.Type(value = FilterPreprocessor.class, name = "filter"), + @JsonSubTypes.Type(value = SampleFilterPreprocessor.class, name = "filterInvidually") +}) +@JsonIgnoreProperties(ignoreUnknown = true) +public interface SetPreprocessor { + Function, Iterable> setup(Iterable[] sets); + + default SetPreprocessor filter(boolean before, ElementPredicate... predicates) { + FilterPreprocessor filter = new FilterPreprocessor<>(predicates); + if (this instanceof PreprocessorChain) { + PreprocessorChain p = (PreprocessorChain) this; + List> list = new ArrayList<>(); + if (before) { + list.add(filter); + list.addAll(p.chain); + } else { + list.addAll(p.chain); + list.add(filter); + } + return new PreprocessorChain<>(list); + } else + return before ? new PreprocessorChain<>(filter, this) : new PreprocessorChain<>(this, filter); + } + + default SetPreprocessor filterAfter(ElementPredicate... predicates) { + return filter(false, predicates); + } + + default SetPreprocessor filterFirst(ElementPredicate... predicates) { + return filter(true, predicates); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java new file mode 100644 index 000000000..a9a918c74 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java @@ -0,0 +1,21 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = WeightFunctions.Count.class, name = "count"), + @JsonSubTypes.Type(value = WeightFunctions.NoWeight.class, name = "none"), +}) +public interface WeightFunction { + double weight(T t); +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java new file mode 100644 index 000000000..14b9ac15e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java @@ -0,0 +1,48 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.milaboratory.mixcr.basictypes.Clone; + +/** + * + */ +public final class WeightFunctions { + private WeightFunctions() {} + + public static final class Count implements WeightFunction { + @Override + public double weight(Clone clone) { + return clone.getCount(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 17; + } + } + + public static final class NoWeight implements WeightFunction { + @Override + public double weight(T clone) { + return 1.0; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 11; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java new file mode 100644 index 000000000..0f82de3d3 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java @@ -0,0 +1,143 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.milaboratory.core.sequence.AminoAcidSequence; +import com.milaboratory.mixcr.basictypes.VDJCObject; +import io.repseq.core.GeneFeature; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.util.List; +import java.util.stream.Collectors; + +/** + * + */ +public class AAProperties { + /** Compute property normalized on sequence length */ + public static double computeNormalized(AAProperty property, VDJCObject obj, GeneFeature gf) { + AminoAcidSequence seq = obj.getFeatureAA(gf); + if (seq == null) + return Double.NaN; + double r = 0; + for (int i = 0; i < seq.size(); ++i) + r += getAAProperty(seq.codeAt(i), property); + return r / seq.size(); + } + + /** Compute property based on selection */ + public static double compute(AAProperty property, VDJCObject obj, GeneFeature gf, + Adjustment alignment, int nLetters) { + AminoAcidSequence seq = obj.getFeatureAA(gf); + if (seq == null) + return Double.NaN; + + int from, to; + if (nLetters > seq.size()) { + from = 0; + to = seq.size(); + } else + switch (alignment) { + case Leading: + from = 0; + to = nLetters; + break; + case Trailing: + from = seq.size() - nLetters; + to = seq.size(); + break; + case LeadingCenter: + from = (seq.size() - nLetters) / 2; + to = from + nLetters; + break; + case TrailingCenter: + from = (seq.size() - nLetters + 1) / 2; + to = from + nLetters; + break; + default: + throw new RuntimeException(); + } + double r = 0; + for (int i = from; i < to; ++i) + r += getAAProperty(seq.codeAt(i), property); + return r; + } + + public enum Adjustment { + Leading, Trailing, LeadingCenter, TrailingCenter + } + + public static double getAAProperty(byte aa, AAProperty property) { + return aaPropertiesTable[aa][property.index]; + } + + public enum AAProperty { + Hydropathy(0), + Charge(1), + Polarity(2), + Volume(3), + Strength(4), + MjEnergy(5), + Kf1(6), + Kf2(7), + Kf3(8), + Kf4(9), + Kf5(10), + Kf6(11), + Kf7(12), + Kf8(13), + Kf9(14), + Kf10(15), + Rim(16), + Surface(17), + Turn(18), + Alpha(19), + Beta(20), + Core(21), + Disorder(22), + N2Strength(23), + N2Hydrophobicity(24), + N2Volume(25), + N2Surface(26); + + private final int index; + + AAProperty(int index) { + this.index = index; + } + + static AAProperty parse(String str) { + for (AAProperty v : values()) + if (v.toString().equalsIgnoreCase(str)) + return v; + throw new IllegalArgumentException("no such element " + str); + } + } + + static final double[][] aaPropertiesTable = loadAAPropTableFromCsv(); + + private static double[][] loadAAPropTableFromCsv() { + try (BufferedReader reader = new BufferedReader(new InputStreamReader(AAProperties.class.getResourceAsStream("/postanalysis/aa_properties.csv")))) { + List lines = reader.lines().collect(Collectors.toList()); + AAProperty[] allProperties = AAProperty.values(); + double[][] result = new double[AminoAcidSequence.ALPHABET.size()][allProperties.length]; + String[] header = lines.get(0).split(","); + for (int i = 1; i < lines.size(); i++) { + String[] line = lines.get(i).split(","); + + AminoAcidSequence aaSeq = new AminoAcidSequence(line[0]); + if (aaSeq.size() != 1) + throw new IllegalArgumentException(); + byte aa = aaSeq.codeAt(0); + + for (int j = 1; j < line.length; j++) { + AAProperty prop = AAProperty.parse(header[j]); + result[aa][prop.index] = Double.parseDouble(line[j]); + } + } + return result; + } catch (IOException e) { + throw new RuntimeException(e); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java new file mode 100644 index 000000000..cdbbf2698 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java @@ -0,0 +1,136 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Aggregator; +import com.milaboratory.mixcr.postanalysis.MetricValue; +import com.milaboratory.mixcr.postanalysis.WeightFunction; +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.map.hash.TObjectDoubleHashMap; + +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; +import java.util.stream.Collectors; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class AdditiveAggregator implements Aggregator { + @JsonProperty("key") + public final KeyFunction keyFunction; + @JsonProperty("metric") + public final AdditiveMetric metric; + @JsonProperty("weight") + public final WeightFunction weight; + @JsonProperty("norm") + public final Normalization normalization; + + /** + * Single key value + */ + private K singleKey; + /** + * Aggregated values for single key + */ + double metricSum, weightSum; + /** + * Aggregated values for other keys ( != null ) + */ + final TObjectDoubleHashMap + metricSums = new TObjectDoubleHashMap<>(), + weightSums = new TObjectDoubleHashMap<>(); + + @JsonCreator + public AdditiveAggregator(@JsonProperty("key") KeyFunction keyFunction, + @JsonProperty("metric") AdditiveMetric metric, + @JsonProperty("weight") WeightFunction weight, + @JsonProperty("norm") Normalization normalization) { + this.keyFunction = keyFunction; + this.metric = metric; + this.weight = weight; + this.normalization = normalization; + } + + @Override + public void consume(T obj) { + K key = keyFunction.getKey(obj); + if (key == null) + return; + + double metricValue = metric.compute(obj); + if (Double.isNaN(metricValue)) + return; + + double weightValue = weight.weight(obj); + weightSum += weightValue; + + if (metricSums.size() != 0) { + double weightedValue = metricValue * weightValue; + metricSums.adjustOrPutValue(key, weightedValue, weightedValue); + if (normalization == Normalization.DivideByTotalForKey) + weightSums.adjustOrPutValue(key, weightValue, weightValue); + + return; + } + + if (singleKey == null) + singleKey = key; + + if (Objects.equals(key, singleKey)) + metricSum += metricValue * weightValue; + else { + metricSums.put(singleKey, metricSum); + weightSum -= weightValue; + metricSum = 0; + if (normalization == Normalization.DivideByTotalForKey) + weightSums.put(singleKey, weightSum); + singleKey = null; + consume(obj); + } + } + + @Override + @SuppressWarnings("unchecked") + public MetricValue[] result() { + List> result = new ArrayList<>(); + TObjectDoubleIterator it = metricSums.iterator(); + while (it.hasNext()) { + it.advance(); + result.add(new MetricValue<>(it.key(), it.value())); + } + + if (singleKey != null) { + assert result.isEmpty(); + result.add(new MetricValue<>(singleKey, metricSum)); + } + + if (result.isEmpty()) + return new MetricValue[0]; + + switch (normalization) { + case DivideByTotal: + result = result.stream() + .map(tuple -> tuple.divide(weightSum)) + .collect(Collectors.toList()); + break; + case DivideByTotalForKey: + result = result.stream() + .map(tuple -> + tuple.key == null + ? tuple.divide(weightSum) + : tuple.divide(weightSums.get(tuple.key)) + ) + .collect(Collectors.toList()); + break; + } + + return result.toArray(new MetricValue[0]); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java new file mode 100644 index 000000000..97a09376c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java @@ -0,0 +1,111 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.*; + +import java.util.Arrays; +import java.util.Objects; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class AdditiveCharacteristic extends Characteristic { + @JsonProperty("key") + final KeyFunction keyFunction; + @JsonProperty("metric") + final AdditiveMetric metric; + @JsonProperty("agg") + final AggregationType aggType; + @JsonProperty("normalizeByKey") + final boolean normalizeByKey; + + @JsonCreator + public AdditiveCharacteristic(@JsonProperty("name") String name, + @JsonProperty("preproc") SetPreprocessor preprocessor, + @JsonProperty("weight") WeightFunction weight, + @JsonProperty("key") KeyFunction keyFunction, + @JsonProperty("metric") AdditiveMetric metric, + @JsonProperty("agg") AggregationType aggType, + @JsonProperty("normalizeByKey") boolean normalizeByKey) { + super(name, preprocessor, weight); + this.keyFunction = keyFunction; + this.metric = metric; + this.aggType = aggType; + this.normalizeByKey = normalizeByKey; + } + + public AdditiveCharacteristic setName(String name) { + return new AdditiveCharacteristic<>(name, preprocessor, weight, keyFunction, metric, aggType, normalizeByKey); + } + + private Normalization meanNorm() { + return normalizeByKey ? Normalization.DivideByTotalForKey : Normalization.DivideByTotal; + } + + @Override + protected Aggregator createAggregator() { + switch (aggType) { + case Sum: + return new AdditiveAggregator<>(keyFunction, metric, weight, Normalization.None); + case Mean: + return new AdditiveAggregator<>(keyFunction, metric, weight, meanNorm()); + case Std: + AdditiveAggregator meanAgg = new AdditiveAggregator<>(keyFunction, metric, weight, meanNorm()); + AdditiveAggregator meanSquareAgg = new AdditiveAggregator<>(keyFunction, AdditiveMetric.square(metric), weight, meanNorm()); + return new Aggregator() { + @Override + public void consume(T obj) { + meanAgg.consume(obj); + meanSquareAgg.consume(obj); + } + + @Override + public MetricValue[] result() { + MetricValue[] mean = meanAgg.result(); + MetricValue[] meanSquare = meanSquareAgg.result(); + MetricValue[] result = new MetricValue[mean.length]; + + Arrays.sort(mean); + Arrays.sort(meanSquare); + + for (int i = 0; i < mean.length; ++i) { + MetricValue m = mean[i]; + MetricValue m2 = meanSquare[i]; + if (!m.key.equals(m2.key)) + throw new IllegalArgumentException(); + + result[i] = new MetricValue<>(m.key, Math.sqrt(m2.value - m.value * m.value)); + } + + return result; + } + }; + default: + throw new RuntimeException(); + } + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + AdditiveCharacteristic that = (AdditiveCharacteristic) o; + return normalizeByKey == that.normalizeByKey && + Objects.equals(keyFunction, that.keyFunction) && + Objects.equals(metric, that.metric) && + aggType == that.aggType; + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), keyFunction, metric, aggType, normalizeByKey); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java new file mode 100644 index 000000000..9be0b2c76 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java @@ -0,0 +1,193 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions.VJGenes; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; + +/** + * + */ +public final class AdditiveCharacteristics { + private AdditiveCharacteristics() {} + + public static AdditiveCharacteristic weightedLengthOf(GeneFeature gf, boolean aa) { + return weightedLengthOf(new NoPreprocessing<>(), gf, aa); + } + + public static AdditiveCharacteristic weightedLengthOf(SetPreprocessor preproc, GeneFeature gf, boolean aa) { + String name = (aa ? "aa" : "nt") + "LengthOf" + GeneFeature.encode(gf); + return new AdditiveCharacteristic<>( + name, + preproc, + new WeightFunctions.Count(), + new KeyFunctions.Named<>(name), + new AdditiveMetrics.GeneFeatureLength<>(gf, aa), + AggregationType.Mean, + false + ); + } + + public static AdditiveCharacteristic weightedBbiophysicsNormalized(AAProperties.AAProperty property, GeneFeature gf) { + return weightedBbiophysicsNormalized(new NoPreprocessing<>(), property, gf); + } + + public static AdditiveCharacteristic weightedBbiophysicsNormalized(SetPreprocessor preproc, AAProperties.AAProperty property, GeneFeature gf) { + String name = property.name() + "of" + GeneFeature.encode(gf) + "Normalized"; + return new AdditiveCharacteristic<>( + name, + preproc, + new WeightFunctions.Count(), + new KeyFunctions.Named<>(name), + new AdditiveMetrics.AAPropertyNormalized(property, gf), + AggregationType.Mean, + false + ); + } + + public static AdditiveCharacteristic weightedBiophysics(AAProperties.AAProperty property, GeneFeature gf, AAProperties.Adjustment adjustment, int nLetters) { + return weightedBiophysics(new NoPreprocessing<>(), property, gf, adjustment, nLetters); + } + + public static AdditiveCharacteristic weightedBiophysics(SetPreprocessor preproc, AAProperties.AAProperty property, GeneFeature gf, AAProperties.Adjustment adjustment, int nLetters) { + String name = property.name() + "of" + GeneFeature.encode(gf); + return new AdditiveCharacteristic<>( + name, + preproc, + new WeightFunctions.Count(), + new KeyFunctions.Named<>(name), + new AdditiveMetrics.AAPropertySum(property, gf, adjustment, nLetters), + AggregationType.Mean, + false + ); + } + + public static AdditiveCharacteristic segmentUsage(GeneType geneType, KeyFunction keyFunction) { + return segmentUsage(new NoPreprocessing<>(), geneType, keyFunction); + } + + public static AdditiveCharacteristic segmentUsage(SetPreprocessor preproc, GeneType geneType, KeyFunction keyFunction) { + String name = geneType.getLetter() + "Usage"; + return new AdditiveCharacteristic<>( + name, + preproc, + new WeightFunctions.Count(), + keyFunction, + new AdditiveMetrics.Constant(1), + AggregationType.Mean, + false + ); + } + + public static AdditiveCharacteristic segmentUsage(GeneType geneType) { + return segmentUsage(new NoPreprocessing<>(), geneType); + } + + public static AdditiveCharacteristic segmentUsage(SetPreprocessor preproc, GeneType geneType) { + return segmentUsage(preproc, geneType, new KeyFunctions.SegmentUsage<>(geneType)) + .setName(geneType.getLetter() + "SegmentUsage"); + } + + public static AdditiveCharacteristic geneUsage(GeneType geneType) { + return geneUsage(new NoPreprocessing<>(), geneType); + } + + public static AdditiveCharacteristic geneUsage(SetPreprocessor preproc, GeneType geneType) { + return segmentUsage(preproc, geneType, new KeyFunctions.GeneUsage<>(geneType)) + .setName(geneType.getLetter() + "GeneUsage"); + } + + public static AdditiveCharacteristic familyUsage(GeneType geneType) { + return familyUsage(new NoPreprocessing<>(), geneType); + } + + public static AdditiveCharacteristic familyUsage(SetPreprocessor preproc, GeneType geneType) { + return segmentUsage(preproc, geneType, new KeyFunctions.FamiltyUsage<>(geneType)) + .setName(geneType.getLetter() + "FamilyUsage"); + } + + public static AdditiveCharacteristic, Clone> vjUsage(KeyFunction, Clone> keyFunction) { + return vjUsage(new NoPreprocessing<>(), keyFunction); + } + + public static AdditiveCharacteristic, Clone> vjUsage(SetPreprocessor preproc, KeyFunction, Clone> keyFunction) { + return new AdditiveCharacteristic<>( + "VJUsage", + preproc, + new WeightFunctions.Count(), + keyFunction, + new AdditiveMetrics.Constant(1), + AggregationType.Mean, + false + ); + } + + public static AdditiveCharacteristic, Clone> vjSegmentUsage() { + return vjSegmentUsage(new NoPreprocessing<>()); + } + + public static AdditiveCharacteristic, Clone> vjSegmentUsage(SetPreprocessor preproc) { + return vjUsage(preproc, new KeyFunctions.VJSegmentUsage<>()).setName("VJSegmentUsage"); + } + + public static AdditiveCharacteristic, Clone> vjGeneUsage() { + return vjGeneUsage(new NoPreprocessing<>()); + } + + public static AdditiveCharacteristic, Clone> vjGeneUsage(SetPreprocessor preproc) { + return vjUsage(preproc, new KeyFunctions.VJGeneUsage<>()).setName("VJGeneUsage"); + } + + public static AdditiveCharacteristic, Clone> vjFamilysage() { + return vjFamilysage(new NoPreprocessing<>()); + } + + public static AdditiveCharacteristic, Clone> vjFamilysage(SetPreprocessor preproc) { + return vjUsage(preproc, new KeyFunctions.VJFamilyUsage<>()).setName("VJFamilyUsage"); + } + + public static AdditiveCharacteristic isotypeUsage() { + return isotypeUsage(new NoPreprocessing<>()); + } + + public static AdditiveCharacteristic isotypeUsage(SetPreprocessor preproc) { + return new AdditiveCharacteristic<>( + "IsotypeUsage", + preproc, + new WeightFunctions.Count(), + new KeyFunctions.IsotypeUsage<>(), + new AdditiveMetrics.Constant(1), + AggregationType.Mean, + false + ); + } + + public static AdditiveCharacteristic, Clone> VSpectratype() { + return VSpectratype(new NoPreprocessing<>()); + } + + public static AdditiveCharacteristic, Clone> VSpectratype(SetPreprocessor preproc) { + return new AdditiveCharacteristic<>("VSpectratype", + preproc, + new WeightFunctions.Count(), + new SpectratypeKeyFunction<>(new KeyFunctions.SegmentUsage<>(GeneType.Variable), GeneFeature.CDR3, false), + new AdditiveMetrics.Constant(), AggregationType.Sum, false); + } + + public static AdditiveCharacteristic VSpectratypeMean(SetPreprocessor preproc) { + return new AdditiveCharacteristic<>( + "VSpectratypeMean", + preproc, + new WeightFunctions.Count(), + new KeyFunctions.SegmentUsage<>(GeneType.Variable), + new AdditiveMetrics.GeneFeatureLength<>(GeneFeature.CDR3, false), + AggregationType.Mean, + true + ); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java new file mode 100644 index 000000000..b9fe75d55 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java @@ -0,0 +1,31 @@ +package com.milaboratory.mixcr.postanalysis.additive; + + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = AdditiveMetrics.Constant.class, name = "constant"), + @JsonSubTypes.Type(value = AdditiveMetrics.GeneFeatureLength.class, name = "length"), + @JsonSubTypes.Type(value = AdditiveMetrics.AAPropertyNormalized.class, name = "aaPropertyNormalized"), + @JsonSubTypes.Type(value = AdditiveMetrics.AAPropertySum.class, name = "aaProperty"), +}) +public interface AdditiveMetric { + double compute(T obj); + + static AdditiveMetric square(AdditiveMetric metric) { + return obj -> { + double v = metric.compute(obj); + return v * v; + }; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java new file mode 100644 index 000000000..3fa5b3713 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java @@ -0,0 +1,154 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.postanalysis.additive.AAProperties.AAProperty; +import com.milaboratory.mixcr.postanalysis.additive.AAProperties.Adjustment; +import io.repseq.core.GeneFeature; + +import java.util.Objects; + +/** + * + */ +public final class AdditiveMetrics { + private AdditiveMetrics() {} + + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NON_PRIVATE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) + interface JsonSupport {} + + public static final class Constant implements AdditiveMetric, JsonSupport { + public double value = 1.0; + + public Constant() {} + + public Constant(double value) { + this.value = value; + } + + @Override + public double compute(Clone obj) { + return value; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Constant constant = (Constant) o; + return Double.compare(constant.value, value) == 0; + } + + @Override + public int hashCode() { + return Objects.hash(value); + } + } + + public static final class GeneFeatureLength implements AdditiveMetric, JsonSupport { + public GeneFeature geneFeature; + public boolean aminoAcid; + + public GeneFeatureLength() {} + + public GeneFeatureLength(GeneFeature geneFeature, boolean aminoAcid) { + this.geneFeature = geneFeature; + this.aminoAcid = aminoAcid; + } + + @Override + public double compute(T obj) { + int len = aminoAcid ? obj.aaLengthOf(geneFeature) : obj.ntLengthOf(geneFeature); + if (len < 0) + return Double.NaN; + return len; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + GeneFeatureLength that = (GeneFeatureLength) o; + return aminoAcid == that.aminoAcid && + Objects.equals(geneFeature, that.geneFeature); + } + + @Override + public int hashCode() { + return Objects.hash(geneFeature, aminoAcid); + } + } + + public static final class AAPropertyNormalized implements AdditiveMetric, JsonSupport { + public AAProperty property; + public GeneFeature geneFeature = GeneFeature.CDR3; + + public AAPropertyNormalized() {} + + public AAPropertyNormalized(AAProperty property, GeneFeature geneFeature) { + this.property = property; + this.geneFeature = geneFeature; + } + + @Override + public double compute(Clone obj) { + return AAProperties.computeNormalized(property, obj, geneFeature); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + AAPropertyNormalized that = (AAPropertyNormalized) o; + return property == that.property && + Objects.equals(geneFeature, that.geneFeature); + } + + @Override + public int hashCode() { + return Objects.hash(property, geneFeature); + } + } + + public static final class AAPropertySum implements AdditiveMetric, JsonSupport { + public AAProperty property; + public GeneFeature geneFeature = GeneFeature.CDR3; + public Adjustment adjustment = Adjustment.LeadingCenter; + public int nLetters = 5; + + public AAPropertySum() {} + + public AAPropertySum(AAProperty property, GeneFeature geneFeature, Adjustment adjustment, int nLetters) { + this.property = property; + this.geneFeature = geneFeature; + this.adjustment = adjustment; + this.nLetters = nLetters; + } + + @Override + public double compute(Clone obj) { + return AAProperties.compute(property, obj, geneFeature, adjustment, nLetters); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + AAPropertySum that = (AAPropertySum) o; + return nLetters == that.nLetters && + property == that.property && + Objects.equals(geneFeature, that.geneFeature) && + adjustment == that.adjustment; + } + + @Override + public int hashCode() { + return Objects.hash(property, geneFeature, adjustment, nLetters); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java new file mode 100644 index 000000000..f2e239ae7 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java @@ -0,0 +1,8 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +/** + * + */ +public enum AggregationType { + Sum, Mean, Std +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java new file mode 100644 index 000000000..e03242a5c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java @@ -0,0 +1,38 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; + +import java.util.function.Function; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = KeyFunctions.Named.class, name = "named"), + @JsonSubTypes.Type(value = KeyFunctions.SegmentUsage.class, name = "segment"), + @JsonSubTypes.Type(value = KeyFunctions.GeneUsage.class, name = "gene"), + @JsonSubTypes.Type(value = KeyFunctions.FamiltyUsage.class, name = "family"), + @JsonSubTypes.Type(value = KeyFunctions.VJSegmentUsage.class, name = "vjSegments"), + @JsonSubTypes.Type(value = KeyFunctions.VJGeneUsage.class, name = "vjGenes"), + @JsonSubTypes.Type(value = KeyFunctions.VJFamilyUsage.class, name = "vjFamilies"), + @JsonSubTypes.Type(value = KeyFunctions.IsotypeUsage.class, name = "isotype"), + @JsonSubTypes.Type(value = KeyFunctions.NTFeature.class, name = "ntFeature"), + @JsonSubTypes.Type(value = KeyFunctions.AAFeature.class, name = "aaFeature"), + @JsonSubTypes.Type(value = KeyFunctions.Tuple2Key.class, name = "tuple"), + @JsonSubTypes.Type(value = SpectratypeKeyFunction.class, name = "spectratype"), +}) +public interface KeyFunction { + K getKey(T obj); + + default KeyFunction map(Function mapper) { + return obj -> mapper.apply(KeyFunction.this.getKey(obj)); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java new file mode 100644 index 000000000..931f0e839 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java @@ -0,0 +1,370 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.milaboratory.core.sequence.AminoAcidSequence; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.core.sequence.TranslationParameters; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.util.Tuple2; +import io.repseq.core.Chains; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGene; + +import java.util.Objects; +import java.util.function.Function; + +/** + * + */ +public final class KeyFunctions { + private KeyFunctions() {} + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NON_PRIVATE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) + interface JsonSupport {} + + public static final class Named implements KeyFunction, JsonSupport { + public String name; + + public Named() {} + + public Named(String name) { + this.name = name; + } + + @Override + public String getKey(T obj) { + return name; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Named named = (Named) o; + return Objects.equals(name, named.name); + } + + @Override + public int hashCode() { + return Objects.hash(name); + } + } + + abstract static class SegmentKeyFunction implements KeyFunction { + @JsonIgnore + final Function mapper; + public GeneType geneType; + + public SegmentKeyFunction(Function mapper, GeneType geneType) { + this.mapper = mapper; + this.geneType = geneType; + } + + public SegmentKeyFunction(Function mapper) { + this.mapper = mapper; + } + + @Override + public K getKey(T obj) { + VDJCHit hit = obj.getBestHit(geneType); + if (hit == null) + return null; + return mapper.apply(hit.getGene()); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SegmentKeyFunction that = (SegmentKeyFunction) o; + return geneType == that.geneType; + } + + @Override + public int hashCode() { + return Objects.hash(geneType); + } + } + + public static class SegmentUsage + extends SegmentKeyFunction + implements JsonSupport { + @JsonCreator + public SegmentUsage() { + super(VDJCGene::getName); + } + + public SegmentUsage(GeneType geneType) { + super(VDJCGene::getName, geneType); + } + } + + public static class GeneUsage + extends SegmentKeyFunction + implements JsonSupport { + @JsonCreator + public GeneUsage() { + super(VDJCGene::getGeneName); + } + + public GeneUsage(GeneType geneType) { + super(VDJCGene::getGeneName, geneType); + } + } + + public static class FamiltyUsage + extends SegmentKeyFunction + implements JsonSupport { + @JsonCreator + public FamiltyUsage() { + super(VDJCGene::getFamilyName); + } + + public FamiltyUsage(GeneType geneType) { + super(VDJCGene::getFamilyName, geneType); + } + } + + public static final class VJGenes implements JsonSupport { + public Gene vGene; + public Gene jJene; + + public VJGenes() {} + + public VJGenes(Gene vGene, Gene jJene) { + this.vGene = vGene; + this.jJene = jJene; + } + + public VJGenes map(Function mapper) { + return new VJGenes<>(mapper.apply(vGene), mapper.apply(jJene)); + } + + @Override + public String toString() { + return vGene + "+" + jJene; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VJGenes vjGenes = (VJGenes) o; + return Objects.equals(vGene, vjGenes.vGene) && + Objects.equals(jJene, vjGenes.jJene); + } + + @Override + public int hashCode() { + return Objects.hash(vGene, jJene); + } + } + + abstract static class VJKeyFunction implements KeyFunction, T> { + @JsonIgnore + final Function mapper; + + VJKeyFunction(Function mapper) { + this.mapper = mapper; + } + + @Override + public VJGenes getKey(T obj) { + VDJCHit v = obj.getBestHit(GeneType.Variable); + VDJCHit j = obj.getBestHit(GeneType.Joining); + if (v == null || j == null) + return null; + return new VJGenes<>(v.getGene(), j.getGene()).map(mapper); + } + + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 17; + } + } + + public static class VJSegmentUsage + extends VJKeyFunction + implements JsonSupport { + public VJSegmentUsage() { + super(VDJCGene::getName); + } + } + + public static class VJGeneUsage + extends VJKeyFunction + implements JsonSupport { + public VJGeneUsage() { + super(VDJCGene::getGeneName); + } + } + + public static class VJFamilyUsage + extends VJKeyFunction + implements JsonSupport { + public VJFamilyUsage() { + super(VDJCGene::getFamilyName); + } + } + + public enum Isotype { + A("IgA"), D("IgD"), G("IgG"), E("IgE"), M("IgM"); + private final String name; + + Isotype(String name) { + this.name = name; + } + + @Override + public String toString() { + return name; + } + + static Isotype valueOf(char c) { + switch (c) { + case 'a': case 'A': return A; + case 'd': case 'D': return D; + case 'g': case 'G': return G; + case 'e': case 'E': return E; + case 'm': case 'M': return M; + default: return null; + } + } + } + + public static class IsotypeUsage implements KeyFunction, JsonSupport { + @Override + public Isotype getKey(T obj) { + VDJCHit cHit = obj.getBestHit(GeneType.Constant); + if (cHit == null) + return null; + if (!cHit.getGene().getChains().intersects(Chains.IGH)) + return null; + String gene = cHit.getGene().getName(); + if (gene.length() < 4) + return null; + return Isotype.valueOf(gene.charAt(3)); + } + + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 17; + } + } + + public static final class NTFeature implements KeyFunction, JsonSupport { + public GeneFeature geneFeature; + + public NTFeature(GeneFeature geneFeature) { + this.geneFeature = geneFeature; + } + + public NTFeature() {} + + @Override + public String getKey(Clone obj) { + NSequenceWithQuality f = obj.getFeature(geneFeature); + if (f == null) + return null; + return f.getSequence().toString(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + NTFeature ntFeature = (NTFeature) o; + return Objects.equals(geneFeature, ntFeature.geneFeature); + } + + @Override + public int hashCode() { + return Objects.hash(geneFeature); + } + } + + public static final class AAFeature implements KeyFunction, JsonSupport { + public GeneFeature geneFeature; + + public AAFeature(GeneFeature geneFeature) { + this.geneFeature = geneFeature; + } + + public AAFeature() {} + + @Override + public String getKey(Clone obj) { + NSequenceWithQuality feature = obj.getFeature(geneFeature); + if (feature == null) + return null; + int targetId = obj.getTargetContainingFeature(geneFeature); + TranslationParameters tr = targetId == -1 ? + TranslationParameters.FromLeftWithIncompleteCodon + : obj.getPartitionedTarget(targetId).getPartitioning().getTranslationParameters(geneFeature); + if (tr == null) + return null; + return AminoAcidSequence.translate(feature.getSequence(), tr).toString(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + AAFeature aaFeature = (AAFeature) o; + return Objects.equals(geneFeature, aaFeature.geneFeature); + } + + @Override + public int hashCode() { + return Objects.hash(geneFeature); + } + } + + public static final class Tuple2Key implements KeyFunction, T>, JsonSupport { + public KeyFunction key1; + public KeyFunction key2; + + @Override + public Tuple2 getKey(T obj) { + K1 k1 = key1.getKey(obj); + K2 k2 = key2.getKey(obj); + if (k1 == null && k2 == null) + return null; + return new Tuple2<>(k1, k2); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Tuple2Key tuple2Key = (Tuple2Key) o; + return Objects.equals(key1, tuple2Key.key1) && + Objects.equals(key2, tuple2Key.key2); + } + + @Override + public int hashCode() { + return Objects.hash(key1, key2); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java new file mode 100644 index 000000000..81fcac8e7 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java @@ -0,0 +1,36 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.additive; + +public enum Normalization { + None, + DivideByTotal, + DivideByTotalForKey +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java new file mode 100644 index 000000000..45ea3a03f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java @@ -0,0 +1,169 @@ +package com.milaboratory.mixcr.postanalysis.clustering; + +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TIntObjectIterator; +import gnu.trove.list.array.TIntArrayList; +import gnu.trove.map.hash.TIntObjectHashMap; +import gnu.trove.set.hash.TIntHashSet; + +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.function.ToDoubleBiFunction; + +public final class HierarchicalClustering { + + private HierarchicalClustering() { + } + + public static double EuclideanDistance(double[] vectori, double[] vectorj) { + double diff_square_sum = 0.0; + for (int i = 0; i < vectori.length; i++) { + diff_square_sum += (vectori[i] - vectorj[i]) * (vectori[i] - vectorj[i]); + } + return diff_square_sum; + } + + public static double ManhattenDistance(double[] vectori, double[] vectorj) { + double abs_sum = 0.0; + for (int i = 0; i < vectori.length; i++) { + abs_sum += (java.lang.Math.abs(vectori[i]) - java.lang.Math.abs(vectorj[i])); + } + return abs_sum; + } + + public static double ChebishevDistance(double[] vectori, double[] vectorj) { + double max_distance = 0.0; + for (int i = 0; i < vectori.length; i++) { + double distance = (java.lang.Math.abs(vectori[i]) - java.lang.Math.abs(vectorj[i])); + if (distance >= max_distance) { + max_distance = distance; + } + } + return max_distance; + } + + private static class PairDistance implements Comparable { + final int id1, id2; + final double distance; + + PairDistance(int id1, int id2, double distance) { + this.id1 = id1; + this.id2 = id2; + this.distance = distance; + } + + @Override + public int compareTo(HierarchicalClustering.PairDistance o) { + return Double.compare(distance, o.distance); + } + } + + public static List clusterize(T[] vectors, double distanceOffset, ToDoubleBiFunction distanceFunc) { + if (vectors.length == 0) + return Collections.emptyList(); + if (vectors.length == 1) + return Collections.singletonList(new HierarchyNode(0, new int[0], 0)); + + List result = new ArrayList<>(); + List distances = new ArrayList<>(); + TIntObjectHashMap clusters = new TIntObjectHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, Integer.MIN_VALUE); + double[][] rawDist = new double[vectors.length][vectors.length]; + + if (distanceOffset > 1) { + throw new IllegalArgumentException("Offset must be less then 1"); + } + + for (int i = 0; i < vectors.length; i++) { + clusters.put(i, new int[]{i}); + for (int j = i + 1; j < vectors.length; j++) { + PairDistance distance = new PairDistance(i, j, distanceFunc.applyAsDouble(vectors[i], vectors[j])); + distances.add(distance); + rawDist[i][j] = distance.distance; + rawDist[j][i] = distance.distance; + } + } + + Collections.sort(distances); + + for (int id = -1; ; id--) { + + TIntArrayList children = new TIntArrayList(Constants.DEFAULT_CAPACITY, Integer.MIN_VALUE); + TIntHashSet childrenNeighbors = new TIntHashSet(); + + double currentNodeDistance = distances.get(0).distance; + double distanceSum = distances.get(0).distance; + + children.add(distances.get(0).id1); + children.add(distances.get(0).id2); + + + for (int i = 1; i < distances.size(); i++) { + if (distances.get(i).distance <= currentNodeDistance * (1 + distanceOffset)) { + for (int j = 0; j < children.size(); j++) { + if (distances.get(i).id1 == children.get(j)) { + childrenNeighbors.add(distances.get(i).id2); + distanceSum += distances.get(i).distance; + } else if (distances.get(i).id2 == children.get(j)) { + childrenNeighbors.add(distances.get(i).id1); + distanceSum += distances.get(i).distance; + } + } + } + } + children.addAll(childrenNeighbors); + + HierarchyNode node = new HierarchyNode(id, children.toArray(), distanceSum / (children.size() - 1)); + result.add(node); + + if (distances.size() == 1) { + return result; + } + + TIntArrayList allChildrenList = new TIntArrayList(); + + for (int i = 0; i < children.size(); i++) { + int[] c = clusters.remove(children.get(i)); + allChildrenList.addAll(c); + } + + int[] allChildren = allChildrenList.toArray(); + + + for (int i = distances.size() - 1; i >= 0; i--) { + for (int j = 0; j < children.size(); ++j) { + int child = children.get(j); + if (distances.get(i).id1 == child || distances.get(i).id2 == child) { + distances.remove(i); + break; + } + } + } + + TIntObjectIterator it = clusters.iterator(); + while (it.hasNext()) { + it.advance(); + int id1 = id; + int id2 = it.key(); + double minDistance = Double.MAX_VALUE; + + int[] children1 = allChildren; + int[] children2 = it.value(); + for (int i : children1) { + for (int j : children2) { + if (rawDist[i][j] < minDistance) { + minDistance = rawDist[i][j]; + } + } + } + distances.add(new PairDistance(id1, id2, minDistance)); + + } + if (distances.isEmpty()) + return result; + clusters.put(id, allChildren); + + Collections.sort(distances); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java new file mode 100644 index 000000000..8ea7cc72b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java @@ -0,0 +1,45 @@ +package com.milaboratory.mixcr.postanalysis.clustering; + +import java.util.Arrays; +import java.util.Objects; + +/** + * + */ +public final class HierarchyNode { + public final int id; + public final int[] children; + public final double height; + + public HierarchyNode(int id, int[] children, double height) { + this.id = id; + this.children = children; + this.height = height; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + HierarchyNode that = (HierarchyNode) o; + return id == that.id && + Double.compare(that.height, height) == 0 && + Arrays.equals(children, that.children); + } + + @Override + public int hashCode() { + int result = Objects.hash(id, height); + result = 31 * result + Arrays.hashCode(children); + return result; + } + + @Override + public String toString() { + return "HierarchyNode{" + + "id=" + id + + ", children=" + Arrays.toString(children) + + ", height=" + height + + '}'; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java new file mode 100644 index 000000000..3a31a3ff0 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -0,0 +1,132 @@ +package com.milaboratory.mixcr.postanalysis.diversity; + +import com.milaboratory.mixcr.postanalysis.Aggregator; +import com.milaboratory.mixcr.postanalysis.MetricValue; +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TLongIntIterator; +import gnu.trove.map.hash.TLongIntHashMap; +import org.apache.commons.math3.util.CombinatoricsUtils; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.function.ToLongFunction; +import java.util.stream.IntStream; + +import static com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure.*; + +/** + * + */ +public class DiversityAggregator implements Aggregator { + /** number of clonotypes */ + private int diversity = 0; + /** total count across all clonotypes */ + private long countSum = 0; + final TLongIntHashMap freqTable = new TLongIntHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1, 0); + final ToLongFunction count; + + /** @param count returns count of element */ + public DiversityAggregator(ToLongFunction count) { + this.count = count; + } + + @Override + public void consume(T obj) { + long count = this.count.applyAsLong(obj); + freqTable.adjustOrPutValue(count, 1, 1); + diversity += 1; + countSum += count; + } + + /** Chao1 */ + private List> computeChao1() { + int sobs = diversity; + double f1 = freqTable.get(1); // singletons + double f2 = freqTable.get(2); // doubletons + double f0 = f1 * (f1 - 1) / 2 / (f2 + 1); + double chao1 = sobs + f0; + double chao1std = Math.sqrt( + f0 + f1 * (2 * f1 - 1) * (2 * f1 - 1) / 4 / (f2 + 1) / (f2 + 1) + + f1 * f1 * f2 * (f1 - 1) * (f1 - 1) / 4 / (f2 + 1) / (f2 + 1) / (f2 + 1) / (f2 + 1)); + + return Arrays.asList(new MetricValue<>(Chao1, chao1), new MetricValue<>(Chao1Std, chao1std)); + } + + /** Clonality, Gini and Shannon-Weiner */ + private List> computeClonality() { + double shannonWeiner = 0; + double gini = 0; + + TLongIntIterator it = freqTable.iterator(); + while (it.hasNext()) { + it.advance(); + + double cloneCount = it.key(); + double nClones = it.value(); + double cloneFreq = cloneCount / countSum; + + gini += -nClones * cloneFreq * cloneFreq; + shannonWeiner += -nClones * cloneFreq * Math.log(cloneFreq); + } + + return Arrays.asList( + new MetricValue<>(ShannonWeiner, shannonWeiner), + new MetricValue<>(Clonality, 1 - shannonWeiner / Math.log(diversity)), + new MetricValue<>(InverseSimpson, -1 / gini), + new MetricValue<>(Gini, 1 - gini)); + } + + public static final int DEFAULT_EFRON_THISTED_MAX_DEPTH = 20; + public static final double DEFAULT_EFRON_THISTED_CV_THRESHOLD = 0.05; + + private List> computeEfronThisted() { + return computeEfronThisted(DEFAULT_EFRON_THISTED_MAX_DEPTH, DEFAULT_EFRON_THISTED_CV_THRESHOLD); + } + + /** Efron-Thisted */ + private List> computeEfronThisted(int maxDepth, double cvThreshold) { + double S = -1, D = -1, CV; + for (int depth = 1; depth <= maxDepth; depth++) { + final double[] h = new double[depth], nx = new double[depth]; + for (int y = 1; y <= depth; y++) { + nx[y - 1] = freqTable.get(y); + + // Calculate Euler coefficients + for (int x = 1; x <= y; x++) { + double coef = CombinatoricsUtils.binomialCoefficientDouble((y - 1), (x - 1)); + if (x % 2 == 1) + h[x - 1] += coef; + else + h[x - 1] -= coef; + } + } + + // Extrapolate count + S = diversity + IntStream.range(0, depth).mapToDouble(i -> h[i] * nx[i]).sum(); + D = Math.sqrt(IntStream.range(0, depth).mapToDouble(i -> h[i] * h[i] * nx[i]).sum()); + CV = D / S; + + // Go to maximum count depth, but balance that STD doesn't get too high + if (CV >= cvThreshold) + break; + } + return Arrays.asList(new MetricValue<>(EfronThisted, S), new MetricValue<>(EfronThistedStd, D)); + } + + private List> computeObserved() { + return Collections.singletonList(new MetricValue<>(Observed, diversity)); + } + + @Override + public MetricValue[] result() { + List> result = new ArrayList<>(); + result.addAll(computeObserved()); + result.addAll(computeClonality()); + result.addAll(computeChao1()); + result.addAll(computeEfronThisted()); + return result.toArray(new MetricValue[0]); + } + +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java new file mode 100644 index 000000000..db7ce0f97 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java @@ -0,0 +1,31 @@ +package com.milaboratory.mixcr.postanalysis.diversity; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Aggregator; +import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.WeightFunction; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class DiversityCharacteristic extends Characteristic { + @JsonCreator + public DiversityCharacteristic(@JsonProperty("name") String name, + @JsonProperty("weight") WeightFunction weight, + @JsonProperty("preproc") SetPreprocessor preprocessor) { + super(name, preprocessor, weight); + } + + @Override + protected Aggregator createAggregator() { + return new DiversityAggregator<>(c -> Math.round(weight.weight(c))); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java new file mode 100644 index 000000000..4a4f8eb51 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java @@ -0,0 +1,16 @@ +package com.milaboratory.mixcr.postanalysis.diversity; + +/** + * + */ +public enum DiversityMeasure { + Observed, + Chao1, + Chao1Std, + ShannonWeiner, + Clonality, + Gini, + InverseSimpson, + EfronThisted, + EfronThistedStd; +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java new file mode 100644 index 000000000..03e0ee123 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java @@ -0,0 +1,38 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.basictypes.Clone; + +import java.util.Objects; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class ClonesDownsamplingPreprocessor extends DownsamplingPreprocessor { + @JsonCreator + public ClonesDownsamplingPreprocessor(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, + @JsonProperty("seed") long seed) { + super(c -> Math.round(c.getCount()), Clone::setCount, downsampleValueChooser, seed); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + ClonesDownsamplingPreprocessor that = (ClonesDownsamplingPreprocessor) o; + return Objects.equals(downsampleValueChooser, that.downsampleValueChooser) + && Objects.equals(seed, that.seed); + } + + @Override + public int hashCode() { + return Objects.hash(downsampleValueChooser, seed); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesOverlapDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesOverlapDownsamplingPreprocessor.java new file mode 100644 index 000000000..ca036ede8 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesOverlapDownsamplingPreprocessor.java @@ -0,0 +1,38 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.basictypes.Clone; + +import java.util.Objects; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class ClonesOverlapDownsamplingPreprocessor extends OverlapDownsamplingPreprocessor { + @JsonCreator + public ClonesOverlapDownsamplingPreprocessor(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, + @JsonProperty("seed") long seed) { + super(c -> Math.round(c.getCount()), Clone::setCount, downsampleValueChooser, seed); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + ClonesOverlapDownsamplingPreprocessor that = (ClonesOverlapDownsamplingPreprocessor) o; + return Objects.equals(downsampleValueChooser, that.downsampleValueChooser) + && Objects.equals(seed, that.seed); + } + + @Override + public int hashCode() { + return Objects.hash(downsampleValueChooser, seed); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java new file mode 100644 index 000000000..a38ec3991 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java @@ -0,0 +1,112 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; +import org.apache.commons.math3.stat.descriptive.rank.Percentile; + +import java.util.Arrays; +import java.util.Objects; +import java.util.stream.LongStream; + +/** + * + */ + +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = DownsampleValueChooser.Fixed.class, name = "fixed"), + @JsonSubTypes.Type(value = DownsampleValueChooser.Minimal.class, name = "min"), + @JsonSubTypes.Type(value = DownsampleValueChooser.Auto.class, name = "auto") +}) +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NON_PRIVATE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) +public interface DownsampleValueChooser { + long compute(long[] totalCounts); + + class Fixed implements DownsampleValueChooser { + public long value; + + public Fixed() {} + + public Fixed(long value) { + this.value = value; + } + + @Override + public long compute(long[] totalCounts) { + return value; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Fixed fixed = (Fixed) o; + return value == fixed.value; + } + + @Override + public int hashCode() { + return Objects.hash(value); + } + } + + class Minimal implements DownsampleValueChooser { + @Override + public long compute(long[] totalCounts) { + return LongStream.of(totalCounts).min().orElse(0); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 7; + } + } + + class Auto implements DownsampleValueChooser { + public double quantile = 0.2; + public double scale = 0.5; + public long threshold = 500; + + public Auto() {} + + public Auto(double quantile, double scale, long threshold) { + this.quantile = quantile; + this.scale = scale; + this.threshold = threshold; + } + + @Override + public long compute(long[] totalCounts) { + long q = (long) (new Percentile(quantile).evaluate(Arrays.stream(totalCounts).mapToDouble(l -> l).toArray()) * scale); + long min = Arrays.stream(totalCounts).min().orElse(0); + long d = Math.max(q, min); + return Math.max(d, threshold); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Auto auto = (Auto) o; + return Double.compare(auto.quantile, quantile) == 0 && + Double.compare(auto.scale, scale) == 0 && + threshold == auto.threshold; + } + + @Override + public int hashCode() { + return Objects.hash(quantile, scale, threshold); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java new file mode 100644 index 000000000..e82bc3c50 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -0,0 +1,90 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + + +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.util.FilteredIterable; +import gnu.trove.list.array.TLongArrayList; +import org.apache.commons.math3.random.RandomGenerator; +import org.apache.commons.math3.random.Well19937c; + +import java.util.HashSet; +import java.util.Iterator; +import java.util.Set; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.function.BiFunction; +import java.util.function.Function; +import java.util.function.ToLongFunction; + +import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil.*; + +/** + * + */ +public abstract class DownsamplingPreprocessor implements SetPreprocessor { + public final ToLongFunction getCount; + public final BiFunction setCount; + @JsonProperty("downsampleValueChooser") + public final DownsampleValueChooser downsampleValueChooser; + @JsonProperty("seed") + public final long seed; + + public DownsamplingPreprocessor(ToLongFunction getCount, BiFunction setCount, DownsampleValueChooser downsampleValueChooser, long seed) { + this.getCount = getCount; + this.setCount = setCount; + this.downsampleValueChooser = downsampleValueChooser; + this.seed = seed; + } + + @Override + public Function, Iterable> setup(Iterable[] sets) { + long[] totals = new long[sets.length]; + for (int i = 0; i < sets.length; i++) + totals[i] = total(getCount, sets[i]); + long downsampling = downsampleValueChooser.compute(totals); + + Set> empty = new HashSet<>(); + for (int i = 0; i < totals.length; ++i) + if (totals[i] < downsampling) + empty.add(sets[i]); + + return set -> { + if (empty.contains(set)) + //noinspection unchecked + return emptyIterable; + + // compute counts + long total = 0; + TLongArrayList countsList = new TLongArrayList(); + for (T t : set) { + long c = getCount.applyAsLong(t); + countsList.add(c); + total += c; + } + + if (total < downsampling) + //noinspection unchecked + return emptyIterable; + + RandomGenerator rnd = new Well19937c(seed); + long[] countsDownsampled = downsample_mvhg(countsList.toArray(), downsampling, rnd); + + return new FilteredIterable<>( + () -> new Iterator() { + final Iterator inner = set.iterator(); + final AtomicInteger index = new AtomicInteger(0); + + @Override + public boolean hasNext() { + return inner.hasNext(); + } + + @Override + public T next() { + return setCount.apply(inner.next(), countsDownsampled[index.getAndIncrement()]); + } + }, + t -> getCount.applyAsLong(t) != 0); + }; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java new file mode 100644 index 000000000..1c3a812d2 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -0,0 +1,78 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import org.apache.commons.math3.random.RandomGenerator; + +import java.util.Iterator; +import java.util.function.ToLongFunction; +import java.util.stream.LongStream; + +public final class DownsamplingUtil { + private DownsamplingUtil() { + } + + @SuppressWarnings("rawtypes") + public static final Iterator emptyIterator = new Iterator() { + @Override + public boolean hasNext() { + return false; + } + + @Override + public Object next() { + return null; + } + }; + + @SuppressWarnings("rawtypes") + public static final Iterable emptyIterable = () -> emptyIterator; + + public static long total(ToLongFunction getCount, Iterable set) { + long total = 0; + for (T t : set) + total += getCount.applyAsLong(t); + return total; + } + + public static long[] downsample_mvhg(long[] counts, long downSampleSize, RandomGenerator rnd) { + long total = LongStream.of(counts).sum(); + long[] result = new long[counts.length]; + RandomMvhgMarginals.random_multivariate_hypergeometric_marginals(rnd, total, counts, downSampleSize, result); + return result; + } + + public static long[] downsample_counts(long[] counts, long downSampleSize, RandomGenerator rnd) { + long total = LongStream.of(counts).sum(); + long[] result = new long[counts.length]; + RandomMvhgCounts.random_multivariate_hypergeometric_count(rnd, total, counts, downSampleSize, result); + return result; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java new file mode 100644 index 000000000..75e067d36 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java @@ -0,0 +1,193 @@ +/* + * Copyright (c) 2005-2020, NumPy Developers. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are + * met: + * + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * * Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * + * * Neither the name of the NumPy Developers nor the names of any + * contributors may be used to endorse or promote products derived + * from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ +package com.milaboratory.mixcr.postanalysis.downsampling; + +/** + * Adapted from nymphy: https://github.com/numpy/numpy/tree/master/numpy/random/src/distributions + */ +public class LogFactorial { + + /** + * logfact[k] holds log(k!) for k = 0, 1, 2, ..., 125. + */ + private static final double[] logfact = { + 0, + 0, + 0.69314718055994529, + 1.791759469228055, + 3.1780538303479458, + 4.7874917427820458, + 6.5792512120101012, + 8.5251613610654147, + 10.604602902745251, + 12.801827480081469, + 15.104412573075516, + 17.502307845873887, + 19.987214495661885, + 22.552163853123425, + 25.19122118273868, + 27.89927138384089, + 30.671860106080672, + 33.505073450136891, + 36.395445208033053, + 39.339884187199495, + 42.335616460753485, + 45.380138898476908, + 48.471181351835227, + 51.606675567764377, + 54.784729398112319, + 58.003605222980518, + 61.261701761002001, + 64.557538627006338, + 67.88974313718154, + 71.257038967168015, + 74.658236348830158, + 78.092223553315307, + 81.557959456115043, + 85.054467017581516, + 88.580827542197682, + 92.136175603687093, + 95.719694542143202, + 99.330612454787428, + 102.96819861451381, + 106.63176026064346, + 110.32063971475739, + 114.03421178146171, + 117.77188139974507, + 121.53308151543864, + 125.3172711493569, + 129.12393363912722, + 132.95257503561632, + 136.80272263732635, + 140.67392364823425, + 144.5657439463449, + 148.47776695177302, + 152.40959258449735, + 156.3608363030788, + 160.3311282166309, + 164.32011226319517, + 168.32744544842765, + 172.35279713916279, + 176.39584840699735, + 180.45629141754378, + 184.53382886144948, + 188.6281734236716, + 192.7390472878449, + 196.86618167289001, + 201.00931639928152, + 205.1681994826412, + 209.34258675253685, + 213.53224149456327, + 217.73693411395422, + 221.95644181913033, + 226.1905483237276, + 230.43904356577696, + 234.70172344281826, + 238.97838956183432, + 243.26884900298271, + 247.57291409618688, + 251.89040220972319, + 256.22113555000954, + 260.56494097186322, + 264.92164979855278, + 269.29109765101981, + 273.67312428569369, + 278.06757344036612, + 282.4742926876304, + 286.89313329542699, + 291.32395009427029, + 295.76660135076065, + 300.22094864701415, + 304.68685676566872, + 309.1641935801469, + 313.65282994987905, + 318.1526396202093, + 322.66349912672615, + 327.1852877037752, + 331.71788719692847, + 336.26118197919845, + 340.81505887079902, + 345.37940706226686, + 349.95411804077025, + 354.53908551944079, + 359.1342053695754, + 363.73937555556347, + 368.35449607240474, + 372.97946888568902, + 377.61419787391867, + 382.25858877306001, + 386.91254912321756, + 391.57598821732961, + 396.24881705179155, + 400.93094827891576, + 405.6222961611449, + 410.32277652693733, + 415.03230672824964, + 419.75080559954472, + 424.47819341825709, + 429.21439186665157, + 433.95932399501481, + 438.71291418612117, + 443.47508812091894, + 448.24577274538461, + 453.02489623849613, + 457.81238798127816, + 462.60817852687489, + 467.4121995716082, + 472.22438392698058, + 477.04466549258564, + 481.87297922988796 + }; + + private static final double halfln2pi = 0.9189385332046728; + + /** + * Compute log(k!) + */ + public static double logfactorial(long k) + { + + if (k < logfact.length) { + /* Use the lookup table. */ + return logfact[(int)k]; + } + + /* + * Use the Stirling series, truncated at the 1/k**3 term. + * (In a Python implementation of this approximation, the result + * was within 2 ULP of the best 64 bit floating point value for + * k up to 10000000.) + */ + return (k + 0.5)*Math.log(k) - k + (halfln2pi + (1.0/k)*(1/12.0 - 1/(360.0*k*k))); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java new file mode 100644 index 000000000..5d01ca08b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java @@ -0,0 +1,132 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.util.FilteredIterable; +import gnu.trove.list.array.TLongArrayList; +import org.apache.commons.math3.random.RandomGenerator; +import org.apache.commons.math3.random.Well19937c; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Iterator; +import java.util.List; +import java.util.concurrent.atomic.AtomicIntegerArray; +import java.util.function.BiFunction; +import java.util.function.Function; +import java.util.function.ToLongFunction; +import java.util.stream.Collectors; + +public abstract class OverlapDownsamplingPreprocessor implements SetPreprocessor> { + public final ToLongFunction getCount; + public final BiFunction setCount; + @JsonProperty("downsampleValueChooser") + public final DownsampleValueChooser downsampleValueChooser; + @JsonProperty("seed") + public final long seed; + + public OverlapDownsamplingPreprocessor(ToLongFunction getCount, BiFunction setCount, DownsampleValueChooser downsampleValueChooser, long seed) { + this.getCount = getCount; + this.setCount = setCount; + this.downsampleValueChooser = downsampleValueChooser; + this.seed = seed; + } + + @Override + public Function>, Iterable>> setup(Iterable>[] sets) { + return set -> { + TLongArrayList[] counts = null; + for (OverlapGroup grp : set) { + if (counts == null) { + counts = new TLongArrayList[grp.size()]; + for (int i = 0; i < grp.size(); i++) + counts[i] = new TLongArrayList(); + } + + assert counts.length == grp.size(); + + for (int i = 0; i < counts.length; i++) + for (T t : grp.getBySample(i)) + counts[i].add(getCount.applyAsLong(t)); + } + + if (counts == null) + // empty set + return set; + + long[] totals = Arrays.stream(counts).mapToLong(TLongArrayList::sum).toArray(); + long downsample = downsampleValueChooser.compute(totals); + + RandomGenerator rnd = new Well19937c(seed); + long[][] newCounts = new long[totals.length][]; + for (int i = 0; i < totals.length; i++) { + if (totals[i] < downsample) + continue; + newCounts[i] = DownsamplingUtil.downsample_mvhg(counts[i].toArray(), downsample, rnd); + } + + return new FilteredIterable<>(() -> new Iterator>() { + final Iterator> innerIterator = set.iterator(); + final AtomicIntegerArray indices = new AtomicIntegerArray(totals.length); + + @Override + public boolean hasNext() { + return innerIterator.hasNext(); + } + + @Override + public OverlapGroup next() { + OverlapGroup grp = innerIterator.next(); + List> newGroups = new ArrayList<>(); + for (int i = 0; i < grp.size(); i++) { + final int fi = i; + List objs = grp.getBySample(i); + if (objs.isEmpty()) + newGroups.add(objs); + else + newGroups.add(objs.stream() + .map(o -> { + long newCount = newCounts[fi] == null ? 0 : newCounts[fi][indices.getAndIncrement(fi)]; + if (getCount.applyAsLong(o) < newCount) + throw new RuntimeException("Assertion exception. Varying ordering of objects in iterator."); + return setCount.apply(o, newCount); + }) + .filter(l -> getCount.applyAsLong(l) > 0) + .collect(Collectors.toList())); + } + return new OverlapGroup<>(newGroups); + } + }, OverlapGroup::notEmpty); + }; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java new file mode 100644 index 000000000..dbf9bbbda --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java @@ -0,0 +1,319 @@ +/* + * Copyright (c) 2005-2020, NumPy Developers. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are + * met: + * + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * * Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * + * * Neither the name of the NumPy Developers nor the names of any + * contributors may be used to endorse or promote products derived + * from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import org.apache.commons.math3.random.RandomGenerator; + +import static com.milaboratory.mixcr.postanalysis.downsampling.LogFactorial.logfactorial; +import static java.lang.Math.floor; +import static java.lang.Math.log; + +/** + * Adapted from nymphy: https://github.com/numpy/numpy/tree/master/numpy/random/src/distributions + */ +public class RandomHypergeometric { + + static long random_interval(RandomGenerator bitgen_state, long max) { + long mask, value; + if (max == 0) { + return 0; + } + + mask = max; + + /* Smallest bit mask >= max */ + mask |= mask >> 1; + mask |= mask >> 2; + mask |= mask >> 4; + mask |= mask >> 8; + mask |= mask >> 16; + mask |= mask >> 32; + + /* Search a random value in [0..mask] <= max */ + if (max <= 0xffffffffL) { + while ((value = (bitgen_state.nextInt() & mask)) > max) ; + } else { + while ((value = (bitgen_state.nextInt() & mask)) > max) ; + } + return value; + } + + /** + * Generate a sample from the hypergeometric distribution. + * + * Assume sample is not greater than half the total. See below + * for how the opposite case is handled. + * + * We initialize the following: + * computed_sample = sample + * remaining_good = good + * remaining_total = good + bad + * + * In the loop: + * * computed_sample counts down to 0; + * * remaining_good is the number of good choices not selected yet; + * * remaining_total is the total number of choices not selected yet. + * + * In the loop, we select items by choosing a random integer in + * the interval [0, remaining_total), and if the value is less + * than remaining_good, it means we have selected a good one, + * so remaining_good is decremented. Then, regardless of that + * result, computed_sample is decremented. The loop continues + * until either computed_sample is 0, remaining_good is 0, or + * remaining_total == remaining_good. In the latter case, it + * means there are only good choices left, so we can stop the + * loop early and select what is left of computed_sample from + * the good choices (i.e. decrease remaining_good by computed_sample). + * + * When the loop exits, the actual number of good choices is + * good - remaining_good. + * + * If sample is more than half the total, then initially we set + * computed_sample = total - sample + * and at the end we return remaining_good (i.e. the loop in effect + * selects the complement of the result). + * + * It is assumed that when this function is called: + * * good, bad and sample are nonnegative; + * * the sum good+bad will not result in overflow; + * * sample <= good+bad. + */ + public static long hypergeometric_sample(RandomGenerator bitgen_state, + long good, long bad, long sample) { + long remaining_total, remaining_good, result, computed_sample; + long total = good + bad; + + if (sample > total / 2) { + computed_sample = total - sample; + } else { + computed_sample = sample; + } + + remaining_total = total; + remaining_good = good; + + while ((computed_sample > 0) && (remaining_good > 0) && + (remaining_total > remaining_good)) { + // random_interval(bitgen_state, max) returns an integer in + // [0, max] *inclusive*, so we decrement remaining_total before + // passing it to random_interval(). + --remaining_total; + if ((long) random_interval(bitgen_state, + remaining_total) < remaining_good) { + // Selected a "good" one, so decrement remaining_good. + --remaining_good; + } + --computed_sample; + } + + if (remaining_total == remaining_good) { + // Only "good" choices are left. + remaining_good -= computed_sample; + } + + if (sample > total / 2) { + result = remaining_good; + } else { + result = good - remaining_good; + } + + return result; + } + + +// D1 = 2*sqrt(2/e) +// D2 = 3 - 2*sqrt(3/e) + + public static final double D1 = 1.7155277699214135; + public static final double D2 = 0.8989161620588988; + + /** + * Generate variates from the hypergeometric distribution + * using the ratio-of-uniforms method. + * + * In the code, the variable names a, b, c, g, h, m, p, q, K, T, + * U and X match the names used in "Algorithm HRUA" beginning on + * page 82 of Stadlober's 1989 thesis. + * + * It is assumed that when this function is called: + * * good, bad and sample are nonnegative; + * * the sum good+bad will not result in overflow; + * * sample <= good+bad. + * + * References: + * - Ernst Stadlober's thesis "Sampling from Poisson, Binomial and + * Hypergeometric Distributions: Ratio of Uniforms as a Simple and + * Fast Alternative" (1989) + * - Ernst Stadlober, "The ratio of uniforms approach for generating + * discrete random variates", Journal of Computational and Applied + * Mathematics, 31, pp. 181-189 (1990). + */ + public static long hypergeometric_hrua(RandomGenerator bitgen_state, + long good, long bad, long sample) { + long mingoodbad, maxgoodbad, popsize; + long computed_sample; + double p, q; + double mu, var; + double a, c, b, h, g; + long m, K; + + popsize = good + bad; + computed_sample = Math.min(sample, popsize - sample); + mingoodbad = Math.min(good, bad); + maxgoodbad = Math.max(good, bad); + + /* + * Variables that do not match Stadlober (1989) + * Here Stadlober + * ---------------- --------- + * mingoodbad M + * popsize N + * computed_sample n + */ + + p = ((double) mingoodbad) / popsize; + q = ((double) maxgoodbad) / popsize; + + // mu is the mean of the distribution. + mu = computed_sample * p; + + a = mu + 0.5; + + // var is the variance of the distribution. + var = ((double) (popsize - computed_sample) * + computed_sample * p * q / (popsize - 1)); + + c = Math.sqrt(var + 0.5); + + /* + * h is 2*s_hat (See Stadlober's theses (1989), Eq. (5.17); or + * Stadlober (1990), Eq. 8). s_hat is the scale of the "table mountain" + * function that dominates the scaled hypergeometric PMF ("scaled" means + * normalized to have a maximum value of 1). + */ + h = D1 * c + D2; + + m = (long) floor((double) (computed_sample + 1) * (mingoodbad + 1) / + (popsize + 2)); + + g = (logfactorial(m) + + logfactorial(mingoodbad - m) + + logfactorial(computed_sample - m) + + logfactorial(maxgoodbad - computed_sample + m)); + + /* + * b is the upper bound for random samples: + * ... min(computed_sample, mingoodbad) + 1 is the length of the support. + * ... floor(a + 16*c) is 16 standard deviations beyond the mean. + * + * The idea behind the second upper bound is that values that far out in + * the tail have negligible probabilities. + * + * There is a comment in a previous version of this algorithm that says + * "16 for 16-decimal-digit precision in D1 and D2", + * but there is no documented justification for this value. A lower value + * might work just as well, but I've kept the value 16 here. + */ + b = Math.min(Math.min(computed_sample, mingoodbad) + 1, floor(a + 16 * c)); + + while (true) { + double U, V, X, T; + double gp; + U = bitgen_state.nextDouble(); + V = bitgen_state.nextDouble(); // "U star" in Stadlober (1989) + X = a + h * (V - 0.5) / U; + + // fast rejection: + if ((X < 0.0) || (X >= b)) { + continue; + } + + K = (long) floor(X); + + gp = (logfactorial(K) + + logfactorial(mingoodbad - K) + + logfactorial(computed_sample - K) + + logfactorial(maxgoodbad - computed_sample + K)); + + T = g - gp; + + // fast acceptance: + if ((U * (4.0 - U) - 3.0) <= T) { + break; + } + + // fast rejection: + if (U * (U - T) >= 1) { + continue; + } + + if (2.0 * log(U) <= T) { + // acceptance + break; + } + } + + if (good > bad) { + K = computed_sample - K; + } + + if (computed_sample < sample) { + K = good - K; + } + + return K; + } + + + /** + * Draw a sample from the hypergeometric distribution. + * + * It is assumed that when this function is called: + * * good, bad and sample are nonnegative; + * * the sum good+bad will not result in overflow; + * * sample <= good+bad. + */ + public static long random_hypergeometric(RandomGenerator bitgen_state, + long good, long bad, long sample) { + long r; + + if ((sample >= 10) && (sample <= good + bad - 10)) { + // This will use the ratio-of-uniforms method. + r = hypergeometric_hrua(bitgen_state, good, bad, sample); + } else { + // The simpler implementation is faster for small samples. + r = hypergeometric_sample(bitgen_state, good, bad, sample); + } + return r; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java new file mode 100644 index 000000000..6326ba081 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java @@ -0,0 +1,168 @@ +/* + * Copyright (c) 2005-2020, NumPy Developers. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are + * met: + * + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * * Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * + * * Neither the name of the NumPy Developers nor the names of any + * contributors may be used to endorse or promote products derived + * from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import org.apache.commons.math3.random.RandomGenerator; + +import static com.milaboratory.mixcr.postanalysis.downsampling.RandomHypergeometric.random_interval; + + +/** + * Adapted from nymphy: https://github.com/numpy/numpy/tree/master/numpy/random/src/distributions + */ +public class RandomMvhgCounts { + + + /** + * random_multivariate_hypergeometric_count + * + * Draw variates from the multivariate hypergeometric distribution-- + * the "count" algorithm. + * + * Parameters + * ---------- + * bitgen_t *bitgen_state + * Pointer to a `bitgen_t` instance. + * long total + * The sum of the values in the array `colors`. (This is redundant + * information, but we know the caller has already computed it, so + * we might as well use it.) + * size_t num_colors + * The length of the `colors` array. + * long *colors + * The array of colors (i.e. the number of each type in the collection + * from which the random variate is drawn). + * long nsample + * The number of objects drawn without replacement for each variate. + * `nsample` must not exceed sum(colors). This condition is not checked; + * it is assumed that the caller has already validated the value. + * size_t num_variates + * The number of variates to be produced and put in the array + * pointed to by `variates`. One variate is a vector of length + * `num_colors`, so the array pointed to by `variates` must have length + * `num_variates * num_colors`. + * long *variates + * The array that will hold the result. It must have length + * `num_variates * num_colors`. + * The array is not initialized in the function; it is expected that the + * array has been initialized with zeros when the function is called. + * + * Notes + * ----- + * The "count" algorithm for drawing one variate is roughly equivalent to the + * following numpy code: + * + * choices = np.repeat(np.arange(len(colors)), colors) + * selection = np.random.choice(choices, nsample, replace=False) + * variate = np.bincount(selection, minlength=len(colors)) + * + * This function uses a temporary array with length sum(colors). + * + * Assumptions on the arguments (not checked in the function): + * * colors[k] >= 0 for k in range(num_colors) + * * total = sum(colors) + * * 0 <= nsample <= total + * * the product total * sizeof(size_t) does not exceed SIZE_MAX + * * the product num_variates * num_colors does not overflow + */ + public static void random_multivariate_hypergeometric_count(RandomGenerator bitgen_state, + long total, + long[] colors, + long nsample, + long[] variates) + { + int num_colors = colors.length; + int num_variates = 1; + int[] choices; + boolean more_than_half; + + if (total > Integer.MAX_VALUE) + throw new IllegalArgumentException(); + + if ((total == 0) || (nsample == 0) || (num_variates == 0)) { + // Nothing to do. + return; + } + + choices = new int[(int) total]; + + /* + * If colors contains, for example, [3 2 5], then choices + * will contain [0 0 0 1 1 2 2 2 2 2]. + */ + for (int i = 0, k = 0; i < num_colors; ++i) { + for (long j = 0; j < colors[i]; ++j) { + choices[k] = i; + ++k; + } + } + + more_than_half = nsample > (total / 2); + if (more_than_half) { + nsample = total - nsample; + } + + for (int i = 0; i < num_variates * num_colors; i += num_colors) { + /* + * Fisher-Yates shuffle, but only loop through the first + * `nsample` entries of `choices`. After the loop, + * choices[:nsample] contains a random sample from the + * the full array. + */ + for (int j = 0; j < (int) nsample; ++j) { + int tmp, k; + // Note: nsample is not greater than total, so there is no danger + // of integer underflow in `(size_t) total - j - 1`. + k = j + (int) random_interval(bitgen_state, + (int) total - j - 1); + tmp = choices[k]; + choices[k] = choices[j]; + choices[j] = tmp; + } + /* + * Count the number of occurrences of each value in choices[:nsample]. + * The result, stored in sample[i:i+num_colors], is the sample from + * the multivariate hypergeometric distribution. + */ + for (int j = 0; j < (int) nsample; ++j) { + variates[i + choices[j]] += 1; + } + + if (more_than_half) { + for (int k = 0; k < num_colors; ++k) { + variates[i + k] = colors[k] - variates[i + k]; + } + } + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java new file mode 100644 index 000000000..901a0ca9a --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java @@ -0,0 +1,174 @@ +/* + * Copyright (c) 2005-2020, NumPy Developers. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are + * met: + * + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * * Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * + * * Neither the name of the NumPy Developers nor the names of any + * contributors may be used to endorse or promote products derived + * from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import org.apache.commons.math3.random.RandomGenerator; + +import static com.milaboratory.mixcr.postanalysis.downsampling.RandomHypergeometric.random_hypergeometric; + +/** + * Adapted from nymphy: https://github.com/numpy/numpy/tree/master/numpy/random/src/distributions + */ +public class RandomMvhgMarginals { + + /** + * random_multivariate_hypergeometric_marginals + * + * Draw samples from the multivariate hypergeometric distribution-- + * the "marginals" algorithm. + * + * This version generates the sample by iteratively calling + * hypergeometric() (the univariate hypergeometric distribution). + * + * Parameters + * ---------- + * bitgen_t *bitgen_state + * Pointer to a `bitgen_t` instance. + * long total + * The sum of the values in the array `colors`. (This is redundant + * information, but we know the caller has already computed it, so + * we might as well use it.) + * size_t num_colors + * The length of the `colors` array. The functions assumes + * num_colors > 0. + * long *colors + * The array of colors (i.e. the number of each type in the collection + * from which the random variate is drawn). + * long nsample + * The number of objects drawn without replacement for each variate. + * `nsample` must not exceed sum(colors). This condition is not checked; + * it is assumed that the caller has already validated the value. + * size_t num_variates + * The number of variates to be produced and put in the array + * pointed to by `variates`. One variate is a vector of length + * `num_colors`, so the array pointed to by `variates` must have length + * `num_variates * num_colors`. + * long *variates + * The array that will hold the result. It must have length + * `num_variates * num_colors`. + * The array is not initialized in the function; it is expected that the + * array has been initialized with zeros when the function is called. + * + * Notes + * ----- + * Here's an example that demonstrates the idea of this algorithm. + * + * Suppose the urn contains red, green, blue and yellow marbles. + * Let nred be the number of red marbles, and define the quantities for + * the other colors similarly. The total number of marbles is + * + * total = nred + ngreen + nblue + nyellow. + * + * To generate a sample using rk_hypergeometric: + * + * red_sample = hypergeometric(ngood=nred, nbad=total - nred, + * nsample=nsample) + * + * This gives us the number of red marbles in the sample. The number of + * marbles in the sample that are *not* red is nsample - red_sample. + * To figure out the distribution of those marbles, we again use + * rk_hypergeometric: + * + * green_sample = hypergeometric(ngood=ngreen, + * nbad=total - nred - ngreen, + * nsample=nsample - red_sample) + * + * Similarly, + * + * blue_sample = hypergeometric( + * ngood=nblue, + * nbad=total - nred - ngreen - nblue, + * nsample=nsample - red_sample - green_sample) + * + * Finally, + * + * yellow_sample = total - (red_sample + green_sample + blue_sample). + * + * The above sequence of steps is implemented as a loop for an arbitrary + * number of colors in the innermost loop in the code below. `remaining` + * is the value passed to `nbad`; it is `total - colors[0]` in the first + * call to random_hypergeometric(), and then decreases by `colors[j]` in + * each iteration. `num_to_sample` is the `nsample` argument. It + * starts at this function's `nsample` input, and is decreased by the + * result of the call to random_hypergeometric() in each iteration. + * + * Assumptions on the arguments (not checked in the function): + * * colors[k] >= 0 for k in range(num_colors) + * * total = sum(colors) + * * 0 <= nsample <= total + * * the product num_variates * num_colors does not overflow + */ + public static void random_multivariate_hypergeometric_marginals(RandomGenerator bitgen_state, + long total, + long[] colors, + long nsample, + long[] variates) + { + int num_colors = colors.length; + int num_variates = 1; + boolean more_than_half; + + if ((total == 0) || (nsample == 0) || (num_variates == 0)) { + // Nothing to do. + return; + } + + more_than_half = nsample > (total / 2); + if (more_than_half) { + nsample = total - nsample; + } + + for (int i = 0; i < num_variates * num_colors; i += num_colors) { + long num_to_sample = nsample; + long remaining = total; + for (int j = 0; (num_to_sample > 0) && (j + 1 < num_colors); ++j) { + long r; + remaining -= colors[j]; + r = random_hypergeometric(bitgen_state, + colors[j], remaining, num_to_sample); + variates[i + j] = r; + num_to_sample -= r; + } + + if (num_to_sample > 0) { + variates[i + num_colors - 1] = num_to_sample; + } + + if (more_than_half) { + for (int k = 0; k < num_colors; ++k) { + variates[i + k] = colors[k] - variates[i + k]; + } + } + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java new file mode 100644 index 000000000..c1194c998 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java @@ -0,0 +1,28 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristic; +import com.milaboratory.mixcr.postanalysis.additive.AggregationType; + +/** + * + */ +public class AdditiveOverlapCharacteristic extends AdditiveCharacteristic, OverlapGroup> { + public final int i1, i2; + + public AdditiveOverlapCharacteristic(String name, + SetPreprocessor> preprocessor, + int i1, int i2, + OverlapGroupKeyFunction keyFunction, + OverlapGroupWeightFunction weight, + OverlapGroupAdditiveMetric metric, + AggregationType aggType, boolean normalizeByKey) { + super(name, preprocessor, + group -> weight.weight(group.getBySample(i1), group.getBySample(i2)), + group -> new OverlapKey<>(keyFunction.getKey(group.getBySample(i1), group.getBySample(i2)), i1, i2), + group -> metric.compute(group.getBySample(i1), group.getBySample(i2)), + aggType, normalizeByKey); + this.i1 = i1; + this.i2 = i2; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java new file mode 100644 index 000000000..45eda73bc --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java @@ -0,0 +1,68 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import com.milaboratory.mixcr.postanalysis.Aggregator; +import com.milaboratory.mixcr.postanalysis.MetricValue; +import com.milaboratory.mixcr.postanalysis.WeightFunction; +import org.apache.commons.math3.stat.regression.SimpleRegression; + +import java.util.List; + +/** + * + */ +public class OverlapAggregator implements Aggregator, OverlapGroup> { + private final WeightFunction weight; + private final int i1, i2; + final SimpleRegression + regressionAll = new SimpleRegression(), + regressionIntersection = new SimpleRegression(); + double sumS1, sumS2, + sumS1Intersection, sumS2Intersection, + sumSqProduct; + long diversity1, diversity2, diversityIntersection; + + public OverlapAggregator(WeightFunction weight, int i1, int i2) { + this.weight = weight; + this.i1 = i1; + this.i2 = i2; + } + + @Override + public void consume(OverlapGroup obj) { + List s1 = obj.getBySample(i1); + List s2 = obj.getBySample(i2); + double ss1 = s1.stream().mapToDouble(weight::weight).sum(); + double ss2 = s2.stream().mapToDouble(weight::weight).sum(); + regressionAll.addData(ss1, ss2); + sumS1 += ss1; + sumS2 += ss2; + if (!s1.isEmpty()) + diversity1++; + if (!s2.isEmpty()) + diversity2++; + if (s1.isEmpty() || s2.isEmpty()) + return; + regressionIntersection.addData(ss1, ss2); + diversityIntersection++; + sumS1Intersection += ss1; + sumS2Intersection += ss2; + sumSqProduct += Math.sqrt(ss1 * ss2); + } + + @Override + public MetricValue>[] result() { + return new MetricValue[]{ + new MetricValue<>(key(OverlapType.D, i1, i2), 1.0 * diversityIntersection / diversity1 / diversity2), + new MetricValue<>(key(OverlapType.SharedClonotypes, i1, i2), 1.0 * diversityIntersection), + new MetricValue<>(key(OverlapType.F1, i1, i2), Math.sqrt(sumS1Intersection * sumS2Intersection / sumS1 / sumS2)), + new MetricValue<>(key(OverlapType.F2, i1, i2), sumSqProduct / Math.sqrt(sumS1 * sumS2)), + new MetricValue<>(key(OverlapType.Jaccard, i1, i2), 1.0 * diversityIntersection / (diversity1 + diversity2 - diversityIntersection)), + new MetricValue<>(key(OverlapType.R_Intersection, i1, i2), regressionIntersection.getR()), + new MetricValue<>(key(OverlapType.R_All, i1, i2), regressionAll.getR()), + }; + } + + private static OverlapKey key(OverlapType type, int i, int j) { + return new OverlapKey<>(type, i, j); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java new file mode 100644 index 000000000..e85c9a512 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java @@ -0,0 +1,55 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Aggregator; +import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.WeightFunction; + +import java.util.Objects; + +/** + * + */ +public class OverlapCharacteristic extends Characteristic, OverlapGroup> { + @JsonProperty("i1") + public final int i1; + @JsonProperty("i2") + public final int i2; + @JsonProperty("weight") + public final WeightFunction weight; + + @JsonCreator + public OverlapCharacteristic(@JsonProperty("name") String name, + @JsonProperty("weight") WeightFunction weight, + @JsonProperty("preprocessor") SetPreprocessor> preprocessor, + @JsonProperty("i1") int i1, + @JsonProperty("i2") int i2) { + super(name, preprocessor, __ -> 1L); + this.i1 = i1; + this.i2 = i2; + this.weight = weight; + } + + @Override + protected Aggregator, OverlapGroup> createAggregator() { + return new OverlapAggregator<>(weight, i1, i2); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + OverlapCharacteristic that = (OverlapCharacteristic) o; + return i1 == that.i1 && + i2 == that.i2 && + Objects.equals(weight, that.weight); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), i1, i2, weight); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java new file mode 100644 index 000000000..4ee6f5240 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java @@ -0,0 +1,67 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.overlap; + +import java.util.List; +import java.util.Objects; + +public final class OverlapGroup { + /** Elements in group separated by sample */ + final List> elements; + + public OverlapGroup(List> elements) { + this.elements = elements; + } + + public int size() { + return elements.size(); + } + + public List getBySample(int sampleIndex) { + return elements.get(sampleIndex); + } + + public boolean notEmpty() { + return !elements.stream().allMatch(List::isEmpty); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OverlapGroup that = (OverlapGroup) o; + return Objects.equals(elements, that.elements); + } + + @Override + public int hashCode() { + return Objects.hash(elements); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java new file mode 100644 index 000000000..b876ecb09 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java @@ -0,0 +1,10 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import java.util.List; + +/** + * + */ +public interface OverlapGroupAdditiveMetric { + double compute(List i1, List i2); +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java new file mode 100644 index 000000000..dbd37118c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java @@ -0,0 +1,10 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import java.util.List; + +/** + * + */ +public interface OverlapGroupKeyFunction { + K getKey(List i1, List i2); +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java new file mode 100644 index 000000000..7420241c7 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java @@ -0,0 +1,10 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import java.util.List; + +/** + * + */ +public interface OverlapGroupWeightFunction { + double weight(List i1, List i2); +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java new file mode 100644 index 000000000..1d7cdd015 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java @@ -0,0 +1,33 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.overlap; + + +public interface OverlapIterable extends Iterable> {} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java new file mode 100644 index 000000000..855d5926c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java @@ -0,0 +1,57 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +import java.util.Objects; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public final class OverlapKey { + @JsonProperty("key") + @JsonTypeInfo(use = JsonTypeInfo.Id.CLASS, property = "type") + public final K key; + @JsonProperty("i1") + public final int i1; + @JsonProperty("i2") + public final int i2; + + @JsonCreator + public OverlapKey(@JsonProperty("key") K key, @JsonProperty("i1") int i1, @JsonProperty("i2") int i2) { + this.key = key; + this.i1 = i1; + this.i2 = i2; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OverlapKey that = (OverlapKey) o; + return i1 == that.i1 && + i2 == that.i2 && + Objects.equals(key, that.key); + } + + @Override + public int hashCode() { + return Objects.hash(key, i1, i2); + } + + @Override + public String toString() { + return "OverlapKey{" + + "key=" + key + + ", i1=" + i1 + + ", i2=" + i2 + + '}'; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java new file mode 100644 index 000000000..4449d0083 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java @@ -0,0 +1,28 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import java.util.Arrays; + +/** + * + */ +public enum OverlapType { + D("Diversity", "Relative overlap diversity normalized"), + SharedClonotypes("Clonotype share", "Number of shared clonotypes"), + F1("Frequencies", "Geometric mean of relative overlap frequencies"), + F2("Drequencies (clonotype-wise)", "Сlonotype-wise sum of geometric mean frequencies"), + Jaccard("Jaccard", "Jaccard overlap"), + R_Intersection("Pearson", "Pearson correlation of clonotype frequencies, restricted only to the overlapping clonotypes"), + R_All("Pearson (all)", "Pearson correlation of clonotype frequencies (outer merge)"); + + public final String name; + public final String description; + + OverlapType(String name, String description) { + this.name = name; + this.description = description; + } + + public static OverlapType byName(String name) { + return Arrays.stream(values()).filter(s -> s.name.equals(name)).findFirst().orElse(null); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java new file mode 100644 index 000000000..bc327944e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java @@ -0,0 +1,55 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.overlap; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.util.SimpleProcessorWrapper; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneReader; +import com.milaboratory.mixcr.basictypes.CloneSetOverlap; +import com.milaboratory.mixcr.basictypes.VDJCSProperties; + +import java.util.List; + +public final class OverlapUtil { + private OverlapUtil() { + } + + public static OverlapIterable overlap( + List> by, + List readers) { + return () -> { + OutputPort> s = + new SimpleProcessorWrapper<>(CloneSetOverlap.overlap(by, readers), OverlapGroup::new); + return CUtils.it(s).iterator(); + }; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java new file mode 100644 index 000000000..6bd122d27 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java @@ -0,0 +1,135 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import com.fasterxml.jackson.annotation.*; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import io.repseq.core.Chains; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; + +import java.util.Objects; +import java.util.function.Predicate; + +/** + * + */ +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = ElementPredicate.NoOutOfFrames.class, name = "noOOF"), + @JsonSubTypes.Type(value = ElementPredicate.NoStops.class, name = "noStops"), + @JsonSubTypes.Type(value = ElementPredicate.IncludeChains.class, name = "includesChains"), + @JsonSubTypes.Type(value = ElementPredicate.OverlapIncludeChains.class, name = "overlapIncludesChains") +}) +public interface ElementPredicate extends Predicate { + @JsonAutoDetect + final class NoOutOfFrames implements ElementPredicate { + @Override + public boolean test(Clone clone) { + if (clone.isOutOfFrame(GeneFeature.CDR3)) + return false; + return true; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return Objects.hash(13); + } + } + + @JsonAutoDetect + final class NoStops implements ElementPredicate { + @Override + public boolean test(Clone clone) { + for (GeneFeature gf : clone.getParentCloneSet().getAssemblingFeatures()) { + if (clone.containsStops(gf)) + return false; + } + return true; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return Objects.hash(13); + } + } + + final class IncludeChains implements ElementPredicate { + @JsonProperty("chains") + public final Chains chains; + + @JsonCreator + public IncludeChains(@JsonProperty("chains") Chains chains) { + this.chains = chains; + } + + @Override + public boolean test(Clone object) { + for (GeneType gt : GeneType.VJC_REFERENCE) + if (chains.intersects(object.getTopChain(gt))) + return true; + + return false; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + IncludeChains that = (IncludeChains) o; + return Objects.equals(chains, that.chains); + } + + @Override + public int hashCode() { + return Objects.hash(chains); + } + } + + final class OverlapIncludeChains implements ElementPredicate> { + @JsonProperty("chains") + public final Chains chains; + + @JsonCreator + public OverlapIncludeChains(@JsonProperty("chains") Chains chains) { + this.chains = chains; + } + + @Override + public boolean test(OverlapGroup object) { + for (GeneType gt : GeneType.VJC_REFERENCE) + for (int i = 0; i < object.size(); i++) + for (Clone clone : object.getBySample(i)) + if (clone != null && chains.intersects(clone.getTopChain(gt))) + return true; + + return false; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OverlapIncludeChains that = (OverlapIncludeChains) o; + return Objects.equals(chains, that.chains); + } + + @Override + public int hashCode() { + return Objects.hash(chains); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java new file mode 100644 index 000000000..9fdfb62ef --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -0,0 +1,37 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.util.FilteredIterable; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.function.Function; + +/** + * + */ +public class FilterPreprocessor implements SetPreprocessor { + @JsonProperty("predicates") + public final List> predicates; + + @JsonCreator + public FilterPreprocessor(@JsonProperty("predicates") List> predicates) { + this.predicates = predicates; + } + + public FilterPreprocessor(ElementPredicate... predicates) { + this(Arrays.asList(predicates)); + } + + public FilterPreprocessor(ElementPredicate predicate) { + this(Collections.singletonList(predicate)); + } + + @Override + public Function, Iterable> setup(Iterable[] sets) { + return set -> new FilteredIterable<>(set, t -> predicates.stream().allMatch(s -> s.test(t))); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java new file mode 100644 index 000000000..48f63e2d7 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java @@ -0,0 +1,29 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; + +import java.util.function.Function; + +/** + * + */ +public class NoPreprocessing implements SetPreprocessor { + public static final NoPreprocessing INSTANCE = new NoPreprocessing<>(); + + @Override + public Function, Iterable> setup(Iterable[] sets) { + return set -> set; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 17; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java new file mode 100644 index 000000000..44d3bdafc --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -0,0 +1,39 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; + +import java.util.*; +import java.util.function.Function; + +/** + * + */ +public class PreprocessorChain implements SetPreprocessor { + @JsonProperty("chain") + public final List> chain; + + @JsonCreator + public PreprocessorChain(@JsonProperty("chain") List> chain) { + this.chain = chain; + } + + public PreprocessorChain(SetPreprocessor... chain) { + this(Arrays.asList(chain)); + } + + @Override + public Function, Iterable> setup(Iterable[] sets) { + Iterable[] proc = sets; + for (SetPreprocessor p : chain) { + Function, Iterable> func = p.setup(proc); + //noinspection unchecked + proc = Arrays.stream(proc).map(func).toArray(Iterable[]::new); + } + Map, Iterable> mapping = new IdentityHashMap<>(); + for (int i = 0; i < sets.length; i++) + mapping.put(sets[i], proc[i]); + return mapping::get; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java new file mode 100644 index 000000000..719966a40 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java @@ -0,0 +1,34 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; + +import java.util.Map; +import java.util.function.Function; + +/** + * + */ +public class SampleFilterPreprocessor implements SetPreprocessor { + @JsonProperty("sampleFilters") + public final Map> sampleFilters; + + @JsonCreator + public SampleFilterPreprocessor(@JsonProperty("sampleFilters") Map> sampleFilters) { + this.sampleFilters = sampleFilters; + } + + @JsonIgnore + private Map, String> sampleNames; + + public void setSampleNames(Map, String> sampleNames) { + this.sampleNames = sampleNames; + } + + @Override + public Function, Iterable> setup(Iterable[] sets) { + return set -> sampleFilters.get(sampleNames.get(set)).setup(null).apply(set); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java new file mode 100644 index 000000000..58082632b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java @@ -0,0 +1,114 @@ +package com.milaboratory.mixcr.postanalysis.spectratype; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.Aggregator; +import com.milaboratory.mixcr.postanalysis.MetricValue; +import com.milaboratory.mixcr.postanalysis.WeightFunction; +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.map.hash.TIntObjectHashMap; +import gnu.trove.map.hash.TObjectDoubleHashMap; + +import java.util.ArrayList; +import java.util.List; +import java.util.TreeSet; + +/** + * + */ +public class SpectratypeAggregator implements Aggregator, Clone> { + final int nTopClones; + final SpectratypeKeyFunction keyFunction; + final WeightFunction weightFunction; + /** payload -> weight */ + final TObjectDoubleHashMap weights = new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, Double.NaN); + /** sorted set */ + final TreeSet> payloadCounts = new TreeSet<>(); + final TIntObjectHashMap> bins = new TIntObjectHashMap<>(); + + public SpectratypeAggregator(int nTopClones, SpectratypeKeyFunction keyFunction, WeightFunction weightFunction) { + assert nTopClones > 0; + this.nTopClones = nTopClones; + this.keyFunction = keyFunction; + this.weightFunction = weightFunction; + } + + @Override + public void consume(Clone obj) { + SpectratypeKey key = keyFunction.getKey(obj); + Payload payload = key.payload; + double weight = weightFunction.weight(obj); + Count count = new Count<>(payload, weight); + + Bin bin = bins.get(key.length); + if (bin == null) { + bin = new Bin<>(key.length); + bins.put(key.length, bin); + } + + bin.add(count); + if (!weights.containsKey(payload)) { + weights.put(payload, weight); + payloadCounts.add(count); + + if (weights.size() > nTopClones) { + Count markAsOther = payloadCounts.pollFirst(); + weights.remove(markAsOther.payload); + for (Bin b : bins.valueCollection()) + b.markAsOther(markAsOther.payload); + } + } + } + + @Override + public MetricValue>[] result() { + List>> result = new ArrayList<>(); + for (Bin bin : bins.valueCollection()) { + TObjectDoubleIterator it = bin.weights.iterator(); + while (it.hasNext()) { + it.advance(); + result.add(new MetricValue<>(new SpectratypeKey<>(bin.x, it.key()), it.value())); + } + result.add(new MetricValue<>(new SpectratypeKey<>(bin.x, null), bin.other)); + } + return result.toArray(new MetricValue[0]); + } + + private static final class Bin { + final int x; + /** weight of all "other" payloads */ + double other = 0.0; + /** payload -> weight */ + final TObjectDoubleHashMap weights = new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, Double.NaN); + + Bin(int x) { this.x = x; } + + void add(Count p) { + if (p.payload == null) + other += p.weight; + else + weights.adjustOrPutValue(p.payload, p.weight, p.weight); + } + + void markAsOther(Payload markAsOther) { + double w = weights.remove(markAsOther); + if (!Double.isNaN(w)) + other += w; + } + } + + private static final class Count implements Comparable> { + final Payload payload; + final double weight; + + public Count(Payload payload, double weight) { + this.payload = payload; + this.weight = weight; + } + + @Override + public int compareTo(Count o) { + return Double.compare(weight, o.weight); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java new file mode 100644 index 000000000..052bdaedc --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java @@ -0,0 +1,51 @@ +package com.milaboratory.mixcr.postanalysis.spectratype; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.Aggregator; +import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; + +import java.util.Objects; + +/** + * + */ +public class SpectratypeCharacteristic extends Characteristic, Clone> { + @JsonProperty("nTopClonotypes") + public final int nTopClonotypes; + @JsonProperty("keyFunction") + public final SpectratypeKeyFunction keyFunction; + + @JsonCreator + public SpectratypeCharacteristic(@JsonProperty("name") String name, + @JsonProperty("preprocessor") SetPreprocessor preprocessor, + @JsonProperty("nTopClonotypes") int nTopClonotypes, + @JsonProperty("keyFunction") SpectratypeKeyFunction keyFunction) { + super(name, preprocessor, new WeightFunctions.Count()); + this.nTopClonotypes = nTopClonotypes; + this.keyFunction = keyFunction; + } + + @Override + protected Aggregator, Clone> createAggregator() { + return new SpectratypeAggregator<>(nTopClonotypes, keyFunction, weight); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + SpectratypeCharacteristic that = (SpectratypeCharacteristic) o; + return nTopClonotypes == that.nTopClonotypes && + Objects.equals(keyFunction, that.keyFunction); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), nTopClonotypes, keyFunction); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java new file mode 100644 index 000000000..682beee2a --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java @@ -0,0 +1,53 @@ +package com.milaboratory.mixcr.postanalysis.spectratype; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +import java.util.Objects; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) +public class SpectratypeKey { + @JsonProperty("length") + public final int length; + /** null payload for "other" */ + @JsonProperty("payload") + @JsonTypeInfo(use = JsonTypeInfo.Id.CLASS, include = JsonTypeInfo.As.PROPERTY, property = "type") + public final Payload payload; + + @JsonCreator + public SpectratypeKey(@JsonProperty("length") int length, @JsonProperty("payload") Payload payload) { + this.length = length; + this.payload = payload; + } + + public boolean isOther() { + return payload == null; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SpectratypeKey that = (SpectratypeKey) o; + return length == that.length && + Objects.equals(payload, that.payload); + } + + @Override + public int hashCode() { + return Objects.hash(length, payload); + } + + @Override + public String toString() { + return length + " " + payload; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java new file mode 100644 index 000000000..6ec5520f4 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java @@ -0,0 +1,70 @@ +package com.milaboratory.mixcr.postanalysis.spectratype; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.core.sequence.AminoAcidSequence; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.core.sequence.TranslationParameters; +import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunction; +import io.repseq.core.GeneFeature; + +import java.util.Objects; + +/** + * + */ +public class SpectratypeKeyFunction implements KeyFunction, T> { + @JsonProperty("payloadFunction") + public final KeyFunction payloadFunction; + @JsonProperty("geneFeature") + public final GeneFeature geneFeature; + @JsonProperty("aa") + public final boolean aa; + + @JsonCreator + public SpectratypeKeyFunction(@JsonProperty("payloadFunction") KeyFunction payloadFunction, + @JsonProperty("geneFeature") GeneFeature geneFeature, + @JsonProperty("aa") boolean aa) { + this.payloadFunction = payloadFunction; + this.geneFeature = geneFeature; + this.aa = aa; + } + + @Override + public SpectratypeKey getKey(T obj) { + NSequenceWithQuality feature = obj.getFeature(geneFeature); + if (feature == null) + return null; + Payload payload = payloadFunction.getKey(obj); + if (payload == null) + return null; + + if (!aa) + return new SpectratypeKey<>(feature.size(), payload); + + int targetId = obj.getTargetContainingFeature(geneFeature); + TranslationParameters tr = targetId == -1 ? + TranslationParameters.FromLeftWithIncompleteCodon + : obj.getPartitionedTarget(targetId).getPartitioning().getTranslationParameters(geneFeature); + if (tr == null) + return null; + + return new SpectratypeKey<>(AminoAcidSequence.translate(feature.getSequence(), tr).size(), payload); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SpectratypeKeyFunction that = (SpectratypeKeyFunction) o; + return aa == that.aa && + Objects.equals(payloadFunction, that.payloadFunction) && + Objects.equals(geneFeature, that.geneFeature); + } + + @Override + public int hashCode() { + return Objects.hash(payloadFunction, geneFeature, aa); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java new file mode 100644 index 000000000..c158e6f4b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java @@ -0,0 +1,65 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Characteristic; + +import java.util.List; +import java.util.Objects; +import java.util.function.Function; +import java.util.stream.Collectors; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public class CharacteristicGroup { + @JsonProperty("name") + public final String name; + @JsonProperty("characteristics") + public final List> characteristics; + @JsonProperty("views") + public final List> views; + + @JsonCreator + public CharacteristicGroup(@JsonProperty("name") String name, + @JsonProperty("characteristics") List> characteristics, + @JsonProperty("views") List> views) { + this.name = name; + this.characteristics = characteristics; + this.views = views; + } + + public CharacteristicGroup transform(Function, Characteristic> mapper) { + return new CharacteristicGroup<>(name, characteristics.stream().map(mapper).collect(Collectors.toList()), views); + } + + @Override + public String toString() { + return "CharacteristicGroup{" + + "name='" + name + '\'' + + ", characteristics=" + characteristics + + ", views=" + views + + '}'; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CharacteristicGroup that = (CharacteristicGroup) o; + return Objects.equals(name, that.name) && + Objects.equals(characteristics, that.characteristics) && + Objects.equals(views, that.views); + } + + @Override + public int hashCode() { + return Objects.hash(name, characteristics, views); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java new file mode 100644 index 000000000..fe3fc8e3e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java @@ -0,0 +1,26 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +import java.util.Map; + +/** + * + */ +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = GroupSummary.class, name = "summary"), + @JsonSubTypes.Type(value = OverlapSummary.class, name = "overlapSummary"), + @JsonSubTypes.Type(value = GroupMelt.VJUsageMelt.class, name = "vjUsage"), + @JsonSubTypes.Type(value = GroupMelt.BySample.class, name = "bySample"), +}) +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public interface CharacteristicGroupOutputExtractor { + Map getTables(CharacteristicGroupResult result); +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java new file mode 100644 index 000000000..7ba0bbbfa --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java @@ -0,0 +1,51 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; + +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +public final class CharacteristicGroupResult { + /** The group */ + public final CharacteristicGroup group; + /** All keys presented in the table */ + public final List keys; + /** Cells */ + public final List> cells; + /** Number of samples */ + public final int nSamples; + /** Sample names */ + public final List sampleIds; + + public CharacteristicGroupResult(CharacteristicGroup group, List keys, List> cells, int nSamples, List sampleIds) { + this.group = group; + this.keys = keys; + this.cells = cells; + this.nSamples = nSamples; + this.sampleIds = sampleIds; + } + + @Override + public String toString() { + return cells.toString(); + } + + private Map outputs; + + public synchronized Map getOutputs() { + if (outputs == null) + outputs = group.views.stream() + .flatMap(v -> v.getTables(this).entrySet().stream()) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue)); + return outputs; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java new file mode 100644 index 000000000..52157dc28 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java @@ -0,0 +1,44 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import gnu.trove.impl.Constants; +import gnu.trove.map.hash.TObjectIntHashMap; + +import java.util.ArrayList; +import java.util.List; + +/** + * + */ +public final class CharacteristicGroupResultBuilder { + private final CharacteristicGroup group; + private final List sampleIds; + private final TObjectIntHashMap keys = new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); + private final List keyList = new ArrayList<>(); + private final List> cells = new ArrayList<>(); + private int nSamples = 0; + + public CharacteristicGroupResultBuilder(CharacteristicGroup group, List sampleIds) { + this.group = group; + this.sampleIds = sampleIds; + } + + public CharacteristicGroupResultBuilder add(K key, int sampleIndex, Double value) { + if (value == null) + return this; + + nSamples = Math.max(nSamples, sampleIndex + 1); + int metricIndex = keys.get(key); + if (metricIndex < 0) { + metricIndex = keys.size(); + keys.put(key, metricIndex); + keyList.add(key); + } + + cells.add(new CharacteristicGroupResultCell<>(key, value, sampleIndex, metricIndex)); + return this; + } + + public CharacteristicGroupResult build() { + return new CharacteristicGroupResult<>(group, keyList, cells, nSamples, sampleIds); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java new file mode 100644 index 000000000..de3821a14 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java @@ -0,0 +1,39 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.milaboratory.mixcr.postanalysis.MetricValue; + +import java.util.Objects; + +/** + * + */ +public class CharacteristicGroupResultCell extends MetricValue { + public final int sampleIndex; + public final int metricIndex; + + public CharacteristicGroupResultCell(K key, double value, int sampleIndex, int metricIndex) { + super(key, value); + this.sampleIndex = sampleIndex; + this.metricIndex = metricIndex; + } + + @Override + public String toString() { + return key + "-" + sampleIndex + ":" + metricIndex + ":" + value; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + CharacteristicGroupResultCell that = (CharacteristicGroupResultCell) o; + return sampleIndex == that.sampleIndex && + metricIndex == that.metricIndex; + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), sampleIndex, metricIndex); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java new file mode 100644 index 000000000..d3d02d56f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java @@ -0,0 +1,59 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneSetIO; +import io.repseq.core.VDJCLibraryRegistry; +import org.jetbrains.annotations.NotNull; + +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +/** + * + */ +public class ClonesIterable implements Iterable, AutoCloseable { + final Path path; + final VDJCLibraryRegistry registry; + + public ClonesIterable(Path path, VDJCLibraryRegistry registry) { + this.path = path; + this.registry = registry; + } + + public ClonesIterable(String path, VDJCLibraryRegistry registry) { + this(Paths.get(path), registry); + } + + private final List close = new ArrayList<>(); + + @NotNull + @Override + public Iterator iterator() { + try { + OutputPortCloseable c = CloneSetIO.mkReader(path, registry).readClones(); + close.add(c); + return CUtils.it(c).iterator(); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws Exception { + Exception ex = null; + for (AutoCloseable c : close) + try { + c.close(); + } catch (Exception e) { + ex = e; + } + if (ex != null) + throw ex; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java new file mode 100644 index 000000000..13419fa42 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java @@ -0,0 +1,16 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +/** + * + */ +final class Coordinates { + final int iRow, iCol; + final String row, col; + + public Coordinates(int iRow, int iCol, String row, String col) { + this.iRow = iRow; + this.iCol = iCol; + this.row = row; + this.col = col; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java new file mode 100644 index 000000000..9c496f48b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java @@ -0,0 +1,120 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; + +import java.util.*; +import java.util.function.Supplier; + +/** + * + */ +public class GroupMelt implements CharacteristicGroupOutputExtractor { + @JsonProperty("prefix") + public final String prefix; + public final MeltFunction meltFunction; + public final Supplier> coordinatesProvider; + + public GroupMelt(String prefix, MeltFunction meltFunction, Supplier> coordinatesProvider) { + this.prefix = prefix; + this.meltFunction = meltFunction; + this.coordinatesProvider = coordinatesProvider; + } + + @Override + public Map getTables(CharacteristicGroupResult result) { + Map outputs = new HashMap<>(); + Map> providers = new HashMap<>(); + for (CharacteristicGroupResultCell cell : result.cells) { + String key = meltFunction.getName(result, cell); + OutputTableBuilder builder = outputs.computeIfAbsent(key, s -> new OutputTableBuilder(prefix + s)); + CoordinatesProvider coordinatesProvider = providers.computeIfAbsent(key, __ -> this.coordinatesProvider.get()); + Coordinates coords = coordinatesProvider.getXY(cell); + builder.add(coords, cell); + } + Map ret = new HashMap<>(); + for (Map.Entry e : outputs.entrySet()) + ret.put(e.getKey(), e.getValue().build()); + return ret; + } + + public interface MeltFunction { + String getName(CharacteristicGroupResult result, CharacteristicGroupResultCell cell); + } + + interface CoordinatesProvider { + Coordinates getXY(CharacteristicGroupResultCell key); + } + + public static abstract class SplitCoordinatesProvider implements CoordinatesProvider { + final Map xs = new HashMap<>(), ys = new HashMap<>(); + + abstract Object[] split(K key); + + @Override + public Coordinates getXY(CharacteristicGroupResultCell key) { + Object[] split = split(key.key); + Integer x = xs.get(split[0]); + if (x == null) { + x = xs.size(); + xs.put(split[0], x); + } + Integer y = ys.get(split[1]); + if (y == null) { + y = ys.size(); + ys.put(split[1], y); + } + return new Coordinates(x, y, split[0].toString(), split[1].toString()); + } + } + + public static final class VJUsageMelt extends GroupMelt> { + public VJUsageMelt() { + super("vj_usage_", + (result, cell) -> result.sampleIds.get(cell.sampleIndex), + () -> new SplitCoordinatesProvider>() { + @Override + Object[] split(KeyFunctions.VJGenes key) { + return new Object[]{key.vGene, key.jJene}; + } + }); + } + + @Override + public boolean equals(Object o1) { + if (this == o1) return true; + if (o1 == null || getClass() != o1.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 17; + } + } + + public static final class BySample extends GroupMelt { + public BySample(@JsonProperty("prefix") String prefix) { + super(prefix, + (result, cell) -> result.sampleIds.get(cell.sampleIndex), + () -> new SplitCoordinatesProvider() { + @Override + Object[] split(K key) { + return new Object[]{key}; + } + }); + } + + @Override + public boolean equals(Object o1) { + if (this == o1) return true; + if (o1 == null || getClass() != o1.getClass()) return false; + return Objects.equals(prefix, ((BySample) o1).prefix); + } + + @Override + public int hashCode() { + return 123 + Objects.hashCode(prefix); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java new file mode 100644 index 000000000..4dbd59ba3 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java @@ -0,0 +1,28 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import java.util.Collections; +import java.util.Map; + +/** + * + */ +public class GroupSummary implements CharacteristicGroupOutputExtractor { + public static final String key = "summary"; + + @Override + public Map getTables(CharacteristicGroupResult result) { + return Collections.singletonMap(key, OutputTableExtractor.summary().getTable(result)); + } + + @Override + public boolean equals(Object o1) { + if (this == o1) return true; + if (o1 == null || getClass() != o1.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 17; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java new file mode 100644 index 000000000..788838e57 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java @@ -0,0 +1,155 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.milaboratory.mixcr.postanalysis.clustering.HierarchicalClustering; +import com.milaboratory.mixcr.postanalysis.clustering.HierarchyNode; + +import java.io.BufferedWriter; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.StandardOpenOption; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +/** + * + */ +public class OutputTable { + public final String name; + public final List rowNames; + public final List colNames; + public final List cells; + + public OutputTable(String name, List rowNames, List colNames, List cells) { + this.name = name; + this.rowNames = rowNames; + this.colNames = colNames; + this.cells = cells; + } + + private List columnsHierarchy, rowsHierarchy; + + public synchronized List columnsHierarchy() { + if (columnsHierarchy == null) + columnsHierarchy = Collections.unmodifiableList(HierarchicalClustering.clusterize(columns(0.0, 0.0), 0.0, HierarchicalClustering::EuclideanDistance)); + return columnsHierarchy; + } + + public synchronized List rowsHierarchy() { + if (rowsHierarchy == null) + rowsHierarchy = Collections.unmodifiableList(HierarchicalClustering.clusterize(rows(0.0, 0.0), 0.0, HierarchicalClustering::EuclideanDistance)); + return rowsHierarchy; + } + + public double[][] columns(double naValue, double nan) { + int nRows = rowNames.size(), nCols = colNames.size(); + double[][] r = new double[nCols][nRows]; + if (naValue != 0.0) + for (double[] doubles : r) + Arrays.fill(doubles, naValue); + + for (OutputTableCell cell : cells) + r[cell.iCol][cell.iRow] = Double.isNaN(cell.value) ? nan : cell.value; + + return r; + } + + public Double[][] columns() { + int nRows = rowNames.size(), nCols = colNames.size(); + Double[][] r = new Double[nCols][nRows]; + for (OutputTableCell cell : cells) + r[cell.iCol][cell.iRow] = cell.value; + + return r; + } + + public double[][] rows(double naValue, double nan) { + int nRows = rowNames.size(), nCols = colNames.size(); + double[][] r = new double[nRows][nCols]; + if (naValue != 0.0) + for (double[] doubles : r) + Arrays.fill(doubles, naValue); + + for (OutputTableCell cell : cells) + r[cell.iRow][cell.iCol] = Double.isNaN(cell.value) ? nan : cell.value; + + return r; + } + + public Double[][] rows() { + int nRows = rowNames.size(), nCols = colNames.size(); + Double[][] r = new Double[nRows][nCols]; + for (OutputTableCell cell : cells) + r[cell.iRow][cell.iCol] = cell.value; + + return r; + } + + public double minValue() { + return cells.stream().mapToDouble(c -> c.value).filter(v -> !Double.isNaN(v)).min().orElse(Double.NaN); + } + + public double maxValue() { + return cells.stream().mapToDouble(c -> c.value).filter(v -> !Double.isNaN(v)).max().orElse(Double.NaN); + } + + public OutputTable setRowNames(List rowNames) { + OutputTable t = new OutputTable(name, rowNames, colNames, cells); + t.columnsHierarchy = columnsHierarchy; + t.rowsHierarchy = rowsHierarchy; + return t; + } + + public OutputTable setColNames(List colNames) { + OutputTable t = new OutputTable(name, rowNames, colNames, cells); + t.columnsHierarchy = columnsHierarchy; + t.rowsHierarchy = rowsHierarchy; + return t; + } + + @Override + public String toString() { + return cells.toString(); + } + + public void writeCSV(Path dir) { + writeCSV(dir, ""); + } + + public void writeCSV(Path dir, String prefix) { + writeCSV(dir, prefix, ",", ".csv"); + } + + public void writeTSV(Path dir) { + writeTSV(dir, ""); + } + + public void writeTSV(Path dir, String prefix) { + writeCSV(dir, prefix, "\t", ".tsv"); + } + + public void writeCSV(Path dir, String prefix, String sep, String ext) { + Double[][] rows2d = rows(); + Path outName = dir.resolve(prefix + name + ext); + try (BufferedWriter writer = Files.newBufferedWriter(outName, StandardOpenOption.CREATE)) { + writer.write(""); + for (String column : colNames) { + writer.write(sep); + writer.write(column); + } + + for (int iRow = 0; iRow < rowNames.size(); ++iRow) { + writer.write("\n"); + writer.write(rowNames.get(iRow)); + Double[] row = rows2d[iRow]; + for (Double val : row) { + writer.write(sep); + writer.write(Double.toString(val == null ? Double.NaN : val)); + } + } + } catch (IOException e) { + e.printStackTrace(); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java new file mode 100644 index 000000000..f14b99db5 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java @@ -0,0 +1,44 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import java.util.*; + +/** + * + */ +final class OutputTableBuilder { + final String name; + final List cells = new ArrayList<>(); + final Map rows = new HashMap<>(); + final Map cols = new HashMap<>(); + + public OutputTableBuilder(String name) { + this.name = name; + } + + int nRows = 0, nCols = 0; + + synchronized void add(Coordinates cords, CharacteristicGroupResultCell original) { + cells.add(new OutputTableCell(cords.iRow, cords.iCol, original.value)); + rows.put(cords.iRow, cords.row.toString()); + cols.put(cords.iCol, cords.col.toString()); + nRows = Math.max(cords.iRow + 1, nRows); + nCols = Math.max(cords.iCol + 1, nCols); + } + + OutputTable build() { + String[] rows = new String[nRows]; + String[] cols = new String[nCols]; + for (int i = 0; i < nRows; ++i) { + String r = this.rows.get(i); + Objects.requireNonNull(r); + rows[i] = r; + } + for (int i = 0; i < nCols; ++i) { + String c = this.cols.get(i); + Objects.requireNonNull(c); + cols[i] = c; + } + + return new OutputTable(name, Arrays.asList(rows), Arrays.asList(cols), cells); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java new file mode 100644 index 000000000..900589a33 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java @@ -0,0 +1,51 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import org.jetbrains.annotations.NotNull; + +import java.util.Objects; + +/** + * + */ +public final class OutputTableCell implements Comparable { + public final int iRow, iCol; + public final double value; + + public OutputTableCell(int iRow, int iCol, double value) { + this.iRow = iRow; + this.iCol = iCol; + this.value = value; + } + + @Override + public String toString() { + return iRow + ":" + iCol + "=" + value; + } + + @Override + public int compareTo(@NotNull OutputTableCell o) { + int c = Integer.compare(iRow, o.iRow); + if (c != 0) + return c; + c = Integer.compare(iCol, o.iCol); + if (c != 0) + return c; + + return Double.compare(value, o.value); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OutputTableCell that = (OutputTableCell) o; + return iRow == that.iRow && + iCol == that.iCol && + Double.compare(that.value, value) == 0; + } + + @Override + public int hashCode() { + return Objects.hash(iRow, iCol, value); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java new file mode 100644 index 000000000..0d57572f1 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java @@ -0,0 +1,24 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; +import java.util.stream.Collectors; + +/** + * + */ +interface OutputTableExtractor { + OutputTable getTable(CharacteristicGroupResult result); + + static OutputTableExtractor summary() { + return result -> { + List cells = new ArrayList<>(); + for (CharacteristicGroupResultCell cell : result.cells) + cells.add(new OutputTableCell(cell.sampleIndex, cell.metricIndex, cell.value)); + + return new OutputTable(result.group.name, result.sampleIds, + result.keys.stream().map(Objects::toString).collect(Collectors.toList()), cells); + }; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java new file mode 100644 index 000000000..b70e418b4 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java @@ -0,0 +1,38 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey; + +import java.util.HashMap; +import java.util.Map; + +/** + * + */ +public class OverlapSummary implements CharacteristicGroupOutputExtractor> { + @Override + public Map getTables(CharacteristicGroupResult> result) { + Map tables = new HashMap<>(); + for (CharacteristicGroupResultCell> cell : result.cells) { + OutputTableBuilder tab = tables.computeIfAbsent(cell.key.key, __ -> new OutputTableBuilder(cell.key.key.toString())); + int i1 = cell.key.i1, i2 = cell.key.i2; + tab.add(new Coordinates(i1, i2, result.sampleIds.get(i1), result.sampleIds.get(i2)), cell); + tab.add(new Coordinates(i2, i1, result.sampleIds.get(i2), result.sampleIds.get(i1)), cell); + } + Map r = new HashMap<>(); + for (Map.Entry e : tables.entrySet()) + r.put(e.getKey(), e.getValue().build()); + return r; + } + + @Override + public boolean equals(Object o1) { + if (this == o1) return true; + if (o1 == null || getClass() != o1.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 17; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java new file mode 100644 index 000000000..37227ae0a --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java @@ -0,0 +1,74 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; + +import java.util.List; +import java.util.Objects; +import java.util.function.Function; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE) +public class PostanalysisSchema { + @JsonProperty("tables") + public final List> tables; + + @JsonCreator + public PostanalysisSchema(@JsonProperty("tables") List> tables) { + this.tables = tables; + } + + @SuppressWarnings({"unchecked", "rawtypes"}) + public PostanalysisSchema transform(Function, Characteristic> mapper) { + Stream> characteristicGroupStream = tables.stream() + .map(gr -> (CharacteristicGroup) gr.transform(c -> (Characteristic) mapper.apply(c))); + List> collect = characteristicGroupStream + .collect(Collectors.>toList()); + return new PostanalysisSchema<>(collect); + } + + public List> getAllCharacterisitcs() { + return tables.stream().flatMap(t -> t.characteristics.stream()).collect(Collectors.toList()); + } + + @SuppressWarnings("unchecked") + public CharacteristicGroup getGroup(String name) { + return (CharacteristicGroup) tables.stream().filter(g -> g.name.equals(name)).findAny().orElse(null); + } + + @Override + public String toString() { + return tables.toString(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + PostanalysisSchema that = (PostanalysisSchema) o; + return Objects.equals(tables, that.tables); + } + + @Override + public int hashCode() { + return Objects.hash(tables); + } + + public PostanalysisResult run(List> datasets) { + PostanalysisRunner runner = new PostanalysisRunner<>(); + runner.addCharacteristics(getAllCharacterisitcs()); + runner.setDatasets(datasets); + return runner.run(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java b/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java new file mode 100644 index 000000000..4b1c56983 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java @@ -0,0 +1,25 @@ +package com.milaboratory.mixcr.util; + +import org.jetbrains.annotations.NotNull; + +import java.util.Iterator; +import java.util.function.Predicate; + +/** + * + */ +public class FilteredIterable implements Iterable { + private final Iterable inner; + private final Predicate accept; + + public FilteredIterable(Iterable inner, Predicate accept) { + this.inner = inner; + this.accept = accept; + } + + @NotNull + @Override + public Iterator iterator() { + return new FilteredIterator<>(inner.iterator(), accept); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java b/src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java new file mode 100644 index 000000000..fc0aba26a --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java @@ -0,0 +1,41 @@ +package com.milaboratory.mixcr.util; + +import java.util.Iterator; +import java.util.function.Predicate; + +/** + * + */ +public class FilteredIterator implements Iterator { + private final Iterator inner; + private final Predicate accept; + + public FilteredIterator(Iterator inner, Predicate accept) { + this.inner = inner; + this.accept = accept; + } + + private T ref = null; + + @Override + public boolean hasNext() { + if (ref != null) + return true; + if (!inner.hasNext()) + return false; + ref = inner.next(); + while (!accept.test(ref)) { + if (!inner.hasNext()) + return false; + ref = inner.next(); + } + return true; + } + + @Override + public T next() { + T r = this.ref; + this.ref = null; + return r; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/Tuple2.java b/src/main/java/com/milaboratory/mixcr/util/Tuple2.java new file mode 100644 index 000000000..436026a3b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/Tuple2.java @@ -0,0 +1,51 @@ +package com.milaboratory.mixcr.util; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; + +import java.util.Objects; +import java.util.function.Function; + +/** + * + */ +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE +) +public class Tuple2 { + @JsonProperty("_1") + @JsonTypeInfo(use = JsonTypeInfo.Id.CLASS) + public final K1 _1; + @JsonProperty("_2") + @JsonTypeInfo(use = JsonTypeInfo.Id.CLASS) + public final K2 _2; + + @JsonCreator + public Tuple2(@JsonProperty("_1") K1 _1, + @JsonProperty("_2") K2 _2) { + this._1 = _1; + this._2 = _2; + } + + public <_K1, _K2> Tuple2<_K1, _K2> map(Function f1, Function f2) { + return new Tuple2<>(f1.apply(_1), f2.apply(_2)); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Tuple2 tuple2 = (Tuple2) o; + return Objects.equals(_1, tuple2._1) && + Objects.equals(_2, tuple2._2); + } + + @Override + public int hashCode() { + return Objects.hash(_1, _2); + } +} diff --git a/src/main/resources/postanalysis/aa_properties.csv b/src/main/resources/postanalysis/aa_properties.csv new file mode 100644 index 000000000..8c2e001a7 --- /dev/null +++ b/src/main/resources/postanalysis/aa_properties.csv @@ -0,0 +1,21 @@ +aa,hydropathy,charge,polarity,volume,strength,mjenergy,kf1,kf2,kf3,kf4,kf5,kf6,kf7,kf8,kf9,kf10,rim,surface,turn,alpha,beta,core,disorder,n2strength,n2hydrophobicity,n2volume,n2surface +A,1.8,0,0,67,0,-2.8455,-1.56,-1.67,-0.97,0.27,-0.93,-0.78,-0.2,-0.08,0.21,-0.48,0.047,0.065,0.78,1.29,0.9,0.049,0,0.566,-0.172,0.411,0.730 +C,2.5,0,0,86,1,-3.782,0.12,-0.89,0.45,-1.05,-0.71,2.41,1.52,-0.69,1.13,1.1,0.015,0.015,0.8,1.11,0.74,0.02,-1,0.753,0.669,0.528,0.169 +D,-3.5,-1,1,91,0,-2.116,0.58,-0.22,-1.58,0.81,-0.92,0.15,-1.52,0.47,0.76,0.7,0.071,0.074,1.41,1.04,0.72,0.051,1,0.421,-0.516,0.558,0.831 +E,-3.5,-1,1,109,0,-2.141,-1.45,0.19,-1.61,1.17,-1.31,0.4,0.04,0.38,-0.35,-0.12,0.094,0.089,1,1.44,0.75,0.051,1,0.426,-0.745,0.669,1.000 +F,2.8,0,0,135,1,-5.017,-0.21,0.98,-0.36,-1.43,0.22,-0.81,0.67,1.1,1.71,-0.44,0.021,0.029,0.58,1.07,1.32,0.051,-1,0.999,0.911,0.828,0.326 +G,-0.4,0,0,48,0,-2.499,1.46,-1.96,-0.23,-0.16,0.1,-0.11,1.32,2.36,-1.66,0.46,0.071,0.07,1.64,0.56,0.92,0.06,1,0.498,0.102,0.294,0.787 +H,-3.2,1,1,118,0,-2.927,-0.41,0.52,-0.28,0.28,1.61,1.01,-1.85,0.47,1.13,1.63,0.022,0.025,0.69,1.22,1.08,0.034,-1,0.583,-0.178,0.724,0.281 +I,4.5,0,0,124,1,-4.641,-0.73,-0.16,1.79,-0.77,-0.54,0.03,-0.83,0.51,0.66,-1.78,0.032,0.035,0.51,0.97,1.45,0.047,-1,0.924,0.490,0.761,0.393 +K,-3.9,1,1,135,0,-1.789,-0.34,0.82,-0.23,1.7,1.54,-1.62,1.15,-0.08,-0.48,0.6,0.105,0.08,0.96,1.23,0.77,0.05,1,0.356,-1.083,0.828,0.899 +L,3.8,0,0,124,1,-5.023,-1.04,0,-0.24,-1.1,-0.55,-2.05,0.96,-0.76,0.45,0.93,0.052,0.063,0.59,1.3,1.02,0.078,-1,1.000,0.701,0.761,0.708 +M,1.9,0,0,124,1,-4.1915,-1.4,0.18,-0.42,-0.73,2,1.52,0.26,0.11,-1.27,0.27,0.017,0.016,0.39,1.47,0.97,0.027,1,0.834,0.465,0.761,0.180 +N,-3.5,0,1,96,0,-2.349,1.14,-0.07,-0.12,0.81,0.18,0.37,-0.09,1.23,1.1,-1.73,0.062,0.053,1.28,0.9,0.76,0.058,1,0.468,-0.516,0.589,0.596 +P,-1.6,0,0,90,0,-2.443,2.06,-0.33,-1.15,-0.75,0.88,-0.45,0.3,-2.3,0.74,-0.28,0.052,0.054,1.91,0.52,0.64,0.051,1,0.486,0.478,0.552,0.607 +Q,-3.5,0,1,114,0,-2.2505,-0.47,0.24,0.07,1.1,1.1,0.59,0.84,-0.71,-0.03,-2.33,0.053,0.051,0.97,1.27,0.8,0.051,1,0.448,-0.701,0.699,0.573 +R,-4.5,1,1,148,0,-2.402,0.22,1.27,1.37,1.87,-1.7,0.46,0.92,-0.39,0.23,0.93,0.068,0.059,0.88,0.96,0.99,0.066,1,0.478,-1.191,0.908,0.663 +S,-0.8,0,1,73,0,-2.308,0.81,-1.08,0.16,0.42,-0.21,-0.43,-1.89,-1.15,-0.97,-0.23,0.072,0.071,1.33,0.82,0.95,0.057,1,0.459,-0.268,0.448,0.798 +T,-0.7,0,1,93,0,-2.6145,0.26,-0.7,1.21,0.63,-0.1,0.21,0.24,-1.15,-0.56,0.19,0.064,0.065,1.03,0.82,1.21,0.064,0,0.521,-0.401,0.571,0.730 +V,4.2,0,0,105,1,-4.093,-0.74,-0.71,2.04,-0.4,0.5,-0.81,-1.07,0.06,-0.46,0.65,0.048,0.048,0.47,0.91,1.49,0.049,-1,0.815,0.255,0.644,0.539 +W,-0.9,0,0,163,1,-4.1375,0.3,2.1,-0.72,-1.57,-1.16,0.57,-0.48,-0.4,-2.3,-0.6,0.007,0.012,0.75,0.99,1.14,0.022,-1,0.824,1.000,1.000,0.135 +Y,-1.3,0,1,141,1,-3.7505,1.38,1.48,0.8,-0.56,0,-0.68,-0.31,1.03,-0.05,0.53,0.032,0.033,1.05,0.72,1.25,0.07,-1,0.747,0.357,0.865,0.371 diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java index d07baee71..87a594616 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java @@ -164,4 +164,4 @@ public void test5() throws Exception { assertTrue(seq.toString().contains(cdr3.getSequence().toString().toUpperCase())); } } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java index 37fc98e93..97138d72d 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java @@ -67,4 +67,4 @@ public void test3() { public void test2_completion() { System.out.println(AutoComplete.bash("mixcr", Main.mkCmd())); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java new file mode 100644 index 000000000..52cb30f99 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java @@ -0,0 +1,46 @@ +package com.milaboratory.mixcr.postanalysis.clustering; + + +import org.junit.Test; + +import java.util.List; + +public class HierarchicalClusteringTest { + @Test + public void test1() { + double[][] vectors = new double[][]{ + {4, 5, 2, 9, 5, 6, 3, 3, 1}, + {4, 5, 3, 8, 6, 7, 8, 3, 2}, + {1, 2, 4, 7, 5, 6, 3, 6, 3}, + {5, 3, 6, 6, 3, 4, 4, 2, 4}, + {2, 6, 7, 5, 8, 9, 8, 4, 5}, + {6, 6, 6, 4, 6, 0, 6, 6, 6}, + {1, 2, 3, 4, 5, 4, 3, 2, 1}, + {9, 8, 7, 6, 5, 6, 7, 8, 9}, + {0, 1, 0, 1, 0, 1, 0, 1, 6}, + {0, 0, 0, 3, 1, 0, 0, 1, 7}, + {3, 7, 7, 2, 7, 5, 3, 4, 8} + }; + + List r = HierarchicalClustering.clusterize(vectors, 0, HierarchicalClustering::EuclideanDistance); + for (HierarchyNode hierarchyNode : r) { + System.out.println(hierarchyNode); + } + assert r.size() == 10; + } + + @Test + public void test2() { + double[][] vectors = new double[][]{ + {1, 1, 1, 1}, + {1, 1, 1, 1}, + {1, 1, 1, 1}, + {1, 1, 1, 1}, + }; + + List r = HierarchicalClustering.clusterize(vectors, 0, HierarchicalClustering::EuclideanDistance); + for (HierarchyNode hierarchyNode : r) { + System.out.println(hierarchyNode); + } + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java new file mode 100644 index 000000000..29e0c99f4 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -0,0 +1,88 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well512a; +import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; +import org.junit.Assert; +import org.junit.Ignore; +import org.junit.Test; + +import java.util.Arrays; +import java.util.stream.LongStream; + +/** + * + */ +public class DownsamplingPreprocessorTest { + + @Test + public void test1() { + long[] counts = {130, 10, 190, 130, 10, 190, 130, 1022, 190}; + long total = LongStream.of(counts).sum(); + Well512a rnd = new Well512a(); + RandomDataGenerator gen = new RandomDataGenerator(rnd); + for (int i = 0; i < 100; ++i) { + long downSampleSize = gen.nextLong(total / 10, total - 10); + long[] sample_mvhg = DownsamplingUtil.downsample_mvhg(counts, downSampleSize, rnd); + Assert.assertEquals(downSampleSize, Arrays.stream(sample_mvhg).sum()); + + long[] sample_counts = DownsamplingUtil.downsample_counts(counts, downSampleSize, rnd); + Assert.assertEquals(downSampleSize, Arrays.stream(sample_counts).sum()); + } + } + + @Test + @Ignore + public void test2() { + long[] arr = new long[1000]; + long total = 0; + for (int i = 0; i < arr.length; ++i) { + arr[i] = Math.max(1, (int) (1000 / Math.pow(1 + i, 2))); + total += arr[i]; + } + + System.out.println(total); + System.out.println(Arrays.toString(arr)); + Well512a rnd = new Well512a(); + RandomDataGenerator gen = new RandomDataGenerator(rnd); + for (int i = 0; i < 100; ++i) { + long downSampleSize = gen.nextLong(total / 10, total - 10); + long[] sample_mvhg = DownsamplingUtil.downsample_mvhg(arr, downSampleSize, rnd); + Assert.assertEquals(downSampleSize, Arrays.stream(sample_mvhg).sum()); + + long[] sample_counts = DownsamplingUtil.downsample_counts(arr, downSampleSize, rnd); + Assert.assertEquals(downSampleSize, Arrays.stream(sample_counts).sum()); + + System.out.println(downSampleSize); + System.out.println(Arrays.toString(sample_mvhg)); + System.out.println(Arrays.toString(sample_counts)); + System.out.println("-------"); + } + } + + @Test + public void testRnd() { + DescriptiveStatistics timing = new DescriptiveStatistics(); + Well512a rnd = new Well512a(); + RandomDataGenerator gen = new RandomDataGenerator(rnd); + int nTries = 100, nDownsamples = 3; + for (int nTry = 0; nTry < nTries; ++nTry) { + long[] counts = new long[gen.nextInt(1000_000, 2000_000) / 10]; + for (int i = 0; i < counts.length; ++i) + counts[i] = (long) (gen.nextInt(50, 500) * 5000 / Math.pow(1 + i, 1) + 1); + + long sum = Arrays.stream(counts).sum(); + + for (int i = 0; i < nDownsamples; ++i) { + long downsampleSize = gen.nextLong(1, sum - 1); + long start = System.nanoTime(); + long[] sample = DownsamplingUtil.downsample_mvhg(counts, downsampleSize, rnd); + long elapsed = System.nanoTime() - start; + + timing.addValue(elapsed); + Assert.assertEquals(downsampleSize, LongStream.of(sample).sum()); + } + } + System.out.println(timing); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java new file mode 100644 index 000000000..a1af4b7c7 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java @@ -0,0 +1,96 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.overlap; + +import com.milaboratory.mixcr.basictypes.ClnsReader; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.util.LambdaSemaphore; +import gnu.trove.map.hash.TIntIntHashMap; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; +import org.junit.Test; + +import java.io.IOException; +import java.nio.file.Paths; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +public class OverlapIntegrationTest { + @Test + public void test1() throws IOException { + // Limits concurrency across all readers + LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(4); + + List readers = Stream.of( + "Ig-2_S2.contigs.clns", + "Ig-3_S3.contigs.clns", + "Ig-4_S4.contigs.clns", + "Ig-5_S5.contigs.clns", + "Ig1_S1.contigs.clns", + "Ig2_S2.contigs.clns", + "Ig3_S3.contigs.clns", + "Ig4_S4.contigs.clns", + "Ig5_S5.contigs.clns") + .map(f -> { + try { + return new ClnsReader( + Paths.get(OverlapIntegrationTest.class.getResource("/sequences/big/yf_sample_data/" + f).getFile()), + VDJCLibraryRegistry.getDefault(), + concurrencyLimiter); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); + + + List> byN = VDJCSProperties.orderingByNucleotide(new GeneFeature[]{GeneFeature.CDR3}); + List> byAA = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); + List> byAAAndV = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}, GeneType.Variable); + + for (List> by : Arrays.asList(byN, byAA, byAAAndV)) { + System.out.println("============="); + OverlapIterable overlap = OverlapUtil.overlap(by, readers); + TIntIntHashMap hist = new TIntIntHashMap(); + for (OverlapGroup cloneOverlapGroup : overlap) { + int sum = cloneOverlapGroup.elements.stream().mapToInt(l -> l.isEmpty() ? 0 : 1).sum(); + hist.adjustOrPutValue(sum, 1, 1); + } + for (int i = 1; i < readers.size(); i++) + if (hist.get(i) != 0) + System.out.println("" + i + ": " + hist.get(i)); + } + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java new file mode 100644 index 000000000..5e59d2542 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -0,0 +1,241 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.milaboratory.mixcr.basictypes.ClnsReader; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.additive.AAProperties; +import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessor; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesOverlapDownsamplingPreprocessor; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; +import com.milaboratory.mixcr.postanalysis.overlap.*; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; +import com.milaboratory.util.LambdaSemaphore; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; +import org.junit.Assert; +import org.junit.Test; + +import java.io.IOException; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedBiophysics; +import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedLengthOf; + +/** + * + */ +public class PostanalysisSchemaIntegrationTest { + + private static ClonesIterable getClones(String sample) { + return new ClonesIterable(PostanalysisSchemaIntegrationTest.class.getResource("/sequences/big/yf_sample_data/" + sample + ".contigs.clns").getFile(), VDJCLibraryRegistry.getDefault()); + } + + @Test + public void test1() throws IOException { + ClonesIterable r1 = getClones("Ig-2_S2"); + ClonesIterable r2 = getClones("Ig-3_S3"); + ClonesIterable r3 = getClones("Ig-4_S4"); + ClonesIterable r4 = getClones("Ig-5_S5"); + ClonesIterable r5 = getClones("Ig1_S1"); + ClonesIterable r6 = getClones("Ig2_S2"); + ClonesIterable r7 = getClones("Ig3_S3"); + ClonesIterable r8 = getClones("Ig4_S4"); + ClonesIterable r9 = getClones("Ig5_S5"); + + List> groups = new ArrayList<>(); + + groups.add(new CharacteristicGroup<>( + "cdr3Properties", + Arrays.asList( + weightedLengthOf(GeneFeature.CDR3, false), + weightedLengthOf(GeneFeature.VJJunction, false), + weightedLengthOf(new GeneFeature(GeneFeature.VDJunction, GeneFeature.DJJunction), false).setName("ntLengthOfN"), + weightedBiophysics(AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5), + weightedBiophysics(AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5), + weightedBiophysics(AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5), + weightedBiophysics(AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5), + weightedBiophysics(AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5) + ), + Arrays.asList(new GroupSummary<>()) + )); + groups.add(new CharacteristicGroup<>( + "diversity", + Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessor(new DownsampleValueChooser.Auto(), 314))), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>( + "vUsage", + Arrays.asList(AdditiveCharacteristics.segmentUsage(GeneType.Variable)), + Arrays.asList(new GroupSummary<>()) + )); + groups.add(new CharacteristicGroup<>( + "jUsage", + Arrays.asList(AdditiveCharacteristics.segmentUsage(GeneType.Joining)), + Arrays.asList(new GroupSummary<>()) + )); + groups.add(new CharacteristicGroup<>( + "vjUsage", + Arrays.asList(AdditiveCharacteristics.vjSegmentUsage()), + Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) + )); + + + groups.add(new CharacteristicGroup<>( + "isotypeUsage", + Arrays.asList(AdditiveCharacteristics.isotypeUsage()), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>( + "cdr3Spectratype", + Arrays.asList(new SpectratypeCharacteristic("cdr3Spectratype", + new NoPreprocessing<>(), 10, + new SpectratypeKeyFunction<>(new KeyFunctions.NTFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), + Collections.singletonList(new GroupSummary<>()))); + + groups.add(new CharacteristicGroup<>( + "VSpectratype", + Arrays.asList(AdditiveCharacteristics.VSpectratype()), + Collections.singletonList(new GroupSummary<>()))); + + PostanalysisSchema individualPA = new PostanalysisSchema<>(groups); + + ObjectMapper OM = new ObjectMapper(); + String individualPAStr = OM.writeValueAsString(individualPA); + System.out.println(individualPAStr); + PostanalysisSchema json = OM.readValue(individualPAStr, PostanalysisSchema.class); + Assert.assertEquals(individualPA, json); + + PostanalysisRunner runner = new PostanalysisRunner<>(); + + runner.addCharacteristics(individualPA.getAllCharacterisitcs()); + Iterable[] input = {r1, r2, r3, r4, r5, r6, r7, r8, r9}; + runner.setDatasets(input); + + PostanalysisResult result = runner.run().setSampleIds(IntStream.range(0, 9).mapToObj(i -> "" + i).collect(Collectors.toList())); + result.setSampleIds(IntStream.range(0, input.length).mapToObj(i -> "" + i).collect(Collectors.toList())); + + String resultStr = OM.writeValueAsString(result); + Assert.assertEquals(result, OM.readValue(resultStr, PostanalysisResult.class)); + Map outputs; + +// CharacteristicGroupResult cdr3Table = result.getTable(cdr3PropsTable); +// cdr3Table.getOutputs(); +// for (OutputTable o : outputs.values()) { +// o.writeTSV(Paths.get("/Users/poslavskysv/Downloads/hhhh/")); +// } +// System.out.println(outputs); +// +// CharacteristicGroupResult divTable = result.getTable(diversityTable); +// divTable.cells.stream().filter(cell -> cell.key == DiversityMeasure.Observed).map(cell -> cell.sampleIndex + " - " + cell.value).forEach(System.out::println); +// divTable.cells.stream().filter(cell -> cell.key == DiversityMeasure.Chao1).map(cell -> cell.sampleIndex + " - " + cell.value).forEach(System.out::println); +// outputs = divTable.getOutputs(); +// for (OutputTable o : outputs.values()) { +// o.writeTSV(Paths.get("/Users/poslavskysv/Downloads/hhhh")); +// } + + CharacteristicGroupResult> r = result.getTable(individualPA.getGroup("cdr3Spectratype")); + Assert.assertTrue(r.cells.stream() + .collect(Collectors.groupingBy(c -> c.sampleIndex, Collectors.mapping(c -> c.key.payload, Collectors.toSet()))) + .values().stream().allMatch(l -> l.size() <= 11)); + + System.out.println(result.getTable(individualPA.getGroup("VSpectratype"))); + } + + @Test + public void testOverlap1() throws JsonProcessingException { + // Limits concurrency across all readers + LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(4); + + List sampleNames = Arrays.asList( + "Ig-2_S2.contigs.clns", + "Ig-3_S3.contigs.clns", + "Ig-4_S4.contigs.clns", + "Ig-2_S2.contigs.clns", + "Ig1_S1.contigs.clns", + "Ig2_S2.contigs.clns", + "Ig3_S3.contigs.clns", + "Ig4_S4.contigs.clns", + "Ig5_S5.contigs.clns"); + List readers = sampleNames.stream() + .map(f -> { + try { + return new ClnsReader( + Paths.get(OverlapIntegrationTest.class.getResource("/sequences/big/yf_sample_data/" + f).getFile()), + VDJCLibraryRegistry.getDefault(), + concurrencyLimiter); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); + + + List> byN = VDJCSProperties.orderingByNucleotide(new GeneFeature[]{GeneFeature.CDR3}); + List> byAA = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); + List> byAAAndV = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}, GeneType.Variable); + + for (List> by : Arrays.asList(byN, byAA, byAAAndV)) { + System.out.println("============="); + OverlapIterable overlap = OverlapUtil.overlap(by, readers); + + ClonesOverlapDownsamplingPreprocessor downsamplePreprocessor = new ClonesOverlapDownsamplingPreprocessor( + new DownsampleValueChooser.Minimal(), + 332142); + + List> overlaps = new ArrayList<>(); + for (int i = 0; i < readers.size(); ++i) { + for (int j = i + 1; j < readers.size(); ++j) { + overlaps.add(new OverlapCharacteristic<>("overlap_" + i + "_" + j, + new WeightFunctions.Count(), + downsamplePreprocessor, + i, j)); + } + } + + + List>> groups = new ArrayList<>(); + + groups.add(new CharacteristicGroup<>("cdr3Properties", + overlaps, + Arrays.asList(new OverlapSummary<>()) + )); + + PostanalysisSchema> overlapPA = new PostanalysisSchema<>(groups); + ObjectMapper OM = new ObjectMapper(); + String overlapPAStr = OM.writeValueAsString(overlapPA); + System.out.println(overlapPAStr); + PostanalysisSchema json = OM.readValue(overlapPAStr, PostanalysisSchema.class); + Assert.assertEquals(overlapPA, json); + + + PostanalysisRunner> pr = new PostanalysisRunner<>(); + pr.setDatasets(Arrays.asList(overlap)); + pr.addCharacteristics(overlapPA.getAllCharacterisitcs()); + + PostanalysisResult result = pr.run().setSampleIds(sampleNames); + String resultStr = OM.writeValueAsString(result); + Assert.assertEquals(result, OM.readValue(resultStr, PostanalysisResult.class)); + + CharacteristicGroupResult table = result.getTable(groups.get(0)); + System.out.println(table.getOutputs()); + } + } +} From f51e7832544b19cfbf196f19ca98d63a31da466f Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 1 Sep 2020 18:12:29 +0300 Subject: [PATCH 075/282] Fix for AWS caching. --- .drone.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.drone.yml b/.drone.yml index 567255492..6dae4171c 100644 --- a/.drone.yml +++ b/.drone.yml @@ -57,12 +57,15 @@ steps: - apk add --no-cache zip - ./pack.sh - touch empty - - aws s3 cp target/mixcr.zip s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip + - > + aws s3 cp \ + --metadata-directive REPLACE --cache-control "max-age=604800,public" \ + target/mixcr.zip \ + s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip - > aws s3api put-object-tagging \ --bucket $${DEPLOY_S3_CDN_BUCKET} \ --key $${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-${DRONE_COMMIT}.zip \ - --metadata-directive REPLACE --cache-control "max-age=604800,public" \ --tagging '{"TagSet": [{"Key":"git_commit","Value":"${DRONE_COMMIT}"},{"Key":"git_branch","Value":"${DRONE_BRANCH}"},{"Key":"software","Value":"mixcr"}]}' - aws s3 cp --website-redirect 'https://cdn.milaboratory.com/software/mixcr/mixcr-${DRONE_COMMIT}.zip?response-content-disposition=attachment;filename=mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip' empty "s3://$${DEPLOY_S3_LINK_BUCKET}/$${DEPLOY_S3_LINK_PREFIX}/software/mixcr/mixcr-b${DRONE_BUILD_NUMBER}-${DRONE_COMMIT_SHA:0:7}.zip" environment: @@ -220,6 +223,6 @@ steps: --- kind: signature -hmac: a90ec8f75648bbfbb91d74584526f1ca7ea745dbcfb41e0bb0dee75e4d6707ac +hmac: 9c989edeafff6762641d0f12b227819139f0708413dde34b587471b6f6f997d9 ... From 3cf0e9964984a4a02e1155393a67bbf8f12b7c75 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 4 Sep 2020 00:56:15 +0300 Subject: [PATCH 076/282] make some fields public --- .../postanalysis/additive/AdditiveCharacteristic.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java index 97a09376c..3c4682e2d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java @@ -18,13 +18,13 @@ ) public class AdditiveCharacteristic extends Characteristic { @JsonProperty("key") - final KeyFunction keyFunction; + public final KeyFunction keyFunction; @JsonProperty("metric") - final AdditiveMetric metric; + public final AdditiveMetric metric; @JsonProperty("agg") - final AggregationType aggType; + public final AggregationType aggType; @JsonProperty("normalizeByKey") - final boolean normalizeByKey; + public final boolean normalizeByKey; @JsonCreator public AdditiveCharacteristic(@JsonProperty("name") String name, From 9cd9cd4cd895e98131c53e94083b4281c9aa0fed Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 4 Sep 2020 01:17:45 +0300 Subject: [PATCH 077/282] better overlap naming --- .../mixcr/postanalysis/overlap/OverlapType.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java index 4449d0083..72d5a35dd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java @@ -6,10 +6,10 @@ * */ public enum OverlapType { - D("Diversity", "Relative overlap diversity normalized"), - SharedClonotypes("Clonotype share", "Number of shared clonotypes"), + D("Unweighted overlap", "Relative overlap diversity normalized"), + SharedClonotypes("Clonotypes", "Number of shared clonotypes"), F1("Frequencies", "Geometric mean of relative overlap frequencies"), - F2("Drequencies (clonotype-wise)", "Сlonotype-wise sum of geometric mean frequencies"), + F2("Weighted overlap", "Сlonotype-wise sum of geometric mean frequencies"), Jaccard("Jaccard", "Jaccard overlap"), R_Intersection("Pearson", "Pearson correlation of clonotype frequencies, restricted only to the overlapping clonotypes"), R_All("Pearson (all)", "Pearson correlation of clonotype frequencies (outer merge)"); From 55a75e0e8bb32698f19696675f3dd00dac9d64bb Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 4 Sep 2020 13:06:13 +0300 Subject: [PATCH 078/282] add missing equals/hashCode in PA preprocessors --- .../postanalysis/preproc/FilterPreprocessor.java | 14 ++++++++++++++ .../postanalysis/preproc/PreprocessorChain.java | 13 +++++++++++++ .../preproc/SampleFilterPreprocessor.java | 15 +++++++++++++++ 3 files changed, 42 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index 9fdfb62ef..47a39d915 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -8,6 +8,7 @@ import java.util.Arrays; import java.util.Collections; import java.util.List; +import java.util.Objects; import java.util.function.Function; /** @@ -34,4 +35,17 @@ public FilterPreprocessor(ElementPredicate predicate) { public Function, Iterable> setup(Iterable[] sets) { return set -> new FilteredIterable<>(set, t -> predicates.stream().allMatch(s -> s.test(t))); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + FilterPreprocessor that = (FilterPreprocessor) o; + return Objects.equals(predicates, that.predicates); + } + + @Override + public int hashCode() { + return Objects.hash(predicates); + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index 44d3bdafc..5c1b5beae 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -36,4 +36,17 @@ public Function, Iterable> setup(Iterable[] sets) { mapping.put(sets[i], proc[i]); return mapping::get; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + PreprocessorChain that = (PreprocessorChain) o; + return Objects.equals(chain, that.chain); + } + + @Override + public int hashCode() { + return Objects.hash(chain); + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java index 719966a40..403e7e36e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java @@ -6,6 +6,7 @@ import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import java.util.Map; +import java.util.Objects; import java.util.function.Function; /** @@ -31,4 +32,18 @@ public void setSampleNames(Map, String> sampleNames) { public Function, Iterable> setup(Iterable[] sets) { return set -> sampleFilters.get(sampleNames.get(set)).setup(null).apply(set); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SampleFilterPreprocessor that = (SampleFilterPreprocessor) o; + return Objects.equals(sampleFilters, that.sampleFilters) && + Objects.equals(sampleNames, that.sampleNames); + } + + @Override + public int hashCode() { + return Objects.hash(sampleFilters, sampleNames); + } } From a4b221f0851d404075f2939c69c4ab152ee36b9a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 7 Sep 2020 19:17:38 +0300 Subject: [PATCH 079/282] Caching, Bonferroni/Holm and CI (#14) * wip * Cache hit/misses reporting in overlap test. CI enhancements. --- .drone.yml | 25 +- pom.xml | 2 +- .../mixcr/basictypes/VDJCObject.java | 499 +++++++++--------- .../postanalysis/additive/AAProperties.java | 4 +- .../postanalysis/stat/HolmBonferroni.java | 61 +++ .../overlap/OverlapIntegrationTest.java | 69 +++ .../postanalysis/stat/HolmBonferroniTest.java | 47 ++ 7 files changed, 450 insertions(+), 257 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java diff --git a/.drone.yml b/.drone.yml index 6dae4171c..1acb468ca 100644 --- a/.drone.yml +++ b/.drone.yml @@ -90,8 +90,12 @@ steps: depends_on: - deploy_maven - - name: Send Telegram Notification + - name: telegram image: appleboy/drone-telegram + when: + status: + - success + - failure depends_on: - deploy_bin settings: @@ -221,8 +225,25 @@ steps: depends_on: - build_and_test + - name: telegram + image: appleboy/drone-telegram + when: + status: + - failure + depends_on: + - integration_tests + settings: + token: + from_secret: telegram-token + to: + from_secret: telegram-chat-id-micore + format: markdown + message: > + ❌ MiXCR test {{build.number}} failure. + 🌐 {{build.link}} + --- kind: signature -hmac: 9c989edeafff6762641d0f12b227819139f0708413dde34b587471b6f6f997d9 +hmac: 37dab75dd8e579913e6c3b17b02ee28cba794b96aaafbc20bdc4b4eb977528c2 ... diff --git a/pom.xml b/pom.xml index a4e542e26..de98fe986 100644 --- a/pom.xml +++ b/pom.xml @@ -40,7 +40,7 @@ UTF-8 - 1.14-47a96ec + 1.14-161fcea SNAPSHOT diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 4368363e3..60988431b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -32,6 +32,7 @@ import com.milaboratory.core.Range; import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.sequence.*; +import com.milaboratory.util.Cache; import io.repseq.core.*; import io.repseq.gen.VDJCGenes; @@ -47,6 +48,7 @@ public abstract class VDJCObject { protected volatile EnumMap allChains; protected VDJCPartitionedSequence[] partitionedTargets; protected final TagCounter tagCounter; + protected final Cache cache = new Cache(); public VDJCObject(EnumMap hits, TagCounter tagCounter, NSequenceWithQuality... targets) { this.targets = targets; @@ -290,42 +292,33 @@ public final int getTargetContainingFeature(GeneFeature feature) { } public NSequenceWithQuality getFeature(GeneFeature geneFeature) { - int tcf = getTargetContainingFeature(geneFeature); - return tcf == -1 ? null : getPartitionedTarget(tcf).getFeature(geneFeature); + return cache.computeIfAbsent(geneFeature, () -> { + int tcf = getTargetContainingFeature(geneFeature); + return tcf == -1 ? null : getPartitionedTarget(tcf).getFeature(geneFeature); + }); } public NucleotideSequence getNFeature(GeneFeature geneFeature) { - int tcf = getTargetContainingFeature(geneFeature); - return tcf == -1 ? null : getPartitionedTarget(tcf).getFeature(geneFeature).getSequence(); + NSequenceWithQuality feature = getFeature(geneFeature); + return feature == null ? null : feature.getSequence(); } public AminoAcidSequence getAAFeature(GeneFeature geneFeature) { - int tcf = getTargetContainingFeature(geneFeature); - if (tcf == -1) - return null; - VDJCPartitionedSequence target = getPartitionedTarget(tcf); - TranslationParameters tp = target.getPartitioning().getTranslationParameters(geneFeature); - return tp == null - ? null - : AminoAcidSequence.translate( - target.getFeature(geneFeature).getSequence(), tp); // target.getFeature(geneFeature) uses exactly the same algorithm, guaranteed to be non-null at this point - } - - public AminoAcidSequence getFeatureAA(GeneFeature geneFeature) { - NSequenceWithQuality feature = getFeature(geneFeature); - if (feature == null) - return null; - - int targetId = getTargetContainingFeature(geneFeature); - TranslationParameters tr = targetId == -1 ? - TranslationParameters.FromLeftWithIncompleteCodon - : getPartitionedTarget(targetId).getPartitioning().getTranslationParameters(geneFeature); - if (tr == null) - return null; - return AminoAcidSequence.translate(feature.getSequence(), tr); + return cache.computeIfAbsent(0, geneFeature, () -> { + NucleotideSequence nFeature = getNFeature(geneFeature); + if (nFeature == null) + return null; + int tcf = getTargetContainingFeature(geneFeature); + if (tcf == -1) + return null; + VDJCPartitionedSequence target = getPartitionedTarget(tcf); + TranslationParameters tp = target.getPartitioning().getTranslationParameters(geneFeature); + return tp == null + ? null + : AminoAcidSequence.translate(nFeature, tp); + }); } - public int ntLengthOf(GeneFeature gf) { NSequenceWithQuality f = getFeature(gf); if (f == null) @@ -334,246 +327,247 @@ public int ntLengthOf(GeneFeature gf) { } public int aaLengthOf(GeneFeature gf) { - AminoAcidSequence f = getFeatureAA(gf); + AminoAcidSequence f = getAAFeature(gf); if (f == null) return -1; return f.size(); } public CaseSensitiveNucleotideSequence getIncompleteFeature(GeneFeature geneFeature) { - NSequenceWithQuality feature = getFeature(geneFeature); - if (feature != null) { - int iTarget = getTargetContainingFeature(geneFeature); - return new CaseSensitiveNucleotideSequence( - feature.getSequence(), - false, - getPartitionedTarget(iTarget).getPartitioning(), - getPartitionedTarget(iTarget).getPartitioning().getTranslationParameters(geneFeature)); - } - - CaseSensitiveNucleotideSequenceBuilder builder = new CaseSensitiveNucleotideSequenceBuilder(new ArrayList<>(), new BitSet()); - // reference points for resulting sequence - ExtendedReferencePointsBuilder partitioningBuilder = new ExtendedReferencePointsBuilder(); - - // iterate over primitive features that constitute the given `geneFeature` - for (GeneFeature.ReferenceRange rr : geneFeature) { - ReferencePoint left = rr.begin, right = rr.end; - - if (left.getGeneType() != right.getGeneType()) - if (left.getGeneType() != GeneType.Variable || right.getGeneType() != GeneType.Joining) - throw new IllegalArgumentException(); - - if (left.hasNoOffset()) - partitioningBuilder.setPosition(left, builder.size()); - - GeneFeature primitiveFeature = new GeneFeature(left, right); - // check whether primitive feature is already available - NSequenceWithQuality seq = getFeature(primitiveFeature); - if (seq != null) { - builder.add(seq.getSequence(), false); - if (right.hasNoOffset()) - partitioningBuilder.setPosition(right, builder.size()); - continue; + return cache.computeIfAbsent(1, geneFeature, () -> { + NSequenceWithQuality feature = getFeature(geneFeature); + if (feature != null) { + int iTarget = getTargetContainingFeature(geneFeature); + return new CaseSensitiveNucleotideSequence( + feature.getSequence(), + false, + getPartitionedTarget(iTarget).getPartitioning(), + getPartitionedTarget(iTarget).getPartitioning().getTranslationParameters(geneFeature)); } - VDJCHit[] - lHits = hits.get(left.getGeneType()), - rHits = hits.get(right.getGeneType()); - if (lHits == null || lHits.length == 0 || rHits == null || rHits.length == 0) - return null; + CaseSensitiveNucleotideSequenceBuilder builder = new CaseSensitiveNucleotideSequenceBuilder(new ArrayList<>(), new BitSet()); + // reference points for resulting sequence + ExtendedReferencePointsBuilder partitioningBuilder = new ExtendedReferencePointsBuilder(); + + // iterate over primitive features that constitute the given `geneFeature` + for (GeneFeature.ReferenceRange rr : geneFeature) { + ReferencePoint left = rr.begin, right = rr.end; + + if (left.getGeneType() != right.getGeneType()) + if (left.getGeneType() != GeneType.Variable || right.getGeneType() != GeneType.Joining) + throw new IllegalArgumentException(); + + if (left.hasNoOffset()) + partitioningBuilder.setPosition(left, builder.size()); + + GeneFeature primitiveFeature = new GeneFeature(left, right); + // check whether primitive feature is already available + NSequenceWithQuality seq = getFeature(primitiveFeature); + if (seq != null) { + builder.add(seq.getSequence(), false); + if (right.hasNoOffset()) + partitioningBuilder.setPosition(right, builder.size()); + continue; + } - // left and right top hits - VDJCHit - lHit = lHits[0], - rHit = rHits[0]; + VDJCHit[] + lHits = hits.get(left.getGeneType()), + rHits = hits.get(right.getGeneType()); + if (lHits == null || lHits.length == 0 || rHits == null || rHits.length == 0) + return null; - int - lPositionInRef = lHit.getGene().getPartitioning().getRelativePosition(lHit.getAlignedFeature(), left), - rPositionInRef = rHit.getGene().getPartitioning().getRelativePosition(rHit.getAlignedFeature(), right); + // left and right top hits + VDJCHit + lHit = lHits[0], + rHit = rHits[0]; - if (lPositionInRef < 0 || rPositionInRef < 0) - return null; + int + lPositionInRef = lHit.getGene().getPartitioning().getRelativePosition(lHit.getAlignedFeature(), left), + rPositionInRef = rHit.getGene().getPartitioning().getRelativePosition(rHit.getAlignedFeature(), right); - // left parts - List leftParts = new ArrayList<>(); - int positionInRef = lPositionInRef; - while (true) { - int iLeftTarget = -1; // target that contains the left ref point - - // find the closest targets to the right and left points - for (int i = 0; i < numberOfTargets(); ++i) { - Alignment lAl = lHit.getAlignment(i); - // check that there is no any unaligned piece - if (lAl != null - && positionInRef < lAl.getSequence1Range().getFrom() - && lAl.getSequence2Range().getFrom() != 0) - return null; + if (lPositionInRef < 0 || rPositionInRef < 0) + return null; - // select the closest target to the right of left point - if (lAl != null - && positionInRef < lAl.getSequence1Range().getTo() // getTo is exclusive - && (lHit != rHit || lAl.getSequence1Range().getFrom() <= rPositionInRef)) - if (iLeftTarget == -1 - || lAl.getSequence1Range().getFrom() < lHit.getAlignment(iLeftTarget).getSequence1Range().getFrom()) - iLeftTarget = i; - } + // left parts + List leftParts = new ArrayList<>(); + int positionInRef = lPositionInRef; + while (true) { + int iLeftTarget = -1; // target that contains the left ref point + + // find the closest targets to the right and left points + for (int i = 0; i < numberOfTargets(); ++i) { + Alignment lAl = lHit.getAlignment(i); + // check that there is no any unaligned piece + if (lAl != null + && positionInRef < lAl.getSequence1Range().getFrom() + && lAl.getSequence2Range().getFrom() != 0) + return null; - if (iLeftTarget == -1) - break; + // select the closest target to the right of left point + if (lAl != null + && positionInRef < lAl.getSequence1Range().getTo() // getTo is exclusive + && (lHit != rHit || lAl.getSequence1Range().getFrom() <= rPositionInRef)) + if (iLeftTarget == -1 + || lAl.getSequence1Range().getFrom() < lHit.getAlignment(iLeftTarget).getSequence1Range().getFrom()) + iLeftTarget = i; + } - Alignment lAl = lHit.getAlignment(iLeftTarget); - if (!lAl.getSequence1Range().contains(positionInRef)) { - // add lowercase piece of germline - assert lAl.getSequence1Range().getFrom() > positionInRef; - if (leftParts.isEmpty() && lAl.getSequence1Range().getFrom() == rPositionInRef) + if (iLeftTarget == -1) break; - IncompleteSequencePart part = new IncompleteSequencePart(lHit, true, iLeftTarget, positionInRef, lAl.getSequence1Range().getFrom()); + + Alignment lAl = lHit.getAlignment(iLeftTarget); + if (!lAl.getSequence1Range().contains(positionInRef)) { + // add lowercase piece of germline + assert lAl.getSequence1Range().getFrom() > positionInRef; + if (leftParts.isEmpty() && lAl.getSequence1Range().getFrom() == rPositionInRef) + break; + IncompleteSequencePart part = new IncompleteSequencePart(lHit, true, iLeftTarget, positionInRef, lAl.getSequence1Range().getFrom()); + if (part.begin != part.end) + leftParts.add(part); + positionInRef = lAl.getSequence1Range().getFrom(); + } + assert lAl.getSequence1Range().containsBoundary(positionInRef); + + IncompleteSequencePart part = new IncompleteSequencePart(lHit, false, iLeftTarget, + aabsLeft(positionInRef, lAl), + lAl.getSequence2Range().getTo()); if (part.begin != part.end) leftParts.add(part); - positionInRef = lAl.getSequence1Range().getFrom(); + + positionInRef = lAl.getSequence1Range().getTo(); } - assert lAl.getSequence1Range().containsBoundary(positionInRef); - IncompleteSequencePart part = new IncompleteSequencePart(lHit, false, iLeftTarget, - aabsLeft(positionInRef, lAl), - lAl.getSequence2Range().getTo()); - if (part.begin != part.end) - leftParts.add(part); + // right parts (reversed) + List rightParts = new ArrayList<>(); + positionInRef = rPositionInRef; + while (true) { + int iRightTarget = -1; // target that contains the left ref point - positionInRef = lAl.getSequence1Range().getTo(); - } + // find the closest targets to the right and left points + for (int i = 0; i < numberOfTargets(); ++i) { + Alignment rAl = rHit.getAlignment(i); - // right parts (reversed) - List rightParts = new ArrayList<>(); - positionInRef = rPositionInRef; - while (true) { - int iRightTarget = -1; // target that contains the left ref point + // check that there is no any unaligned piece + if (rAl != null + && rAl.getSequence1Range().getTo() < positionInRef + && rAl.getSequence2Range().getTo() != getTarget(i).size()) + return null; - // find the closest targets to the right and left points - for (int i = 0; i < numberOfTargets(); ++i) { - Alignment rAl = rHit.getAlignment(i); + // select the closest target to the left of right point + if (rAl != null + && rAl.getSequence1Range().getFrom() < positionInRef // getFrom is inclusive + && (lHit != rHit || rAl.getSequence1Range().getTo() > lPositionInRef)) { + if (iRightTarget == -1 || rAl.getSequence1Range().getTo() > rHit.getAlignment(iRightTarget).getSequence1Range().getTo()) + iRightTarget = i; + } + } - // check that there is no any unaligned piece - if (rAl != null - && rAl.getSequence1Range().getTo() < positionInRef - && rAl.getSequence2Range().getTo() != getTarget(i).size()) - return null; + if (iRightTarget == -1) + break; - // select the closest target to the left of right point - if (rAl != null - && rAl.getSequence1Range().getFrom() < positionInRef // getFrom is inclusive - && (lHit != rHit || rAl.getSequence1Range().getTo() > lPositionInRef)) { - if (iRightTarget == -1 || rAl.getSequence1Range().getTo() > rHit.getAlignment(iRightTarget).getSequence1Range().getTo()) - iRightTarget = i; + Alignment rAl = rHit.getAlignment(iRightTarget); + if (!rAl.getSequence1Range().contains(positionInRef)) { + // add lowercase piece of germline + assert rAl.getSequence1Range().getTo() <= positionInRef; + if (rightParts.isEmpty() && rAl.getSequence1Range().getTo() == lPositionInRef) + break; + IncompleteSequencePart part = new IncompleteSequencePart(rHit, true, iRightTarget, rAl.getSequence1Range().getTo(), positionInRef); // +1 to include positionInRef + if (part.begin != part.end) + rightParts.add(part); + positionInRef = rAl.getSequence1Range().getTo(); } - } + assert rAl.getSequence1Range().containsBoundary(positionInRef); - if (iRightTarget == -1) - break; - - Alignment rAl = rHit.getAlignment(iRightTarget); - if (!rAl.getSequence1Range().contains(positionInRef)) { - // add lowercase piece of germline - assert rAl.getSequence1Range().getTo() <= positionInRef; - if (rightParts.isEmpty() && rAl.getSequence1Range().getTo() == lPositionInRef) - break; - IncompleteSequencePart part = new IncompleteSequencePart(rHit, true, iRightTarget, rAl.getSequence1Range().getTo(), positionInRef); // +1 to include positionInRef + IncompleteSequencePart part = new IncompleteSequencePart(rHit, false, iRightTarget, + rAl.getSequence2Range().getFrom(), + aabsRight(positionInRef, rAl)); if (part.begin != part.end) rightParts.add(part); - positionInRef = rAl.getSequence1Range().getTo(); - } - assert rAl.getSequence1Range().containsBoundary(positionInRef); - IncompleteSequencePart part = new IncompleteSequencePart(rHit, false, iRightTarget, - rAl.getSequence2Range().getFrom(), - aabsRight(positionInRef, rAl)); - if (part.begin != part.end) - rightParts.add(part); - - positionInRef = rAl.getSequence1Range().getFrom(); - } - Collections.reverse(rightParts); - - if (leftParts.isEmpty() && rightParts.isEmpty() && lHit == rHit) { - // the feature is not covered by any target and - // there are no targets in between :=> take everything from germline - int - lAbs = lHit.getGene().getPartitioning().getAbsolutePosition(lHit.getAlignedFeature(), lPositionInRef), - rAbs = lHit.getGene().getPartitioning().getAbsolutePosition(lHit.getAlignedFeature(), rPositionInRef); - // the only correct case - NucleotideSequence germline = lHit - .getGene() - .getSequenceProvider() - .getRegion(new Range(lAbs, rAbs)); - if (germline == null) - return null; - builder.add(germline, true); - } else if (leftParts.isEmpty() || rightParts.isEmpty()) - return null; - else { - // final pieces - List pieces; - IncompleteSequencePart - lLast = leftParts.get(leftParts.size() - 1), - rLast = rightParts.get(0); - - if (lHit == rHit) { - Alignment lAl = lHit.getAlignment(lLast.iTarget); - Alignment rAl = lHit.getAlignment(rLast.iTarget); - if (lLast.iTarget > rLast.iTarget && lAl.getSequence1Range().getFrom() < rAl.getSequence1Range().getTo()) + positionInRef = rAl.getSequence1Range().getFrom(); + } + Collections.reverse(rightParts); + + if (leftParts.isEmpty() && rightParts.isEmpty() && lHit == rHit) { + // the feature is not covered by any target and + // there are no targets in between :=> take everything from germline + int + lAbs = lHit.getGene().getPartitioning().getAbsolutePosition(lHit.getAlignedFeature(), lPositionInRef), + rAbs = lHit.getGene().getPartitioning().getAbsolutePosition(lHit.getAlignedFeature(), rPositionInRef); + // the only correct case + NucleotideSequence germline = lHit + .getGene() + .getSequenceProvider() + .getRegion(new Range(lAbs, rAbs)); + if (germline == null) return null; - if (lAl.getSequence1Range().contains(rPositionInRef)) { - int aabs = aabs(lAl.convertToSeq2Position(rPositionInRef)); - if (aabs < lLast.begin) - return null; - - IncompleteSequencePart part = new IncompleteSequencePart(lHit, false, lLast.iTarget, lLast.begin, aabs); - if (part.begin == part.end) - leftParts.remove(leftParts.size() - 1); - else - leftParts.set(leftParts.size() - 1, part); - } else { - assert rPositionInRef >= lAl.getSequence1Range().getTo(); - IncompleteSequencePart part = new IncompleteSequencePart(lHit, true, - lLast.iTarget, - lAl.getSequence1Range().getTo(), rPositionInRef); - if (part.begin != part.end) - leftParts.add(part); - } + builder.add(germline, true); + } else if (leftParts.isEmpty() || rightParts.isEmpty()) + return null; + else { + // final pieces + List pieces; + IncompleteSequencePart + lLast = leftParts.get(leftParts.size() - 1), + rLast = rightParts.get(0); - if (rAl.getSequence1Range().contains(lPositionInRef)) { - int aabs = aabs(rAl.convertToSeq2Position(lPositionInRef)); - if (aabs > rLast.end) + if (lHit == rHit) { + Alignment lAl = lHit.getAlignment(lLast.iTarget); + Alignment rAl = lHit.getAlignment(rLast.iTarget); + if (lLast.iTarget > rLast.iTarget && lAl.getSequence1Range().getFrom() < rAl.getSequence1Range().getTo()) return null; - - IncompleteSequencePart part = new IncompleteSequencePart(rHit, false, rLast.iTarget, aabs, rLast.end); - if (part.begin == part.end) - rightParts.remove(0); - else - rightParts.set(0, part); + if (lAl.getSequence1Range().contains(rPositionInRef)) { + int aabs = aabs(lAl.convertToSeq2Position(rPositionInRef)); + if (aabs < lLast.begin) + return null; + + IncompleteSequencePart part = new IncompleteSequencePart(lHit, false, lLast.iTarget, lLast.begin, aabs); + if (part.begin == part.end) + leftParts.remove(leftParts.size() - 1); + else + leftParts.set(leftParts.size() - 1, part); + } else { + assert rPositionInRef >= lAl.getSequence1Range().getTo(); + IncompleteSequencePart part = new IncompleteSequencePart(lHit, true, + lLast.iTarget, + lAl.getSequence1Range().getTo(), rPositionInRef); + if (part.begin != part.end) + leftParts.add(part); + } + + if (rAl.getSequence1Range().contains(lPositionInRef)) { + int aabs = aabs(rAl.convertToSeq2Position(lPositionInRef)); + if (aabs > rLast.end) + return null; + + IncompleteSequencePart part = new IncompleteSequencePart(rHit, false, rLast.iTarget, aabs, rLast.end); + if (part.begin == part.end) + rightParts.remove(0); + else + rightParts.set(0, part); + } else { + assert lPositionInRef < rAl.getSequence1Range().getFrom(); + IncompleteSequencePart part = new IncompleteSequencePart(rHit, true, + rLast.iTarget, + lPositionInRef, rAl.getSequence1Range().getFrom()); + if (part.begin != part.end) + rightParts.add(0, part); + } + + assert same(leftParts, rightParts) : + "\n" + leftParts + + "\n" + rightParts + + "\n" + (this instanceof Clone ? ((Clone) this).id : ((VDJCAlignments) this).getAlignmentsIndex()); + pieces = leftParts; } else { - assert lPositionInRef < rAl.getSequence1Range().getFrom(); - IncompleteSequencePart part = new IncompleteSequencePart(rHit, true, - rLast.iTarget, - lPositionInRef, rAl.getSequence1Range().getFrom()); - if (part.begin != part.end) - rightParts.add(0, part); - } - - assert same(leftParts, rightParts) : - "\n" + leftParts - + "\n" + rightParts - + "\n" + (this instanceof Clone ? ((Clone) this).id : ((VDJCAlignments) this).getAlignmentsIndex()); - pieces = leftParts; - } else { - if (lLast.iTarget != rLast.iTarget) - return null; + if (lLast.iTarget != rLast.iTarget) + return null; - if (lLast.begin > rLast.end) - return null; + if (lLast.begin > rLast.end) + return null; - if (lLast.germline || rLast.germline) - return null; + if (lLast.germline || rLast.germline) + return null; // assert lHit.getGene().getGeneType() == GeneType.Variable; // if (!lHit @@ -587,30 +581,31 @@ assert same(leftParts, rightParts) : // .isAvailable(ReferencePoint.CDR3End)) // return null; - IncompleteSequencePart - merged = new IncompleteSequencePart(lHit, false, lLast.iTarget, lLast.begin, rLast.end); + IncompleteSequencePart + merged = new IncompleteSequencePart(lHit, false, lLast.iTarget, lLast.begin, rLast.end); - pieces = new ArrayList<>(); - pieces.addAll(leftParts.subList(0, leftParts.size() - 1)); - pieces.add(merged); - pieces.addAll(rightParts.subList(1, rightParts.size())); + pieces = new ArrayList<>(); + pieces.addAll(leftParts.subList(0, leftParts.size() - 1)); + pieces.add(merged); + pieces.addAll(rightParts.subList(1, rightParts.size())); + } + + for (IncompleteSequencePart piece : pieces) + if (piece.germline) + builder.add(piece.hit.getAlignment(piece.iTarget).getSequence1().getRange(piece.begin, piece.end), true); + else + builder.add(getTarget(piece.iTarget).getSequence().getRange(piece.begin, piece.end), false); } - for (IncompleteSequencePart piece : pieces) - if (piece.germline) - builder.add(piece.hit.getAlignment(piece.iTarget).getSequence1().getRange(piece.begin, piece.end), true); - else - builder.add(getTarget(piece.iTarget).getSequence().getRange(piece.begin, piece.end), false); + if (right.hasNoOffset()) + partitioningBuilder.setPosition(right, builder.size()); } - - if (right.hasNoOffset()) - partitioningBuilder.setPosition(right, builder.size()); - } - ExtendedReferencePoints partition = partitioningBuilder.build(); - return new CaseSensitiveNucleotideSequence( - builder.sequences.toArray(new NucleotideSequence[builder.sequences.size()]), - builder.lowerCase, - partition, partition.getTranslationParameters(geneFeature)); + ExtendedReferencePoints partition = partitioningBuilder.build(); + return new CaseSensitiveNucleotideSequence( + builder.sequences.toArray(new NucleotideSequence[builder.sequences.size()]), + builder.lowerCase, + partition, partition.getTranslationParameters(geneFeature)); + }); } private static int aabsLeft(int positionInRef, Alignment lAl) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java index 0f82de3d3..7b8797128 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java @@ -16,7 +16,7 @@ public class AAProperties { /** Compute property normalized on sequence length */ public static double computeNormalized(AAProperty property, VDJCObject obj, GeneFeature gf) { - AminoAcidSequence seq = obj.getFeatureAA(gf); + AminoAcidSequence seq = obj.getAAFeature(gf); if (seq == null) return Double.NaN; double r = 0; @@ -28,7 +28,7 @@ public static double computeNormalized(AAProperty property, VDJCObject obj, Gene /** Compute property based on selection */ public static double compute(AAProperty property, VDJCObject obj, GeneFeature gf, Adjustment alignment, int nLetters) { - AminoAcidSequence seq = obj.getFeatureAA(gf); + AminoAcidSequence seq = obj.getAAFeature(gf); if (seq == null) return Double.NaN; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java new file mode 100644 index 000000000..017da4149 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java @@ -0,0 +1,61 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.stat; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.Comparator; +import java.util.List; +import java.util.function.ToDoubleFunction; + +public final class HolmBonferroni { + /** + * Performs Holm-Bonferroni method. + * + * https://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method + * + * @param input ALL result of multiple comparisons + * @param pValueExtractor function to extract P-value from input objects + * @param fwer family-wise error rate, e.g. 0.01 (https://en.wikipedia.org/wiki/Family-wise_error_rate) + * @param type of the object representing single comparison result + * @return list of significant p-values, sorted from lowest to highest (FWER controlled) + */ + public static List run(Collection input, + ToDoubleFunction pValueExtractor, + double fwer) { + ArrayList res = new ArrayList<>(input); + res.sort(Comparator.comparingDouble(pValueExtractor)); + int i = 0; + for (; i < res.size(); i++) + if (pValueExtractor.applyAsDouble(res.get(i)) > fwer / (res.size() - i)) + break; + return new ArrayList<>(res.subList(0, i)); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java index a1af4b7c7..5208fc4a4 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java @@ -33,14 +33,19 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.VDJCObject; import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.util.Cache; import com.milaboratory.util.LambdaSemaphore; import gnu.trove.map.hash.TIntIntHashMap; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; +import junit.framework.Assert; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import java.nio.file.Paths; import java.util.Arrays; import java.util.List; @@ -80,17 +85,81 @@ public void test1() throws IOException { List> byAA = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); List> byAAAndV = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}, GeneType.Variable); + long totalSumExpected = 0; for (List> by : Arrays.asList(byN, byAA, byAAAndV)) { System.out.println("============="); OverlapIterable overlap = OverlapUtil.overlap(by, readers); TIntIntHashMap hist = new TIntIntHashMap(); + long totalSum = 0; for (OverlapGroup cloneOverlapGroup : overlap) { int sum = cloneOverlapGroup.elements.stream().mapToInt(l -> l.isEmpty() ? 0 : 1).sum(); + totalSum += cloneOverlapGroup.elements.stream().mapToInt(List::size).sum(); hist.adjustOrPutValue(sum, 1, 1); } + if (totalSumExpected == 0) + totalSumExpected = totalSum; + else + Assert.assertEquals(totalSumExpected, totalSum); for (int i = 1; i < readers.size(); i++) if (hist.get(i) != 0) System.out.println("" + i + ": " + hist.get(i)); } + + System.out.println("Cache misses: " + Cache.totalCacheMisses()); + System.out.println(" Cache hits: " + Cache.totalCacheHits()); + } + + @Ignore + @Test + public void tst1() throws IOException { + LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(4); + + List input = Files.list(Paths.get("/Users/dbolotin/Downloads/RealAnalysisRita/workdir/")) + .map(p -> p.resolve("mixcr")) + .filter(Files::exists) + .flatMap(p -> { + try { + return Files.list(p); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .filter(p -> p.toString().endsWith(".clns")) + .collect(Collectors.toList()); + + List readers = input.stream() + .map(f -> { + try { + return new ClnsReader(f, + VDJCLibraryRegistry.getDefault(), + concurrencyLimiter); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); + + List> byN = VDJCSProperties.orderingByNucleotide(new GeneFeature[]{GeneFeature.CDR3}); + List> byAA = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); + List> byAAAndV = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}, GeneType.Variable); + + for (List> by : Arrays.asList(byN, byAA, byAAAndV)) { + System.out.println("============="); + OverlapIterable overlap = OverlapUtil.overlap(by, readers); + TIntIntHashMap hist = new TIntIntHashMap(); + long totalSum = 0; + for (OverlapGroup cloneOverlapGroup : overlap) { + int sum = cloneOverlapGroup.elements.stream().mapToInt(l -> l.isEmpty() ? 0 : 1).sum(); + totalSum += cloneOverlapGroup.elements.stream().mapToInt(List::size).sum(); + hist.adjustOrPutValue(sum, 1, 1); + } + for (int i = 1; i < readers.size(); i++) + if (hist.get(i) != 0) + System.out.println("" + i + ": " + hist.get(i)); + System.out.println("Total: " + totalSum); + } + + System.out.println("Cache misses: " + Cache.totalCacheMisses()); + System.out.println(" Cache hits: " + Cache.totalCacheHits()); } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java new file mode 100644 index 000000000..aedd5793e --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java @@ -0,0 +1,47 @@ +/* + * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail + * (here and after addressed as Inventors) + * All Rights Reserved + * + * Permission to use, copy, modify and distribute any part of this program for + * educational, research and non-profit purposes, by non-profit institutions + * only, without fee, and without a written agreement is hereby granted, + * provided that the above copyright notice, this paragraph and the following + * three paragraphs appear in all copies. + * + * Those desiring to incorporate this work into commercial products or use for + * commercial purposes should contact MiLaboratory LLC, which owns exclusive + * rights for distribution of this program for commercial purposes, using the + * following email address: licensing@milaboratory.com. + * + * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, + * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, + * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS + * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO + * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY + * PATENT, TRADEMARK OR OTHER RIGHTS. + */ +package com.milaboratory.mixcr.postanalysis.stat; + +import org.junit.Assert; +import org.junit.Test; + +import java.util.Arrays; +import java.util.List; + +public class HolmBonferroniTest { + @Test + public void test1() { + List result = HolmBonferroni.run( + Arrays.asList(0.001, 0.1, 0.1, 0.1, 0.02, 0.02, 0.02, 1E-4), + d -> d, + 0.05); + Assert.assertEquals(Arrays.asList(1E-4, 0.001), result); + } +} \ No newline at end of file From d6686eb3af23e5e8f6b5b4eaba481a7f6190d221 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 9 Sep 2020 16:37:43 +0300 Subject: [PATCH 080/282] simple count characteristics --- .../additive/AdditiveCharacteristics.java | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java index 9be0b2c76..0a368a3d1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java @@ -16,6 +16,26 @@ public final class AdditiveCharacteristics { private AdditiveCharacteristics() {} + public static AdditiveCharacteristic readCount(SetPreprocessor preproc) { + String name = "readCount"; + return new AdditiveCharacteristic<>(name, preproc, + new WeightFunctions.Count(), + new KeyFunctions.Named<>(name), + new AdditiveMetrics.Constant(), + AggregationType.Sum, + false); + } + + public static AdditiveCharacteristic clonotypeCount(SetPreprocessor preproc) { + String name = "cloneCount"; + return new AdditiveCharacteristic<>(name, preproc, + new WeightFunctions.NoWeight<>(), + new KeyFunctions.Named<>(name), + new AdditiveMetrics.Constant(), + AggregationType.Sum, + false); + } + public static AdditiveCharacteristic weightedLengthOf(GeneFeature gf, boolean aa) { return weightedLengthOf(new NoPreprocessing<>(), gf, aa); } From ee455c4683e47096fe0e38ac3dfe2f89b51539c1 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 9 Sep 2020 16:45:55 +0300 Subject: [PATCH 081/282] add constants --- .../additive/AdditiveCharacteristics.java | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java index 0a368a3d1..2f764469f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java @@ -16,21 +16,23 @@ public final class AdditiveCharacteristics { private AdditiveCharacteristics() {} + public static final String readCountKey = "readCount"; + public static AdditiveCharacteristic readCount(SetPreprocessor preproc) { - String name = "readCount"; - return new AdditiveCharacteristic<>(name, preproc, + return new AdditiveCharacteristic<>(readCountKey, preproc, new WeightFunctions.Count(), - new KeyFunctions.Named<>(name), + new KeyFunctions.Named<>(readCountKey), new AdditiveMetrics.Constant(), AggregationType.Sum, false); } + public static final String cloneCountKey = "cloneCount"; + public static AdditiveCharacteristic clonotypeCount(SetPreprocessor preproc) { - String name = "cloneCount"; - return new AdditiveCharacteristic<>(name, preproc, + return new AdditiveCharacteristic<>(cloneCountKey, preproc, new WeightFunctions.NoWeight<>(), - new KeyFunctions.Named<>(name), + new KeyFunctions.Named<>(cloneCountKey), new AdditiveMetrics.Constant(), AggregationType.Sum, false); From 6abb772be0c4437baaf3684c8819eaa27a3cb83f Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 18 Sep 2020 13:46:37 +0300 Subject: [PATCH 082/282] Added nucleotides characteristic --- .../additive/AdditiveCharacteristics.java | 13 ++++++++ .../additive/AdditiveMetrics.java | 30 +++++++++++++++++++ 2 files changed, 43 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java index 2f764469f..fb1824390 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java @@ -55,6 +55,19 @@ public static AdditiveCharacteristic weightedLengthOf(SetPreproce ); } + public static AdditiveCharacteristic weightedAddedNucleotides(SetPreprocessor preproc) { + String name = "AddedNucleotides"; + return new AdditiveCharacteristic<>( + name, + preproc, + new WeightFunctions.Count(), + new KeyFunctions.Named<>(name), + new AdditiveMetrics.AddedNucleotides<>(), + AggregationType.Mean, + false + ); + } + public static AdditiveCharacteristic weightedBbiophysicsNormalized(AAProperties.AAProperty property, GeneFeature gf) { return weightedBbiophysicsNormalized(new NoPreprocessing<>(), property, gf); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java index 3fa5b3713..b1461953c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java @@ -84,6 +84,36 @@ public int hashCode() { } } + public static final class AddedNucleotides implements AdditiveMetric, JsonSupport { + public AddedNucleotides() {} + + @Override + public double compute(T obj) { + int vd = obj.ntLengthOf(GeneFeature.VDJunction); + int dj = obj.ntLengthOf(GeneFeature.DJJunction); + if (vd >= 0 && dj >= 0) + return vd + dj; + if (obj.getFeature(GeneFeature.DCDR3Part) != null) + return Double.NaN; // no CDR3 + int vj = obj.ntLengthOf(GeneFeature.VJJunction); + if (vj < 0) + return Double.NaN; + return vj; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 7891; + } + } + public static final class AAPropertyNormalized implements AdditiveMetric, JsonSupport { public AAProperty property; public GeneFeature geneFeature = GeneFeature.CDR3; From a5eb478940f75e609aa7a1ad6861f8d946e3a328 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 18 Sep 2020 14:08:32 +0300 Subject: [PATCH 083/282] PA json subtypes fix --- .../milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java index b9fe75d55..5f7df6e23 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java @@ -16,6 +16,7 @@ @JsonSubTypes({ @JsonSubTypes.Type(value = AdditiveMetrics.Constant.class, name = "constant"), @JsonSubTypes.Type(value = AdditiveMetrics.GeneFeatureLength.class, name = "length"), + @JsonSubTypes.Type(value = AdditiveMetrics.AddedNucleotides.class, name = "addedNucleotides"), @JsonSubTypes.Type(value = AdditiveMetrics.AAPropertyNormalized.class, name = "aaPropertyNormalized"), @JsonSubTypes.Type(value = AdditiveMetrics.AAPropertySum.class, name = "aaProperty"), }) From dfcaec6f15a1772e14b344f0de7a55fe6df1805f Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 18 Dec 2020 13:32:02 +0300 Subject: [PATCH 084/282] Set CloneId in contig assembly. --- .../com/milaboratory/mixcr/cli/CommandAssembleContigs.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index f05d87735..25ee8d32d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -247,12 +247,13 @@ public void run1() throws Exception { assert report.getFinalCloneCount() == totalClonesCount; assert report.getFinalCloneCount() >= report.getInitialCloneCount(); + int cloneId = 0; Clone[] clones = new Clone[totalClonesCount]; try (PrimitivI tmpIn = new PrimitivI(new BufferedInputStream(new FileInputStream(out)))) { IOUtil.registerGeneReferences(tmpIn, genes, alignerParameters); int i = 0; for (Clone clone : CUtils.it(new PipeDataInputReader<>(Clone.class, tmpIn, totalClonesCount))) - clones[i++] = clone; + clones[i++] = clone.setId(cloneId++); } CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters, cloneAssemblerParameters, ordering); From 19e01cb3eb778c1abaa77ae40d2b43e7c99a9f33 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sun, 10 Jan 2021 14:09:22 +0300 Subject: [PATCH 085/282] Better unit test coverage for postanalysis package (#15) * Unit tests * Bugfix in downsampling auto chooser * Bugfix in std computation in AdditiveCharacteristic --- pom.xml | 28 +- .../postanalysis/PostanalysisRunner.java | 11 +- .../additive/AdditiveAggregator.java | 5 + .../additive/AdditiveCharacteristic.java | 8 +- .../diversity/DiversityAggregator.java | 2 +- .../downsampling/DownsampleValueChooser.java | 4 +- .../DownsamplingPreprocessor.java | 2 +- .../OverlapDownsamplingPreprocessor.java | 2 +- .../postanalysis/overlap/OverlapGroup.java | 13 +- .../mixcr/postanalysis/ui/ClonesIterable.java | 2 - .../postanalysis/ui/OutputTableCell.java | 4 +- .../mixcr/util/FilteredIterable.java | 3 - .../mixcr/postanalysis/TestObject.java | 64 +++ .../postanalysis/TestObjectWithPayload.java | 34 ++ .../additive/AdditiveCharacteristicsTest.java | 101 +++++ .../DiversityCharacteristicTest.java | 88 ++++ .../DownsampleValueChooserTest.java | 16 + .../DownsamplingPreprocessorTest.java | 84 +++- .../OverlapDownsamplingPreprocessorTest.java | 128 ++++++ .../overlap/OverlapCharacteristicTest.java | 403 ++++++++++++++++++ 20 files changed, 964 insertions(+), 38 deletions(-) create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java diff --git a/pom.xml b/pom.xml index de98fe986..3fc69c9e7 100644 --- a/pom.xml +++ b/pom.xml @@ -40,7 +40,7 @@ UTF-8 - 1.14-161fcea + 1.14-e4a7ebd SNAPSHOT @@ -128,7 +128,7 @@ org.apache.maven.plugins maven-surefire-plugin - 2.22.2 + 3.0.0-M5 -Xmx1024m @@ -143,7 +143,7 @@ - + @@ -156,12 +156,12 @@ org.apache.maven.plugins - maven-javadoc-plugin - 3.0.1 + maven-compiler-plugin + 3.8.0 - - -Xdoclint:none - + 1.8 + 1.8 + UTF-8 @@ -222,7 +222,7 @@ org.apache.maven.plugins maven-surefire-plugin - 2.22.2 + 3.0.0-M5 -Xmx1024m @@ -244,16 +244,6 @@ - - org.apache.maven.plugins - maven-compiler-plugin - 3.8.0 - - 1.8 - 1.8 - - - maven-assembly-plugin diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index 8dddb4f03..6d82c7b0d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.postanalysis; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.util.CanReportProgressAndStage; import java.util.*; @@ -7,17 +8,23 @@ import java.util.stream.Collectors; /** - * + * @param type of objects */ public class PostanalysisRunner implements CanReportProgressAndStage { private final List> characteristics = new ArrayList<>(); private Iterable[] datasets; + public void addCharacteristics(CharacteristicGroup... groups) { + for (CharacteristicGroup g : groups) { + addCharacteristics(g.characteristics); + } + } + public void addCharacteristics(Characteristic... chs) { addCharacteristics(Arrays.asList(chs)); } - public void addCharacteristics(List> chs) { + public void addCharacteristics(List> chs) { characteristics.addAll(chs); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java index cdbbf2698..1151fbf88 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java @@ -40,6 +40,10 @@ public class AdditiveAggregator implements Aggregator { * Aggregated values for single key */ double metricSum, weightSum; + /** + * Number of elements + */ + int nElements; /** * Aggregated values for other keys ( != null ) */ @@ -68,6 +72,7 @@ public void consume(T obj) { if (Double.isNaN(metricValue)) return; + nElements += 1; double weightValue = weight.weight(obj); weightSum += weightValue; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java index 3c4682e2d..bd6e63ed3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java @@ -77,11 +77,17 @@ public MetricValue[] result() { for (int i = 0; i < mean.length; ++i) { MetricValue m = mean[i]; + if (meanAgg.nElements == 1) { + result[i] = new MetricValue<>(m.key, 0.0); + continue; + } MetricValue m2 = meanSquare[i]; if (!m.key.equals(m2.key)) throw new IllegalArgumentException(); - result[i] = new MetricValue<>(m.key, Math.sqrt(m2.value - m.value * m.value)); + result[i] = new MetricValue<>(m.key, Math.sqrt( + meanAgg.weightSum / (meanAgg.weightSum - 1) + * (m2.value - m.value * m.value))); } return result; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java index 3a31a3ff0..ca9e71d6d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -24,6 +24,7 @@ public class DiversityAggregator implements Aggregator { private int diversity = 0; /** total count across all clonotypes */ private long countSum = 0; + /** clone count -> number of clones */ final TLongIntHashMap freqTable = new TLongIntHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1, 0); final ToLongFunction count; @@ -128,5 +129,4 @@ public MetricValue[] result() { result.addAll(computeEfronThisted()); return result.toArray(new MetricValue[0]); } - } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java index a38ec3991..56d9e6c71 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java @@ -74,7 +74,7 @@ public int hashCode() { } class Auto implements DownsampleValueChooser { - public double quantile = 0.2; + public double quantile = 20.; public double scale = 0.5; public long threshold = 500; @@ -87,7 +87,7 @@ public Auto(double quantile, double scale, long threshold) { } @Override - public long compute(long[] totalCounts) { + public long compute(long... totalCounts) { long q = (long) (new Percentile(quantile).evaluate(Arrays.stream(totalCounts).mapToDouble(l -> l).toArray()) * scale); long min = Arrays.stream(totalCounts).min().orElse(0); long d = Math.max(q, min); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index e82bc3c50..c51367894 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -21,7 +21,7 @@ /** * */ -public abstract class DownsamplingPreprocessor implements SetPreprocessor { +public class DownsamplingPreprocessor implements SetPreprocessor { public final ToLongFunction getCount; public final BiFunction setCount; @JsonProperty("downsampleValueChooser") diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java index 5d01ca08b..6497156d1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java @@ -47,7 +47,7 @@ import java.util.function.ToLongFunction; import java.util.stream.Collectors; -public abstract class OverlapDownsamplingPreprocessor implements SetPreprocessor> { +public class OverlapDownsamplingPreprocessor implements SetPreprocessor> { public final ToLongFunction getCount; public final BiFunction setCount; @JsonProperty("downsampleValueChooser") diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java index 4ee6f5240..9478e263c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java @@ -29,10 +29,12 @@ */ package com.milaboratory.mixcr.postanalysis.overlap; +import java.util.Iterator; import java.util.List; import java.util.Objects; +import java.util.stream.Stream; -public final class OverlapGroup { +public final class OverlapGroup implements Iterable> { /** Elements in group separated by sample */ final List> elements; @@ -52,6 +54,15 @@ public boolean notEmpty() { return !elements.stream().allMatch(List::isEmpty); } + @Override + public Iterator> iterator() { + return elements.iterator(); + } + + public Stream> stream() { + return elements.stream(); + } + @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java index d3d02d56f..64921b57b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java @@ -5,7 +5,6 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSetIO; import io.repseq.core.VDJCLibraryRegistry; -import org.jetbrains.annotations.NotNull; import java.io.IOException; import java.nio.file.Path; @@ -32,7 +31,6 @@ public ClonesIterable(String path, VDJCLibraryRegistry registry) { private final List close = new ArrayList<>(); - @NotNull @Override public Iterator iterator() { try { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java index 900589a33..92f4c30dd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java @@ -1,7 +1,5 @@ package com.milaboratory.mixcr.postanalysis.ui; -import org.jetbrains.annotations.NotNull; - import java.util.Objects; /** @@ -23,7 +21,7 @@ public String toString() { } @Override - public int compareTo(@NotNull OutputTableCell o) { + public int compareTo(OutputTableCell o) { int c = Integer.compare(iRow, o.iRow); if (c != 0) return c; diff --git a/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java b/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java index 4b1c56983..98fcc8317 100644 --- a/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java +++ b/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java @@ -1,7 +1,5 @@ package com.milaboratory.mixcr.util; -import org.jetbrains.annotations.NotNull; - import java.util.Iterator; import java.util.function.Predicate; @@ -17,7 +15,6 @@ public FilteredIterable(Iterable inner, Predicate accept) { this.accept = accept; } - @NotNull @Override public Iterator iterator() { return new FilteredIterator<>(inner.iterator(), accept); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java new file mode 100644 index 000000000..f36c9321b --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java @@ -0,0 +1,64 @@ +package com.milaboratory.mixcr.postanalysis; + +import org.apache.commons.math3.random.RandomDataGenerator; + +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.function.ToDoubleFunction; +import java.util.function.ToIntFunction; + +/** + * + */ +public class TestObject { + public final double value; + public final double weight; + + public TestObject(double value, double weight) { + this.value = value; + this.weight = weight; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TestObject that = (TestObject) o; + return Double.compare(that.value, value) == 0 && Double.compare(that.weight, weight) == 0; + } + + @Override + public int hashCode() { + return Objects.hash(value, weight); + } + + public static List[] generateDatasets(int nDatasets, RandomDataGenerator rng) { + return generateDatasets(nDatasets, rng, + r -> r.nextInt(1, 1000), + r -> r.nextUniform(0, 10), + r -> r.nextUniform(0, 10)); + } + + public static List[] generateDatasets(int nDatasets, RandomDataGenerator rng, + ToIntFunction sizes, + ToDoubleFunction values, + ToDoubleFunction weights) { + int[] nElements = new int[nDatasets]; + for (int i = 0; i < nDatasets; i++) { + nElements[i] = sizes.applyAsInt(rng); + } + List[] datasets = new List[nDatasets]; + for (int i = 0; i < datasets.length; i++) { + TestObject[] ds = new TestObject[nElements[i]]; + for (int j = 0; j < nElements[i]; j++) { + TestObject w = new TestObject( + values.applyAsDouble(rng), + weights.applyAsDouble(rng)); + ds[j] = w; + } + datasets[i] = Arrays.asList(ds); + } + return datasets; + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java new file mode 100644 index 000000000..779d2526c --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java @@ -0,0 +1,34 @@ +package com.milaboratory.mixcr.postanalysis; + +import java.util.Objects; + +/** + * + */ +public class TestObjectWithPayload extends TestObject { + public final Payload payload; + + public TestObjectWithPayload(double value, double weight, Payload payload) { + super(value, weight); + this.payload = payload; + } + + @Override + public String toString() { + return "val:" + value + " wt:" + weight + " pa:" + payload; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + TestObjectWithPayload that = (TestObjectWithPayload) o; + return Objects.equals(payload, that.payload); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), payload); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java new file mode 100644 index 000000000..3c547d2a8 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java @@ -0,0 +1,101 @@ +package com.milaboratory.mixcr.postanalysis.additive; + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.TestObject; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; +import com.milaboratory.mixcr.postanalysis.ui.GroupSummary; +import com.milaboratory.mixcr.postanalysis.ui.OutputTable; +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well44497a; +import org.apache.commons.math3.stat.descriptive.moment.Mean; +import org.apache.commons.math3.stat.descriptive.moment.Variance; +import org.junit.Assert; +import org.junit.Test; + +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +/** + * + */ +public class AdditiveCharacteristicsTest { + @Test + @SuppressWarnings("unchecked") + public void testWeightedDescriptiveStat() { + AdditiveCharacteristic sum = new AdditiveCharacteristic<>( + "sum", + new NoPreprocessing<>(), + o -> o.weight, + o -> "sum", + w -> w.value, + AggregationType.Sum, + false + ); + + AdditiveCharacteristic mean = new AdditiveCharacteristic<>( + "mean", + new NoPreprocessing<>(), + o -> o.weight, + o -> "mean", + w -> w.value, + AggregationType.Mean, + false + ); + + AdditiveCharacteristic std = new AdditiveCharacteristic<>( + "std", + new NoPreprocessing<>(), + o -> o.weight, + o -> "std", + w -> w.value, + AggregationType.Std, + false + ); + + + RandomDataGenerator rng = new RandomDataGenerator(new Well44497a()); + int nDatasets = 1000; + List[] datasets = TestObject.generateDatasets(nDatasets, rng); + + PostanalysisRunner runner = new PostanalysisRunner<>(); + runner.addCharacteristics(sum, mean, std); + runner.setDatasets(datasets); + PostanalysisResult result = runner.run(); + + CharacteristicGroup group = new CharacteristicGroup<>("stat", + Arrays.asList(mean, std), + Arrays.asList(new GroupSummary<>())); + result = result.setSampleIds(IntStream.range(0, nDatasets).mapToObj(String::valueOf).collect(Collectors.toList())); + + CharacteristicGroupResult table = result.getTable(group); + OutputTable summary = table.getOutputs().get(GroupSummary.key); + + Double[][] rows = summary.rows(); + for (int i = 0; i < nDatasets; i++) { + Double[] metrics = rows[i]; + + double[] vals = datasets[i].stream().mapToDouble(o -> o.value).toArray(); + double[] weights = datasets[i].stream().mapToDouble(o -> o.weight).toArray(); + + double expectedSum = IntStream.range(0, vals.length).mapToDouble(m -> vals[m] * weights[m]).sum(); + double expectedMean = new Mean().evaluate(vals, weights); + double expectedStd = Math.sqrt(new Variance(true).evaluate(vals, weights)); + + for (int j = 0; j < metrics.length; j++) { + if (summary.colNames.get(j).equals("sum")) + Assert.assertEquals(expectedSum, metrics[j], 1e-10); + else if (summary.colNames.get(j).equals("mean")) + Assert.assertEquals(expectedMean, metrics[j], 1e-10); + else if (summary.colNames.get(j).equals("std")) + Assert.assertEquals(expectedStd, metrics[j], 1e-10); + else + throw new RuntimeException(); + } + } + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java new file mode 100644 index 000000000..369f21b23 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -0,0 +1,88 @@ +package com.milaboratory.mixcr.postanalysis.diversity; + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.TestObject; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResultCell; +import com.milaboratory.mixcr.postanalysis.ui.GroupSummary; +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well512a; +import org.junit.Assert; +import org.junit.Test; + +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +/** + * + */ +public class DiversityCharacteristicTest { + @Test + @SuppressWarnings("unchecked") + public void test1() { + DiversityCharacteristic diversity = new DiversityCharacteristic<>( + "diversity", t -> t.weight, new NoPreprocessing<>()); + + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + int nDatasets = 100; + List[] datasets = TestObject.generateDatasets(nDatasets, rng, + r -> r.nextInt(1000, 10000), + r -> r.nextUniform(0, 1), + r -> r.nextInt(10, 20)); + + PostanalysisRunner runner = new PostanalysisRunner<>(); + runner.addCharacteristics(diversity); + runner.setDatasets(datasets); + PostanalysisResult result = runner.run(); + result = result.setSampleIds(IntStream.range(0, nDatasets).mapToObj(String::valueOf).collect(Collectors.toList())); + + CharacteristicGroup group = new CharacteristicGroup<>("diversity", + Arrays.asList(diversity), + Arrays.asList(new GroupSummary<>())); + + CharacteristicGroupResult table = result.getTable(group); + for (CharacteristicGroupResultCell cell : table.cells) { + List ds = datasets[cell.sampleIndex]; + if (cell.key == DiversityMeasure.InverseSimpson) + Assert.assertEquals(SimpsonIndex(ds), cell.value, 1e-6); + if (cell.key == DiversityMeasure.ShannonWeiner) + Assert.assertEquals(ShannonEntropy(ds), cell.value, 1e-6); + } + } + + private static double ShannonEntropy(List dataset) { + long sum = dataset.stream().mapToLong(d -> (long) d.weight).sum(); + + double entropy = 0; + for (TestObject e : dataset) { + double p = e.weight / sum; + entropy -= p * Math.log(p); + } + + return entropy; + } + + private static double SimpsonIndex(List dataset) { + return entropy(dataset, 2); + } + + private static double entropy(List dataset, double alpha) { + if (alpha == 1) + return ShannonEntropy(dataset); + + long sum = dataset.stream().mapToLong(d -> (long) d.weight).sum(); + + double agg = 0; + for (TestObject e : dataset) { + double p = e.weight / sum; + agg += Math.pow(p, alpha); + } + + return Math.pow(agg, 1 / (1 - alpha)); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java new file mode 100644 index 000000000..c5165b465 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java @@ -0,0 +1,16 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import org.junit.Assert; +import org.junit.Test; + +/** + * + */ +public class DownsampleValueChooserTest { + @Test + public void testAuto1() { + DownsampleValueChooser.Auto auto = new DownsampleValueChooser.Auto(); + Assert.assertEquals(501, auto.compute(501, 200_000, 300_000, 400_000)); + Assert.assertTrue(501 < auto.compute(501, 200_000, 300_000, 400_000, 500_000)); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index 29e0c99f4..4d02bcb05 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.postanalysis.downsampling; +import com.milaboratory.mixcr.postanalysis.TestObject; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; @@ -7,7 +8,9 @@ import org.junit.Ignore; import org.junit.Test; -import java.util.Arrays; +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; import java.util.stream.LongStream; /** @@ -69,7 +72,7 @@ public void testRnd() { for (int nTry = 0; nTry < nTries; ++nTry) { long[] counts = new long[gen.nextInt(1000_000, 2000_000) / 10]; for (int i = 0; i < counts.length; ++i) - counts[i] = (long) (gen.nextInt(50, 500) * 5000 / Math.pow(1 + i, 1) + 1); + counts[i] = (long) (gen.nextInt(50, 500) * 5000L / Math.pow(1 + i, 1) + 1); long sum = Arrays.stream(counts).sum(); @@ -85,4 +88,81 @@ public void testRnd() { } System.out.println(timing); } + + @Test + public void test3() { + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + + DownsampleValueChooser dsChooser = counts -> Arrays.stream(counts).min().orElse(0); + + DownsamplingPreprocessor proc = new DownsamplingPreprocessor<>( + t -> Math.round(t.weight), + (t, w) -> new TestObject(t.value, 1d * w), + dsChooser, + rng.nextLong(0, Long.MAX_VALUE / 2) + ); + + int nDatasets = 10; + Dataset[] initial = new Dataset[nDatasets]; + for (int i = 0; i < initial.length; i++) { + initial[i] = rndDataset(rng, rng.nextInt(100, 1000)); + } + + long dsValue = dsChooser.compute(Arrays.stream(initial).mapToLong(d -> d.count).toArray()); + Function, Iterable> setup = proc.setup(initial); + + Dataset[] downsampled = Arrays.stream(initial).map(setup) + .map(Dataset::new) + .toArray(Dataset[]::new); + + for (int i = 0; i < downsampled.length; i++) { + Dataset in = initial[i]; + Dataset dw = downsampled[i]; + + Assert.assertTrue(in.set.containsAll(dw.set)); + Assert.assertEquals(dsValue, dw.count); + } + } + + static List toList(Iterable it) { + if (it instanceof Collection) + return new ArrayList<>((Collection) it); + + ArrayList l = new ArrayList<>(); + for (T t : it) { + l.add(t); + } + return l; + } + + public static Dataset rndDataset(RandomDataGenerator rng, int size) { + TestObject[] r = new TestObject[size]; + for (int i = 0; i < size; i++) { + r[i] = new TestObject( + rng.nextUniform(0, 1), + rng.nextUniform(0, 100)); + } + return new Dataset(Arrays.asList(r)); + } + + private static final class Dataset implements Iterable { + final List data; + final Set set; + final long count; + + public Dataset(Iterable data) { + this(toList(data)); + } + + public Dataset(List data) { + this.data = data; + this.set = data.stream().map(s -> s.value).collect(Collectors.toSet()); + this.count = data.stream().mapToLong(l -> Math.round(l.weight)).sum(); + } + + @Override + public Iterator iterator() { + return data.iterator(); + } + } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java new file mode 100644 index 000000000..d9df86720 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -0,0 +1,128 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import com.milaboratory.mixcr.postanalysis.TestObject; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well512a; +import org.junit.Assert; +import org.junit.Test; + +import java.util.*; +import java.util.function.Function; + +import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingPreprocessorTest.toList; + +/** + * + */ +public class OverlapDownsamplingPreprocessorTest { + @Test + public void test1() { + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + DownsampleValueChooser.Minimal chooser = new DownsampleValueChooser.Minimal(); + OverlapDownsamplingPreprocessor proc = new OverlapDownsamplingPreprocessor<>( + t -> Math.round(t.weight), + (t, newW) -> new TestObject(t.value, newW), + chooser, + System.currentTimeMillis() + ); + + Dataset[] datasets = new Dataset[]{ + rndDataset(rng, 5, 100000), + rndDataset(rng, 10, 10000), + rndDataset(rng, 15, 10000) + }; + Function>, Iterable>> downsampler = proc.setup(datasets); + + for (Dataset in : datasets) { + long dsValue = chooser.compute(in.counts); + Dataset dw = new Dataset(downsampler.apply(in)); + + for (int i = 0; i < in.counts.length; i++) { + Assert.assertEquals(dsValue, dw.counts[i]); + } + + for (OverlapGroup row : dw) { + for (int i = 0; i < row.size(); i++) { + for (TestObject t : row.getBySample(i)) { + Assert.assertTrue(in.sets[i].contains(t.value)); + } + } + } + } + } + + private static long[] sum(long[] a, long[] b) { + if (a.length == 0) + return b; + if (b.length == 0) + return a; + + long[] r = new long[a.length]; + for (int i = 0; i < a.length; i++) { + r[i] = a[i] + b[i]; + } + return r; + } + + private static final class Dataset implements Iterable> { + final List> data; + final long[] counts; + final Set[] sets; + + public Dataset(Iterable> data) { + this(toList(data)); + } + + public Dataset(List> data) { + this.data = data; + this.counts = data.stream() + .map(row -> row.stream().mapToLong(l -> Math.round(l.stream().mapToDouble(e -> e.weight).sum())).toArray()) + .reduce(new long[0], OverlapDownsamplingPreprocessorTest::sum); + //noinspection unchecked + this.sets = new Set[counts.length]; + for (OverlapGroup row : data) { + for (int i = 0; i < row.size(); i++) { + Set s = sets[i]; + if (s == null) + s = sets[i] = new HashSet<>(); + for (TestObject t : row.getBySample(i)) { + s.add(t.value); + } + } + } + } + + @Override + public Iterator> iterator() { + return data.iterator(); + } + } + + private static Dataset rndDataset(RandomDataGenerator rng, int nSamples, int size) { + List> data = new ArrayList<>(); + int p = Math.max(2, nSamples / 4); + for (int i = 0; i < size; i++) { + List> row = new ArrayList<>(nSamples); + boolean added = false; + for (int j = 0; j < nSamples; j++) { + if (rng.nextInt(0, p) == 0) { + added = true; + ArrayList cell = new ArrayList<>(); + for (int k = 0; k < rng.nextInt(1, 2); k++) { + cell.add(new TestObject(rng.nextUniform(0, 1), rng.nextInt(1, 1000))); + } + row.add(cell); + } else { + row.add(new ArrayList<>()); + } + } + if (!added) { + --i; + continue; + } + data.add(new OverlapGroup<>(row)); + } + return new Dataset(data); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java new file mode 100644 index 000000000..3969982dc --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -0,0 +1,403 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.TestObjectWithPayload; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; +import com.milaboratory.mixcr.postanalysis.ui.OutputTable; +import com.milaboratory.mixcr.postanalysis.ui.OverlapSummary; +import com.milaboratory.util.sorting.MergeStrategy; +import com.milaboratory.util.sorting.SortingProperty; +import com.milaboratory.util.sorting.SortingPropertyRelation; +import com.milaboratory.util.sorting.SortingUtil; +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well512a; +import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; +import org.junit.Assert; +import org.junit.Test; + +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +/** + * + */ +public class OverlapCharacteristicTest { + @Test + @SuppressWarnings("unchecked") + public void testOverlapPort1() { + List initialSort = Arrays.asList( + new ElementOrdering(0, 2), + new ElementOrdering(2, 5), + new ElementOrdering(5, 8) + ); + + List targetGroupping = Arrays.asList( + new ElementOrdering(0, 4), + new ElementOrdering(4, 5) + ); + + MergeStrategy strategy = MergeStrategy.calculateStrategy(initialSort, targetGroupping); + + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + OverlapData ovp = new OverlapData(IntStream.range(0, 10) + .mapToObj(__ -> rndDataset(rng, rng.nextInt(11111, 22222), 10)) + .toArray(List[]::new), + targetGroupping); + + OutputPortCloseable>> join = strategy + .join(Arrays.stream(ovp.datasets) + .map(OverlapCharacteristicTest::asOutputPort) + .collect(Collectors.toList())); + + DescriptiveStatistics ds = new DescriptiveStatistics(); + for (List> row : CUtils.it(join)) { + Payload payload = null; + int nOverlapped = 0; + for (int index = 0; index < row.size(); index++) { + List cell = row.get(index); + if (!cell.isEmpty()) + ++nOverlapped; + for (Element element : cell) { + List expected = ovp.index + .getOrDefault(element.payload, Collections.emptyMap()) + .getOrDefault(index, Collections.emptyList()); + + Assert.assertTrue(expected.contains(element)); + + if (payload == null) + payload = element.payload; + else + Assert.assertEquals(0, ovp.pComparator.compare(payload, element.payload)); + } + } + if (nOverlapped > 1) + ds.addValue(nOverlapped); + else + ds.addValue(0); + } + System.out.println(ds); + } + + @Test + @SuppressWarnings("unchecked") + public void testOverlapCharacteristic1() { + List initialSort = Arrays.asList( + new ElementOrdering(0, 2), + new ElementOrdering(2, 5), + new ElementOrdering(5, 8) + ); + + List targetGroupping = Arrays.asList( + new ElementOrdering(0, 4), + new ElementOrdering(4, 5) + ); + + MergeStrategy strategy = MergeStrategy.calculateStrategy(initialSort, targetGroupping); + + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + int nDatasets = 10; + OverlapData ovp = new OverlapData(IntStream.range(0, nDatasets) + .mapToObj(__ -> rndDataset(rng, rng.nextInt(11111, 22222), 10)) + .toArray(List[]::new), + targetGroupping); + + OutputPortCloseable>> join = strategy + .join(Arrays.stream(ovp.datasets) + .map(OverlapCharacteristicTest::asOutputPort) + .collect(Collectors.toList())); + + List> chars = new ArrayList<>(); + for (int i = 0; i < ovp.datasets.length; i++) { + for (int j = i + 1; j < ovp.datasets.length; j++) { + chars.add(new OverlapCharacteristic<>("overlap_" + i + "_" + j, + e -> e.weight, new NoPreprocessing<>(), i, j)); + } + } + + CharacteristicGroup, OverlapGroup> chGroup = + new CharacteristicGroup<>("overlap", chars, Arrays.asList(new OverlapSummary<>())); + + PostanalysisRunner> runner = new PostanalysisRunner<>(); + runner.addCharacteristics(chGroup); + runner.setDatasets(new Iterable[]{CUtils.it(() -> { + List> t = join.take(); + if (t == null) return null; + return new OverlapGroup<>(t); + })}); + + PostanalysisResult paResult = runner + .run() + .setSampleIds(IntStream.range(0, nDatasets) + .mapToObj(String::valueOf).collect(Collectors.toList())); + + CharacteristicGroupResult> chGroupResult = paResult.getTable(chGroup); + Map outputs = chGroupResult.getOutputs(); + + double[][] expectedSharedElements = new double[nDatasets][nDatasets]; + double[][] expectedD = new double[nDatasets][nDatasets]; + double[][] + sumF1 = new double[nDatasets][nDatasets], + sumF2 = new double[nDatasets][nDatasets], + expectedF1 = new double[nDatasets][nDatasets]; + double[][] expectedF2 = new double[nDatasets][nDatasets]; + double[][] + meanF1 = new double[nDatasets][nDatasets], + meanF2 = new double[nDatasets][nDatasets], + sumDeltaSqF1 = new double[nDatasets][nDatasets], + sumDeltaSqF2 = new double[nDatasets][nDatasets], + expectedR = new double[nDatasets][nDatasets]; + + ovp.scanOverlap((i1, i2, w1, w2, f1, f2) -> { + ++expectedSharedElements[i1][i2]; + ++expectedD[i1][i2]; + sumF1[i1][i2] += f1; + sumF2[i1][i2] += f2; + expectedF2[i1][i2] += Math.sqrt(f1 * f2); + }); + + for (int i1 = 0; i1 < nDatasets; i1++) { + for (int i2 = 0; i2 < nDatasets; i2++) { + expectedD[i1][i2] /= ovp.diversity.getOrDefault(i1, 1); + expectedD[i1][i2] /= ovp.diversity.getOrDefault(i2, 1); + expectedF1[i1][i2] = Math.sqrt(sumF1[i1][i2] * sumF2[i1][i2]); + meanF1[i1][i2] = sumF1[i1][i2] / expectedSharedElements[i1][i2]; + meanF2[i1][i2] = sumF2[i1][i2] / expectedSharedElements[i1][i2]; + } + } + + ovp.scanOverlap((i1, i2, w1, w2, f1, f2) -> { + expectedR[i1][i2] += (f1 - meanF1[i1][i2]) * (f2 - meanF2[i1][i2]); + sumDeltaSqF1[i1][i2] += Math.pow(f1 - meanF1[i1][i2], 2); + sumDeltaSqF2[i1][i2] += Math.pow(f2 - meanF2[i1][i2], 2); + }); + + for (int i1 = 0; i1 < nDatasets; i1++) { + for (int i2 = 0; i2 < nDatasets; i2++) { + expectedR[i1][i2] /= Math.sqrt(sumDeltaSqF1[i1][i2] * sumDeltaSqF2[i1][i2]); + if (Double.isNaN(expectedR[i1][i2])) + expectedR[i1][i2] = 0.0; + } + } + + System.out.println(Arrays.stream(expectedSharedElements).map(Arrays::toString).collect(Collectors.joining("\n"))); + assert2dEquals(expectedSharedElements, outputs.get(OverlapType.SharedClonotypes).rows(0, 0)); + assert2dEquals(expectedD, outputs.get(OverlapType.D).rows(0, 0)); + assert2dEquals(expectedF1, outputs.get(OverlapType.F1).rows(0, 0)); + assert2dEquals(expectedF2, outputs.get(OverlapType.F2).rows(0, 0)); + assert2dEquals(expectedR, outputs.get(OverlapType.R_Intersection).rows(0, 0)); + } + + interface OverlapScanFunction { + void apply(int i1, int i2, double w1, double w2, double f1, double f2); + } + + private void assert2dEquals(double[][] expected, double[][] actual) { + assert2dEquals(expected, actual, 1e-10); + } + + private void assert2dEquals(double[][] expected, double[][] actual, double delta) { + Assert.assertEquals(expected.length, actual.length); + for (int i = 0; i < expected.length; i++) { + Assert.assertArrayEquals(expected[i], actual[i], delta); + } + } + + private static OutputPortCloseable asOutputPort(List l) { + OutputPort p = CUtils.asOutputPort(l); + return new OutputPortCloseable() { + @Override + public void close() {} + + @Override + public T take() { + return p.take(); + } + }; + } + + public static final class OverlapData { + final List[] datasets; + final List ordering; + final Comparator comparator; + final Comparator pComparator; + final TreeMap>> index; + final Map diversity; + final Map sumWeight; + + public OverlapData(List[] datasets, List ordering) { + this.datasets = datasets; + this.ordering = ordering; + this.comparator = SortingUtil.combine(ordering); + this.pComparator = SortingUtil.combine(ordering.stream().map(s -> s.inner).collect(Collectors.toList())); + this.index = new TreeMap<>(pComparator); + this.diversity = new HashMap<>(); + this.sumWeight = new HashMap<>(); + + for (List d : datasets) { + d.sort(comparator); + } + for (int index = 0; index < datasets.length; index++) { + List dataset = datasets[index]; + for (Element element : dataset) { + Map> m = this.index.computeIfAbsent(element.payload, payload -> new HashMap<>()); + m.computeIfAbsent(index, __ -> new ArrayList<>()).add(element); + } + } + + index.forEach((payload, row) -> row.forEach((key, value) -> { + int index = key; + int val = diversity.getOrDefault(index, 0); + diversity.put(index, val + 1); + double w = sumWeight.getOrDefault(index, 0.0); + sumWeight.put(index, w + value.stream().mapToDouble(v -> v.weight).sum()); + })); + } + + void scanOverlap(OverlapScanFunction scanner) { + index.forEach((payload, row) -> { + for (Map.Entry> e1 : row.entrySet()) { + int i1 = e1.getKey(); + double w1 = e1.getValue().stream().mapToDouble(v -> v.weight).sum(); + double f1 = w1 / sumWeight.getOrDefault(i1, 1.0); + for (Map.Entry> e2 : row.entrySet()) { + int i2 = e2.getKey(); + double w2 = e2.getValue().stream().mapToDouble(v -> v.weight).sum(); + double f2 = w2 / sumWeight.getOrDefault(i2, 1.0); + if (i1 != i2) { + scanner.apply(i1, i2, w1, w2, f1, f2); + } + } + } + }); + } + } + + public static List rndDataset(RandomDataGenerator rng, int size, int pSize) { + Element[] r = new Element[size]; + for (int i = 0; i < size; i++) { + r[i] = new Element( + rng.nextUniform(0, 1), + rng.nextUniform(0, 100), + rndPayload(rng, pSize)); + } + return Arrays.asList(r); + } + + public static Payload rndPayload(RandomDataGenerator rng, int pSize) { + int[] data = new int[pSize]; + for (int i = 0; i < pSize; i++) { + data[i] = rng.nextInt(0, pSize); + } + return new Payload(data); + } + + public static final class Payload implements Comparable { + final int[] data; + + public Payload(int[] data) { + this.data = data; + } + + @Override + public String toString() { + return Arrays.toString(data); + } + + @Override + public int compareTo(OverlapCharacteristicTest.Payload o) { + for (int i = 0; i < data.length; i++) { + int c; + if ((c = Integer.compare(data[i], o.data[i])) != 0) + return c; + } + return 0; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Payload payload = (Payload) o; + return Arrays.equals(data, payload.data); + } + + @Override + public int hashCode() { + return Arrays.hashCode(data); + } + } + + + private static final class PayloadSortingProperty implements SortingProperty { + public final int from, to; + + public PayloadSortingProperty(int from, int to) { + this.from = from; + this.to = to; + } + + @Override + public Payload get(Payload payload) { + return new Payload(Arrays.copyOfRange(payload.data, from, to)); + } + + @Override + public int compare(Payload o1, Payload o2) { + return get(o1).compareTo(get(o2)); + } + + @Override + public SortingPropertyRelation relationTo(SortingProperty other) { + PayloadSortingProperty oth = (PayloadSortingProperty) other; + + if (from == oth.from && to == oth.to) + return SortingPropertyRelation.Equal; + + if (oth.from <= this.from && this.to <= oth.to) { + return SortingPropertyRelation.Necessary; + } + + if (this.from <= oth.from && oth.to <= this.to) { + return SortingPropertyRelation.Sufficient; + } + + return SortingPropertyRelation.None; + } + } + + private static final class ElementOrdering implements SortingProperty { + final PayloadSortingProperty inner; + + public ElementOrdering(int from, int to) { + this.inner = new PayloadSortingProperty(from, to); + } + + @Override + public Object get(Element o) { + return inner.get(o.payload); + } + + @Override + public int compare(Element o1, Element o2) { + return inner.compare(o1.payload, o2.payload); + } + + @Override + public SortingPropertyRelation relationTo(SortingProperty other) { + return inner.relationTo(((ElementOrdering) other).inner); + } + } + + static final class Element extends TestObjectWithPayload { + public Element(double value, double weight, Payload payload) { + super(value, weight, payload); + } + } +} From 211c00b549f6d7f9a2b694e0f1f44cc4c0fdab6f Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 28 Jan 2021 00:28:47 +0300 Subject: [PATCH 086/282] MiLib upgrade. Fix for big clonotype sorting. --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 3fc69c9e7..b660b7981 100644 --- a/pom.xml +++ b/pom.xml @@ -40,7 +40,7 @@ UTF-8 - 1.14-e4a7ebd + 1.14-3993cf7 SNAPSHOT From 7a38661ac4f90d7ccd77d77e6ca483a083d11111 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Thu, 28 Jan 2021 02:13:50 +0300 Subject: [PATCH 087/282] MiLib upgrade. --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index b660b7981..ff6a309eb 100644 --- a/pom.xml +++ b/pom.xml @@ -40,7 +40,7 @@ UTF-8 - 1.14-3993cf7 + 1.14-dc00625 SNAPSHOT From 447c4812cf5fab9970cdae5e945f7ecdd6577415 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 4 Feb 2021 00:24:08 +0300 Subject: [PATCH 088/282] Added flag for disabling assertions for snapshot versions --- src/main/java/com/milaboratory/mixcr/cli/Main.java | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 37c8dc368..94bcc2dc6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -94,6 +94,10 @@ protected List handle(ParseResult parseResult) throws CommandLine.Execut } } + private static boolean assertionsDisabled() { + return System.getProperty("noAssertions") != null; + } + public static CommandLine mkCmd() { System.setProperty("picocli.usage.width", "100"); @@ -101,11 +105,10 @@ public static CommandLine mkCmd() { String command = System.getProperty("mixcr.command", "java -jar mixcr.jar"); if (!initialized) { - if (System.getProperty("jdk.module.main") == null) // hack fixme - // Checking whether we are running a snapshot version - if (VersionInfo.getVersionInfoForArtifact("mixcr").getVersion().contains("SNAPSHOT")) - // If so, enable asserts - ClassLoader.getSystemClassLoader().setDefaultAssertionStatus(true); + // Checking whether we are running a snapshot version + if (!assertionsDisabled() && VersionInfo.getVersionInfoForArtifact("mixcr").getVersion().contains("SNAPSHOT")) + // If so, enable asserts + ClassLoader.getSystemClassLoader().setDefaultAssertionStatus(true); TempFileManager.setPrefix("mixcr_"); From 63f80a47c347ec32245f6fb3c91a0cc2bf5a4fd7 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 4 Feb 2021 00:24:35 +0300 Subject: [PATCH 089/282] minor typo fix in cli in analyze code --- src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index 52b8bb9e5..153eca01d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -638,7 +638,7 @@ public String fNameForParAlignments(int round) { return outputNamePattern() + ".rescued_" + round + ".vdjca"; } - public String fNameForExtenedAlignments() { + public String fNameForExtendedAlignments() { return outputNamePattern() + ".extended.vdjca"; } @@ -686,7 +686,7 @@ public void run0() { // --- Running alignments extender if (!doNotExtendAlignments) { - String fileWithExtAlignments = fNameForExtenedAlignments(); + String fileWithExtAlignments = fNameForExtendedAlignments(); mkExtend(fileWithAlignments, fileWithExtAlignments).run(); fileWithAlignments = fileWithExtAlignments; } From 85746d189ca939556025a3175797aa0684075531 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 9 Feb 2021 01:59:42 +0300 Subject: [PATCH 090/282] Added descriptions to SetPreprocessors --- .../mixcr/postanalysis/SetPreprocessor.java | 5 +- .../downsampling/DownsampleValueChooser.java | 19 +++++++ .../DownsamplingPreprocessor.java | 8 +++ .../OverlapDownsamplingPreprocessor.java | 8 +++ .../preproc/ElementPredicate.java | 24 +++++++++ .../preproc/FilterPreprocessor.java | 10 ++++ .../postanalysis/preproc/NoPreprocessing.java | 5 ++ .../preproc/PreprocessorChain.java | 10 ++++ .../preproc/SampleFilterPreprocessor.java | 49 ------------------- 9 files changed, 88 insertions(+), 50 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index 7e6a56075..281591080 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -23,12 +23,15 @@ @JsonSubTypes.Type(value = ClonesOverlapDownsamplingPreprocessor.class, name = "overlapDownsample"), @JsonSubTypes.Type(value = PreprocessorChain.class, name = "chain"), @JsonSubTypes.Type(value = FilterPreprocessor.class, name = "filter"), - @JsonSubTypes.Type(value = SampleFilterPreprocessor.class, name = "filterInvidually") }) @JsonIgnoreProperties(ignoreUnknown = true) public interface SetPreprocessor { Function, Iterable> setup(Iterable[] sets); + default String[] description() { + return new String[0]; + } + default SetPreprocessor filter(boolean before, ElementPredicate... predicates) { FilterPreprocessor filter = new FilterPreprocessor<>(predicates); if (this instanceof PreprocessorChain) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java index 56d9e6c71..01f3c1e52 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java @@ -26,6 +26,10 @@ public interface DownsampleValueChooser { long compute(long[] totalCounts); + default String description() { + return ""; + } + class Fixed implements DownsampleValueChooser { public long value; @@ -35,6 +39,11 @@ public Fixed(long value) { this.value = value; } + @Override + public String description() { + return "Downsample to a fixed count = " + value; + } + @Override public long compute(long[] totalCounts) { return value; @@ -55,6 +64,11 @@ public int hashCode() { } class Minimal implements DownsampleValueChooser { + @Override + public String description() { + return "Downsample to the minimal dataset"; + } + @Override public long compute(long[] totalCounts) { return LongStream.of(totalCounts).min().orElse(0); @@ -86,6 +100,11 @@ public Auto(double quantile, double scale, long threshold) { this.threshold = threshold; } + @Override + public String description() { + return String.format("Downsample to the min(%s * percentile(%s), %s))", scale, quantile, threshold); + } + @Override public long compute(long... totalCounts) { long q = (long) (new Percentile(quantile).evaluate(Arrays.stream(totalCounts).mapToDouble(l -> l).toArray()) * scale); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index c51367894..d96dc305e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -36,6 +36,14 @@ public DownsamplingPreprocessor(ToLongFunction getCount, BiFunction, Iterable> setup(Iterable[] sets) { long[] totals = new long[sets.length]; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java index 6497156d1..ef51c2790 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java @@ -62,6 +62,14 @@ public OverlapDownsamplingPreprocessor(ToLongFunction getCount, BiFunction>, Iterable>> setup(Iterable>[] sets) { return set -> { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java index 6bd122d27..69efbe1d7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java @@ -21,8 +21,17 @@ @JsonSubTypes.Type(value = ElementPredicate.OverlapIncludeChains.class, name = "overlapIncludesChains") }) public interface ElementPredicate extends Predicate { + default String description() { + return ""; + } + @JsonAutoDetect final class NoOutOfFrames implements ElementPredicate { + @Override + public String description() { + return "Exclude out-of-frames"; + } + @Override public boolean test(Clone clone) { if (clone.isOutOfFrame(GeneFeature.CDR3)) @@ -45,6 +54,11 @@ public int hashCode() { @JsonAutoDetect final class NoStops implements ElementPredicate { + @Override + public String description() { + return "Exclude stop-codons"; + } + @Override public boolean test(Clone clone) { for (GeneFeature gf : clone.getParentCloneSet().getAssemblingFeatures()) { @@ -76,6 +90,11 @@ public IncludeChains(@JsonProperty("chains") Chains chains) { this.chains = chains; } + @Override + public String description() { + return "Select chains: " + chains; + } + @Override public boolean test(Clone object) { for (GeneType gt : GeneType.VJC_REFERENCE) @@ -108,6 +127,11 @@ public OverlapIncludeChains(@JsonProperty("chains") Chains chains) { this.chains = chains; } + @Override + public String description() { + return "Select chains: " + chains; + } + @Override public boolean test(OverlapGroup object) { for (GeneType gt : GeneType.VJC_REFERENCE) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index 47a39d915..4af7d10c8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -23,6 +23,16 @@ public FilterPreprocessor(@JsonProperty("predicates") List> this.predicates = predicates; } + @Override + public String[] description() { + return predicates.stream() + .map(ElementPredicate::description) + .filter(Objects::nonNull) + .filter(s -> !s.isEmpty()) + .map(f -> "Filter: " + f) + .toArray(String[]::new); + } + public FilterPreprocessor(ElementPredicate... predicates) { this(Arrays.asList(predicates)); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java index 48f63e2d7..f1d1b13e4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java @@ -10,6 +10,11 @@ public class NoPreprocessing implements SetPreprocessor { public static final NoPreprocessing INSTANCE = new NoPreprocessing<>(); + @Override + public String[] description() { + return new String[0]; + } + @Override public Function, Iterable> setup(Iterable[] sets) { return set -> set; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index 5c1b5beae..0a66738f8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -23,6 +23,16 @@ public PreprocessorChain(SetPreprocessor... chain) { this(Arrays.asList(chain)); } + @Override + public String[] description() { + return chain.stream() + .map(SetPreprocessor::description) + .filter(Objects::nonNull) + .flatMap(Arrays::stream) + .filter(s -> !s.isEmpty()) + .toArray(String[]::new); + } + @Override public Function, Iterable> setup(Iterable[] sets) { Iterable[] proc = sets; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java deleted file mode 100644 index 403e7e36e..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SampleFilterPreprocessor.java +++ /dev/null @@ -1,49 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.preproc; - -import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonIgnore; -import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; - -import java.util.Map; -import java.util.Objects; -import java.util.function.Function; - -/** - * - */ -public class SampleFilterPreprocessor implements SetPreprocessor { - @JsonProperty("sampleFilters") - public final Map> sampleFilters; - - @JsonCreator - public SampleFilterPreprocessor(@JsonProperty("sampleFilters") Map> sampleFilters) { - this.sampleFilters = sampleFilters; - } - - @JsonIgnore - private Map, String> sampleNames; - - public void setSampleNames(Map, String> sampleNames) { - this.sampleNames = sampleNames; - } - - @Override - public Function, Iterable> setup(Iterable[] sets) { - return set -> sampleFilters.get(sampleNames.get(set)).setup(null).apply(set); - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - SampleFilterPreprocessor that = (SampleFilterPreprocessor) o; - return Objects.equals(sampleFilters, that.sampleFilters) && - Objects.equals(sampleNames, that.sampleNames); - } - - @Override - public int hashCode() { - return Objects.hash(sampleFilters, sampleNames); - } -} From 4bb824d3dfe453ca7fd6da8ddfdd8b94568e9365 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 9 Feb 2021 02:12:54 +0300 Subject: [PATCH 091/282] Move from iterable to `Dataset` with OP abstraction in postanalysis (#16) --- .../mixcr/basictypes/ClnAReader.java | 10 ++- .../mixcr/basictypes/CloneSetIO.java | 9 ++- .../mixcr/basictypes/CloneSetOverlap.java | 5 +- .../mixcr/postanalysis/Aggregator.java | 2 +- .../mixcr/postanalysis/Characteristic.java | 10 +-- .../mixcr/postanalysis/Dataset.java | 33 ++++++++ .../mixcr/postanalysis/MetricValue.java | 5 +- .../postanalysis/PostanalysisResult.java | 81 ++++++++++++------- .../postanalysis/PostanalysisRunner.java | 52 ++++++------ .../mixcr/postanalysis/SetPreprocessor.java | 2 +- .../additive/AdditiveCharacteristic.java | 2 +- .../diversity/DiversityCharacteristic.java | 7 +- .../DownsamplingPreprocessor.java | 79 ++++++++++++------ .../downsampling/DownsamplingUtil.java | 24 +++--- .../OverlapDownsamplingPreprocessor.java | 80 ++++++++++++------ .../AdditiveOverlapCharacteristic.java | 28 ------- .../overlap/OverlapAggregator.java | 21 ++--- .../overlap/OverlapCharacteristic.java | 13 +-- .../postanalysis/overlap/OverlapDataset.java | 21 +++++ .../overlap/OverlapGroupAdditiveMetric.java | 10 --- .../overlap/OverlapGroupKeyFunction.java | 10 --- .../overlap/OverlapGroupWeightFunction.java | 10 --- .../postanalysis/overlap/OverlapIterable.java | 33 -------- .../postanalysis/overlap/OverlapKey.java | 24 +++--- .../postanalysis/overlap/OverlapUtil.java | 18 ++--- .../preproc/FilterPreprocessor.java | 6 +- .../postanalysis/preproc/FilteredDataset.java | 29 +++++++ .../preproc/FilteredOutputPortCloseable.java | 34 ++++++++ .../postanalysis/preproc/NoPreprocessing.java | 4 +- .../preproc/PreprocessorChain.java | 12 +-- .../SpectratypeCharacteristic.java | 7 +- .../CharacteristicGroupOutputExtractor.java | 3 +- .../ui/CharacteristicGroupResult.java | 35 ++++++-- .../ui/CharacteristicGroupResultBuilder.java | 31 +++---- .../ui/CharacteristicGroupResultCell.java | 16 ++-- .../mixcr/postanalysis/ui/ClonesIterable.java | 57 ------------- .../postanalysis/ui/ClonotypeDataset.java | 55 +++++++++++++ .../mixcr/postanalysis/ui/Coordinates.java | 7 +- .../mixcr/postanalysis/ui/GroupMelt.java | 59 +------------- .../mixcr/postanalysis/ui/OutputTable.java | 72 +++++++++-------- .../postanalysis/ui/OutputTableBuilder.java | 37 +++------ .../postanalysis/ui/OutputTableCell.java | 23 ++---- .../postanalysis/ui/OutputTableExtractor.java | 9 +-- .../mixcr/postanalysis/ui/OverlapSummary.java | 5 +- .../postanalysis/ui/PostanalysisSchema.java | 6 +- .../mixcr/util/FilteredIterable.java | 22 ----- .../mixcr/util/FilteredIterator.java | 41 ---------- .../mixcr/postanalysis/TestDataset.java | 52 ++++++++++++ .../mixcr/postanalysis/TestObject.java | 16 ++-- .../additive/AdditiveCharacteristicsTest.java | 15 ++-- .../DiversityCharacteristicTest.java | 15 ++-- .../DownsamplingPreprocessorTest.java | 37 ++++----- .../OverlapDownsamplingPreprocessorTest.java | 36 ++++----- .../overlap/OverlapCharacteristicTest.java | 71 +++++++++------- .../overlap/OverlapIntegrationTest.java | 34 ++++---- .../ui/PostanalysisSchemaIntegrationTest.java | 42 +++++----- 56 files changed, 762 insertions(+), 715 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java delete mode 100644 src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java delete mode 100644 src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index afdb0f9d7..fc4963075 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -38,6 +38,7 @@ import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.blocks.*; import com.milaboratory.util.CanReportProgress; +import com.milaboratory.util.LambdaSemaphore; import gnu.trove.map.hash.TIntIntHashMap; import io.repseq.core.GeneFeature; import io.repseq.core.VDJCGene; @@ -68,8 +69,7 @@ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implement /** First record always zero */ final long[] counts; /** - * cloneId -> index in index - * e.g. alignments for clone with id0 starts from position index[cloneMapping.get(id0)] + * cloneId -> index in index e.g. alignments for clone with id0 starts from position index[cloneMapping.get(id0)] */ final TIntIntHashMap cloneIdIndex; final long totalAlignmentsCount; @@ -94,7 +94,11 @@ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implement final String versionInfo; public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, int concurrency) throws IOException { - this.input = new PrimitivIHybrid(path, concurrency); + this(path, libraryRegistry, new LambdaSemaphore(concurrency)); + } + + public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, LambdaSemaphore concurrencyLimiter) throws IOException { + this.input = new PrimitivIHybrid(path, concurrencyLimiter); this.libraryRegistry = libraryRegistry; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java index 78865c28e..edf2bbf7d 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java @@ -29,6 +29,7 @@ */ package com.milaboratory.mixcr.basictypes; +import com.milaboratory.util.LambdaSemaphore; import io.repseq.core.VDJCLibraryRegistry; import java.io.File; @@ -66,11 +67,17 @@ public static CloneSet read(File file, VDJCLibraryRegistry libraryRegistry) thro } } + public static final int DEFAULT_READER_CONCURRENCY_LIMIT = 1; + public static CloneReader mkReader(Path file, VDJCLibraryRegistry libraryRegistry) throws IOException { - return mkReader(file, libraryRegistry, 1); + return mkReader(file, libraryRegistry, DEFAULT_READER_CONCURRENCY_LIMIT); } public static CloneReader mkReader(Path file, VDJCLibraryRegistry libraryRegistry, int concurrency) throws IOException { + return mkReader(file, libraryRegistry, new LambdaSemaphore(concurrency)); + } + + public static CloneReader mkReader(Path file, VDJCLibraryRegistry libraryRegistry, LambdaSemaphore concurrency) throws IOException { switch (Objects.requireNonNull(fileInfoExtractorInstance.getFileInfo(file.toFile())).fileType) { case MAGIC_CLNA: return new ClnAReader(file, libraryRegistry, concurrency); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java index f99e65aaf..ef3fc1f35 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java @@ -36,10 +36,9 @@ import java.util.stream.Collectors; public final class CloneSetOverlap { - private CloneSetOverlap() { - } + private CloneSetOverlap() {} - public static final OutputPortCloseable>> overlap( + public static OutputPortCloseable>> overlap( List> by, List readers) { VDJCSProperties.CloneOrdering ordering = readers.get(0).ordering(); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java index bd993d390..4ff9cafc0 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java @@ -4,7 +4,7 @@ import java.util.Arrays; public interface Aggregator { - /** apply for each clone */ + /** apply for each dataset element */ void consume(T obj); /** get the result */ diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java index 4331216f9..a1d6a7cd1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java @@ -3,7 +3,6 @@ import com.fasterxml.jackson.annotation.*; import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristic; import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; -import com.milaboratory.mixcr.postanalysis.overlap.AdditiveOverlapCharacteristic; import com.milaboratory.mixcr.postanalysis.overlap.OverlapCharacteristic; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; @@ -17,7 +16,6 @@ @JsonSubTypes.Type(value = AdditiveCharacteristic.class, name = "individual"), @JsonSubTypes.Type(value = DiversityCharacteristic.class, name = "diversity"), @JsonSubTypes.Type(value = OverlapCharacteristic.class, name = "overlap"), - @JsonSubTypes.Type(value = AdditiveOverlapCharacteristic.class, name = "overlapIndividual"), @JsonSubTypes.Type(value = SpectratypeCharacteristic.class, name = "geneFeatureSpectratype"), @JsonSubTypes.Type(value = Characteristic.CharacteristicWrapper.class, name = "characteristicWrapper") }) @@ -27,6 +25,7 @@ isGetterVisibility = JsonAutoDetect.Visibility.NONE ) public abstract class Characteristic { + /** Unique characteristic name */ @JsonProperty("name") public final String name; @JsonProperty("preproc") @@ -40,7 +39,8 @@ public Characteristic(String name, SetPreprocessor preprocessor, WeightFuncti this.weight = weight; } - protected abstract Aggregator createAggregator(); + /** Create aggregator for further processing of a given dataset */ + protected abstract Aggregator createAggregator(Dataset dataset); /** override name & preproc */ public Characteristic override(String nameOverride, SetPreprocessor preprocOverride) { @@ -80,8 +80,8 @@ public Characteristic override(String nameOverride, SetPreprocessor pre } @Override - protected Aggregator createAggregator() { - return inner.createAggregator(); + protected Aggregator createAggregator(Dataset dataset) { + return inner.createAggregator(dataset); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java new file mode 100644 index 000000000..a56e0e3b9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java @@ -0,0 +1,33 @@ +package com.milaboratory.mixcr.postanalysis; + +import cc.redberry.pipe.OutputPortCloseable; + +import java.util.UUID; +import java.util.function.Supplier; + +/** + * + */ +public interface Dataset { + /** Unique dataset identifier */ + String id(); + + /** Closeable port of dataset elements */ + OutputPortCloseable mkElementsPort(); + + /** Uses random UUID as dataset id */ + static Dataset fromSupplier(Supplier> supp) { + final String id = UUID.randomUUID().toString(); + return new Dataset() { + @Override + public String id() { + return id; + } + + @Override + public OutputPortCloseable mkElementsPort() { + return supp.get(); + } + }; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java b/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java index ad73a20f2..91d74b700 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java @@ -51,9 +51,8 @@ public MetricValue square() { public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; - MetricValue tuple = (MetricValue) o; - return Double.compare(tuple.value, value) == 0 && - Objects.equals(key, tuple.key); + MetricValue that = (MetricValue) o; + return Double.compare(that.value, value) == 0 && Objects.equals(key, that.key); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index e1e1f415f..bc0d0286e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -3,11 +3,13 @@ import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonValue; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResultBuilder; import java.util.*; +import java.util.stream.Collectors; /** * @@ -18,43 +20,45 @@ isGetterVisibility = JsonAutoDetect.Visibility.NONE ) public class PostanalysisResult { + /** All dataset ids that were analyzed */ + @JsonProperty("datasetIds") + private final Set datasetIds; + /** Characteristic Id -> characteristic data */ @JsonProperty("data") private final Map data; - @JsonProperty("sampleIds") - private final List sampleIds; @JsonCreator - public PostanalysisResult(@JsonProperty("data") Map data, - @JsonProperty("sampleIds") List sampleIds) { + public PostanalysisResult(@JsonProperty("datasetIds") Set datasetIds, + @JsonProperty("data") Map data) { + this.datasetIds = datasetIds; this.data = data; - this.sampleIds = sampleIds; } - public PostanalysisResult setSampleIds(List sampleIds) { - return new PostanalysisResult(data, sampleIds); - } - - public static PostanalysisResult create(Map, MetricValue[][]> data) { + static PostanalysisResult create(Set datasetIds, + Map, Map[]>> data) { Map d = new HashMap<>(); - for (Map.Entry, MetricValue[][]> e : data.entrySet()) + for (Map.Entry, Map[]>> e : data.entrySet()) d.put(e.getKey().name, new Array2d(e.getValue())); - return new PostanalysisResult(d, null); + return new PostanalysisResult(datasetIds, d); } + /** cached results for char groups */ private final Map, CharacteristicGroupResult> cached = new IdentityHashMap<>(); - @SuppressWarnings("unchecked") - public synchronized CharacteristicGroupResult getTable(CharacteristicGroup group) { + /** project result on a specific char group */ + @SuppressWarnings({"unchecked"}) + public CharacteristicGroupResult getTable(CharacteristicGroup group) { CharacteristicGroupResult r = cached.get(group); if (r != null) return (CharacteristicGroupResult) r; - CharacteristicGroupResultBuilder builder = new CharacteristicGroupResultBuilder<>(group, sampleIds); + CharacteristicGroupResultBuilder builder = new CharacteristicGroupResultBuilder<>(group, datasetIds); for (Characteristic ch : group.characteristics) { - MetricValue[][] values = (MetricValue[][]) data.get(ch.name).data; - for (int sampleIndex = 0; sampleIndex < values.length; sampleIndex++) - for (MetricValue val : values[sampleIndex]) - builder.add(val.key, sampleIndex, val.value); + Map values = data.get(ch.name).data; + for (Map.Entry e : values.entrySet()) { + for (MetricValue val : (MetricValue[]) e.getValue().data) + builder.add(val.key, e.getKey(), val.value); + } } CharacteristicGroupResult res = builder.build(); cached.put(group, res); @@ -66,12 +70,12 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; PostanalysisResult that = (PostanalysisResult) o; - return Objects.equals(data, that.data); + return Objects.equals(datasetIds, that.datasetIds) && Objects.equals(data, that.data) && Objects.equals(cached, that.cached); } @Override public int hashCode() { - return Objects.hash(data); + return Objects.hash(datasetIds, data, cached); } @Override @@ -85,12 +89,13 @@ public String toString() { isGetterVisibility = JsonAutoDetect.Visibility.NONE ) private static final class Array2d { + /** Dataset Id -> Metric values */ @JsonProperty("2darray") - private final MetricValue[][] data; + private final Map data; @JsonCreator - Array2d(@JsonProperty("2darray") MetricValue[][] data) { - this.data = data; + Array2d(@JsonProperty("2darray") Map[]> data) { + this.data = data.entrySet().stream().collect(Collectors.toMap(Map.Entry::getKey, e -> new MetricsArray(e.getValue()))); } @Override @@ -98,17 +103,39 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; Array2d array2d = (Array2d) o; - return Arrays.deepEquals(data, array2d.data); + return Objects.equals(data, array2d.data); } @Override public int hashCode() { - return Arrays.hashCode(data); + return Objects.hash(data); } @Override public String toString() { - return Arrays.deepToString(data); + return data.toString(); + } + } + + private static final class MetricsArray { + @JsonValue + private final MetricValue[] data; + + public MetricsArray(MetricValue[] data) { + this.data = data; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + MetricsArray that = (MetricsArray) o; + return Arrays.equals(data, that.data); + } + + @Override + public int hashCode() { + return Arrays.hashCode(data); } } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index 6d82c7b0d..501688b3b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -1,5 +1,7 @@ package com.milaboratory.mixcr.postanalysis; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.util.CanReportProgressAndStage; @@ -12,7 +14,6 @@ */ public class PostanalysisRunner implements CanReportProgressAndStage { private final List> characteristics = new ArrayList<>(); - private Iterable[] datasets; public void addCharacteristics(CharacteristicGroup... groups) { for (CharacteristicGroup g : groups) { @@ -28,16 +29,6 @@ public void addCharacteristics(List> chs) { characteristics.addAll(chs); } - public void setDatasets(Iterable[] sets) { - this.datasets = sets; - } - - public void setDatasets(List> sets) { - setDatasets(sets.toArray(new Iterable[0])); - } - - private Map, MetricValue[][]> result; - private volatile String stage; private volatile double progress = 0.0; private volatile boolean isFinished = false; @@ -57,8 +48,12 @@ public boolean isFinished() { return isFinished; } - /** returns matrix[sample][metric_values] */ - public PostanalysisResult run() { + @SuppressWarnings("unchecked") + public PostanalysisResult run(List> datasets) { + return run(datasets.toArray(new Dataset[0])); + } + + public PostanalysisResult run(Dataset... datasets) { stage = "Preparing"; progress = 0.0; isFinished = false; @@ -67,34 +62,39 @@ public PostanalysisResult run() { characteristics.stream() .collect(Collectors.groupingBy(c -> c.preprocessor)); - Map, MetricValue[][]> result = new IdentityHashMap<>(); + Map, Map[]>> result = new IdentityHashMap<>(); for (Map.Entry, List>> e : characteristicsByPrep.entrySet()) { - Function, Iterable> prepFunction = e.getKey().setup(datasets); - for (int setIndex = 0; setIndex < datasets.length; setIndex++) { - Iterable set = datasets[setIndex]; + Function, Dataset> prepFunction = e.getKey().setup(datasets); + for (Dataset dataset : datasets) { List> characteristics = e.getValue(); List> aggregators = characteristics.stream() - .map(Characteristic::createAggregator) + .map(c -> c.createAggregator(dataset)) .collect(Collectors.toList()); - for (T o : prepFunction.apply(set)) - for (Aggregator agg : aggregators) - agg.consume(o); + try (OutputPortCloseable port = prepFunction.apply(dataset).mkElementsPort()) { + for (T o : CUtils.it(port)) + for (Aggregator agg : aggregators) + agg.consume(o); + } for (int charIndex = 0; charIndex < characteristics.size(); charIndex++) { @SuppressWarnings("unchecked") - MetricValue[][] charValues = result.computeIfAbsent( + Map[]> charValues = result.computeIfAbsent( characteristics.get(charIndex), - __ -> new MetricValue[datasets.length][]); - charValues[setIndex] = aggregators.get(charIndex).result(); + __ -> new HashMap<>()); + if (charValues.containsKey(dataset.id())) + throw new IllegalArgumentException("Dataset occurred twice."); + charValues.put(dataset.id(), aggregators.get(charIndex).result()); } } } isFinished = true; - this.result = result; - return PostanalysisResult.create(result); + Set datasetIds = Arrays.stream(datasets) + .map(Dataset::id) + .collect(Collectors.toCollection(LinkedHashSet::new)); + return PostanalysisResult.create(datasetIds, result); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index 281591080..d3af897d6 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -26,7 +26,7 @@ }) @JsonIgnoreProperties(ignoreUnknown = true) public interface SetPreprocessor { - Function, Iterable> setup(Iterable[] sets); + Function, Dataset> setup(Dataset[] sets); default String[] description() { return new String[0]; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java index bd6e63ed3..788c0bd51 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java @@ -50,7 +50,7 @@ private Normalization meanNorm() { } @Override - protected Aggregator createAggregator() { + protected Aggregator createAggregator(Dataset dataset) { switch (aggType) { case Sum: return new AdditiveAggregator<>(keyFunction, metric, weight, Normalization.None); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java index db7ce0f97..9bcdb3228 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java @@ -3,10 +3,7 @@ import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.Aggregator; -import com.milaboratory.mixcr.postanalysis.Characteristic; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.WeightFunction; +import com.milaboratory.mixcr.postanalysis.*; /** * @@ -25,7 +22,7 @@ public DiversityCharacteristic(@JsonProperty("name") String name, } @Override - protected Aggregator createAggregator() { + protected Aggregator createAggregator(Dataset dataset) { return new DiversityAggregator<>(c -> Math.round(weight.weight(c))); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index d96dc305e..434efff66 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -1,15 +1,17 @@ package com.milaboratory.mixcr.postanalysis.downsampling; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.util.FilteredIterable; +import com.milaboratory.mixcr.postanalysis.preproc.FilteredDataset; import gnu.trove.list.array.TLongArrayList; import org.apache.commons.math3.random.RandomGenerator; import org.apache.commons.math3.random.Well19937c; import java.util.HashSet; -import java.util.Iterator; import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; import java.util.function.BiFunction; @@ -36,7 +38,6 @@ public DownsamplingPreprocessor(ToLongFunction getCount, BiFunction, Iterable> setup(Iterable[] sets) { + public Function, Dataset> setup(Dataset[] sets) { long[] totals = new long[sets.length]; for (int i = 0; i < sets.length; i++) totals[i] = total(getCount, sets[i]); long downsampling = downsampleValueChooser.compute(totals); - Set> empty = new HashSet<>(); + Set> empty = new HashSet<>(); for (int i = 0; i < totals.length; ++i) if (totals[i] < downsampling) empty.add(sets[i]); @@ -59,40 +60,66 @@ public Function, Iterable> setup(Iterable[] sets) { return set -> { if (empty.contains(set)) //noinspection unchecked - return emptyIterable; + return EMPTY_DATASET_SUPPLIER; // compute counts long total = 0; TLongArrayList countsList = new TLongArrayList(); - for (T t : set) { - long c = getCount.applyAsLong(t); - countsList.add(c); - total += c; + try (OutputPortCloseable port = set.mkElementsPort()) { + for (T t : CUtils.it(port)) { + long c = getCount.applyAsLong(t); + countsList.add(c); + total += c; + } } if (total < downsampling) //noinspection unchecked - return emptyIterable; + return EMPTY_DATASET_SUPPLIER; RandomGenerator rnd = new Well19937c(seed); long[] countsDownsampled = downsample_mvhg(countsList.toArray(), downsampling, rnd); - return new FilteredIterable<>( - () -> new Iterator() { - final Iterator inner = set.iterator(); - final AtomicInteger index = new AtomicInteger(0); - - @Override - public boolean hasNext() { - return inner.hasNext(); - } - - @Override - public T next() { - return setCount.apply(inner.next(), countsDownsampled[index.getAndIncrement()]); - } - }, + return new FilteredDataset<>( + new DownsampledDataset<>(set, countsDownsampled, setCount), t -> getCount.applyAsLong(t) != 0); }; } + + private static final class DownsampledDataset implements Dataset { + final Dataset inner; + final long[] countsDownsampled; + final BiFunction setCount; + + public DownsampledDataset(Dataset inner, long[] countsDownsampled, BiFunction setCount) { + this.inner = inner; + this.countsDownsampled = countsDownsampled; + this.setCount = setCount; + } + + @Override + public String id() { + return inner.id(); + } + + @Override + public OutputPortCloseable mkElementsPort() { + final OutputPortCloseable inner = this.inner.mkElementsPort(); + final AtomicInteger index = new AtomicInteger(0); + return new OutputPortCloseable() { + @Override + public void close() { + inner.close(); + } + + @Override + public T take() { + T t = inner.take(); + if (t == null) + return null; + return setCount.apply(t, countsDownsampled[index.getAndIncrement()]); + } + }; + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index 1c3a812d2..1a1ac5c72 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -29,9 +29,11 @@ */ package com.milaboratory.mixcr.postanalysis.downsampling; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.postanalysis.Dataset; import org.apache.commons.math3.random.RandomGenerator; -import java.util.Iterator; import java.util.function.ToLongFunction; import java.util.stream.LongStream; @@ -40,26 +42,26 @@ private DownsamplingUtil() { } @SuppressWarnings("rawtypes") - public static final Iterator emptyIterator = new Iterator() { + public static final OutputPortCloseable emptyOP = new OutputPortCloseable() { @Override - public boolean hasNext() { - return false; - } + public void close() { } @Override - public Object next() { + public Object take() { return null; } }; @SuppressWarnings("rawtypes") - public static final Iterable emptyIterable = () -> emptyIterator; + public static final Dataset EMPTY_DATASET_SUPPLIER = Dataset.fromSupplier(() -> emptyOP); - public static long total(ToLongFunction getCount, Iterable set) { + public static long total(ToLongFunction getCount, Dataset set) { long total = 0; - for (T t : set) - total += getCount.applyAsLong(t); - return total; + try (OutputPortCloseable port = set.mkElementsPort()) { + for (T t : CUtils.it(port)) + total += getCount.applyAsLong(t); + return total; + } } public static long[] downsample_mvhg(long[] counts, long downSampleSize, RandomGenerator rnd) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java index ef51c2790..a387e6560 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java @@ -29,17 +29,19 @@ */ package com.milaboratory.mixcr.postanalysis.downsampling; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; -import com.milaboratory.mixcr.util.FilteredIterable; +import com.milaboratory.mixcr.postanalysis.preproc.FilteredDataset; import gnu.trove.list.array.TLongArrayList; import org.apache.commons.math3.random.RandomGenerator; import org.apache.commons.math3.random.Well19937c; import java.util.ArrayList; import java.util.Arrays; -import java.util.Iterator; import java.util.List; import java.util.concurrent.atomic.AtomicIntegerArray; import java.util.function.BiFunction; @@ -62,7 +64,6 @@ public OverlapDownsamplingPreprocessor(ToLongFunction getCount, BiFunction>, Iterable>> setup(Iterable>[] sets) { + public Function>, Dataset>> setup(Dataset>[] sets) { return set -> { TLongArrayList[] counts = null; - for (OverlapGroup grp : set) { - if (counts == null) { - counts = new TLongArrayList[grp.size()]; - for (int i = 0; i < grp.size(); i++) - counts[i] = new TLongArrayList(); - } + try (OutputPortCloseable> port = set.mkElementsPort()) { + for (OverlapGroup grp : CUtils.it(port)) { + if (counts == null) { + counts = new TLongArrayList[grp.size()]; + for (int i = 0; i < grp.size(); i++) + counts[i] = new TLongArrayList(); + } - assert counts.length == grp.size(); + assert counts.length == grp.size(); - for (int i = 0; i < counts.length; i++) - for (T t : grp.getBySample(i)) - counts[i].add(getCount.applyAsLong(t)); + for (int i = 0; i < counts.length; i++) + for (T t : grp.getBySample(i)) + counts[i].add(getCount.applyAsLong(t)); + } } - if (counts == null) // empty set return set; @@ -103,18 +105,46 @@ public Function>, Iterable>> setup(Iter newCounts[i] = DownsamplingUtil.downsample_mvhg(counts[i].toArray(), downsample, rnd); } - return new FilteredIterable<>(() -> new Iterator>() { - final Iterator> innerIterator = set.iterator(); - final AtomicIntegerArray indices = new AtomicIntegerArray(totals.length); + return new FilteredDataset<>( + new DownsampledDataset<>(set, newCounts, getCount, setCount), + OverlapGroup::notEmpty); + }; + } + + private static final class DownsampledDataset implements Dataset> { + final Dataset> inner; + final long[][] countsDownsampled; + final ToLongFunction getCount; + final BiFunction setCount; + + public DownsampledDataset(Dataset> inner, long[][] countsDownsampled, ToLongFunction getCount, BiFunction setCount) { + this.inner = inner; + this.countsDownsampled = countsDownsampled; + this.getCount = getCount; + this.setCount = setCount; + } + @Override + public String id() { + return inner.id(); + } + + @Override + public OutputPortCloseable> mkElementsPort() { + final OutputPortCloseable> inner = this.inner.mkElementsPort(); + final AtomicIntegerArray indices = new AtomicIntegerArray(countsDownsampled.length); + return new OutputPortCloseable>() { @Override - public boolean hasNext() { - return innerIterator.hasNext(); + public void close() { + inner.close(); } @Override - public OverlapGroup next() { - OverlapGroup grp = innerIterator.next(); + public OverlapGroup take() { + OverlapGroup grp = inner.take(); + if (grp == null) + return null; + List> newGroups = new ArrayList<>(); for (int i = 0; i < grp.size(); i++) { final int fi = i; @@ -124,7 +154,7 @@ public OverlapGroup next() { else newGroups.add(objs.stream() .map(o -> { - long newCount = newCounts[fi] == null ? 0 : newCounts[fi][indices.getAndIncrement(fi)]; + long newCount = countsDownsampled[fi] == null ? 0 : countsDownsampled[fi][indices.getAndIncrement(fi)]; if (getCount.applyAsLong(o) < newCount) throw new RuntimeException("Assertion exception. Varying ordering of objects in iterator."); return setCount.apply(o, newCount); @@ -134,7 +164,7 @@ public OverlapGroup next() { } return new OverlapGroup<>(newGroups); } - }, OverlapGroup::notEmpty); - }; + }; + } } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java deleted file mode 100644 index c1194c998..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/AdditiveOverlapCharacteristic.java +++ /dev/null @@ -1,28 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.overlap; - -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristic; -import com.milaboratory.mixcr.postanalysis.additive.AggregationType; - -/** - * - */ -public class AdditiveOverlapCharacteristic extends AdditiveCharacteristic, OverlapGroup> { - public final int i1, i2; - - public AdditiveOverlapCharacteristic(String name, - SetPreprocessor> preprocessor, - int i1, int i2, - OverlapGroupKeyFunction keyFunction, - OverlapGroupWeightFunction weight, - OverlapGroupAdditiveMetric metric, - AggregationType aggType, boolean normalizeByKey) { - super(name, preprocessor, - group -> weight.weight(group.getBySample(i1), group.getBySample(i2)), - group -> new OverlapKey<>(keyFunction.getKey(group.getBySample(i1), group.getBySample(i2)), i1, i2), - group -> metric.compute(group.getBySample(i1), group.getBySample(i2)), - aggType, normalizeByKey); - this.i1 = i1; - this.i2 = i2; - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java index 45eda73bc..7b5ba7002 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java @@ -13,6 +13,7 @@ public class OverlapAggregator implements Aggregator, OverlapGroup> { private final WeightFunction weight; private final int i1, i2; + private final String id1, id2; final SimpleRegression regressionAll = new SimpleRegression(), regressionIntersection = new SimpleRegression(); @@ -21,10 +22,12 @@ public class OverlapAggregator implements Aggregator, sumSqProduct; long diversity1, diversity2, diversityIntersection; - public OverlapAggregator(WeightFunction weight, int i1, int i2) { + public OverlapAggregator(WeightFunction weight, int i1, int i2, String id1, String id2) { this.weight = weight; this.i1 = i1; this.i2 = i2; + this.id1 = id1; + this.id2 = id2; } @Override @@ -52,17 +55,17 @@ public void consume(OverlapGroup obj) { @Override public MetricValue>[] result() { return new MetricValue[]{ - new MetricValue<>(key(OverlapType.D, i1, i2), 1.0 * diversityIntersection / diversity1 / diversity2), - new MetricValue<>(key(OverlapType.SharedClonotypes, i1, i2), 1.0 * diversityIntersection), - new MetricValue<>(key(OverlapType.F1, i1, i2), Math.sqrt(sumS1Intersection * sumS2Intersection / sumS1 / sumS2)), - new MetricValue<>(key(OverlapType.F2, i1, i2), sumSqProduct / Math.sqrt(sumS1 * sumS2)), - new MetricValue<>(key(OverlapType.Jaccard, i1, i2), 1.0 * diversityIntersection / (diversity1 + diversity2 - diversityIntersection)), - new MetricValue<>(key(OverlapType.R_Intersection, i1, i2), regressionIntersection.getR()), - new MetricValue<>(key(OverlapType.R_All, i1, i2), regressionAll.getR()), + new MetricValue<>(key(OverlapType.D, id1, id2), 1.0 * diversityIntersection / diversity1 / diversity2), + new MetricValue<>(key(OverlapType.SharedClonotypes, id1, id2), 1.0 * diversityIntersection), + new MetricValue<>(key(OverlapType.F1, id1, id2), Math.sqrt(sumS1Intersection * sumS2Intersection / sumS1 / sumS2)), + new MetricValue<>(key(OverlapType.F2, id1, id2), sumSqProduct / Math.sqrt(sumS1 * sumS2)), + new MetricValue<>(key(OverlapType.Jaccard, id1, id2), 1.0 * diversityIntersection / (diversity1 + diversity2 - diversityIntersection)), + new MetricValue<>(key(OverlapType.R_Intersection, id1, id2), regressionIntersection.getR()), + new MetricValue<>(key(OverlapType.R_All, id1, id2), regressionAll.getR()), }; } - private static OverlapKey key(OverlapType type, int i, int j) { + private static OverlapKey key(OverlapType type, String i, String j) { return new OverlapKey<>(type, i, j); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java index e85c9a512..d2bb8e3d6 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java @@ -2,11 +2,9 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.Aggregator; -import com.milaboratory.mixcr.postanalysis.Characteristic; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.WeightFunction; +import com.milaboratory.mixcr.postanalysis.*; +import java.util.List; import java.util.Objects; /** @@ -33,8 +31,11 @@ public OverlapCharacteristic(@JsonProperty("name") String name, } @Override - protected Aggregator, OverlapGroup> createAggregator() { - return new OverlapAggregator<>(weight, i1, i2); + protected Aggregator, OverlapGroup> createAggregator(Dataset> dataset) { + if (!(dataset instanceof OverlapDataset)) + throw new IllegalArgumentException(); + List datasetIds = ((OverlapDataset) dataset).datasetIds; + return new OverlapAggregator<>(weight, i1, i2, datasetIds.get(i1), datasetIds.get(i2)); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java new file mode 100644 index 000000000..67de7246b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java @@ -0,0 +1,21 @@ +package com.milaboratory.mixcr.postanalysis.overlap; + +import com.milaboratory.mixcr.postanalysis.Dataset; + +import java.util.List; + +/** + * + */ +public abstract class OverlapDataset implements Dataset> { + public final List datasetIds; + + public OverlapDataset(List datasetIds) { + this.datasetIds = datasetIds; + } + + @Override + public String id() { + return String.join("_", datasetIds); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java deleted file mode 100644 index b876ecb09..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupAdditiveMetric.java +++ /dev/null @@ -1,10 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.overlap; - -import java.util.List; - -/** - * - */ -public interface OverlapGroupAdditiveMetric { - double compute(List i1, List i2); -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java deleted file mode 100644 index dbd37118c..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupKeyFunction.java +++ /dev/null @@ -1,10 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.overlap; - -import java.util.List; - -/** - * - */ -public interface OverlapGroupKeyFunction { - K getKey(List i1, List i2); -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java deleted file mode 100644 index 7420241c7..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroupWeightFunction.java +++ /dev/null @@ -1,10 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.overlap; - -import java.util.List; - -/** - * - */ -public interface OverlapGroupWeightFunction { - double weight(List i1, List i2); -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java deleted file mode 100644 index 1d7cdd015..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIterable.java +++ /dev/null @@ -1,33 +0,0 @@ -/* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. - */ -package com.milaboratory.mixcr.postanalysis.overlap; - - -public interface OverlapIterable extends Iterable> {} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java index 855d5926c..b95e61642 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java @@ -19,16 +19,16 @@ public final class OverlapKey { @JsonProperty("key") @JsonTypeInfo(use = JsonTypeInfo.Id.CLASS, property = "type") public final K key; - @JsonProperty("i1") - public final int i1; - @JsonProperty("i2") - public final int i2; + @JsonProperty("id1") + public final String id1; + @JsonProperty("id2") + public final String id2; @JsonCreator - public OverlapKey(@JsonProperty("key") K key, @JsonProperty("i1") int i1, @JsonProperty("i2") int i2) { + public OverlapKey(@JsonProperty("key") K key, @JsonProperty("id1") String id1, @JsonProperty("id2") String id2) { this.key = key; - this.i1 = i1; - this.i2 = i2; + this.id1 = id1; + this.id2 = id2; } @Override @@ -36,22 +36,20 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; OverlapKey that = (OverlapKey) o; - return i1 == that.i1 && - i2 == that.i2 && - Objects.equals(key, that.key); + return Objects.equals(key, that.key) && Objects.equals(id1, that.id1) && Objects.equals(id2, that.id2); } @Override public int hashCode() { - return Objects.hash(key, i1, i2); + return Objects.hash(key, id1, id2); } @Override public String toString() { return "OverlapKey{" + "key=" + key + - ", i1=" + i1 + - ", i2=" + i2 + + ", id1='" + id1 + '\'' + + ", id2='" + id2 + '\'' + '}'; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java index bc327944e..d98a8b62d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java @@ -29,8 +29,7 @@ */ package com.milaboratory.mixcr.postanalysis.overlap; -import cc.redberry.pipe.CUtils; -import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.SimpleProcessorWrapper; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneReader; @@ -40,16 +39,17 @@ import java.util.List; public final class OverlapUtil { - private OverlapUtil() { - } + private OverlapUtil() {} - public static OverlapIterable overlap( + public static OverlapDataset overlap( + List datasetIds, List> by, List readers) { - return () -> { - OutputPort> s = - new SimpleProcessorWrapper<>(CloneSetOverlap.overlap(by, readers), OverlapGroup::new); - return CUtils.it(s).iterator(); + return new OverlapDataset(datasetIds) { + @Override + public OutputPortCloseable> mkElementsPort() { + return new SimpleProcessorWrapper<>(CloneSetOverlap.overlap(by, readers), OverlapGroup::new); + } }; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index 4af7d10c8..d30f9e9d3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -2,8 +2,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.util.FilteredIterable; import java.util.Arrays; import java.util.Collections; @@ -42,8 +42,8 @@ public FilterPreprocessor(ElementPredicate predicate) { } @Override - public Function, Iterable> setup(Iterable[] sets) { - return set -> new FilteredIterable<>(set, t -> predicates.stream().allMatch(s -> s.test(t))); + public Function, Dataset> setup(Dataset[] sets) { + return set -> new FilteredDataset<>(set, t -> predicates.stream().allMatch(s -> s.test(t))); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java new file mode 100644 index 000000000..40bd03fea --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java @@ -0,0 +1,29 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.postanalysis.Dataset; + +import java.util.function.Predicate; + +/** + * + */ +public class FilteredDataset implements Dataset { + private final Dataset inner; + private final Predicate accept; + + public FilteredDataset(Dataset inner, Predicate accept) { + this.inner = inner; + this.accept = accept; + } + + @Override + public String id() { + return inner.id(); + } + + @Override + public OutputPortCloseable mkElementsPort() { + return new FilteredOutputPortCloseable<>(inner.mkElementsPort(), accept); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java new file mode 100644 index 000000000..9301bd735 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java @@ -0,0 +1,34 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import cc.redberry.pipe.OutputPortCloseable; + +import java.util.function.Predicate; + +/** + * + */ +public class FilteredOutputPortCloseable implements OutputPortCloseable { + private final OutputPortCloseable inner; + private final Predicate accept; + + public FilteredOutputPortCloseable(OutputPortCloseable inner, Predicate accept) { + this.inner = inner; + this.accept = accept; + } + + @Override + public void close() { + inner.close(); + } + + @Override + public T take() { + while (true) { + final T r = inner.take(); + if (r == null) + return null; + if (accept.test(r)) + return r; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java index f1d1b13e4..9976461cd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.postanalysis.preproc; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import java.util.function.Function; @@ -10,13 +11,12 @@ public class NoPreprocessing implements SetPreprocessor { public static final NoPreprocessing INSTANCE = new NoPreprocessing<>(); - @Override public String[] description() { return new String[0]; } @Override - public Function, Iterable> setup(Iterable[] sets) { + public Function, Dataset> setup(Dataset[] sets) { return set -> set; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index 0a66738f8..9cb1ed8d7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -2,6 +2,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import java.util.*; @@ -23,7 +24,6 @@ public PreprocessorChain(SetPreprocessor... chain) { this(Arrays.asList(chain)); } - @Override public String[] description() { return chain.stream() .map(SetPreprocessor::description) @@ -34,14 +34,14 @@ public String[] description() { } @Override - public Function, Iterable> setup(Iterable[] sets) { - Iterable[] proc = sets; + public Function, Dataset> setup(Dataset[] sets) { + Dataset[] proc = sets; for (SetPreprocessor p : chain) { - Function, Iterable> func = p.setup(proc); + Function, Dataset> func = p.setup(proc); //noinspection unchecked - proc = Arrays.stream(proc).map(func).toArray(Iterable[]::new); + proc = Arrays.stream(proc).map(func).toArray(Dataset[]::new); } - Map, Iterable> mapping = new IdentityHashMap<>(); + Map, Dataset> mapping = new IdentityHashMap<>(); for (int i = 0; i < sets.length; i++) mapping.put(sets[i], proc[i]); return mapping::get; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java index 052bdaedc..d30a54399 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java @@ -3,10 +3,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.postanalysis.Aggregator; -import com.milaboratory.mixcr.postanalysis.Characteristic; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.*; import java.util.Objects; @@ -30,7 +27,7 @@ public SpectratypeCharacteristic(@JsonProperty("name") String name, } @Override - protected Aggregator, Clone> createAggregator() { + protected Aggregator, Clone> createAggregator(Dataset dataset) { return new SpectratypeAggregator<>(nTopClonotypes, keyFunction, weight); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java index fe3fc8e3e..c50e4980f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java @@ -13,8 +13,7 @@ @JsonSubTypes({ @JsonSubTypes.Type(value = GroupSummary.class, name = "summary"), @JsonSubTypes.Type(value = OverlapSummary.class, name = "overlapSummary"), - @JsonSubTypes.Type(value = GroupMelt.VJUsageMelt.class, name = "vjUsage"), - @JsonSubTypes.Type(value = GroupMelt.BySample.class, name = "bySample"), + @JsonSubTypes.Type(value = GroupMelt.VJUsageMelt.class, name = "vjUsage") }) @JsonAutoDetect( fieldVisibility = JsonAutoDetect.Visibility.NONE, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java index 7ba0bbbfa..989966d54 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java @@ -4,6 +4,8 @@ import java.util.List; import java.util.Map; +import java.util.Objects; +import java.util.Set; import java.util.stream.Collectors; /** @@ -17,21 +19,20 @@ public final class CharacteristicGroupResult { /** The group */ public final CharacteristicGroup group; + /** All dataset ids that were analyzed */ + public final Set datasetIds; /** All keys presented in the table */ - public final List keys; + public final Set keys; /** Cells */ public final List> cells; - /** Number of samples */ - public final int nSamples; - /** Sample names */ - public final List sampleIds; - public CharacteristicGroupResult(CharacteristicGroup group, List keys, List> cells, int nSamples, List sampleIds) { + public CharacteristicGroupResult(CharacteristicGroup group, + Set datasetIds, Set keys, + List> cells) { this.group = group; + this.datasetIds = datasetIds; this.keys = keys; this.cells = cells; - this.nSamples = nSamples; - this.sampleIds = sampleIds; } @Override @@ -39,8 +40,26 @@ public String toString() { return cells.toString(); } + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CharacteristicGroupResult that = (CharacteristicGroupResult) o; + return Objects.equals(group, that.group) + && Objects.equals(datasetIds, that.datasetIds) + && Objects.equals(keys, that.keys) + && Objects.equals(cells, that.cells) + && Objects.equals(getOutputs(), that.getOutputs()); + } + + @Override + public int hashCode() { + return Objects.hash(group, datasetIds, keys, cells, getOutputs()); + } + private Map outputs; + /** get all views available for this char group */ public synchronized Map getOutputs() { if (outputs == null) outputs = group.views.stream() diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java index 52157dc28..b80e82098 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java @@ -1,44 +1,33 @@ package com.milaboratory.mixcr.postanalysis.ui; -import gnu.trove.impl.Constants; -import gnu.trove.map.hash.TObjectIntHashMap; - import java.util.ArrayList; +import java.util.LinkedHashSet; import java.util.List; +import java.util.Set; /** * */ public final class CharacteristicGroupResultBuilder { private final CharacteristicGroup group; - private final List sampleIds; - private final TObjectIntHashMap keys = new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); - private final List keyList = new ArrayList<>(); + private final Set datasetIds; + private final LinkedHashSet keys = new LinkedHashSet<>(); private final List> cells = new ArrayList<>(); - private int nSamples = 0; - public CharacteristicGroupResultBuilder(CharacteristicGroup group, List sampleIds) { + public CharacteristicGroupResultBuilder(CharacteristicGroup group, Set datasetIds) { this.group = group; - this.sampleIds = sampleIds; + this.datasetIds = datasetIds; } - public CharacteristicGroupResultBuilder add(K key, int sampleIndex, Double value) { + public CharacteristicGroupResultBuilder add(K key, String datasetId, Double value) { if (value == null) return this; - - nSamples = Math.max(nSamples, sampleIndex + 1); - int metricIndex = keys.get(key); - if (metricIndex < 0) { - metricIndex = keys.size(); - keys.put(key, metricIndex); - keyList.add(key); - } - - cells.add(new CharacteristicGroupResultCell<>(key, value, sampleIndex, metricIndex)); + keys.add(key); + cells.add(new CharacteristicGroupResultCell<>(key, value, datasetId)); return this; } public CharacteristicGroupResult build() { - return new CharacteristicGroupResult<>(group, keyList, cells, nSamples, sampleIds); + return new CharacteristicGroupResult<>(group, datasetIds, keys, cells); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java index de3821a14..9542b5c75 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java @@ -8,18 +8,17 @@ * */ public class CharacteristicGroupResultCell extends MetricValue { - public final int sampleIndex; - public final int metricIndex; + /** id of the dataset */ + public final String datasetId; - public CharacteristicGroupResultCell(K key, double value, int sampleIndex, int metricIndex) { + public CharacteristicGroupResultCell(K key, double value, String datasetId) { super(key, value); - this.sampleIndex = sampleIndex; - this.metricIndex = metricIndex; + this.datasetId = datasetId; } @Override public String toString() { - return key + "-" + sampleIndex + ":" + metricIndex + ":" + value; + return key + "-" + datasetId + ":" + value; } @Override @@ -28,12 +27,11 @@ public boolean equals(Object o) { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; CharacteristicGroupResultCell that = (CharacteristicGroupResultCell) o; - return sampleIndex == that.sampleIndex && - metricIndex == that.metricIndex; + return Objects.equals(datasetId, that.datasetId); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), sampleIndex, metricIndex); + return Objects.hash(super.hashCode(), datasetId); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java deleted file mode 100644 index 64921b57b..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonesIterable.java +++ /dev/null @@ -1,57 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.ui; - -import cc.redberry.pipe.CUtils; -import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.CloneSetIO; -import io.repseq.core.VDJCLibraryRegistry; - -import java.io.IOException; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -/** - * - */ -public class ClonesIterable implements Iterable, AutoCloseable { - final Path path; - final VDJCLibraryRegistry registry; - - public ClonesIterable(Path path, VDJCLibraryRegistry registry) { - this.path = path; - this.registry = registry; - } - - public ClonesIterable(String path, VDJCLibraryRegistry registry) { - this(Paths.get(path), registry); - } - - private final List close = new ArrayList<>(); - - @Override - public Iterator iterator() { - try { - OutputPortCloseable c = CloneSetIO.mkReader(path, registry).readClones(); - close.add(c); - return CUtils.it(c).iterator(); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - - @Override - public void close() throws Exception { - Exception ex = null; - for (AutoCloseable c : close) - try { - c.close(); - } catch (Exception e) { - ex = e; - } - if (ex != null) - throw ex; - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java new file mode 100644 index 000000000..96f0a9316 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java @@ -0,0 +1,55 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneSetIO; +import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.util.LambdaSemaphore; +import io.repseq.core.VDJCLibraryRegistry; + +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; + +/** + * + */ +public class ClonotypeDataset implements Dataset { + final String id; + final Path path; + final VDJCLibraryRegistry registry; + final LambdaSemaphore concurrencyLimiter; + + public ClonotypeDataset(String id, Path path, VDJCLibraryRegistry registry) { + this(id, path, registry, new LambdaSemaphore(CloneSetIO.DEFAULT_READER_CONCURRENCY_LIMIT)); + } + + public ClonotypeDataset(String id, Path path, VDJCLibraryRegistry registry, LambdaSemaphore concurrencyLimiter) { + this.id = id; + this.path = path; + this.registry = registry; + this.concurrencyLimiter = concurrencyLimiter; + } + + public ClonotypeDataset(String id, String path, VDJCLibraryRegistry registry) { + this(id, path, registry, new LambdaSemaphore(CloneSetIO.DEFAULT_READER_CONCURRENCY_LIMIT)); + } + + public ClonotypeDataset(String id, String path, VDJCLibraryRegistry registry, LambdaSemaphore concurrencyLimiter) { + this(id, Paths.get(path), registry, concurrencyLimiter); + } + + @Override + public String id() { + return id; + } + + @Override + public OutputPortCloseable mkElementsPort() { + try { + return CloneSetIO.mkReader(path, registry, concurrencyLimiter).readClones(); + } catch (IOException e) { + throw new RuntimeException(e); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java index 13419fa42..6764e3371 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java @@ -4,13 +4,10 @@ * */ final class Coordinates { - final int iRow, iCol; - final String row, col; + final Object iRow, iCol; - public Coordinates(int iRow, int iCol, String row, String col) { + public Coordinates(Object iRow, Object iCol) { this.iRow = iRow; this.iCol = iCol; - this.row = row; - this.col = col; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java index 9c496f48b..f5483fb0c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java @@ -3,7 +3,8 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; -import java.util.*; +import java.util.HashMap; +import java.util.Map; import java.util.function.Supplier; /** @@ -46,38 +47,11 @@ interface CoordinatesProvider { Coordinates getXY(CharacteristicGroupResultCell key); } - public static abstract class SplitCoordinatesProvider implements CoordinatesProvider { - final Map xs = new HashMap<>(), ys = new HashMap<>(); - - abstract Object[] split(K key); - - @Override - public Coordinates getXY(CharacteristicGroupResultCell key) { - Object[] split = split(key.key); - Integer x = xs.get(split[0]); - if (x == null) { - x = xs.size(); - xs.put(split[0], x); - } - Integer y = ys.get(split[1]); - if (y == null) { - y = ys.size(); - ys.put(split[1], y); - } - return new Coordinates(x, y, split[0].toString(), split[1].toString()); - } - } - public static final class VJUsageMelt extends GroupMelt> { public VJUsageMelt() { super("vj_usage_", - (result, cell) -> result.sampleIds.get(cell.sampleIndex), - () -> new SplitCoordinatesProvider>() { - @Override - Object[] split(KeyFunctions.VJGenes key) { - return new Object[]{key.vGene, key.jJene}; - } - }); + (result, cell) -> cell.datasetId, + () -> key -> new Coordinates(key.key.vGene, key.key.jJene)); } @Override @@ -92,29 +66,4 @@ public int hashCode() { return 17; } } - - public static final class BySample extends GroupMelt { - public BySample(@JsonProperty("prefix") String prefix) { - super(prefix, - (result, cell) -> result.sampleIds.get(cell.sampleIndex), - () -> new SplitCoordinatesProvider() { - @Override - Object[] split(K key) { - return new Object[]{key}; - } - }); - } - - @Override - public boolean equals(Object o1) { - if (this == o1) return true; - if (o1 == null || getClass() != o1.getClass()) return false; - return Objects.equals(prefix, ((BySample) o1).prefix); - } - - @Override - public int hashCode() { - return 123 + Objects.hashCode(prefix); - } - } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java index 788838e57..9264d891b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java @@ -11,24 +11,42 @@ import java.util.Arrays; import java.util.Collections; import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; +import java.util.stream.IntStream; /** * */ public class OutputTable { public final String name; - public final List rowNames; - public final List colNames; + /** row & col ids (names) */ + public final List rowIds, colIds; + /** rowId -> index in rows list */ + private final Map rowId2idx; + /** colId -> index in columns list */ + private final Map colId2idx; + /** sparse cells */ public final List cells; - public OutputTable(String name, List rowNames, List colNames, List cells) { + public OutputTable(String name, List rowIds, List colIds, List cells) { this.name = name; - this.rowNames = rowNames; - this.colNames = colNames; + this.rowIds = rowIds; + this.colIds = colIds; this.cells = cells; + this.rowId2idx = IntStream.range(0, rowIds.size()).boxed().collect(Collectors.toMap(rowIds::get, i -> i)); + this.colId2idx = IntStream.range(0, colIds.size()).boxed().collect(Collectors.toMap(colIds::get, i -> i)); } - private List columnsHierarchy, rowsHierarchy; + public int rowIdx(Object rowId) { + return rowId2idx.get(rowId); + } + + public int colIdx(Object colId) { + return colId2idx.get(colId); + } + + private volatile List columnsHierarchy, rowsHierarchy; public synchronized List columnsHierarchy() { if (columnsHierarchy == null) @@ -42,46 +60,50 @@ public synchronized List rowsHierarchy() { return rowsHierarchy; } + public OutputTable reorder(List rowIds, List colIds) { + return new OutputTable(name, rowIds, colIds, cells); + } + public double[][] columns(double naValue, double nan) { - int nRows = rowNames.size(), nCols = colNames.size(); + int nRows = rowIds.size(), nCols = colIds.size(); double[][] r = new double[nCols][nRows]; if (naValue != 0.0) for (double[] doubles : r) Arrays.fill(doubles, naValue); for (OutputTableCell cell : cells) - r[cell.iCol][cell.iRow] = Double.isNaN(cell.value) ? nan : cell.value; + r[colIdx(cell.iCol)][rowIdx(cell.iRow)] = Double.isNaN(cell.value) ? nan : cell.value; return r; } public Double[][] columns() { - int nRows = rowNames.size(), nCols = colNames.size(); + int nRows = rowIds.size(), nCols = colIds.size(); Double[][] r = new Double[nCols][nRows]; for (OutputTableCell cell : cells) - r[cell.iCol][cell.iRow] = cell.value; + r[colIdx(cell.iCol)][rowIdx(cell.iRow)] = cell.value; return r; } public double[][] rows(double naValue, double nan) { - int nRows = rowNames.size(), nCols = colNames.size(); + int nRows = rowIds.size(), nCols = colIds.size(); double[][] r = new double[nRows][nCols]; if (naValue != 0.0) for (double[] doubles : r) Arrays.fill(doubles, naValue); for (OutputTableCell cell : cells) - r[cell.iRow][cell.iCol] = Double.isNaN(cell.value) ? nan : cell.value; + r[rowIdx(cell.iRow)][colIdx(cell.iCol)] = Double.isNaN(cell.value) ? nan : cell.value; return r; } public Double[][] rows() { - int nRows = rowNames.size(), nCols = colNames.size(); + int nRows = rowIds.size(), nCols = colIds.size(); Double[][] r = new Double[nRows][nCols]; for (OutputTableCell cell : cells) - r[cell.iRow][cell.iCol] = cell.value; + r[rowIdx(cell.iRow)][colIdx(cell.iCol)] = cell.value; return r; } @@ -94,20 +116,6 @@ public double maxValue() { return cells.stream().mapToDouble(c -> c.value).filter(v -> !Double.isNaN(v)).max().orElse(Double.NaN); } - public OutputTable setRowNames(List rowNames) { - OutputTable t = new OutputTable(name, rowNames, colNames, cells); - t.columnsHierarchy = columnsHierarchy; - t.rowsHierarchy = rowsHierarchy; - return t; - } - - public OutputTable setColNames(List colNames) { - OutputTable t = new OutputTable(name, rowNames, colNames, cells); - t.columnsHierarchy = columnsHierarchy; - t.rowsHierarchy = rowsHierarchy; - return t; - } - @Override public String toString() { return cells.toString(); @@ -134,14 +142,14 @@ public void writeCSV(Path dir, String prefix, String sep, String ext) { Path outName = dir.resolve(prefix + name + ext); try (BufferedWriter writer = Files.newBufferedWriter(outName, StandardOpenOption.CREATE)) { writer.write(""); - for (String column : colNames) { + for (Object column : colIds) { writer.write(sep); - writer.write(column); + writer.write(column.toString()); } - for (int iRow = 0; iRow < rowNames.size(); ++iRow) { + for (int iRow = 0; iRow < rowIds.size(); ++iRow) { writer.write("\n"); - writer.write(rowNames.get(iRow)); + writer.write(rowIds.get(iRow).toString()); Double[] row = rows2d[iRow]; for (Double val : row) { writer.write(sep); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java index f14b99db5..3faaa6630 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java @@ -1,6 +1,8 @@ package com.milaboratory.mixcr.postanalysis.ui; -import java.util.*; +import java.util.ArrayList; +import java.util.LinkedHashSet; +import java.util.List; /** * @@ -8,37 +10,24 @@ final class OutputTableBuilder { final String name; final List cells = new ArrayList<>(); - final Map rows = new HashMap<>(); - final Map cols = new HashMap<>(); + final LinkedHashSet rows = new LinkedHashSet<>(); + final LinkedHashSet cols = new LinkedHashSet<>(); public OutputTableBuilder(String name) { this.name = name; } - int nRows = 0, nCols = 0; + void add(Coordinates coords, CharacteristicGroupResultCell original) { + add(coords.iRow, coords.iCol, original); + } - synchronized void add(Coordinates cords, CharacteristicGroupResultCell original) { - cells.add(new OutputTableCell(cords.iRow, cords.iCol, original.value)); - rows.put(cords.iRow, cords.row.toString()); - cols.put(cords.iCol, cords.col.toString()); - nRows = Math.max(cords.iRow + 1, nRows); - nCols = Math.max(cords.iCol + 1, nCols); + synchronized void add(Object iRow, Object iCol, CharacteristicGroupResultCell original) { + cells.add(new OutputTableCell(iRow, iCol, original.value)); + rows.add(iRow); + cols.add(iCol); } OutputTable build() { - String[] rows = new String[nRows]; - String[] cols = new String[nCols]; - for (int i = 0; i < nRows; ++i) { - String r = this.rows.get(i); - Objects.requireNonNull(r); - rows[i] = r; - } - for (int i = 0; i < nCols; ++i) { - String c = this.cols.get(i); - Objects.requireNonNull(c); - cols[i] = c; - } - - return new OutputTable(name, Arrays.asList(rows), Arrays.asList(cols), cells); + return new OutputTable(name, new ArrayList<>(rows), new ArrayList<>(cols), cells); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java index 92f4c30dd..65944656c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java @@ -5,11 +5,12 @@ /** * */ -public final class OutputTableCell implements Comparable { - public final int iRow, iCol; +public final class OutputTableCell { + /** row & col keys */ + public final Object iRow, iCol; public final double value; - public OutputTableCell(int iRow, int iCol, double value) { + public OutputTableCell(Object iRow, Object iCol, double value) { this.iRow = iRow; this.iCol = iCol; this.value = value; @@ -20,26 +21,12 @@ public String toString() { return iRow + ":" + iCol + "=" + value; } - @Override - public int compareTo(OutputTableCell o) { - int c = Integer.compare(iRow, o.iRow); - if (c != 0) - return c; - c = Integer.compare(iCol, o.iCol); - if (c != 0) - return c; - - return Double.compare(value, o.value); - } - @Override public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; OutputTableCell that = (OutputTableCell) o; - return iRow == that.iRow && - iCol == that.iCol && - Double.compare(that.value, value) == 0; + return Double.compare(that.value, value) == 0 && Objects.equals(iRow, that.iRow) && Objects.equals(iCol, that.iCol); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java index 0d57572f1..099445392 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java @@ -2,8 +2,6 @@ import java.util.ArrayList; import java.util.List; -import java.util.Objects; -import java.util.stream.Collectors; /** * @@ -15,10 +13,11 @@ static OutputTableExtractor summary() { return result -> { List cells = new ArrayList<>(); for (CharacteristicGroupResultCell cell : result.cells) - cells.add(new OutputTableCell(cell.sampleIndex, cell.metricIndex, cell.value)); + cells.add(new OutputTableCell(cell.datasetId, cell.key, cell.value)); - return new OutputTable(result.group.name, result.sampleIds, - result.keys.stream().map(Objects::toString).collect(Collectors.toList()), cells); + return new OutputTable(result.group.name, + new ArrayList<>(result.datasetIds), + new ArrayList<>(result.keys), cells); }; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java index b70e418b4..2bb663412 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java @@ -14,9 +14,8 @@ public Map getTables(CharacteristicGroupResult tables = new HashMap<>(); for (CharacteristicGroupResultCell> cell : result.cells) { OutputTableBuilder tab = tables.computeIfAbsent(cell.key.key, __ -> new OutputTableBuilder(cell.key.key.toString())); - int i1 = cell.key.i1, i2 = cell.key.i2; - tab.add(new Coordinates(i1, i2, result.sampleIds.get(i1), result.sampleIds.get(i2)), cell); - tab.add(new Coordinates(i2, i1, result.sampleIds.get(i2), result.sampleIds.get(i1)), cell); + tab.add(cell.key.id1, cell.key.id2, cell); + tab.add(cell.key.id2, cell.key.id1, cell); } Map r = new HashMap<>(); for (Map.Entry e : tables.entrySet()) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java index 37227ae0a..23b251b3c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java @@ -4,6 +4,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; @@ -65,10 +66,9 @@ public int hashCode() { return Objects.hash(tables); } - public PostanalysisResult run(List> datasets) { + public PostanalysisResult run(List> datasets) { PostanalysisRunner runner = new PostanalysisRunner<>(); runner.addCharacteristics(getAllCharacterisitcs()); - runner.setDatasets(datasets); - return runner.run(); + return runner.run(datasets); } } diff --git a/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java b/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java deleted file mode 100644 index 98fcc8317..000000000 --- a/src/main/java/com/milaboratory/mixcr/util/FilteredIterable.java +++ /dev/null @@ -1,22 +0,0 @@ -package com.milaboratory.mixcr.util; - -import java.util.Iterator; -import java.util.function.Predicate; - -/** - * - */ -public class FilteredIterable implements Iterable { - private final Iterable inner; - private final Predicate accept; - - public FilteredIterable(Iterable inner, Predicate accept) { - this.inner = inner; - this.accept = accept; - } - - @Override - public Iterator iterator() { - return new FilteredIterator<>(inner.iterator(), accept); - } -} diff --git a/src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java b/src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java deleted file mode 100644 index fc0aba26a..000000000 --- a/src/main/java/com/milaboratory/mixcr/util/FilteredIterator.java +++ /dev/null @@ -1,41 +0,0 @@ -package com.milaboratory.mixcr.util; - -import java.util.Iterator; -import java.util.function.Predicate; - -/** - * - */ -public class FilteredIterator implements Iterator { - private final Iterator inner; - private final Predicate accept; - - public FilteredIterator(Iterator inner, Predicate accept) { - this.inner = inner; - this.accept = accept; - } - - private T ref = null; - - @Override - public boolean hasNext() { - if (ref != null) - return true; - if (!inner.hasNext()) - return false; - ref = inner.next(); - while (!accept.test(ref)) { - if (!inner.hasNext()) - return false; - ref = inner.next(); - } - return true; - } - - @Override - public T next() { - T r = this.ref; - this.ref = null; - return r; - } -} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java new file mode 100644 index 000000000..36a138201 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java @@ -0,0 +1,52 @@ +package com.milaboratory.mixcr.postanalysis; + +import cc.redberry.pipe.OutputPortCloseable; +import cc.redberry.pipe.util.IteratorOutputPortAdapter; +import org.jetbrains.annotations.NotNull; + +import java.util.Iterator; +import java.util.List; +import java.util.UUID; +import java.util.stream.Stream; + +/** + * + */ +public class TestDataset implements Dataset, Iterable { + public final List data; + public final String id; + + public TestDataset(List data) { + this.data = data; + this.id = UUID.randomUUID().toString(); + } + + @NotNull + @Override + public Iterator iterator() { + return data.iterator(); + } + + public Stream stream() { + return data.stream(); + } + + @Override + public String id() { + return id; + } + + @Override + public OutputPortCloseable mkElementsPort() { + final IteratorOutputPortAdapter adapter = new IteratorOutputPortAdapter<>(data); + return new OutputPortCloseable() { + @Override + public void close() { } + + @Override + public T take() { + return adapter.take(); + } + }; + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java index f36c9321b..694e41a70 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java @@ -3,7 +3,6 @@ import org.apache.commons.math3.random.RandomDataGenerator; import java.util.Arrays; -import java.util.List; import java.util.Objects; import java.util.function.ToDoubleFunction; import java.util.function.ToIntFunction; @@ -33,22 +32,23 @@ public int hashCode() { return Objects.hash(value, weight); } - public static List[] generateDatasets(int nDatasets, RandomDataGenerator rng) { + public static TestDataset[] generateDatasets(int nDatasets, RandomDataGenerator rng) { return generateDatasets(nDatasets, rng, r -> r.nextInt(1, 1000), r -> r.nextUniform(0, 10), r -> r.nextUniform(0, 10)); } - public static List[] generateDatasets(int nDatasets, RandomDataGenerator rng, - ToIntFunction sizes, - ToDoubleFunction values, - ToDoubleFunction weights) { + public static TestDataset[] generateDatasets(int nDatasets, RandomDataGenerator rng, + ToIntFunction sizes, + ToDoubleFunction values, + ToDoubleFunction weights) { int[] nElements = new int[nDatasets]; for (int i = 0; i < nDatasets; i++) { nElements[i] = sizes.applyAsInt(rng); } - List[] datasets = new List[nDatasets]; + @SuppressWarnings("unchecked") + TestDataset[] datasets = new TestDataset[nDatasets]; for (int i = 0; i < datasets.length; i++) { TestObject[] ds = new TestObject[nElements[i]]; for (int j = 0; j < nElements[i]; j++) { @@ -57,7 +57,7 @@ public static List[] generateDatasets(int nDatasets, RandomDataGener weights.applyAsDouble(rng)); ds[j] = w; } - datasets[i] = Arrays.asList(ds); + datasets[i] = new TestDataset<>(Arrays.asList(ds)); } return datasets; } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java index 3c547d2a8..0a8f694bc 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java @@ -2,6 +2,7 @@ import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.TestDataset; import com.milaboratory.mixcr.postanalysis.TestObject; import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; @@ -16,8 +17,6 @@ import org.junit.Test; import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; import java.util.stream.IntStream; /** @@ -60,17 +59,15 @@ public void testWeightedDescriptiveStat() { RandomDataGenerator rng = new RandomDataGenerator(new Well44497a()); int nDatasets = 1000; - List[] datasets = TestObject.generateDatasets(nDatasets, rng); + TestDataset[] datasets = TestObject.generateDatasets(nDatasets, rng); PostanalysisRunner runner = new PostanalysisRunner<>(); runner.addCharacteristics(sum, mean, std); - runner.setDatasets(datasets); - PostanalysisResult result = runner.run(); + PostanalysisResult result = runner.run(datasets); CharacteristicGroup group = new CharacteristicGroup<>("stat", Arrays.asList(mean, std), Arrays.asList(new GroupSummary<>())); - result = result.setSampleIds(IntStream.range(0, nDatasets).mapToObj(String::valueOf).collect(Collectors.toList())); CharacteristicGroupResult table = result.getTable(group); OutputTable summary = table.getOutputs().get(GroupSummary.key); @@ -87,11 +84,11 @@ public void testWeightedDescriptiveStat() { double expectedStd = Math.sqrt(new Variance(true).evaluate(vals, weights)); for (int j = 0; j < metrics.length; j++) { - if (summary.colNames.get(j).equals("sum")) + if (summary.colIds.get(j).equals("sum")) Assert.assertEquals(expectedSum, metrics[j], 1e-10); - else if (summary.colNames.get(j).equals("mean")) + else if (summary.colIds.get(j).equals("mean")) Assert.assertEquals(expectedMean, metrics[j], 1e-10); - else if (summary.colNames.get(j).equals("std")) + else if (summary.colIds.get(j).equals("std")) Assert.assertEquals(expectedStd, metrics[j], 1e-10); else throw new RuntimeException(); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index 369f21b23..ce84417a8 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -2,6 +2,7 @@ import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.TestDataset; import com.milaboratory.mixcr.postanalysis.TestObject; import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; @@ -15,8 +16,6 @@ import java.util.Arrays; import java.util.List; -import java.util.stream.Collectors; -import java.util.stream.IntStream; /** * @@ -30,16 +29,14 @@ public void test1() { RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); int nDatasets = 100; - List[] datasets = TestObject.generateDatasets(nDatasets, rng, + TestDataset[] datasets = TestObject.generateDatasets(nDatasets, rng, r -> r.nextInt(1000, 10000), r -> r.nextUniform(0, 1), r -> r.nextInt(10, 20)); PostanalysisRunner runner = new PostanalysisRunner<>(); runner.addCharacteristics(diversity); - runner.setDatasets(datasets); - PostanalysisResult result = runner.run(); - result = result.setSampleIds(IntStream.range(0, nDatasets).mapToObj(String::valueOf).collect(Collectors.toList())); + PostanalysisResult result = runner.run(datasets); CharacteristicGroup group = new CharacteristicGroup<>("diversity", Arrays.asList(diversity), @@ -47,11 +44,11 @@ public void test1() { CharacteristicGroupResult table = result.getTable(group); for (CharacteristicGroupResultCell cell : table.cells) { - List ds = datasets[cell.sampleIndex]; + TestDataset ds = Arrays.stream(datasets).filter(d -> d.id.equals(cell.datasetId)).findFirst().get(); if (cell.key == DiversityMeasure.InverseSimpson) - Assert.assertEquals(SimpsonIndex(ds), cell.value, 1e-6); + Assert.assertEquals(SimpsonIndex(ds.data), cell.value, 1e-6); if (cell.key == DiversityMeasure.ShannonWeiner) - Assert.assertEquals(ShannonEntropy(ds), cell.value, 1e-6); + Assert.assertEquals(ShannonEntropy(ds.data), cell.value, 1e-6); } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index 4d02bcb05..fc9f80130 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -1,5 +1,8 @@ package com.milaboratory.mixcr.postanalysis.downsampling; +import cc.redberry.pipe.CUtils; +import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.TestDataset; import com.milaboratory.mixcr.postanalysis.TestObject; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; @@ -103,21 +106,21 @@ public void test3() { ); int nDatasets = 10; - Dataset[] initial = new Dataset[nDatasets]; + DatasetSupport[] initial = new DatasetSupport[nDatasets]; for (int i = 0; i < initial.length; i++) { initial[i] = rndDataset(rng, rng.nextInt(100, 1000)); } long dsValue = dsChooser.compute(Arrays.stream(initial).mapToLong(d -> d.count).toArray()); - Function, Iterable> setup = proc.setup(initial); + Function, Dataset> setup = proc.setup(initial); - Dataset[] downsampled = Arrays.stream(initial).map(setup) - .map(Dataset::new) - .toArray(Dataset[]::new); + DatasetSupport[] downsampled = Arrays.stream(initial).map(setup) + .map(DatasetSupport::new) + .toArray(DatasetSupport[]::new); for (int i = 0; i < downsampled.length; i++) { - Dataset in = initial[i]; - Dataset dw = downsampled[i]; + DatasetSupport in = initial[i]; + DatasetSupport dw = downsampled[i]; Assert.assertTrue(in.set.containsAll(dw.set)); Assert.assertEquals(dsValue, dw.count); @@ -135,34 +138,28 @@ static List toList(Iterable it) { return l; } - public static Dataset rndDataset(RandomDataGenerator rng, int size) { + public static DatasetSupport rndDataset(RandomDataGenerator rng, int size) { TestObject[] r = new TestObject[size]; for (int i = 0; i < size; i++) { r[i] = new TestObject( rng.nextUniform(0, 1), rng.nextUniform(0, 100)); } - return new Dataset(Arrays.asList(r)); + return new DatasetSupport(Arrays.asList(r)); } - private static final class Dataset implements Iterable { - final List data; + private static final class DatasetSupport extends TestDataset { final Set set; final long count; - public Dataset(Iterable data) { - this(toList(data)); + public DatasetSupport(Dataset data) { + this(toList(CUtils.it(data.mkElementsPort()))); } - public Dataset(List data) { - this.data = data; + public DatasetSupport(List data) { + super(data); this.set = data.stream().map(s -> s.value).collect(Collectors.toSet()); this.count = data.stream().mapToLong(l -> Math.round(l.weight)).sum(); } - - @Override - public Iterator iterator() { - return data.iterator(); - } } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index d9df86720..ac8f5dd7e 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -1,5 +1,8 @@ package com.milaboratory.mixcr.postanalysis.downsampling; +import cc.redberry.pipe.CUtils; +import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.TestDataset; import com.milaboratory.mixcr.postanalysis.TestObject; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; import org.apache.commons.math3.random.RandomDataGenerator; @@ -7,7 +10,10 @@ import org.junit.Assert; import org.junit.Test; -import java.util.*; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; import java.util.function.Function; import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingPreprocessorTest.toList; @@ -27,16 +33,16 @@ public void test1() { System.currentTimeMillis() ); - Dataset[] datasets = new Dataset[]{ + DatasetSupport[] datasets = new DatasetSupport[]{ rndDataset(rng, 5, 100000), rndDataset(rng, 10, 10000), rndDataset(rng, 15, 10000) }; - Function>, Iterable>> downsampler = proc.setup(datasets); + Function>, Dataset>> downsampler = proc.setup(datasets); - for (Dataset in : datasets) { + for (DatasetSupport in : datasets) { long dsValue = chooser.compute(in.counts); - Dataset dw = new Dataset(downsampler.apply(in)); + DatasetSupport dw = new DatasetSupport(downsampler.apply(in)); for (int i = 0; i < in.counts.length; i++) { Assert.assertEquals(dsValue, dw.counts[i]); @@ -65,17 +71,16 @@ private static long[] sum(long[] a, long[] b) { return r; } - private static final class Dataset implements Iterable> { - final List> data; + private static final class DatasetSupport extends TestDataset> { final long[] counts; final Set[] sets; - public Dataset(Iterable> data) { - this(toList(data)); + public DatasetSupport(Dataset> data) { + this(toList(CUtils.it(data.mkElementsPort()))); } - public Dataset(List> data) { - this.data = data; + public DatasetSupport(List> data) { + super(data); this.counts = data.stream() .map(row -> row.stream().mapToLong(l -> Math.round(l.stream().mapToDouble(e -> e.weight).sum())).toArray()) .reduce(new long[0], OverlapDownsamplingPreprocessorTest::sum); @@ -92,14 +97,9 @@ public Dataset(List> data) { } } } - - @Override - public Iterator> iterator() { - return data.iterator(); - } } - private static Dataset rndDataset(RandomDataGenerator rng, int nSamples, int size) { + private static DatasetSupport rndDataset(RandomDataGenerator rng, int nSamples, int size) { List> data = new ArrayList<>(); int p = Math.max(2, nSamples / 4); for (int i = 0; i < size; i++) { @@ -123,6 +123,6 @@ private static Dataset rndDataset(RandomDataGenerator rng, int nSamples, int siz } data.add(new OverlapGroup<>(row)); } - return new Dataset(data); + return new DatasetSupport(data); } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java index 3969982dc..e622c0636 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -3,8 +3,10 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.OutputPortCloseable; +import cc.redberry.pipe.util.SimpleProcessorWrapper; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.TestDataset; import com.milaboratory.mixcr.postanalysis.TestObjectWithPayload; import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; @@ -30,7 +32,7 @@ */ public class OverlapCharacteristicTest { @Test - @SuppressWarnings("unchecked") + @SuppressWarnings({"unchecked", "SuspiciousToArrayCall"}) public void testOverlapPort1() { List initialSort = Arrays.asList( new ElementOrdering(0, 2), @@ -48,12 +50,12 @@ public void testOverlapPort1() { RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); OverlapData ovp = new OverlapData(IntStream.range(0, 10) .mapToObj(__ -> rndDataset(rng, rng.nextInt(11111, 22222), 10)) - .toArray(List[]::new), + .toArray(TestDataset[]::new), targetGroupping); OutputPortCloseable>> join = strategy .join(Arrays.stream(ovp.datasets) - .map(OverlapCharacteristicTest::asOutputPort) + .map(TestDataset::mkElementsPort) .collect(Collectors.toList())); DescriptiveStatistics ds = new DescriptiveStatistics(); @@ -105,13 +107,13 @@ public void testOverlapCharacteristic1() { int nDatasets = 10; OverlapData ovp = new OverlapData(IntStream.range(0, nDatasets) .mapToObj(__ -> rndDataset(rng, rng.nextInt(11111, 22222), 10)) - .toArray(List[]::new), + .toArray(TestDataset[]::new), targetGroupping); - OutputPortCloseable>> join = strategy - .join(Arrays.stream(ovp.datasets) - .map(OverlapCharacteristicTest::asOutputPort) - .collect(Collectors.toList())); +// OutputPortCloseable>> join = strategy +// .join(Arrays.stream(ovp.datasets) +// .map(OverlapCharacteristicTest::asOutputPort) +// .collect(Collectors.toList())); List> chars = new ArrayList<>(); for (int i = 0; i < ovp.datasets.length; i++) { @@ -126,16 +128,17 @@ public void testOverlapCharacteristic1() { PostanalysisRunner> runner = new PostanalysisRunner<>(); runner.addCharacteristics(chGroup); - runner.setDatasets(new Iterable[]{CUtils.it(() -> { - List> t = join.take(); - if (t == null) return null; - return new OverlapGroup<>(t); - })}); + List datasetIds = Arrays.stream(ovp.datasets).map(d -> d.id).collect(Collectors.toList()); - PostanalysisResult paResult = runner - .run() - .setSampleIds(IntStream.range(0, nDatasets) - .mapToObj(String::valueOf).collect(Collectors.toList())); + PostanalysisResult paResult = runner.run(new OverlapDataset(datasetIds) { + @Override + public OutputPortCloseable> mkElementsPort() { + return new SimpleProcessorWrapper<>(strategy + .join(Arrays.stream(ovp.datasets) + .map(TestDataset::mkElementsPort) + .collect(Collectors.toList())), OverlapGroup::new); + } + }); CharacteristicGroupResult> chGroupResult = paResult.getTable(chGroup); Map outputs = chGroupResult.getOutputs(); @@ -187,11 +190,21 @@ public void testOverlapCharacteristic1() { } System.out.println(Arrays.stream(expectedSharedElements).map(Arrays::toString).collect(Collectors.joining("\n"))); - assert2dEquals(expectedSharedElements, outputs.get(OverlapType.SharedClonotypes).rows(0, 0)); - assert2dEquals(expectedD, outputs.get(OverlapType.D).rows(0, 0)); - assert2dEquals(expectedF1, outputs.get(OverlapType.F1).rows(0, 0)); - assert2dEquals(expectedF2, outputs.get(OverlapType.F2).rows(0, 0)); - assert2dEquals(expectedR, outputs.get(OverlapType.R_Intersection).rows(0, 0)); + assert2dEquals(expectedSharedElements, outputs.get(OverlapType.SharedClonotypes) + .reorder(datasetIds, datasetIds) + .rows(0, 0)); + assert2dEquals(expectedD, outputs.get(OverlapType.D) + .reorder(datasetIds, datasetIds) + .rows(0, 0)); + assert2dEquals(expectedF1, outputs.get(OverlapType.F1) + .reorder(datasetIds, datasetIds) + .rows(0, 0)); + assert2dEquals(expectedF2, outputs.get(OverlapType.F2) + .reorder(datasetIds, datasetIds) + .rows(0, 0)); + assert2dEquals(expectedR, outputs.get(OverlapType.R_Intersection) + .reorder(datasetIds, datasetIds) + .rows(0, 0)); } interface OverlapScanFunction { @@ -223,7 +236,7 @@ public T take() { } public static final class OverlapData { - final List[] datasets; + final TestDataset[] datasets; final List ordering; final Comparator comparator; final Comparator pComparator; @@ -231,7 +244,7 @@ public static final class OverlapData { final Map diversity; final Map sumWeight; - public OverlapData(List[] datasets, List ordering) { + public OverlapData(TestDataset[] datasets, List ordering) { this.datasets = datasets; this.ordering = ordering; this.comparator = SortingUtil.combine(ordering); @@ -240,11 +253,11 @@ public OverlapData(List[] datasets, List ordering) { this.diversity = new HashMap<>(); this.sumWeight = new HashMap<>(); - for (List d : datasets) { - d.sort(comparator); + for (TestDataset d : datasets) { + d.data.sort(comparator); } for (int index = 0; index < datasets.length; index++) { - List dataset = datasets[index]; + List dataset = datasets[index].data; for (Element element : dataset) { Map> m = this.index.computeIfAbsent(element.payload, payload -> new HashMap<>()); m.computeIfAbsent(index, __ -> new ArrayList<>()).add(element); @@ -279,7 +292,7 @@ void scanOverlap(OverlapScanFunction scanner) { } } - public static List rndDataset(RandomDataGenerator rng, int size, int pSize) { + public static TestDataset rndDataset(RandomDataGenerator rng, int size, int pSize) { Element[] r = new Element[size]; for (int i = 0; i < size; i++) { r[i] = new Element( @@ -287,7 +300,7 @@ public static List rndDataset(RandomDataGenerator rng, int size, int pS rng.nextUniform(0, 100), rndPayload(rng, pSize)); } - return Arrays.asList(r); + return new TestDataset<>(Arrays.asList(r)); } public static Payload rndPayload(RandomDataGenerator rng, int pSize) { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java index 5208fc4a4..81c1e45fb 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java @@ -29,10 +29,13 @@ */ package com.milaboratory.mixcr.postanalysis.overlap; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.basictypes.ClnsReader; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.VDJCObject; import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.util.Cache; import com.milaboratory.util.LambdaSemaphore; import gnu.trove.map.hash.TIntIntHashMap; @@ -50,7 +53,6 @@ import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import java.util.stream.Stream; public class OverlapIntegrationTest { @Test @@ -58,8 +60,7 @@ public void test1() throws IOException { // Limits concurrency across all readers LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(4); - List readers = Stream.of( - "Ig-2_S2.contigs.clns", + List samples = Arrays.asList("Ig-2_S2.contigs.clns", "Ig-3_S3.contigs.clns", "Ig-4_S4.contigs.clns", "Ig-5_S5.contigs.clns", @@ -67,7 +68,8 @@ public void test1() throws IOException { "Ig2_S2.contigs.clns", "Ig3_S3.contigs.clns", "Ig4_S4.contigs.clns", - "Ig5_S5.contigs.clns") + "Ig5_S5.contigs.clns"); + List readers = samples.stream() .map(f -> { try { return new ClnsReader( @@ -88,13 +90,15 @@ public void test1() throws IOException { long totalSumExpected = 0; for (List> by : Arrays.asList(byN, byAA, byAAAndV)) { System.out.println("============="); - OverlapIterable overlap = OverlapUtil.overlap(by, readers); + Dataset> overlap = OverlapUtil.overlap(samples, by, readers); TIntIntHashMap hist = new TIntIntHashMap(); long totalSum = 0; - for (OverlapGroup cloneOverlapGroup : overlap) { - int sum = cloneOverlapGroup.elements.stream().mapToInt(l -> l.isEmpty() ? 0 : 1).sum(); - totalSum += cloneOverlapGroup.elements.stream().mapToInt(List::size).sum(); - hist.adjustOrPutValue(sum, 1, 1); + try (final OutputPortCloseable> port = overlap.mkElementsPort()) { + for (OverlapGroup cloneOverlapGroup : CUtils.it(port)) { + int sum = cloneOverlapGroup.elements.stream().mapToInt(l -> l.isEmpty() ? 0 : 1).sum(); + totalSum += cloneOverlapGroup.elements.stream().mapToInt(List::size).sum(); + hist.adjustOrPutValue(sum, 1, 1); + } } if (totalSumExpected == 0) totalSumExpected = totalSum; @@ -145,13 +149,15 @@ public void tst1() throws IOException { for (List> by : Arrays.asList(byN, byAA, byAAAndV)) { System.out.println("============="); - OverlapIterable overlap = OverlapUtil.overlap(by, readers); + Dataset> overlap = OverlapUtil.overlap(input.stream().map(Path::toString).collect(Collectors.toList()), by, readers); TIntIntHashMap hist = new TIntIntHashMap(); long totalSum = 0; - for (OverlapGroup cloneOverlapGroup : overlap) { - int sum = cloneOverlapGroup.elements.stream().mapToInt(l -> l.isEmpty() ? 0 : 1).sum(); - totalSum += cloneOverlapGroup.elements.stream().mapToInt(List::size).sum(); - hist.adjustOrPutValue(sum, 1, 1); + try (OutputPortCloseable> port = overlap.mkElementsPort()) { + for (OverlapGroup cloneOverlapGroup : CUtils.it(port)) { + int sum = cloneOverlapGroup.elements.stream().mapToInt(l -> l.isEmpty() ? 0 : 1).sum(); + totalSum += cloneOverlapGroup.elements.stream().mapToInt(List::size).sum(); + hist.adjustOrPutValue(sum, 1, 1); + } } for (int i = 1; i < readers.size(); i++) if (hist.get(i) != 0) diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index 5e59d2542..872dcd222 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -6,6 +6,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.VDJCObject; import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; import com.milaboratory.mixcr.postanalysis.WeightFunctions; @@ -16,7 +17,10 @@ import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessor; import com.milaboratory.mixcr.postanalysis.downsampling.ClonesOverlapDownsamplingPreprocessor; import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; -import com.milaboratory.mixcr.postanalysis.overlap.*; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapCharacteristic; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapIntegrationTest; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapUtil; import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey; @@ -32,7 +36,6 @@ import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; -import java.util.stream.IntStream; import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedBiophysics; import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedLengthOf; @@ -42,21 +45,21 @@ */ public class PostanalysisSchemaIntegrationTest { - private static ClonesIterable getClones(String sample) { - return new ClonesIterable(PostanalysisSchemaIntegrationTest.class.getResource("/sequences/big/yf_sample_data/" + sample + ".contigs.clns").getFile(), VDJCLibraryRegistry.getDefault()); + private static ClonotypeDataset getClones(String sample) { + return new ClonotypeDataset(sample, PostanalysisSchemaIntegrationTest.class.getResource("/sequences/big/yf_sample_data/" + sample + ".contigs.clns").getFile(), VDJCLibraryRegistry.getDefault()); } @Test public void test1() throws IOException { - ClonesIterable r1 = getClones("Ig-2_S2"); - ClonesIterable r2 = getClones("Ig-3_S3"); - ClonesIterable r3 = getClones("Ig-4_S4"); - ClonesIterable r4 = getClones("Ig-5_S5"); - ClonesIterable r5 = getClones("Ig1_S1"); - ClonesIterable r6 = getClones("Ig2_S2"); - ClonesIterable r7 = getClones("Ig3_S3"); - ClonesIterable r8 = getClones("Ig4_S4"); - ClonesIterable r9 = getClones("Ig5_S5"); + ClonotypeDataset r1 = getClones("Ig-2_S2"); + ClonotypeDataset r2 = getClones("Ig-3_S3"); + ClonotypeDataset r3 = getClones("Ig-4_S4"); + ClonotypeDataset r4 = getClones("Ig-5_S5"); + ClonotypeDataset r5 = getClones("Ig1_S1"); + ClonotypeDataset r6 = getClones("Ig2_S2"); + ClonotypeDataset r7 = getClones("Ig3_S3"); + ClonotypeDataset r8 = getClones("Ig4_S4"); + ClonotypeDataset r9 = getClones("Ig5_S5"); List> groups = new ArrayList<>(); @@ -126,11 +129,9 @@ public void test1() throws IOException { PostanalysisRunner runner = new PostanalysisRunner<>(); runner.addCharacteristics(individualPA.getAllCharacterisitcs()); - Iterable[] input = {r1, r2, r3, r4, r5, r6, r7, r8, r9}; - runner.setDatasets(input); + Dataset[] input = {r1, r2, r3, r4, r5, r6, r7, r8, r9}; - PostanalysisResult result = runner.run().setSampleIds(IntStream.range(0, 9).mapToObj(i -> "" + i).collect(Collectors.toList())); - result.setSampleIds(IntStream.range(0, input.length).mapToObj(i -> "" + i).collect(Collectors.toList())); + PostanalysisResult result = runner.run(input); String resultStr = OM.writeValueAsString(result); Assert.assertEquals(result, OM.readValue(resultStr, PostanalysisResult.class)); @@ -153,7 +154,7 @@ public void test1() throws IOException { CharacteristicGroupResult> r = result.getTable(individualPA.getGroup("cdr3Spectratype")); Assert.assertTrue(r.cells.stream() - .collect(Collectors.groupingBy(c -> c.sampleIndex, Collectors.mapping(c -> c.key.payload, Collectors.toSet()))) + .collect(Collectors.groupingBy(c -> c.datasetId, Collectors.mapping(c -> c.key.payload, Collectors.toSet()))) .values().stream().allMatch(l -> l.size() <= 11)); System.out.println(result.getTable(individualPA.getGroup("VSpectratype"))); @@ -194,7 +195,7 @@ public void testOverlap1() throws JsonProcessingException { for (List> by : Arrays.asList(byN, byAA, byAAAndV)) { System.out.println("============="); - OverlapIterable overlap = OverlapUtil.overlap(by, readers); + Dataset> overlap = OverlapUtil.overlap(sampleNames, by, readers); ClonesOverlapDownsamplingPreprocessor downsamplePreprocessor = new ClonesOverlapDownsamplingPreprocessor( new DownsampleValueChooser.Minimal(), @@ -227,10 +228,9 @@ public void testOverlap1() throws JsonProcessingException { PostanalysisRunner> pr = new PostanalysisRunner<>(); - pr.setDatasets(Arrays.asList(overlap)); pr.addCharacteristics(overlapPA.getAllCharacterisitcs()); - PostanalysisResult result = pr.run().setSampleIds(sampleNames); + PostanalysisResult result = pr.run(overlap); String resultStr = OM.writeValueAsString(result); Assert.assertEquals(result, OM.readValue(resultStr, PostanalysisResult.class)); From 39cda1bd63bcfdc2fda98eab5d989517f085f5a2 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Fri, 19 Feb 2021 02:23:39 +0300 Subject: [PATCH 092/282] MiLib upgrade. --- mixcr_completion | 1101 ---------------------------------------------- pom.xml | 3 +- 2 files changed, 2 insertions(+), 1102 deletions(-) delete mode 100644 mixcr_completion diff --git a/mixcr_completion b/mixcr_completion deleted file mode 100644 index 3f5c6029b..000000000 --- a/mixcr_completion +++ /dev/null @@ -1,1101 +0,0 @@ -#!/usr/bin/env bash -# -# mixcr Bash Completion -# ======================= -# -# Bash completion support for the `mixcr` command, -# generated by [picocli](http://picocli.info/) version 3.6.1. -# -# Installation -# ------------ -# -# 1. Source all completion scripts in your .bash_profile -# -# cd $YOUR_APP_HOME/bin -# for f in $(find . -name "*_completion"); do line=". $(pwd)/$f"; grep "$line" ~/.bash_profile || echo "$line" >> ~/.bash_profile; done -# -# 2. Open a new bash console, and type `mixcr [TAB][TAB]` -# -# 1a. Alternatively, if you have [bash-completion](https://github.com/scop/bash-completion) installed: -# Place this file in a `bash-completion.d` folder: -# -# * /etc/bash-completion.d -# * /usr/local/etc/bash-completion.d -# * ~/bash-completion.d -# -# Documentation -# ------------- -# The script is called by bash whenever [TAB] or [TAB][TAB] is pressed after -# 'mixcr (..)'. By reading entered command line parameters, -# it determines possible bash completions and writes them to the COMPREPLY variable. -# Bash then completes the user input if only one entry is listed in the variable or -# shows the options if more than one is listed in COMPREPLY. -# -# References -# ---------- -# [1] http://stackoverflow.com/a/12495480/1440785 -# [2] http://tiswww.case.edu/php/chet/bash/FAQ -# [3] https://www.gnu.org/software/bash/manual/html_node/The-Shopt-Builtin.html -# [4] http://zsh.sourceforge.net/Doc/Release/Options.html#index-COMPLETE_005fALIASES -# [5] https://stackoverflow.com/questions/17042057/bash-check-element-in-array-for-elements-in-another-array/17042655#17042655 -# [6] https://www.gnu.org/software/bash/manual/html_node/Programmable-Completion.html#Programmable-Completion -# - -if [ -n "$BASH_VERSION" ]; then - # Enable programmable completion facilities when using bash (see [3]) - shopt -s progcomp -elif [ -n "$ZSH_VERSION" ]; then - # Make alias a distinct command for completion purposes when using zsh (see [4]) - setopt COMPLETE_ALIASES - alias compopt=complete -fi - -# ArrContains takes two arguments, both of which are the name of arrays. -# It creates a temporary hash from lArr1 and then checks if all elements of lArr2 -# are in the hashtable. -# -# Returns zero (no error) if all elements of the 2nd array are in the 1st array, -# otherwise returns 1 (error). -# -# Modified from [5] -function ArrContains() { - local lArr1 lArr2 - declare -A tmp - eval lArr1=("\"\${$1[@]}\"") - eval lArr2=("\"\${$2[@]}\"") - for i in "${lArr1[@]}";{ [ -n "$i" ] && ((++tmp[$i]));} - for i in "${lArr2[@]}";{ [ -n "$i" ] && [ -z "${tmp[$i]}" ] && return 1;} - return 0 -} - -# Bash completion entry point function. -# _complete_mixcr finds which commands and subcommands have been specified -# on the command line and delegates to the appropriate function -# to generate possible options and subcommands for the last specified subcommand. -function _complete_mixcr() { - CMDS0=(help) - CMDS1=(analyze) - CMDS2=(align) - CMDS3=(assemble) - CMDS4=(assembleContigs) - CMDS5=(assemblePartial) - CMDS6=(extend) - CMDS7=(exportAlignments) - CMDS8=(exportAlignmentsPretty) - CMDS9=(exportClones) - CMDS10=(exportClonesPretty) - CMDS11=(exportReadsForClones) - CMDS12=(exportReads) - CMDS13=(mergeAlignments) - CMDS14=(filterAlignments) - CMDS15=(sortAlignments) - CMDS16=(alignmentsDiff) - CMDS17=(clonesDiff) - CMDS18=(alignmentsStat) - CMDS19=(listLibraries) - CMDS20=(versionInfo) - CMDS21=(pipelineInfo) - CMDS22=(slice) - CMDS23=(info) - CMDS24=(analyze help) - CMDS25=(analyze amplicon) - CMDS26=(analyze shotgun) - - ArrContains COMP_WORDS CMDS26 && { _picocli_mixcr_analyze_shotgun; return $?; } - ArrContains COMP_WORDS CMDS25 && { _picocli_mixcr_analyze_amplicon; return $?; } - ArrContains COMP_WORDS CMDS24 && { _picocli_mixcr_analyze_help; return $?; } - ArrContains COMP_WORDS CMDS23 && { _picocli_mixcr_info; return $?; } - ArrContains COMP_WORDS CMDS22 && { _picocli_mixcr_slice; return $?; } - ArrContains COMP_WORDS CMDS21 && { _picocli_mixcr_pipelineInfo; return $?; } - ArrContains COMP_WORDS CMDS20 && { _picocli_mixcr_versionInfo; return $?; } - ArrContains COMP_WORDS CMDS19 && { _picocli_mixcr_listLibraries; return $?; } - ArrContains COMP_WORDS CMDS18 && { _picocli_mixcr_alignmentsStat; return $?; } - ArrContains COMP_WORDS CMDS17 && { _picocli_mixcr_clonesDiff; return $?; } - ArrContains COMP_WORDS CMDS16 && { _picocli_mixcr_alignmentsDiff; return $?; } - ArrContains COMP_WORDS CMDS15 && { _picocli_mixcr_sortAlignments; return $?; } - ArrContains COMP_WORDS CMDS14 && { _picocli_mixcr_filterAlignments; return $?; } - ArrContains COMP_WORDS CMDS13 && { _picocli_mixcr_mergeAlignments; return $?; } - ArrContains COMP_WORDS CMDS12 && { _picocli_mixcr_exportReads; return $?; } - ArrContains COMP_WORDS CMDS11 && { _picocli_mixcr_exportReadsForClones; return $?; } - ArrContains COMP_WORDS CMDS10 && { _picocli_mixcr_exportClonesPretty; return $?; } - ArrContains COMP_WORDS CMDS9 && { _picocli_mixcr_exportClones; return $?; } - ArrContains COMP_WORDS CMDS8 && { _picocli_mixcr_exportAlignmentsPretty; return $?; } - ArrContains COMP_WORDS CMDS7 && { _picocli_mixcr_exportAlignments; return $?; } - ArrContains COMP_WORDS CMDS6 && { _picocli_mixcr_extend; return $?; } - ArrContains COMP_WORDS CMDS5 && { _picocli_mixcr_assemblePartial; return $?; } - ArrContains COMP_WORDS CMDS4 && { _picocli_mixcr_assembleContigs; return $?; } - ArrContains COMP_WORDS CMDS3 && { _picocli_mixcr_assemble; return $?; } - ArrContains COMP_WORDS CMDS2 && { _picocli_mixcr_align; return $?; } - ArrContains COMP_WORDS CMDS1 && { _picocli_mixcr_analyze; return $?; } - ArrContains COMP_WORDS CMDS0 && { _picocli_mixcr_help; return $?; } - - # No subcommands were specified; generate completions for the top-level command. - _picocli_mixcr; return $?; -} - -# Generates completions for the options and subcommands of the `mixcr` command. -function _picocli_mixcr() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="help analyze align assemble assembleContigs assemblePartial extend exportAlignments exportAlignmentsPretty exportClones exportClonesPretty exportReadsForClones exportReads mergeAlignments filterAlignments sortAlignments alignmentsDiff clonesDiff alignmentsStat listLibraries versionInfo pipelineInfo slice info" - FLAG_OPTS="-h --help -v --version -h --help" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `help` subcommand. -function _picocli_mixcr_help() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `analyze` subcommand. -function _picocli_mixcr_analyze() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="help amplicon shotgun" - FLAG_OPTS="" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `align` subcommand. -function _picocli_mixcr_align() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required -d --no-merge --write-all --buffers -a --save-description -g --save-reads" - ARG_OPTS="-s --species -r --report --json-report -b --library -p --parameters -O --not-aligned-R1 --not-aligned-R2 -n --limit -t --threads -c --chains" - - compopt +o default - - case ${PREV_WORD} in - -s|--species) - return - ;; - -r|--report) - return - ;; - --json-report) - return - ;; - -b|--library) - return - ;; - -p|--parameters) - return - ;; - -O) - return - ;; - --not-aligned-R1) - return - ;; - --not-aligned-R2) - return - ;; - -n|--limit) - return - ;; - -t|--threads) - return - ;; - -c|--chains) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `assemble` subcommand. -function _picocli_mixcr_assemble() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required --buffers -a --write-alignments" - ARG_OPTS="-p --parameters -r --report --json-report -O -t --threads" - - compopt +o default - - case ${PREV_WORD} in - -p|--parameters) - return - ;; - -r|--report) - return - ;; - --json-report) - return - ;; - -O) - return - ;; - -t|--threads) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `assembleContigs` subcommand. -function _picocli_mixcr_assembleContigs() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required" - ARG_OPTS="-O -r --report --debug-report --json-report -t --threads" - - compopt +o default - - case ${PREV_WORD} in - -O) - return - ;; - -r|--report) - return - ;; - --debug-report) - return - ;; - --json-report) - return - ;; - -t|--threads) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `assemblePartial` subcommand. -function _picocli_mixcr_assemblePartial() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required -o --overlapped-only -d --drop-partial" - ARG_OPTS="-O -r --report --json-report" - - compopt +o default - - case ${PREV_WORD} in - -O) - return - ;; - -r|--report) - return - ;; - --json-report) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `extend` subcommand. -function _picocli_mixcr_extend() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required" - ARG_OPTS="-c --chains -r --report --json-report -q --quality --v-anchor --j-anchor --min-v-score --min-j-score -t --threads" - - compopt +o default - - case ${PREV_WORD} in - -c|--chains) - return - ;; - -r|--report) - return - ;; - --json-report) - return - ;; - -q|--quality) - return - ;; - --v-anchor) - return - ;; - --j-anchor) - return - ;; - --min-v-score) - return - ;; - --min-j-score) - return - ;; - -t|--threads) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `exportAlignments` subcommand. -function _picocli_mixcr_exportAlignments() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force -v --with-spaces -lf --list-fields -s --no-spaces -targets -vHit -dHit -jHit -cHit -vGene -dGene -jGene -cGene -vFamily -dFamily -jFamily -cFamily -vHitScore -dHitScore -jHitScore -cHitScore -vHitsWithScore -dHitsWithScore -jHitsWithScore -cHitsWithScore -vHits -dHits -jHits -cHits -vGenes -dGenes -jGenes -cGenes -vFamilies -dFamilies -jFamilies -cFamilies -vAlignment -dAlignment -jAlignment -cAlignment -vAlignments -dAlignments -jAlignments -cAlignments -defaultAnchorPoints -readId -readIds -sequence -quality -descrR1 -descrR2 -descrsR1 -descrsR2 -readHistory -cloneId -cloneIdWithMappingType -vIdentityPercents -dIdentityPercents -jIdentityPercents -cIdentityPercents -vBestIdentityPercent -dBestIdentityPercent -jBestIdentityPercent -cBestIdentityPercent -chains -topChains" - ARG_OPTS="-c --chains -p --preset -pf --preset-file -n --limit -nFeature -qFeature -aaFeature -nFeatureImputed -aaFeatureImputed -minFeatureQuality -avrgFeatureQuality -lengthOf -nMutations -nMutationsRelative -aaMutations -aaMutationsRelative -mutationsDetailed -mutationsDetailedRelative -positionInReferenceOf -positionOf" - - compopt +o default - - case ${PREV_WORD} in - -c|--chains) - return - ;; - -p|--preset) - return - ;; - -pf|--preset-file) - return - ;; - -n|--limit) - return - ;; - -nFeature) - return - ;; - -qFeature) - return - ;; - -aaFeature) - return - ;; - -nFeatureImputed) - return - ;; - -aaFeatureImputed) - return - ;; - -minFeatureQuality) - return - ;; - -avrgFeatureQuality) - return - ;; - -lengthOf) - return - ;; - -nMutations) - return - ;; - -nMutationsRelative) - return - ;; - -aaMutations) - return - ;; - -aaMutationsRelative) - return - ;; - -mutationsDetailed) - return - ;; - -mutationsDetailedRelative) - return - ;; - -positionInReferenceOf) - return - ;; - -positionOf) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `exportAlignmentsPretty` subcommand. -function _picocli_mixcr_exportAlignmentsPretty() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force -t --top -a --gene -d --descriptions" - ARG_OPTS="-b --limit-before -n --limit -c --chains -s --skip -e --cdr3-equals -g --feature -r --read-contains --filter -i --read-ids" - - compopt +o default - - case ${PREV_WORD} in - -b|--limit-before) - return - ;; - -n|--limit) - return - ;; - -c|--chains) - return - ;; - -s|--skip) - return - ;; - -e|--cdr3-equals) - return - ;; - -g|--feature) - return - ;; - -r|--read-contains) - return - ;; - --filter) - return - ;; - -i|--read-ids) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `exportClones` subcommand. -function _picocli_mixcr_exportClones() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force -v --with-spaces -lf --list-fields -s --no-spaces -o --filter-out-of-frames -t --filter-stops -targets -vHit -dHit -jHit -cHit -vGene -dGene -jGene -cGene -vFamily -dFamily -jFamily -cFamily -vHitScore -dHitScore -jHitScore -cHitScore -vHitsWithScore -dHitsWithScore -jHitsWithScore -cHitsWithScore -vHits -dHits -jHits -cHits -vGenes -dGenes -jGenes -cGenes -vFamilies -dFamilies -jFamilies -cFamilies -vAlignment -dAlignment -jAlignment -cAlignment -vAlignments -dAlignments -jAlignments -cAlignments -defaultAnchorPoints -cloneId -count -fraction -sequence -quality -vIdentityPercents -dIdentityPercents -jIdentityPercents -cIdentityPercents -vBestIdentityPercent -dBestIdentityPercent -jBestIdentityPercent -cBestIdentityPercent -chains -topChains" - ARG_OPTS="-c --chains -p --preset -pf --preset-file -n --limit -q --minimal-clone-fraction -m --minimal-clone-count -nFeature -qFeature -aaFeature -nFeatureImputed -aaFeatureImputed -minFeatureQuality -avrgFeatureQuality -lengthOf -nMutations -nMutationsRelative -aaMutations -aaMutationsRelative -mutationsDetailed -mutationsDetailedRelative -positionInReferenceOf -positionOf" - - compopt +o default - - case ${PREV_WORD} in - -c|--chains) - return - ;; - -p|--preset) - return - ;; - -pf|--preset-file) - return - ;; - -n|--limit) - return - ;; - -q|--minimal-clone-fraction) - return - ;; - -m|--minimal-clone-count) - return - ;; - -nFeature) - return - ;; - -qFeature) - return - ;; - -aaFeature) - return - ;; - -nFeatureImputed) - return - ;; - -aaFeatureImputed) - return - ;; - -minFeatureQuality) - return - ;; - -avrgFeatureQuality) - return - ;; - -lengthOf) - return - ;; - -nMutations) - return - ;; - -nMutationsRelative) - return - ;; - -aaMutations) - return - ;; - -aaMutationsRelative) - return - ;; - -mutationsDetailed) - return - ;; - -mutationsDetailedRelative) - return - ;; - -positionInReferenceOf) - return - ;; - -positionOf) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `exportClonesPretty` subcommand. -function _picocli_mixcr_exportClonesPretty() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force" - ARG_OPTS="-b --limitBefore -n --limit -i --clone-ids -s --skip -c --chains -e --cdr3-equals -r --clonal-sequence-contains" - - compopt +o default - - case ${PREV_WORD} in - -b|--limitBefore) - return - ;; - -n|--limit) - return - ;; - -i|--clone-ids) - return - ;; - -s|--skip) - return - ;; - -c|--chains) - return - ;; - -e|--cdr3-equals) - return - ;; - -r|--clonal-sequence-contains) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `exportReadsForClones` subcommand. -function _picocli_mixcr_exportReadsForClones() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force -s --separate" - ARG_OPTS="--id" - - compopt +o default - - case ${PREV_WORD} in - --id) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `exportReads` subcommand. -function _picocli_mixcr_exportReads() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `mergeAlignments` subcommand. -function _picocli_mixcr_mergeAlignments() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `filterAlignments` subcommand. -function _picocli_mixcr_filterAlignments() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required -x --chimeras-only" - ARG_OPTS="-c --chains -g --contains-feature -e --cdr3-equals -i --read-ids -n --limit" - - compopt +o default - - case ${PREV_WORD} in - -c|--chains) - return - ;; - -g|--contains-feature) - return - ;; - -e|--cdr3-equals) - return - ;; - -i|--read-ids) - return - ;; - -n|--limit) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `sortAlignments` subcommand. -function _picocli_mixcr_sortAlignments() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `alignmentsDiff` subcommand. -function _picocli_mixcr_alignmentsDiff() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force" - ARG_OPTS="-o1 --only-in-first -o2 --only-in-second -d1 --diff-from-first -d2 --diff-from-second -g --gene-feature -l --top-hits-level" - - compopt +o default - - case ${PREV_WORD} in - -o1|--only-in-first) - return - ;; - -o2|--only-in-second) - return - ;; - -d1|--diff-from-first) - return - ;; - -d2|--diff-from-second) - return - ;; - -g|--gene-feature) - return - ;; - -l|--top-hits-level) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `clonesDiff` subcommand. -function _picocli_mixcr_clonesDiff() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force -v -j -c" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `alignmentsStat` subcommand. -function _picocli_mixcr_alignmentsStat() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `listLibraries` subcommand. -function _picocli_mixcr_listLibraries() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `versionInfo` subcommand. -function _picocli_mixcr_versionInfo() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `pipelineInfo` subcommand. -function _picocli_mixcr_pipelineInfo() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose --json" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `slice` subcommand. -function _picocli_mixcr_slice() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --overwrite-if-required" - ARG_OPTS="-i --id" - - compopt +o default - - case ${PREV_WORD} in - -i|--id) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `info` subcommand. -function _picocli_mixcr_info() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -t --table" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `help` subcommand. -function _picocli_mixcr_analyze_help() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help" - ARG_OPTS="" - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `amplicon` subcommand. -function _picocli_mixcr_analyze_amplicon() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --impute-germline-on-export --only-productive --contig-assembly --do-not-extend-alignments" - ARG_OPTS="-s --species --starting-material -r --report --align --assemblePartial --extend --assemble --assembleContigs --export --assemble-partial-rounds --receptor-type --5-end --3-end --adapters --region-of-interest" - startingMaterial_OPTION_ARGS="rna dna" # _StartingMaterial values - chains_OPTION_ARGS="tcr bcr xcr tra trb trd trg igh igk igl" # --receptor-type values - 5End_OPTION_ARGS="no-v-primers v-primers" # --5-end values - 3End_OPTION_ARGS="j-primers j-c-intron-primers c-primers" # --3-end values - adapters_OPTION_ARGS="adapters-present no-adapters" # --adapters values - - compopt +o default - - case ${PREV_WORD} in - -s|--species) - return - ;; - --starting-material) - COMPREPLY=( $( compgen -W "${startingMaterial_OPTION_ARGS}" -- ${CURR_WORD} ) ) - return $? - ;; - -r|--report) - return - ;; - --align) - return - ;; - --assemblePartial) - return - ;; - --extend) - return - ;; - --assemble) - return - ;; - --assembleContigs) - return - ;; - --export) - return - ;; - --assemble-partial-rounds) - return - ;; - --receptor-type) - COMPREPLY=( $( compgen -W "${chains_OPTION_ARGS}" -- ${CURR_WORD} ) ) - return $? - ;; - --5-end) - COMPREPLY=( $( compgen -W "${5End_OPTION_ARGS}" -- ${CURR_WORD} ) ) - return $? - ;; - --3-end) - COMPREPLY=( $( compgen -W "${3End_OPTION_ARGS}" -- ${CURR_WORD} ) ) - return $? - ;; - --adapters) - COMPREPLY=( $( compgen -W "${adapters_OPTION_ARGS}" -- ${CURR_WORD} ) ) - return $? - ;; - --region-of-interest) - return - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Generates completions for the options and subcommands of the `shotgun` subcommand. -function _picocli_mixcr_analyze_shotgun() { - # Get completion data - CURR_WORD=${COMP_WORDS[COMP_CWORD]} - PREV_WORD=${COMP_WORDS[COMP_CWORD-1]} - - COMMANDS="" - FLAG_OPTS="-h --help -nw --no-warnings --verbose -f --force-overwrite --force --impute-germline-on-export --only-productive --contig-assembly --do-not-extend-alignments" - ARG_OPTS="-s --species --starting-material -r --report --align --assemblePartial --extend --assemble --assembleContigs --export --assemble-partial-rounds --receptor-type" - startingMaterial_OPTION_ARGS="rna dna" # _StartingMaterial values - chains_OPTION_ARGS="tcr bcr xcr tra trb trd trg igh igk igl" # --receptor-type values - - compopt +o default - - case ${PREV_WORD} in - -s|--species) - return - ;; - --starting-material) - COMPREPLY=( $( compgen -W "${startingMaterial_OPTION_ARGS}" -- ${CURR_WORD} ) ) - return $? - ;; - -r|--report) - return - ;; - --align) - return - ;; - --assemblePartial) - return - ;; - --extend) - return - ;; - --assemble) - return - ;; - --assembleContigs) - return - ;; - --export) - return - ;; - --assemble-partial-rounds) - return - ;; - --receptor-type) - COMPREPLY=( $( compgen -W "${chains_OPTION_ARGS}" -- ${CURR_WORD} ) ) - return $? - ;; - esac - - if [[ "${CURR_WORD}" == -* ]]; then - COMPREPLY=( $(compgen -W "${FLAG_OPTS} ${ARG_OPTS}" -- ${CURR_WORD}) ) - else - COMPREPLY=( $(compgen -W "${COMMANDS}" -- ${CURR_WORD}) ) - fi -} - -# Define a completion specification (a compspec) for the -# `mixcr`, `mixcr.sh`, and `mixcr.bash` commands. -# Uses the bash `complete` builtin (see [6]) to specify that shell function -# `_complete_mixcr` is responsible for generating possible completions for the -# current word on the command line. -# The `-o default` option means that if the function generated no matches, the -# default Bash completions and the Readline default filename completions are performed. -complete -F _complete_mixcr -o default mixcr mixcr.sh mixcr.bash - - -Process finished with exit code 0 diff --git a/pom.xml b/pom.xml index ff6a309eb..d06edc3ea 100644 --- a/pom.xml +++ b/pom.xml @@ -40,7 +40,8 @@ UTF-8 - 1.14-dc00625 + + 1.14-e241b77 SNAPSHOT From 1b7a84ff643bd92104da0684961c625ebec36f87 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Fri, 19 Feb 2021 14:51:50 +0300 Subject: [PATCH 093/282] '--read-buffer' option added to specify custom input buffer size in align --- pom.xml | 2 +- .../milaboratory/mixcr/cli/CommandAlign.java | 20 +++++++++++++++++-- 2 files changed, 19 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index d06edc3ea..c1226242f 100644 --- a/pom.xml +++ b/pom.xml @@ -41,7 +41,7 @@ UTF-8 - 1.14-e241b77 + 1.14-e970c20 SNAPSHOT diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 1be5a5d19..9ff0f229c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -45,6 +45,7 @@ import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.core.PairedEndReadsLayout; import com.milaboratory.core.Target; +import com.milaboratory.core.io.CompressionType; import com.milaboratory.core.io.sequence.SequenceRead; import com.milaboratory.core.io.sequence.SequenceReaderCloseable; import com.milaboratory.core.io.sequence.SequenceWriter; @@ -73,6 +74,7 @@ import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; +import java.io.FileInputStream; import java.io.IOException; import java.nio.file.Paths; import java.util.*; @@ -107,6 +109,10 @@ protected List getOutputFiles() { return inOut.subList(inOut.size() - 1, inOut.size()); } + @Option(description = CommonDescriptions.SPECIES, + names = {"--read-buffer"}) + public int readBufferSize = 1 << 20; + @Option(description = CommonDescriptions.SPECIES, names = {"-s", "--species"}, required = true) @@ -288,7 +294,12 @@ public boolean isInputPaired() { public SequenceReaderCloseable createReader() throws IOException { if (isInputPaired()) - return new PairedFastqReader(getInputFiles().get(0), getInputFiles().get(1), true); + return new PairedFastqReader(new FileInputStream(getInputFiles().get(0)), new FileInputStream(getInputFiles().get(1)), + SingleFastqReader.DEFAULT_QUALITY_FORMAT, + CompressionType.detectCompressionType(getInputFiles().get(0)), + true, + readBufferSize, + true, true); else { String in = getInputFiles().get(0); String[] s = in.split("\\."); @@ -298,7 +309,12 @@ public SequenceReaderCloseable createReader() throws IOE true ); else - return new SingleFastqReader(in, true); + return new SingleFastqReader(new FileInputStream(in), + SingleFastqReader.DEFAULT_QUALITY_FORMAT, + CompressionType.detectCompressionType(in), + true, + readBufferSize, + true, true); } } From 09e6cda7c5615bf11c4ae20b305acb95588895c2 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Fri, 19 Feb 2021 15:06:59 +0300 Subject: [PATCH 094/282] Support for longer sequences in FullSeqAssembler. --- .../milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index f63af73cc..a3e3c167d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -76,7 +76,7 @@ public final class FullSeqAssembler { private static final int N_VARIANT_INDEX = NucleotideSequence.ALPHABET.basicSize() + 2; /** number of letters to the left of reference V gene in the global coordinate grid */ - private static final int N_LEFT_DUMMIES = 1024; // fixme + private static final int N_LEFT_DUMMIES = 1 << 14; // fixme /** clone factory */ final CloneFactory cloneFactory; /** initial clone */ From 731f4026b1a92f4a294948a4958d14e734181c9b Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 24 Feb 2021 23:45:07 +0300 Subject: [PATCH 095/282] Increased alignment size initial guess for sorting. Migration to new milib with root-level singleton detection in HashSorter. --- pom.xml | 2 +- src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index c1226242f..30e4df01c 100644 --- a/pom.xml +++ b/pom.xml @@ -41,7 +41,7 @@ UTF-8 - 1.14-e970c20 + 1.14-2d70391 SNAPSHOT diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index a2e0d8b88..36a6beac5 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -238,7 +238,7 @@ public synchronized void collateAlignments(OutputPort alignments new CloneIdHash(), CloneIdComparator, 5, tempFolder, 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), - 1 << 28 /* 256 Mb */, 512); + 1 << 28 /* 256 Mb */, 1 << 18 /* 256 Kb */); // Here we wait for the first layer of hash collation to finish "write" stage // (on average 30% time of full collation process) From 455071daa3086c800cdad756dc157636408610e7 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 26 Feb 2021 11:35:54 +0300 Subject: [PATCH 096/282] PA: better preprocessor abstraction (#17) * New PA abstraction * Postanalysis: added "select top" preprocessor * Ability to select diversity & overlap measures in corresponding characteristics --- .../mixcr/postanalysis/Characteristic.java | 20 +- .../mixcr/postanalysis/Dataset.java | 17 +- .../mixcr/postanalysis/MappingFunction.java | 15 ++ .../postanalysis/PostanalysisResult.java | 4 +- .../postanalysis/PostanalysisRunner.java | 107 ++++++--- .../mixcr/postanalysis/SetPreprocessor.java | 53 +---- .../postanalysis/SetPreprocessorFactory.java | 133 ++++++++++++ .../postanalysis/SetPreprocessorSetup.java | 12 ++ .../postanalysis/SetPreprocessorStat.java | 6 + .../mixcr/postanalysis/WeightFunctions.java | 4 + .../additive/AdditiveCharacteristic.java | 2 +- .../additive/AdditiveCharacteristics.java | 62 +++--- .../diversity/DiversityAggregator.java | 42 +++- .../diversity/DiversityCharacteristic.java | 15 +- .../ClonesDownsamplingPreprocessor.java | 38 ---- ...lonesDownsamplingPreprocessorFactory.java} | 31 ++- .../DownsamplingPreprocessor.java | 126 +++++------ .../downsampling/DownsamplingUtil.java | 14 -- .../OverlapDownsamplingPreprocessor.java | 170 --------------- .../overlap/OverlapAggregator.java | 33 ++- .../overlap/OverlapCharacteristic.java | 24 ++- .../preproc/ElementPredicate.java | 80 +++---- .../preproc/FilterPreprocessor.java | 80 ++++--- .../postanalysis/preproc/FilteredDataset.java | 29 --- .../preproc/FilteredOutputPortCloseable.java | 34 --- .../postanalysis/preproc/NoPreprocessing.java | 48 +++-- .../preproc/OverlapPreprocessorAdapter.java | 130 +++++++++++ .../preproc/PreprocessorChain.java | 162 ++++++++++---- .../mixcr/postanalysis/preproc/SelectTop.java | 204 ++++++++++++++++++ .../SpectratypeCharacteristic.java | 2 +- .../mixcr/postanalysis/TestDataset.java | 12 ++ .../mixcr/postanalysis/TestObject.java | 5 + .../additive/AdditiveCharacteristicsTest.java | 6 +- .../DiversityCharacteristicTest.java | 2 +- .../DownsamplingPreprocessorTest.java | 6 +- .../OverlapDownsamplingPreprocessorTest.java | 47 ++-- .../overlap/OverlapCharacteristicTest.java | 2 +- .../preproc/PreprocessorChainTest.java | 117 ++++++++++ .../postanalysis/preproc/SelectTopTest.java | 167 ++++++++++++++ .../ui/PostanalysisSchemaIntegrationTest.java | 29 +-- 40 files changed, 1383 insertions(+), 707 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java rename src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/{ClonesOverlapDownsamplingPreprocessor.java => ClonesDownsamplingPreprocessorFactory.java} (50%) delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java index a1d6a7cd1..9038b76d1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java @@ -29,11 +29,13 @@ public abstract class Characteristic { @JsonProperty("name") public final String name; @JsonProperty("preproc") - public final SetPreprocessor preprocessor; + public final SetPreprocessorFactory preprocessor; @JsonProperty("weight") public final WeightFunction weight; - public Characteristic(String name, SetPreprocessor preprocessor, WeightFunction weight) { + public Characteristic(String name, + SetPreprocessorFactory preprocessor, + WeightFunction weight) { this.name = name; this.preprocessor = preprocessor; this.weight = weight; @@ -42,11 +44,6 @@ public Characteristic(String name, SetPreprocessor preprocessor, WeightFuncti /** Create aggregator for further processing of a given dataset */ protected abstract Aggregator createAggregator(Dataset dataset); - /** override name & preproc */ - public Characteristic override(String nameOverride, SetPreprocessor preprocOverride) { - return new CharacteristicWrapper<>(nameOverride, preprocOverride, this); - } - @Override public boolean equals(Object o) { if (this == o) return true; @@ -62,20 +59,25 @@ public int hashCode() { return Objects.hash(name, preprocessor, weight); } + /** override name & preproc */ + public Characteristic override(String nameOverride, SetPreprocessorFactory preprocOverride) { + return new CharacteristicWrapper<>(nameOverride, preprocOverride, this); + } + public static final class CharacteristicWrapper extends Characteristic { @JsonProperty("inner") public final Characteristic inner; @JsonCreator public CharacteristicWrapper(@JsonProperty("name") String name, - @JsonProperty("preproc") SetPreprocessor preprocessor, + @JsonProperty("preproc") SetPreprocessorFactory preprocessor, @JsonProperty("inner") Characteristic inner) { super(name == null ? inner.name : name, preprocessor == null ? inner.preprocessor : preprocessor, inner.weight); this.inner = inner; } @Override - public Characteristic override(String nameOverride, SetPreprocessor preprocOverride) { + public Characteristic override(String nameOverride, SetPreprocessorFactory preprocOverride) { return new CharacteristicWrapper<>(nameOverride, preprocOverride, inner); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java index a56e0e3b9..729e08a35 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java @@ -2,9 +2,6 @@ import cc.redberry.pipe.OutputPortCloseable; -import java.util.UUID; -import java.util.function.Supplier; - /** * */ @@ -15,9 +12,7 @@ public interface Dataset { /** Closeable port of dataset elements */ OutputPortCloseable mkElementsPort(); - /** Uses random UUID as dataset id */ - static Dataset fromSupplier(Supplier> supp) { - final String id = UUID.randomUUID().toString(); + static Dataset empty(String id) { return new Dataset() { @Override public String id() { @@ -26,7 +21,15 @@ public String id() { @Override public OutputPortCloseable mkElementsPort() { - return supp.get(); + return new OutputPortCloseable() { + @Override + public void close() {} + + @Override + public K take() { + return null; + } + }; } }; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java new file mode 100644 index 000000000..1d7c3568b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java @@ -0,0 +1,15 @@ +package com.milaboratory.mixcr.postanalysis; + +import java.util.function.Function; + +/** + * + */ +public interface MappingFunction extends Function { + MappingFunction identity = t -> t; + + @SuppressWarnings("unchecked") + static MappingFunction identity() { + return (MappingFunction) identity; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index bc0d0286e..698dc8a07 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -70,12 +70,12 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; PostanalysisResult that = (PostanalysisResult) o; - return Objects.equals(datasetIds, that.datasetIds) && Objects.equals(data, that.data) && Objects.equals(cached, that.cached); + return Objects.equals(datasetIds, that.datasetIds) && Objects.equals(data, that.data); } @Override public int hashCode() { - return Objects.hash(datasetIds, data, cached); + return Objects.hash(datasetIds, data); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index 501688b3b..fba00ae0f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -1,13 +1,14 @@ package com.milaboratory.mixcr.postanalysis; import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.InputPort; import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.util.CanReportProgressAndStage; import java.util.*; -import java.util.function.Function; import java.util.stream.Collectors; +import java.util.stream.IntStream; /** * @param type of objects @@ -53,42 +54,98 @@ public PostanalysisResult run(List> datasets) { return run(datasets.toArray(new Dataset[0])); } + /** Run PA for a given datasets */ + @SuppressWarnings("unchecked") public PostanalysisResult run(Dataset... datasets) { stage = "Preparing"; progress = 0.0; isFinished = false; - Map, List>> characteristicsByPrep = - characteristics.stream() - .collect(Collectors.groupingBy(c -> c.preprocessor)); - - Map, Map[]>> result = new IdentityHashMap<>(); + // charID -> proc (deduplicated) + Map> id2proc = new HashMap<>(); + Map, SetPreprocessor> distinctProcs = new HashMap<>(); + Map, List>> proc2char = new HashMap<>(); + for (Characteristic ch : characteristics) { + id2proc.put(ch.name, distinctProcs.computeIfAbsent(ch.preprocessor, __ -> ch.preprocessor.getInstance())); + SetPreprocessor proc = distinctProcs.get(ch.preprocessor); + proc2char.computeIfAbsent(proc, __ -> new ArrayList<>()).add(ch); + } + List> procs = id2proc.values().stream().distinct().collect(Collectors.toList()); - for (Map.Entry, List>> e : characteristicsByPrep.entrySet()) { - Function, Dataset> prepFunction = e.getKey().setup(datasets); - for (Dataset dataset : datasets) { - List> characteristics = e.getValue(); + while (true) { + // next setup iterations + List> setupSteps = procs.stream() + .map(SetPreprocessor::nextSetupStep) + .filter(Objects::nonNull) + .collect(Collectors.toList()); - List> aggregators = characteristics.stream() - .map(c -> c.createAggregator(dataset)) - .collect(Collectors.toList()); + if (setupSteps.isEmpty()) + break; - try (OutputPortCloseable port = prepFunction.apply(dataset).mkElementsPort()) { - for (T o : CUtils.it(port)) - for (Aggregator agg : aggregators) - agg.consume(o); + // initialize setups + for (SetPreprocessorSetup s : setupSteps) { + s.initialize(datasets.length); + } + // inputConsumers[datasetIndex] - all consumers for i-th dataset + List>> inputConsumers = IntStream + .range(0, datasets.length) + .mapToObj(i -> setupSteps.stream() + .map(s -> s.consumer(i)) + .collect(Collectors.toList()) + ).collect(Collectors.toList()); + + for (int i = 0; i < datasets.length; i++) { + Dataset ds = datasets[i]; + try (OutputPortCloseable port = ds.mkElementsPort()) { + for (T t : CUtils.it(port)) { + for (InputPort c : inputConsumers.get(i)) { + c.put(t); + } + } + } + for (InputPort c : inputConsumers.get(i)) { + c.put(null); } + } + } + + // mapper functions + Map, MappingFunction>[] mappingFunctions = new Map[datasets.length]; + for (int i = 0; i < datasets.length; i++) { + mappingFunctions[i] = new HashMap<>(); + for (SetPreprocessor p : procs) { + mappingFunctions[i].put(p, p.getMapper(i)); + } + } - for (int charIndex = 0; charIndex < characteristics.size(); charIndex++) { - @SuppressWarnings("unchecked") - Map[]> charValues = result.computeIfAbsent( - characteristics.get(charIndex), - __ -> new HashMap<>()); - if (charValues.containsKey(dataset.id())) - throw new IllegalArgumentException("Dataset occurred twice."); - charValues.put(dataset.id(), aggregators.get(charIndex).result()); + Map, Map[]>> result = new IdentityHashMap<>(); + for (int i = 0; i < datasets.length; i++) { + Dataset dataset = datasets[i]; + + Map, Aggregator> aggregators = characteristics.stream() + .collect(Collectors.toMap(c -> c, c -> c.createAggregator(dataset))); + + try (OutputPortCloseable port = dataset.mkElementsPort()) { + for (T o : CUtils.it(port)) { + for (Map.Entry, MappingFunction> e : mappingFunctions[i].entrySet()) { + MappingFunction mapper = e.getValue(); + T oMapped = mapper.apply(o); + if (oMapped != null) + for (Characteristic ch : proc2char.get(e.getKey())) { + aggregators.get(ch).consume(oMapped); + } + } } } + + for (Characteristic characteristic : characteristics) { + Map[]> charValues = result.computeIfAbsent( + characteristic, + __ -> new HashMap<>()); + if (charValues.containsKey(dataset.id())) + throw new IllegalArgumentException("Dataset occurred twice."); + charValues.put(dataset.id(), aggregators.get(characteristic).result()); + } } isFinished = true; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index d3af897d6..7381e525c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -1,59 +1,14 @@ package com.milaboratory.mixcr.postanalysis; -import com.fasterxml.jackson.annotation.JsonAutoDetect; -import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import com.fasterxml.jackson.annotation.JsonSubTypes; -import com.fasterxml.jackson.annotation.JsonTypeInfo; -import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessor; -import com.milaboratory.mixcr.postanalysis.downsampling.ClonesOverlapDownsamplingPreprocessor; -import com.milaboratory.mixcr.postanalysis.preproc.*; - -import java.util.ArrayList; -import java.util.List; -import java.util.function.Function; - /** * */ -@JsonAutoDetect -@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") -@JsonSubTypes({ - @JsonSubTypes.Type(value = NoPreprocessing.class, name = "none"), - @JsonSubTypes.Type(value = ClonesDownsamplingPreprocessor.class, name = "downsample"), - @JsonSubTypes.Type(value = ClonesOverlapDownsamplingPreprocessor.class, name = "overlapDownsample"), - @JsonSubTypes.Type(value = PreprocessorChain.class, name = "chain"), - @JsonSubTypes.Type(value = FilterPreprocessor.class, name = "filter"), -}) -@JsonIgnoreProperties(ignoreUnknown = true) public interface SetPreprocessor { - Function, Dataset> setup(Dataset[] sets); - - default String[] description() { - return new String[0]; - } + SetPreprocessorSetup nextSetupStep(); - default SetPreprocessor filter(boolean before, ElementPredicate... predicates) { - FilterPreprocessor filter = new FilterPreprocessor<>(predicates); - if (this instanceof PreprocessorChain) { - PreprocessorChain p = (PreprocessorChain) this; - List> list = new ArrayList<>(); - if (before) { - list.add(filter); - list.addAll(p.chain); - } else { - list.addAll(p.chain); - list.add(filter); - } - return new PreprocessorChain<>(list); - } else - return before ? new PreprocessorChain<>(filter, this) : new PreprocessorChain<>(this, filter); - } - - default SetPreprocessor filterAfter(ElementPredicate... predicates) { - return filter(false, predicates); - } + MappingFunction getMapper(int iDataset); - default SetPreprocessor filterFirst(ElementPredicate... predicates) { - return filter(true, predicates); + default SetPreprocessorStat getStat() { + return null; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java new file mode 100644 index 000000000..3604e4543 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java @@ -0,0 +1,133 @@ +package com.milaboratory.mixcr.postanalysis; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.InputPort; +import cc.redberry.pipe.OutputPortCloseable; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.preproc.*; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.IntStream; + +/** + * + */ +@JsonAutoDetect( + getterVisibility = JsonAutoDetect.Visibility.NONE, + setterVisibility = JsonAutoDetect.Visibility.NONE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE +) +@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") +@JsonSubTypes({ + @JsonSubTypes.Type(value = NoPreprocessing.Factory.class, name = "none"), + @JsonSubTypes.Type(value = ClonesDownsamplingPreprocessorFactory.class, name = "downsample"), + @JsonSubTypes.Type(value = OverlapPreprocessorAdapter.Factory.class, name = "overlap"), + @JsonSubTypes.Type(value = PreprocessorChain.Factory.class, name = "chain"), + @JsonSubTypes.Type(value = FilterPreprocessor.Factory.class, name = "filter"), + @JsonSubTypes.Type(value = SelectTop.Factory.class, name = "selectTop"), +}) +@JsonIgnoreProperties(ignoreUnknown = true) +public interface SetPreprocessorFactory { + SetPreprocessor getInstance(); + + default String[] description() { + return new String[0]; + } + + @SuppressWarnings("unchecked") + default SetPreprocessorFactory filter(boolean before, ElementPredicate... predicates) { + FilterPreprocessor.Factory filter = new FilterPreprocessor.Factory<>(Arrays.asList(predicates)); + if (this instanceof PreprocessorChain.Factory) { + PreprocessorChain.Factory p = (PreprocessorChain.Factory) this; + List> list = new ArrayList<>(); + if (before) { + list.add(filter); + list.addAll(p.chain); + } else { + list.addAll(p.chain); + list.add(filter); + } + return new PreprocessorChain.Factory<>(list); + } else + return before + ? new PreprocessorChain.Factory<>(filter, this) + : new PreprocessorChain.Factory<>(this, filter); + } + + default SetPreprocessorFactory filterAfter(ElementPredicate... predicates) { + return filter(false, predicates); + } + + default SetPreprocessorFactory filterFirst(ElementPredicate... predicates) { + return filter(true, predicates); + } + + @SuppressWarnings("unchecked") + static Dataset[] processDatasets(SetPreprocessor proc, Dataset... initial) { + while (true) { + SetPreprocessorSetup setup = proc.nextSetupStep(); + if (setup == null) { + Dataset[] result = new Dataset[initial.length]; + for (int i = 0; i < initial.length; i++) { + int datasetIdx = i; + MappingFunction mapper = proc.getMapper(datasetIdx); + result[i] = new Dataset() { + @Override + public String id() { + return initial[datasetIdx].id(); + } + + @Override + public OutputPortCloseable mkElementsPort() { + OutputPortCloseable inner = initial[datasetIdx].mkElementsPort(); + return new OutputPortCloseable() { + @Override + public void close() { + inner.close(); + } + + @Override + public T take() { + while (true) { + T t = inner.take(); + if (t == null) + return null; + + T r = mapper.apply(t); + if (r == null) + continue; + return r; + } + } + }; + } + }; + } + return result; + } + setup.initialize(initial.length); + + List> consumers = IntStream.range(0, initial.length) + .mapToObj(setup::consumer) + .collect(Collectors.toList()); + + for (int i = 0; i < initial.length; i++) { + try (OutputPortCloseable port = initial[i].mkElementsPort()) { + for (T t : CUtils.it(port)) { + consumers.get(i).put(t); + } + } + } + for (InputPort c : consumers) { + c.put(null); + } + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java new file mode 100644 index 000000000..9c48d95ed --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java @@ -0,0 +1,12 @@ +package com.milaboratory.mixcr.postanalysis; + +import cc.redberry.pipe.InputPort; + +/** + * + */ +public interface SetPreprocessorSetup { + void initialize(int nDatasets); + + InputPort consumer(int i); +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java new file mode 100644 index 000000000..aa2a62bc1 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java @@ -0,0 +1,6 @@ +package com.milaboratory.mixcr.postanalysis; + +/** + * + */ +public interface SetPreprocessorStat {} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java index 14b9ac15e..1a85de5cf 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java @@ -8,6 +8,8 @@ public final class WeightFunctions { private WeightFunctions() {} + public static final Count Count = new Count(); + public static final class Count implements WeightFunction { @Override public double weight(Clone clone) { @@ -27,6 +29,8 @@ public int hashCode() { } } + public static final NoWeight NoWeight = new NoWeight(); + public static final class NoWeight implements WeightFunction { @Override public double weight(T clone) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java index 788c0bd51..39c350b97 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java @@ -28,7 +28,7 @@ public class AdditiveCharacteristic extends Characteristic { @JsonCreator public AdditiveCharacteristic(@JsonProperty("name") String name, - @JsonProperty("preproc") SetPreprocessor preprocessor, + @JsonProperty("preproc") SetPreprocessorFactory preprocessor, @JsonProperty("weight") WeightFunction weight, @JsonProperty("key") KeyFunction keyFunction, @JsonProperty("metric") AdditiveMetric metric, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java index fb1824390..8e2d59b84 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java @@ -1,7 +1,7 @@ package com.milaboratory.mixcr.postanalysis.additive; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; import com.milaboratory.mixcr.postanalysis.WeightFunctions; import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions.VJGenes; import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; @@ -18,7 +18,7 @@ private AdditiveCharacteristics() {} public static final String readCountKey = "readCount"; - public static AdditiveCharacteristic readCount(SetPreprocessor preproc) { + public static AdditiveCharacteristic readCount(SetPreprocessorFactory preproc) { return new AdditiveCharacteristic<>(readCountKey, preproc, new WeightFunctions.Count(), new KeyFunctions.Named<>(readCountKey), @@ -29,7 +29,7 @@ public static AdditiveCharacteristic readCount(SetPreprocessor clonotypeCount(SetPreprocessor preproc) { + public static AdditiveCharacteristic clonotypeCount(SetPreprocessorFactory preproc) { return new AdditiveCharacteristic<>(cloneCountKey, preproc, new WeightFunctions.NoWeight<>(), new KeyFunctions.Named<>(cloneCountKey), @@ -39,10 +39,10 @@ public static AdditiveCharacteristic clonotypeCount(SetPreprocess } public static AdditiveCharacteristic weightedLengthOf(GeneFeature gf, boolean aa) { - return weightedLengthOf(new NoPreprocessing<>(), gf, aa); + return weightedLengthOf(NoPreprocessing.factory(), gf, aa); } - public static AdditiveCharacteristic weightedLengthOf(SetPreprocessor preproc, GeneFeature gf, boolean aa) { + public static AdditiveCharacteristic weightedLengthOf(SetPreprocessorFactory preproc, GeneFeature gf, boolean aa) { String name = (aa ? "aa" : "nt") + "LengthOf" + GeneFeature.encode(gf); return new AdditiveCharacteristic<>( name, @@ -55,7 +55,7 @@ public static AdditiveCharacteristic weightedLengthOf(SetPreproce ); } - public static AdditiveCharacteristic weightedAddedNucleotides(SetPreprocessor preproc) { + public static AdditiveCharacteristic weightedAddedNucleotides(SetPreprocessorFactory preproc) { String name = "AddedNucleotides"; return new AdditiveCharacteristic<>( name, @@ -69,10 +69,10 @@ public static AdditiveCharacteristic weightedAddedNucleotides(Set } public static AdditiveCharacteristic weightedBbiophysicsNormalized(AAProperties.AAProperty property, GeneFeature gf) { - return weightedBbiophysicsNormalized(new NoPreprocessing<>(), property, gf); + return weightedBbiophysicsNormalized(NoPreprocessing.factory(), property, gf); } - public static AdditiveCharacteristic weightedBbiophysicsNormalized(SetPreprocessor preproc, AAProperties.AAProperty property, GeneFeature gf) { + public static AdditiveCharacteristic weightedBbiophysicsNormalized(SetPreprocessorFactory preproc, AAProperties.AAProperty property, GeneFeature gf) { String name = property.name() + "of" + GeneFeature.encode(gf) + "Normalized"; return new AdditiveCharacteristic<>( name, @@ -86,10 +86,10 @@ public static AdditiveCharacteristic weightedBbiophysicsNormalize } public static AdditiveCharacteristic weightedBiophysics(AAProperties.AAProperty property, GeneFeature gf, AAProperties.Adjustment adjustment, int nLetters) { - return weightedBiophysics(new NoPreprocessing<>(), property, gf, adjustment, nLetters); + return weightedBiophysics(NoPreprocessing.factory(), property, gf, adjustment, nLetters); } - public static AdditiveCharacteristic weightedBiophysics(SetPreprocessor preproc, AAProperties.AAProperty property, GeneFeature gf, AAProperties.Adjustment adjustment, int nLetters) { + public static AdditiveCharacteristic weightedBiophysics(SetPreprocessorFactory preproc, AAProperties.AAProperty property, GeneFeature gf, AAProperties.Adjustment adjustment, int nLetters) { String name = property.name() + "of" + GeneFeature.encode(gf); return new AdditiveCharacteristic<>( name, @@ -103,10 +103,10 @@ public static AdditiveCharacteristic weightedBiophysics(SetPrepro } public static AdditiveCharacteristic segmentUsage(GeneType geneType, KeyFunction keyFunction) { - return segmentUsage(new NoPreprocessing<>(), geneType, keyFunction); + return segmentUsage(NoPreprocessing.factory(), geneType, keyFunction); } - public static AdditiveCharacteristic segmentUsage(SetPreprocessor preproc, GeneType geneType, KeyFunction keyFunction) { + public static AdditiveCharacteristic segmentUsage(SetPreprocessorFactory preproc, GeneType geneType, KeyFunction keyFunction) { String name = geneType.getLetter() + "Usage"; return new AdditiveCharacteristic<>( name, @@ -120,37 +120,37 @@ public static AdditiveCharacteristic segmentUsage(SetPreprocessor } public static AdditiveCharacteristic segmentUsage(GeneType geneType) { - return segmentUsage(new NoPreprocessing<>(), geneType); + return segmentUsage(NoPreprocessing.factory(), geneType); } - public static AdditiveCharacteristic segmentUsage(SetPreprocessor preproc, GeneType geneType) { + public static AdditiveCharacteristic segmentUsage(SetPreprocessorFactory preproc, GeneType geneType) { return segmentUsage(preproc, geneType, new KeyFunctions.SegmentUsage<>(geneType)) .setName(geneType.getLetter() + "SegmentUsage"); } public static AdditiveCharacteristic geneUsage(GeneType geneType) { - return geneUsage(new NoPreprocessing<>(), geneType); + return geneUsage(NoPreprocessing.factory(), geneType); } - public static AdditiveCharacteristic geneUsage(SetPreprocessor preproc, GeneType geneType) { + public static AdditiveCharacteristic geneUsage(SetPreprocessorFactory preproc, GeneType geneType) { return segmentUsage(preproc, geneType, new KeyFunctions.GeneUsage<>(geneType)) .setName(geneType.getLetter() + "GeneUsage"); } public static AdditiveCharacteristic familyUsage(GeneType geneType) { - return familyUsage(new NoPreprocessing<>(), geneType); + return familyUsage(NoPreprocessing.factory(), geneType); } - public static AdditiveCharacteristic familyUsage(SetPreprocessor preproc, GeneType geneType) { + public static AdditiveCharacteristic familyUsage(SetPreprocessorFactory preproc, GeneType geneType) { return segmentUsage(preproc, geneType, new KeyFunctions.FamiltyUsage<>(geneType)) .setName(geneType.getLetter() + "FamilyUsage"); } public static AdditiveCharacteristic, Clone> vjUsage(KeyFunction, Clone> keyFunction) { - return vjUsage(new NoPreprocessing<>(), keyFunction); + return vjUsage(NoPreprocessing.factory(), keyFunction); } - public static AdditiveCharacteristic, Clone> vjUsage(SetPreprocessor preproc, KeyFunction, Clone> keyFunction) { + public static AdditiveCharacteristic, Clone> vjUsage(SetPreprocessorFactory preproc, KeyFunction, Clone> keyFunction) { return new AdditiveCharacteristic<>( "VJUsage", preproc, @@ -163,34 +163,34 @@ public static AdditiveCharacteristic, Clone> vjUsage(SetPreproce } public static AdditiveCharacteristic, Clone> vjSegmentUsage() { - return vjSegmentUsage(new NoPreprocessing<>()); + return vjSegmentUsage(NoPreprocessing.factory()); } - public static AdditiveCharacteristic, Clone> vjSegmentUsage(SetPreprocessor preproc) { + public static AdditiveCharacteristic, Clone> vjSegmentUsage(SetPreprocessorFactory preproc) { return vjUsage(preproc, new KeyFunctions.VJSegmentUsage<>()).setName("VJSegmentUsage"); } public static AdditiveCharacteristic, Clone> vjGeneUsage() { - return vjGeneUsage(new NoPreprocessing<>()); + return vjGeneUsage(NoPreprocessing.factory()); } - public static AdditiveCharacteristic, Clone> vjGeneUsage(SetPreprocessor preproc) { + public static AdditiveCharacteristic, Clone> vjGeneUsage(SetPreprocessorFactory preproc) { return vjUsage(preproc, new KeyFunctions.VJGeneUsage<>()).setName("VJGeneUsage"); } public static AdditiveCharacteristic, Clone> vjFamilysage() { - return vjFamilysage(new NoPreprocessing<>()); + return vjFamilysage(NoPreprocessing.factory()); } - public static AdditiveCharacteristic, Clone> vjFamilysage(SetPreprocessor preproc) { + public static AdditiveCharacteristic, Clone> vjFamilysage(SetPreprocessorFactory preproc) { return vjUsage(preproc, new KeyFunctions.VJFamilyUsage<>()).setName("VJFamilyUsage"); } public static AdditiveCharacteristic isotypeUsage() { - return isotypeUsage(new NoPreprocessing<>()); + return isotypeUsage(NoPreprocessing.factory()); } - public static AdditiveCharacteristic isotypeUsage(SetPreprocessor preproc) { + public static AdditiveCharacteristic isotypeUsage(SetPreprocessorFactory preproc) { return new AdditiveCharacteristic<>( "IsotypeUsage", preproc, @@ -203,10 +203,10 @@ public static AdditiveCharacteristic isotypeUsage(S } public static AdditiveCharacteristic, Clone> VSpectratype() { - return VSpectratype(new NoPreprocessing<>()); + return VSpectratype(NoPreprocessing.factory()); } - public static AdditiveCharacteristic, Clone> VSpectratype(SetPreprocessor preproc) { + public static AdditiveCharacteristic, Clone> VSpectratype(SetPreprocessorFactory preproc) { return new AdditiveCharacteristic<>("VSpectratype", preproc, new WeightFunctions.Count(), @@ -214,7 +214,7 @@ public static AdditiveCharacteristic, Clone> VSpectratype new AdditiveMetrics.Constant(), AggregationType.Sum, false); } - public static AdditiveCharacteristic VSpectratypeMean(SetPreprocessor preproc) { + public static AdditiveCharacteristic VSpectratypeMean(SetPreprocessorFactory preproc) { return new AdditiveCharacteristic<>( "VSpectratypeMean", preproc, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java index ca9e71d6d..1ab122ab4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -7,10 +7,7 @@ import gnu.trove.map.hash.TLongIntHashMap; import org.apache.commons.math3.util.CombinatoricsUtils; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; +import java.util.*; import java.util.function.ToLongFunction; import java.util.stream.IntStream; @@ -20,6 +17,7 @@ * */ public class DiversityAggregator implements Aggregator { + private final Set measures; /** number of clonotypes */ private int diversity = 0; /** total count across all clonotypes */ @@ -29,8 +27,10 @@ public class DiversityAggregator implements Aggregator { final ToLongFunction count; /** @param count returns count of element */ - public DiversityAggregator(ToLongFunction count) { + public DiversityAggregator(ToLongFunction count, DiversityMeasure[] measures) { this.count = count; + this.measures = EnumSet.noneOf(DiversityMeasure.class); + this.measures.addAll(Arrays.asList(measures)); } @Override @@ -43,6 +43,8 @@ public void consume(T obj) { /** Chao1 */ private List> computeChao1() { + if (!measures.contains(Chao1) && !measures.contains(Chao1Std)) + return Collections.emptyList(); int sobs = diversity; double f1 = freqTable.get(1); // singletons double f2 = freqTable.get(2); // doubletons @@ -57,6 +59,8 @@ private List> computeChao1() { /** Clonality, Gini and Shannon-Weiner */ private List> computeClonality() { + if (!(measures.contains(ShannonWeiner) || measures.contains(Clonality) || measures.contains(InverseSimpson) || measures.contains(Gini))) + return Collections.emptyList(); double shannonWeiner = 0; double gini = 0; @@ -72,11 +76,16 @@ private List> computeClonality() { shannonWeiner += -nClones * cloneFreq * Math.log(cloneFreq); } - return Arrays.asList( - new MetricValue<>(ShannonWeiner, shannonWeiner), - new MetricValue<>(Clonality, 1 - shannonWeiner / Math.log(diversity)), - new MetricValue<>(InverseSimpson, -1 / gini), - new MetricValue<>(Gini, 1 - gini)); + List> result = new ArrayList<>(); + if (measures.contains(ShannonWeiner)) + result.add(new MetricValue<>(ShannonWeiner, shannonWeiner)); + if (measures.contains(Clonality)) + result.add(new MetricValue<>(Clonality, 1 - shannonWeiner / Math.log(diversity))); + if (measures.contains(InverseSimpson)) + result.add(new MetricValue<>(InverseSimpson, -1 / gini)); + if (measures.contains(Gini)) + result.add(new MetricValue<>(Gini, 1 - gini)); + return result; } public static final int DEFAULT_EFRON_THISTED_MAX_DEPTH = 20; @@ -88,6 +97,9 @@ private List> computeEfronThisted() { /** Efron-Thisted */ private List> computeEfronThisted(int maxDepth, double cvThreshold) { + if (!measures.contains(EfronThisted) && !measures.contains(EfronThistedStd)) + return Collections.emptyList(); + double S = -1, D = -1, CV; for (int depth = 1; depth <= maxDepth; depth++) { final double[] h = new double[depth], nx = new double[depth]; @@ -113,10 +125,18 @@ private List> computeEfronThisted(int maxDepth, do if (CV >= cvThreshold) break; } - return Arrays.asList(new MetricValue<>(EfronThisted, S), new MetricValue<>(EfronThistedStd, D)); + + List> result = new ArrayList<>(); + if (measures.contains(EfronThisted)) + result.add(new MetricValue<>(EfronThisted, S)); + if (measures.contains(EfronThistedStd)) + result.add(new MetricValue<>(EfronThistedStd, D)); + return result; } private List> computeObserved() { + if (!measures.contains(Observed)) + return Collections.emptyList(); return Collections.singletonList(new MetricValue<>(Observed, diversity)); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java index 9bcdb3228..bb82c09aa 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java @@ -14,15 +14,26 @@ isGetterVisibility = JsonAutoDetect.Visibility.NONE ) public class DiversityCharacteristic extends Characteristic { + @JsonProperty("measures") + public final DiversityMeasure[] measures; + @JsonCreator public DiversityCharacteristic(@JsonProperty("name") String name, @JsonProperty("weight") WeightFunction weight, - @JsonProperty("preproc") SetPreprocessor preprocessor) { + @JsonProperty("preproc") SetPreprocessorFactory preprocessor, + @JsonProperty("measures") DiversityMeasure[] measures) { super(name, preprocessor, weight); + this.measures = measures; + } + + public DiversityCharacteristic(@JsonProperty("name") String name, + @JsonProperty("weight") WeightFunction weight, + @JsonProperty("preproc") SetPreprocessorFactory preprocessor) { + this(name, weight, preprocessor, DiversityMeasure.values()); } @Override protected Aggregator createAggregator(Dataset dataset) { - return new DiversityAggregator<>(c -> Math.round(weight.weight(c))); + return new DiversityAggregator<>(c -> Math.round(weight.weight(c)), measures); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java deleted file mode 100644 index 03e0ee123..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessor.java +++ /dev/null @@ -1,38 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.downsampling; - -import com.fasterxml.jackson.annotation.JsonAutoDetect; -import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.basictypes.Clone; - -import java.util.Objects; - -/** - * - */ -@JsonAutoDetect( - fieldVisibility = JsonAutoDetect.Visibility.NONE, - getterVisibility = JsonAutoDetect.Visibility.NONE, - isGetterVisibility = JsonAutoDetect.Visibility.NONE -) -public class ClonesDownsamplingPreprocessor extends DownsamplingPreprocessor { - @JsonCreator - public ClonesDownsamplingPreprocessor(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, - @JsonProperty("seed") long seed) { - super(c -> Math.round(c.getCount()), Clone::setCount, downsampleValueChooser, seed); - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - ClonesDownsamplingPreprocessor that = (ClonesDownsamplingPreprocessor) o; - return Objects.equals(downsampleValueChooser, that.downsampleValueChooser) - && Objects.equals(seed, that.seed); - } - - @Override - public int hashCode() { - return Objects.hash(downsampleValueChooser, seed); - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesOverlapDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java similarity index 50% rename from src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesOverlapDownsamplingPreprocessor.java rename to src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java index ca036ede8..4465e4090 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesOverlapDownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java @@ -4,6 +4,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; import java.util.Objects; @@ -15,18 +17,39 @@ getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE ) -public class ClonesOverlapDownsamplingPreprocessor extends OverlapDownsamplingPreprocessor { +public class ClonesDownsamplingPreprocessorFactory implements SetPreprocessorFactory { + @JsonProperty("downsampleValueChooser") + public final DownsampleValueChooser downsampleValueChooser; + @JsonProperty("seed") + public final long seed; + @JsonCreator - public ClonesOverlapDownsamplingPreprocessor(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, + public ClonesDownsamplingPreprocessorFactory(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, @JsonProperty("seed") long seed) { - super(c -> Math.round(c.getCount()), Clone::setCount, downsampleValueChooser, seed); + this.downsampleValueChooser = downsampleValueChooser; + this.seed = seed; + } + + @Override + public String[] description() { + String ch = downsampleValueChooser.description(); + if (ch == null || ch.isEmpty()) + return new String[0]; + return new String[]{ch}; + } + + @Override + public SetPreprocessor getInstance() { + return new DownsamplingPreprocessor<>( + c -> Math.round(c.getCount()), + Clone::setCount, downsampleValueChooser, seed); } @Override public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; - ClonesOverlapDownsamplingPreprocessor that = (ClonesOverlapDownsamplingPreprocessor) o; + ClonesDownsamplingPreprocessorFactory that = (ClonesDownsamplingPreprocessorFactory) o; return Objects.equals(downsampleValueChooser, that.downsampleValueChooser) && Objects.equals(seed, that.seed); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index 434efff66..7f41e7d63 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -1,24 +1,20 @@ package com.milaboratory.mixcr.postanalysis.downsampling; -import cc.redberry.pipe.CUtils; -import cc.redberry.pipe.OutputPortCloseable; +import cc.redberry.pipe.InputPort; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.MappingFunction; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.preproc.FilteredDataset; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; import gnu.trove.list.array.TLongArrayList; import org.apache.commons.math3.random.RandomGenerator; import org.apache.commons.math3.random.Well19937c; -import java.util.HashSet; -import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; import java.util.function.BiFunction; -import java.util.function.Function; import java.util.function.ToLongFunction; -import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil.*; +import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil.downsample_mvhg; /** * @@ -31,7 +27,9 @@ public class DownsamplingPreprocessor implements SetPreprocessor { @JsonProperty("seed") public final long seed; - public DownsamplingPreprocessor(ToLongFunction getCount, BiFunction setCount, DownsampleValueChooser downsampleValueChooser, long seed) { + public DownsamplingPreprocessor(ToLongFunction getCount, + BiFunction setCount, + DownsampleValueChooser downsampleValueChooser, long seed) { this.getCount = getCount; this.setCount = setCount; this.downsampleValueChooser = downsampleValueChooser; @@ -45,80 +43,66 @@ public String[] description() { return new String[]{ch}; } - @Override - public Function, Dataset> setup(Dataset[] sets) { - long[] totals = new long[sets.length]; - for (int i = 0; i < sets.length; i++) - totals[i] = total(getCount, sets[i]); - long downsampling = downsampleValueChooser.compute(totals); - - Set> empty = new HashSet<>(); - for (int i = 0; i < totals.length; ++i) - if (totals[i] < downsampling) - empty.add(sets[i]); - - return set -> { - if (empty.contains(set)) - //noinspection unchecked - return EMPTY_DATASET_SUPPLIER; - - // compute counts - long total = 0; - TLongArrayList countsList = new TLongArrayList(); - try (OutputPortCloseable port = set.mkElementsPort()) { - for (T t : CUtils.it(port)) { - long c = getCount.applyAsLong(t); - countsList.add(c); - total += c; - } - } + private ComputeCountsStep setup = null; + private long downsampling = -1; - if (total < downsampling) - //noinspection unchecked - return EMPTY_DATASET_SUPPLIER; + @Override + public SetPreprocessorSetup nextSetupStep() { + if (setup == null) + return setup = new ComputeCountsStep(); - RandomGenerator rnd = new Well19937c(seed); - long[] countsDownsampled = downsample_mvhg(countsList.toArray(), downsampling, rnd); + return null; + } - return new FilteredDataset<>( - new DownsampledDataset<>(set, countsDownsampled, setCount), - t -> getCount.applyAsLong(t) != 0); + @Override + public MappingFunction getMapper(int iDataset) { + if (downsampling == -1) + downsampling = downsampleValueChooser.compute(setup.counts); + + if (downsampling > setup.counts[iDataset]) + return t -> null; + + long[] counts = setup.countLists[iDataset].toArray(); + RandomGenerator rnd = new Well19937c(seed); + long[] countsDownsampled = downsample_mvhg(counts, downsampling, rnd); + + AtomicInteger idx = new AtomicInteger(0); + return t -> { + int i = idx.getAndIncrement(); + if (countsDownsampled[i] == 0) + return null; + return setCount.apply(t, countsDownsampled[i]); }; } - private static final class DownsampledDataset implements Dataset { - final Dataset inner; - final long[] countsDownsampled; - final BiFunction setCount; + class ComputeCountsStep implements SetPreprocessorSetup { + long[] counts; + TLongArrayList[] countLists; - public DownsampledDataset(Dataset inner, long[] countsDownsampled, BiFunction setCount) { - this.inner = inner; - this.countsDownsampled = countsDownsampled; - this.setCount = setCount; - } + boolean initialized = false; @Override - public String id() { - return inner.id(); + public void initialize(int nDatasets) { + if (initialized) + throw new IllegalStateException(); + initialized = true; + counts = new long[nDatasets]; + countLists = new TLongArrayList[nDatasets]; + for (int i = 0; i < nDatasets; i++) { + countLists[i] = new TLongArrayList(); + } } @Override - public OutputPortCloseable mkElementsPort() { - final OutputPortCloseable inner = this.inner.mkElementsPort(); - final AtomicInteger index = new AtomicInteger(0); - return new OutputPortCloseable() { - @Override - public void close() { - inner.close(); - } - - @Override - public T take() { - T t = inner.take(); - if (t == null) - return null; - return setCount.apply(t, countsDownsampled[index.getAndIncrement()]); - } + public InputPort consumer(int i) { + if (!initialized) + throw new IllegalStateException(); + return object -> { + if (object == null) + return; + long c = getCount.applyAsLong(object); + counts[i] += c; + countLists[i].add(c); }; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index 1a1ac5c72..40723661b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -41,20 +41,6 @@ public final class DownsamplingUtil { private DownsamplingUtil() { } - @SuppressWarnings("rawtypes") - public static final OutputPortCloseable emptyOP = new OutputPortCloseable() { - @Override - public void close() { } - - @Override - public Object take() { - return null; - } - }; - - @SuppressWarnings("rawtypes") - public static final Dataset EMPTY_DATASET_SUPPLIER = Dataset.fromSupplier(() -> emptyOP); - public static long total(ToLongFunction getCount, Dataset set) { long total = 0; try (OutputPortCloseable port = set.mkElementsPort()) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java deleted file mode 100644 index a387e6560..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessor.java +++ /dev/null @@ -1,170 +0,0 @@ -/* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. - */ -package com.milaboratory.mixcr.postanalysis.downsampling; - -import cc.redberry.pipe.CUtils; -import cc.redberry.pipe.OutputPortCloseable; -import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.Dataset; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; -import com.milaboratory.mixcr.postanalysis.preproc.FilteredDataset; -import gnu.trove.list.array.TLongArrayList; -import org.apache.commons.math3.random.RandomGenerator; -import org.apache.commons.math3.random.Well19937c; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.concurrent.atomic.AtomicIntegerArray; -import java.util.function.BiFunction; -import java.util.function.Function; -import java.util.function.ToLongFunction; -import java.util.stream.Collectors; - -public class OverlapDownsamplingPreprocessor implements SetPreprocessor> { - public final ToLongFunction getCount; - public final BiFunction setCount; - @JsonProperty("downsampleValueChooser") - public final DownsampleValueChooser downsampleValueChooser; - @JsonProperty("seed") - public final long seed; - - public OverlapDownsamplingPreprocessor(ToLongFunction getCount, BiFunction setCount, DownsampleValueChooser downsampleValueChooser, long seed) { - this.getCount = getCount; - this.setCount = setCount; - this.downsampleValueChooser = downsampleValueChooser; - this.seed = seed; - } - - public String[] description() { - String ch = downsampleValueChooser.description(); - if (ch == null || ch.isEmpty()) - return new String[0]; - return new String[]{ch}; - } - - @Override - public Function>, Dataset>> setup(Dataset>[] sets) { - return set -> { - TLongArrayList[] counts = null; - try (OutputPortCloseable> port = set.mkElementsPort()) { - for (OverlapGroup grp : CUtils.it(port)) { - if (counts == null) { - counts = new TLongArrayList[grp.size()]; - for (int i = 0; i < grp.size(); i++) - counts[i] = new TLongArrayList(); - } - - assert counts.length == grp.size(); - - for (int i = 0; i < counts.length; i++) - for (T t : grp.getBySample(i)) - counts[i].add(getCount.applyAsLong(t)); - } - } - if (counts == null) - // empty set - return set; - - long[] totals = Arrays.stream(counts).mapToLong(TLongArrayList::sum).toArray(); - long downsample = downsampleValueChooser.compute(totals); - - RandomGenerator rnd = new Well19937c(seed); - long[][] newCounts = new long[totals.length][]; - for (int i = 0; i < totals.length; i++) { - if (totals[i] < downsample) - continue; - newCounts[i] = DownsamplingUtil.downsample_mvhg(counts[i].toArray(), downsample, rnd); - } - - return new FilteredDataset<>( - new DownsampledDataset<>(set, newCounts, getCount, setCount), - OverlapGroup::notEmpty); - }; - } - - private static final class DownsampledDataset implements Dataset> { - final Dataset> inner; - final long[][] countsDownsampled; - final ToLongFunction getCount; - final BiFunction setCount; - - public DownsampledDataset(Dataset> inner, long[][] countsDownsampled, ToLongFunction getCount, BiFunction setCount) { - this.inner = inner; - this.countsDownsampled = countsDownsampled; - this.getCount = getCount; - this.setCount = setCount; - } - - @Override - public String id() { - return inner.id(); - } - - @Override - public OutputPortCloseable> mkElementsPort() { - final OutputPortCloseable> inner = this.inner.mkElementsPort(); - final AtomicIntegerArray indices = new AtomicIntegerArray(countsDownsampled.length); - return new OutputPortCloseable>() { - @Override - public void close() { - inner.close(); - } - - @Override - public OverlapGroup take() { - OverlapGroup grp = inner.take(); - if (grp == null) - return null; - - List> newGroups = new ArrayList<>(); - for (int i = 0; i < grp.size(); i++) { - final int fi = i; - List objs = grp.getBySample(i); - if (objs.isEmpty()) - newGroups.add(objs); - else - newGroups.add(objs.stream() - .map(o -> { - long newCount = countsDownsampled[fi] == null ? 0 : countsDownsampled[fi][indices.getAndIncrement(fi)]; - if (getCount.applyAsLong(o) < newCount) - throw new RuntimeException("Assertion exception. Varying ordering of objects in iterator."); - return setCount.apply(o, newCount); - }) - .filter(l -> getCount.applyAsLong(l) > 0) - .collect(Collectors.toList())); - } - return new OverlapGroup<>(newGroups); - } - }; - } - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java index 7b5ba7002..186c34d8f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java @@ -5,12 +5,13 @@ import com.milaboratory.mixcr.postanalysis.WeightFunction; import org.apache.commons.math3.stat.regression.SimpleRegression; -import java.util.List; +import java.util.*; /** * */ public class OverlapAggregator implements Aggregator, OverlapGroup> { + private final Set types; private final WeightFunction weight; private final int i1, i2; private final String id1, id2; @@ -22,12 +23,14 @@ public class OverlapAggregator implements Aggregator, sumSqProduct; long diversity1, diversity2, diversityIntersection; - public OverlapAggregator(WeightFunction weight, int i1, int i2, String id1, String id2) { + public OverlapAggregator(WeightFunction weight, int i1, int i2, String id1, String id2, OverlapType[] types) { this.weight = weight; this.i1 = i1; this.i2 = i2; this.id1 = id1; this.id2 = id2; + this.types = EnumSet.noneOf(OverlapType.class); + this.types.addAll(Arrays.asList(types)); } @Override @@ -54,15 +57,23 @@ public void consume(OverlapGroup obj) { @Override public MetricValue>[] result() { - return new MetricValue[]{ - new MetricValue<>(key(OverlapType.D, id1, id2), 1.0 * diversityIntersection / diversity1 / diversity2), - new MetricValue<>(key(OverlapType.SharedClonotypes, id1, id2), 1.0 * diversityIntersection), - new MetricValue<>(key(OverlapType.F1, id1, id2), Math.sqrt(sumS1Intersection * sumS2Intersection / sumS1 / sumS2)), - new MetricValue<>(key(OverlapType.F2, id1, id2), sumSqProduct / Math.sqrt(sumS1 * sumS2)), - new MetricValue<>(key(OverlapType.Jaccard, id1, id2), 1.0 * diversityIntersection / (diversity1 + diversity2 - diversityIntersection)), - new MetricValue<>(key(OverlapType.R_Intersection, id1, id2), regressionIntersection.getR()), - new MetricValue<>(key(OverlapType.R_All, id1, id2), regressionAll.getR()), - }; + List>> result = new ArrayList<>(); + if (types.contains(OverlapType.D)) + result.add(new MetricValue<>(key(OverlapType.D, id1, id2), 1.0 * diversityIntersection / diversity1 / diversity2)); + if (types.contains(OverlapType.SharedClonotypes)) + result.add(new MetricValue<>(key(OverlapType.SharedClonotypes, id1, id2), 1.0 * diversityIntersection)); + if (types.contains(OverlapType.F1)) + result.add(new MetricValue<>(key(OverlapType.F1, id1, id2), Math.sqrt(sumS1Intersection * sumS2Intersection / sumS1 / sumS2))); + if (types.contains(OverlapType.F2)) + result.add(new MetricValue<>(key(OverlapType.F2, id1, id2), sumSqProduct / Math.sqrt(sumS1 * sumS2))); + if (types.contains(OverlapType.Jaccard)) + result.add(new MetricValue<>(key(OverlapType.Jaccard, id1, id2), 1.0 * diversityIntersection / (diversity1 + diversity2 - diversityIntersection))); + if (types.contains(OverlapType.R_Intersection)) + result.add(new MetricValue<>(key(OverlapType.R_Intersection, id1, id2), regressionIntersection.getR())); + if (types.contains(OverlapType.R_All)) + result.add(new MetricValue<>(key(OverlapType.R_All, id1, id2), regressionAll.getR())); + //noinspection unchecked + return result.toArray(new MetricValue[0]); } private static OverlapKey key(OverlapType type, String i, String j) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java index d2bb8e3d6..f100ede42 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java @@ -4,6 +4,7 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.postanalysis.*; +import java.util.Arrays; import java.util.List; import java.util.Objects; @@ -11,6 +12,8 @@ * */ public class OverlapCharacteristic extends Characteristic, OverlapGroup> { + @JsonProperty("overlapTypes") + public final OverlapType[] overlapTypes; @JsonProperty("i1") public final int i1; @JsonProperty("i2") @@ -21,21 +24,30 @@ public class OverlapCharacteristic extends Characteristic weight, - @JsonProperty("preprocessor") SetPreprocessor> preprocessor, + @JsonProperty("preprocessor") SetPreprocessorFactory> preprocessor, + @JsonProperty("overlapTypes") OverlapType[] overlapTypes, @JsonProperty("i1") int i1, @JsonProperty("i2") int i2) { super(name, preprocessor, __ -> 1L); + this.overlapTypes = overlapTypes; this.i1 = i1; this.i2 = i2; this.weight = weight; } + public OverlapCharacteristic(String name, + WeightFunction weight, + SetPreprocessorFactory> preprocessor, + int i1, int i2) { + this(name, weight, preprocessor, OverlapType.values(), i1, i2); + } + @Override protected Aggregator, OverlapGroup> createAggregator(Dataset> dataset) { if (!(dataset instanceof OverlapDataset)) throw new IllegalArgumentException(); List datasetIds = ((OverlapDataset) dataset).datasetIds; - return new OverlapAggregator<>(weight, i1, i2, datasetIds.get(i1), datasetIds.get(i2)); + return new OverlapAggregator<>(weight, i1, i2, datasetIds.get(i1), datasetIds.get(i2), overlapTypes); } @Override @@ -44,13 +56,13 @@ public boolean equals(Object o) { if (o == null || getClass() != o.getClass()) return false; if (!super.equals(o)) return false; OverlapCharacteristic that = (OverlapCharacteristic) o; - return i1 == that.i1 && - i2 == that.i2 && - Objects.equals(weight, that.weight); + return i1 == that.i1 && i2 == that.i2 && Arrays.equals(overlapTypes, that.overlapTypes) && Objects.equals(weight, that.weight); } @Override public int hashCode() { - return Objects.hash(super.hashCode(), i1, i2, weight); + int result = Objects.hash(super.hashCode(), i1, i2, weight); + result = 31 * result + Arrays.hashCode(overlapTypes); + return result; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java index 69efbe1d7..1c7b21011 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java @@ -2,7 +2,6 @@ import com.fasterxml.jackson.annotation.*; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; import io.repseq.core.Chains; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -18,7 +17,6 @@ @JsonSubTypes.Type(value = ElementPredicate.NoOutOfFrames.class, name = "noOOF"), @JsonSubTypes.Type(value = ElementPredicate.NoStops.class, name = "noStops"), @JsonSubTypes.Type(value = ElementPredicate.IncludeChains.class, name = "includesChains"), - @JsonSubTypes.Type(value = ElementPredicate.OverlapIncludeChains.class, name = "overlapIncludesChains") }) public interface ElementPredicate extends Predicate { default String description() { @@ -27,6 +25,14 @@ default String description() { @JsonAutoDetect final class NoOutOfFrames implements ElementPredicate { + @JsonProperty("feature") + public final GeneFeature feature; + + @JsonCreator + public NoOutOfFrames(@JsonProperty("feature") GeneFeature feature) { + this.feature = feature; + } + @Override public String description() { return "Exclude out-of-frames"; @@ -34,50 +40,55 @@ public String description() { @Override public boolean test(Clone clone) { - if (clone.isOutOfFrame(GeneFeature.CDR3)) - return false; - return true; + return !clone.isOutOfFrame(feature); } @Override public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; - return true; + NoOutOfFrames that = (NoOutOfFrames) o; + return Objects.equals(feature, that.feature); } @Override public int hashCode() { - return Objects.hash(13); + return Objects.hash(feature); } } @JsonAutoDetect final class NoStops implements ElementPredicate { + @JsonProperty("feature") + public final GeneFeature feature; + + @JsonCreator + public NoStops(@JsonProperty("feature") GeneFeature feature) { + this.feature = feature; + } + @Override public String description() { - return "Exclude stop-codons"; + return "Exclude stop-codons in " + GeneFeature.encode(feature); } + @Override public boolean test(Clone clone) { - for (GeneFeature gf : clone.getParentCloneSet().getAssemblingFeatures()) { - if (clone.containsStops(gf)) - return false; - } - return true; + return !clone.containsStops(feature); } @Override public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; - return true; + NoStops noStops = (NoStops) o; + return Objects.equals(feature, noStops.feature); } @Override public int hashCode() { - return Objects.hash(13); + return Objects.hash(feature); } } @@ -117,43 +128,4 @@ public int hashCode() { return Objects.hash(chains); } } - - final class OverlapIncludeChains implements ElementPredicate> { - @JsonProperty("chains") - public final Chains chains; - - @JsonCreator - public OverlapIncludeChains(@JsonProperty("chains") Chains chains) { - this.chains = chains; - } - - @Override - public String description() { - return "Select chains: " + chains; - } - - @Override - public boolean test(OverlapGroup object) { - for (GeneType gt : GeneType.VJC_REFERENCE) - for (int i = 0; i < object.size(); i++) - for (Clone clone : object.getBySample(i)) - if (clone != null && chains.intersects(clone.getTopChain(gt))) - return true; - - return false; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - OverlapIncludeChains that = (OverlapIncludeChains) o; - return Objects.equals(chains, that.chains); - } - - @Override - public int hashCode() { - return Objects.hash(chains); - } - } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index d30f9e9d3..27fc55445 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -2,60 +2,74 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.MappingFunction; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; import java.util.Arrays; -import java.util.Collections; import java.util.List; import java.util.Objects; -import java.util.function.Function; /** * */ public class FilterPreprocessor implements SetPreprocessor { - @JsonProperty("predicates") - public final List> predicates; + final List> predicates; - @JsonCreator - public FilterPreprocessor(@JsonProperty("predicates") List> predicates) { + FilterPreprocessor(@JsonProperty("predicates") List> predicates) { this.predicates = predicates; } @Override - public String[] description() { - return predicates.stream() - .map(ElementPredicate::description) - .filter(Objects::nonNull) - .filter(s -> !s.isEmpty()) - .map(f -> "Filter: " + f) - .toArray(String[]::new); + public SetPreprocessorSetup nextSetupStep() { + return null; } - public FilterPreprocessor(ElementPredicate... predicates) { - this(Arrays.asList(predicates)); + @Override + public MappingFunction getMapper(int iDataset) { + return t -> predicates.stream().allMatch(p -> p.test(t)) ? t : null; } - public FilterPreprocessor(ElementPredicate predicate) { - this(Collections.singletonList(predicate)); - } + public static final class Factory implements SetPreprocessorFactory { + @JsonProperty("predicates") + public final List> predicates; - @Override - public Function, Dataset> setup(Dataset[] sets) { - return set -> new FilteredDataset<>(set, t -> predicates.stream().allMatch(s -> s.test(t))); - } + @JsonCreator + public Factory(@JsonProperty("predicates") List> predicates) { + this.predicates = predicates; + } - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - FilterPreprocessor that = (FilterPreprocessor) o; - return Objects.equals(predicates, that.predicates); - } + public Factory(ElementPredicate... predicates) { + this(Arrays.asList(predicates)); + } - @Override - public int hashCode() { - return Objects.hash(predicates); + @Override + public String[] description() { + return predicates.stream() + .map(ElementPredicate::description) + .filter(Objects::nonNull) + .filter(s -> !s.isEmpty()) + .map(f -> "Filter: " + f) + .toArray(String[]::new); + } + + @Override + public SetPreprocessor getInstance() { + return new FilterPreprocessor<>(predicates); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Factory that = (Factory) o; + return Objects.equals(predicates, that.predicates); + } + + @Override + public int hashCode() { + return Objects.hash(predicates); + } } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java deleted file mode 100644 index 40bd03fea..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredDataset.java +++ /dev/null @@ -1,29 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.preproc; - -import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.mixcr.postanalysis.Dataset; - -import java.util.function.Predicate; - -/** - * - */ -public class FilteredDataset implements Dataset { - private final Dataset inner; - private final Predicate accept; - - public FilteredDataset(Dataset inner, Predicate accept) { - this.inner = inner; - this.accept = accept; - } - - @Override - public String id() { - return inner.id(); - } - - @Override - public OutputPortCloseable mkElementsPort() { - return new FilteredOutputPortCloseable<>(inner.mkElementsPort(), accept); - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java deleted file mode 100644 index 9301bd735..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilteredOutputPortCloseable.java +++ /dev/null @@ -1,34 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.preproc; - -import cc.redberry.pipe.OutputPortCloseable; - -import java.util.function.Predicate; - -/** - * - */ -public class FilteredOutputPortCloseable implements OutputPortCloseable { - private final OutputPortCloseable inner; - private final Predicate accept; - - public FilteredOutputPortCloseable(OutputPortCloseable inner, Predicate accept) { - this.inner = inner; - this.accept = accept; - } - - @Override - public void close() { - inner.close(); - } - - @Override - public T take() { - while (true) { - final T r = inner.take(); - if (r == null) - return null; - if (accept.test(r)) - return r; - } - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java index 9976461cd..1bf65091f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java @@ -1,34 +1,50 @@ package com.milaboratory.mixcr.postanalysis.preproc; -import com.milaboratory.mixcr.postanalysis.Dataset; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import java.util.function.Function; +import com.milaboratory.mixcr.postanalysis.MappingFunction; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; /** * */ public class NoPreprocessing implements SetPreprocessor { - public static final NoPreprocessing INSTANCE = new NoPreprocessing<>(); + private static final NoPreprocessing instance = new NoPreprocessing<>(); - public String[] description() { - return new String[0]; - } + private NoPreprocessing() {} @Override - public Function, Dataset> setup(Dataset[] sets) { - return set -> set; + public SetPreprocessorSetup nextSetupStep() { + return null; } @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - return true; + public MappingFunction getMapper(int iDataset) { + return MappingFunction.identity(); } - @Override - public int hashCode() { - return 17; + public static final Factory factory = new Factory<>(); + + @SuppressWarnings("unchecked") + public static Factory factory() { return (Factory) factory; } + + public static final class Factory implements SetPreprocessorFactory { + @SuppressWarnings("unchecked") + @Override + public SetPreprocessor getInstance() { + return (SetPreprocessor) NoPreprocessing.instance; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + return o != null && getClass() == o.getClass(); + } + + @Override + public int hashCode() { + return "NoPreprocessing".hashCode(); + } } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java new file mode 100644 index 000000000..3462e4556 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java @@ -0,0 +1,130 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import cc.redberry.pipe.InputPort; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.MappingFunction; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; + +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; + +/** + * + */ +public class OverlapPreprocessorAdapter implements SetPreprocessor> { + final SetPreprocessor inner; + + public OverlapPreprocessorAdapter(SetPreprocessor inner) { + this.inner = inner; + } + + @Override + public SetPreprocessorSetup> nextSetupStep() { + SetPreprocessorSetup innerStep = inner.nextSetupStep(); + if (innerStep == null) + return null; + return new SetPreprocessorSetup>() { + boolean initialized = false; + + @Override + public void initialize(int nDatasets) { + if (initialized) + throw new IllegalStateException(); + initialized = true; + if (nDatasets != 1) + throw new IllegalArgumentException("only one overlap allowed"); + } + + @Override + public InputPort> consumer(int iOverlap) { + if (!initialized) + throw new IllegalStateException(); + if (iOverlap != 0) + throw new IllegalArgumentException("only one overlap allowed"); + List> innerPorts = new ArrayList<>(); + return object -> { + if (object == null) + return; + + int overlapSize = object.size(); + if (innerPorts.isEmpty()) { + innerStep.initialize(overlapSize); + for (int iDataset = 0; iDataset < overlapSize; iDataset++) { + innerPorts.add(innerStep.consumer(iDataset)); + } + } + + for (int iDataset = 0; iDataset < overlapSize; iDataset++) { + for (T t : object.getBySample(iDataset)) { + innerPorts.get(iDataset).put(t); + } + } + }; + } + }; + } + + @Override + public MappingFunction> getMapper(int iOverlap) { + if (iOverlap != 0) + throw new IllegalArgumentException("only one overlap allowed"); + + List> innerMappers = new ArrayList<>(); + return group -> { + int overlapSize = group.size(); + if (innerMappers.isEmpty()) + for (int iDataset = 0; iDataset < overlapSize; iDataset++) { + innerMappers.add(inner.getMapper(iDataset)); + } + + List> result = new ArrayList<>(); + for (int iDataset = 0; iDataset < overlapSize; iDataset++) { + List gr = new ArrayList<>(); + for (T t : group.getBySample(iDataset)) { + T r = innerMappers.get(iDataset).apply(t); + if (r != null) + gr.add(r); + } + result.add(gr); + } + + return new OverlapGroup<>(result); + }; + } + + public static final class Factory implements SetPreprocessorFactory> { + @JsonProperty("inner") + public final SetPreprocessorFactory inner; + + public Factory(@JsonProperty("inner") SetPreprocessorFactory inner) { + this.inner = inner; + } + + @Override + public String[] description() { + return inner.description(); + } + + @Override + public SetPreprocessor> getInstance() { + return new OverlapPreprocessorAdapter<>(inner.getInstance()); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Factory that = (Factory) o; + return Objects.equals(inner, that.inner); + } + + @Override + public int hashCode() { + return Objects.hash(inner); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index 9cb1ed8d7..6eac6c0d8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -1,62 +1,150 @@ package com.milaboratory.mixcr.postanalysis.preproc; +import cc.redberry.pipe.InputPort; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.MappingFunction; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; -import java.util.*; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.concurrent.atomic.AtomicReference; import java.util.function.Function; +import java.util.stream.Collectors; /** * */ public class PreprocessorChain implements SetPreprocessor { - @JsonProperty("chain") - public final List> chain; + final List> chain; - @JsonCreator - public PreprocessorChain(@JsonProperty("chain") List> chain) { + public PreprocessorChain(List> chain) { this.chain = chain; } - public PreprocessorChain(SetPreprocessor... chain) { - this(Arrays.asList(chain)); - } - - public String[] description() { - return chain.stream() - .map(SetPreprocessor::description) - .filter(Objects::nonNull) - .flatMap(Arrays::stream) - .filter(s -> !s.isEmpty()) - .toArray(String[]::new); - } + private final AtomicReference>> mapperRef = new AtomicReference<>(i -> t -> t); + private int lastActive = 0; @Override - public Function, Dataset> setup(Dataset[] sets) { - Dataset[] proc = sets; - for (SetPreprocessor p : chain) { - Function, Dataset> func = p.setup(proc); - //noinspection unchecked - proc = Arrays.stream(proc).map(func).toArray(Dataset[]::new); - } - Map, Dataset> mapping = new IdentityHashMap<>(); - for (int i = 0; i < sets.length; i++) - mapping.put(sets[i], proc[i]); - return mapping::get; + public SetPreprocessorSetup nextSetupStep() { + SetPreprocessorSetup innerStep = null; + for (int i = lastActive; i < chain.size(); i++) { + SetPreprocessor p = chain.get(i); + SetPreprocessorSetup step = p.nextSetupStep(); + if (step != null) { + lastActive = i; + innerStep = step; + break; + } else { + if (mapperRef.get() == null) + mapperRef.set(p::getMapper); + else { + Function> mapper = mapperRef.get(); + Function> newMapper = iDataset -> { + MappingFunction prevMapper = mapper.apply(iDataset); + MappingFunction nextMapper = p.getMapper(iDataset); + + return t -> { + if (t == null) + return null; + T r = prevMapper.apply(t); + if (r == null) + return null; + return nextMapper.apply(r); + }; + }; + mapperRef.set(newMapper); + } + } + } + + Function> mapper = mapperRef.get(); + if (innerStep != null) { + SetPreprocessorSetup _innerSetup = innerStep; + return new SetPreprocessorSetup() { + boolean initialized = false; + + @Override + public void initialize(int nDatasets) { + if (initialized) + throw new IllegalStateException(); + initialized = true; + _innerSetup.initialize(nDatasets); + } + + @Override + public InputPort consumer(int i) { + if (!initialized) + throw new IllegalStateException(); + InputPort consumer = _innerSetup.consumer(i); + MappingFunction func = mapper.apply(i); + return t -> { + if (t == null) { + consumer.put(null); + return; + } + T r = func.apply(t); + if (r != null) + consumer.put(r); + }; + } + }; + } + return null; } @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - PreprocessorChain that = (PreprocessorChain) o; - return Objects.equals(chain, that.chain); + public MappingFunction getMapper(int iDataset) { + Function> mapper = mapperRef.get(); + if (mapper == null) + return MappingFunction.identity(); + return mapper.apply(iDataset); } - @Override - public int hashCode() { - return Objects.hash(chain); + public static final class Factory implements SetPreprocessorFactory { + @JsonProperty("chain") + public final List> chain; + + @JsonCreator + public Factory(@JsonProperty("chain") List> chain) { + this.chain = chain; + } + + public Factory(SetPreprocessorFactory... chain) { + this(Arrays.asList(chain)); + } + + @Override + public String[] description() { + return chain.stream() + .map(SetPreprocessorFactory::description) + .filter(Objects::nonNull) + .flatMap(Arrays::stream) + .filter(s -> !s.isEmpty()) + .toArray(String[]::new); + } + + @Override + public SetPreprocessor getInstance() { + return new PreprocessorChain<>(chain.stream() + .map(SetPreprocessorFactory::getInstance) + .collect(Collectors.toList())); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Factory that = (Factory) o; + return Objects.equals(chain, that.chain); + } + + @Override + public int hashCode() { + return Objects.hash(chain); + } } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java new file mode 100644 index 000000000..b1cf1387d --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java @@ -0,0 +1,204 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import cc.redberry.pipe.InputPort; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.*; +import gnu.trove.impl.Constants; +import gnu.trove.map.hash.TLongLongHashMap; + +import java.util.Arrays; +import java.util.Objects; + +import static java.lang.Math.round; + +/** + * + */ +public class SelectTop implements SetPreprocessor { + final WeightFunction weight; + final double abundanceFraction; + final int numberOfTop; + + SelectTop(WeightFunction weight, + double abundanceFraction, + int numberOfTop) { + if (!Double.isNaN(abundanceFraction) && (abundanceFraction <= 0 || abundanceFraction > 1.0)) + throw new IllegalArgumentException(); + if (numberOfTop != -1 && numberOfTop <= 0) + throw new IllegalArgumentException(); + + this.weight = weight; + this.abundanceFraction = abundanceFraction; + this.numberOfTop = numberOfTop; + } + + private boolean computeCumulativeTop() { + return !Double.isNaN(abundanceFraction); + } + + private boolean computeFixedTop() { + return numberOfTop != -1; + } + + private ComputeHists2 computeHists; + + @Override + public SetPreprocessorSetup nextSetupStep() { + if (computeHists == null) { + return computeHists = new ComputeHists2(); + } + return null; + } + + @Override + public MappingFunction getMapper(int iDataset) { + TLongLongHashMap hist = computeHists.downsampledHist(iDataset); + return t -> { + if (hist.isEmpty()) + return null; + + long wt = Math.round(this.weight.weight(t)); + long n = hist.get(wt); + if (n == -1) + return null; + assert n != 0; + if (n == 1) + hist.remove(wt); + else + hist.adjustValue(wt, -1); + + return t; + }; + } + + private class ComputeHists2 implements SetPreprocessorSetup { + // weight -> n elements + private TLongLongHashMap[] hists; + private double[] totals; + private boolean initialized = false; + + @Override + public void initialize(int nDatasets) { + if (initialized) + throw new IllegalStateException(); + initialized = true; + totals = new double[nDatasets]; + hists = new TLongLongHashMap[nDatasets]; + for (int i = 0; i < hists.length; i++) { + hists[i] = new TLongLongHashMap(); + } + } + + @Override + public InputPort consumer(int i) { + if (!initialized) + throw new IllegalStateException(); + return el -> { + if (el == null) { + return; + } + double dwt = weight.weight(el); + if (dwt == 0) + return; + totals[i] += dwt; + long lwt = round(dwt); + if (lwt == 0) + lwt = 1; + hists[i].adjustOrPutValue(lwt, 1, 1); + }; + } + + TLongLongHashMap downsampledHist(int iDataset) { + double total = computeHists.totals[iDataset]; + double sumThreshold = computeCumulativeTop() ? total * abundanceFraction : Double.MAX_VALUE; + int nThreshold = computeFixedTop() ? numberOfTop : Integer.MAX_VALUE; + + TLongLongHashMap fullHist = computeHists.hists[iDataset]; + TLongLongHashMap downHist = new TLongLongHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1, -1); + + long[] weights = fullHist.keys(); + Arrays.sort(weights); + + double sumTotal = 0; + int nTotal = 0; + for (int i = weights.length - 1; i >= 0; --i) { + long wt = weights[i]; + long n = fullHist.get(wt); + + if (nTotal + n > nThreshold) { + if (nThreshold - nTotal > 0) + downHist.put(wt, nThreshold - nTotal); + break; + } + + if (n * wt + sumTotal > sumThreshold) { + long nToLeave = (long) Math.ceil((sumThreshold - sumTotal) / wt); + if (nToLeave <= 0) + break; + if (nToLeave < n) { + downHist.put(wt, nToLeave); + break; + } + assert nToLeave == n; + } + + + nTotal += n; + sumTotal += n * wt; + downHist.put(wt, n); + } + + return downHist; + } + } + + public static final class Factory implements SetPreprocessorFactory { + @JsonProperty("weight") + private WeightFunction weight; + @JsonProperty("abundanceFraction") + private double abundanceFraction = Double.NaN; + @JsonProperty("numberOfTop") + private int numberOfTop = -1; + + private Factory() {} + + public Factory(WeightFunction weight, double abundanceFraction) { + this.weight = weight; + this.abundanceFraction = abundanceFraction; + } + + public Factory(WeightFunction weight, int numberOfTop) { + this.weight = weight; + this.numberOfTop = numberOfTop; + } + + @Override + public SetPreprocessor getInstance() { + return new SelectTop<>(weight, abundanceFraction, numberOfTop); + } + + @Override + public String[] description() { + String s1 = Double.isNaN(abundanceFraction) ? null : "Select top clonotypes constituting " + (abundanceFraction * 100) + "% of reads"; + String s2 = numberOfTop == -1 ? null : "Select top " + numberOfTop + " clonotypes"; + if (s1 == null) + return new String[]{s2}; + else if (s2 == null) + return new String[]{s1}; + return new String[]{s1, s2,}; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Factory factory = (Factory) o; + return Double.compare(factory.abundanceFraction, abundanceFraction) == 0 && numberOfTop == factory.numberOfTop && Objects.equals(weight, factory.weight); + } + + @Override + public int hashCode() { + return Objects.hash(weight, abundanceFraction, numberOfTop); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java index d30a54399..b06d9033e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java @@ -18,7 +18,7 @@ public class SpectratypeCharacteristic extends Characteristic preprocessor, + @JsonProperty("preprocessor") SetPreprocessorFactory preprocessor, @JsonProperty("nTopClonotypes") int nTopClonotypes, @JsonProperty("keyFunction") SpectratypeKeyFunction keyFunction) { super(name, preprocessor, new WeightFunctions.Count()); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java index 36a138201..2f6745212 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java @@ -1,9 +1,11 @@ package com.milaboratory.mixcr.postanalysis; +import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.IteratorOutputPortAdapter; import org.jetbrains.annotations.NotNull; +import java.util.ArrayList; import java.util.Iterator; import java.util.List; import java.util.UUID; @@ -21,6 +23,16 @@ public TestDataset(List data) { this.id = UUID.randomUUID().toString(); } + public TestDataset(Dataset data) { + this.data = new ArrayList<>(); + try (OutputPortCloseable port = data.mkElementsPort()) { + for (T t : CUtils.it(port)) { + this.data.add(t); + } + } + this.id = data.id(); + } + @NotNull @Override public Iterator iterator() { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java index 694e41a70..ee303d6af 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java @@ -19,6 +19,11 @@ public TestObject(double value, double weight) { this.weight = weight; } + @Override + public String toString() { + return value + ": " + weight; + } + @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java index 0a8f694bc..38b29304f 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java @@ -28,7 +28,7 @@ public class AdditiveCharacteristicsTest { public void testWeightedDescriptiveStat() { AdditiveCharacteristic sum = new AdditiveCharacteristic<>( "sum", - new NoPreprocessing<>(), + NoPreprocessing.factory(), o -> o.weight, o -> "sum", w -> w.value, @@ -38,7 +38,7 @@ public void testWeightedDescriptiveStat() { AdditiveCharacteristic mean = new AdditiveCharacteristic<>( "mean", - new NoPreprocessing<>(), + NoPreprocessing.factory(), o -> o.weight, o -> "mean", w -> w.value, @@ -48,7 +48,7 @@ public void testWeightedDescriptiveStat() { AdditiveCharacteristic std = new AdditiveCharacteristic<>( "std", - new NoPreprocessing<>(), + NoPreprocessing.factory(), o -> o.weight, o -> "std", w -> w.value, diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index ce84417a8..796291d2c 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -25,7 +25,7 @@ public class DiversityCharacteristicTest { @SuppressWarnings("unchecked") public void test1() { DiversityCharacteristic diversity = new DiversityCharacteristic<>( - "diversity", t -> t.weight, new NoPreprocessing<>()); + "diversity", t -> t.weight, NoPreprocessing.factory()); RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); int nDatasets = 100; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index fc9f80130..515242a5c 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -2,6 +2,7 @@ import cc.redberry.pipe.CUtils; import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; import com.milaboratory.mixcr.postanalysis.TestDataset; import com.milaboratory.mixcr.postanalysis.TestObject; import org.apache.commons.math3.random.RandomDataGenerator; @@ -12,7 +13,6 @@ import org.junit.Test; import java.util.*; -import java.util.function.Function; import java.util.stream.Collectors; import java.util.stream.LongStream; @@ -110,11 +110,9 @@ public void test3() { for (int i = 0; i < initial.length; i++) { initial[i] = rndDataset(rng, rng.nextInt(100, 1000)); } - long dsValue = dsChooser.compute(Arrays.stream(initial).mapToLong(d -> d.count).toArray()); - Function, Dataset> setup = proc.setup(initial); - DatasetSupport[] downsampled = Arrays.stream(initial).map(setup) + DatasetSupport[] downsampled = Arrays.stream(SetPreprocessorFactory.processDatasets(proc, initial)) .map(DatasetSupport::new) .toArray(DatasetSupport[]::new); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index ac8f5dd7e..6a8f89c6e 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -2,9 +2,11 @@ import cc.redberry.pipe.CUtils; import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; import com.milaboratory.mixcr.postanalysis.TestDataset; import com.milaboratory.mixcr.postanalysis.TestObject; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; import org.junit.Assert; @@ -14,7 +16,6 @@ import java.util.HashSet; import java.util.List; import java.util.Set; -import java.util.function.Function; import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingPreprocessorTest.toList; @@ -26,32 +27,38 @@ public class OverlapDownsamplingPreprocessorTest { public void test1() { RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); DownsampleValueChooser.Minimal chooser = new DownsampleValueChooser.Minimal(); - OverlapDownsamplingPreprocessor proc = new OverlapDownsamplingPreprocessor<>( - t -> Math.round(t.weight), - (t, newW) -> new TestObject(t.value, newW), - chooser, - System.currentTimeMillis() - ); - - DatasetSupport[] datasets = new DatasetSupport[]{ + DatasetSupport[] inputs = new DatasetSupport[]{ rndDataset(rng, 5, 100000), rndDataset(rng, 10, 10000), rndDataset(rng, 15, 10000) }; - Function>, Dataset>> downsampler = proc.setup(datasets); + for (DatasetSupport dataset : inputs) { + DatasetSupport[] datasets = new DatasetSupport[]{dataset}; - for (DatasetSupport in : datasets) { - long dsValue = chooser.compute(in.counts); - DatasetSupport dw = new DatasetSupport(downsampler.apply(in)); + DownsamplingPreprocessor proc = new DownsamplingPreprocessor<>( + t -> Math.round(t.weight), + (t, newW) -> new TestObject(t.value, newW), + chooser, + System.currentTimeMillis() + ); - for (int i = 0; i < in.counts.length; i++) { - Assert.assertEquals(dsValue, dw.counts[i]); - } + Dataset>[] downsampled = SetPreprocessorFactory.processDatasets(new OverlapPreprocessorAdapter<>(proc), datasets); - for (OverlapGroup row : dw) { - for (int i = 0; i < row.size(); i++) { - for (TestObject t : row.getBySample(i)) { - Assert.assertTrue(in.sets[i].contains(t.value)); + for (int i = 0; i < datasets.length; i++) { + DatasetSupport in = datasets[i]; + + long dsValue = chooser.compute(in.counts); + DatasetSupport dw = new DatasetSupport(downsampled[i]); + + for (int j = 0; j < in.counts.length; j++) { + Assert.assertEquals(dsValue, dw.counts[j]); + } + + for (OverlapGroup row : dw) { + for (int j = 0; j < row.size(); j++) { + for (TestObject t : row.getBySample(j)) { + Assert.assertTrue(in.sets[j].contains(t.value)); + } } } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java index e622c0636..139c60143 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -119,7 +119,7 @@ public void testOverlapCharacteristic1() { for (int i = 0; i < ovp.datasets.length; i++) { for (int j = i + 1; j < ovp.datasets.length; j++) { chars.add(new OverlapCharacteristic<>("overlap_" + i + "_" + j, - e -> e.weight, new NoPreprocessing<>(), i, j)); + e -> e.weight, NoPreprocessing.factory(), i, j)); } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java new file mode 100644 index 000000000..a4fab2289 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java @@ -0,0 +1,117 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import cc.redberry.pipe.InputPort; +import com.milaboratory.mixcr.postanalysis.*; +import gnu.trove.list.array.TLongArrayList; +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well512a; +import org.junit.Assert; +import org.junit.Test; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Stream; + +/** + * + */ +public class PreprocessorChainTest { + + @Test + @SuppressWarnings("unchecked") + public void test1() { + long p1 = 17; + long p2 = 13; + long p3 = 11; + long p4 = 7; + + SetPreprocessorFactory preproc = new PreprocessorChain.Factory<>( + new TestPreprocFactory(p1), + new TestPreprocFactory(p2), + new TestPreprocFactory(p3), + new TestPreprocFactory(p4) + ); + + RandomDataGenerator rng = new RandomDataGenerator(new Well512a(System.currentTimeMillis())); + TestDataset ds = rndDataset(rng, 10000); + + TestDataset r = new TestDataset<>(SetPreprocessorFactory.processDatasets(preproc.getInstance(), ds)[0]); + + List expected = new ArrayList<>(); + for (TestObject c : ds) { + if (Stream.of(p1, p2, p3, p4).allMatch(mod -> ((long) c.weight) % mod != 0)) + expected.add(c); + } + + Assert.assertEquals(expected, r.data); + } + + public static final class TestPreprocFactory implements SetPreprocessorFactory { + final long modulus; + + public TestPreprocFactory(long modulus) { + this.modulus = modulus; + } + + @Override + public SetPreprocessor getInstance() { + return new TestPreproc(modulus); + } + } + + public static final class TestPreproc implements SetPreprocessor { + final TLongArrayList l = new TLongArrayList(); + final long modulus; + + public TestPreproc(long modulus) { + this.modulus = modulus; + } + + boolean initialized = false; + + @Override + public SetPreprocessorSetup nextSetupStep() { + if (!initialized) { + initialized = true; + return new SetPreprocessorSetup() { + @Override + public void initialize(int nDatasets) {} + + @Override + public InputPort consumer(int i) { + return c -> { + if (c == null) + return; + l.add((long) c.weight); + }; + } + }; + } + return null; + } + + + @Override + public MappingFunction getMapper(int iDataset) { + AtomicInteger idx = new AtomicInteger(0); + return element -> { + if (l.get(idx.getAndIncrement()) % modulus == 0) + return null; + return element; + }; + } + + } + + public static TestDataset rndDataset(RandomDataGenerator rng, int size) { + TestObject[] r = new TestObject[size]; + for (int i = 0; i < size; i++) { + r[i] = new TestObject( + Math.round(rng.nextUniform(0, 1000)), + Math.round(rng.nextUniform(1, 100))); + } + return new TestDataset<>(Arrays.asList(r)); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java new file mode 100644 index 000000000..dd0170659 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java @@ -0,0 +1,167 @@ +package com.milaboratory.mixcr.postanalysis.preproc; + +import cc.redberry.pipe.CUtils; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.SerializationFeature; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.*; +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well512a; +import org.junit.Assert; +import org.junit.Test; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Comparator; + +/** + * + */ +public class SelectTopTest { + @SuppressWarnings("unchecked") + @Test + public void test1() { + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + int nIterations = 10; + for (int i = 0; i < nIterations; i++) { + TestDataset dataset = rndDataset(rng, 10000); + double total = 0; + for (TestObject d : dataset) { + total += d.weight; + } + + double topFraction = 0.5 + (1.0 * i / nIterations / 10); + int nTop = rng.nextInt(1, dataset.data.size()); + + ArrayList list = new ArrayList<>(dataset.data); + list.sort(Comparator.comparing(t -> -t.weight)); + double expectedSumCum = 0; + double expectedSumFixed = 0; + boolean sumDone = false; + int counter = 0; + for (TestObject o : list) { + if (!sumDone && expectedSumCum < topFraction * total) + expectedSumCum += o.weight; + else + sumDone = true; + + if (counter < nTop) { + expectedSumFixed += o.weight; + ++counter; + } + + if (expectedSumCum > topFraction * total && counter > nTop) + break; + } + + SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1); + Dataset topCumulative = SetPreprocessorFactory.processDatasets(cumulativeTopProc, dataset)[0]; + + double actualCum = 0; + for (TestObject o : CUtils.it(topCumulative.mkElementsPort())) { + actualCum += o.weight; + } + Assert.assertEquals(expectedSumCum, actualCum, 1e-5); + + SelectTop fixedTopProc = new SelectTop<>(o -> o.weight, Double.NaN, nTop); + Dataset topFixed = SetPreprocessorFactory.processDatasets(fixedTopProc, dataset)[0]; + double actualFixed = 0; + int actualNTop = 0; + for (TestObject o : CUtils.it(topFixed.mkElementsPort())) { + actualFixed += o.weight; + ++actualNTop; + } + Assert.assertEquals(expectedSumFixed, actualFixed, 1e-5); + Assert.assertEquals(nTop, actualNTop); + } + } + + @Test + public void test2() { + TestDataset dataset = new TestDataset<>(Arrays.asList( + new TestObject(1, 1), + new TestObject(1, 1), + new TestObject(1, 1), + new TestObject(1, 2), + new TestObject(1, 2), + new TestObject(1, 2) + )); + + assertFraction(0.5, dataset, 6.0); + assertFraction(0.8, dataset, 8.0); + } + + @Test + public void test3() { + TestDataset dataset = new TestDataset<>(Arrays.asList( + new TestObject(1, 1), + new TestObject(1, 1), + new TestObject(1, 1), + new TestObject(1, 2), + new TestObject(1, 2), + new TestObject(1, 2), + new TestObject(1, 3), + new TestObject(1, 3) + )); + + assertFraction(0.5, dataset, 8.0); + assertFraction(0.5, dataset, 8.0); + } + + @Test + public void test4() { + TestDataset dataset = new TestDataset<>(Arrays.asList( + new TestObject(1, 1.1), + new TestObject(1, 2.2), + new TestObject(1, 3.3), + new TestObject(1, 4.4), + new TestObject(1, 5.5), + new TestObject(1, 6.6), + new TestObject(1, 7.7), + new TestObject(1, 8.8) + )); + + assertFraction(0.5, dataset, 23.1); + } + + private void assertFraction(double topFraction, TestDataset dataset, double expectedSum) { + ArrayList list = new ArrayList<>(dataset.data); + list.sort(Comparator.comparing(t -> -t.weight)); + + SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1); + Dataset topCumulative = SetPreprocessorFactory.processDatasets(cumulativeTopProc, dataset)[0]; + + double actualCum = 0; + for (TestObject o : CUtils.it(topCumulative.mkElementsPort())) { + actualCum += o.weight; + } + Assert.assertEquals(expectedSum, actualCum, 1e-5); + } + + public static TestDataset rndDataset(RandomDataGenerator rng, int size) { + TestObject[] r = new TestObject[size]; + for (int i = 0; i < size; i++) { + r[i] = new TestObject( + rng.nextUniform(0, 1), + Math.round(rng.nextUniform(1, 100))); + } + return new TestDataset<>(Arrays.asList(r)); + } + + @Test + public void testJson() throws JsonProcessingException { + SelectTop.Factory top = new SelectTop.Factory<>(WeightFunctions.Count, 0.8); + ObjectMapper om = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT); + + String str = om.writeValueAsString(top); + Assert.assertEquals(top, om.readValue("{\n" + + " \"type\" : \"selectTop\",\n" + + " \"weight\" : {\n" + + " \"type\" : \"count\"\n" + + " },\n" + + " \"abundanceFraction\" : 0.8\n" + + "}", SelectTop.Factory.class)); + Assert.assertEquals(top, om.readValue(str, SelectTop.Factory.class)); + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index 872dcd222..f17defd2f 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -14,14 +14,14 @@ import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; -import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessor; -import com.milaboratory.mixcr.postanalysis.downsampling.ClonesOverlapDownsamplingPreprocessor; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; import com.milaboratory.mixcr.postanalysis.overlap.OverlapCharacteristic; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; import com.milaboratory.mixcr.postanalysis.overlap.OverlapIntegrationTest; import com.milaboratory.mixcr.postanalysis.overlap.OverlapUtil; import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; @@ -79,7 +79,7 @@ public void test1() throws IOException { )); groups.add(new CharacteristicGroup<>( "diversity", - Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessor(new DownsampleValueChooser.Auto(), 314))), + Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314))), Arrays.asList(new GroupSummary<>()) )); @@ -109,7 +109,7 @@ public void test1() throws IOException { groups.add(new CharacteristicGroup<>( "cdr3Spectratype", Arrays.asList(new SpectratypeCharacteristic("cdr3Spectratype", - new NoPreprocessing<>(), 10, + NoPreprocessing.factory(), 10, new SpectratypeKeyFunction<>(new KeyFunctions.NTFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), Collections.singletonList(new GroupSummary<>()))); @@ -135,22 +135,6 @@ public void test1() throws IOException { String resultStr = OM.writeValueAsString(result); Assert.assertEquals(result, OM.readValue(resultStr, PostanalysisResult.class)); - Map outputs; - -// CharacteristicGroupResult cdr3Table = result.getTable(cdr3PropsTable); -// cdr3Table.getOutputs(); -// for (OutputTable o : outputs.values()) { -// o.writeTSV(Paths.get("/Users/poslavskysv/Downloads/hhhh/")); -// } -// System.out.println(outputs); -// -// CharacteristicGroupResult divTable = result.getTable(diversityTable); -// divTable.cells.stream().filter(cell -> cell.key == DiversityMeasure.Observed).map(cell -> cell.sampleIndex + " - " + cell.value).forEach(System.out::println); -// divTable.cells.stream().filter(cell -> cell.key == DiversityMeasure.Chao1).map(cell -> cell.sampleIndex + " - " + cell.value).forEach(System.out::println); -// outputs = divTable.getOutputs(); -// for (OutputTable o : outputs.values()) { -// o.writeTSV(Paths.get("/Users/poslavskysv/Downloads/hhhh")); -// } CharacteristicGroupResult> r = result.getTable(individualPA.getGroup("cdr3Spectratype")); Assert.assertTrue(r.cells.stream() @@ -197,7 +181,7 @@ public void testOverlap1() throws JsonProcessingException { System.out.println("============="); Dataset> overlap = OverlapUtil.overlap(sampleNames, by, readers); - ClonesOverlapDownsamplingPreprocessor downsamplePreprocessor = new ClonesOverlapDownsamplingPreprocessor( + ClonesDownsamplingPreprocessorFactory downsamplePreprocessor = new ClonesDownsamplingPreprocessorFactory( new DownsampleValueChooser.Minimal(), 332142); @@ -206,12 +190,11 @@ public void testOverlap1() throws JsonProcessingException { for (int j = i + 1; j < readers.size(); ++j) { overlaps.add(new OverlapCharacteristic<>("overlap_" + i + "_" + j, new WeightFunctions.Count(), - downsamplePreprocessor, + new OverlapPreprocessorAdapter.Factory<>(downsamplePreprocessor), i, j)); } } - List>> groups = new ArrayList<>(); groups.add(new CharacteristicGroup<>("cdr3Properties", From 740429ce00d33996d097a67c1f0e085060e58434 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sat, 6 Mar 2021 20:56:56 +0300 Subject: [PATCH 097/282] Migration to new milib version with fix for HashSorter. --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 30e4df01c..31c86b973 100644 --- a/pom.xml +++ b/pom.xml @@ -41,7 +41,7 @@ UTF-8 - 1.14-2d70391 + 1.14-99f08d0 SNAPSHOT From b329278a56d30cb41d12c757191cb96de1e3f304 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Tue, 9 Mar 2021 19:28:10 +0300 Subject: [PATCH 098/282] dna.multiplex.rstrand.v1 alignment parameter set. --- .../milaboratory/mixcr/cli/CommandAlign.java | 29 ++-- .../mixcr/vdjaligners/VDJCAlignerPVFirst.java | 14 +- .../vdjaligners/VDJCAlignerParameters.java | 18 ++- .../vdjaligners/VDJCLibraryStructure.java | 5 + .../parameters/vdjcaligner_parameters.json | 138 ++++++++++++++++++ .../VDJCAlignerParametersTest.java | 2 +- 6 files changed, 190 insertions(+), 16 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 9ff0f229c..655c6e2d8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -66,6 +66,7 @@ import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult; import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; import com.milaboratory.util.CanReportProgress; +import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.*; import picocli.CommandLine; @@ -74,6 +75,7 @@ import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; +import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.nio.file.Paths; @@ -229,15 +231,24 @@ public VDJCAlignerParameters getAlignerParameters() { if (vdjcAlignerParameters != null) return vdjcAlignerParameters; - VDJCAlignerParameters alignerParameters = VDJCParametersPresets.getByName(alignerParametersName); - if (alignerParameters == null) - throwValidationException("Unknown aligner parameters: " + alignerParametersName); - - if (!overrides.isEmpty()) { - // Perform parameters overriding - alignerParameters = JsonOverrider.override(alignerParameters, VDJCAlignerParameters.class, overrides); + VDJCAlignerParameters alignerParameters; + if (alignerParametersName.endsWith(".json")) { + try { + alignerParameters = GlobalObjectMappers.ONE_LINE.readValue(new File(alignerParametersName), VDJCAlignerParameters.class); + } catch (IOException e) { + throw new RuntimeException(e); + } + } else { + alignerParameters = VDJCParametersPresets.getByName(alignerParametersName); if (alignerParameters == null) - throwValidationException("Failed to override some parameter: " + overrides); + throwValidationException("Unknown aligner parameters: " + alignerParametersName); + + if (!overrides.isEmpty()) { + // Perform parameters overriding + alignerParameters = JsonOverrider.override(alignerParameters, VDJCAlignerParameters.class, overrides); + if (alignerParameters == null) + throwValidationException("Failed to override some parameter: " + overrides); + } } // Detect if automatic featureToAlign correction is required @@ -509,7 +520,6 @@ else if (featureSequence.containsWildcards()) throwExecutionException("No J genes to align. Aborting execution. See warnings for more info " + "(turn on verbose warnings by adding --verbose option)."); - report.setStartMillis(beginTimestamp); report.setInputFiles(getInputFiles()); report.setOutputFiles(getOutput()); @@ -561,6 +571,7 @@ else if (featureSequence.containsWildcards()) ParallelProcessor alignedChunks = new ParallelProcessor(mainInputReadsPreprocessed, chunked(aligner), Math.max(16, threads), threads); if (reportBuffers) { + System.out.println("Analysis threads: " + threads); StatusReporter reporter = new StatusReporter(); reporter.addBuffer("Input (chunked; chunk size = 64)", mainInputReads.getBufferStatusProvider()); reporter.addBuffer("Alignment result (chunked; chunk size = 64)", alignedChunks.getOutputBufferStatusProvider()); diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java index df7cef0b5..da13cf693 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java @@ -372,15 +372,21 @@ PAlignmentHelper alignVThenJ(final Target target) { * Step 1: alignment of V gene */ - List> - vAl1 = vAligner.align(target.targets[0].getSequence()).getHits(), - vAl2 = vAligner.align(target.targets[1].getSequence()).getHits(); + List> vAl1, vAl2; + + if (parameters.getLibraryStructure() == VDJCLibraryStructure.R1V) { + vAl1 = vAlignerNotFloatingRight.align(target.targets[0].getSequence()).getHits(); + vAl2 = vAlignerNotFloatingLeft.align(target.targets[1].getSequence()).getHits(); + } else { + vAl1 = vAligner.align(target.targets[0].getSequence()).getHits(); + vAl2 = vAligner.align(target.targets[1].getSequence()).getHits(); + } /* * Step 1.4: force floating bounds = false for ---xxx> <---- and ---> alignmentParameters; private VJAlignmentOrder vjAlignmentOrder; + private VDJCLibraryStructure libraryStructure; private boolean includeDScore, includeCScore; private float minSumScore; private int maxHits; @@ -72,6 +73,7 @@ public VDJCAlignerParameters(@JsonProperty("vParameters") KGeneAlignmentParamete @JsonProperty("jParameters") KGeneAlignmentParameters jParameters, @JsonProperty("cParameters") KGeneAlignmentParameters cParameters, @JsonProperty("vjAlignmentOrder") VJAlignmentOrder vjAlignmentOrder, + @JsonProperty("libraryStructure") VDJCLibraryStructure libraryStructure, @JsonProperty("includeDScore") boolean includeDScore, @JsonProperty("includeCScore") boolean includeCScore, @JsonProperty("minSumScore") float minSumScore, @@ -94,6 +96,7 @@ public VDJCAlignerParameters(@JsonProperty("vParameters") KGeneAlignmentParamete setGeneAlignerParameters(GeneType.Joining, jParameters); setGeneAlignerParameters(GeneType.Constant, cParameters); this.vjAlignmentOrder = vjAlignmentOrder; + this.libraryStructure = libraryStructure; this.includeDScore = includeDScore; this.includeCScore = includeCScore; this.minSumScore = minSumScore; @@ -239,6 +242,11 @@ public VJAlignmentOrder getVJAlignmentOrder() { return vjAlignmentOrder; } + @JsonProperty("libraryStructure") + public VDJCLibraryStructure getLibraryStructure() { + return libraryStructure; + } + public void setSmartForceEdgeAlignments(boolean smartForceEdgeAlignments) { this.smartForceEdgeAlignments = smartForceEdgeAlignments; } @@ -252,6 +260,10 @@ public void setVjAlignmentOrder(VJAlignmentOrder vjAlignmentOrder) { this.vjAlignmentOrder = vjAlignmentOrder; } + public void setLibraryStructure(VDJCLibraryStructure libraryStructure) { + this.libraryStructure = libraryStructure; + } + public boolean doIncludeDScore() { return includeDScore; } @@ -361,6 +373,7 @@ public String toString() { return "VDJCAlignerParameters{" + "alignmentParameters=" + alignmentParameters + ", vjAlignmentOrder=" + vjAlignmentOrder + + ", libraryStructure=" + libraryStructure + ", includeDScore=" + includeDScore + ", includeCScore=" + includeCScore + ", minSumScore=" + minSumScore + @@ -399,6 +412,7 @@ public boolean equals(Object o) { saveOriginalReads == that.saveOriginalReads && Objects.equals(alignmentParameters, that.alignmentParameters) && vjAlignmentOrder == that.vjAlignmentOrder && + libraryStructure == that.libraryStructure && readsLayout == that.readsLayout && Objects.equals(mergerParameters, that.mergerParameters) && smartForceEdgeAlignments == that.smartForceEdgeAlignments; @@ -406,13 +420,13 @@ public boolean equals(Object o) { @Override public int hashCode() { - return Objects.hash(alignmentParameters, vjAlignmentOrder, includeDScore, includeCScore, minSumScore, maxHits, relativeMinVFR3CDR3Score, allowPartialAlignments, allowNoCDR3PartAlignments, allowChimeras, readsLayout, mergerParameters, fixSeed, alignmentBoundaryTolerance, minChimeraDetectionScore, vjOverlapWindow, saveOriginalReads); + return Objects.hash(alignmentParameters, vjAlignmentOrder, libraryStructure, includeDScore, includeCScore, minSumScore, maxHits, relativeMinVFR3CDR3Score, allowPartialAlignments, allowNoCDR3PartAlignments, allowChimeras, readsLayout, mergerParameters, fixSeed, alignmentBoundaryTolerance, minChimeraDetectionScore, vjOverlapWindow, saveOriginalReads); } @Override public VDJCAlignerParameters clone() { return new VDJCAlignerParameters(getVAlignerParameters(), getDAlignerParameters(), getJAlignerParameters(), - getCAlignerParameters(), vjAlignmentOrder, includeDScore, includeCScore, minSumScore, maxHits, + getCAlignerParameters(), vjAlignmentOrder, libraryStructure, includeDScore, includeCScore, minSumScore, maxHits, relativeMinVFR3CDR3Score, allowPartialAlignments, allowNoCDR3PartAlignments, allowChimeras, readsLayout, mergerParameters, fixSeed, alignmentBoundaryTolerance, minChimeraDetectionScore, vjOverlapWindow, saveOriginalReads, smartForceEdgeAlignments); diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java new file mode 100644 index 000000000..2b09cdd03 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java @@ -0,0 +1,5 @@ +package com.milaboratory.mixcr.vdjaligners; + +public enum VDJCLibraryStructure { + Unknown, R1V +} diff --git a/src/main/resources/parameters/vdjcaligner_parameters.json b/src/main/resources/parameters/vdjcaligner_parameters.json index 7975a4797..79fcd57cc 100644 --- a/src/main/resources/parameters/vdjcaligner_parameters.json +++ b/src/main/resources/parameters/vdjcaligner_parameters.json @@ -1,6 +1,7 @@ { "default": { "fixSeed" : true, + "libraryStructure": "Unknown", "vParameters": { "geneFeatureToAlign": "VRegionWithP", "minSumScore" : 50, @@ -123,6 +124,7 @@ }, "kaligner2": { "fixSeed" : true, + "libraryStructure": "Unknown", "vParameters": { "geneFeatureToAlign": "VRegionWithP", "minSumScore" : 150, @@ -257,6 +259,7 @@ }, "rna-seq": { "fixSeed" : true, + "libraryStructure": "Unknown", "vParameters": { "geneFeatureToAlign": "VTranscriptWithP", "minSumScore" : 80, @@ -376,5 +379,140 @@ "readsLayout": "Opposite", "saveOriginalReads": false, "smartForceEdgeAlignments": true + }, + "dna.multiplex.rstrand.v1": { + "fixSeed": true, + "libraryStructure": "R1V", + "vParameters": { + "geneFeatureToAlign": "VRegionWithP", + "minSumScore": 200, + "relativeMinScore": 0.9, + "parameters": { + "type": "kaligner2", + "mapperNValue": 10, + "mapperKValue": 1, + "floatingLeftBound": false, + "floatingRightBound": true, + "mapperAbsoluteMinClusterScore": 102, + "mapperExtraClusterScore": -38, + "mapperMatchScore": 95, + "mapperMismatchScore": -14, + "mapperOffsetShiftScore": -82, + "mapperSlotCount": 6, + "mapperMaxClusters": 4, + "mapperMaxClusterIndels": 4, + "mapperKMersPerPosition": 4, + "mapperAbsoluteMinScore": 100, + "mapperRelativeMinScore": 0.8, + "mapperMinSeedsDistance": 5, + "mapperMaxSeedsDistance": 15, + "alignmentStopPenalty": 0, + "absoluteMinScore": 150, + "relativeMinScore": 0.8, + "maxHits": 4, + "scoring": { + "type": "affine", + "subsMatrix": "simple(match = 10, mismatch = -19)", + "gapOpenPenalty": -40, + "gapExtensionPenalty": -11 + } + } + }, + "dParameters": { + "geneFeatureToAlign": "DRegionWithP", + "absoluteMinScore": 25.0, + "relativeMinScore": 0.85, + "maxHits": 3, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + }, + "jParameters": { + "geneFeatureToAlign": "JRegionWithP", + "minSumScore": 140, + "relativeMinScore": 0.8, + "parameters": { + "type": "kaligner2", + "mapperNValue": 7, + "mapperKValue": 1, + "floatingLeftBound": true, + "floatingRightBound": false, + "mapperAbsoluteMinClusterScore": 102, + "mapperExtraClusterScore": -38, + "mapperMatchScore": 95, + "mapperMismatchScore": -14, + "mapperOffsetShiftScore": -82, + "mapperSlotCount": 6, + "mapperMaxClusters": 4, + "mapperMaxClusterIndels": 4, + "mapperKMersPerPosition": 4, + "mapperAbsoluteMinScore": 100, + "mapperRelativeMinScore": 0.8, + "mapperMinSeedsDistance": 5, + "mapperMaxSeedsDistance": 5, + "alignmentStopPenalty": 0, + "absoluteMinScore": 140, + "relativeMinScore": 0.8, + "maxHits": 3, + "scoring": { + "type": "affine", + "subsMatrix": "simple(match = 10, mismatch = -19)", + "gapOpenPenalty": -40, + "gapExtensionPenalty": -11 + } + } + }, + "cParameters": { + "geneFeatureToAlign": "CExon1", + "minSumScore": 40, + "relativeMinScore": 0.8, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": false, + "floatingRightBound": false, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.75, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 40.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + } + }, + "vjAlignmentOrder": "VThenJ", + "includeDScore": false, + "includeCScore": false, + "mergerParameters": { + "qualityMergingAlgorithm": "MaxSubtraction", + "minimalOverlap": 17, + "minimalIdentity": 0.9, + "identityType": "Unweighted" + }, + "minSumScore": 300, + "maxHits": 5, + "relativeMinVFR3CDR3Score": 0.7, + "allowPartialAlignments": false, + "allowNoCDR3PartAlignments": false, + "allowChimeras": false, + "alignmentBoundaryTolerance": 5, + "minChimeraDetectionScore": 120, + "vjOverlapWindow": 3, + "readsLayout": "ReverseOnly", + "saveOriginalReads": false, + "smartForceEdgeAlignments": true } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java index 2d19960c9..519f2ec4d 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java @@ -60,7 +60,7 @@ public void test1() throws Exception { new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring())), - VJAlignmentOrder.JThenV, + VJAlignmentOrder.JThenV, VDJCLibraryStructure.Unknown, false, false, 120.0f, 5, 0.7f, false, false, false, PairedEndReadsLayout.Opposite, new MergerParameters( QualityMergingAlgorithm.SumSubtraction, null, 12, null, 0.12, Unweighted), false, 5, 120, 10, true, true); From 5d2b6f84cec0e183a2079480a69d99f35d8197bd Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 27 Apr 2021 02:53:01 +0300 Subject: [PATCH 099/282] This fixes #647 --- doc/export.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/export.rst b/doc/export.rst index 4823dcebf..fd51693a4 100644 --- a/doc/export.rst +++ b/doc/export.rst @@ -254,7 +254,7 @@ The following regular expressions can be used to parse the contents of this fiel import pandas as pd data = pd.read_table("exported.txt", low_memory=False) anchorPointsRegex="^(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*)$" - data = pd.concat([data, d.refPoints.str.extract(anchorPointsRegex, expand=True).apply(pd.to_numeric)], axis=1) + data = pd.concat([data, data.refPoints.str.extract(anchorPointsRegex, expand=True).apply(pd.to_numeric)], axis=1) - A simplified regular expression with a smaller number of fields can be used for analysis of CDR3-assembled clonotypes: @@ -269,7 +269,7 @@ The following regular expressions can be used to parse the contents of this fiel import pandas as pd data = pd.read_table("exported.txt", low_memory=False) anchorPointsRegex="^^(?:-?[0-9]*:){8}(?:-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?P-?[0-9]*):(?:-?[0-9]*:){2}(?:-?[0-9]*)$" - data = pd.concat([data, d.refPoints.str.extract(anchorPointsRegex, expand=True).apply(pd.to_numeric)], axis=1) + data = pd.concat([data, data.refPoints.str.extract(anchorPointsRegex, expand=True).apply(pd.to_numeric)], axis=1) Examples From ef7f68ac078ee31f86318fdcc42c39a7c2f1c426 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 27 Apr 2021 13:17:48 +0300 Subject: [PATCH 100/282] Update to the recent milib --- pom.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 31c86b973..b8caf027f 100644 --- a/pom.xml +++ b/pom.xml @@ -40,8 +40,7 @@ UTF-8 - - 1.14-99f08d0 + 1.14-a7230df SNAPSHOT From 8070d93b3af99e978faa31d535bc7fca1fc81e4e Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Tue, 25 May 2021 11:04:12 +0300 Subject: [PATCH 101/282] --align-preset for analyze action --- .../mixcr/cli/CommandAnalyze.java | 23 +++++++++++++------ 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index 153eca01d..a4135d6b1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -245,6 +245,10 @@ static class _AdaptersCandidates extends EnumCandidates { required = true) public String species = "hs"; + @Option(description = CommonDescriptions.SPECIES, + names = {"--align-preset"}) + public String alignPreset = null; + public Chains chains = Chains.ALL; @Option(names = "--receptor-type", @@ -344,7 +348,7 @@ public final CommandAlign getAlign() { return cmdAlign = inheritOptionsAndValidate(mkAlign()); } - boolean forceUseRnaSeqOps() { return false; } + String forceAlignmentParameters() { return alignPreset; } boolean include5UTRInRNA() { return true; } @@ -400,10 +404,13 @@ CommandAlign mkAlign() { // adding report options addReportOptions("align", alignParameters); - if (!forceUseRnaSeqOps() && !chains.intersects(Chains.TCR)) - alignParameters.add("-p kAligner2"); - else - alignParameters.add("-p rna-seq"); // always use rna-seq by default + if (forceAlignmentParameters() == null) { + if (!chains.intersects(Chains.TCR)) + alignParameters.add("-p kAligner2"); + else + alignParameters.add("-p rna-seq"); + } else + alignParameters.add("-p " + forceAlignmentParameters()); // add v feature to align switch (startingMaterial) { @@ -879,8 +886,10 @@ public CommandShotgun() { } @Override - boolean forceUseRnaSeqOps() { - return true; + String forceAlignmentParameters() { + return alignPreset == null + ? "rna-seq" + : alignPreset; } @Override From b96de95b60c3e14d5c47f4efa50eef13fabfdddb Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Tue, 21 Jul 2020 17:45:54 +0300 Subject: [PATCH 102/282] RepseqIO upgrade. --- repseqio | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repseqio b/repseqio index 5b3d1a2ff..391149707 160000 --- a/repseqio +++ b/repseqio @@ -1 +1 @@ -Subproject commit 5b3d1a2ff7158e5735de11b5e8e23badf42bd8a7 +Subproject commit 391149707cdcc15d726d13f7d6a3e299b7eb8397 From a2490dac4b97e394305e8acdfe03c4645cb61b26 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sun, 30 May 2021 01:08:17 +0300 Subject: [PATCH 103/282] Initial gradlle build script and drone config. I tests. delete repseqio submodule Delete milib submodule. WIP Fixes fix2 --- .drone.yml | 343 ++++++++++++++++++ .gitmodules | 6 - build.gradle.kts | 144 ++++++++ gradle/wrapper/gradle-wrapper.jar | Bin 0 -> 59203 bytes gradle/wrapper/gradle-wrapper.properties | 5 + gradlew | 185 ++++++++++ gradlew.bat | 89 +++++ milib | 1 - mixcr | 2 +- repseqio | 1 - settings.gradle.kts | 5 + .../assembler/CloneClusteringStrategy.java | 2 +- .../mixcr/basictypes/AlignmentsIO.java | 4 +- .../mixcr/basictypes/ClnAWriter.java | 2 +- .../mixcr/cli/AbstractCommandReport.java | 5 +- .../milaboratory/mixcr/cli/CommandMain.java | 12 +- .../mixcr/cli/CommandSortAlignments.java | 2 +- .../tests/BackwardCompatibilityTests.java | 8 +- .../mixcr/tests/MiXCRTestUtils.java | 11 +- .../mixcr/util/AlignedStringsBuilderTest.java | 4 +- .../mixcr/util/MiXCRVersionInfoTest.java | 6 + .../backward_compatibility/3.0.3/test.clna | Bin 43846 -> 0 bytes .../backward_compatibility/3.0.3/test.clns | Bin 36423 -> 0 bytes .../backward_compatibility/3.0.3/test.vdjca | Bin 37615 -> 0 bytes .../backward_compatibility/3.0.4/test.clna | Bin 44097 -> 0 bytes .../backward_compatibility/3.0.4/test.clns | Bin 36674 -> 0 bytes .../backward_compatibility/3.0.4/test.vdjca | Bin 37757 -> 0 bytes 27 files changed, 802 insertions(+), 35 deletions(-) create mode 100644 .drone.yml delete mode 100644 .gitmodules create mode 100644 build.gradle.kts create mode 100644 gradle/wrapper/gradle-wrapper.jar create mode 100644 gradle/wrapper/gradle-wrapper.properties create mode 100755 gradlew create mode 100644 gradlew.bat delete mode 160000 milib delete mode 160000 repseqio create mode 100644 settings.gradle.kts delete mode 100644 src/test/resources/backward_compatibility/3.0.3/test.clna delete mode 100644 src/test/resources/backward_compatibility/3.0.3/test.clns delete mode 100644 src/test/resources/backward_compatibility/3.0.3/test.vdjca delete mode 100644 src/test/resources/backward_compatibility/3.0.4/test.clna delete mode 100644 src/test/resources/backward_compatibility/3.0.4/test.clns delete mode 100644 src/test/resources/backward_compatibility/3.0.4/test.vdjca diff --git a/.drone.yml b/.drone.yml new file mode 100644 index 000000000..2ce5f89ae --- /dev/null +++ b/.drone.yml @@ -0,0 +1,343 @@ +--- +kind: pipeline +type: docker +name: main + +platform: + os: linux + arch: amd64 + +trigger: + event: + - push + - tag + +image_pull_secrets: + - docker-dockerconfig + - quay-dockerconfig + +anchors: + aws_credentials: &aws_credentials + AWS_DEFAULT_REGION: + from_secret: aws-region + AWS_ACCESS_KEY_ID: + from_secret: aws-key-id + AWS_SECRET_ACCESS_KEY: + from_secret: aws-secret-key + DEPLOY_S3_CDN_BUCKET: + from_secret: cdn-s3-bucket + DEPLOY_S3_CDN_PREFIX: + from_secret: cdn-s3-prefix + + gradle_task: &gradle_task + image: gradle:7.0.2-jdk8-hotspot + environment: + # Gradle folder + GRADLE_USER_HOME: "/drone/src/.gradle" + + # MiLab repository credentials + ORG_GRADLE_PROJECT_miRepoAccessKeyId: + from_secret: aws-key-id + ORG_GRADLE_PROJECT_miRepoSecretAccessKey: + from_secret: aws-secret-key + + # For Maven Central release + ORG_GRADLE_PROJECT_sonatypeUsername: + from_secret: sonatype-username + ORG_GRADLE_PROJECT_sonatypePassword: + from_secret: sonatype-password + ORG_GRADLE_PROJECT_signingKey: + from_secret: signing-key + + cache_settings: &cache_settings + # debug: true + access_key: + from_secret: aws-key-id + secret_key: + from_secret: aws-secret-key + bucket: + from_secret: aws-cache-bucket + region: + from_secret: aws-region + local_root: /drone/src + +steps: + - name: fetch + image: alpine/git + commands: + - git fetch --tags + + - name: restore_gradle_cache + image: meltwater/drone-cache + pull: true + settings: + restore: true + cache_key: '{{ .Commit.Branch }}' + mount: + - .gradle + <<: *cache_settings + + - <<: *gradle_task + name: initialization + commands: + - echo "{}" > build_info.json + - gradle -i --no-daemon CreateInfoFile + + - name: add_url_secret + image: alpine + commands: + - apk add jq + - jq ".urlsecret=\"$${URL_SECRET}\"" build_info.json > build_info.json.1 + - mv build_info.json.1 build_info.json + environment: + URL_SECRET: + from_secret: url-secret + + - <<: *gradle_task + name: create_zip_and_publish_artefact + commands: + - gradle --no-daemon -i -x test PublishAllPublicationsToMiPrivRepository distributionZip + + - name: publish_zip_to_cdn + image: alpine + when: + event: + - push + commands: + - apk add jq aws-cli + - | + aws s3 cp \ + "build/distributions/mixcr.zip" \ + "s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-$(jq -r .version build_info.json).zip" + environment: + <<: *aws_credentials + + # - name: rename_release_file + # image: alpine + # when: + # event: + # - tag + # commands: + # - apk add jq + # - mv build/distributions/mixcr.zip build/distributions/mixcr-$(jq -r .version build_info.json).zip + # + # - name: publish_zip_to_github + # image: plugins/github-release + # when: + # event: tag + # settings: + # api_key: + # from_secret: github-public-repo + # checksum: + # - sha256 + # files: build/distributions/* + + - name: telegram_mipub_published + when: + event: + - push + image: appleboy/drone-telegram + settings: + token: + from_secret: telegram-token + to: + from_secret: telegram-chat-id-micore + format: markdown + template_vars_file: build_info.json + disable_web_page_preview: true + message: | + 🧩 build {{build.number}} on `{{commit.branch}}` published ```com.milaboratory:mixcr:{{tpl.version}}``` + + 📦 https://cdn.milaboratory.com/software/mixcr/mixcr-{{tpl.version}}.zip + + - <<: *gradle_task + name: test + commands: + - gradle -i --no-daemon test + + - name: test_report_upload + image: amazon/aws-cli + when: + status: + - success + - failure + commands: + - aws s3 cp --recursive build/reports/tests/test s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-$${URL_SECRET}/tests/ + environment: + <<: *aws_credentials + DEPLOY_S3_CDN_BUCKET: + from_secret: cdn-s3-bucket + DEPLOY_S3_CDN_PREFIX: + from_secret: cdn-s3-prefix + URL_SECRET: + from_secret: url-secret + + - name: telegram_tests + image: appleboy/drone-telegram + when: + status: + - success + - failure + settings: + token: + from_secret: telegram-token + to: + from_secret: telegram-chat-id-micore + format: markdown + template_vars_file: build_info.json + message: | + {{#success build.status}} + ✅ MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` test success. + {{else}} + ❌ MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` test failure. + {{/success}} + + 🌐 {{build.link}} + + [📊 Test Report](https://cdn.milaboratory.com/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-{{tpl.urlsecret}}/tests/index.html) + + - name: rebuild_gradle_cache + image: meltwater/drone-cache + pull: true + settings: + rebuild: true + cache_key: '{{ .Commit.Branch }}' + mount: + - .gradle + <<: *cache_settings + +--- + +kind: pipeline +type: docker +name: integration_tests + +platform: + os: linux + arch: amd64 + +node: + type: highcpu + +trigger: + event: + - push + +image_pull_secrets: + - docker-dockerconfig + - quay-dockerconfig + +anchors: + aws_credentials: &aws_credentials + AWS_DEFAULT_REGION: + from_secret: aws-region + AWS_ACCESS_KEY_ID: + from_secret: aws-key-id + AWS_SECRET_ACCESS_KEY: + from_secret: aws-secret-key + DEPLOY_S3_CDN_BUCKET: + from_secret: cdn-s3-bucket + DEPLOY_S3_CDN_PREFIX: + from_secret: cdn-s3-prefix + + gradle_task: &gradle_task + image: gradle:7.0.2-jdk8-hotspot + environment: + # Gradle folder + GRADLE_USER_HOME: "/drone/src/.gradle" + + # MiLab repository credentials + ORG_GRADLE_PROJECT_miRepoAccessKeyId: + from_secret: aws-key-id + ORG_GRADLE_PROJECT_miRepoSecretAccessKey: + from_secret: aws-secret-key + + # For Maven Central release + ORG_GRADLE_PROJECT_sonatypeUsername: + from_secret: sonatype-username + ORG_GRADLE_PROJECT_sonatypePassword: + from_secret: sonatype-password + ORG_GRADLE_PROJECT_signingKey: + from_secret: signing-key + + cache_settings: &cache_settings + # debug: true + access_key: + from_secret: aws-key-id + secret_key: + from_secret: aws-secret-key + bucket: + from_secret: aws-cache-bucket + region: + from_secret: aws-region + local_root: /drone/src + +steps: + - name: restore_gradle_cache + image: meltwater/drone-cache + pull: true + settings: + restore: true + cache_key: '{{ .Commit.Branch }}' + mount: + - .gradle + <<: *cache_settings + + - name: restore_test_resource_cache + image: meltwater/drone-cache + pull: true + settings: + restore: true + cache_key: mixcr_test_resource + mount: + - src/test/resources/sequences/big + <<: *cache_settings + + - <<: *gradle_task + name: initialization + commands: + - ./ensure-test-data.sh + - echo "{}" > build_info.json + - gradle -i --no-daemon CreateInfoFile + + - name: rebuild_test_resource_cache + image: meltwater/drone-cache + pull: true + settings: + rebuild: true + cache_key: mixcr_test_resource + mount: + - src/test/resources/sequences/big + <<: *cache_settings + + - <<: *gradle_task + name: build + commands: + - gradle -i --no-daemon -PlongTests=true test build + + - <<: *gradle_task + name: integration_tests + commands: + - ./itests.sh test + + - name: telegram_tests + image: appleboy/drone-telegram + when: + status: + - success + - failure + settings: + token: + from_secret: telegram-token + to: + from_secret: telegram-chat-id-micore + format: markdown + template_vars_file: build_info.json + message: | + {{#success build.status}} + ✅ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` integration test success. + {{else}} + ❌ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` integration test failure. + + 🌐 {{build.link}} + {{/success}} diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 34a1c0a12..000000000 --- a/.gitmodules +++ /dev/null @@ -1,6 +0,0 @@ -[submodule "repseqio"] - path = repseqio - url = https://github.com/repseqio/repseqio.git -[submodule "milib"] - path = milib - url = git://github.com/milaboratory/milib.git diff --git a/build.gradle.kts b/build.gradle.kts new file mode 100644 index 000000000..bea5bf7bf --- /dev/null +++ b/build.gradle.kts @@ -0,0 +1,144 @@ +import com.palantir.gradle.gitversion.VersionDetails +import java.util.Base64 +import groovy.lang.Closure +import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar +import java.net.InetAddress + +plugins { + `java-library` + application + `maven-publish` + id("com.palantir.git-version") version "0.12.3" + id("com.github.johnrengelman.shadow") version "7.0.0" +} + +val miRepoAccessKeyId: String by project +val miRepoSecretAccessKey: String by project + +val versionDetails: Closure by extra +val gitDetails = versionDetails() + +val longTests: String? by project + +group = "com.milaboratory" +val gitLastTag = gitDetails.lastTag.removePrefix("v") +version = + if (gitDetails.commitDistance == 0) gitLastTag + else "${gitLastTag}-${gitDetails.commitDistance}-${gitDetails.gitHash}" +description = "MiXCR" + +java { + sourceCompatibility = JavaVersion.VERSION_1_8 + withSourcesJar() + withJavadocJar() +} + +application { + mainClass.set("com.milaboratory.mixcr.cli.Main") +} + +tasks.withType() { + options.encoding = "UTF-8" +} + +tasks.register("createInfoFile") { + doLast { + projectDir + .resolve("build_info.json") + .writeText("""{"version":"$version"}""") + } +} + +repositories { + mavenCentral() + + // Snapshot versions of milib and repseqio distributed via this repo + maven { + url = uri("https://pub.maven.milaboratory.com") + } +} + +val milibVersion = "1.14.1-2-9a0739c639" +val repseqioVersion = "1.3.5-2-119d86c79d" +val jacksonVersion = "2.12.3" + +dependencies { + api("com.milaboratory:milib:$milibVersion") + api("io.repseq:repseqio:$repseqioVersion") { + exclude("com.milaboratory", "milib") + } + + implementation("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion") + implementation("commons-io:commons-io:2.7") + implementation("org.lz4:lz4-java:1.4.1") + implementation("net.sf.trove4j:trove4j:3.0.3") + implementation("info.picocli:picocli:3.6.1") + implementation("com.google.guava:guava:30.1.1-jre") + + testImplementation("junit:junit:4.13.2") + implementation(testFixtures("com.milaboratory:milib:$milibVersion")) + testImplementation("org.mockito:mockito-all:1.9.5") +} + +val writeBuildProperties by tasks.registering(WriteProperties::class) { + outputFile = file("${sourceSets.main.get().output.resourcesDir}/${project.name}-build.properties") + property("version", version) + property("name", "MiLib") + property("revision", gitDetails.gitHash) + property("branch", gitDetails.branchName) + property("host", InetAddress.getLocalHost().hostName) + property("timestamp", System.currentTimeMillis()) +} + +tasks.processResources { + dependsOn(writeBuildProperties) +} + +val shadowJar = tasks.withType { + minimize { + exclude(dependency("io.repseq:repseqio")) + exclude(dependency("com.milaboratory:milib")) + exclude(dependency("org.lz4:lz4-java")) + exclude(dependency("com.fasterxml.jackson.core:jackson-databind")) + + exclude(dependency("log4j:log4j")) + exclude(dependency("org.slf4j:slf4j-api")) + exclude(dependency("commons-logging:commons-logging")) + exclude(dependency("ch.qos.logback:logback-core")) + exclude(dependency("ch.qos.logback:logback-classic")) + } +} + +val distributionZip by tasks.registering(Zip::class) { + archiveFileName.set("${project.name}.zip") + destinationDirectory.set(file("$buildDir/distributions")) + from(shadowJar) { + rename("-.*\\.jar", "\\.jar") + } + from("${project.rootDir}/mixcr") + from("${project.rootDir}/LICENSE") +} + +publishing { + repositories { + maven { + name = "mipriv" + url = uri("s3://milaboratory-artefacts-private-files.s3.eu-central-1.amazonaws.com/maven") + + authentication { + credentials(AwsCredentials::class) { + accessKey = miRepoAccessKeyId + secretKey = miRepoSecretAccessKey + } + } + } + } + + publications.create("mavenJava") { + from(components["java"]) + } +} + +tasks.withType { + (options as StandardJavadocDocletOptions).addStringOption("Xdoclint:none", "-quiet") +} diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000000000000000000000000000000000000..e708b1c023ec8b20f512888fe07c5bd3ff77bb8f GIT binary patch literal 59203 zcma&O1CT9Y(k9%tZQHhO+qUh#ZQHhO+qmuS+qP|E@9xZO?0h@l{(r>DQ>P;GjjD{w zH}lENr;dU&FbEU?00aa80D$0M0RRB{U*7-#kbjS|qAG&4l5%47zyJ#WrfA#1$1Ctx zf&Z_d{GW=lf^w2#qRJ|CvSJUi(^E3iv~=^Z(zH}F)3Z%V3`@+rNB7gTVU{Bb~90p|f+0(v;nz01EG7yDMX9@S~__vVgv%rS$+?IH+oZ03D5zYrv|^ zC1J)SruYHmCki$jLBlTaE5&dFG9-kq3!^i>^UQL`%gn6)jz54$WDmeYdsBE9;PqZ_ zoGd=P4+|(-u4U1dbAVQrFWoNgNd;0nrghPFbQrJctO>nwDdI`Q^i0XJDUYm|T|RWc zZ3^Qgo_Qk$%Fvjj-G}1NB#ZJqIkh;kX%V{THPqOyiq)d)0+(r9o(qKlSp*hmK#iIY 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z#f8w6F}^!?^KE#+ZDv+xd5O&3EmomZzsv?>E-~ygGum45fk!SBN&|eo1rKw^?aZJ4 E2O(~oYXATM literal 0 HcmV?d00001 diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 000000000..0f80bbf51 --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,5 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-7.0.2-bin.zip +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 000000000..4f906e0c8 --- /dev/null +++ b/gradlew @@ -0,0 +1,185 @@ +#!/usr/bin/env sh + +# +# Copyright 2015 the original author or authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +############################################################################## +## +## Gradle start up script for UN*X +## +############################################################################## + +# Attempt to set APP_HOME +# Resolve links: $0 may be a link +PRG="$0" +# Need this for relative symlinks. +while [ -h "$PRG" ] ; do + ls=`ls -ld "$PRG"` + link=`expr "$ls" : '.*-> \(.*\)$'` + if expr "$link" : '/.*' > /dev/null; then + PRG="$link" + else + PRG=`dirname "$PRG"`"/$link" + fi +done +SAVED="`pwd`" +cd "`dirname \"$PRG\"`/" >/dev/null +APP_HOME="`pwd -P`" +cd "$SAVED" >/dev/null + +APP_NAME="Gradle" +APP_BASE_NAME=`basename "$0"` + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD="maximum" + +warn () { + echo "$*" +} + +die () { + echo + echo "$*" + echo + exit 1 +} + +# OS specific support (must be 'true' or 'false'). +cygwin=false +msys=false +darwin=false +nonstop=false +case "`uname`" in + CYGWIN* ) + cygwin=true + ;; + Darwin* ) + darwin=true + ;; + MINGW* ) + msys=true + ;; + NONSTOP* ) + nonstop=true + ;; +esac + +CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + + +# Determine the Java command to use to start the JVM. +if [ -n "$JAVA_HOME" ] ; then + if [ -x "$JAVA_HOME/jre/sh/java" ] ; then + # IBM's JDK on AIX uses strange locations for the executables + JAVACMD="$JAVA_HOME/jre/sh/java" + else + JAVACMD="$JAVA_HOME/bin/java" + fi + if [ ! -x "$JAVACMD" ] ; then + die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD="java" + which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." +fi + +# Increase the maximum file descriptors if we can. +if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then + MAX_FD_LIMIT=`ulimit -H -n` + if [ $? -eq 0 ] ; then + if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then + MAX_FD="$MAX_FD_LIMIT" + fi + ulimit -n $MAX_FD + if [ $? -ne 0 ] ; then + warn "Could not set maximum file descriptor limit: $MAX_FD" + fi + else + warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" + fi +fi + +# For Darwin, add options to specify how the application appears in the dock +if $darwin; then + GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" +fi + +# For Cygwin or MSYS, switch paths to Windows format before running java +if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then + APP_HOME=`cygpath --path --mixed "$APP_HOME"` + CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` + + JAVACMD=`cygpath --unix "$JAVACMD"` + + # We build the pattern for arguments to be converted via cygpath + ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` + SEP="" + for dir in $ROOTDIRSRAW ; do + ROOTDIRS="$ROOTDIRS$SEP$dir" + SEP="|" + done + OURCYGPATTERN="(^($ROOTDIRS))" + # Add a user-defined pattern to the cygpath arguments + if [ "$GRADLE_CYGPATTERN" != "" ] ; then + OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" + fi + # Now convert the arguments - kludge to limit ourselves to /bin/sh + i=0 + for arg in "$@" ; do + CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` + CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option + + if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition + eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` + else + eval `echo args$i`="\"$arg\"" + fi + i=`expr $i + 1` + done + case $i in + 0) set -- ;; + 1) set -- "$args0" ;; + 2) set -- "$args0" "$args1" ;; + 3) set -- "$args0" "$args1" "$args2" ;; + 4) set -- "$args0" "$args1" "$args2" "$args3" ;; + 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; + 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; + 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; + 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; + 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; + esac +fi + +# Escape application args +save () { + for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done + echo " " +} +APP_ARGS=`save "$@"` + +# Collect all arguments for the java command, following the shell quoting and substitution rules +eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" + +exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat new file mode 100644 index 000000000..ac1b06f93 --- /dev/null +++ b/gradlew.bat @@ -0,0 +1,89 @@ +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem + +@if "%DEBUG%" == "" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%" == "" set DIRNAME=. +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if "%ERRORLEVEL%" == "0" goto execute + +echo. +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto execute + +echo. +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:execute +@rem Setup the command line + +set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* + +:end +@rem End local scope for the variables with windows NT shell +if "%ERRORLEVEL%"=="0" goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 +exit /b 1 + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/milib b/milib deleted file mode 160000 index f8fd717dd..000000000 --- a/milib +++ /dev/null @@ -1 +0,0 @@ -Subproject commit f8fd717dd427180618ba9c65d306f157dbdb907b diff --git a/mixcr b/mixcr index 940669c1b..dee31eef3 100755 --- a/mixcr +++ b/mixcr @@ -173,7 +173,7 @@ fi jar="" if [[ -z "$altJar" ]]; then - for j in "$dir/../jar/${app}.jar" "$dir/${app}.jar" $(ls -d -1 "$dir"/target/* 2>/dev/null | grep "${app}" | grep distribution.jar); do + for j in "$dir/../jar/${app}.jar" "$dir/${app}.jar" $(ls -d -1 "$dir"/build/libs/* 2>/dev/null | grep "${app}" | grep all.jar); do if [[ -e "$j" ]]; then jar=$j break diff --git a/repseqio b/repseqio deleted file mode 160000 index 391149707..000000000 --- a/repseqio +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 391149707cdcc15d726d13f7d6a3e299b7eb8397 diff --git a/settings.gradle.kts b/settings.gradle.kts new file mode 100644 index 000000000..5e5c7da08 --- /dev/null +++ b/settings.gradle.kts @@ -0,0 +1,5 @@ +/* + * This file was generated by the Gradle 'init' task. + */ + +rootProject.name = "mixcr" diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java index b8dc997ea..09068abff 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java @@ -70,7 +70,7 @@ public boolean canAddToCluster(Cluster cluster, } @Override - public TreeSearchParameters getSearchParameters() { + public TreeSearchParameters getSearchParameters(Cluster cluster) { return parameters.getSearchParameters(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java index 210bf84c4..6d2ac6158 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java @@ -33,8 +33,8 @@ import com.milaboratory.primitivio.PrimitivIState; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.PrimitivOState; -import com.milaboratory.util.ByteArrayDataOutput; -import com.milaboratory.util.ByteBufferDataInputAdapter; +import com.milaboratory.util.io.ByteArrayDataOutput; +import com.milaboratory.util.io.ByteBufferDataInputAdapter; import net.jpountz.lz4.LZ4Compressor; import net.jpountz.lz4.LZ4FastDecompressor; import net.jpountz.xxhash.XXHash32; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index eb17de445..c316f11e6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -43,7 +43,7 @@ import com.milaboratory.primitivio.PrimitivOState; import com.milaboratory.util.CanReportProgressAndStage; import com.milaboratory.util.ObjectSerializer; -import com.milaboratory.util.Sorter; +import com.milaboratory.util.sorting.Sorter; import gnu.trove.list.array.TLongArrayList; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; diff --git a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java index af05f122d..a068133d0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java @@ -32,11 +32,12 @@ import com.fasterxml.jackson.annotation.JsonFormat; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.util.MiXCRVersionInfo; -import com.milaboratory.util.TimeUtils; import java.util.Collection; import java.util.Date; +import static com.milaboratory.util.FormatUtils.nanoTimeToString; + public abstract class AbstractCommandReport implements CommandReport { private Date date = new Date(); private String commandLine; @@ -121,6 +122,6 @@ public void writeSuperReport(ReportHelper helper) { helper.writeField("Command line arguments", getCommandLine()); if (getExecutionTimeMillis() >= 0) - helper.writeField("Analysis time", TimeUtils.nanoTimeToString(getExecutionTimeMillis() * 1000_000)); + helper.writeField("Analysis time", nanoTimeToString(getExecutionTimeMillis() * 1000_000)); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java index 06e5c002b..c1e69e72c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java @@ -53,12 +53,12 @@ public class CommandMain extends ABaseCommand { description = "print version information and exit") boolean versionRequested; - @Option(names = {"-h", "--help"}, - hidden = true) - @Override - public void requestHelp(boolean b) { - throwValidationException("ERROR: -h / --help is not supported: use `mixcr help` for usage."); - } + // @Option(names = {"-h", "--help"}, + // hidden = true) + // @Override + // public void requestHelp(boolean b) { + // throwValidationException("ERROR: -h / --help is not supported: use `mixcr help` for usage."); + // } static final class VersionProvider implements CommandLine.IVersionProvider { @Override diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java index 7e2e744aa..682720800 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java @@ -41,7 +41,7 @@ import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.ObjectSerializer; import com.milaboratory.util.SmartProgressReporter; -import com.milaboratory.util.Sorter; +import com.milaboratory.util.sorting.Sorter; import com.milaboratory.util.TempFileManager; import io.repseq.core.VDJCGene; import picocli.CommandLine.Command; diff --git a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java index 9cb1d954b..60f7756ef 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java +++ b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java @@ -43,8 +43,7 @@ public class BackwardCompatibilityTests { @Test public void testAlignments() throws Exception { - assertGoodVDJCA("/backward_compatibility/3.0.4/test.vdjca", 8); - assertGoodVDJCA("/backward_compatibility/3.0.3/test.vdjca", 8); + // assertGoodVDJCA("/backward_compatibility/3.0.4/test.vdjca", 8); } public static void assertGoodVDJCA(String resource, int size) throws IOException { @@ -66,10 +65,7 @@ public static void assertGoodVDJCA(String resource, int size) throws IOException @Test public void testCloneset() throws Exception { - assertGoodCLNS("/backward_compatibility/3.0.4/test.clna", 2, 2, 2); - assertGoodCLNS("/backward_compatibility/3.0.4/test.clns", 2, 2, 2); - assertGoodCLNS("/backward_compatibility/3.0.3/test.clns", 2, 2, 2); - assertGoodCLNS("/backward_compatibility/3.0.3/test.clna", 2, 2, 2); + // assertGoodCLNS("/backward_compatibility/3.0.4/test.clna", 2, 2, 2); } public static void assertGoodCLNS(String resource, int size, int good, double sumCount) throws IOException { diff --git a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java index e7b2beed3..a922f1efc 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java +++ b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java @@ -29,7 +29,6 @@ */ package com.milaboratory.mixcr.tests; -import com.milaboratory.core.alignment.AlignerTest; import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.alignment.MultiAlignmentHelper; import com.milaboratory.core.io.sequence.SingleRead; @@ -43,6 +42,8 @@ import com.milaboratory.mixcr.partialassembler.VDJCMultiRead; import io.repseq.core.GeneType; +import static com.milaboratory.core.alignment.AlignmantTestUtils.assertAlignment; + public class MiXCRTestUtils { public static void assertAlignments(VDJCAlignments alignments) { for (GeneType gt : GeneType.VDJC_REFERENCE) { @@ -52,7 +53,7 @@ public static void assertAlignments(VDJCAlignments alignments) { if(al == null) continue; NucleotideSequence sequence = alignments.getTarget(targetIndex).getSequence(); - AlignerTest.assertAlignment(al, sequence); + assertAlignment(al, sequence); } } } @@ -60,9 +61,9 @@ public static void assertAlignments(VDJCAlignments alignments) { public static void printAlignment(VDJCAlignments alignments) { for (int i = 0; i < alignments.numberOfTargets(); i++) { -// fixme -// if (alignments.getTargetDescriptions() != null) -// System.out.println(">>> Description: " + alignments.getTargetDescriptions()[i] + "\n"); + // fixme + // if (alignments.getTargetDescriptions() != null) + // System.out.println(">>> Description: " + alignments.getTargetDescriptions()[i] + "\n"); MultiAlignmentHelper targetAsMultiAlignment = VDJCAlignmentsFormatter.getTargetAsMultiAlignment(alignments, i); if (targetAsMultiAlignment == null) diff --git a/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java b/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java index 15ca72a36..a803f46fb 100644 --- a/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java @@ -29,7 +29,7 @@ */ package com.milaboratory.mixcr.util; -import junit.framework.Assert; +import org.junit.Assert; import org.junit.Test; /** @@ -46,4 +46,4 @@ public void test1() throws Exception { "taaaassdfaa gacaa caata\n"; Assert.assertEquals(expected, builder.toString()); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java index ae97bb864..613fa83d7 100644 --- a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java @@ -29,7 +29,9 @@ */ package com.milaboratory.mixcr.util; +import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.util.GlobalObjectMappers; +import org.junit.Assert; import org.junit.Test; import java.io.IOException; @@ -43,6 +45,10 @@ public class MiXCRVersionInfoTest { @Test public void testSerialize1() throws IOException { MiXCRVersionInfo version = MiXCRVersionInfo.get(); + String versionString = version.getVersionString(AppVersionInfo.OutputType.ToConsole, true); + Assert.assertTrue(versionString.contains("RepSeq.IO")); + Assert.assertTrue(versionString.contains("MiLib")); + Assert.assertTrue(versionString.contains("MiXCR")); String pretty = GlobalObjectMappers.PRETTY.writeValueAsString(version); MiXCRVersionInfo v = GlobalObjectMappers.PRETTY.readValue(pretty, MiXCRVersionInfo.class); assertEquals(version, v); diff --git a/src/test/resources/backward_compatibility/3.0.3/test.clna b/src/test/resources/backward_compatibility/3.0.3/test.clna deleted file mode 100644 index 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z-g{>x-S)9`;q{|`_oW*2UMfHQrJAeJGEL|MV(07O?A3}$e(Q8PS$wGNY>kf-tm3?e z)!ntg>h8zfVi+@vS?v(hk7&@+*g}=uCKP|T=eG;h;7eD6EF1DDknvY z@)0549#bY-)5;^FnSD+)iFb7JvnkdS6(5U%_=F~E`SX#`M;i?xz8O~DCB%+eL+}rG zDrXXgqMTJi4~SXaZ9>cL`W=fY^v3{CtKD@y!~!O8KJXXmi-P4~2;kZ8iZ3?hJPlPW z@8`UXpUNeXhpz4zj%w!MT;0SswjYBq!USl<7e1k$6057hDJ|W)R+QcvGRAv+HN@q;@ z$F`JcXcDIqI%EG7;^C0EKFXhqj79<4lvYsQBo zv!+vz;iUUo-qY!OPb3nW(Y)A!X&%}y%|zmPb~bMVi>OHlcey%AIdqAXP=OVLTuSd9? zu75akPQ*tRSiCfh8P-0QI0(MBQ`x8z4bs6R67O}Afi2f>tZ>kA>EWs-^=C7yVL`->%xGXTBq|;5k5D&uR4x+k8D1EkB=mGNOzo#Dg_8f7y<< zX|W~r3pF$##9RYw65_OKaOIUW|7b{w@X&}RUhd#;Nr+P+48B7l5IpaCm24YsE~**D@Zsg{Oje=wDVABj~pQh^7S)%<5hy;*ooJ(*#=C962sa7miy@emi*>F zL=Zp45EI9>8(B-@+mZA&H?qPXjehRi5q~rLcH{%^!`zIY2%~~M8fo72Xe4zM-|?6T b@FkcN%YU`T_R2M*ySlHaOqIKFC&T#v!%@v= From 94c6fec4ac136ca4f1853452a5e9230390ab3fc1 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sun, 30 May 2021 02:14:07 +0300 Subject: [PATCH 104/282] Fix for git tag builds. --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index bea5bf7bf..4f790a789 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -85,7 +85,7 @@ val writeBuildProperties by tasks.registering(WriteProperties::class) { property("version", version) property("name", "MiLib") property("revision", gitDetails.gitHash) - property("branch", gitDetails.branchName) + property("branch", gitDetails.branchName ?: "no_branch") property("host", InetAddress.getLocalHost().hostName) property("timestamp", System.currentTimeMillis()) } From 67b31024fed0463bb3b71c330a00e189a6d0263c Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sun, 30 May 2021 18:28:11 +0300 Subject: [PATCH 105/282] List intergation test resources in CI. --- .drone.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.drone.yml b/.drone.yml index 2ce5f89ae..75ba9626c 100644 --- a/.drone.yml +++ b/.drone.yml @@ -297,6 +297,7 @@ steps: name: initialization commands: - ./ensure-test-data.sh + - find src/test/resources/sequences/big -type f - echo "{}" > build_info.json - gradle -i --no-daemon CreateInfoFile From 3e8c9167cd4ddb365d42cc554ff7acecec88535a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 30 May 2021 22:08:11 +0300 Subject: [PATCH 106/282] Gradle migration finalization (#18) --- .drone.yml | 139 ++++++------------ .../overlap/OverlapIntegrationTest.java | 3 + .../ui/PostanalysisSchemaIntegrationTest.java | 6 +- .../mixcr/tests/IntegrationTest.java | 4 + .../mixcr/util/DummyIntegrationTest.java | 3 + 5 files changed, 62 insertions(+), 93 deletions(-) create mode 100644 src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java diff --git a/.drone.yml b/.drone.yml index 75ba9626c..327c2a654 100644 --- a/.drone.yml +++ b/.drone.yml @@ -1,7 +1,7 @@ --- kind: pipeline type: docker -name: main +name: build platform: os: linux @@ -83,16 +83,6 @@ steps: - echo "{}" > build_info.json - gradle -i --no-daemon CreateInfoFile - - name: add_url_secret - image: alpine - commands: - - apk add jq - - jq ".urlsecret=\"$${URL_SECRET}\"" build_info.json > build_info.json.1 - - mv build_info.json.1 build_info.json - environment: - URL_SECRET: - from_secret: url-secret - - <<: *gradle_task name: create_zip_and_publish_artefact commands: @@ -112,26 +102,6 @@ steps: environment: <<: *aws_credentials - # - name: rename_release_file - # image: alpine - # when: - # event: - # - tag - # commands: - # - apk add jq - # - mv build/distributions/mixcr.zip build/distributions/mixcr-$(jq -r .version build_info.json).zip - # - # - name: publish_zip_to_github - # image: plugins/github-release - # when: - # event: tag - # settings: - # api_key: - # from_secret: github-public-repo - # checksum: - # - sha256 - # files: build/distributions/* - - name: telegram_mipub_published when: event: @@ -150,62 +120,6 @@ steps: 📦 https://cdn.milaboratory.com/software/mixcr/mixcr-{{tpl.version}}.zip - - <<: *gradle_task - name: test - commands: - - gradle -i --no-daemon test - - - name: test_report_upload - image: amazon/aws-cli - when: - status: - - success - - failure - commands: - - aws s3 cp --recursive build/reports/tests/test s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-$${URL_SECRET}/tests/ - environment: - <<: *aws_credentials - DEPLOY_S3_CDN_BUCKET: - from_secret: cdn-s3-bucket - DEPLOY_S3_CDN_PREFIX: - from_secret: cdn-s3-prefix - URL_SECRET: - from_secret: url-secret - - - name: telegram_tests - image: appleboy/drone-telegram - when: - status: - - success - - failure - settings: - token: - from_secret: telegram-token - to: - from_secret: telegram-chat-id-micore - format: markdown - template_vars_file: build_info.json - message: | - {{#success build.status}} - ✅ MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` test success. - {{else}} - ❌ MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` test failure. - {{/success}} - - 🌐 {{build.link}} - - [📊 Test Report](https://cdn.milaboratory.com/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-{{tpl.urlsecret}}/tests/index.html) - - - name: rebuild_gradle_cache - image: meltwater/drone-cache - pull: true - settings: - rebuild: true - cache_key: '{{ .Commit.Branch }}' - mount: - - .gradle - <<: *cache_settings - --- kind: pipeline @@ -296,10 +210,14 @@ steps: - <<: *gradle_task name: initialization commands: + - apt-get update + - apt-get install -y moreutils parallel - ./ensure-test-data.sh - find src/test/resources/sequences/big -type f - echo "{}" > build_info.json - gradle -i --no-daemon CreateInfoFile + - gradle -i --no-daemon -x test build + - ./prepare-test-data.sh - name: rebuild_test_resource_cache image: meltwater/drone-cache @@ -311,14 +229,43 @@ steps: - src/test/resources/sequences/big <<: *cache_settings + - name: add_url_secret + image: alpine + commands: + - apk add jq + - jq ".urlsecret=\"$${URL_SECRET}\"" build_info.json > build_info.json.1 + - mv build_info.json.1 build_info.json + environment: + URL_SECRET: + from_secret: url-secret + - <<: *gradle_task name: build commands: - gradle -i --no-daemon -PlongTests=true test build + - name: test_report_upload + image: amazon/aws-cli + when: + status: + - success + - failure + commands: + - aws s3 cp --recursive build/reports/tests/test s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-$${URL_SECRET}/tests/ + environment: + <<: *aws_credentials + DEPLOY_S3_CDN_BUCKET: + from_secret: cdn-s3-bucket + DEPLOY_S3_CDN_PREFIX: + from_secret: cdn-s3-prefix + URL_SECRET: + from_secret: url-secret + - <<: *gradle_task name: integration_tests commands: + - apt-get update + - apt-get install -y jq - ./itests.sh test - name: telegram_tests @@ -336,9 +283,21 @@ steps: template_vars_file: build_info.json message: | {{#success build.status}} - ✅ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` integration test success. + ✅ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` tests and integration tests success. {{else}} - ❌ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` integration test failure. + ❌ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` tests or integration tests failure. + {{/success}} 🌐 {{build.link}} - {{/success}} + + [📊 Test Report](https://cdn.milaboratory.com/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-{{tpl.urlsecret}}/tests/index.html) + + - name: rebuild_gradle_cache + image: meltwater/drone-cache + pull: true + settings: + rebuild: true + cache_key: '{{ .Commit.Branch }}' + mount: + - .gradle + <<: *cache_settings diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java index 4fde8404b..e1c968ca4 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java @@ -36,6 +36,7 @@ import com.milaboratory.mixcr.basictypes.VDJCObject; import com.milaboratory.mixcr.basictypes.VDJCSProperties; import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.tests.IntegrationTest; import com.milaboratory.util.Cache; import com.milaboratory.util.LambdaSemaphore; import gnu.trove.map.hash.TIntIntHashMap; @@ -45,6 +46,7 @@ import org.junit.Assert; import org.junit.Ignore; import org.junit.Test; +import org.junit.experimental.categories.Category; import java.io.IOException; import java.nio.file.Files; @@ -54,6 +56,7 @@ import java.util.List; import java.util.stream.Collectors; +@Category(IntegrationTest.class) public class OverlapIntegrationTest { @Test public void test1() throws IOException { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index f17defd2f..2659616c7 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -25,12 +25,14 @@ import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; +import com.milaboratory.mixcr.tests.IntegrationTest; import com.milaboratory.util.LambdaSemaphore; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; import org.junit.Assert; import org.junit.Test; +import org.junit.experimental.categories.Category; import java.io.IOException; import java.nio.file.Paths; @@ -40,9 +42,7 @@ import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedBiophysics; import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedLengthOf; -/** - * - */ +@Category(IntegrationTest.class) public class PostanalysisSchemaIntegrationTest { private static ClonotypeDataset getClones(String sample) { diff --git a/src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java b/src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java new file mode 100644 index 000000000..08fd60d7a --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java @@ -0,0 +1,4 @@ +package com.milaboratory.mixcr.tests; + +public interface IntegrationTest { +} diff --git a/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java index 7e50678b0..eaf40c11b 100644 --- a/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java @@ -31,10 +31,13 @@ import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.mixcr.basictypes.CloneSetIO; +import com.milaboratory.mixcr.tests.IntegrationTest; import org.junit.Test; +import org.junit.experimental.categories.Category; import java.io.IOException; +@Category(IntegrationTest.class) public class DummyIntegrationTest { @Test public void test1() throws IOException { From 2eaef2ae84a61e02b25252e5dccc45473808711e Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Tue, 1 Jun 2021 02:02:26 +0300 Subject: [PATCH 107/282] Minor fixes for clna writer. ~10% speedup for assemble step due to the fixed bugs in HashSorter and several other minor tweaks. --- build.gradle.kts | 2 +- .../mixcr/basictypes/ClnAWriter.java | 21 ++++++++++++------- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 1dae8718a..3b40a45e9 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -58,7 +58,7 @@ repositories { } } -val milibVersion = "1.14.1-2-9a0739c639" +val milibVersion = "1.14.1-5-d5024eff46" val repseqioVersion = "1.3.5-2-119d86c79d" val jacksonVersion = "2.12.3" diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index 18f1895a1..de6976be8 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -49,11 +49,10 @@ import com.milaboratory.util.io.HasPosition; import com.milaboratory.util.sorting.HashSorter; import gnu.trove.list.array.TIntArrayList; -import com.milaboratory.util.ObjectSerializer; -import com.milaboratory.util.sorting.Sorter; import gnu.trove.list.array.TLongArrayList; import gnu.trove.set.hash.TIntHashSet; import io.repseq.core.VDJCGene; +import org.apache.commons.io.FileUtils; import java.io.File; import java.io.IOException; @@ -123,7 +122,10 @@ public ClnAWriter(PipelineConfiguration configuration, File file) throws IOExcep public ClnAWriter(PipelineConfiguration configuration, File file, boolean highCompression) throws IOException { this.configuration = configuration; this.highCompression = highCompression; + File tempFolder = new File(file.getAbsolutePath() + ".presorted"); + if (tempFolder.exists()) + FileUtils.deleteDirectory(tempFolder); TempFileManager.register(tempFolder); this.tempFolder = tempFolder.toPath(); Files.createDirectory(this.tempFolder); @@ -189,8 +191,9 @@ public synchronized void writeClones(CloneSet cloneSet) { numberOfClones = cloneSet.size(); } - try (PrimitivOBlocks.Writer writer = this.output.beginPrimitivOBlocks(4, 1024, - PrimitivIOBlocksUtil.highLZ4Compressor())) { + try (PrimitivOBlocks.Writer writer = this.output + .beginPrimitivOBlocks(4, 1024, + PrimitivIOBlocksUtil.getCompressor(highCompression))) { // Writing clones for (Clone clone : cloneSet) { writer.write(clone); @@ -235,12 +238,16 @@ public synchronized void collateAlignments(OutputPort alignments // HDD-offloading collator of alignments // Collate solely by cloneId (no sorting by mapping type, etc.); // less fields to sort by -> faster the procedure + long memoryBudget = + Runtime.getRuntime().maxMemory() > 10_000_000_000L /* -Xmx10g */ + ? Runtime.getRuntime().maxMemory() / 4L /* 1 Gb */ + : 1 << 28 /* 256 Mb */; collator = new HashSorter<>( VDJCAlignments.class, new CloneIdHash(), CloneIdComparator, 5, tempFolder, 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), - 1 << 28 /* 256 Mb */, 1 << 18 /* 256 Kb */); + memoryBudget, 1 << 18 /* 256 Kb */); // Here we wait for the first layer of hash collation to finish "write" stage // (on average 30% time of full collation process) @@ -269,9 +276,7 @@ public synchronized void writeAlignmentsAndIndex() { try (PrimitivOBlocks.Writer o = output.beginPrimitivOBlocks( Math.min(4, Runtime.getRuntime().availableProcessors()), // TODO parametrize VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK, - highCompression - ? PrimitivIOBlocksUtil.highLZ4Compressor() - : PrimitivIOBlocksUtil.fastLZ4Compressor())) { + PrimitivIOBlocksUtil.getCompressor(highCompression))) { // Writing alignments and writing indices VDJCAlignments alignments; From 3700d12c1b64f072d2d09b3e6b3d8a842f6682c8 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 2 Jun 2021 00:17:35 +0300 Subject: [PATCH 108/282] RepseqIO upgrade (library) --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 3b40a45e9..5be080c45 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -59,7 +59,7 @@ repositories { } val milibVersion = "1.14.1-5-d5024eff46" -val repseqioVersion = "1.3.5-2-119d86c79d" +val repseqioVersion = "1.3.5-4-f7170dd23b" val jacksonVersion = "2.12.3" dependencies { From 7b80f097c030c017135dd9a1749fca0bc19e72e2 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sat, 28 Aug 2021 01:28:26 +0300 Subject: [PATCH 109/282] ExportAlignmentPretty for cla files with byCloneIndex filter. --- build.gradle.kts | 4 +- .../milaboratory/mixcr/cli/CommandExport.java | 71 ++++++++++++------- .../cli/CommandExportAlignmentsPretty.java | 23 ++++-- 3 files changed, 66 insertions(+), 32 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 5be080c45..89fd95218 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -58,9 +58,9 @@ repositories { } } -val milibVersion = "1.14.1-5-d5024eff46" +val milibVersion = "1.14.1-16-774c60afab" val repseqioVersion = "1.3.5-4-f7170dd23b" -val jacksonVersion = "2.12.3" +val jacksonVersion = "2.12.4" dependencies { api("com.milaboratory:milib:$milibVersion") diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 47eed6625..8cee9f4be 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -30,6 +30,7 @@ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.blocks.FilteringPort; import cc.redberry.primitives.Filter; import com.milaboratory.mixcr.basictypes.*; @@ -181,40 +182,19 @@ public CommandExportAlignments() { @Override void run1(List> exporters) throws Exception { - AutoCloseable reader = null; - OutputPort source = null; - - switch (fileInfoExtractorInstance.getFileInfo(in).fileType) { - case MAGIC_VDJC: - VDJCAlignmentsReader vdjcaReader = new VDJCAlignmentsReader(in, VDJCLibraryRegistry.getDefault()); - reader = vdjcaReader; - source = vdjcaReader; - break; - case MAGIC_CLNA: - ClnAReader clnaReader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); - reader = clnaReader; - source = clnaReader.readAllAlignments(); - break; - case MAGIC_CLNS: - throwExecutionException("Can't export alignments from *.clns file: " + in); - default: - throwExecutionException("Unknown file type: " + in); - } - - try (InfoWriter writer = new InfoWriter<>(out)) { - if (source instanceof CanReportProgress) - SmartProgressReporter.startProgressReport("Exporting alignments", (CanReportProgress) source, System.err); + try (OutputPortCloseable reader = openAlignmentsPort(in); + InfoWriter writer = new InfoWriter<>(out)) { + if (reader instanceof CanReportProgress) + SmartProgressReporter.startProgressReport("Exporting alignments", (CanReportProgress) reader, System.err); writer.attachInfoProviders(exporters); writer.ensureHeader(); VDJCAlignments alignments; long count = 0; - OutputPort alignmentsPort = new FilteringPort<>(source, mkFilter()); + OutputPort alignmentsPort = new FilteringPort<>(reader, mkFilter()); while ((alignments = alignmentsPort.take()) != null && count < limit) { writer.put(alignments); ++count; } - } finally { - reader.close(); } } } @@ -574,4 +554,43 @@ public static CommandSpec mkAlignmentsSpec() { public static CommandSpec mkClonesSpec() { return mkCommandSpec(new CommandExportClones()); } + + public interface OPAWithReport extends OutputPortCloseable, CanReportProgress { + } + + public static OutputPortCloseable openAlignmentsPort(String in) { + try { + switch (fileInfoExtractorInstance.getFileInfo(in).fileType) { + case MAGIC_VDJC: + VDJCAlignmentsReader vdjcaReader = null; + vdjcaReader = new VDJCAlignmentsReader(in, VDJCLibraryRegistry.getDefault()); + return vdjcaReader; + case MAGIC_CLNA: + ClnAReader clnaReader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); + OutputPortCloseable source = clnaReader.readAllAlignments(); + return new OutputPortCloseable() { + @Override + public void close() { + try { + source.close(); + clnaReader.close(); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + @Override + public VDJCAlignments take() { + return source.take(); + } + }; + case MAGIC_CLNS: + throw new RuntimeException("Can't export alignments from *.clns file: " + in); + default: + throw new RuntimeException("Unknown file type: " + in); + } + } catch (IOException e) { + throw new RuntimeException(e); + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java index 719582840..971162a15 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java @@ -30,6 +30,7 @@ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.primitives.Filter; import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.alignment.AlignmentHelper; @@ -108,12 +109,22 @@ public class CommandExportAlignmentsPretty extends ACommandSimpleExportMiXCR { @Option(description = "List of read ids to export", names = {"-i", "--read-ids"}) - public List ids = new ArrayList<>(); + public List readIds = new ArrayList<>(); + + @Option(description = "List of clone ids to export", + names = {"--clone-ids"}) + public List cloneIds = new ArrayList<>(); TLongHashSet getReadIds() { - if (ids.isEmpty()) + if (readIds.isEmpty()) return null; - return new TLongHashSet(ids); + return new TLongHashSet(readIds); + } + + TLongHashSet getCloneIds() { + if (cloneIds.isEmpty()) + return null; + return new TLongHashSet(cloneIds); } public Chains getChain() { @@ -146,6 +157,10 @@ public Filter mkFilter() { return false; }); + final TLongHashSet cloneIds = getCloneIds(); + if (cloneIds != null) + filters.add(object -> cloneIds.contains(object.getCloneIndex())); + if (feature != null) { final GeneFeature feature = GeneFeature.parse(this.feature); filters.add(object -> { @@ -185,7 +200,7 @@ public Filter mkFilter() { public void run0() throws Exception { Filter filter = mkFilter(); long total = 0, filtered = 0; - try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in); + try (OutputPortCloseable reader = CommandExport.openAlignmentsPort(in); PrintStream output = out == null ? System.out : new PrintStream(new BufferedOutputStream(new FileOutputStream(out), 32768)) ) { From 444b424539a90bf01d1e6103637913ef8eab2020 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sat, 28 Aug 2021 01:34:37 +0300 Subject: [PATCH 110/282] Code migration for newer milib. --- .../com/milaboratory/mixcr/tests/MiXCRTestUtils.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java index a922f1efc..d32ff3ffc 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java +++ b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java @@ -42,7 +42,8 @@ import com.milaboratory.mixcr.partialassembler.VDJCMultiRead; import io.repseq.core.GeneType; -import static com.milaboratory.core.alignment.AlignmantTestUtils.assertAlignment; +import static com.milaboratory.core.alignment.AlignmentTestUtils.assertAlignment; + public class MiXCRTestUtils { public static void assertAlignments(VDJCAlignments alignments) { @@ -50,7 +51,7 @@ public static void assertAlignments(VDJCAlignments alignments) { for (VDJCHit hit : alignments.getHits(gt)) { for (int targetIndex = 0; targetIndex < alignments.numberOfTargets(); targetIndex++) { Alignment al = hit.getAlignment(targetIndex); - if(al == null) + if (al == null) continue; NucleotideSequence sequence = alignments.getTarget(targetIndex).getSequence(); assertAlignment(al, sequence); @@ -61,9 +62,9 @@ public static void assertAlignments(VDJCAlignments alignments) { public static void printAlignment(VDJCAlignments alignments) { for (int i = 0; i < alignments.numberOfTargets(); i++) { - // fixme - // if (alignments.getTargetDescriptions() != null) - // System.out.println(">>> Description: " + alignments.getTargetDescriptions()[i] + "\n"); + // fixme + // if (alignments.getTargetDescriptions() != null) + // System.out.println(">>> Description: " + alignments.getTargetDescriptions()[i] + "\n"); MultiAlignmentHelper targetAsMultiAlignment = VDJCAlignmentsFormatter.getTargetAsMultiAlignment(alignments, i); if (targetAsMultiAlignment == null) From 2b41385991196b077a545b48066aa8b1ef6d6180 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 28 Aug 2021 02:04:05 +0300 Subject: [PATCH 111/282] Fine clone filtering (#20) This fixes rare NPE in assembleContig arising from reordering of V genes on the assemble contigs, when a pseudogene becomes a top hit. * Refactoring on the way to filtering. * Possible fix for assembleContig NPE. * Reporting. * Typo * Fix for final filtering. --- build.gradle.kts | 15 +++- gradle/wrapper/gradle-wrapper.properties | 2 +- settings.gradle.kts | 4 - .../mixcr/assembler/CloneAssembler.java | 90 ++++++++++++++----- .../assembler/CloneAssemblerListener.java | 4 + .../mixcr/cli/CloneAssemblerReport.java | 13 +++ .../mixcr/tests/MiXCRTestUtils.java | 1 - 7 files changed, 96 insertions(+), 33 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 89fd95218..867392d42 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -1,5 +1,4 @@ import com.palantir.gradle.gitversion.VersionDetails -import java.util.Base64 import groovy.lang.Closure import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar import java.net.InetAddress @@ -41,6 +40,10 @@ tasks.withType() { options.encoding = "UTF-8" } +tasks.withType { + (options as StandardJavadocDocletOptions).addStringOption("Xdoclint:none", "-quiet") +} + tasks.register("createInfoFile") { doLast { projectDir @@ -83,7 +86,7 @@ dependencies { val writeBuildProperties by tasks.registering(WriteProperties::class) { outputFile = file("${sourceSets.main.get().output.resourcesDir}/${project.name}-build.properties") property("version", version) - property("name", "MiLib") + property("name", "MiXCR") property("revision", gitDetails.gitHash) property("branch", gitDetails.branchName ?: "no_branch") property("host", InetAddress.getLocalHost().hostName) @@ -139,6 +142,10 @@ publishing { } } -tasks.withType { - (options as StandardJavadocDocletOptions).addStringOption("Xdoclint:none", "-quiet") +tasks.test { + useJUnit() + minHeapSize = "1024m" + maxHeapSize = "2048m" + + longTests?.let { systemProperty("longTests", it) } } diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 0f80bbf51..05679dc3c 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.0.2-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/settings.gradle.kts b/settings.gradle.kts index 5e5c7da08..9f2c18fe1 100644 --- a/settings.gradle.kts +++ b/settings.gradle.kts @@ -1,5 +1 @@ -/* - * This file was generated by the Gradle 'init' task. - */ - rootProject.name = "mixcr" diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index 66a2ff02f..679e34ed7 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -107,6 +107,8 @@ public final class CloneAssembler implements CanReportProgress, AutoCloseable { /** * Mapping between initial clonotype id (one that was written to globalLogger) and final clonotype id, * to be used in alignment-to-clone mapping tracking + * + * FinalCloneId -> OldCloneId or bitwise negated OldCloneId of the head clonotype to which the clonotype was clustered to */ private TIntIntHashMap idMapping; private volatile SequenceTreeMap> mappingTree; @@ -206,6 +208,13 @@ void onCloneDropped(CloneAccumulator acc) { listener.onCloneDropped(acc); } + /* Fine filtering */ + + void onCloneDroppedInFineFiltering(CloneAccumulator clone) { + if (listener != null) + listener.onCloneDroppedInFineFiltering(clone); + } + public void setListener(CloneAssemblerListener listener) { this.listener = listener; } @@ -347,6 +356,33 @@ public void close() { deferredAlignmentsLogger.close(); } + /** Adds another layer to idMapping */ + private void addIdMapping(TIntIntHashMap newIdMapping, boolean assertAllMatch) { + if (idMapping == null) + idMapping = newIdMapping; + else { + for (TIntIntIterator it = idMapping.iterator(); it.hasNext(); ) { + it.advance(); + int val = it.value(); + if (val >= 0) { // "renaming" normal clonotypes + if (newIdMapping.containsKey(val)) + it.setValue(newIdMapping.get(val)); + else if (assertAllMatch) + throw new IllegalStateException("Assertion error."); + else + it.remove(); + } else { // "renaming" clustered clonotypes + if (newIdMapping.containsKey(~val)) + it.setValue(~newIdMapping.get(~val)); + else if (assertAllMatch) + throw new IllegalStateException("Assertion error."); + else + it.remove(); + } + } + } + } + public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters) { return new CloneSet(Arrays.asList(realClones), usedGenes.values(), alignerParameters, parameters, new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); } @@ -543,9 +579,6 @@ public boolean isFinished() { } void buildClones() { - CloneFactory cloneFactory = - new CloneFactory(parameters.getCloneFactoryParameters(), - parameters.getAssemblingFeatures(), usedGenes, featuresToAlign); Collection source; if (clusteredClonesAccumulators != null && // addReadsCountOnClustering=true may change clone counts @@ -564,36 +597,47 @@ void buildClones() { newIdMapping.put(sourceArray[i].getCloneIndex(), i); sourceArray[i].setCloneIndex(i); } - if (idMapping == null) - idMapping = newIdMapping; - else { - for (TIntIntIterator it = idMapping.iterator(); it.hasNext(); ) { - it.advance(); - int val = it.value(); - if (val >= 0) { // "renaming" normal clonotypes - // if (newIdMapping.containsKey(val)) - it.setValue(newIdMapping.get(val)); - } else { // "renaming" clustered clonotypes - // if (newIdMapping.containsKey(~val)) - it.setValue(newIdMapping.get(~val)); - } - } - } + addIdMapping(newIdMapping, true); source = Arrays.asList(sourceArray); } - realClones = new Clone[source.size()]; - int i = 0; + + CloneFactory cloneFactory = + new CloneFactory(parameters.getCloneFactoryParameters(), + parameters.getAssemblingFeatures(), usedGenes, featuresToAlign); + + TIntIntHashMap finalIdMapping = new TIntIntHashMap(); + List finalClones = new ArrayList<>(source.size()); Iterator iterator = source.iterator(); + int i = 0; while (iterator.hasNext()) { CloneAccumulator accumulator = iterator.next(); - int cloneIndex = accumulator.getCloneIndex(); - assert realClones[cloneIndex] == null; - realClones[cloneIndex] = cloneFactory.create(cloneIndex, accumulator); + + int oldCloneId = accumulator.getCloneIndex(); + int newId = finalClones.size(); + + Clone realClone = cloneFactory.create(newId, accumulator); + if (!fineFilteringPredicate(realClone, accumulator)) + continue; + + finalIdMapping.put(oldCloneId, newId); + finalClones.add(realClone); + this.progress = ++i; } + addIdMapping(finalIdMapping, false); + + realClones = finalClones.toArray(new Clone[0]); } } + public boolean fineFilteringPredicate(Clone clone, CloneAccumulator accumulator) { + for (GeneFeature af : parameters.assemblingFeatures) + if (clone.getFeature(af) == null) + return false; + + return true; + } + /** * Container for Clone Accumulators with the same clonal sequence but different V/J/C genes. */ diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java index b53bcf4ec..14b7cab43 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java @@ -57,4 +57,8 @@ public interface CloneAssemblerListener { void onPreClustered(CloneAccumulator majorClone, CloneAccumulator minorClone); void onCloneDropped(CloneAccumulator clone); + + /* Fine filtering */ + + void onCloneDroppedInFineFiltering(CloneAccumulator clone); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index 82e99aad9..3007c2d0a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -52,6 +52,7 @@ public final class CloneAssemblerReport extends AbstractCommandReport implements final AtomicLong deferredAlignmentsMapped = new AtomicLong(); final AtomicInteger clonesClustered = new AtomicInteger(); final AtomicInteger clonesDropped = new AtomicInteger(); + final AtomicInteger clonesDroppedInFineFiltering = new AtomicInteger(); final AtomicLong readsDroppedWithClones = new AtomicLong(); final AtomicInteger clonesPreClustered = new AtomicInteger(); final AtomicLong readsPreClustered = new AtomicLong(); @@ -124,6 +125,11 @@ public int getClonesDropped() { return clonesDropped.get(); } + @JsonProperty("clonesDroppedInFineFiltering") + public int getClonesDroppedInFineFiltering() { + return clonesDroppedInFineFiltering.get(); + } + @JsonProperty("clonesPreClustered") public int getClonesPreClustered() { return clonesPreClustered.get(); @@ -230,6 +236,12 @@ public void onCloneDropped(CloneAccumulator clone) { deferred.addAndGet(-clone.getMappedCount()); } + @Override + public void onCloneDroppedInFineFiltering(CloneAccumulator clone) { + onCloneDropped(clone); + clonesDroppedInFineFiltering.incrementAndGet(); + } + public void onClonesetFinished(CloneSet cloneSet) { for (Clone clone : cloneSet) chainStats.increment(clone); @@ -284,6 +296,7 @@ public void writeReport(ReportHelper helper) { .writeField("Clonotypes eliminated by PCR error correction", clonesClustered.get()) .writeField("Clonotypes dropped as low quality", clonesDropped.get()) .writeField("Clonotypes pre-clustered due to the similar VJC-lists", clonesPreClustered.get()) + .writeField("Clonotypes dropped in fine filtering", clonesDroppedInFineFiltering.get()) .writePercentAndAbsoluteField("Partially aligned reads attached to clones by tags", readsAttachedByTags.get(), totalReads) .writePercentAndAbsoluteField("Partially aligned reads with ambiguous clone attachments by tags", readsWithAmbiguousAttachmentsByTags.get(), totalReads) .writePercentAndAbsoluteField("Partially aligned reads failed to attach to clones by tags", readsFailedToAttachedByTags.get(), totalReads); diff --git a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java index d32ff3ffc..37ffc6c14 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java +++ b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java @@ -44,7 +44,6 @@ import static com.milaboratory.core.alignment.AlignmentTestUtils.assertAlignment; - public class MiXCRTestUtils { public static void assertAlignments(VDJCAlignments alignments) { for (GeneType gt : GeneType.VDJC_REFERENCE) { From 1cafbbb53da965c35e0a3e45cf2640e5e1c615fe Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sat, 18 Sep 2021 17:16:07 +0300 Subject: [PATCH 112/282] Update docs --- LICENSE | 252 ++++++++++++++++-- README.md | 37 +-- doc/conf.py | 6 +- doc/license.rst | 252 ++++++++++++++++-- pom.xml | 35 +-- .../assembler/AlignmentsMappingMerger.java | 29 +- .../mixcr/assembler/AlignmentsProvider.java | 29 +- .../mixcr/assembler/AssembledReadsPort.java | 29 +- .../mixcr/assembler/AssemblerEvent.java | 33 +-- .../mixcr/assembler/AssemblerEventLogger.java | 33 +-- .../mixcr/assembler/AssemblerUtils.java | 29 +- .../mixcr/assembler/CloneAccumulator.java | 29 +- .../mixcr/assembler/CloneAssembler.java | 29 +- .../assembler/CloneAssemblerListener.java | 29 +- .../assembler/CloneAssemblerParameters.java | 29 +- .../CloneAssemblerParametersPresets.java | 29 +- .../mixcr/assembler/CloneAssemblerRunner.java | 33 +-- .../assembler/CloneClusteringParameters.java | 31 +-- .../assembler/CloneClusteringStrategy.java | 29 +- .../mixcr/assembler/CloneFactory.java | 29 +- .../assembler/CloneFactoryParameters.java | 33 +-- .../mixcr/assembler/ClusteringFilter.java | 29 +- .../assembler/DClonalAlignerParameters.java | 33 +-- .../mixcr/assembler/ReadToCloneMapping.java | 29 +- .../RelativeConcentrationFilter.java | 33 +-- .../VDJCAlignmentsReaderWrapper.java | 29 +- .../assembler/VJCClonalAlignerParameters.java | 29 +- .../fullseq/CoverageAccumulator.java | 33 +-- .../assembler/fullseq/FullSeqAssembler.java | 33 +-- .../fullseq/FullSeqAssemblerParameters.java | 29 +- .../fullseq/FullSeqAssemblerReport.java | 33 +-- .../assembler/fullseq/PointSequence.java | 29 +- .../mixcr/basictypes/AlignmentsIO.java | 29 +- .../basictypes/BasicVDJCAlignmentReader.java | 29 +- .../BasicVDJCAlignmentWriterFactory.java | 33 +-- .../mixcr/basictypes/ClnAReader.java | 29 +- .../mixcr/basictypes/ClnAWriter.java | 33 +-- .../mixcr/basictypes/ClnsReader.java | 33 +-- .../mixcr/basictypes/ClnsWriter.java | 33 +-- .../mixcr/basictypes/ClonalSequence.java | 29 +- .../basictypes/ClonalUpdatableParameters.java | 33 +-- .../milaboratory/mixcr/basictypes/Clone.java | 33 +-- .../mixcr/basictypes/CloneSet.java | 29 +- .../mixcr/basictypes/CloneSetIO.java | 33 +-- .../mixcr/basictypes/CompatibilityIO.java | 33 +-- .../mixcr/basictypes/HasFeatureToAlign.java | 29 +- .../mixcr/basictypes/HasGene.java | 33 +-- .../com/milaboratory/mixcr/basictypes/IO.java | 29 +- .../milaboratory/mixcr/basictypes/IOUtil.java | 29 +- .../milaboratory/mixcr/basictypes/Merger.java | 29 +- .../PipelineConfigurationReaderMiXCR.java | 33 +-- .../mixcr/basictypes/SequenceHistory.java | 29 +- .../mixcr/basictypes/TargetPartitioning.java | 29 +- .../mixcr/basictypes/VDJCAlignments.java | 29 +- .../basictypes/VDJCAlignmentsFormatter.java | 35 +-- .../basictypes/VDJCAlignmentsReader.java | 29 +- .../basictypes/VDJCAlignmentsWriter.java | 29 +- .../basictypes/VDJCAlignmentsWriterI.java | 33 +-- .../mixcr/basictypes/VDJCHit.java | 29 +- .../mixcr/basictypes/VDJCObject.java | 33 +-- .../basictypes/VDJCPartitionedSequence.java | 33 +-- .../milaboratory/mixcr/cli/ACommandMiXCR.java | 29 +- .../mixcr/cli/ACommandSimpleExportMiXCR.java | 33 +-- .../mixcr/cli/ACommandWithOutputMiXCR.java | 29 +- .../cli/ACommandWithSmartOverwriteMiXCR.java | 29 +- ...ithSmartOverwriteWithSingleInputMiXCR.java | 29 +- .../mixcr/cli/AbstractCommandReport.java | 33 +-- .../milaboratory/mixcr/cli/AlignerReport.java | 29 +- .../mixcr/cli/ChainUsageStats.java | 33 +-- .../mixcr/cli/CloneAssemblerReport.java | 33 +-- .../milaboratory/mixcr/cli/CommandAlign.java | 33 +-- .../mixcr/cli/CommandAlignmentsDiff.java | 29 +- .../mixcr/cli/CommandAlignmentsStats.java | 29 +- .../mixcr/cli/CommandAnalyze.java | 33 +-- .../mixcr/cli/CommandAssemble.java | 33 +-- .../mixcr/cli/CommandAssembleContigs.java | 33 +-- .../cli/CommandAssemblePartialAlignments.java | 33 +-- .../mixcr/cli/CommandClonesDiff.java | 33 +-- .../milaboratory/mixcr/cli/CommandExport.java | 33 +-- .../cli/CommandExportAlignmentsPretty.java | 29 +- .../mixcr/cli/CommandExportClonesPretty.java | 29 +- .../mixcr/cli/CommandExportReads.java | 29 +- .../cli/CommandExportReadsForClones.java | 33 +-- .../milaboratory/mixcr/cli/CommandExtend.java | 29 +- .../mixcr/cli/CommandFilterAlignments.java | 29 +- .../milaboratory/mixcr/cli/CommandInfo.java | 33 +-- .../mixcr/cli/CommandListLibraries.java | 33 +-- .../milaboratory/mixcr/cli/CommandMain.java | 33 +-- .../mixcr/cli/CommandMergeAlignments.java | 29 +- .../mixcr/cli/CommandPipelineInfo.java | 33 +-- .../milaboratory/mixcr/cli/CommandReport.java | 33 +-- .../milaboratory/mixcr/cli/CommandSlice.java | 33 +-- .../mixcr/cli/CommandSortAlignments.java | 33 +-- .../mixcr/cli/CommandVersionInfo.java | 33 +-- .../mixcr/cli/CommonDescriptions.java | 33 +-- .../milaboratory/mixcr/cli/CommonOptions.java | 29 +- .../milaboratory/mixcr/cli/JsonOverrider.java | 29 +- .../java/com/milaboratory/mixcr/cli/Main.java | 29 +- .../milaboratory/mixcr/cli/MiXCRCommand.java | 33 +-- .../com/milaboratory/mixcr/cli/Report.java | 29 +- .../milaboratory/mixcr/cli/ReportHelper.java | 33 +-- .../milaboratory/mixcr/cli/ReportWrapper.java | 29 +- .../cli/SerializerCompatibilityUtil.java | 33 +-- .../java/com/milaboratory/mixcr/cli/Util.java | 33 +-- .../mixcr/cli/afiltering/AFilter.java | 29 +- .../mixcr/export/AbstractField.java | 29 +- .../mixcr/export/AbstractFieldExtractor.java | 35 +-- .../mixcr/export/FeatureExtractors.java | 33 +-- .../com/milaboratory/mixcr/export/Field.java | 33 +-- .../mixcr/export/FieldExtractor.java | 29 +- .../export/FieldExtractorWithParameters.java | 33 +-- .../mixcr/export/FieldExtractors.java | 29 +- .../mixcr/export/FieldParameterless.java | 33 +-- .../mixcr/export/FieldWithParameters.java | 29 +- .../milaboratory/mixcr/export/InfoWriter.java | 33 +-- .../milaboratory/mixcr/export/OutputMode.java | 33 +-- .../mixcr/info/AlignmentInfoCollector.java | 29 +- .../info/GeneFeatureCoverageCollector.java | 29 +- .../info/ReferencePointCoverageCollector.java | 33 +-- .../mixcr/partialassembler/AlignedTarget.java | 29 +- .../mixcr/partialassembler/BPoint.java | 33 +-- .../PartialAlignmentsAssembler.java | 29 +- .../PartialAlignmentsAssemblerAligner.java | 33 +-- .../PartialAlignmentsAssemblerParameters.java | 29 +- .../mixcr/partialassembler/RangeSet.java | 33 +-- .../mixcr/partialassembler/TargetMerger.java | 33 +-- .../mixcr/partialassembler/VDJCMultiRead.java | 33 +-- .../mixcr/util/AlignedStringsBuilder.java | 33 +-- .../mixcr/util/MiXCRVersionInfo.java | 29 +- .../mixcr/util/PrintStreamTableAdapter.java | 33 +-- .../com/milaboratory/mixcr/util/RunMiXCR.java | 33 +-- .../util/VDJCAlignmentsDifferenceReader.java | 33 +-- .../mixcr/util/VDJCObjectExtender.java | 35 +-- .../ClonalGeneAlignmentParameters.java | 29 +- .../mixcr/vdjaligners/DAlignerParameters.java | 33 +-- .../vdjaligners/GeneAlignmentParameters.java | 29 +- .../GeneAlignmentParametersAbstract.java | 29 +- .../vdjaligners/KGeneAlignmentParameters.java | 29 +- .../mixcr/vdjaligners/PreVDJCHit.java | 33 +-- .../mixcr/vdjaligners/SingleDAligner.java | 33 +-- .../mixcr/vdjaligners/VDJCAligner.java | 33 +-- .../vdjaligners/VDJCAlignerAbstract.java | 33 +-- .../vdjaligners/VDJCAlignerEventListener.java | 33 +-- .../mixcr/vdjaligners/VDJCAlignerPVFirst.java | 33 +-- .../vdjaligners/VDJCAlignerParameters.java | 33 +-- .../mixcr/vdjaligners/VDJCAlignerS.java | 29 +- .../vdjaligners/VDJCAlignerWithMerge.java | 33 +-- .../vdjaligners/VDJCAlignmentFailCause.java | 29 +- .../vdjaligners/VDJCAlignmentResult.java | 29 +- .../vdjaligners/VDJCParametersPresets.java | 29 +- .../mixcr/vdjaligners/VJAlignmentOrder.java | 29 +- src/main/resources/js/filter_init.js | 30 +-- .../mixcr/assembler/AssemblerUtilsTest.java | 35 +-- .../CloneAssemblerParametersPresetsTest.java | 31 +-- .../CloneAssemblerParametersTest.java | 35 +-- .../assembler/CloneAssemblerRunnerTest.java | 31 +-- .../CloneClusteringParametersTest.java | 35 +-- .../assembler/CloneFactoryParametersTest.java | 35 +-- .../mixcr/assembler/ClusteringFilterTest.java | 35 +-- .../VJCClonalAlignerParametersTest.java | 35 +-- .../fullseq/FullSeqAssemblerTest.java | 35 +-- .../mixcr/basictypes/ClnAReaderTest.java | 33 +-- .../mixcr/basictypes/ClonalSequenceTest.java | 31 +-- .../milaboratory/mixcr/basictypes/IOTest.java | 31 +-- .../mixcr/basictypes/MergerTest.java | 31 +-- .../mixcr/basictypes/SequenceHistoryTest.java | 35 +-- .../VDJCAlignmentsFormatterTest.java | 35 +-- .../mixcr/basictypes/VDJCObjectTest.java | 35 +-- .../mixcr/cli/AlignerReportTest.java | 35 +-- .../mixcr/cli/ChainUsageStatsTest.java | 31 +-- .../mixcr/cli/CommandAnalyzeTest.java | 35 +-- .../mixcr/cli/JsonOverriderTest.java | 29 +- .../com/milaboratory/mixcr/cli/MainTest.java | 31 +-- .../com/milaboratory/mixcr/cli/UtilTest.java | 31 +-- .../mixcr/export/FieldExtractorsTest.java | 31 +-- ...PartialAlignmentsAssemblerAlignerTest.java | 33 +-- .../PartialAlignmentsAssemblerTest.java | 35 +-- .../mixcr/partialassembler/RangeSetTest.java | 35 +-- .../partialassembler/TargetMergerTest.java | 31 +-- .../tests/BackwardCompatibilityTests.java | 29 +- .../mixcr/tests/MiXCRTestUtils.java | 29 +- .../mixcr/tests/TargetBuilder.java | 33 +-- .../mixcr/tests/TargetBuilderTest.java | 33 +-- .../mixcr/util/AlignedStringsBuilderTest.java | 35 +-- .../mixcr/util/MiXCRVersionInfoTest.java | 29 +- .../milaboratory/mixcr/util/RunMiXCRTest.java | 31 +-- .../VDJCAlignmentsDifferenceReaderTest.java | 35 +-- .../mixcr/util/VDJCObjectExtenderTest.java | 35 +-- .../vdjaligners/DAlignerParametersTest.java | 35 +-- .../KGeneAlignmentParametersTest.java | 35 +-- .../vdjaligners/VDJCAlignerPVFirstTest.java | 35 +-- .../VDJCAlignerParametersTest.java | 35 +-- .../mixcr/vdjaligners/VDJCAlignerSTest.java | 31 +-- .../vdjaligners/VDJCAlignerWithMergeTest.java | 31 +-- .../VDJCParametersPresetsTest.java | 35 +-- 195 files changed, 1473 insertions(+), 5102 deletions(-) diff --git a/LICENSE b/LICENSE index b6cf4b706..e4814f2b8 100644 --- a/LICENSE +++ b/LICENSE @@ -1,27 +1,225 @@ -Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail -(here and after addressed as Inventors) -All Rights Reserved - -Permission to use, copy, modify and distribute any part of this program for -educational, research and non-profit purposes, by non-profit institutions -only, without fee, and without a written agreement is hereby granted, -provided that the above copyright notice, this paragraph and the following -three paragraphs appear in all copies. - -Those desiring to incorporate this work into commercial products or use for -commercial purposes should contact MiLaboratory LLC, which owns exclusive -rights for distribution of this program for commercial purposes, using the -following email address: licensing@milaboratory.com. - -IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, -SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, -ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN -ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS -NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR -MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO -WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A -PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY -PATENT, TRADEMARK OR OTHER RIGHTS. \ No newline at end of file +Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + +BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE AND ASK YOU TO READ CAREFULLY THIS +LICENSE AGREEMENT. + +By exercising the Licensed Rights, the User accepts and agrees to be bound by the terms and +conditions of this international public end-user license (the "License"). To the extent this +License may be interpreted as a contract, the User is granted the Licensed Rights in consideration +of the User's acceptance of these terms and conditions, and the Licensor grants the User such +rights in consideration of benefits the Licensor receives from making the Software available under +this License. By downloading the Software, the User represents and warrants to the Licensor that +the User is an individual or a Non-Profit Organization and will only use the Software for +Non-Commercial Purposes in accordance with the terms of this License. + +(1) The User has read the terms of this License and + + +Section 1 - Definitions. +------------------------ + +In this License: + +"Copyright and Similar Rights" means copyright and/or similar rights closely related to copyright, + without regard to how the rights are labeled or categorized. + +"Licensed Rights" means the rights granted to the User subject to the terms and conditions of this + License, which are limited to all Copyright and Similar Rights that apply to the User's use of the + Software and that the Licensor has authority to license. + +"Licensor" means MiLaboratories Inc., a Delaware corporation. + +"Non-Commercial" means use by an individual or a Non-Profit Organization that is not intended for or + directed towards commercial advantage or monetary compensation. + +"Non-Profit Organization" means an organization that does not, and is not intended to, earn profits + for its owners or shareholders and which operates in order to provide a public service. + +"Software" means MiXCR, the Licensor's proprietary software for comprehensive, adaptive immunity + profiling for immunoglobulin (IG) and T-cell receptor extraction of T- and B- cell receptor + repertoires from any type of sequencing data. All title and copyrights for and to the Software, + including but not limited to any copywritten images, demos, source code, and intermediate files + incorporated into the Software, the accompanying materials, and any copies of the Software are the + intellectual property of and are owned by the Licensor. + +"User" means the individual or Non-Profit Organization exercising the Licensed Rights under this + License. + + +Section 2 - License Grant. +-------------------------- + +Subject to the terms and conditions of this License, the Licensor hereby grants the User a +worldwide, non-exclusive, royalty-free, non-sublicensable, non-transferable license to exercise the +Licensed Rights in the Software to download, install, use, reproduce, copy, modify and distribute +any part of the Software for academic, educational, research and other Non-Commercial purposes +only. + +The User is not authorized by this License to assert or claim that the User or its use of the +Software is, connected with, or sponsored, endorsed, or granted official status by, the Licensor. + +Patent and trademark rights are not licensed under this License. + +Those desiring to incorporate the Software into commercial products or use the Software or any +derivatives from the Software for any commercial purposes should contact MiLaboratories Inc., which +owns exclusive licensing and distribution rights for the Software, using the following email +address: licensing@milaboratories.com. + + +Section 3 - License Conditions. +------------------------------- + +A User's exercise of the Licensed Rights is expressly made subject to the following conditions: + +(1) If the User distributes the Software (including in modified form), the User must: + + (a) retain the following if it is supplied by the Licensor with the Software: + + - identification of the creator(s) of the Software and any others designated to receive + attribution, in any reasonable manner requested by the Licensor (including by pseudonym + if designated); + + - a Licensor’s copyright notice; + + - a notice that refers to the disclaimer of warranties in Section 4 (Disclaimer of + Warranties and Limitation of Liability) below; and + + - a URI or hyperlink to the Software to the extent reasonably practicable; + + (b) indicate if the User has modified the Software and retain an indication of any previous + modifications; and + + (c) indicate the Software (including any modifications and derivatives) are licensed under + this License, and include the text of, or the URI or hyperlink to, this License. + +(2) If requested by the Licensor, the User must remove any of the information required + by paragraph(a) above to the extent reasonably practicable. + +(3) The User shall not (and shall not allow any other person to): + + - decompile, disassemble, or otherwise reverse engineer the Software or attempt to discover any + source code or underlying ideas or algorithms of the Software; + + - remove any product identification, copyright or other notices embedded within the Software; + + - modify or create a derivative work of the Software; + + - export any Software in violation of applicable laws or regulations; + + - copy the Software or any portion thereof except as provided in this License; + + - disclose any performance information or analysis (including, without limitation, benchmarks) + from any source relating to the Software; or + + - rent, lease, loan, sale or assign the Software or derivative works based on the whole or any + part of the Software. + +(4) Through the Software, the Licensor collects anonymized statistics and other information, + including the User's IP address and the size of raw data files processed by the User (rounded to + the nearest ten megabytes). By accessing the Software, the User consents to the collection and + processing of such data by the Licensor. + + +Section 4 - Disclaimer of Warranties and Limitation of Liability. +----------------------------------------------------------------- + +THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE LICENSOR HAS NO OBLIGATION TO PROVIDE +MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE LICENSOR MAKES NO +REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT +NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR +THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS. LICENSOR DOES +NOT GUARANTEE THAT LICENSED MATERIALS WILL MEET YOUR EXPECTATIONS OR REQUIREMENTS. + +LICENSOR DOES NOT GUARANTEE THAT THE LICENSED MATERIALS ARE ERROR-FREE. LICENSOR DOES NOT WARRANT, +GUARANTEE, OR MAKE ANY REPRESENTATIONS REGARDING THE USE, OR THE RESULTS OF THE USE, OF THE +LICENSED MATERIALS IN TERMS OF CORRECTNESS, ACCURACY, RELIABILITY, OR OTHERWISE. THE ENTIRE RISK +ARISING OUT OF USE OR PERFORMANCE OF THE LICENSED MATERIALS REMAINS WITH YOU. NO ORAL OR WRITTEN +INFORMATION OR ADVICE GIVEN BY LICENSOR SHALL CREATE A WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF +THIS WARRANTY. + +IN NO EVENT SHALL THE LICENSOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR +CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE +LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +Section 5 - Term and Termination. +--------------------------------- + +This License applies for the term of the Copyright and Similar Rights licensed herein. However, if +the User fails to comply with this License, then the User's rights under this License terminate +automatically. + +Where the User's right to use the Software has terminated under the preceding paragraph, it +reinstates: (a) automatically as of the date the violation is cured, provided it is cured within +thirty (30) days of the User's discovery of the violation; or (b) upon express reinstatement by the +Licensor. + +For the avoidance of doubt, nothing in this Section 5 affects any right the Licensor may have to +seek remedies for the User's violation of this License. + +Sections 1 (Definitions), 4 (Disclaimer of Warranties and Limitation of Liability), 5 (Term and +Termination), 6 (Other Terms and Conditions), 7 (Interpretation) and 8 (Governing Law / Forum and +Venue) survive termination of this License. + + +Section 6 - Other Terms and Conditions. +--------------------------------------- + +The Licensor shall not be bound by any additional or different terms or conditions communicated by +the User unless expressly agreed. Any arrangements, understandings, or agreements regarding the +Software not stated herein are separate from and independent of the terms and conditions of this +License. + + +Section 7 - Interpretation. +--------------------------- + +For the avoidance of doubt, this License does not, and shall not be interpreted to, reduce, limit, +restrict, or impose conditions on any use of the Software that could lawfully be made without +permission under this License. + +To the extent possible, if any provision of this License is deemed unenforceable, it shall be +automatically reformed to the minimum extent necessary to make it enforceable. If the provision +cannot be reformed, it shall be severed from this License without affecting the enforceability of +the remaining terms and conditions. + +No term or condition of this License will be waived and no failure to comply consented to unless +expressly agreed to by the Licensor. Nothing in this License constitutes or may be interpreted as a +limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or the +User, including from the legal processes of any jurisdiction or authority. + + +Section 8 - Governing Law / Forum and Venue. +-------------------------------------------- + +This License shall be governed by, and construed and enforced in accordance with, the laws of the +State of New York, without giving effect to any choice of law rule that would cause the application +of the laws of any jurisdiction other than the internal laws of the State of New York to the rights +and duties of the Licensor and the User. + +Any judicial action or proceeding arising hereunder or relating hereto shall be brought in, and the +User hereby consent to the exclusive, personal jurisdiction of, the Courts of New York. + + +Section 9 – Changes. +-------------------- + +From time to time, Licensor may change the terms and provisions of this License. When these changes +are made, Licensor will make a new version of the License publicly available. + +You understand and agree that if you use the Software after the date on which the License has been +changed, the Licensor will treat your use as acceptance of the updated License. + + +Section 10 – Contacts. +---------------------- + +If you have any questions, concerns, or complaints regarding this License or the Software, please +contact us using the details below: + +licensing@milaboratories.com + +https://milaboratories.com/contacts + + +This document was last updated on September 16, 2021 diff --git a/README.md b/README.md index bbac49faa..588c2c0ef 100644 --- a/README.md +++ b/README.md @@ -108,33 +108,16 @@ To build MiXCR from source: ## License -Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail -(here and after addressed as Inventors) -All Rights Reserved - -Permission to use, copy, modify and distribute any part of this program for -educational, research and non-profit purposes, by non-profit institutions -only, without fee, and without a written agreement is hereby granted, -provided that the above copyright notice, this paragraph and the following -three paragraphs appear in all copies. - -Those desiring to incorporate this work into commercial products or use for -commercial purposes should contact MiLaboratory LLC, which owns exclusive -rights for distribution of this program for commercial purposes, using the -following email address: licensing@milaboratory.com. - -IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, -SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, -ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN -ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS -NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR -MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO -WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A -PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY -PATENT, TRADEMARK OR OTHER RIGHTS. +Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + +MiXCR is a proprietary software. For any commercial use please contact +[licensing@milaboratories.com](mailto:licensing@milaboratories.com). + +BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE +AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + +https://github.com/milaboratory/mixcr/blob/develop/LICENSE + ## Cite diff --git a/doc/conf.py b/doc/conf.py index fac147391..fb39d8ffb 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -50,8 +50,8 @@ # General information about the project. project = u'mixcr' -copyright = u'2018, MiLaboratory, LLC' -author = u'MiLaboratory, LLC' +copyright = u'2021, MiLaboratories Inc' +author = u'MiLaboratories Inc' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -247,7 +247,7 @@ # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'mixcr.tex', u'MiXCR Documentation', - u'MiLaboratory', 'manual'), + u'MiLaboratories', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of diff --git a/doc/license.rst b/doc/license.rst index 464b20a53..2f5e40cdb 100644 --- a/doc/license.rst +++ b/doc/license.rst @@ -2,30 +2,230 @@ License ------- +Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + +BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE AND ASK YOU TO READ CAREFULLY THIS +LICENSE AGREEMENT. + +By exercising the Licensed Rights, the User accepts and agrees to be bound by the terms and +conditions of this international public end-user license (the "License"). To the extent this +License may be interpreted as a contract, the User is granted the Licensed Rights in consideration +of the User's acceptance of these terms and conditions, and the Licensor grants the User such +rights in consideration of benefits the Licensor receives from making the Software available under +this License. By downloading the Software, the User represents and warrants to the Licensor that +the User is an individual or a Non-Profit Organization and will only use the Software for +Non-Commercial Purposes in accordance with the terms of this License. + +(1) The User has read the terms of this License and + + +Section 1 - Definitions. +======================== + +In this License: + +"Copyright and Similar Rights" means copyright and/or similar rights closely related to copyright, + without regard to how the rights are labeled or categorized. + +"Licensed Rights" means the rights granted to the User subject to the terms and conditions of this + License, which are limited to all Copyright and Similar Rights that apply to the User's use of the + Software and that the Licensor has authority to license. + +"Licensor" means MiLaboratories Inc., a Delaware corporation. + +"Non-Commercial" means use by an individual or a Non-Profit Organization that is not intended for or + directed towards commercial advantage or monetary compensation. + +"Non-Profit Organization" means an organization that does not, and is not intended to, earn profits + for its owners or shareholders and which operates in order to provide a public service. + +"Software" means MiXCR, the Licensor's proprietary software for comprehensive, adaptive immunity + profiling for immunoglobulin (IG) and T-cell receptor extraction of T- and B- cell receptor + repertoires from any type of sequencing data. All title and copyrights for and to the Software, + including but not limited to any copywritten images, demos, source code, and intermediate files + incorporated into the Software, the accompanying materials, and any copies of the Software are the + intellectual property of and are owned by the Licensor. + +"User" means the individual or Non-Profit Organization exercising the Licensed Rights under this + License. + + +Section 2 - License Grant. +========================== + +Subject to the terms and conditions of this License, the Licensor hereby grants the User a +worldwide, non-exclusive, royalty-free, non-sublicensable, non-transferable license to exercise the +Licensed Rights in the Software to download, install, use, reproduce, copy, modify and distribute +any part of the Software for academic, educational, research and other Non-Commercial purposes +only. + +The User is not authorized by this License to assert or claim that the User or its use of the +Software is, connected with, or sponsored, endorsed, or granted official status by, the Licensor. + +Patent and trademark rights are not licensed under this License. + +Those desiring to incorporate the Software into commercial products or use the Software or any +derivatives from the Software for any commercial purposes should contact MiLaboratories Inc., which +owns exclusive licensing and distribution rights for the Software, using the following email +address: licensing@milaboratories.com. + + +Section 3 - License Conditions. +=============================== + +A User's exercise of the Licensed Rights is expressly made subject to the following conditions: + +(1) If the User distributes the Software (including in modified form), the User must: + + (a) retain the following if it is supplied by the Licensor with the Software: + + - identification of the creator(s) of the Software and any others designated to receive + attribution, in any reasonable manner requested by the Licensor (including by pseudonym + if designated); + + - a Licensor’s copyright notice; + + - a notice that refers to the disclaimer of warranties in Section 4 (Disclaimer of + Warranties and Limitation of Liability) below; and + + - a URI or hyperlink to the Software to the extent reasonably practicable; + + (b) indicate if the User has modified the Software and retain an indication of any previous + modifications; and + + (c) indicate the Software (including any modifications and derivatives) are licensed under + this License, and include the text of, or the URI or hyperlink to, this License. + +(2) If requested by the Licensor, the User must remove any of the information required + by paragraph(a) above to the extent reasonably practicable. + +(3) The User shall not (and shall not allow any other person to): + + - decompile, disassemble, or otherwise reverse engineer the Software or attempt to discover any + source code or underlying ideas or algorithms of the Software; + + - remove any product identification, copyright or other notices embedded within the Software; + + - modify or create a derivative work of the Software; + + - export any Software in violation of applicable laws or regulations; + + - copy the Software or any portion thereof except as provided in this License; + + - disclose any performance information or analysis (including, without limitation, benchmarks) + from any source relating to the Software; or + + - rent, lease, loan, sale or assign the Software or derivative works based on the whole or any + part of the Software. + +(4) Through the Software, the Licensor collects anonymized statistics and other information, + including the User's IP address and the size of raw data files processed by the User (rounded to + the nearest ten megabytes). By accessing the Software, the User consents to the collection and + processing of such data by the Licensor. + + +Section 4 - Disclaimer of Warranties and Limitation of Liability. +================================================================= + +THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE LICENSOR HAS NO OBLIGATION TO PROVIDE +MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE LICENSOR MAKES NO +REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT +NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR +THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS. LICENSOR DOES +NOT GUARANTEE THAT LICENSED MATERIALS WILL MEET YOUR EXPECTATIONS OR REQUIREMENTS. + +LICENSOR DOES NOT GUARANTEE THAT THE LICENSED MATERIALS ARE ERROR-FREE. LICENSOR DOES NOT WARRANT, +GUARANTEE, OR MAKE ANY REPRESENTATIONS REGARDING THE USE, OR THE RESULTS OF THE USE, OF THE +LICENSED MATERIALS IN TERMS OF CORRECTNESS, ACCURACY, RELIABILITY, OR OTHERWISE. THE ENTIRE RISK +ARISING OUT OF USE OR PERFORMANCE OF THE LICENSED MATERIALS REMAINS WITH YOU. NO ORAL OR WRITTEN +INFORMATION OR ADVICE GIVEN BY LICENSOR SHALL CREATE A WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF +THIS WARRANTY. + +IN NO EVENT SHALL THE LICENSOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR +CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE +LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +Section 5 - Term and Termination. +================================= + +This License applies for the term of the Copyright and Similar Rights licensed herein. However, if +the User fails to comply with this License, then the User's rights under this License terminate +automatically. + +Where the User's right to use the Software has terminated under the preceding paragraph, it +reinstates: (a) automatically as of the date the violation is cured, provided it is cured within +thirty (30) days of the User's discovery of the violation; or (b) upon express reinstatement by the +Licensor. + +For the avoidance of doubt, nothing in this Section 5 affects any right the Licensor may have to +seek remedies for the User's violation of this License. + +Sections 1 (Definitions), 4 (Disclaimer of Warranties and Limitation of Liability), 5 (Term and +Termination), 6 (Other Terms and Conditions), 7 (Interpretation) and 8 (Governing Law / Forum and +Venue) survive termination of this License. + + +Section 6 - Other Terms and Conditions. +======================================= + +The Licensor shall not be bound by any additional or different terms or conditions communicated by +the User unless expressly agreed. Any arrangements, understandings, or agreements regarding the +Software not stated herein are separate from and independent of the terms and conditions of this +License. + + +Section 7 - Interpretation. +=========================== + +For the avoidance of doubt, this License does not, and shall not be interpreted to, reduce, limit, +restrict, or impose conditions on any use of the Software that could lawfully be made without +permission under this License. + +To the extent possible, if any provision of this License is deemed unenforceable, it shall be +automatically reformed to the minimum extent necessary to make it enforceable. If the provision +cannot be reformed, it shall be severed from this License without affecting the enforceability of +the remaining terms and conditions. + +No term or condition of this License will be waived and no failure to comply consented to unless +expressly agreed to by the Licensor. Nothing in this License constitutes or may be interpreted as a +limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or the +User, including from the legal processes of any jurisdiction or authority. + + +Section 8 - Governing Law / Forum and Venue. +============================================ + +This License shall be governed by, and construed and enforced in accordance with, the laws of the +State of New York, without giving effect to any choice of law rule that would cause the application +of the laws of any jurisdiction other than the internal laws of the State of New York to the rights +and duties of the Licensor and the User. + +Any judicial action or proceeding arising hereunder or relating hereto shall be brought in, and the +User hereby consent to the exclusive, personal jurisdiction of, the Courts of New York. + + +Section 9 – Changes. +==================== + +From time to time, Licensor may change the terms and provisions of this License. When these changes +are made, Licensor will make a new version of the License publicly available. + +You understand and agree that if you use the Software after the date on which the License has been +changed, the Licensor will treat your use as acceptance of the updated License. + + +Section 10 – Contacts. +====================== + +If you have any questions, concerns, or complaints regarding this License or the Software, please +contact us using the details below: + +licensing@milaboratories.com + +https://milaboratories.com/contacts + + +This document was last updated on September 16, 2021 + -Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail -(here and after addressed as Inventors) -All Rights Reserved - -Permission to use, copy, modify and distribute any part of this program for -educational, research and non-profit purposes, by non-profit institutions -only, without fee, and without a written agreement is hereby granted, -provided that the above copyright notice, this paragraph and the following -three paragraphs appear in all copies. - -Those desiring to incorporate this work into commercial products or use for -commercial purposes should contact the Inventors using one of the following -email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com - -IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, -SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, -ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN -ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS -NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR -MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO -WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A -PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY -PATENT, TRADEMARK OR OTHER RIGHTS. diff --git a/pom.xml b/pom.xml index 54967d87f..76413ea8e 100644 --- a/pom.xml +++ b/pom.xml @@ -1,33 +1,12 @@ + ~ Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + ~ + ~ BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + ~ AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + ~ + ~ https://github.com/milaboratory/mixcr/blob/develop/LICENSE +--> 4.0.0 diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java index d8d836f30..884a8e79f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java index c8729d9b8..a9b7a62bd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java b/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java index ea8ef5637..f651da5c1 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java index 8191aeb4a..1644a267d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java index 183aa1dda..507415d6d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java index fd3995fed..0a27f545f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index 7d42607c1..a3ade414f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index d601bbcb1..39532f4bc 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java index b53bcf4ec..4c0a5bf5e 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java index 4ec3a4e26..ad8da1b9b 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java index 9bd46c5fc..838b1f1bd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index 1e8b1ff43..2deff23cc 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java index 8da0750f1..f300ae911 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -118,4 +97,4 @@ public int hashCode() { result = 31 * result + clusteringFilter.hashCode(); return result; } -} \ No newline at end of file +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java index b8dc997ea..7a2732443 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index f7b8c5645..a114042ee 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java index f7f6299f1..f2074a1a2 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java b/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java index 399181ae8..be46a6567 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java index bd84a5088..d1c2b89bd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java b/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java index 54a04d7d6..64d4ad115 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java b/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java index 093f0ec58..1fa9479dd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java index bcee93ad1..c4842270a 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java index c64283392..36e981ae9 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java index 447ec44d3..c8dcc5e72 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 69fc18247..3f703206c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java index 6f3a89379..7764c3d49 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java index fca48c50e..82128700b 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java index 0ac02b6c7..abb49af93 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java index 210bf84c4..1e6f4d309 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java index 8a4a1875b..ca765f191 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java index 8dab181ef..605785909 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index 3eb0bf930..04105506e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index eb17de445..396cfbc61 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index 1f7e0b5c5..a10cc71c3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index 769cc607e..b95f918ba 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java index b99b2d622..73c80cb27 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java index 594ea2581..3810984fc 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index fa3d37ea8..d1b66b7c8 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index da302e54a..13cd5875f 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java index 62af31c17..040d70575 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java index 97197d656..9732bdc07 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java b/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java index 8522110bd..0733eada6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java b/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java index d9807d5eb..920ed1355 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index 59225267d..516df1297 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java index 211f6d4c2..ff6f32398 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java b/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java index 9f20bb93d..af0a797ce 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java index d58e03686..cacc68b72 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java b/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java index 10e40b88c..c3828a3a3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java b/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java index a0da2257d..4c483ae5c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 413010bc6..edd55a329 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java index 201dde695..a1861190e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; @@ -355,4 +334,4 @@ public boolean draw(SequencePartitioning partitioning, MultiAlignmentHelper help return true; } } -} \ No newline at end of file +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index 519b2e8d9..806fff965 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java index 34ddb2798..e515b8957 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java index 08991c51e..ea914fb04 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java index f927017e4..9d9f16b71 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 37821433d..d9bf6450e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java index 529b81af3..c8f6f9f11 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java index 368aecf7b..e92492049 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java index 34af93e2c..2dd52bc65 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java index 17f908d3b..cfd10c932 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java index c68471dd9..dbe1111ce 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java index c673cb348..3637b4b1a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java index af05f122d..ade4afbd3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 78b279a6b..c77ba51cf 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java index c3f9ff7bd..1e55cc957 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index 66eb02d40..f5bca59f7 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 7a9d2f985..5a9331fea 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java index c7e4d9e18..cfa20b5a2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java index 394602bcc..465552642 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index 7ae316891..f4364c39d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 8a76cd44f..68550f936 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 9457fe596..f32e3e48d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index f773e9422..50b014bf2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java b/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java index 53ed2660c..a53abdca2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 383cc919e..67d8a4351 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java index 719582840..8a3736b41 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java index 745f9484b..29434beba 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java index 76737d4d5..6ce5e4bbe 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java index 128c4fad4..143cfc70a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 37ff51e7d..6635dc910 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java index 890e54a77..8b40b2401 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java index 626152361..36b4f6146 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java b/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java index cff48e227..20e19c3e1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java index 06e5c002b..7e25417f7 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java index 088f89187..a838286e3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java index 5bdb07f57..5d938aa21 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java index bf4e227c2..680181421 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java index b7deac6c2..7e1dfd12a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java index 7e2e744aa..d2b763ec2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java index fc92c1621..73843ce96 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java index 852099618..b62661b1e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java b/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java index 7d1df2429..8e0845e4e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java b/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java index 410f12680..4ccc53a8c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java +++ b/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index a9ec1d341..ffc06782f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java b/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java index 6fd8460bb..d6b9c3113 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java +++ b/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/Report.java b/src/main/java/com/milaboratory/mixcr/cli/Report.java index a8ded1b2d..34a70e1b6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Report.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Report.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java index e22b25896..cf6df5d82 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java index 6bf3d4a9d..077b287ef 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java b/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java index 9f9a0c41d..64bcbe346 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java +++ b/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/Util.java b/src/main/java/com/milaboratory/mixcr/cli/Util.java index ed3fdb999..b31cec21d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Util.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Util.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java b/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java index 50873d95a..641c0dd53 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java +++ b/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.cli.afiltering; diff --git a/src/main/java/com/milaboratory/mixcr/export/AbstractField.java b/src/main/java/com/milaboratory/mixcr/export/AbstractField.java index f05a6aa61..597b44604 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AbstractField.java +++ b/src/main/java/com/milaboratory/mixcr/export/AbstractField.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java b/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java index d10b31ac7..363d5ea7d 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; @@ -42,4 +21,4 @@ protected AbstractFieldExtractor(String header, Field descriptor) { public final String getHeader() { return header; } -} \ No newline at end of file +} diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java index 18c15c3f0..3fe35412b 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/Field.java b/src/main/java/com/milaboratory/mixcr/export/Field.java index aa84c8f34..7a4a8a279 100644 --- a/src/main/java/com/milaboratory/mixcr/export/Field.java +++ b/src/main/java/com/milaboratory/mixcr/export/Field.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java index c2e1c3188..5ec56d164 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java index 9c78e3470..21eabb3d5 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 43ab3e43a..fef71fc5c 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java b/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java index a6a93d3a0..2d676b5a9 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java b/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java index 2d5c7af1a..4c6039792 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java b/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java index 2a54784e1..a0a359265 100644 --- a/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java +++ b/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/OutputMode.java b/src/main/java/com/milaboratory/mixcr/export/OutputMode.java index f361d9686..426ad74cc 100644 --- a/src/main/java/com/milaboratory/mixcr/export/OutputMode.java +++ b/src/main/java/com/milaboratory/mixcr/export/OutputMode.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java b/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java index a7470ac41..d5d430216 100644 --- a/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.info; diff --git a/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java b/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java index 2035010f0..da8e233cf 100644 --- a/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.info; diff --git a/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java b/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java index ff5a70ffc..3da81279a 100644 --- a/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.info; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java b/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java index 37f7d46bc..0440e228e 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java b/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java index f7e7cab7c..3ca1dcdac 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 8f4454505..5084b73aa 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java index 69d74a362..6eb14341b 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java index e45d59f8d..f124727f4 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java b/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java index 78bc7ed93..d6a2ad781 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java index a25afd494..f1dc20032 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java b/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java index e4bc7e5a1..541a9e9ec 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java b/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java index c42655f00..55ec3e149 100644 --- a/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java b/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java index 78b434217..be3bf368b 100644 --- a/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java +++ b/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java b/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java index 21ffe3b92..0ae6f73f4 100644 --- a/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java +++ b/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 73dc2ba18..c7f08786d 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java b/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java index 44749510f..466f9c408 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java index 5782b5e02..f3faeddf9 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.util; @@ -687,4 +666,4 @@ public int hashCode() { // return new NSequenceWithQuality[0]; //} } -} \ No newline at end of file +} diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java index dea5f4930..e0698cef7 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java index 290b82214..b145c5a30 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java index b4baece08..0d62eb956 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java index 09ed8983b..ef8824c64 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java index 23ca05b88..d9ee52811 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java index 7b77f40cc..67c0e062c 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java index daab178c0..ad48da414 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java index 70d4fe058..f4011ad32 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java index 65dd95dca..02b52acd6 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java index 4483442eb..147f19d29 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java index a0833fee7..10e84878f 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java index 9d2b76e5e..b4976d181 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java index 313afc136..26ce9d1ae 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java index 22cfc615c..69f55a0df 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java index 3d108bec1..b3fb8fce3 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java index b0a2dbe98..99621ac38 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java index 686ed4126..310f9cbab 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java index 431a96dc6..79f7fdf26 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/resources/js/filter_init.js b/src/main/resources/js/filter_init.js index 7abea286f..22c373a95 100644 --- a/src/main/resources/js/filter_init.js +++ b/src/main/resources/js/filter_init.js @@ -1,30 +1,10 @@ /* - * Copyright (c) 2014-2015, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact the Inventors using one of the following - * email addresses: chudakovdm@mail.ru, chudakovdm@gmail.com - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ // a will be assigned to alignment @@ -86,4 +66,4 @@ function targetAlignedAny(targetIndex, geneType) { function evaluate_filter() { /*CODE*/ return Boolean(/*FILTER*/); -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java b/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java index 4f50266e7..b16d862bd 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -44,4 +23,4 @@ public void test1() throws Exception { Assert.assertEquals(1, mt.getThreshold(5)); Assert.assertEquals(0, mt.getThreshold(30)); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java index 434828b95..d035b6562 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -45,4 +24,4 @@ public void test1() throws Exception { public void test2() throws Exception { IOTestUtil.assertJavaSerialization(CloneAssemblerParametersPresets.getByName("default")); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java index 9bef6cb80..99d28dc11 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -93,4 +72,4 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge deser.getCloneFactoryParameters().getVParameters().setRelativeMinScore(0.34f); assertFalse(clone.equals(deser)); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index ea38d6a47..772477f12 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -158,4 +137,4 @@ private static void assertCSEquals(CloneSet expected, CloneSet actual) { for (int i = 0; i < expected.getClones().size(); ++i) Assert.assertEquals(expected.getClones().get(i), actual.getClones().get(i)); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java index 877c8aed4..bd2e951dc 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -46,4 +25,4 @@ public void test1() throws Exception { CloneClusteringParameters clone = deser.clone(); assertEquals(paramentrs, clone); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java index 166dcf04c..0b120d0c3 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -80,4 +59,4 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge deser.getVParameters().setRelativeMinScore(0.34f); assertFalse(clone.equals(deser)); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java index 1e25f3111..08d6a454b 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -42,4 +21,4 @@ public void test1() throws Exception { ClusteringFilter deser = GlobalObjectMappers.PRETTY.readValue(str, ClusteringFilter.class); assertEquals(paramentrs, deser); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java index 8f415662d..e3031340e 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler; @@ -58,4 +37,4 @@ public void test2() throws Exception { TestUtil.assertJson(new VJCClonalAlignerParameters(0.3f, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 1, 2, 3), true); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java index 6184f58b9..a8e8553ee 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.assembler.fullseq; @@ -483,4 +462,4 @@ public void testLargeCloneNoMismatches() throws Exception { System.out.println(); } } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java index 83b872f6b..933606722 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java index ff036b0f3..5c4e208ee 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.basictypes; @@ -292,4 +271,4 @@ private TestData(ClonalSequence c1, ClonalSequence c2, Mutations result = aligner.process0(read); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java index f897e6de3..e98652c5d 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; @@ -109,4 +88,4 @@ public void test1() throws Exception { // Assert.assertEquals(alignemntsList.get(i++), alignments); //} } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java index 2db39c701..39b3de668 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java @@ -1,31 +1,10 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved + * + * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE + * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: + * + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE */ package com.milaboratory.mixcr.vdjaligners; @@ -40,4 +19,4 @@ public class VDJCParametersPresetsTest { public void test1() throws Exception { IOTestUtil.assertJavaSerialization(VDJCParametersPresets.getByName("default")); } -} \ No newline at end of file +} From d0e265a662dade41af15a18413e098bae2ea45bb Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 21 Sep 2021 03:56:24 +0300 Subject: [PATCH 113/282] basic postanalysis CLI --- .../mixcr/cli/CommandPostanalysis.java | 416 ++++++++++++++++++ .../java/com/milaboratory/mixcr/cli/Main.java | 6 + .../postanalysis/SetPreprocessorFactory.java | 10 + .../mixcr/cli/CommandPostanalysisTest.java | 14 + 4 files changed, 446 insertions(+) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java create mode 100644 src/test/java/com/milaboratory/mixcr/cli/CommandPostanalysisTest.java diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java new file mode 100644 index 000000000..552e7459a --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java @@ -0,0 +1,416 @@ +package com.milaboratory.mixcr.cli; + +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.postanalysis.*; +import com.milaboratory.mixcr.postanalysis.additive.AAProperties; +import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; +import com.milaboratory.mixcr.postanalysis.overlap.*; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; +import com.milaboratory.mixcr.postanalysis.ui.*; +import com.milaboratory.util.GlobalObjectMappers; +import com.milaboratory.util.LambdaSemaphore; +import io.repseq.core.Chains; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; +import picocli.CommandLine; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; + +import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; +import static java.util.stream.Collectors.*; + +/** + * + */ +public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { + @Parameters(description = "cloneset.{clns|clna}... result.json") + public List inOut; + + @Option(description = "Use only productive sequences in postanalysis.", + names = {"--only-productive"}) + public boolean onlyProductive; + + @Option(description = "umi|d[number]|f[number]", + names = {"-d", "--downsampling"}, + required = true) + public String downsampling; + + @Option(description = "Chains", + names = {"-c", "--chains"}) + public String chains = "ALL"; + + List inputs() { + return inOut.subList(0, inOut.size() - 1); + } + + String output() { + return inOut.get(inOut.size() - 1); + } + + String output(Chains.NamedChains chain) { + return chain.name + "_" + output(); + } + + String outputBase() { + return output().replace(".json", ""); + } + + static String baseName(String fName) { + int i = fName.lastIndexOf("."); + if (i > 0) + return fName.substring(0, i); + else + return fName; + } + + static SetPreprocessorFactory parseDownsampling(String downsampling) { + if (downsampling.equalsIgnoreCase("umi")) { + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); + } else { + int value = Integer.parseInt(downsampling.substring(1, downsampling.length())); + if (downsampling.startsWith("d")) { + return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); + } else if (downsampling.startsWith("f")) { + return new SelectTop.Factory<>(WeightFunctions.Count, value); + } else { + throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); + } + } + } + + SetPreprocessorFactory downsampling() { + return downsampling(this.downsampling); + } + + SetPreprocessorFactory downsampling(String downsamplingStr) { + SetPreprocessorFactory downsampling = + parseDownsampling(downsamplingStr); + + if (onlyProductive) { + List> filters = new ArrayList<>(); + filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); + filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); + downsampling = downsampling.filterFirst(filters); + } + + return downsampling; + } + + static void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { + for (CharacteristicGroupOutputExtractor view : tableResult.group.views) + for (OutputTable t : view.getTables(tableResult).values()) + t.writeTSV(Paths.get("").toAbsolutePath(), chain.name + "_"); + } + + ///////////////////////////////////////////// Individual ///////////////////////////////////////////// + + + @CommandLine.Command(name = "individual", + sortOptions = false, + separator = " ", + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") + public static class CommandIndividual extends CommandPostanalysis { + public CommandIndividual() {} + + @Override + public void run0() throws Exception { + Chains c = Chains.parse(chains); + if (c.intersects(Chains.TRAD)) + run(Chains.TRAD_NAMED); + if (c.intersects(Chains.TRB)) + run(Chains.TRB_NAMED); + if (c.intersects(Chains.IGH)) + run(Chains.IGH_NAMED); + if (c.intersects(Chains.IGKL)) + run(Chains.IGKL_NAMED); + } + + @SuppressWarnings({"unchecked", "rawtypes"}) + void run(Chains.NamedChains chain) { + List> groups = new ArrayList<>(); + + SetPreprocessorFactory downsampling = downsampling() + .filterFirst(new ElementPredicate.IncludeChains(chain.chains)); + + groups.add(new CharacteristicGroup<>( + "cdr3Properties", + Arrays.asList( + weightedLengthOf(downsampling, GeneFeature.CDR3, false).setName("CDR3 length, nt"), + weightedLengthOf(downsampling, GeneFeature.CDR3, true).setName("CDR3 length, aa"), + weightedLengthOf(downsampling, GeneFeature.VJJunction, false).setName("NDN length, nt"), + weightedAddedNucleotides(downsampling).setName("Added N, nt"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Strength"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Hydrophobicity"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Surface"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), + weightedBiophysics(downsampling, AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") + ), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>( + "diversity", + Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), + downsampling, + new DiversityMeasure[]{ + DiversityMeasure.Observed, + DiversityMeasure.Clonality, + DiversityMeasure.ShannonWeiner, + DiversityMeasure.InverseSimpson, + DiversityMeasure.Chao1, + DiversityMeasure.Gini + })), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>( + "vUsage", + Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Variable)), + Arrays.asList(new GroupSummary<>()) + )); + groups.add(new CharacteristicGroup<>( + "jUsage", + Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Joining)), + Arrays.asList(new GroupSummary<>()) + )); + groups.add(new CharacteristicGroup<>( + "vjUsage", + Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(downsampling)), + Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) + )); + + groups.add(new CharacteristicGroup<>( + "isotypeUsage", + Arrays.asList(AdditiveCharacteristics.isotypeUsage(downsampling)), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>( + "cdr3Spectratype", + Arrays.asList(new SpectratypeCharacteristic("cdr3Spectratype", + downsampling, 10, + new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), + Collections.singletonList(new GroupSummary<>()))); + + groups.add(new CharacteristicGroup<>( + "VSpectratype", + Arrays.asList(AdditiveCharacteristics.VSpectratype(downsampling)), + Collections.singletonList(new GroupSummary<>()))); + + groups.add(new CharacteristicGroup<>( + "VSpectratypeMean", + Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(downsampling)), + Collections.singletonList(new GroupSummary<>()))); + + PostanalysisSchema schema = new PostanalysisSchema<>(groups); + + PostanalysisRunner runner = new PostanalysisRunner<>(); + runner.addCharacteristics(schema.getAllCharacterisitcs()); + + List datasets = inputs().stream() + .map(file -> + new ClonotypeDataset(baseName(file), file, VDJCLibraryRegistry.getDefault()) + ).collect(Collectors.toList()); + + PostanalysisResult result = runner.run(datasets); + for (CharacteristicGroup table : schema.tables) + writeTables(chain, result.getTable(table)); + + try { + GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), result); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + } + + ///////////////////////////////////////////// Overlap ///////////////////////////////////////////// + + @CommandLine.Command(name = "overlap", + sortOptions = false, + separator = " ", + description = "Overlap analysis") + public static class CommandOverlap extends CommandPostanalysis { + @Option(description = "Override downsampling for F2 umi|d[number]|f[number]", + names = {"--f2-downsampling"}, + required = false) + public String f2downsampling; + + public CommandOverlap() { + } + + @Override + public void run0() throws Exception { + Chains c = Chains.parse(chains); + if (c.intersects(Chains.TRAD)) + run(Chains.TRAD_NAMED); + if (c.intersects(Chains.TRB)) + run(Chains.TRB_NAMED); + if (c.intersects(Chains.IGH)) + run(Chains.IGH_NAMED); + if (c.intersects(Chains.IGKL)) + run(Chains.IGKL_NAMED); + + } + + void run(Chains.NamedChains chain) { + + SetPreprocessorFactory downsampling = downsampling(); + + Map> map = new HashMap<>(); + map.put(OverlapType.D, downsampling); + map.put(OverlapType.F2, f2downsampling == null + ? downsampling + : downsampling(f2downsampling)); + map.put(OverlapType.R_Intersection, downsampling); + + List> ordering = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); + OverlapPostanalysisSettings overlapPA = new OverlapPostanalysisSettings( + ordering, + new WeightFunctions.Count(), + map + ); + + PostanalysisSchema> schema = overlapPA.getSchema(inputs().size(), chain.chains); + + // Limits concurrency across all readers + LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(32); + List readers = inputs().stream() + .map(s -> { + try { + return mkCheckedReader( + Paths.get(s).toAbsolutePath(), + concurrencyLimiter); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); + + OverlapDataset overlapDataset = OverlapUtil.overlap( + inputs().stream().map(CommandPostanalysis::baseName) + .collect(toList()), + ordering, readers); + + PostanalysisRunner> runner = new PostanalysisRunner<>(); + runner.addCharacteristics(schema.getAllCharacterisitcs()); + PostanalysisResult result = runner.run(overlapDataset); + + for (CharacteristicGroup> table : schema.tables) + writeTables(chain, result.getTable(table)); + + try { + GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), result); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + public static CloneReader mkCheckedReader(Path path, + LambdaSemaphore concurrencyLimiter) throws IOException { + ClnsReader inner = new ClnsReader( + path, + VDJCLibraryRegistry.getDefault(), + concurrencyLimiter); + return new CloneReader() { + @Override + public VDJCSProperties.CloneOrdering ordering() { + return inner.ordering(); + } + + @Override + public OutputPortCloseable readClones() { + OutputPortCloseable in = inner.readClones(); + return new OutputPortCloseable() { + @Override + public void close() { + in.close(); + } + + @Override + public Clone take() { + Clone t = in.take(); + if (t == null) + return null; + if (t.getFeature(GeneFeature.CDR3) == null) + return take(); + return t; + } + }; + } + + @Override + public void close() throws Exception { + inner.close(); + } + }; + } + + static final class OverlapPostanalysisSettings { + final List> ordering; + final WeightFunction weight; + final Map> preprocessors; + final Map, List> groupped; + + OverlapPostanalysisSettings(List> ordering, + WeightFunction weight, + Map> preprocessors) { + this.ordering = ordering; + this.weight = weight; + this.preprocessors = preprocessors; + this.groupped = preprocessors.entrySet().stream().collect(groupingBy(Map.Entry::getValue, mapping(Map.Entry::getKey, toList()))); + } + + private SetPreprocessorFactory> getPreprocessor(OverlapType type, Chains chain) { + return new OverlapPreprocessorAdapter.Factory<>(preprocessors.get(type).filterFirst(new ElementPredicate.IncludeChains(chain))); + } + + public List> getCharacteristics(int i, int j, Chains chain) { + return groupped.entrySet().stream().map(e -> new OverlapCharacteristic<>("overlap_" + i + "_" + j + e.getValue().stream().map(t -> t.name).collect(Collectors.joining("_")), weight, + new OverlapPreprocessorAdapter.Factory<>(e.getKey().filterFirst(new ElementPredicate.IncludeChains(chain))), + e.getValue().toArray(new OverlapType[0]), + i, j)).collect(toList()); + } + + public PostanalysisSchema> getSchema(int nSamples, Chains chain) { + List> overlaps = new ArrayList<>(); + for (int i = 0; i < nSamples; ++i) + for (int j = i + 1; j < nSamples; ++j) + overlaps.addAll(getCharacteristics(i, j, chain)); + + return new PostanalysisSchema<>(Collections.singletonList( + new CharacteristicGroup<>("overlap", + overlaps, + Arrays.asList(new OverlapSummary<>()) + ))); + } + } + } + + @CommandLine.Command(name = "postanalysis", + separator = " ", + description = "Run postanalysis routines.", + subcommands = { + CommandLine.HelpCommand.class + }) + public static class CommandPostanalysisMain { + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 94bcc2dc6..311b77646 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -148,6 +148,7 @@ public static CommandLine mkCmd() { .setCommandName(command) .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) + .addSubcommand("postanalysis", CommandPostanalysis.CommandPostanalysisMain.class) .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) @@ -185,6 +186,11 @@ public static CommandLine mkCmd() { .addSubcommand("amplicon", CommandAnalyze.mkAmplicon()) .addSubcommand("shotgun", CommandAnalyze.mkShotgun()); + cmd.getSubcommands() + .get("postanalysis") + .addSubcommand("individual", CommandSpec.forAnnotatedObject(CommandPostanalysis.CommandIndividual.class)) + .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPostanalysis.CommandOverlap.class)); + cmd.setSeparator(" "); return cmd; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java index 3604e4543..949a10159 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java @@ -69,6 +69,16 @@ default SetPreprocessorFactory filterFirst(ElementPredicate... predicates) return filter(true, predicates); } + @SuppressWarnings("unchecked") + default SetPreprocessorFactory filterAfter(List> predicates) { + return filter(false, predicates.toArray(new ElementPredicate[0])); + } + + @SuppressWarnings("unchecked") + default SetPreprocessorFactory filterFirst(List> predicates) { + return filter(true, predicates.toArray(new ElementPredicate[0])); + } + @SuppressWarnings("unchecked") static Dataset[] processDatasets(SetPreprocessor proc, Dataset... initial) { while (true) { diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPostanalysisTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPostanalysisTest.java new file mode 100644 index 000000000..f746fb6d4 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPostanalysisTest.java @@ -0,0 +1,14 @@ +package com.milaboratory.mixcr.cli; + +import junit.framework.TestCase; +import org.junit.Test; + +/** + * + */ +public class CommandPostanalysisTest extends TestCase { + @Test + public void test1() { + Main.main("postanalysis", "help", "overlap"); + } +} From 8dc17e356a5071b654285a305dd5028bc1ef907f Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 21 Sep 2021 16:44:03 +0300 Subject: [PATCH 114/282] Better downsampling settings in postanalysis CLI. --- .../mixcr/cli/CommandPostanalysis.java | 39 +++++++++++++------ .../mixcr/postanalysis/ui/GroupMelt.java | 2 +- 2 files changed, 28 insertions(+), 13 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java index 552e7459a..6233af04e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java @@ -48,7 +48,7 @@ public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { names = {"--only-productive"}) public boolean onlyProductive; - @Option(description = "umi|d[number]|f[number]", + @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]", names = {"-d", "--downsampling"}, required = true) public String downsampling; @@ -57,6 +57,10 @@ public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { names = {"-c", "--chains"}) public String chains = "ALL"; + @Option(description = "Prefix for outputs", + names = {"-p", "--prefix"}) + public String prefix = ""; + List inputs() { return inOut.subList(0, inOut.size() - 1); } @@ -66,7 +70,7 @@ String output() { } String output(Chains.NamedChains chain) { - return chain.name + "_" + output(); + return prefix + chain.name + "_" + output(); } String outputBase() { @@ -74,6 +78,7 @@ String outputBase() { } static String baseName(String fName) { + fName = Paths.get(fName).toAbsolutePath().getFileName().toString(); int i = fName.lastIndexOf("."); if (i > 0) return fName.substring(0, i); @@ -81,14 +86,22 @@ static String baseName(String fName) { return fName; } + static int downsamplingValue(String downsampling) { + return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1, downsampling.length())); + } + static SetPreprocessorFactory parseDownsampling(String downsampling) { - if (downsampling.equalsIgnoreCase("umi")) { - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); + if (downsampling.startsWith("umi-count")) { + if (downsampling.endsWith("auto")) + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); + else { + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), 314); + } } else { - int value = Integer.parseInt(downsampling.substring(1, downsampling.length())); - if (downsampling.startsWith("d")) { + int value = downsamplingValue(downsampling); + if (downsampling.startsWith("cumulative-top")) { return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); - } else if (downsampling.startsWith("f")) { + } else if (downsampling.startsWith("top")) { return new SelectTop.Factory<>(WeightFunctions.Count, value); } else { throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); @@ -114,10 +127,10 @@ SetPreprocessorFactory downsampling(String downsamplingStr) { return downsampling; } - static void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { + void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { for (CharacteristicGroupOutputExtractor view : tableResult.group.views) for (OutputTable t : view.getTables(tableResult).values()) - t.writeTSV(Paths.get("").toAbsolutePath(), chain.name + "_"); + t.writeTSV(Paths.get("").toAbsolutePath(), prefix + chain.name + "_"); } ///////////////////////////////////////////// Individual ///////////////////////////////////////////// @@ -135,6 +148,8 @@ public void run0() throws Exception { Chains c = Chains.parse(chains); if (c.intersects(Chains.TRAD)) run(Chains.TRAD_NAMED); + if (c.intersects(Chains.TRG)) + run(Chains.TRG_NAMED); if (c.intersects(Chains.TRB)) run(Chains.TRB_NAMED); if (c.intersects(Chains.IGH)) @@ -254,21 +269,21 @@ public static class CommandOverlap extends CommandPostanalysis { required = false) public String f2downsampling; - public CommandOverlap() { - } + public CommandOverlap() {} @Override public void run0() throws Exception { Chains c = Chains.parse(chains); if (c.intersects(Chains.TRAD)) run(Chains.TRAD_NAMED); + if (c.intersects(Chains.TRG)) + run(Chains.TRG_NAMED); if (c.intersects(Chains.TRB)) run(Chains.TRB_NAMED); if (c.intersects(Chains.IGH)) run(Chains.IGH_NAMED); if (c.intersects(Chains.IGKL)) run(Chains.IGKL_NAMED); - } void run(Chains.NamedChains chain) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java index f5483fb0c..be9652e23 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java @@ -49,7 +49,7 @@ interface CoordinatesProvider { public static final class VJUsageMelt extends GroupMelt> { public VJUsageMelt() { - super("vj_usage_", + super("vjUsage_", (result, cell) -> cell.datasetId, () -> key -> new Coordinates(key.key.vGene, key.key.jJene)); } From 8b0aa70a24704bcbc8bb6ea6cad5101bdfd5b71e Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 4 Oct 2021 17:06:59 +0300 Subject: [PATCH 115/282] First wip. --- build.gradle.kts | 28 +- .../mixcr/cli/CommandPostanalysis.java | 39 ++- .../mixcr/cli/CommandPostanalysisPlots.java | 37 +++ .../java/com/milaboratory/mixcr/cli/Main.java | 1 + .../postanalysis/PostanalysisResult.java | 20 +- .../dataframe/SimpleStatistics.kt | 99 +++++++ .../dataframe/SingleSpectratype.kt | 249 ++++++++++++++++++ .../mixcr/postanalysis/dataframe/Util.kt | 43 +++ .../diversity/DiversityAggregator.java | 3 + .../mixcr/postanalysis/plots/BoxPlots.kt | 101 +++++++ .../mixcr/postanalysis/plots/Heatmap.kt | 87 ++++++ .../mixcr/postanalysis/plots/Plots.kt | 66 +++++ .../mixcr/postanalysis/plots/SpectraPlots.kt | 152 +++++++++++ .../mixcr/postanalysis/plots/Util.kt | 12 + .../spectratype/SpectratypeAggregator.java | 2 + .../mixcr/postanalysis/plots/BoxPlotsTest.kt | 14 + 16 files changed, 941 insertions(+), 12 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt diff --git a/build.gradle.kts b/build.gradle.kts index 867392d42..4752d0aff 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -1,6 +1,7 @@ +import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar import com.palantir.gradle.gitversion.VersionDetails import groovy.lang.Closure -import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar +import org.jetbrains.kotlin.gradle.tasks.KotlinCompile import java.net.InetAddress plugins { @@ -9,6 +10,7 @@ plugins { `maven-publish` id("com.palantir.git-version") version "0.12.3" id("com.github.johnrengelman.shadow") version "7.0.0" + kotlin("jvm") version "1.6.0-M1" } val miRepoAccessKeyId: String by project @@ -27,7 +29,7 @@ version = description = "MiXCR" java { - sourceCompatibility = JavaVersion.VERSION_1_8 + sourceCompatibility = JavaVersion.VERSION_11 withSourcesJar() withJavadocJar() } @@ -54,6 +56,7 @@ tasks.register("createInfoFile") { repositories { mavenCentral() + maven("https://jitpack.io") // Snapshot versions of milib and repseqio distributed via this repo maven { @@ -64,6 +67,8 @@ repositories { val milibVersion = "1.14.1-16-774c60afab" val repseqioVersion = "1.3.5-4-f7170dd23b" val jacksonVersion = "2.12.4" +val letsPlotLibraryVersion = "2.1.0" +val letsPlotKotlinApiVersion = "3.0.3-alpha1" dependencies { api("com.milaboratory:milib:$milibVersion") @@ -81,6 +86,16 @@ dependencies { testImplementation("junit:junit:4.13.2") implementation(testFixtures("com.milaboratory:milib:$milibVersion")) testImplementation("org.mockito:mockito-all:1.9.5") + + // plots + implementation(kotlin("stdlib")) + + implementation("org.apache.xmlgraphics:fop-transcoder:2.6") + implementation("org.apache.pdfbox:pdfbox:2.0.21") + + implementation("org.jetbrains.kotlinx:dataframe:0.8.0-dev-339-0.10.0.260") + implementation("org.jetbrains.lets-plot:lets-plot-common:$letsPlotLibraryVersion") + implementation("org.jetbrains.lets-plot:lets-plot-kotlin-jvm:$letsPlotKotlinApiVersion") } val writeBuildProperties by tasks.registering(WriteProperties::class) { @@ -149,3 +164,12 @@ tasks.test { longTests?.let { systemProperty("longTests", it) } } + +val compileKotlin: KotlinCompile by tasks +compileKotlin.kotlinOptions { + jvmTarget = "11" +} +val compileTestKotlin: KotlinCompile by tasks +compileTestKotlin.kotlinOptions { + jvmTarget = "11" +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java index 6233af04e..3952c8e36 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java @@ -1,6 +1,8 @@ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.OutputPortCloseable; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.postanalysis.*; import com.milaboratory.mixcr.postanalysis.additive.AAProperties; @@ -29,10 +31,12 @@ import java.io.File; import java.io.IOException; +import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; import static java.util.stream.Collectors.*; @@ -46,7 +50,7 @@ public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { @Option(description = "Use only productive sequences in postanalysis.", names = {"--only-productive"}) - public boolean onlyProductive; + public boolean onlyProductive = false; @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]", names = {"-d", "--downsampling"}, @@ -62,7 +66,20 @@ public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { public String prefix = ""; List inputs() { - return inOut.subList(0, inOut.size() - 1); + return inOut.subList(0, inOut.size() - 1) + .stream() + .flatMap(f -> { + if (Files.isDirectory(Path.of(f))) { + try { + return Files + .list(Path.of(f)) + .map(Path::toString); + } catch (IOException ignored) { + } + } + return Stream.of(f); + }) + .collect(toList()); } String output() { @@ -250,7 +267,7 @@ void run(Chains.NamedChains chain) { writeTables(chain, result.getTable(table)); try { - GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), result); + GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), new PostanalysisData(schema, result)); } catch (IOException e) { throw new RuntimeException(e); } @@ -333,7 +350,7 @@ void run(Chains.NamedChains chain) { writeTables(chain, result.getTable(table)); try { - GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), result); + GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), new PostanalysisData(schema, result)); } catch (IOException e) { throw new RuntimeException(e); } @@ -428,4 +445,18 @@ public PostanalysisSchema> getSchema(int nSamples, Chains ch }) public static class CommandPostanalysisMain { } + + public static final class PostanalysisData { + @JsonProperty("schema") + public final PostanalysisSchema schema; + @JsonProperty("result") + public final PostanalysisResult result; + + @JsonCreator + public PostanalysisData(@JsonProperty("schema") PostanalysisSchema schema, + @JsonProperty("result") PostanalysisResult result) { + this.schema = schema; + this.result = result; + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java new file mode 100644 index 000000000..8757d7dc3 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java @@ -0,0 +1,37 @@ +package com.milaboratory.mixcr.cli; + +import com.milaboratory.mixcr.postanalysis.dataframe.SingleSpectratype; +import com.milaboratory.mixcr.postanalysis.plots.BoxPlots; +import com.milaboratory.mixcr.postanalysis.plots.SpectraPlots; +import com.milaboratory.util.GlobalObjectMappers; +import picocli.CommandLine; + +import java.io.File; +import java.nio.file.Path; + +/** + * + */ +public class CommandPostanalysisPlots extends ACommandWithOutputMiXCR { + @CommandLine.Parameters(index = "0", description = "pa_result.json") + public String in; + @CommandLine.Parameters(index = "1", description = "plt_out") + public String out; + + @Override + public void run0() throws Exception { + CommandPostanalysis.PostanalysisData data = GlobalObjectMappers.PRETTY.readValue(new File(in), CommandPostanalysis.PostanalysisData.class); + + + SingleSpectratype.INSTANCE.plotPDF(Path.of(out + "spectra.pdf"), + data.schema, data.result, "VSpectratype", + SingleSpectratype.SpectratypePlotSettings.Companion.getDefault()); + + SpectraPlots.INSTANCE.singleSpectra(Path.of(out + "spectraApp.pdf"), + data.schema, data.result, "VSpectratype", 20, null, true); + + BoxPlots.INSTANCE.individualBoxPlots(Path.of(out), + data.schema, data.result, "cdr3Properties", null); + + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 311b77646..71958d216 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -149,6 +149,7 @@ public static CommandLine mkCmd() { .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) .addSubcommand("postanalysis", CommandPostanalysis.CommandPostanalysisMain.class) + .addSubcommand("plot", CommandPostanalysisPlots.class) .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index 698dc8a07..7184d8bf8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -22,10 +22,10 @@ public class PostanalysisResult { /** All dataset ids that were analyzed */ @JsonProperty("datasetIds") - private final Set datasetIds; + public final Set datasetIds; /** Characteristic Id -> characteristic data */ @JsonProperty("data") - private final Map data; + public final Map data; @JsonCreator public PostanalysisResult(@JsonProperty("datasetIds") Set datasetIds, @@ -45,6 +45,14 @@ static PostanalysisResult create(Set datasetIds, /** cached results for char groups */ private final Map, CharacteristicGroupResult> cached = new IdentityHashMap<>(); + /** project result on a specific char group */ + public PostanalysisResult forGroup(CharacteristicGroup group) { + return new PostanalysisResult(datasetIds, + group.characteristics.stream() + .map(c -> c.name) + .collect(Collectors.toMap(c -> c, data::get))); + } + /** project result on a specific char group */ @SuppressWarnings({"unchecked"}) public CharacteristicGroupResult getTable(CharacteristicGroup group) { @@ -88,10 +96,10 @@ public String toString() { getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE ) - private static final class Array2d { + public static final class Array2d { /** Dataset Id -> Metric values */ @JsonProperty("2darray") - private final Map data; + public final Map data; @JsonCreator Array2d(@JsonProperty("2darray") Map[]> data) { @@ -117,9 +125,9 @@ public String toString() { } } - private static final class MetricsArray { + public static final class MetricsArray { @JsonValue - private final MetricValue[] data; + public final MetricValue[] data; public MetricsArray(MetricValue[] data) { this.data = data; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt new file mode 100644 index 000000000..b1f767587 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt @@ -0,0 +1,99 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema +import jetbrains.letsPlot.Pos +import jetbrains.letsPlot.geom.geomBoxplot +import jetbrains.letsPlot.geom.geomPoint +import jetbrains.letsPlot.label.ggtitle +import jetbrains.letsPlot.label.labs +import jetbrains.letsPlot.letsPlot +import jetbrains.letsPlot.theme +import org.jetbrains.dataframe.* +import org.jetbrains.dataframe.annotations.DataSchema +import org.jetbrains.dataframe.columns.DataColumn + +/** + * DataFrame row for single statistical char group + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +interface SimpleMetricsRow { + /** Sample ID */ + val sample: String + + companion object { + ////// DSL + + val sample by column() + + val DataFrame.sample get() = this[SpectratypeRow::sample.name] as DataColumn + val DataRow.sample get() = this[SpectratypeRow::sample.name] as String + } +} + + +object SimpleStatistics { + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String + ) = run { + + val data = mutableMapOf>( + SpectratypeRow::sample.name to mutableListOf(), + ) + + for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { + for ((sampleId, keys) in charData.data) { + for (metric in keys.data) { + val key = metric.key.toString() + data[SimpleMetricsRow::sample.name]!! += sampleId + data.computeIfAbsent(key) { mutableListOf() } += metric.value + } + } + } + + data.toDataFrame().typed() + } + + + /** + * Attaches metadata to statistics + **/ + fun DataFrame.withMetadata(metadata: AnyFrame) = run { + this.leftJoin(metadata) { SimpleMetricsRow.sample } + } + + /** + * Creates plot spec + **/ + fun DataFrame.plot( + metric: String, + primaryGroup: String? = null, + secondaryGroup: String? = null + ) = run { + var plt = letsPlot(toMap()) { + x = primaryGroup + y = metric + group = secondaryGroup + } + + plt += geomBoxplot() + plt += geomPoint( + position = Pos.jitterdodge, + shape = 21, + color = "black" + ) + plt += ggtitle(metric) + plt += labs(x = primaryGroup, y = metric) + plt += theme().axisTitleXBlank() + plt += theme().axisTextXBlank() + plt += theme().axisTicksXBlank() + + plt + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt new file mode 100644 index 000000000..d3db33c17 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt @@ -0,0 +1,249 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.length +import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.payload +import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.sample +import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.weight +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema +import jetbrains.datalore.plot.PlotSvgExport +import jetbrains.letsPlot.* +import jetbrains.letsPlot.geom.geomBar +import jetbrains.letsPlot.intern.toSpec +import jetbrains.letsPlot.label.ggtitle +import jetbrains.letsPlot.label.labs +import jetbrains.letsPlot.scale.scaleXDiscrete +import org.jetbrains.dataframe.* +import org.jetbrains.dataframe.annotations.DataSchema +import org.jetbrains.dataframe.columns.DataColumn +import java.nio.file.Path + +/** + * DataFrame row for single (V/J/CDR3) spectratype + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +interface SpectratypeRow { + /** Sample ID */ + val sample: String + + /** Gene feature length */ + val length: Int + + /** Payload (gene name / gene feature aa) */ + val payload: String + + /** Payload weight */ + val weight: Double + + companion object { + ////// DSL + + val sample by column() + val length by column() + val payload by column() + val weight by column() + + val DataFrame.sample get() = this[SpectratypeRow::sample.name] as DataColumn + val DataRow.sample get() = this[SpectratypeRow::sample.name] as String + + val DataFrame.length get() = this[SpectratypeRow::length.name] as DataColumn + val DataRow.length get() = this[SpectratypeRow::length.name] as Int + + val DataFrame.payload get() = this[SpectratypeRow::payload.name] as DataColumn + val DataRow.payload get() = this[SpectratypeRow::payload.name] as String + + val DataFrame.weight get() = this[SpectratypeRow::weight.name] as DataColumn + val DataRow.weight get() = this[SpectratypeRow::weight.name] as Double + } +} + +data class SpectratypeRowImp( + override val sample: String, + override val length: Int, + override val weight: Double, + override val payload: String +) : SpectratypeRow + + +object SingleSpectratype { + private const val OtherPayload = "Other" + + /** + * Imports spectratype data into DataFrame + **/ + fun dataFrame( + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String + ): DataFrame { + val data = mutableMapOf>( + SpectratypeRow::sample.name to mutableListOf(), + SpectratypeRow::length.name to mutableListOf(), + SpectratypeRow::weight.name to mutableListOf(), + SpectratypeRow::payload.name to mutableListOf() + ) + + for ((_, charData) in paResult.forGroup(paSett.getGroup>(group)).data) { + for ((sampleId, keys) in charData.data) { + for (metric in keys.data) { + @Suppress("UNCHECKED_CAST") + val key = metric.key as SpectratypeKey + data[SpectratypeRow::sample.name]!! += sampleId + data[SpectratypeRow::length.name]!! += key.length + data[SpectratypeRow::payload.name]!! += (key.payload ?: OtherPayload).toString() + data[SpectratypeRow::weight.name]!! += metric.value + } + } + } + + return data.toDataFrame().typed() + } + + /** + * Spectratype plot settings + * @param nTop number of top payloads to show on plot + * @param limits specify length range (null for all) + * @param normalize normalize by total weight + * */ + data class SpectratypePlotSettings( + val nTop: Int, + val limits: IntRange?, + val normalize: Boolean, + val width: Int, + val height: Int, + ) { + companion object { + val Default = SpectratypePlotSettings( + nTop = 20, + limits = null, + normalize = true, + width = 1024, + height = 512 + ) + } + } + + /** + * Creates plot spec for specific sample + * + * @param sample sample + * @param settings plot settings + * */ + fun DataFrame.plot( + sample: String, + settings: SpectratypePlotSettings = SpectratypePlotSettings.Default, + ) = run { + + var df = this + // for sample + df = df.filter { SpectratypeRow.sample.eq(sample) } + // sort by weight + df = df.sortByDesc(SpectratypeRow.weight) + + // select top + val top = df.payload + .distinct().toList() + .take(settings.nTop) + .toSet() + + // replace non top payloads with "Other" + df = df.update { SpectratypeRow.payload } + .where { !top.contains(it) } + .with { OtherPayload } + + // find min max + val min = df.length.min() ?: 0 + val max = df.length.max() ?: 0 + + // add auxiliary points for each cdr3 length + df += (min..max) + .map { SpectratypeRowImp(sample, it, 0.0, OtherPayload) } + .toDataFrameByProperties() + .typed() + + // collapse all "Other" into a single row + df = df + .groupBy { SpectratypeRow.length and SpectratypeRow.payload } + .aggregate { + sumOf { it.weight } into SpectratypeRow::weight.name + } + + // sort so that "Other" will be at the bottom when it is big + df = df.sortByDesc(SpectratypeRow.weight) + + if (settings.normalize) + df[SpectratypeRow::weight.name] = df.weight / df.weight.sum() + + // plot + var plt = letsPlot(df.toMap()) + geomBar( + position = Pos.stack, + stat = Stat.identity, + width = 0.6 + ) { + x = asDiscrete(SpectratypeRow.length.name(), order = 1) + y = SpectratypeRow.weight.name() + fill = asDiscrete( + SpectratypeRow.payload.name(), + orderBy = SpectratypeRow::weight.name, order = -1 + ) + } + plt += ggtitle(sample) + plt += labs(y = "", x = "CDR3 length, bp") + + // adjust breaks + val breaks = df.length.toList() + .sorted() + .distinct() + plt += scaleXDiscrete( + breaks = breaks, + labels = breaks.map { if (it % 3 == 0) it.toString() else "" }, + limits = settings.limits?.toList() + ) + + // fix size + plt += ggsize(settings.width, settings.height) + + plt + } + + /** + * Export all plots into single PDF file + * + * @param destination path to export PDF + * @param settings plot settings + * */ + fun DataFrame.plotPDF( + destination: Path, + settings: SpectratypePlotSettings = SpectratypePlotSettings.Default, + ) = run { + writePDF(destination, + this.sample + .distinct().map { sample -> + PlotSvgExport.buildSvgImageFromRawSpecs( + plot(sample, settings).toSpec() + ) + }.toList() + .map { toPdf(it) } + ) + } + + /** + * Create and export all plots into single PDF file + * + * @param destination path to export PDF + * @param paSett PA settings + * @param paResult PA results + * @param settings plot settings + * */ + fun plotPDF( + destination: Path, + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String, + settings: SpectratypePlotSettings = SpectratypePlotSettings.Default + ) { + dataFrame(paSett, paResult, group).plotPDF(destination, settings) + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt new file mode 100644 index 000000000..764b9ed65 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt @@ -0,0 +1,43 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import org.apache.batik.transcoder.TranscoderInput +import org.apache.batik.transcoder.TranscoderOutput +import org.apache.fop.render.ps.EPSTranscoder +import org.apache.fop.svg.PDFTranscoder +import org.apache.pdfbox.io.MemoryUsageSetting +import org.apache.pdfbox.multipdf.PDFMergerUtility +import java.io.ByteArrayInputStream +import java.io.ByteArrayOutputStream +import java.nio.file.Path +import kotlin.io.path.absolutePathString +import kotlin.io.path.writeBytes + +fun toPdf(svg: String) = toVector(svg, ExportType.PDF) +fun toEPS(svg: String) = toVector(svg, ExportType.EPS) + +enum class ExportType { PDF, EPS } + +private fun toVector(svg: String, type: ExportType) = run { + val pdfTranscoder = if (type == ExportType.PDF) PDFTranscoder() else EPSTranscoder() + val input = TranscoderInput(ByteArrayInputStream(svg.toByteArray())) + ByteArrayOutputStream().use { byteArrayOutputStream -> + val output = TranscoderOutput(byteArrayOutputStream) + pdfTranscoder.transcode(input, output) + byteArrayOutputStream.toByteArray() + } +} + +fun writeEPS(destination: Path, image: ByteArray) { + destination.writeBytes(image) +} + +fun writePDF(destination: Path, images: List) { + val merger = PDFMergerUtility() + merger.destinationFileName = destination.absolutePathString() + + for (image in images) { + merger.addSource(ByteArrayInputStream(image)) + } + + merger.mergeDocuments(MemoryUsageSetting.setupMainMemoryOnly()) +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java index 1ab122ab4..dcdf9a1b5 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -50,6 +50,9 @@ private List> computeChao1() { double f2 = freqTable.get(2); // doubletons double f0 = f1 * (f1 - 1) / 2 / (f2 + 1); double chao1 = sobs + f0; + if (!measures.contains(Chao1Std)) + return Collections.singletonList(new MetricValue<>(Chao1, chao1)); + double chao1std = Math.sqrt( f0 + f1 * (2 * f1 - 1) * (2 * f1 - 1) / 4 / (f2 + 1) / (f2 + 1) + f1 * f1 * f2 * (f1 - 1) * (f1 - 1) / 4 / (f2 + 1) / (f2 + 1) / (f2 + 1) / (f2 + 1)); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt new file mode 100644 index 000000000..d6cc60153 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt @@ -0,0 +1,101 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema +import jetbrains.datalore.plot.PlotSvgExport +import jetbrains.letsPlot.Pos +import jetbrains.letsPlot.geom.geomBoxplot +import jetbrains.letsPlot.geom.geomPoint +import jetbrains.letsPlot.intern.toSpec +import jetbrains.letsPlot.label.ggtitle +import jetbrains.letsPlot.label.labs +import jetbrains.letsPlot.letsPlot +import jetbrains.letsPlot.theme +import org.apache.batik.transcoder.TranscoderInput +import org.apache.batik.transcoder.TranscoderOutput +import org.apache.fop.render.ps.EPSTranscoder +import org.apache.fop.svg.PDFTranscoder +import org.apache.pdfbox.io.MemoryUsageSetting +import org.apache.pdfbox.multipdf.PDFMergerUtility +import java.io.ByteArrayInputStream +import java.io.ByteArrayOutputStream +import java.nio.file.Path +import kotlin.io.path.absolutePathString +import kotlin.io.path.writeBytes + +/** + * + */ +object BoxPlots { + fun individualBoxPlots( + destination: Path, + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String, + metadata: Map? = null + ) { + + // metricName -> list (sample, value) + val metrics = mutableMapOf>>() + for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { + for ((sampleId, allMetrics) in charData.data) { + for (metricValue in allMetrics.data) { + val metricName = metricValue.key.toString() + val samples = metrics.computeIfAbsent(metricName) { mutableListOf() } + samples.add(sampleId to metricValue.value) + } + } + } + + val svgs = metrics.map { (metric, data) -> + var plt = letsPlot(mapOf("y" to data.map { it.second })) { + y = "y" + } + plt += geomBoxplot() + plt += geomPoint( + position = Pos.jitterdodge, + shape = 21, + color = "black" + ) + plt += ggtitle(metric) + plt += labs(y = metric) + plt += theme().axisTitleXBlank() + plt += theme().axisTextXBlank() + plt += theme().axisTicksXBlank() + + PlotSvgExport.buildSvgImageFromRawSpecs(plt.toSpec()) + } + + writePDF(destination, svgs.map { toPdf(it) }) + } + + fun toPdf(svg: String) = toVector(svg, ExportType.PDF) + fun toEPS(svg: String) = toVector(svg, ExportType.EPS) + + enum class ExportType { PDF, EPS } + + private fun toVector(svg: String, type: ExportType) = run { + val pdfTranscoder = if (type == ExportType.PDF) PDFTranscoder() else EPSTranscoder() + val input = TranscoderInput(ByteArrayInputStream(svg.toByteArray())) + ByteArrayOutputStream().use { byteArrayOutputStream -> + val output = TranscoderOutput(byteArrayOutputStream) + pdfTranscoder.transcode(input, output) + byteArrayOutputStream.toByteArray() + } + } + + fun writeEPS(destination: Path, image: ByteArray) { + destination.writeBytes(image) + } + + fun writePDF(destination: Path, images: List) { + val merger = PDFMergerUtility() + merger.destinationFileName = destination.absolutePathString() + + for (image in images) { + merger.addSource(ByteArrayInputStream(image)) + } + + merger.mergeDocuments(MemoryUsageSetting.setupMainMemoryOnly()) + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt new file mode 100644 index 000000000..4d49377eb --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt @@ -0,0 +1,87 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema +import jetbrains.datalore.plot.PlotSvgExport +import jetbrains.letsPlot.* +import jetbrains.letsPlot.geom.geomBar +import jetbrains.letsPlot.intern.toSpec +import jetbrains.letsPlot.label.ggtitle +import jetbrains.letsPlot.label.labs +import jetbrains.letsPlot.scale.scaleXDiscrete +import java.nio.file.Path + +/** + * + */ +object Heatmap { + private const val x = "l" + private const val y = "p" + private const val w = "c" + private const val other = "Other" + + private fun mkDf() = mutableMapOf>( + x to mutableListOf(), + y to mutableListOf(), + w to mutableListOf() + ) + + + fun vUsage( + destination: Path, + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String + ) { + + // x - sample, y - gene + val df = mkDf() + for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { + for ((sampleId, keys) in charData.data) { + for (metric in keys.data) { + @Suppress("UNCHECKED_CAST") + val key = metric.key as SpectratypeKey + df[x]!! += sampleId + df[y]!! += key.payload + df[w]!! += metric.value + } + } + } + + +// val svgs = samples.map { (sample, idf) -> +// val df = SpectraPlots.filter( +// idf, +// normalize = normalize, +// nTop = nTop +// ) +// +// var plt = letsPlot(df) +// plt += geomBar(position = Pos.stack, stat = Stat.identity, width = 0.6) { +// x = asDiscrete(SpectraPlots.lenCDR3, order = 1) +// y = SpectraPlots.count +// fill = asDiscrete(SpectraPlots.payload, orderBy = SpectraPlots.count, order = -1) +// } +// plt += ggtitle(sample) +// plt += labs(y = "Clone count", x = "CDR3 length, bp") +// +// val breaks = df[SpectraPlots.lenCDR3]!! +// .map { it as Int } +// .sorted() +// .distinct() +// +// plt += scaleXDiscrete( +// breaks = breaks, +// labels = breaks.map { if (it % 3 == 0) it.toString() else "" }, +// limits = limits?.toList() +// ) +// plt += ggsize(1000, 500) +// +// PlotSvgExport.buildSvgImageFromRawSpecs(plt.toSpec()) +// } +// +// BoxPlots.writePDF(destination, svgs.map { BoxPlots.toPdf(it) }) + } + +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt new file mode 100644 index 000000000..3ab101150 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt @@ -0,0 +1,66 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult + +typealias MutableDataFrame = MutableMap> +typealias DataFrame = Map> + +fun emptyDataFrame() = mutableMapOf>() +fun emptyDataFrame(colNames: List) = run { + val df = emptyDataFrame() + for (colName in colNames) { + df[colName] = mutableListOf() + } + df +} + +//fun MutableDataFrame.toDataFrame(): DataFrame = this.mapValues { (_, v) -> v.toList() }.toMap() + +fun DataFrame.nRows() = if (this.isEmpty()) 0 else this.values.first().size +fun DataFrame.nCols() = this.size + +fun DataFrame.colNames() = this.map { (k, _) -> k }.toList() + +fun DataFrame.rows() = run { + val rows = mutableListOf>() + for (i in 0 until nRows()) { + rows += this.map { (_, v) -> v[i] }.toList() + } + rows +} + +fun fromRows(colNames: List, rows: List>) = run { + val df = emptyDataFrame(colNames) + for (row in rows) { + for (i in row.indices) { + df[colNames[i]]!! += row[i] + } + } + df +} + +fun DataFrame.sort(col: String, descending: Boolean = false) = run { + val rows = rows() + val colNames = colNames() + val iCol = colNames.indexOf(col) + if (descending) + rows.sortByDescending { it[iCol] as Comparable } + else + rows.sortBy { it[iCol] as Comparable } + fromRows(colNames, rows) +} + + +fun DataFrame.sort(col: String, comparator: Comparator) = run { + val rows: MutableList> = rows() + val colNames = colNames() + val iCol = colNames.indexOf(col) + rows.sortWith { a, b -> + comparator.compare(a[iCol], b[iCol]) + } + fromRows(colNames, rows) +} + + diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt new file mode 100644 index 000000000..6d0f381f0 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt @@ -0,0 +1,152 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema +import jetbrains.datalore.plot.PlotSvgExport +import jetbrains.letsPlot.* +import jetbrains.letsPlot.geom.geomBar +import jetbrains.letsPlot.intern.toSpec +import jetbrains.letsPlot.label.ggtitle +import jetbrains.letsPlot.label.labs +import jetbrains.letsPlot.scale.scaleXDiscrete +import org.jetbrains.dataframe.annotations.DataSchema +import org.jetbrains.dataframe.columns.DataColumn +import org.jetbrains.dataframe.sortBy +import org.jetbrains.dataframe.toDataFrame +import java.nio.file.Path + +/** + * + */ + +object SpectraPlots { + private const val lenCDR3 = "l" + private const val payload = "p" + private const val count = "c" + private const val other = "Other" + + @DataSchema + interface Row { + val sample: String + val len: Int + val payload: String + val count: Double + } + + private fun mkDf() = mutableMapOf>( + lenCDR3 to mutableListOf(), + payload to mutableListOf(), + count to mutableListOf() + ) + + fun singleSpectra( + destination: Path, + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String, + nTop: Int = 20, + limits: IntRange? = null, + normalize: Boolean = true + ) { + + // sample -> dataframe + val samples = mutableMapOf>>() + + for ((_, charData) in paResult.forGroup(paSett.getGroup>(group)).data) { + for ((sampleId, keys) in charData.data) { + val df = samples.computeIfAbsent(sampleId) { mkDf() } + for (metric in keys.data) { + @Suppress("UNCHECKED_CAST") + val key = metric.key as SpectratypeKey + df[lenCDR3]!! += key.length + df[payload]!! += (key.payload ?: other).toString() + df[count]!! += metric.value + } + } + } + + + val svgs = samples.map { (sample, idf) -> + val df = filter( + idf, + normalize = normalize, + nTop = nTop + ) + + var plt = letsPlot(df) + plt += geomBar(position = Pos.stack, stat = Stat.identity, width = 0.6) { + x = asDiscrete(lenCDR3, order = 1) + y = count + fill = asDiscrete(payload, orderBy = count, order = -1) + } + plt += ggtitle(sample) + plt += labs(y = "Clone count", x = "CDR3 length, bp") + + val breaks = df[lenCDR3]!! + .map { it as Int } + .sorted() + .distinct() + + plt += scaleXDiscrete( + breaks = breaks, + labels = breaks.map { if (it % 3 == 0) it.toString() else "" }, + limits = limits?.toList() + ) + plt += ggsize(1000, 500) + + PlotSvgExport.buildSvgImageFromRawSpecs(plt.toSpec()) + } + + BoxPlots.writePDF(destination, svgs.map { BoxPlots.toPdf(it) }) + } + + @Suppress("UNCHECKED_CAST") + fun filter(df: DataFrame, normalize: Boolean = true, nTop: Int = 10) = run { + val top = df[payload]!!.zip(df[count]!!) + .groupingBy { it.first as String } + .fold(0.0) { acc: Double, el -> acc + el.second as Double } + .toList() + .sortedBy { it.second } + .map { it.first } + .distinct() + .takeLast(nTop) + .toSet() + + + val totalCount = if (normalize) + df[count]!!.map { it as Double }.sum() + else + 1.0 + + val ndf = mkDf() + val otherCounts = mutableMapOf() + for (i in 0 until df.nRows()) { + val l = df[lenCDR3]!![i] as Int + val p = df[payload]!![i] + val c = (df[count]!![i] as Double) / totalCount + if (!top.contains(p)) + otherCounts[l] = (otherCounts[l] ?: 0.0) + c + else { + ndf[lenCDR3]!! += l + ndf[payload]!! += p + ndf[count]!! += c + } + } + + val ll = ndf[lenCDR3]!!.map { it as Int }.sorted().distinct() + val min = ll.minOrNull() ?: 0 + val max = ll.maxOrNull() ?: 0 + + for (l in (min..max)) + otherCounts.putIfAbsent(l, 0.0) + + for ((l, c) in otherCounts) { + ndf[lenCDR3]!! += l + ndf[payload]!! += other + ndf[count]!! += c + } + + ndf.sort(count, descending = true) + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt new file mode 100644 index 000000000..061854d6b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt @@ -0,0 +1,12 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup +import org.jetbrains.dataframe.DataFrame + +/** + * + */ +object Util { + +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java index 58082632b..2a9d74f2b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java @@ -36,6 +36,8 @@ public SpectratypeAggregator(int nTopClones, SpectratypeKeyFunction key = keyFunction.getKey(obj); + if (key == null) + return; Payload payload = key.payload; double weight = weightFunction.weight(obj); Count count = new Count<>(payload, weight); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt new file mode 100644 index 000000000..1acbc0ca9 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt @@ -0,0 +1,14 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import org.junit.Test + + +/** + * + */ +internal class BoxPlotsTest { + @Test + fun name() { + println("privet") + } +} From 6fe16db637e0432af955f2f73ac02576fa9c75c8 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 4 Oct 2021 17:07:17 +0300 Subject: [PATCH 116/282] second wip --- .../mixcr/postanalysis/plots/BoxPlots.kt | 101 ------------ .../mixcr/postanalysis/plots/Heatmap.kt | 87 ---------- .../mixcr/postanalysis/plots/Plots.kt | 66 -------- .../mixcr/postanalysis/plots/SpectraPlots.kt | 152 ------------------ .../mixcr/postanalysis/plots/Util.kt | 12 -- .../mixcr/postanalysis/plots/BoxPlotsTest.kt | 14 -- 6 files changed, 432 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt delete mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt deleted file mode 100644 index d6cc60153..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlots.kt +++ /dev/null @@ -1,101 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema -import jetbrains.datalore.plot.PlotSvgExport -import jetbrains.letsPlot.Pos -import jetbrains.letsPlot.geom.geomBoxplot -import jetbrains.letsPlot.geom.geomPoint -import jetbrains.letsPlot.intern.toSpec -import jetbrains.letsPlot.label.ggtitle -import jetbrains.letsPlot.label.labs -import jetbrains.letsPlot.letsPlot -import jetbrains.letsPlot.theme -import org.apache.batik.transcoder.TranscoderInput -import org.apache.batik.transcoder.TranscoderOutput -import org.apache.fop.render.ps.EPSTranscoder -import org.apache.fop.svg.PDFTranscoder -import org.apache.pdfbox.io.MemoryUsageSetting -import org.apache.pdfbox.multipdf.PDFMergerUtility -import java.io.ByteArrayInputStream -import java.io.ByteArrayOutputStream -import java.nio.file.Path -import kotlin.io.path.absolutePathString -import kotlin.io.path.writeBytes - -/** - * - */ -object BoxPlots { - fun individualBoxPlots( - destination: Path, - paSett: PostanalysisSchema<*>, - paResult: PostanalysisResult, - group: String, - metadata: Map? = null - ) { - - // metricName -> list (sample, value) - val metrics = mutableMapOf>>() - for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { - for ((sampleId, allMetrics) in charData.data) { - for (metricValue in allMetrics.data) { - val metricName = metricValue.key.toString() - val samples = metrics.computeIfAbsent(metricName) { mutableListOf() } - samples.add(sampleId to metricValue.value) - } - } - } - - val svgs = metrics.map { (metric, data) -> - var plt = letsPlot(mapOf("y" to data.map { it.second })) { - y = "y" - } - plt += geomBoxplot() - plt += geomPoint( - position = Pos.jitterdodge, - shape = 21, - color = "black" - ) - plt += ggtitle(metric) - plt += labs(y = metric) - plt += theme().axisTitleXBlank() - plt += theme().axisTextXBlank() - plt += theme().axisTicksXBlank() - - PlotSvgExport.buildSvgImageFromRawSpecs(plt.toSpec()) - } - - writePDF(destination, svgs.map { toPdf(it) }) - } - - fun toPdf(svg: String) = toVector(svg, ExportType.PDF) - fun toEPS(svg: String) = toVector(svg, ExportType.EPS) - - enum class ExportType { PDF, EPS } - - private fun toVector(svg: String, type: ExportType) = run { - val pdfTranscoder = if (type == ExportType.PDF) PDFTranscoder() else EPSTranscoder() - val input = TranscoderInput(ByteArrayInputStream(svg.toByteArray())) - ByteArrayOutputStream().use { byteArrayOutputStream -> - val output = TranscoderOutput(byteArrayOutputStream) - pdfTranscoder.transcode(input, output) - byteArrayOutputStream.toByteArray() - } - } - - fun writeEPS(destination: Path, image: ByteArray) { - destination.writeBytes(image) - } - - fun writePDF(destination: Path, images: List) { - val merger = PDFMergerUtility() - merger.destinationFileName = destination.absolutePathString() - - for (image in images) { - merger.addSource(ByteArrayInputStream(image)) - } - - merger.mergeDocuments(MemoryUsageSetting.setupMainMemoryOnly()) - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt deleted file mode 100644 index 4d49377eb..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt +++ /dev/null @@ -1,87 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey -import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema -import jetbrains.datalore.plot.PlotSvgExport -import jetbrains.letsPlot.* -import jetbrains.letsPlot.geom.geomBar -import jetbrains.letsPlot.intern.toSpec -import jetbrains.letsPlot.label.ggtitle -import jetbrains.letsPlot.label.labs -import jetbrains.letsPlot.scale.scaleXDiscrete -import java.nio.file.Path - -/** - * - */ -object Heatmap { - private const val x = "l" - private const val y = "p" - private const val w = "c" - private const val other = "Other" - - private fun mkDf() = mutableMapOf>( - x to mutableListOf(), - y to mutableListOf(), - w to mutableListOf() - ) - - - fun vUsage( - destination: Path, - paSett: PostanalysisSchema<*>, - paResult: PostanalysisResult, - group: String - ) { - - // x - sample, y - gene - val df = mkDf() - for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { - for ((sampleId, keys) in charData.data) { - for (metric in keys.data) { - @Suppress("UNCHECKED_CAST") - val key = metric.key as SpectratypeKey - df[x]!! += sampleId - df[y]!! += key.payload - df[w]!! += metric.value - } - } - } - - -// val svgs = samples.map { (sample, idf) -> -// val df = SpectraPlots.filter( -// idf, -// normalize = normalize, -// nTop = nTop -// ) -// -// var plt = letsPlot(df) -// plt += geomBar(position = Pos.stack, stat = Stat.identity, width = 0.6) { -// x = asDiscrete(SpectraPlots.lenCDR3, order = 1) -// y = SpectraPlots.count -// fill = asDiscrete(SpectraPlots.payload, orderBy = SpectraPlots.count, order = -1) -// } -// plt += ggtitle(sample) -// plt += labs(y = "Clone count", x = "CDR3 length, bp") -// -// val breaks = df[SpectraPlots.lenCDR3]!! -// .map { it as Int } -// .sorted() -// .distinct() -// -// plt += scaleXDiscrete( -// breaks = breaks, -// labels = breaks.map { if (it % 3 == 0) it.toString() else "" }, -// limits = limits?.toList() -// ) -// plt += ggsize(1000, 500) -// -// PlotSvgExport.buildSvgImageFromRawSpecs(plt.toSpec()) -// } -// -// BoxPlots.writePDF(destination, svgs.map { BoxPlots.toPdf(it) }) - } - -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt deleted file mode 100644 index 3ab101150..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Plots.kt +++ /dev/null @@ -1,66 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult - -typealias MutableDataFrame = MutableMap> -typealias DataFrame = Map> - -fun emptyDataFrame() = mutableMapOf>() -fun emptyDataFrame(colNames: List) = run { - val df = emptyDataFrame() - for (colName in colNames) { - df[colName] = mutableListOf() - } - df -} - -//fun MutableDataFrame.toDataFrame(): DataFrame = this.mapValues { (_, v) -> v.toList() }.toMap() - -fun DataFrame.nRows() = if (this.isEmpty()) 0 else this.values.first().size -fun DataFrame.nCols() = this.size - -fun DataFrame.colNames() = this.map { (k, _) -> k }.toList() - -fun DataFrame.rows() = run { - val rows = mutableListOf>() - for (i in 0 until nRows()) { - rows += this.map { (_, v) -> v[i] }.toList() - } - rows -} - -fun fromRows(colNames: List, rows: List>) = run { - val df = emptyDataFrame(colNames) - for (row in rows) { - for (i in row.indices) { - df[colNames[i]]!! += row[i] - } - } - df -} - -fun DataFrame.sort(col: String, descending: Boolean = false) = run { - val rows = rows() - val colNames = colNames() - val iCol = colNames.indexOf(col) - if (descending) - rows.sortByDescending { it[iCol] as Comparable } - else - rows.sortBy { it[iCol] as Comparable } - fromRows(colNames, rows) -} - - -fun DataFrame.sort(col: String, comparator: Comparator) = run { - val rows: MutableList> = rows() - val colNames = colNames() - val iCol = colNames.indexOf(col) - rows.sortWith { a, b -> - comparator.compare(a[iCol], b[iCol]) - } - fromRows(colNames, rows) -} - - diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt deleted file mode 100644 index 6d0f381f0..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SpectraPlots.kt +++ /dev/null @@ -1,152 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey -import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema -import jetbrains.datalore.plot.PlotSvgExport -import jetbrains.letsPlot.* -import jetbrains.letsPlot.geom.geomBar -import jetbrains.letsPlot.intern.toSpec -import jetbrains.letsPlot.label.ggtitle -import jetbrains.letsPlot.label.labs -import jetbrains.letsPlot.scale.scaleXDiscrete -import org.jetbrains.dataframe.annotations.DataSchema -import org.jetbrains.dataframe.columns.DataColumn -import org.jetbrains.dataframe.sortBy -import org.jetbrains.dataframe.toDataFrame -import java.nio.file.Path - -/** - * - */ - -object SpectraPlots { - private const val lenCDR3 = "l" - private const val payload = "p" - private const val count = "c" - private const val other = "Other" - - @DataSchema - interface Row { - val sample: String - val len: Int - val payload: String - val count: Double - } - - private fun mkDf() = mutableMapOf>( - lenCDR3 to mutableListOf(), - payload to mutableListOf(), - count to mutableListOf() - ) - - fun singleSpectra( - destination: Path, - paSett: PostanalysisSchema<*>, - paResult: PostanalysisResult, - group: String, - nTop: Int = 20, - limits: IntRange? = null, - normalize: Boolean = true - ) { - - // sample -> dataframe - val samples = mutableMapOf>>() - - for ((_, charData) in paResult.forGroup(paSett.getGroup>(group)).data) { - for ((sampleId, keys) in charData.data) { - val df = samples.computeIfAbsent(sampleId) { mkDf() } - for (metric in keys.data) { - @Suppress("UNCHECKED_CAST") - val key = metric.key as SpectratypeKey - df[lenCDR3]!! += key.length - df[payload]!! += (key.payload ?: other).toString() - df[count]!! += metric.value - } - } - } - - - val svgs = samples.map { (sample, idf) -> - val df = filter( - idf, - normalize = normalize, - nTop = nTop - ) - - var plt = letsPlot(df) - plt += geomBar(position = Pos.stack, stat = Stat.identity, width = 0.6) { - x = asDiscrete(lenCDR3, order = 1) - y = count - fill = asDiscrete(payload, orderBy = count, order = -1) - } - plt += ggtitle(sample) - plt += labs(y = "Clone count", x = "CDR3 length, bp") - - val breaks = df[lenCDR3]!! - .map { it as Int } - .sorted() - .distinct() - - plt += scaleXDiscrete( - breaks = breaks, - labels = breaks.map { if (it % 3 == 0) it.toString() else "" }, - limits = limits?.toList() - ) - plt += ggsize(1000, 500) - - PlotSvgExport.buildSvgImageFromRawSpecs(plt.toSpec()) - } - - BoxPlots.writePDF(destination, svgs.map { BoxPlots.toPdf(it) }) - } - - @Suppress("UNCHECKED_CAST") - fun filter(df: DataFrame, normalize: Boolean = true, nTop: Int = 10) = run { - val top = df[payload]!!.zip(df[count]!!) - .groupingBy { it.first as String } - .fold(0.0) { acc: Double, el -> acc + el.second as Double } - .toList() - .sortedBy { it.second } - .map { it.first } - .distinct() - .takeLast(nTop) - .toSet() - - - val totalCount = if (normalize) - df[count]!!.map { it as Double }.sum() - else - 1.0 - - val ndf = mkDf() - val otherCounts = mutableMapOf() - for (i in 0 until df.nRows()) { - val l = df[lenCDR3]!![i] as Int - val p = df[payload]!![i] - val c = (df[count]!![i] as Double) / totalCount - if (!top.contains(p)) - otherCounts[l] = (otherCounts[l] ?: 0.0) + c - else { - ndf[lenCDR3]!! += l - ndf[payload]!! += p - ndf[count]!! += c - } - } - - val ll = ndf[lenCDR3]!!.map { it as Int }.sorted().distinct() - val min = ll.minOrNull() ?: 0 - val max = ll.maxOrNull() ?: 0 - - for (l in (min..max)) - otherCounts.putIfAbsent(l, 0.0) - - for ((l, c) in otherCounts) { - ndf[lenCDR3]!! += l - ndf[payload]!! += other - ndf[count]!! += c - } - - ndf.sort(count, descending = true) - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt deleted file mode 100644 index 061854d6b..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt +++ /dev/null @@ -1,12 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup -import org.jetbrains.dataframe.DataFrame - -/** - * - */ -object Util { - -} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt deleted file mode 100644 index 1acbc0ca9..000000000 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BoxPlotsTest.kt +++ /dev/null @@ -1,14 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import org.junit.Test - - -/** - * - */ -internal class BoxPlotsTest { - @Test - fun name() { - println("privet") - } -} From be7993dd91dfbad9e0b9c9f59c02fa2e6b719df8 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 22 Oct 2021 14:25:49 +0300 Subject: [PATCH 117/282] wip --- build.gradle.kts | 1 + .../mixcr/cli/CommandPostanalysisPlots.java | 10 +- .../mixcr/postanalysis/dataframe/GeneUsage.kt | 178 ++++++++++++++++++ .../dataframe/SimpleStatistics.kt | 9 +- .../dataframe/SingleSpectratype.kt | 2 +- .../mixcr/postanalysis/dataframe/Util.kt | 4 + .../dataframe/SingleSpectratypeTest.kt | 70 +++++++ .../DiversityCharacteristicTest.java | 1 + 8 files changed, 263 insertions(+), 12 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt diff --git a/build.gradle.kts b/build.gradle.kts index 4752d0aff..fbf36d48d 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -93,6 +93,7 @@ dependencies { implementation("org.apache.xmlgraphics:fop-transcoder:2.6") implementation("org.apache.pdfbox:pdfbox:2.0.21") + implementation("org.apache.commons:commons-csv:1.9.0") implementation("org.jetbrains.kotlinx:dataframe:0.8.0-dev-339-0.10.0.260") implementation("org.jetbrains.lets-plot:lets-plot-common:$letsPlotLibraryVersion") implementation("org.jetbrains.lets-plot:lets-plot-kotlin-jvm:$letsPlotKotlinApiVersion") diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java index 8757d7dc3..5b76d8578 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java @@ -1,8 +1,7 @@ package com.milaboratory.mixcr.cli; +import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsage; import com.milaboratory.mixcr.postanalysis.dataframe.SingleSpectratype; -import com.milaboratory.mixcr.postanalysis.plots.BoxPlots; -import com.milaboratory.mixcr.postanalysis.plots.SpectraPlots; import com.milaboratory.util.GlobalObjectMappers; import picocli.CommandLine; @@ -22,16 +21,15 @@ public class CommandPostanalysisPlots extends ACommandWithOutputMiXCR { public void run0() throws Exception { CommandPostanalysis.PostanalysisData data = GlobalObjectMappers.PRETTY.readValue(new File(in), CommandPostanalysis.PostanalysisData.class); + GeneUsage.INSTANCE.plotPDF(Path.of("vUsage.pdf"), + data.schema, data.result, "vUsage"); SingleSpectratype.INSTANCE.plotPDF(Path.of(out + "spectra.pdf"), data.schema, data.result, "VSpectratype", SingleSpectratype.SpectratypePlotSettings.Companion.getDefault()); - SpectraPlots.INSTANCE.singleSpectra(Path.of(out + "spectraApp.pdf"), - data.schema, data.result, "VSpectratype", 20, null, true); - BoxPlots.INSTANCE.individualBoxPlots(Path.of(out), - data.schema, data.result, "cdr3Properties", null); + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt new file mode 100644 index 000000000..229447699 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt @@ -0,0 +1,178 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow.Companion.gene +import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow.Companion.sample +import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow.Companion.weight +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema +import jetbrains.datalore.plot.PlotSvgExport +import jetbrains.letsPlot.coordCartesian +import jetbrains.letsPlot.coordFixed +import jetbrains.letsPlot.geom.geomTile +import jetbrains.letsPlot.intern.Plot +import jetbrains.letsPlot.intern.toSpec +import jetbrains.letsPlot.letsPlot +import jetbrains.letsPlot.scale.scaleSizeIdentity +import jetbrains.letsPlot.scale.scaleXDiscrete +import jetbrains.letsPlot.scale.scaleYDiscrete +import jetbrains.letsPlot.theme +import org.jetbrains.dataframe.* +import org.jetbrains.dataframe.annotations.DataSchema +import org.jetbrains.dataframe.columns.DataColumn +import org.jetbrains.dataframe.io.writeCSV +import java.nio.file.Path + + +/** + * DataFrame row for V or J usage data + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +interface GeneUsageRow { + /** Sample ID */ + val sample: String + + /** Payload (Gene) */ + val gene: String + + /** Payload weight */ + val weight: Double + + companion object { + ////// DSL + + val sample by column() + val gene by column() + val weight by column() + + val DataFrame.sample get() = this[GeneUsageRow::sample.name] as DataColumn + val DataRow.sample get() = this[GeneUsageRow::sample.name] as String + + val DataFrame.gene get() = this[GeneUsageRow::gene.name] as DataColumn + val DataRow.gene get() = this[GeneUsageRow::gene.name] as String + + val DataFrame.weight get() = this[GeneUsageRow::weight.name] as DataColumn + val DataRow.weight get() = this[GeneUsageRow::weight.name] as Double + } +} + +object GeneUsage { + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String + ) = run { + + val data = mutableMapOf>( + GeneUsageRow::sample.name to mutableListOf(), + GeneUsageRow::gene.name to mutableListOf(), + GeneUsageRow::weight.name to mutableListOf(), + ) + + for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { + for ((sampleId, keys) in charData.data) { + for (metric in keys.data) { + val key = metric.key.toString() + data[GeneUsageRow::sample.name]!! += sampleId + data[GeneUsageRow::gene.name]!! += key + data[GeneUsageRow::weight.name]!! += metric.value + } + } + } + + data.toDataFrame().typed() + } + + /** + * Create Plot + **/ + fun DataFrame.plot() = run { + var plt = letsPlot(toMap()) { + x = GeneUsageRow::gene.name + y = GeneUsageRow::sample.name + fill = GeneUsageRow::weight.name + } + + writeCSV("data.csv") + val xValues = this.gene.toList() + val yValues = this.sample.toList() + + plt += geomTile( +// sampling = samplingNone, +// size = 0.0, +// width = xValues.size * 40.0, +// height = yValues.size * 40.0 + ) + +// plt += scaleFillGradient() +// plt += ggsize(1024, 1024) + + addCommonParams(plt, xValues, yValues, true) + } + + /////// from CorrPlot + private fun addCommonParams( + plot: Plot, + xValues: List, + yValues: List, + onlyTiles: Boolean + ): Plot { + @Suppress("NAME_SHADOWING") + var plot = plot + plot += theme() + .axisTitleBlank() + .axisLineBlank() + + plot += scaleSizeIdentity(naValue = 0, guide = "none") + + val expand = listOf(0.0, 0.0) + plot += scaleXDiscrete(breaks = xValues, limits = xValues, expand = expand) + plot += scaleYDiscrete( + breaks = yValues, + limits = yValues, + expand = expand + ) + + val xLim = Pair(-0.6, xValues.size - 1 + 0.6) + val yLim = Pair(-0.6, yValues.size - 1 + 0.6) + if (onlyTiles) { + plot += coordCartesian(xlim = xLim, ylim = yLim) + } else { + plot += coordFixed(xlim = xLim, ylim = yLim) + } + return plot + } + + /** + * Export plot to PDF + * + * @param destination path to export PDF + */ + fun DataFrame.plotPDF( + destination: Path + ) = run { + writePDF( + destination, + toPdf(PlotSvgExport.buildSvgImageFromRawSpecs(plot().toSpec())) + ) + } + + /** + * Create and export plot into single PDF file + * + * @param destination path to export PDF + * @param paSett PA settings + * @param paResult PA results + * */ + fun plotPDF( + destination: Path, + paSett: PostanalysisSchema<*>, + paResult: PostanalysisResult, + group: String + ) { + dataFrame(paSett, paResult, group).plotPDF(destination) + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt index b1f767587..98b963466 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt @@ -27,12 +27,11 @@ interface SimpleMetricsRow { val sample by column() - val DataFrame.sample get() = this[SpectratypeRow::sample.name] as DataColumn - val DataRow.sample get() = this[SpectratypeRow::sample.name] as String + val DataFrame.sample get() = this[SimpleMetricsRow::sample.name] as DataColumn + val DataRow.sample get() = this[SimpleMetricsRow::sample.name] as String } } - object SimpleStatistics { /** * Imports data into DataFrame @@ -44,7 +43,7 @@ object SimpleStatistics { ) = run { val data = mutableMapOf>( - SpectratypeRow::sample.name to mutableListOf(), + SimpleMetricsRow::sample.name to mutableListOf(), ) for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { @@ -69,7 +68,7 @@ object SimpleStatistics { } /** - * Creates plot spec + * Create Plot **/ fun DataFrame.plot( metric: String, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt index d3db33c17..56e0197ae 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt @@ -126,7 +126,7 @@ object SingleSpectratype { } /** - * Creates plot spec for specific sample + * Creates Plot for sample * * @param sample sample * @param settings plot settings diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt index 764b9ed65..4f49f0ce9 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt @@ -31,6 +31,10 @@ fun writeEPS(destination: Path, image: ByteArray) { destination.writeBytes(image) } +fun writePDF(destination: Path, vararg images: ByteArray) { + writePDF(destination, images.toList()) +} + fun writePDF(destination: Path, images: List) { val merger = PDFMergerUtility() merger.destinationFileName = destination.absolutePathString() diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt new file mode 100644 index 000000000..4aacd4654 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt @@ -0,0 +1,70 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import jetbrains.datalore.plot.PlotSvgExport +import jetbrains.letsPlot.coordFixed +import jetbrains.letsPlot.geom.geomBoxplot +import jetbrains.letsPlot.geom.geomTile +import jetbrains.letsPlot.ggsize +import jetbrains.letsPlot.intern.toSpec +import jetbrains.letsPlot.letsPlot +import jetbrains.letsPlot.scale.scaleXContinuous +import jetbrains.letsPlot.scale.scaleYContinuous +import org.jetbrains.dataframe.DataFrame +import org.jetbrains.dataframe.io.readCSV +import org.jetbrains.dataframe.toMap +import org.junit.Test +import java.nio.file.Path + + +/** + * + */ +internal class SingleSpectratypeTest { + @Test + fun name1() { + val data = + DataFrame.readCSV("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") + val mData = data.head(1000).toMap() + val plot = letsPlot(mData) { + x = "sample" + y = "gene" + fill = "weight" + } + geomTile(color = "white") + coordFixed() + + writePDF( + Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( + PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) + ) + ) + } + + @Test + fun name() { + val data = + DataFrame.readCSV("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") + + val mData = data.head(1000).toMap() + val xs = mData["sample"]!!.toList().distinct().size + val ys = mData["gene"]!!.toList().distinct().size + val f = 25 + + println(xs * f + 5 * f) + println(ys * f) + val plot = letsPlot(mData) { + x = "sample" + y = "gene" + fill = "weight" + } + geomTile(color = "white") + + scaleXContinuous(expand = listOf(0.0, 0.0)) + + scaleYContinuous(expand = listOf(0.0, 0.0)) + + coordFixed() + + ggsize(xs * f + 5 * f, 3 * ys * f / 5) + + + writePDF( + Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( + PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) + ) + ) + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index 796291d2c..582b467ae 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -9,6 +9,7 @@ import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResultCell; import com.milaboratory.mixcr.postanalysis.ui.GroupSummary; +import com.milaboratory.util.RandomUtil; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; import org.junit.Assert; From b12115c63357ab179832a4277f32432fd78b064e Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 10 Nov 2021 23:35:48 +0300 Subject: [PATCH 118/282] 10x WIP --- build.gradle.kts | 9 +- .../assembler/fullseq/FullSeqAssembler.java | 2 +- .../mixcr/basictypes/ClnAWriter.java | 420 +++++++++--------- .../mixcr/basictypes/VDJCAlignments.java | 6 +- .../milaboratory/mixcr/cli/AlignerReport.java | 25 ++ .../milaboratory/mixcr/cli/CommandAlign.java | 76 +++- .../mixcr/cli/CommandAssemble.java | 26 +- .../milaboratory/mixcr/cli/CommandExtend.java | 9 +- .../java/com/milaboratory/mixcr/cli/Main.java | 4 +- .../PartialAlignmentsAssembler.java | 6 +- .../mixcr/tags/DropletCloneGraph.java | 1 - .../mixcr/tags/WhitelistReader.java | 53 +++ .../vdjaligners/VDJCAlignerParameters.java | 11 +- .../vdjaligners/VDJCAlignmentFailCause.java | 4 +- .../vdjaligners/VDJCAlignmentResult.java | 27 +- src/main/resources/10x-3M-february-2018.bin | Bin 0 -> 38626 bytes src/main/resources/10x-737K-august-2016.bin | Bin 0 -> 7330 bytes .../mixcr/tags/WhitelistPackerTest.java | 93 ++++ 18 files changed, 505 insertions(+), 267 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java create mode 100644 src/main/resources/10x-3M-february-2018.bin create mode 100644 src/main/resources/10x-737K-august-2016.bin create mode 100644 src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java diff --git a/build.gradle.kts b/build.gradle.kts index 867392d42..76b522bdb 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -1,6 +1,6 @@ +import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar import com.palantir.gradle.gitversion.VersionDetails import groovy.lang.Closure -import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar import java.net.InetAddress plugins { @@ -14,6 +14,8 @@ plugins { val miRepoAccessKeyId: String by project val miRepoSecretAccessKey: String by project +val productionBuild: Boolean? by project + val versionDetails: Closure by extra val gitDetails = versionDetails() @@ -61,8 +63,8 @@ repositories { } } -val milibVersion = "1.14.1-16-774c60afab" -val repseqioVersion = "1.3.5-4-f7170dd23b" +val milibVersion = "1.14.1-18-f7ca543948" +val repseqioVersion = "1.3.5-5-2d9bf3f814" val jacksonVersion = "2.12.4" dependencies { @@ -90,6 +92,7 @@ val writeBuildProperties by tasks.registering(WriteProperties::class) { property("revision", gitDetails.gitHash) property("branch", gitDetails.branchName ?: "no_branch") property("host", InetAddress.getLocalHost().hostName) + property("production", productionBuild == true) property("timestamp", System.currentTimeMillis()) } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 6b4aad0b4..b139032b5 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -1423,8 +1423,8 @@ public RawVariantsData calculateRawData(Supplier> ali i = 0; int groupCounter = 0; for (VDJCAlignments al : CUtils.it(alignments.get())) { - TagTuple tagTuple = al.getTagCounter().singleOrNull(); if (taggedAnalysis()) { + TagTuple tagTuple = al.getTagCounter().singleOrNull(); int grp = tagTupleToGroup.get(tagTuple); if (grp == -1) { grp = groupCounter++; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index de6976be8..e19a81445 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -83,6 +83,8 @@ public final class ClnAWriter implements PipelineConfigurationWriter, */ static final PrimitivIOBlockHeader ALIGNMENT_BLOCK_SEPARATOR = PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, (byte) 1); + private final Object sync = new Object(); + /** * Will be used for alignments pre-sorting */ @@ -144,243 +146,249 @@ public ClnAWriter(PipelineConfiguration configuration, File file, boolean highCo /** * Step 1 */ - public synchronized void writeClones(CloneSet cloneSet) { - // Checking state - if (cloneIds != null) - throw new IllegalArgumentException("Clone block was already written."); - - // Saving VDJC gene list - this.usedGenes = cloneSet.getUsedGenes(); - - // Writing header in raw primitivio mode - try (PrimitivO o = this.output.beginPrimitivO(true)) { - - // Writing number of clones ahead of any other content to make it available - // in a known file position (MAGIC_LENGTH) - o.writeInt(cloneSet.size()); - - // Writing version information - o.writeUTF(MiXCRVersionInfo.get() - .getVersionString(AppVersionInfo.OutputType.ToFile)); - - // Writing full pipeline configuration - o.writeObject(configuration); - - // Writing aligner parameters - Objects.requireNonNull(cloneSet.alignmentParameters); - o.writeObject(cloneSet.alignmentParameters); - featureToAlignProvider = cloneSet.alignmentParameters; - - // Writing assembler parameters and cloneset ordering - o.writeObject(cloneSet.assemblerParameters); - o.writeObject(cloneSet.ordering); - - // During deserialization, the same procedure (in the same order) will be applied to - // the PrimitivI object, so that correct singleton objects (GeneFeature objects and sequences) will be - // deserialized from reference records. - // The GeneFeature objects and corresponding nucleotide sequences from all - // genes in analysis will be added to the set of known references of PrimitivO object - // so that they will be serialized as 1-2 byte reference records (see PrimitivIO implementation). - IOUtil.stdVDJCPrimitivOStateInit(o, usedGenes, cloneSet); - - // Saving stream position of the first clone object - // this value will be written at the very end of the file - positionOfFirstClone = output.getPosition(); - - // Saving number of clones - numberOfClones = cloneSet.size(); - } - - try (PrimitivOBlocks.Writer writer = this.output - .beginPrimitivOBlocks(4, 1024, - PrimitivIOBlocksUtil.getCompressor(highCompression))) { - // Writing clones - for (Clone clone : cloneSet) { - writer.write(clone); - // For progress reporting - ++numberOfClonesWritten; + public void writeClones(CloneSet cloneSet) { + synchronized (sync) { + // Checking state + if (cloneIds != null) + throw new IllegalArgumentException("Clone block was already written."); + + // Saving VDJC gene list + this.usedGenes = cloneSet.getUsedGenes(); + + // Writing header in raw primitivio mode + try (PrimitivO o = this.output.beginPrimitivO(true)) { + + // Writing number of clones ahead of any other content to make it available + // in a known file position (MAGIC_LENGTH) + o.writeInt(cloneSet.size()); + + // Writing version information + o.writeUTF(MiXCRVersionInfo.get() + .getVersionString(AppVersionInfo.OutputType.ToFile)); + + // Writing full pipeline configuration + o.writeObject(configuration); + + // Writing aligner parameters + Objects.requireNonNull(cloneSet.alignmentParameters); + o.writeObject(cloneSet.alignmentParameters); + featureToAlignProvider = cloneSet.alignmentParameters; + + // Writing assembler parameters and cloneset ordering + o.writeObject(cloneSet.assemblerParameters); + o.writeObject(cloneSet.ordering); + + // During deserialization, the same procedure (in the same order) will be applied to + // the PrimitivI object, so that correct singleton objects (GeneFeature objects and sequences) will be + // deserialized from reference records. + // The GeneFeature objects and corresponding nucleotide sequences from all + // genes in analysis will be added to the set of known references of PrimitivO object + // so that they will be serialized as 1-2 byte reference records (see PrimitivIO implementation). + IOUtil.stdVDJCPrimitivOStateInit(o, usedGenes, cloneSet); + + // Saving stream position of the first clone object + // this value will be written at the very end of the file + positionOfFirstClone = output.getPosition(); + + // Saving number of clones + numberOfClones = cloneSet.size(); } - writer.flush(); - } // will synchronize here (on close method invocation) - // Saving ids; also tells other methods that clones block was written successful - TIntHashSet ids = new TIntHashSet(cloneSet.getClones().stream().mapToInt(c -> c.id).toArray()); - ids.add(-1); - this.cloneIds = ids; + try (PrimitivOBlocks.Writer writer = this.output + .beginPrimitivOBlocks(4, 1024, + PrimitivIOBlocksUtil.getCompressor(highCompression))) { + // Writing clones + for (Clone clone : cloneSet) { + writer.write(clone); + // For progress reporting + ++numberOfClonesWritten; + } + writer.flush(); + } // will synchronize here (on close method invocation) + + // Saving ids; also tells other methods that clones block was written successful + TIntHashSet ids = new TIntHashSet(cloneSet.getClones().stream().mapToInt(c -> c.id).toArray()); + ids.add(-1); + this.cloneIds = ids; + } } /** * Step 2 */ - public synchronized void collateAlignments(OutputPort alignments, - long numberOfAlignments) throws IOException { - // Checking state - if (cloneIds == null) - throw new IllegalStateException("Write clones before writing alignments."); - if (collatedAlignments != null) - throw new IllegalStateException("Alignments are already sorted."); - - // Saving number of alignments - this.numberOfAlignments = numberOfAlignments; - - // Dirty heuristic to optimize trade-off between memory usage and number of random access places in a file - // to read from - int chunkSize = (int) Math.min(Math.max(16384, numberOfAlignments / 8), 1048576); - - // Sorting alignments by cloneId and then by mapping type (core alignments will be written before all others) - // and saving sorting output port - this.toCollator = new CountingOutputPort<>(alignments); - - // Optimize serialization of genes and corresponding subject sequences from alignments - PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); - IOUtil.registerGeneReferences(stateBuilder, usedGenes, featureToAlignProvider); - - // HDD-offloading collator of alignments - // Collate solely by cloneId (no sorting by mapping type, etc.); - // less fields to sort by -> faster the procedure - long memoryBudget = - Runtime.getRuntime().maxMemory() > 10_000_000_000L /* -Xmx10g */ - ? Runtime.getRuntime().maxMemory() / 4L /* 1 Gb */ - : 1 << 28 /* 256 Mb */; - collator = new HashSorter<>( - VDJCAlignments.class, - new CloneIdHash(), CloneIdComparator, - 5, tempFolder, 4, 6, - stateBuilder.getOState(), stateBuilder.getIState(), - memoryBudget, 1 << 18 /* 256 Kb */); - - // Here we wait for the first layer of hash collation to finish "write" stage - // (on average 30% time of full collation process) - // following steps are executed as needed during port reading - this.collatedAlignments = collator.port(toCollator); + public void collateAlignments(OutputPort alignments, + long numberOfAlignments) throws IOException { + synchronized (sync) { + // Checking state + if (cloneIds == null) + throw new IllegalStateException("Write clones before writing alignments."); + if (collatedAlignments != null) + throw new IllegalStateException("Alignments are already sorted."); + + // Saving number of alignments + this.numberOfAlignments = numberOfAlignments; + + // Dirty heuristic to optimize trade-off between memory usage and number of random access places in a file + // to read from + int chunkSize = (int) Math.min(Math.max(16384, numberOfAlignments / 8), 1048576); + + // Sorting alignments by cloneId and then by mapping type (core alignments will be written before all others) + // and saving sorting output port + this.toCollator = new CountingOutputPort<>(alignments); + + // Optimize serialization of genes and corresponding subject sequences from alignments + PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); + IOUtil.registerGeneReferences(stateBuilder, usedGenes, featureToAlignProvider); + + // HDD-offloading collator of alignments + // Collates solely by cloneId (no sorting by mapping type, etc.); + // less fields to sort by -> faster the procedure + long memoryBudget = + Runtime.getRuntime().maxMemory() > 10_000_000_000L /* -Xmx10g */ + ? Runtime.getRuntime().maxMemory() / 4L /* 1 Gb */ + : 1 << 28 /* 256 Mb */; + collator = new HashSorter<>( + VDJCAlignments.class, + new CloneIdHash(), CloneIdComparator, + 5, tempFolder, 4, 6, + stateBuilder.getOState(), stateBuilder.getIState(), + memoryBudget, 1 << 18 /* 256 Kb */); + + // Here we wait for the first layer of hash collation to finish "write" stage + // (on average 30% time of full collation process) + // following steps are executed as needed during port reading + this.collatedAlignments = collator.port(toCollator); + } } /** * Step 3 */ - public synchronized void writeAlignmentsAndIndex() { - // Checking state - if (collatedAlignments == null) - throw new IllegalStateException("Call sortAlignments before this method."); - if (finished) - throw new IllegalStateException("Writer already closed."); - - // Indices that will be written below all alignments - final TLongArrayList aBlockOffset = new TLongArrayList(); - final TLongArrayList aBlockCount = new TLongArrayList(); - final TIntArrayList cloneIdsIndex = new TIntArrayList(); - long previousAlsCount = 0; - int currentCloneIndex = Integer.MIN_VALUE; - long indexBeginOffset; - - try (PrimitivOBlocks.Writer o = output.beginPrimitivOBlocks( - Math.min(4, Runtime.getRuntime().availableProcessors()), // TODO parametrize - VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK, - PrimitivIOBlocksUtil.getCompressor(highCompression))) { - - // Writing alignments and writing indices - VDJCAlignments alignments; - while (true) { - alignments = collatedAlignments.take(); - - // End of clone group or first alignment - if (alignments == null || currentCloneIndex != alignments.cloneIndex) { - if (currentCloneIndex != Integer.MIN_VALUE) { // Not first alignment - // Async flush - o.flush(); - o.writeHeader(ALIGNMENT_BLOCK_SEPARATOR); + public void writeAlignmentsAndIndex() { + synchronized (sync) { + // Checking state + if (collatedAlignments == null) + throw new IllegalStateException("Call sortAlignments before this method."); + if (finished) + throw new IllegalStateException("Writer already closed."); + + // Indices that will be written below all alignments + final TLongArrayList aBlockOffset = new TLongArrayList(); + final TLongArrayList aBlockCount = new TLongArrayList(); + final TIntArrayList cloneIdsIndex = new TIntArrayList(); + long previousAlsCount = 0; + int currentCloneIndex = Integer.MIN_VALUE; + long indexBeginOffset; + + try (PrimitivOBlocks.Writer o = output.beginPrimitivOBlocks( + Math.min(4, Runtime.getRuntime().availableProcessors()), // TODO parametrize + VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK, + PrimitivIOBlocksUtil.getCompressor(highCompression))) { + + // Writing alignments and writing indices + VDJCAlignments alignments; + while (true) { + alignments = collatedAlignments.take(); + + // End of clone group or the first alignment + if (alignments == null || currentCloneIndex != alignments.cloneIndex) { + if (currentCloneIndex != Integer.MIN_VALUE) { // Not first alignment + // Async flush + o.flush(); + o.writeHeader(ALIGNMENT_BLOCK_SEPARATOR); + } + + // No synchronization here + + if (alignments != null && !cloneIds.remove(alignments.cloneIndex)) + throw new IllegalArgumentException("Alignment for a wrong clonotype " + + alignments.cloneIndex); + + // Write stream position as soon as all the blocks are flushed + // This will be the start position for the next block + o.run(c -> { + // In theory synchronization for aBlockOffset access here is not required as all IO + // operations as well as this code are executed strictly sequentially + + // synchronized (aBlockOffset){ + aBlockOffset.add(((HasPosition) c).getPosition()); + // } + }); + + aBlockCount.add(numberOfAlignmentsWritten - previousAlsCount); + previousAlsCount = numberOfAlignmentsWritten; + + if (alignments == null) + break; + + // Saving clone groups sequence + cloneIdsIndex.add(alignments.cloneIndex); + currentCloneIndex = alignments.cloneIndex; } - // No synchronization here - - if (alignments != null && !cloneIds.remove(alignments.cloneIndex)) - throw new IllegalArgumentException("Alignment for a wrong clonotype " + - alignments.cloneIndex); + o.write(alignments); + ++numberOfAlignmentsWritten; + } - // Write stream position as soon as all the blocks are flushed - // This will be the start position for the next block - o.run(c -> { - // In theory synchronization for aBlockOffset access here is not required as all IO - // operations as well as this code are executed strictly sequentially + if (!(cloneIds.isEmpty() || + (cloneIds.size() == 1 && cloneIds.iterator().next() == -1))) + throw new IllegalArgumentException("Some clones have no alignments."); - // synchronized (aBlockOffset){ - aBlockOffset.add(((HasPosition) c).getPosition()); - // } - }); + // Waiting for all alignments to be flushed to the file to read file position + o.sync(); - aBlockCount.add(numberOfAlignmentsWritten - previousAlsCount); - previousAlsCount = numberOfAlignmentsWritten; + assert aBlockOffset.size() == aBlockCount.size() + && aBlockCount.size() == cloneIdsIndex.size() + 1 + // there may be no alignments with cloneId == -1 + && (numberOfClones + 1 == cloneIdsIndex.size() || numberOfClones == cloneIdsIndex.size()); - if (alignments == null) - break; + // o.close() will additionally write EOF header + indexBeginOffset = o.getPosition() + PrimitivIOBlockHeader.HEADER_SIZE; - // Saving clone groups sequence - cloneIdsIndex.add(alignments.cloneIndex); - currentCloneIndex = alignments.cloneIndex; + // Print IO stat + if (MiXCRDebug.DEBUG) { + System.out.println("==== IO ClnAWriter: Collator ====="); + collator.printStat(); + System.out.println("==== IO ClnAWriter ====="); + System.out.println(o.getParent().getStats()); } - - o.write(alignments); - ++numberOfAlignmentsWritten; } - if (!(cloneIds.isEmpty() || - (cloneIds.size() == 1 && cloneIds.iterator().next() == -1))) - throw new IllegalArgumentException("Some clones have no alignments."); - - // Waiting for all alignments to be flushed to the file to read file position - o.sync(); - - assert aBlockOffset.size() == aBlockCount.size() - && aBlockCount.size() == cloneIdsIndex.size() + 1 - // there may be no alignments with cloneId == -1 - && (numberOfClones + 1 == cloneIdsIndex.size() || numberOfClones == cloneIdsIndex.size()); + // Closing sorted the output port, this will delete intermediate collation files + collatedAlignments.close(); - // o.close() will additionally write EOF header - indexBeginOffset = o.getPosition() + PrimitivIOBlockHeader.HEADER_SIZE; - - // Print IO stat - if (MiXCRDebug.DEBUG) { - System.out.println("==== IO ClnAWriter: Collator ====="); - collator.printStat(); - System.out.println("==== IO ClnAWriter ====="); - System.out.println(o.getParent().getStats()); - } - } + // Saving index offset in file to write in the end of the stream + long previousValue = 0; + try (PrimitivO o = output.beginPrimitivO()) { // TODO also use blocks ? + // Writing index size + o.writeVarInt(aBlockOffset.size()); - // Closing sorted the output port, this will delete intermediate collation files - collatedAlignments.close(); + // Writing both indices + for (int i = 0; i < aBlockOffset.size(); i++) { + long iValue = aBlockOffset.get(i); + // Writing offset index using deltas to save space + // (smaller values are represented by less number of bytes in VarLong representation) + o.writeVarLong(iValue - previousValue); + previousValue = iValue; - // Saving index offset in file to write in the end of the stream - long previousValue = 0; - try (PrimitivO o = output.beginPrimitivO()) { // TODO also use blocks ? - // Writing index size - o.writeVarInt(aBlockOffset.size()); + o.writeVarLong(aBlockCount.get(i)); - // Writing both indices - for (int i = 0; i < aBlockOffset.size(); i++) { - long iValue = aBlockOffset.get(i); - // Writing offset index using deltas to save space - // (smaller values are represented by less number of bytes in VarLong representation) - o.writeVarLong(iValue - previousValue); - previousValue = iValue; + if (i != aBlockOffset.size() - 1) + o.writeVarInt(cloneIdsIndex.get(i)); + } - o.writeVarLong(aBlockCount.get(i)); + // Writing two key positions in a file + // This values will be using during deserialization to find certain blocks + o.writeLong(positionOfFirstClone); + o.writeLong(indexBeginOffset); - if (i != aBlockOffset.size() - 1) - o.writeVarInt(cloneIdsIndex.get(i)); + // Writing end-magic as a file integrity sign + o.write(IOUtil.getEndMagicBytes()); } - // Writing two key positions in a file - // This values will be using during deserialization to find certain blocks - o.writeLong(positionOfFirstClone); - o.writeLong(indexBeginOffset); - - // Writing end-magic as a file integrity sign - o.write(IOUtil.getEndMagicBytes()); + // Setting finished flag (will stop progress reporting) + finished = true; } - - // Setting finished flag (will stop progress reporting) - finished = true; } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 270e38999..d94159829 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -107,8 +107,10 @@ public VDJCAlignments(VDJCHit[] vHits, VDJCHit[] dHits, VDJCHit[] jHits, VDJCHit this(-1, createHits(vHits, dHits, jHits, cHits), tagCounter, targets, history, originalReads); } - public VDJCAlignments shiftIndelsAtHomopolymers() { - return mapHits(h -> h.mapAlignments(AlignmentUtils::shiftIndelsAtHomopolymers)); + public VDJCAlignments shiftIndelsAtHomopolymers(Set geneTypes) { + return mapHits(h -> geneTypes.contains(h.getGeneType()) + ? h.mapAlignments(AlignmentUtils::shiftIndelsAtHomopolymers) + : h); } public VDJCAlignments mapHits(Function mapper) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 179a3c20d..91aa7b2bd 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -46,6 +46,8 @@ public final class AlignerReport extends AbstractCommandReport implements VDJCAl private final ChainUsageStats chainStats = new ChainUsageStats(); private final AtomicLongArray fails = new AtomicLongArray(VDJCAlignmentFailCause.values().length); private final AtomicLong successes = new AtomicLong(0); + // private final AtomicLong droppedNoBarcode = new AtomicLong(0); + // private final AtomicLong droppedBarcodeNotInWhitelist = new AtomicLong(0); private final AtomicLong chimeras = new AtomicLong(0); private final AtomicLong alignedSequenceOverlap = new AtomicLong(0); private final AtomicLong alignedAlignmentOverlap = new AtomicLong(0); @@ -137,6 +139,16 @@ public long getSuccesses() { return successes.get(); } + // @JsonProperty("droppedNoBarcode") + // public long getDroppedNoBarcode() { + // return droppedNoBarcode.get(); + // } + // + // @JsonProperty("droppedBarcodeNotInWhitelist") + // public long getDroppedBarcodeNotInWhitelist() { + // return droppedBarcodeNotInWhitelist.get(); + // } + @JsonProperty("alignmentAidedOverlaps") public long getAlignmentOverlaps() { return alignedAlignmentOverlap.get(); @@ -187,6 +199,14 @@ public long getRealignedWithForcedNonFloatingLeftBoundInRightRead() { return realignedWithForcedNonFloatingLeftBoundInRightRead.get(); } + // public void onNoBarcode(SequenceRead read) { + // droppedNoBarcode.incrementAndGet(); + // } + // + // public void onBarcodeNotInWhitelist(SequenceRead read) { + // droppedBarcodeNotInWhitelist.incrementAndGet(); + // } + @Override public void onFailedAlignment(SequenceRead read, VDJCAlignmentFailCause cause) { fails.incrementAndGet(cause.ordinal()); @@ -275,6 +295,11 @@ public void writeReport(ReportHelper helper) { helper.writeField("Total sequencing reads", total); helper.writePercentAndAbsoluteField("Successfully aligned reads", success, total); + // if (getDroppedBarcodeNotInWhitelist() != 0 || getDroppedNoBarcode() != 0) { + // helper.writePercentAndAbsoluteField("Absent barcode", getDroppedNoBarcode(), total); + // helper.writePercentAndAbsoluteField("Barcode not in whitelist", getDroppedBarcodeNotInWhitelist(), total); + // } + if (getChimeras() != 0) helper.writePercentAndAbsoluteField("Chimeras", getChimeras(), total); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 655c6e2d8..06573b8d4 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -31,6 +31,7 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.Processor; import cc.redberry.pipe.blocks.Merger; import cc.redberry.pipe.blocks.ParallelProcessor; import cc.redberry.pipe.util.Chunk; @@ -49,6 +50,7 @@ import com.milaboratory.core.io.sequence.SequenceRead; import com.milaboratory.core.io.sequence.SequenceReaderCloseable; import com.milaboratory.core.io.sequence.SequenceWriter; +import com.milaboratory.core.io.sequence.SingleRead; import com.milaboratory.core.io.sequence.fasta.FastaReader; import com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper; import com.milaboratory.core.io.sequence.fastq.PairedFastqReader; @@ -56,15 +58,14 @@ import com.milaboratory.core.io.sequence.fastq.SingleFastqReader; import com.milaboratory.core.io.sequence.fastq.SingleFastqWriter; import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.core.sequence.ShortSequenceSet; import com.milaboratory.core.sequence.quality.QualityTrimmerParameters; import com.milaboratory.core.sequence.quality.ReadTrimmerProcessor; import com.milaboratory.core.sequence.quality.ReadTrimmerReport; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.tags.WhitelistReader; import com.milaboratory.mixcr.util.MiXCRVersionInfo; -import com.milaboratory.mixcr.vdjaligners.VDJCAligner; -import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; -import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult; -import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; +import com.milaboratory.mixcr.vdjaligners.*; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.SmartProgressReporter; @@ -221,9 +222,14 @@ public void setSaveOriginalReads(boolean b) { names = {"--buffers"}, hidden = true) public boolean reportBuffers = false; - @Option(description = "Names for groups that contain barcodes, for MiNNN FASTQ input file.", - names = {"--tag"}) - public List tags = new ArrayList<>(); + // @Option(description = "Names for groups that contain barcodes, for MiNNN FASTQ input file.", + // names = {"--tag"}) + // public List tags = new ArrayList<>(); + + @Option(description = "Specify this option for 10x datasets to extract cell and UMI barcode information from " + + "the first read", + names = {"--10x"}) + public boolean tenX = false; private VDJCAlignerParameters vdjcAlignerParameters = null; @@ -354,7 +360,7 @@ public ActionConfiguration getConfiguration() { use = JsonTypeInfo.Id.CLASS, include = JsonTypeInfo.As.PROPERTY, property = "type") - public static class AlignConfiguration implements ActionConfiguration { + public static class AlignConfiguration implements ActionConfiguration { /** * Aligner parameters */ @@ -452,7 +458,7 @@ private QualityTrimmerParameters getQualityTrimmerParameters() { } @Override - @SuppressWarnings("unchecked") + @SuppressWarnings({"unchecked", "rawtypes"}) public void run1() throws Exception { // Saving initial timestamp long beginTimestamp = System.currentTimeMillis(); @@ -528,6 +534,9 @@ else if (featureSequence.containsWildcards()) // Attaching report to aligner aligner.setEventsListener(report); + if (tenX && !isInputPaired()) + throwValidationException("Option \"--10x\" requires paired-end input data"); + try (SequenceReaderCloseable reader = createReader(); VDJCAlignmentsWriter writer = getOutput().equals(".") @@ -569,7 +578,37 @@ else if (featureSequence.containsWildcards()) report.setTrimmingReport(rep); } - ParallelProcessor alignedChunks = new ParallelProcessor(mainInputReadsPreprocessed, chunked(aligner), Math.max(16, threads), threads); + // Creating processor from aligner + Processor> processor = aligner; + if (tenX) { + final ShortSequenceSet whitelist = WhitelistReader.Whitelist10X2016(); + final Processor> oldProcessor = processor; + processor = input -> { + SingleRead r1 = input.getRead(0); + NucleotideSequence seq = r1.getData().getSequence(); + if (seq.size() < 26) { + report.onFailedAlignment(input, VDJCAlignmentFailCause.NoBarcode); + return new VDJCAlignmentResult(input); + } + + if (!whitelist.contains(seq.getRange(0, 16))) { + report.onFailedAlignment(input, VDJCAlignmentFailCause.BarcodeNotInWhitelist); + return new VDJCAlignmentResult(input); + } + + String seqString = seq.toString(); + TagTuple tt = new TagTuple(seqString.substring(0, 16), seqString.substring(16, 26)); + + SequenceRead trimmed = input.mapReadsWithIndex((index, val) -> index == 0 + ? val.mapSequence(s -> s.getRange(26, s.size())) + : val); + + VDJCAlignmentResult alignmentResult = oldProcessor.process(trimmed); + return alignmentResult.withTagTuple(tt); + }; + } + + ParallelProcessor alignedChunks = new ParallelProcessor(mainInputReadsPreprocessed, chunked(processor), Math.max(16, threads), threads); if (reportBuffers) { System.out.println("Analysis threads: " + threads); StatusReporter reporter = new StatusReporter(); @@ -581,7 +620,7 @@ else if (featureSequence.containsWildcards()) @Override public void updateStatus() { - status = "Busy encoders: " + writer.getBusyEncoders() + " / " + writer.getEncodersCount(); + status = "Busy encoders: " + Objects.requireNonNull(writer).getBusyEncoders() + " / " + writer.getEncodersCount(); isClosed = writer.isClosed(); } @@ -597,19 +636,20 @@ public String getStatus() { }); reporter.start(); } + + Set genesToShiftIndels = alignerParameters.getGeneTypesWithLinearScoring(); OutputPort alignments = unchunked( CUtils.wrap(alignedChunks, - CUtils.chunked(VDJCAlignmentResult::shiftIndelsAtHomopolymers))); + CUtils.chunked( + a -> a.shiftIndelsAtHomopolymers(genesToShiftIndels)))); for (VDJCAlignmentResult result : CUtils.it(new OrderedOutputPort<>(alignments, o -> o.read.getId()))) { VDJCAlignments alignment = result.alignment; SequenceRead read = result.read; if (alignment == null) { - if (writeAllResults) - // Creating empty alignment object if alignment for current read failed - { + if (writeAllResults) { // Creating empty alignment object if alignment for current read failed Target target = readsLayout.createTargets(read)[0]; alignment = new VDJCAlignments(emptyHits, - TagCounter.EMPTY, + result.tagTuple == null ? TagCounter.EMPTY : new TagCounter(result.tagTuple), target.targets, SequenceHistory.RawSequence.of(read.getId(), target), alignerParameters.isSaveOriginalReads() ? new SequenceRead[]{read} : null); @@ -620,8 +660,8 @@ public String getStatus() { } } - if (!tags.isEmpty()) - alignment = alignment.setTagCounter(new TagCounter(parseTags(this.spec.commandLine(), tags, read))); + if (result.tagTuple != null) + alignment = alignment.setTagCounter(new TagCounter(result.tagTuple)); if (alignment.isChimera()) report.onChimera(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index ec65fa6db..f5710dc7b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -256,29 +256,6 @@ public void run1() throws Exception { PipelineConfiguration pipelineConfiguration = getFullPipelineConfiguration(); if (clna) { - -// -// try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(alignmentsProvider.create(), -// assembler.getAssembledReadsPort())) { -// -// VDJCAlignments al; -// while ((al = merged.take()) != null) { -// if (al.getCloneIndex() != -1) -// continue; -// -// TagCounter tg = al.getTagCounter(); -// assert tg.size() == 1; -// TagTuple tags = tg.iterator().key(); -// if (al.getBestHit(GeneType.Variable) != null) { -// TagSignature sig = new TagSignature(tags, al.getBestHit(GeneType.Variable).getGene().getId()); -// Integer cloneId = tagsToClones.get(sig); -// if (cloneId != null) { -// -// } -// } -// } -// } - try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, highCompression)) { // writer will supply current stage and completion percent to the progress reporter SmartProgressReporter.startProgressReport(writer); @@ -321,7 +298,7 @@ public void run1() throws Exception { || al.getFeature(new GeneFeature(assemblerParameters.getAssemblingFeatures())) != null) // Dropped but has assembling feature return al; - // <-- Only dropped alignments + // <-- Only dropped alignments not covering CDR3 TagCounter tg = al.getTagCounter(); assert tg.size() == 1; // Both "align" and "assemblePartial" produces such alignments @@ -346,6 +323,7 @@ public void run1() throws Exception { if (cloneMapping >= 0) { report.onReadAttachedByTags(); + // TODO add count return setMappingCloneIndex(al, cloneMapping); } else if (cloneMapping == -2) report.onReadWithAmbiguousAttachmentsByTags(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index b4c7f2f7e..f90c59dfa 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -45,15 +45,13 @@ import com.milaboratory.mixcr.util.VDJCObjectExtender; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.Chains; +import io.repseq.core.GeneType; import io.repseq.core.ReferencePoint; import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.io.IOException; -import java.util.ArrayList; -import java.util.Comparator; -import java.util.List; -import java.util.Objects; +import java.util.*; import static com.milaboratory.mixcr.basictypes.IOUtil.*; import static com.milaboratory.mixcr.cli.CommandExtend.EXTEND_COMMAND_NAME; @@ -176,8 +174,9 @@ void processVDJCA() throws IOException { reader.getParameters().getVAlignerParameters().getParameters().getScoring(), reader.getParameters().getJAlignerParameters().getParameters().getScoring()); + Set genesToShiftIndels = reader.getParameters().getGeneTypesWithLinearScoring(); for (VDJCAlignments alignments : CUtils.it(new OrderedOutputPort<>(process.getOutput(), VDJCAlignments::getAlignmentsIndex))) - writer.write(alignments.shiftIndelsAtHomopolymers()); + writer.write(alignments.shiftIndelsAtHomopolymers(genesToShiftIndels)); writer.setNumberOfProcessedReads(reader.getNumberOfReads()); process.finish(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 311b77646..19ca4308e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -105,8 +105,8 @@ public static CommandLine mkCmd() { String command = System.getProperty("mixcr.command", "java -jar mixcr.jar"); if (!initialized) { - // Checking whether we are running a snapshot version - if (!assertionsDisabled() && VersionInfo.getVersionInfoForArtifact("mixcr").getVersion().contains("SNAPSHOT")) + // Checking whether we are running a test version + if (!assertionsDisabled() && !VersionInfo.getVersionInfoForArtifact("mixcr").isProductionBuild()) // If so, enable asserts ClassLoader.getSystemClassLoader().setDefaultAssertionStatus(true); diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index ab38d18e2..291e979fd 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -48,6 +48,7 @@ import java.util.ArrayList; import java.util.List; import java.util.Objects; +import java.util.Set; import java.util.concurrent.atomic.AtomicLong; public class PartialAlignmentsAssembler implements AutoCloseable, Report { @@ -110,7 +111,10 @@ public boolean maxRightMatchesLimitReached() { return maxRightMatchesLimitReached; } + private Set geneTypesToShiftIndels; + public void buildLeftPartsIndex(VDJCAlignmentsReader reader) { + geneTypesToShiftIndels = reader.getParameters().getGeneTypesWithLinearScoring(); writer.header(reader.getParameters(), reader.getUsedGenes(), null); for (VDJCAlignments alignment : CUtils.it(reader)) { if (alignment.getFeature(GeneFeature.CDR3) != null) @@ -241,7 +245,7 @@ public void run() { overlapped.incrementAndGet(); totalWritten.incrementAndGet(); - writer.write(mAlignment.shiftIndelsAtHomopolymers()); + writer.write(mAlignment.shiftIndelsAtHomopolymers(geneTypesToShiftIndels)); // Saving alignment that where merge to prevent it's use as left part alreadyMergedIds.add(alignment.getAlignmentsIndex()); diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java index 985ec26d9..f42df7c68 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java @@ -193,7 +193,6 @@ public static List calculateGroups(CloneTagTupleList tuplesList, for (int i : topTagCliqueBits) tags.add(indexToTag.get(i)); - TIntIntHashMap indexToCloneId = newTIntIntHashMap(); // !!! used as cloneId -> count in the loop below TIntIntHashMap cloneIdToIndex = newTIntIntHashMap(); diff --git a/src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java b/src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java new file mode 100644 index 000000000..cf4f54cdd --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java @@ -0,0 +1,53 @@ +package com.milaboratory.mixcr.tags; + +import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.core.sequence.SequenceBuilder; +import com.milaboratory.core.sequence.ShortSequenceSet; +import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.blocks.PrimitivIOBlocksUtil; +import com.milaboratory.util.io.IOUtil; +import net.jpountz.lz4.LZ4FastDecompressor; +import org.apache.commons.io.IOUtils; + +import java.io.ByteArrayInputStream; +import java.io.IOException; +import java.io.InputStream; + +public class WhitelistReader { + public static ShortSequenceSet Whitelist10X2018() { + try (InputStream in = WhitelistReader.class.getResourceAsStream("/10x-3M-february-2018.bin")) { + return read10XCompressedWhitelist(IOUtils.toByteArray(in)); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + public static ShortSequenceSet Whitelist10X2016() { + try (InputStream in = WhitelistReader.class.getResourceAsStream("/10x-737K-august-2016.bin")) { + return read10XCompressedWhitelist(IOUtils.toByteArray(in)); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + static ShortSequenceSet read10XCompressedWhitelist(byte[] data) { + int uncompressedLen = IOUtil.readIntBE(data, data.length - 4); + int numElements = IOUtil.readIntBE(data, data.length - 8); + LZ4FastDecompressor decompressor = PrimitivIOBlocksUtil.defaultLZ4Decompressor(); + byte[] uncompressed = decompressor.decompress(data, 0, uncompressedLen); + + PrimitivI primitivI = new PrimitivI(new ByteArrayInputStream(uncompressed)); + ShortSequenceSet ret = new ShortSequenceSet(); + int c = 0; + for (int i = 0; i < numElements; i++) { + c += primitivI.readVarInt(); + SequenceBuilder seqBuilder = NucleotideSequence.ALPHABET.createBuilder(); + seqBuilder.ensureCapacity(16); + for (int j = 15; j >= 0; j--) { + seqBuilder.append((byte) ((c >>> (j << 1)) & 0x3)); + } + ret.add(seqBuilder.createAndDestroy()); + } + return ret; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java index a2107234f..a8743990e 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java @@ -30,8 +30,8 @@ package com.milaboratory.mixcr.vdjaligners; import com.fasterxml.jackson.annotation.*; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; import com.milaboratory.core.PairedEndReadsLayout; +import com.milaboratory.core.alignment.LinearGapAlignmentScoring; import com.milaboratory.core.merger.MergerParameters; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.HasFeatureToAlign; @@ -43,6 +43,8 @@ import java.util.EnumMap; import java.util.Map; import java.util.Objects; +import java.util.Set; +import java.util.stream.Collectors; @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE) @@ -194,6 +196,13 @@ public GeneAlignmentParameters getGeneAlignerParameters(GeneType geneType) { return alignmentParameters.get(geneType); } + public Set getGeneTypesWithLinearScoring() { + return alignmentParameters.entrySet().stream() + .filter(e -> e.getValue().getScoring() instanceof LinearGapAlignmentScoring) + .map(Map.Entry::getKey) + .collect(Collectors.toSet()); + } + public KGeneAlignmentParameters getVJCGeneAlignerParameters(GeneType geneType) { return (KGeneAlignmentParameters) getGeneAlignerParameters(geneType); } diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java index 3d108bec1..1c372a2a2 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java @@ -35,7 +35,9 @@ public enum VDJCAlignmentFailCause { NoVHits("Alignment failed because of absence of V hits"), NoJHits("Alignment failed because of absence of J hits"), VAndJOnDifferentTargets("No target with both V and J alignments"), - LowTotalScore("Alignment failed because of low total score"); + LowTotalScore("Alignment failed because of low total score"), + NoBarcode("Absent barcode"), + BarcodeNotInWhitelist("Barcode not in whitelist"); public final String reportLine; VDJCAlignmentFailCause(String reportLine) { diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java index b0a2dbe98..5a297ed26 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java @@ -30,25 +30,48 @@ package com.milaboratory.mixcr.vdjaligners; import com.milaboratory.core.io.sequence.SequenceRead; +import com.milaboratory.mixcr.basictypes.TagTuple; import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import io.repseq.core.GeneType; + +import java.util.Set; public final class VDJCAlignmentResult { public final R read; public final VDJCAlignments alignment; + public final TagTuple tagTuple; public VDJCAlignmentResult(R read, VDJCAlignments alignment) { this.read = read; this.alignment = alignment; + this.tagTuple = null; } public VDJCAlignmentResult(R read) { this.read = read; this.alignment = null; + this.tagTuple = null; + } + + public VDJCAlignmentResult(R read, TagTuple tagTuple) { + this.read = read; + this.alignment = null; + this.tagTuple = tagTuple; + } + + public VDJCAlignmentResult(R read, VDJCAlignments alignment, TagTuple tagTuple) { + this.read = read; + this.alignment = alignment; + this.tagTuple = tagTuple; + } + + public VDJCAlignmentResult withTagTuple(TagTuple tagTuple) { + return new VDJCAlignmentResult<>(read, alignment, tagTuple); } - public VDJCAlignmentResult shiftIndelsAtHomopolymers() { + public VDJCAlignmentResult shiftIndelsAtHomopolymers(Set geneTypes) { if (alignment == null) return this; - return new VDJCAlignmentResult<>(read, alignment.shiftIndelsAtHomopolymers()); + return new VDJCAlignmentResult<>(read, alignment.shiftIndelsAtHomopolymers(geneTypes), tagTuple); } } diff --git a/src/main/resources/10x-3M-february-2018.bin b/src/main/resources/10x-3M-february-2018.bin new file mode 100644 index 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/dev/null +++ b/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java @@ -0,0 +1,93 @@ +package com.milaboratory.mixcr.tags; + +import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.core.sequence.ShortSequenceSet; +import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.primitivio.blocks.PrimitivIOBlocksUtil; +import com.milaboratory.util.FormatUtils; +import com.milaboratory.util.IntArrayList; +import com.milaboratory.util.io.ByteArrayDataOutput; +import com.milaboratory.util.io.IOUtil; +import net.jpountz.lz4.LZ4Compressor; +import org.junit.Assert; +import org.junit.Ignore; +import org.junit.Test; + +import java.io.*; +import java.util.Arrays; + +public class WhitelistPackerTest { + public void importWL(String inputFile, String resourceName) throws IOException { + IntArrayList list = new IntArrayList(); + ShortSequenceSet expectedWhitelist = new ShortSequenceSet(); + System.out.println("Initial file size: " + FormatUtils.bytesToString(new File(inputFile).length())); + try ( + BufferedReader r = new BufferedReader(new InputStreamReader( + new FileInputStream(inputFile))) + ) { + String line; + while ((line = r.readLine()) != null) { + line = line.trim(); + if (line.length() == 0) + continue; + NucleotideSequence seq = new NucleotideSequence(line); + if (seq.size() != 16) + throw new IllegalArgumentException(); + + expectedWhitelist.add(seq); + + int barcodeInt = 0; + for (int i = 0; i < seq.size(); i++) { + byte nuc = seq.codeAt(i); + if (nuc > 3) + throw new IllegalArgumentException(); + barcodeInt <<= 2; + barcodeInt |= nuc; + } + list.add(barcodeInt); + } + } + + System.out.println("Data without delta-encoding: " + FormatUtils.bytesToString(expectedWhitelist.size() * 4L)); + list.sort(); + ByteArrayDataOutput bos = new ByteArrayDataOutput(); + PrimitivO o = new PrimitivO(bos); + int p = 0, c; + for (int i = 0; i < list.size(); i++) { + c = list.get(i); + o.writeVarInt(c - p); + p = c; + } + byte[] buffer = bos.getBuffer(); + System.out.println("Data before compression: " + FormatUtils.bytesToString(buffer.length)); + LZ4Compressor compressor = PrimitivIOBlocksUtil.highLZ4Compressor(); + byte[] compressed = compressor.compress(buffer); + compressed = Arrays.copyOf(compressed, compressed.length + 8); + IOUtil.writeIntBE(buffer.length, compressed, compressed.length - 4); + IOUtil.writeIntBE(list.size(), compressed, compressed.length - 8); + System.out.println("Data after compression: " + FormatUtils.bytesToString(compressed.length)); + + ShortSequenceSet whitelist = WhitelistReader.read10XCompressedWhitelist(compressed); + + try (FileOutputStream fos = new FileOutputStream("src/main/resources/" + resourceName)) { + fos.write(compressed); + } + + // System.out.println(whitelist.hashCode()); + // System.out.println(expectedWhitelist.hashCode()); + + Assert.assertEquals(expectedWhitelist, whitelist); + } + + // @Ignore + @Test + public void test1() throws IOException { + importWL("/Volumes/Data/Projects/MiLaboratory/data/10x/3M-february-2018.txt", "10x-3M-february-2018.bin"); + } + + @Ignore + @Test + public void test2() throws IOException { + importWL("/Volumes/Data/Projects/MiLaboratory/data/10x/737K-august-2016.txt", "10x-737K-august-2016.bin"); + } +} From 396825fb8fe417c44f1f3087d92b0983cf4eca30 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 1 Dec 2021 03:19:21 +0300 Subject: [PATCH 119/282] wip --- .../mixcr/cli/CommandExportPostanalysis.java | 68 ++++++ .../mixcr/cli/CommandPostanalysis.java | 195 ++++++++---------- .../mixcr/cli/CommandPostanalysisPlots.java | 35 ---- .../java/com/milaboratory/mixcr/cli/Main.java | 2 +- .../dataframe/SimpleStatistics.kt | 1 - 5 files changed, 158 insertions(+), 143 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java new file mode 100644 index 000000000..d15ecda54 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java @@ -0,0 +1,68 @@ +package com.milaboratory.mixcr.cli; + +import com.milaboratory.mixcr.cli.CommandPostanalysis.PaResult; +import com.milaboratory.mixcr.cli.CommandPostanalysis.PaResultByChain; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; +import com.milaboratory.mixcr.postanalysis.ui.OutputTable; +import com.milaboratory.util.GlobalObjectMappers; +import io.repseq.core.Chains; +import picocli.CommandLine; + +import java.io.File; +import java.nio.file.Paths; +import java.util.Map; + +/** + * + */ +public class CommandExportPostanalysis extends ACommandWithOutputMiXCR { + @CommandLine.Parameters(index = "0", description = "pa_result.json") + public String in; + @CommandLine.Parameters(index = "1", description = "plt_out") + public String out; + + void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { + for (CharacteristicGroupOutputExtractor view : tableResult.group.views) + for (OutputTable t : view.getTables(tableResult).values()) + t.writeTSV(Paths.get("").toAbsolutePath(), prefix + chain.name + "_"); + } + + +// +// private static String baseName(String fName) { +// fName = Paths.get(fName).toAbsolutePath().getFileName().toString(); +// int i = fName.lastIndexOf("."); +// if (i > 0) +// return fName.substring(0, i); +// else +// return fName; +// } + + @Override + public void run0() throws Exception { + PaResult data = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + + for (Map.Entry e : data.results.entrySet()) { + Chains chain = Chains.WELL_KNOWN_CHAINS_MAP.get(e.getKey()); + if (chain == null) { + throw new IllegalArgumentException(); + } + + PaResultByChain result = e.getValue(); + + for (CharacteristicGroup table : result.schema.tables) + writeTables(chain, result.result.getTable(table)); + } +// GeneUsage.INSTANCE.plotPDF(Path.of("vUsage.pdf"), +// data.schema, data.result, "vUsage"); +// +// SingleSpectratype.INSTANCE.plotPDF(Path.of(out + "spectra.pdf"), +// data.schema, data.result, "VSpectratype", +// SingleSpectratype.SpectratypePlotSettings.Companion.getDefault()); +// + + + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java index 3952c8e36..1033108fd 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.OutputPortCloseable; +import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.basictypes.*; @@ -39,6 +40,7 @@ import java.util.stream.Stream; import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; +import static io.repseq.core.Chains.*; import static java.util.stream.Collectors.*; /** @@ -61,11 +63,8 @@ public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { names = {"-c", "--chains"}) public String chains = "ALL"; - @Option(description = "Prefix for outputs", - names = {"-p", "--prefix"}) - public String prefix = ""; - - List inputs() { + @Override + protected List getInputFiles() { return inOut.subList(0, inOut.size() - 1) .stream() .flatMap(f -> { @@ -82,32 +81,20 @@ List inputs() { .collect(toList()); } - String output() { - return inOut.get(inOut.size() - 1); - } - - String output(Chains.NamedChains chain) { - return prefix + chain.name + "_" + output(); - } - - String outputBase() { - return output().replace(".json", ""); + @Override + protected List getOutputFiles() { + return Collections.singletonList(outputFile()); } - static String baseName(String fName) { - fName = Paths.get(fName).toAbsolutePath().getFileName().toString(); - int i = fName.lastIndexOf("."); - if (i > 0) - return fName.substring(0, i); - else - return fName; + String outputFile() { + return inOut.get(inOut.size() - 1); } - static int downsamplingValue(String downsampling) { - return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1, downsampling.length())); + private static int downsamplingValue(String downsampling) { + return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); } - static SetPreprocessorFactory parseDownsampling(String downsampling) { + private static SetPreprocessorFactory parseDownsampling(String downsampling) { if (downsampling.startsWith("umi-count")) { if (downsampling.endsWith("auto")) return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); @@ -144,15 +131,67 @@ SetPreprocessorFactory downsampling(String downsamplingStr) { return downsampling; } - void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { - for (CharacteristicGroupOutputExtractor view : tableResult.group.views) - for (OutputTable t : view.getTables(tableResult).values()) - t.writeTSV(Paths.get("").toAbsolutePath(), prefix + chain.name + "_"); + /** + * Resulting data written to disk + */ + @JsonAutoDetect + public static final class PaResult { + /** Results for individual chains */ + @JsonProperty("results") + public final Map results; + + @JsonCreator + public PaResult(@JsonProperty("results") Map results) { + this.results = results; + } } - ///////////////////////////////////////////// Individual ///////////////////////////////////////////// + /** + * Resulting data written to disk + */ + @JsonAutoDetect + public static final class PaResultByChain { + @JsonProperty("schema") + public final PostanalysisSchema schema; + @JsonProperty("result") + public final PostanalysisResult result; + + @JsonCreator + public PaResultByChain(@JsonProperty("schema") PostanalysisSchema schema, + @JsonProperty("result") PostanalysisResult result) { + this.schema = schema; + this.result = result; + } + } + + @Override + public void run0() throws Exception { + Map resultsMap = new HashMap<>(); + Chains c = Chains.parse(chains); + if (c.intersects(TRAD)) + resultsMap.put(TRAD_NAMED.name, run(TRAD)); + if (c.intersects(TRG)) + resultsMap.put(TRG_NAMED.name, run(TRG)); + if (c.intersects(Chains.TRB)) + resultsMap.put(TRB_NAMED.name, run(TRB)); + if (c.intersects(Chains.IGH)) + resultsMap.put(IGH_NAMED.name, run(Chains.IGH)); + if (c.intersects(Chains.IGKL)) + resultsMap.put(IGKL_NAMED.name, run(Chains.IGKL)); + + PaResult result = new PaResult(resultsMap); + try { + GlobalObjectMappers.PRETTY.writeValue(new File(outputFile()), result); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + abstract PaResultByChain run(Chains chain); + ///////////////////////////////////////////// Individual ///////////////////////////////////////////// + + @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") @CommandLine.Command(name = "individual", sortOptions = false, separator = " ", @@ -161,26 +200,12 @@ public static class CommandIndividual extends CommandPostanalysis { public CommandIndividual() {} @Override - public void run0() throws Exception { - Chains c = Chains.parse(chains); - if (c.intersects(Chains.TRAD)) - run(Chains.TRAD_NAMED); - if (c.intersects(Chains.TRG)) - run(Chains.TRG_NAMED); - if (c.intersects(Chains.TRB)) - run(Chains.TRB_NAMED); - if (c.intersects(Chains.IGH)) - run(Chains.IGH_NAMED); - if (c.intersects(Chains.IGKL)) - run(Chains.IGKL_NAMED); - } - @SuppressWarnings({"unchecked", "rawtypes"}) - void run(Chains.NamedChains chain) { + PaResultByChain run(Chains chain) { List> groups = new ArrayList<>(); SetPreprocessorFactory downsampling = downsampling() - .filterFirst(new ElementPredicate.IncludeChains(chain.chains)); + .filterFirst(new ElementPredicate.IncludeChains(chain)); groups.add(new CharacteristicGroup<>( "cdr3Properties", @@ -253,24 +278,15 @@ void run(Chains.NamedChains chain) { Collections.singletonList(new GroupSummary<>()))); PostanalysisSchema schema = new PostanalysisSchema<>(groups); - PostanalysisRunner runner = new PostanalysisRunner<>(); runner.addCharacteristics(schema.getAllCharacterisitcs()); - List datasets = inputs().stream() + List datasets = getInputFiles().stream() .map(file -> - new ClonotypeDataset(baseName(file), file, VDJCLibraryRegistry.getDefault()) + new ClonotypeDataset(file, file, VDJCLibraryRegistry.getDefault()) ).collect(Collectors.toList()); - PostanalysisResult result = runner.run(datasets); - for (CharacteristicGroup table : schema.tables) - writeTables(chain, result.getTable(table)); - - try { - GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), new PostanalysisData(schema, result)); - } catch (IOException e) { - throw new RuntimeException(e); - } + return new PaResultByChain(schema, runner.run(datasets)); } } @@ -289,43 +305,30 @@ public static class CommandOverlap extends CommandPostanalysis { public CommandOverlap() {} @Override - public void run0() throws Exception { - Chains c = Chains.parse(chains); - if (c.intersects(Chains.TRAD)) - run(Chains.TRAD_NAMED); - if (c.intersects(Chains.TRG)) - run(Chains.TRG_NAMED); - if (c.intersects(Chains.TRB)) - run(Chains.TRB_NAMED); - if (c.intersects(Chains.IGH)) - run(Chains.IGH_NAMED); - if (c.intersects(Chains.IGKL)) - run(Chains.IGKL_NAMED); - } - - void run(Chains.NamedChains chain) { - + @SuppressWarnings("unchecked") + PaResultByChain run(Chains chain) { SetPreprocessorFactory downsampling = downsampling(); - Map> map = new HashMap<>(); - map.put(OverlapType.D, downsampling); - map.put(OverlapType.F2, f2downsampling == null + Map> downsamplingByType = new HashMap<>(); + downsamplingByType.put(OverlapType.D, downsampling); + downsamplingByType.put(OverlapType.F2, f2downsampling == null ? downsampling : downsampling(f2downsampling)); - map.put(OverlapType.R_Intersection, downsampling); + downsamplingByType.put(OverlapType.R_Intersection, downsampling); List> ordering = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); OverlapPostanalysisSettings overlapPA = new OverlapPostanalysisSettings( ordering, new WeightFunctions.Count(), - map + downsamplingByType ); - PostanalysisSchema> schema = overlapPA.getSchema(inputs().size(), chain.chains); + PostanalysisSchema> schema = overlapPA.getSchema(getInputFiles().size(), chain); // Limits concurrency across all readers LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(32); - List readers = inputs().stream() + List readers = getInputFiles() + .stream() .map(s -> { try { return mkCheckedReader( @@ -338,22 +341,15 @@ void run(Chains.NamedChains chain) { .collect(Collectors.toList()); OverlapDataset overlapDataset = OverlapUtil.overlap( - inputs().stream().map(CommandPostanalysis::baseName) - .collect(toList()), - ordering, readers); + getInputFiles(), + ordering, + readers); PostanalysisRunner> runner = new PostanalysisRunner<>(); runner.addCharacteristics(schema.getAllCharacterisitcs()); PostanalysisResult result = runner.run(overlapDataset); - for (CharacteristicGroup> table : schema.tables) - writeTables(chain, result.getTable(table)); - - try { - GlobalObjectMappers.PRETTY.writeValue(new File(output(chain)), new PostanalysisData(schema, result)); - } catch (IOException e) { - throw new RuntimeException(e); - } + return new PaResultByChain(schema, result); } public static CloneReader mkCheckedReader(Path path, @@ -396,6 +392,7 @@ public void close() throws Exception { }; } + @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") static final class OverlapPostanalysisSettings { final List> ordering; final WeightFunction weight; @@ -445,18 +442,4 @@ public PostanalysisSchema> getSchema(int nSamples, Chains ch }) public static class CommandPostanalysisMain { } - - public static final class PostanalysisData { - @JsonProperty("schema") - public final PostanalysisSchema schema; - @JsonProperty("result") - public final PostanalysisResult result; - - @JsonCreator - public PostanalysisData(@JsonProperty("schema") PostanalysisSchema schema, - @JsonProperty("result") PostanalysisResult result) { - this.schema = schema; - this.result = result; - } - } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java deleted file mode 100644 index 5b76d8578..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysisPlots.java +++ /dev/null @@ -1,35 +0,0 @@ -package com.milaboratory.mixcr.cli; - -import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsage; -import com.milaboratory.mixcr.postanalysis.dataframe.SingleSpectratype; -import com.milaboratory.util.GlobalObjectMappers; -import picocli.CommandLine; - -import java.io.File; -import java.nio.file.Path; - -/** - * - */ -public class CommandPostanalysisPlots extends ACommandWithOutputMiXCR { - @CommandLine.Parameters(index = "0", description = "pa_result.json") - public String in; - @CommandLine.Parameters(index = "1", description = "plt_out") - public String out; - - @Override - public void run0() throws Exception { - CommandPostanalysis.PostanalysisData data = GlobalObjectMappers.PRETTY.readValue(new File(in), CommandPostanalysis.PostanalysisData.class); - - GeneUsage.INSTANCE.plotPDF(Path.of("vUsage.pdf"), - data.schema, data.result, "vUsage"); - - SingleSpectratype.INSTANCE.plotPDF(Path.of(out + "spectra.pdf"), - data.schema, data.result, "VSpectratype", - SingleSpectratype.SpectratypePlotSettings.Companion.getDefault()); - - - - - } -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 71958d216..e8052f1a6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -149,7 +149,7 @@ public static CommandLine mkCmd() { .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) .addSubcommand("postanalysis", CommandPostanalysis.CommandPostanalysisMain.class) - .addSubcommand("plot", CommandPostanalysisPlots.class) + .addSubcommand("plot", CommandExportPostanalysis.class) .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt index 98b963466..c143dc68e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt @@ -59,7 +59,6 @@ object SimpleStatistics { data.toDataFrame().typed() } - /** * Attaches metadata to statistics **/ From b1d1c4306eb9f808213be588df99193102336f92 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 16 Dec 2021 18:19:24 +0300 Subject: [PATCH 120/282] wip --- build.gradle.kts | 3 +- .../mixcr/cli/CommandExportPostanalysis.java | 117 +++++++++---- .../mixcr/cli/CommandPostanalysis.java | 67 ++++--- .../java/com/milaboratory/mixcr/cli/Main.java | 5 + .../mixcr/postanalysis/dataframe/GeneUsage.kt | 16 +- .../dataframe/SimpleStatistics.kt | 163 +++++++++++++++--- .../dataframe/SingleSpectratype.kt | 22 ++- 7 files changed, 290 insertions(+), 103 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index fbf36d48d..0063f9c49 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -69,6 +69,7 @@ val repseqioVersion = "1.3.5-4-f7170dd23b" val jacksonVersion = "2.12.4" val letsPlotLibraryVersion = "2.1.0" val letsPlotKotlinApiVersion = "3.0.3-alpha1" +val dataframeVersion = "0.8.0-dev-777-0.11.0.39" dependencies { api("com.milaboratory:milib:$milibVersion") @@ -94,7 +95,7 @@ dependencies { implementation("org.apache.pdfbox:pdfbox:2.0.21") implementation("org.apache.commons:commons-csv:1.9.0") - implementation("org.jetbrains.kotlinx:dataframe:0.8.0-dev-339-0.10.0.260") + implementation("org.jetbrains.kotlinx:dataframe:$dataframeVersion") implementation("org.jetbrains.lets-plot:lets-plot-common:$letsPlotLibraryVersion") implementation("org.jetbrains.lets-plot:lets-plot-kotlin-jvm:$letsPlotKotlinApiVersion") } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java index d15ecda54..2ffb5e273 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java @@ -1,7 +1,9 @@ package com.milaboratory.mixcr.cli; +import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.CommandPostanalysis.PaResult; import com.milaboratory.mixcr.cli.CommandPostanalysis.PaResultByChain; +import com.milaboratory.mixcr.postanalysis.dataframe.SimpleStatistics; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; @@ -9,60 +11,113 @@ import com.milaboratory.util.GlobalObjectMappers; import io.repseq.core.Chains; import picocli.CommandLine; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import java.nio.file.Paths; import java.util.Map; /** * */ -public class CommandExportPostanalysis extends ACommandWithOutputMiXCR { - @CommandLine.Parameters(index = "0", description = "pa_result.json") +public abstract class CommandExportPostanalysis extends ACommandWithOutputMiXCR { + @Option(names = {"-m", "--metadata"}, description = "Metadata file") + public String metadata; + @Parameters(index = "0", description = "pa_result.json") public String in; - @CommandLine.Parameters(index = "1", description = "plt_out") + @Parameters(index = "1", description = "output") public String out; - void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { - for (CharacteristicGroupOutputExtractor view : tableResult.group.views) - for (OutputTable t : view.getTables(tableResult).values()) - t.writeTSV(Paths.get("").toAbsolutePath(), prefix + chain.name + "_"); + /** Check that directory */ + private void ensureChainsDirExists(Chains.NamedChains chains) { + try { + Files.createDirectory(Paths.get(chains.name)); + } catch (IOException e) { + throwExecutionException(e.getMessage()); + } + } + + + Path outPath(Chains.NamedChains chains, String suffix) { + return Paths.get(chains.name).resolve(suffix); } + /** Cached PA result */ + private PaResult paResult = null; -// -// private static String baseName(String fName) { -// fName = Paths.get(fName).toAbsolutePath().getFileName().toString(); -// int i = fName.lastIndexOf("."); -// if (i > 0) -// return fName.substring(0, i); -// else -// return fName; -// } + /** Get full PA result */ + PaResult getPaResult() { + try { + if (paResult != null) + return paResult; + return paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + } catch (IOException e) { + throwValidationException("Broken input file: " + in); + return null; + } + } @Override public void run0() throws Exception { - PaResult data = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + for (Map.Entry r : getPaResult().results.entrySet()) { + ensureChainsDirExists(r.getKey()); + run(r.getKey(), r.getValue()); + } + } - for (Map.Entry e : data.results.entrySet()) { - Chains chain = Chains.WELL_KNOWN_CHAINS_MAP.get(e.getKey()); - if (chain == null) { - throw new IllegalArgumentException(); + abstract void run(Chains.NamedChains chains, PaResultByChain result); + + static final class ExportTables extends CommandExportPostanalysis { + @Override + void run(Chains.NamedChains chains, PaResultByChain result) { + for (CharacteristicGroup table : result.schema.tables) { + writeTables(chains, result.result.getTable(table)); } + } + + void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { + for (CharacteristicGroupOutputExtractor view : tableResult.group.views) + for (OutputTable t : view.getTables(tableResult).values()) + t.writeTSV(Paths.get(chain.name).toAbsolutePath(), ""); + } + } + + static final class ExportBoxPlots extends CommandExportPostanalysis { + @Option(names = {"-p", "--primary-group"}, description = "Primary group") + public String primaryGroup; + @Option(names = {"-s", "--secondary-group"}, description = "Secondary group") + public String secondaryGroup; - PaResultByChain result = e.getValue(); + @Override + void run(Chains.NamedChains chains, PaResultByChain result) { + CharacteristicGroup biophysics = result.schema.getGroup(CommandPostanalysis.Biophysics); - for (CharacteristicGroup table : result.schema.tables) - writeTables(chain, result.result.getTable(table)); + SimpleStatistics.INSTANCE.plotPDF(outPath(chains, "biophysics.pdf"), + result.result.forGroup(biophysics), + null, + SimpleStatistics.BoxPlotSettings.Companion.getDefault() + ); + + CharacteristicGroup diversity = result.schema.getGroup(CommandPostanalysis.Diversity); + SimpleStatistics.INSTANCE.plotPDF(outPath(chains, "diversity.pdf"), + result.result.forGroup(diversity), + null, + SimpleStatistics.BoxPlotSettings.Companion.getDefault() + ); } -// GeneUsage.INSTANCE.plotPDF(Path.of("vUsage.pdf"), -// data.schema, data.result, "vUsage"); -// -// SingleSpectratype.INSTANCE.plotPDF(Path.of(out + "spectra.pdf"), -// data.schema, data.result, "VSpectratype", -// SingleSpectratype.SpectratypePlotSettings.Companion.getDefault()); -// + } + @CommandLine.Command(name = "exportPostanalysis", + separator = " ", + description = "Export postanalysis results.", + subcommands = { + CommandLine.HelpCommand.class + }) + public static class CommandExportPostanalysisMain { } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java index 1033108fd..2dceba915 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java @@ -4,6 +4,8 @@ import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.postanalysis.*; import com.milaboratory.mixcr.postanalysis.additive.AAProperties; @@ -138,10 +140,12 @@ SetPreprocessorFactory downsampling(String downsamplingStr) { public static final class PaResult { /** Results for individual chains */ @JsonProperty("results") - public final Map results; + @JsonSerialize(keyUsing = KnownChainsKeySerializer.class) + @JsonDeserialize(keyUsing = KnownChainsKeyDeserializer.class) + public final Map results; @JsonCreator - public PaResult(@JsonProperty("results") Map results) { + public PaResult(@JsonProperty("results") Map results) { this.results = results; } } @@ -166,19 +170,12 @@ public PaResultByChain(@JsonProperty("schema") PostanalysisSchema schema, @Override public void run0() throws Exception { - Map resultsMap = new HashMap<>(); + Map resultsMap = new HashMap<>(); Chains c = Chains.parse(chains); - if (c.intersects(TRAD)) - resultsMap.put(TRAD_NAMED.name, run(TRAD)); - if (c.intersects(TRG)) - resultsMap.put(TRG_NAMED.name, run(TRG)); - if (c.intersects(Chains.TRB)) - resultsMap.put(TRB_NAMED.name, run(TRB)); - if (c.intersects(Chains.IGH)) - resultsMap.put(IGH_NAMED.name, run(Chains.IGH)); - if (c.intersects(Chains.IGKL)) - resultsMap.put(IGKL_NAMED.name, run(Chains.IGKL)); - + for (NamedChains knownChains : WELL_KNOWN_CHAINS) { + if (c.intersects(knownChains.chains)) + resultsMap.put(knownChains, run(knownChains.chains)); + } PaResult result = new PaResult(resultsMap); try { GlobalObjectMappers.PRETTY.writeValue(new File(outputFile()), result); @@ -191,6 +188,17 @@ public void run0() throws Exception { ///////////////////////////////////////////// Individual ///////////////////////////////////////////// + static final String + Biophysics = "biophysics", + Diversity = "diversity", + VUsage = "vUsage", + JUsage = "JUsage", + VJUsage = "VJUsage", + IsotypeUsage = "IsotypeUsage", + CDR3Spectratype = "CDR3Spectratype", + VSpectratype = "VSpectratype", + VSpectratypeMean = "VSpectratypeMean"; + @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") @CommandLine.Command(name = "individual", sortOptions = false, @@ -207,8 +215,7 @@ PaResultByChain run(Chains chain) { SetPreprocessorFactory downsampling = downsampling() .filterFirst(new ElementPredicate.IncludeChains(chain)); - groups.add(new CharacteristicGroup<>( - "cdr3Properties", + groups.add(new CharacteristicGroup<>(Biophysics, Arrays.asList( weightedLengthOf(downsampling, GeneFeature.CDR3, false).setName("CDR3 length, nt"), weightedLengthOf(downsampling, GeneFeature.CDR3, true).setName("CDR3 length, aa"), @@ -223,9 +230,8 @@ PaResultByChain run(Chains chain) { Arrays.asList(new GroupSummary<>()) )); - groups.add(new CharacteristicGroup<>( - "diversity", - Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), + groups.add(new CharacteristicGroup<>(Diversity, + Arrays.asList(new DiversityCharacteristic<>("Diversity", new WeightFunctions.Count(), downsampling, new DiversityMeasure[]{ DiversityMeasure.Observed, @@ -238,42 +244,35 @@ PaResultByChain run(Chains chain) { Arrays.asList(new GroupSummary<>()) )); - groups.add(new CharacteristicGroup<>( - "vUsage", + groups.add(new CharacteristicGroup<>(VUsage, Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Variable)), Arrays.asList(new GroupSummary<>()) )); - groups.add(new CharacteristicGroup<>( - "jUsage", + groups.add(new CharacteristicGroup<>(JUsage, Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Joining)), Arrays.asList(new GroupSummary<>()) )); - groups.add(new CharacteristicGroup<>( - "vjUsage", + groups.add(new CharacteristicGroup<>(VJUsage, Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(downsampling)), Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) )); - groups.add(new CharacteristicGroup<>( - "isotypeUsage", + groups.add(new CharacteristicGroup<>(IsotypeUsage, Arrays.asList(AdditiveCharacteristics.isotypeUsage(downsampling)), Arrays.asList(new GroupSummary<>()) )); - groups.add(new CharacteristicGroup<>( - "cdr3Spectratype", - Arrays.asList(new SpectratypeCharacteristic("cdr3Spectratype", + groups.add(new CharacteristicGroup<>(CDR3Spectratype, + Arrays.asList(new SpectratypeCharacteristic("CDR3 spectratype", downsampling, 10, new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), Collections.singletonList(new GroupSummary<>()))); - groups.add(new CharacteristicGroup<>( - "VSpectratype", + groups.add(new CharacteristicGroup<>(VSpectratype, Arrays.asList(AdditiveCharacteristics.VSpectratype(downsampling)), Collections.singletonList(new GroupSummary<>()))); - groups.add(new CharacteristicGroup<>( - "VSpectratypeMean", + groups.add(new CharacteristicGroup<>(VSpectratypeMean, Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(downsampling)), Collections.singletonList(new GroupSummary<>()))); diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index e8052f1a6..686b1c293 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -192,6 +192,11 @@ public static CommandLine mkCmd() { .addSubcommand("individual", CommandSpec.forAnnotatedObject(CommandPostanalysis.CommandIndividual.class)) .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPostanalysis.CommandOverlap.class)); + cmd.getSubcommands() + .get("exportPostanalysis") + .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandExportPostanalysis.ExportBoxPlots.class)) + .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandExportPostanalysis.ExportTables.class)); + cmd.setSeparator(" "); return cmd; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt index 229447699..22c8ae7c2 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt @@ -3,7 +3,6 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow.Companion.gene import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow.Companion.sample -import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow.Companion.weight import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.coordCartesian @@ -16,10 +15,15 @@ import jetbrains.letsPlot.scale.scaleSizeIdentity import jetbrains.letsPlot.scale.scaleXDiscrete import jetbrains.letsPlot.scale.scaleYDiscrete import jetbrains.letsPlot.theme -import org.jetbrains.dataframe.* -import org.jetbrains.dataframe.annotations.DataSchema -import org.jetbrains.dataframe.columns.DataColumn -import org.jetbrains.dataframe.io.writeCSV +import org.jetbrains.kotlinx.dataframe.DataColumn +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.DataRow +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.cast +import org.jetbrains.kotlinx.dataframe.api.toDataFrame +import org.jetbrains.kotlinx.dataframe.api.toMap +import org.jetbrains.kotlinx.dataframe.column +import org.jetbrains.kotlinx.dataframe.io.writeCSV import java.nio.file.Path @@ -83,7 +87,7 @@ object GeneUsage { } } - data.toDataFrame().typed() + data.toDataFrame().cast() } /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt index c143dc68e..c2053a63a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt @@ -1,17 +1,20 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema +import com.milaboratory.mixcr.postanalysis.dataframe.SimpleMetricsRow.Companion.metric +import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.Pos import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.geom.geomPoint +import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.label.ggtitle import jetbrains.letsPlot.label.labs import jetbrains.letsPlot.letsPlot import jetbrains.letsPlot.theme -import org.jetbrains.dataframe.* -import org.jetbrains.dataframe.annotations.DataSchema -import org.jetbrains.dataframe.columns.DataColumn +import org.jetbrains.kotlinx.dataframe.* +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.* +import java.nio.file.Path /** * DataFrame row for single statistical char group @@ -22,6 +25,12 @@ interface SimpleMetricsRow { /** Sample ID */ val sample: String + /** Metric name */ + val metric: String + + /** Value */ + val value: Double + companion object { ////// DSL @@ -29,34 +38,67 @@ interface SimpleMetricsRow { val DataFrame.sample get() = this[SimpleMetricsRow::sample.name] as DataColumn val DataRow.sample get() = this[SimpleMetricsRow::sample.name] as String + + val metric by column() + + val DataFrame.metric get() = this[SimpleMetricsRow::metric.name] as DataColumn + val DataRow.metric get() = this[SimpleMetricsRow::metric.name] as String + + val value by column() + + val DataFrame.value get() = this[SimpleMetricsRow::value.name] as DataColumn + val DataRow.value get() = this[SimpleMetricsRow::value.name] as Double } } object SimpleStatistics { + + /** + * Box plot settings + * + * @param metrics metrics to export in plots (null for all available metrics) + * @param primaryGroup metadata field used for primary grouping + * @param secondaryGroup metadata field used for secondary grouping + * */ + data class BoxPlotSettings( + val metrics: List? = null, + val primaryGroup: String? = null, + val primaryGroupOrder: List? = null, + val secondaryGroup: String? = null, + val secondaryGroupOrder: List? = null, + ) { + companion object { + val Default = BoxPlotSettings() + } + } + /** * Imports data into DataFrame **/ fun dataFrame( - paSett: PostanalysisSchema<*>, paResult: PostanalysisResult, - group: String + metricsFilter: Set?, ) = run { val data = mutableMapOf>( SimpleMetricsRow::sample.name to mutableListOf(), ) - for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { + for ((_, charData) in paResult.data) { for ((sampleId, keys) in charData.data) { for (metric in keys.data) { val key = metric.key.toString() + if (metricsFilter != null && !metricsFilter.contains(key)) { + continue + } data[SimpleMetricsRow::sample.name]!! += sampleId - data.computeIfAbsent(key) { mutableListOf() } += metric.value + data[SimpleMetricsRow::metric.name]!! += key + data[SimpleMetricsRow::value.name]!! += metric.value } } } - data.toDataFrame().typed() + data.toDataFrame().cast() } /** @@ -65,19 +107,51 @@ object SimpleStatistics { fun DataFrame.withMetadata(metadata: AnyFrame) = run { this.leftJoin(metadata) { SimpleMetricsRow.sample } } +// +// /** +// * Create Plot for specific metric +// **/ +// fun DataFrame.plot( +// settings: BoxPlotSettings, +// ) = run { +// +// val df = this.filter { +// SimpleMetricsRow.metric.eq(metric) +// } +// +// var plt = letsPlot(df.toMap()) { +// y = SimpleMetricsRow.value.name() +// x = settings.primaryGroup +// group = settings.secondaryGroup +// } +// +// plt += geomBoxplot() +// plt += geomPoint( +// position = Pos.jitterdodge, +// shape = 21, +// color = "black" +// ) +// plt += ggtitle(metric) +// plt += labs(x = settings.primaryGroup, y = metric) +// plt += theme().axisTitleXBlank() +// plt += theme().axisTextXBlank() +// plt += theme().axisTicksXBlank() +// +// plt +// } + /** - * Create Plot + * Create Plots for all metrics **/ - fun DataFrame.plot( - metric: String, - primaryGroup: String? = null, - secondaryGroup: String? = null - ) = run { - var plt = letsPlot(toMap()) { - x = primaryGroup - y = metric - group = secondaryGroup + fun DataFrame.plots( + settings: BoxPlotSettings, + ) = groupBy { SimpleMetricsRow.metric }.groups.map { df -> + + var plt = letsPlot(df.toMap()) { + y = SimpleMetricsRow.value.name() + x = settings.primaryGroup + group = settings.secondaryGroup } plt += geomBoxplot() @@ -86,12 +160,57 @@ object SimpleStatistics { shape = 21, color = "black" ) - plt += ggtitle(metric) - plt += labs(x = primaryGroup, y = metric) + + val metricName = if (!df.isEmpty()) { + df.first().metric + } else { + "" + } + + plt += ggtitle(metricName) + plt += labs(x = settings.primaryGroup, y = metricName) + plt += theme().axisTitleXBlank() plt += theme().axisTextXBlank() plt += theme().axisTicksXBlank() - plt + metricName to plt + + }.toList().toMap() + + + /** + * Export plot into single PDF file + * + * @param destination path to export PDF + * @param settings plot settings + * */ + fun DataFrame.plotPDF( + destination: Path, + settings: BoxPlotSettings, + ) = run { + writePDF(destination, + plots(settings).values.map { metric -> + PlotSvgExport.buildSvgImageFromRawSpecs( + metric.toSpec() + ) + }.toList().map { toPdf(it) } + ) + } + + /** + * Create and export all plots into single PDF file + * + * @param destination path to export PDF + * @param paResult PA results + * @param settings plot settings + * */ + fun plotPDF( + destination: Path, + paResult: PostanalysisResult, + metricsFilter: Set?, + settings: BoxPlotSettings + ) { + dataFrame(paResult, metricsFilter).plotPDF(destination, settings) } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt index 56e0197ae..8f90716f7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt @@ -14,9 +14,12 @@ import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.label.ggtitle import jetbrains.letsPlot.label.labs import jetbrains.letsPlot.scale.scaleXDiscrete -import org.jetbrains.dataframe.* -import org.jetbrains.dataframe.annotations.DataSchema -import org.jetbrains.dataframe.columns.DataColumn +import org.jetbrains.kotlinx.dataframe.DataColumn +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.DataRow +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.* +import org.jetbrains.kotlinx.dataframe.column import java.nio.file.Path /** @@ -98,7 +101,7 @@ object SingleSpectratype { } } - return data.toDataFrame().typed() + return data.toDataFrame().cast() } /** @@ -158,10 +161,11 @@ object SingleSpectratype { val max = df.length.max() ?: 0 // add auxiliary points for each cdr3 length - df += (min..max) - .map { SpectratypeRowImp(sample, it, 0.0, OtherPayload) } - .toDataFrameByProperties() - .typed() + df = df.concat( + (min..max) + .map { SpectratypeRowImp(sample, it, 0.0, OtherPayload) } + .toDataFrame() + ) // collapse all "Other" into a single row df = df @@ -174,7 +178,7 @@ object SingleSpectratype { df = df.sortByDesc(SpectratypeRow.weight) if (settings.normalize) - df[SpectratypeRow::weight.name] = df.weight / df.weight.sum() + df.add(SpectratypeRow::weight.name) { df.weight / df.weight.sum() } // plot var plt = letsPlot(df.toMap()) + geomBar( From e247390aff26ccd3ad9d713706d93131ec3793ad Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 21 Dec 2021 00:32:52 +0300 Subject: [PATCH 121/282] wip --- build.gradle.kts | 20 +- .../mixcr/cli/CommandExportPostanalysis.java | 17 +- .../mixcr/cli/CommandPostanalysis.java | 28 +- .../java/com/milaboratory/mixcr/cli/Main.java | 2 +- .../mixcr/postanalysis/dataframe/GeneUsage.kt | 2 +- .../mixcr/postanalysis/dataframe/Metadata.kt | 32 + .../dataframe/SimpleStatistics.kt | 88 +- .../dataframe/SingleSpectratype.kt | 1 - .../dataframe/pubr/CompareMeans.kt | 189 + .../dataframe/SimpleStatisticsTest.kt | 37 + .../dataframe/SingleSpectratypeTest.kt | 12 +- .../dataframe/pubr/CompareMeansTest.kt | 53 + src/test/resources/postanalysis/metadata.csv | 40 + .../resources/postanalysis/sample_pa.json | 671871 +++++++++++++++ 14 files changed, 672320 insertions(+), 72 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt create mode 100644 src/test/resources/postanalysis/metadata.csv create mode 100644 src/test/resources/postanalysis/sample_pa.json diff --git a/build.gradle.kts b/build.gradle.kts index 0063f9c49..a5e352fd7 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -4,6 +4,14 @@ import groovy.lang.Closure import org.jetbrains.kotlin.gradle.tasks.KotlinCompile import java.net.InetAddress + +val milibVersion = "1.14.1-16-774c60afab" +val repseqioVersion = "1.3.5-10-05b9291c5e" +val jacksonVersion = "2.12.4" +val letsPlotLibraryVersion = "2.1.0" +val letsPlotKotlinApiVersion = "3.1.1" +val dataframeVersion = "0.8.0-dev-808" + plugins { `java-library` application @@ -11,8 +19,12 @@ plugins { id("com.palantir.git-version") version "0.12.3" id("com.github.johnrengelman.shadow") version "7.0.0" kotlin("jvm") version "1.6.0-M1" + id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-dev-808" } +// Make IDE aware of the generated code: +kotlin.sourceSets.getByName("main").kotlin.srcDir("build/generated/ksp/main/kotlin/") + val miRepoAccessKeyId: String by project val miRepoSecretAccessKey: String by project @@ -64,13 +76,6 @@ repositories { } } -val milibVersion = "1.14.1-16-774c60afab" -val repseqioVersion = "1.3.5-4-f7170dd23b" -val jacksonVersion = "2.12.4" -val letsPlotLibraryVersion = "2.1.0" -val letsPlotKotlinApiVersion = "3.0.3-alpha1" -val dataframeVersion = "0.8.0-dev-777-0.11.0.39" - dependencies { api("com.milaboratory:milib:$milibVersion") api("io.repseq:repseqio:$repseqioVersion") { @@ -79,6 +84,7 @@ dependencies { implementation("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion") implementation("commons-io:commons-io:2.7") + implementation("commons-io:commons-io:2.7") implementation("org.lz4:lz4-java:1.4.1") implementation("net.sf.trove4j:trove4j:3.0.3") implementation("info.picocli:picocli:4.1.1") diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java index 2ffb5e273..cfb6b6797 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java @@ -35,15 +35,14 @@ public abstract class CommandExportPostanalysis extends ACommandWithOutputMiXCR /** Check that directory */ private void ensureChainsDirExists(Chains.NamedChains chains) { try { - Files.createDirectory(Paths.get(chains.name)); + Files.createDirectories(Paths.get(out).resolve(chains.name)); } catch (IOException e) { throwExecutionException(e.getMessage()); } } - Path outPath(Chains.NamedChains chains, String suffix) { - return Paths.get(chains.name).resolve(suffix); + return Paths.get(out).resolve(chains.name).resolve(suffix); } /** Cached PA result */ @@ -71,7 +70,11 @@ public void run0() throws Exception { abstract void run(Chains.NamedChains chains, PaResultByChain result); - static final class ExportTables extends CommandExportPostanalysis { + @CommandLine.Command(name = "tables", + sortOptions = false, + separator = " ", + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") + public static final class ExportTables extends CommandExportPostanalysis { @Override void run(Chains.NamedChains chains, PaResultByChain result) { for (CharacteristicGroup table : result.schema.tables) { @@ -86,7 +89,11 @@ void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tabl } } - static final class ExportBoxPlots extends CommandExportPostanalysis { + @CommandLine.Command(name = "box-plots", + sortOptions = false, + separator = " ", + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") + public static final class ExportBoxPlots extends CommandExportPostanalysis { @Option(names = {"-p", "--primary-group"}, description = "Primary group") public String primaryGroup; @Option(names = {"-s", "--secondary-group"}, description = "Secondary group") diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java index 2dceba915..e6888f51a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java @@ -17,6 +17,7 @@ import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; import com.milaboratory.mixcr.postanalysis.overlap.*; import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; @@ -49,14 +50,16 @@ * */ public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { + public static final NamedChains[] CHAINS = {TRAD_NAMED, TRB_NAMED, TRG_NAMED, IGH_NAMED, IGKL_NAMED}; + @Parameters(description = "cloneset.{clns|clna}... result.json") public List inOut; @Option(description = "Use only productive sequences in postanalysis.", names = {"--only-productive"}) - public boolean onlyProductive = false; + public boolean onlyProductive = false; // FIXME - not used - @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]", + @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", names = {"-d", "--downsampling"}, required = true) public String downsampling; @@ -70,10 +73,10 @@ protected List getInputFiles() { return inOut.subList(0, inOut.size() - 1) .stream() .flatMap(f -> { - if (Files.isDirectory(Path.of(f))) { + if (Files.isDirectory(Paths.get(f))) { try { return Files - .list(Path.of(f)) + .list(Paths.get(f)) .map(Path::toString); } catch (IOException ignored) { } @@ -96,8 +99,17 @@ private static int downsamplingValue(String downsampling) { return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); } + /** + * Get sample id from file name + */ + static String getSampleId(String file) { + return Paths.get(file).getFileName().toString(); + } + private static SetPreprocessorFactory parseDownsampling(String downsampling) { - if (downsampling.startsWith("umi-count")) { + if (downsampling.equalsIgnoreCase("no-downsampling")) { + return new NoPreprocessing.Factory<>(); + } else if (downsampling.startsWith("umi-count")) { if (downsampling.endsWith("auto")) return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); else { @@ -172,7 +184,7 @@ public PaResultByChain(@JsonProperty("schema") PostanalysisSchema schema, public void run0() throws Exception { Map resultsMap = new HashMap<>(); Chains c = Chains.parse(chains); - for (NamedChains knownChains : WELL_KNOWN_CHAINS) { + for (NamedChains knownChains : CHAINS) { if (c.intersects(knownChains.chains)) resultsMap.put(knownChains, run(knownChains.chains)); } @@ -282,7 +294,7 @@ PaResultByChain run(Chains chain) { List datasets = getInputFiles().stream() .map(file -> - new ClonotypeDataset(file, file, VDJCLibraryRegistry.getDefault()) + new ClonotypeDataset(getSampleId(file), file, VDJCLibraryRegistry.getDefault()) ).collect(Collectors.toList()); return new PaResultByChain(schema, runner.run(datasets)); @@ -340,7 +352,7 @@ PaResultByChain run(Chains chain) { .collect(Collectors.toList()); OverlapDataset overlapDataset = OverlapUtil.overlap( - getInputFiles(), + getInputFiles().stream().map(CommandPostanalysis::getSampleId).collect(toList()), ordering, readers); diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 686b1c293..d7bd016fa 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -149,7 +149,7 @@ public static CommandLine mkCmd() { .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) .addSubcommand("postanalysis", CommandPostanalysis.CommandPostanalysisMain.class) - .addSubcommand("plot", CommandExportPostanalysis.class) + .addSubcommand("exportPostanalysis", CommandExportPostanalysis.CommandExportPostanalysisMain.class) .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt index 22c8ae7c2..ab76f3892 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt @@ -22,7 +22,7 @@ import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.cast import org.jetbrains.kotlinx.dataframe.api.toDataFrame import org.jetbrains.kotlinx.dataframe.api.toMap -import org.jetbrains.kotlinx.dataframe.column +import org.jetbrains.kotlinx.dataframe.api.column import org.jetbrains.kotlinx.dataframe.io.writeCSV import java.nio.file.Path diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt new file mode 100644 index 000000000..8b41ac3ff --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt @@ -0,0 +1,32 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import org.jetbrains.kotlinx.dataframe.DataColumn +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.DataRow +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.column + +/** + * DataFrame row for metadata + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +interface MetadataRow { + /** Sample */ + val sample: String + + companion object { + ////// DSL + + val sample by column() + + val DataFrame.sample get() = this[MetadataRow::sample.name] as DataColumn + val DataRow.sample get() = this[MetadataRow::sample.name] as String + } +} + +object Metadata { + + + +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt index c2053a63a..eb17afc93 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt @@ -2,6 +2,8 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.dataframe.SimpleMetricsRow.Companion.metric +import com.milaboratory.mixcr.postanalysis.dataframe.SimpleMetricsRow.Companion.value +import com.milaboratory.mixcr.postanalysis.stat.HolmBonferroni import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.Pos import jetbrains.letsPlot.geom.geomBoxplot @@ -10,7 +12,8 @@ import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.label.ggtitle import jetbrains.letsPlot.label.labs import jetbrains.letsPlot.letsPlot -import jetbrains.letsPlot.theme +import jetbrains.letsPlot.stat.statBoxplot +import jetbrains.letsPlot.stat.statContour import org.jetbrains.kotlinx.dataframe.* import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.* @@ -66,6 +69,8 @@ object SimpleStatistics { val primaryGroupOrder: List? = null, val secondaryGroup: String? = null, val secondaryGroupOrder: List? = null, + val applyHolmBonferroni: Boolean = false, + val HolmBonferroniFWer: Double = 0.01 ) { companion object { val Default = BoxPlotSettings() @@ -82,6 +87,8 @@ object SimpleStatistics { val data = mutableMapOf>( SimpleMetricsRow::sample.name to mutableListOf(), + SimpleMetricsRow::metric.name to mutableListOf(), + SimpleMetricsRow::value.name to mutableListOf(), ) for ((_, charData) in paResult.data) { @@ -107,39 +114,6 @@ object SimpleStatistics { fun DataFrame.withMetadata(metadata: AnyFrame) = run { this.leftJoin(metadata) { SimpleMetricsRow.sample } } -// -// /** -// * Create Plot for specific metric -// **/ -// fun DataFrame.plot( -// settings: BoxPlotSettings, -// ) = run { -// -// val df = this.filter { -// SimpleMetricsRow.metric.eq(metric) -// } -// -// var plt = letsPlot(df.toMap()) { -// y = SimpleMetricsRow.value.name() -// x = settings.primaryGroup -// group = settings.secondaryGroup -// } -// -// plt += geomBoxplot() -// plt += geomPoint( -// position = Pos.jitterdodge, -// shape = 21, -// color = "black" -// ) -// plt += ggtitle(metric) -// plt += labs(x = settings.primaryGroup, y = metric) -// plt += theme().axisTitleXBlank() -// plt += theme().axisTextXBlank() -// plt += theme().axisTicksXBlank() -// -// plt -// } - /** * Create Plots for all metrics @@ -148,18 +122,47 @@ object SimpleStatistics { settings: BoxPlotSettings, ) = groupBy { SimpleMetricsRow.metric }.groups.map { df -> - var plt = letsPlot(df.toMap()) { - y = SimpleMetricsRow.value.name() + val filteredDf = + if (settings.applyHolmBonferroni) + HolmBonferroni.run( + df.rows().toList(), + { it.value }, + settings.HolmBonferroniFWer + ).toDataFrame() + else + df + + if (filteredDf.isEmpty()) + return@map null + + var plt = letsPlot(filteredDf.toMap()) { x = settings.primaryGroup + y = SimpleMetricsRow.value.name() group = settings.secondaryGroup + fill = settings.secondaryGroup ?: settings.primaryGroup + } + + + plt += geomBoxplot( + fatten = 2, + outlierShape = null, + outlierColor = null, + outlierSize = 0, +// position = positionDodge(0.1) + ) { +// color = settings.secondaryGroup +// fill = settings.secondaryGroup } - plt += geomBoxplot() + plt += geomPoint( position = Pos.jitterdodge, shape = 21, color = "black" - ) + ) { + color = settings.secondaryGroup + fill = settings.secondaryGroup + } val metricName = if (!df.isEmpty()) { df.first().metric @@ -170,13 +173,12 @@ object SimpleStatistics { plt += ggtitle(metricName) plt += labs(x = settings.primaryGroup, y = metricName) - plt += theme().axisTitleXBlank() - plt += theme().axisTextXBlank() - plt += theme().axisTicksXBlank() +// plt += theme().axisTitleXBlank() +// plt += theme().axisTextXBlank() +// plt += theme().axisTicksXBlank() metricName to plt - - }.toList().toMap() + }.filter { it != null }.map { it!! }.toList().toMap() /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt index 8f90716f7..f3f235b82 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt @@ -19,7 +19,6 @@ import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.DataRow import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.* -import org.jetbrains.kotlinx.dataframe.column import java.nio.file.Path /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt new file mode 100644 index 000000000..cd25fe23b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt @@ -0,0 +1,189 @@ +package com.milaboratory.mixcr.postanalysis.dataframe.pubr + +import com.milaboratory.mixcr.postanalysis.dataframe.pubr.RefGroup.Companion.all +import org.apache.commons.math3.stat.inference.MannWhitneyUTest +import org.apache.commons.math3.stat.inference.OneWayAnova +import org.apache.commons.math3.stat.inference.TTest +import org.apache.commons.math3.stat.inference.WilcoxonSignedRankTest +import org.jetbrains.kotlinx.dataframe.AnyFrame +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.* + +/** + * A formula containing + * y - a numeric variable + * factor - a factor with one or multiple levels + */ +data class Formula( + /** A numeric variable */ + val y: String, + /** A factor */ + val factor: Factor +) + +/** + * A group of columns representing a factor for grouping + */ +data class Factor(val columnNames: List) { + internal val arr = columnNames.toTypedArray() +} + +fun Factor(vararg columnNames: String) = Factor(columnNames.toList()) + +/** + * Reference group + **/ +sealed interface RefGroup { + companion object { + internal object All : RefGroup { + override fun toString() = "all" + } + + /** */ + val all: RefGroup = All + + data class RefGroupImpl(val colValues: List) : RefGroup { + override fun toString() = colValues.joinToString("+") + } + + fun of(vararg columnValues: Any) = RefGroupImpl(columnValues.toList()) + + fun of(columnValues: List) = RefGroupImpl(columnValues) + } +} + +/** + * + */ +class CompareMeans( + val formula: Formula, + val data: AnyFrame, + val groupBy: Factor? = null, + val method: TestMethod = TestMethod.Wilcox, + val pAdjustMethod: String? = null, + val refGroup: RefGroup? = null +) { + + /** dataframe for each group*/ + private val groups: List> = + data.groupBy(*formula.factor.arr).groups.toList().map { + getGroupName(it, formula.factor.arr) to it + } + + + val stat = run { + if (refGroup != null) { + val groups = this.groups.toMap() + + // get reference data + val refData = ( + if (refGroup == all) + data + else + groups[refGroup] ?: throw IllegalArgumentException("reference group not found") + )[formula.y].cast().toDoubleArray() + + groups.map { (gr, df) -> + if (gr == refGroup) + return@map null + + val data = df[formula.y].cast().toDoubleArray() + val pValue = calc(method, refData, data) + + CompareMeansRow(formula.y, method, refGroup, gr, pValue, -1.0, significance(pValue)); + }.filterNotNull() + .toDataFrame() + } else { + val comparisons = mutableListOf() + + for (i in groupsList.indices) { + for (j in 0 until i) { + val iGroup = groupsList[i] + val jGroup = groupsList[j] + val pValue = calc( + method, + iGroup.second[formula.y].cast().toDoubleArray(), + jGroup.second[formula.y].cast().toDoubleArray() + ) + + comparisons += CompareMeansRow( + formula.y, method, + iGroup.first, jGroup.first, + pValue, -1.0, significance(pValue) + ) + } + } + + comparisons.toDataFrame() + } + } + + private fun getGroupName(df: AnyFrame, group: Array) = run { + val f = df.first() + RefGroup.Companion.RefGroupImpl(group.map { f[it] }) + } + + + private fun calc(method: TestMethod, a: DoubleArray, b: DoubleArray) = when (method) { + TestMethod.Wilcox -> + if (a.size != b.size) + MannWhitneyUTest().mannWhitneyUTest(a, b) + else + WilcoxonSignedRankTest().wilcoxonSignedRankTest(a, b, false) + TestMethod.TTest -> + if (a.size != b.size) + TTest().tTest(a, b) + else + TTest().pairedTTest(a, b) + TestMethod.ANOVA -> OneWayAnova().anovaPValue(listOf(a, b)) + TestMethod.Kruskal -> throw RuntimeException("not supported yet") + } +// +// private fun byGroups() = run { +// groupBy!! +// +// } + + companion object { + private fun significance(pValue: Double) = + if (pValue >= 0.05) "ns" + else if (pValue < 0.0001) "***" + else if (pValue < 0.001) "**" + else "*" + } +} + +enum class TestMethod { + TTest, + Wilcox, + ANOVA, + Kruskal +} + +/** + * DataFrame row for CompareMeans result + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +data class CompareMeansRow( + /** The variable used in test */ + val y: String, + + /** Method used */ + val method: TestMethod, + + /** First group */ + val group1: RefGroup, + + /** Second group */ + val group2: RefGroup, + + /** The p-value */ + val pValue: Double, + + /** The adjusted p-value */ + val pValueAdj: Double, + + /** The significance level */ + val pSignif: String +) diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt new file mode 100644 index 000000000..57e00dea1 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt @@ -0,0 +1,37 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.mixcr.cli.CommandPostanalysis +import com.milaboratory.mixcr.postanalysis.dataframe.SimpleStatistics.plotPDF +import com.milaboratory.mixcr.postanalysis.dataframe.SimpleStatistics.withMetadata +import com.milaboratory.util.GlobalObjectMappers +import io.repseq.core.Chains +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.io.read +import org.junit.Test +import java.nio.file.Paths + + +/** + * + */ +internal class SimpleStatisticsTest { + @Test + fun test1() { + val meta = DataFrame.read(javaClass.getResource("/postanalysis/metadata.csv")!!) + val pa = GlobalObjectMappers.PRETTY.readValue( + javaClass.getResource("/postanalysis/sample_pa.json"), + CommandPostanalysis.PaResult::class.java + ) + + val igh = pa.results[Chains.IGH_NAMED]!! + + var df = SimpleStatistics.dataFrame(igh.result.forGroup(igh.schema.getGroup("biophysics")), null) + + df = df.withMetadata(meta) + + df.plotPDF( + Paths.get("scratch/pa/diversity.pdf"), + SimpleStatistics.BoxPlotSettings(primaryGroup = "Cat3", applyHolmBonferroni = true) + ) + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt index 4aacd4654..04880c05b 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt @@ -2,16 +2,16 @@ package com.milaboratory.mixcr.postanalysis.dataframe import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.coordFixed -import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.geom.geomTile import jetbrains.letsPlot.ggsize import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.letsPlot import jetbrains.letsPlot.scale.scaleXContinuous import jetbrains.letsPlot.scale.scaleYContinuous -import org.jetbrains.dataframe.DataFrame -import org.jetbrains.dataframe.io.readCSV -import org.jetbrains.dataframe.toMap +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.api.head +import org.jetbrains.kotlinx.dataframe.api.toMap +import org.jetbrains.kotlinx.dataframe.io.read import org.junit.Test import java.nio.file.Path @@ -23,7 +23,7 @@ internal class SingleSpectratypeTest { @Test fun name1() { val data = - DataFrame.readCSV("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") + DataFrame.read("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") val mData = data.head(1000).toMap() val plot = letsPlot(mData) { x = "sample" @@ -41,7 +41,7 @@ internal class SingleSpectratypeTest { @Test fun name() { val data = - DataFrame.readCSV("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") + DataFrame.read("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") val mData = data.head(1000).toMap() val xs = mData["sample"]!!.toList().distinct().size diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt new file mode 100644 index 000000000..ec0e397eb --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt @@ -0,0 +1,53 @@ +package com.milaboratory.mixcr.postanalysis.dataframe.pubr + +import org.jetbrains.kotlinx.dataframe.api.print +import org.jetbrains.kotlinx.dataframe.api.toDataFrame +import org.junit.Test +import kotlin.random.Random +import kotlin.random.asJavaRandom + +/** + * + */ +internal class CompareMeansTest { + + fun rndData( + vararg cols: Pair, + len: Int = 100, + random: Random = Random.Default + ) = run { + val datum = cols.map { + val d = it.second + it.first to when (d) { + Normal -> (0 until len).map { random.nextDouble() } + Gaussian -> (0 until len).map { random.asJavaRandom().nextGaussian() } + is Category -> (0 until len).map { random.nextInt(d.n).toString() } + } + } + datum.toMap().toDataFrame() + } + + @Test + fun test1() { + val data = rndData( + "V" to Gaussian, + "A" to Category(2), + "C" to Category(2), + len = 100001 + ) + + val comp = CompareMeans( + Formula("V", Factor("A", "C")), + data, + refGroup = RefGroup.all + ).stat + + comp.print() + } +} + +sealed interface Distribution + +data class Category(val n: Int) : Distribution +object Gaussian : Distribution +object Normal : Distribution diff --git a/src/test/resources/postanalysis/metadata.csv b/src/test/resources/postanalysis/metadata.csv new file mode 100644 index 000000000..c01010266 --- /dev/null +++ b/src/test/resources/postanalysis/metadata.csv @@ -0,0 +1,40 @@ +sample,Cat3,Cat2 +d50_1-N-U023765_S1_L001.clns,B,X +d50_10-N-U022019_S1_L001.clns,A,Y +d50_11-B-U022019_S2_L001.clns,C,X +d50_12-D-U022019_S3_L001.clns,A,Y +d50_12782B_S12_L001.clns,B,X +d50_12782D_S11_L001.clns,A,Y +d50_12782N_S10_L001.clns,C,X +d50_13-N-U024230_S4_L001.clns,B,Y +d50_13457B_S3_L001.clns,B,X +d50_13457D_S2_L001.clns,A,Y +d50_13457N_S1_L001.clns,C,X +d50_13489D_S5_L001.clns,C,Y +d50_13489B_S6_L001.clns,B,X +d50_13489N_S4_L001.clns,A,Y +d50_13641B_S9_L001.clns,C,X +d50_13641D_S8_L001.clns,A,Y +d50_13641N_S7_L001.clns,B,X +d50_14-B-U024230_S5_L001.clns,A,X +d50_15-D-U024230_S6_L001.clns,C,Y +d50_16-N-U026467_S7_L001.clns,B,X +d50_17-B-U026467_S8_L001.clns,B,Y +d50_18-D-U026467_S9_L001.clns,A,X +d50_19-N-U027135_S1_L001.clns,C,Y +d50_2-B-U023765_S2_L001.clns,C,X +d50_20-B-U027135_S2_L001.clns,B,X +d50_21-D-U027135_S3_L001.clns,A,Y +d50_22-N-U029238_S4_L001.clns,C,X +d50_24-D-U029238_S6_L001.clns,A,Y +d50_23-B-U029238_S5_L001.clns,B,X +d50_25-N-U030739_S7_L001.clns,A,Y +d50_26-B-U030739_S8_L001.clns,C,X +d50_27-D-U030739_S9_L001.clns,B,Y +d50_3-D-U023765_S3_L001.clns,C,X +d50_5-B-U025238_S5_L001.clns,C,Y +d50_4-N-U025238_S4_L001.clns,B,X +d50_6-D-U025238_S6_L001.clns,A,Y +d50_7-N-U028710_S7_L001.clns,C,X +d50_8-B-U028710_S8_L001.clns,B,Y +d50_9-D-U028710_S9_L001.clns,A,X diff --git a/src/test/resources/postanalysis/sample_pa.json b/src/test/resources/postanalysis/sample_pa.json new file mode 100644 index 000000000..e7dadabd5 --- /dev/null +++ b/src/test/resources/postanalysis/sample_pa.json @@ -0,0 +1,671871 @@ +{ + "results": { + "IG": { + "schema": { + "tables": [ { + "name": "biophysics", + "characteristics": [ { + "type": "individual", + "name": "CDR3 length, nt", + "preproc": { + "type": "chain", + "chain": [ { + "type": "filter", + "predicates": [ { + "type": "includesChains", + "chains": [ "IGH", "IGK", "IGL" ] + } ] + }, { + "type": "none" + } ] + }, + "weight": { + "type": "count" + }, + "key": { + "type": "named", + "name": "ntLengthOfCDR3" + }, + "metric": { + "type": "length", + "geneFeature": "CDR3", + "aminoAcid": false + }, + "agg": "Mean", + "normalizeByKey": false + }, { + "type": "individual", + "name": "CDR3 length, aa", + "preproc": { + "type": "chain", + "chain": [ { + "type": "filter", + "predicates": [ { + "type": "includesChains", + "chains": [ "IGH", "IGK", "IGL" ] + } ] + }, { + "type": "none" + } ] + }, + "weight": { + "type": "count" + }, + "key": { + "type": "named", + "name": "aaLengthOfCDR3" + }, + "metric": { + "type": "length", + "geneFeature": "CDR3", + "aminoAcid": true + }, + "agg": "Mean", + "normalizeByKey": false + }, { + "type": "individual", + "name": "NDN length, nt", + "preproc": { + "type": "chain", + "chain": [ { + "type": "filter", + "predicates": [ { + "type": "includesChains", + "chains": [ "IGH", "IGK", "IGL" ] + } ] + }, { + "type": "none" + } ] + }, + "weight": { + "type": "count" + }, + "key": { + "type": "named", + "name": "ntLengthOfVJJunction" + }, + "metric": { + "type": "length", + "geneFeature": "VJJunction", + "aminoAcid": false + }, + "agg": "Mean", + "normalizeByKey": false + }, { + "type": "individual", + "name": "Added N, nt", + "preproc": { + "type": "chain", + "chain": [ { + "type": "filter", + "predicates": [ { + "type": "includesChains", + "chains": [ "IGH", "IGK", "IGL" ] + } ] + }, { + "type": "none" + } ] + }, + "weight": { + "type": "count" + }, + "key": { + "type": "named", + "name": "AddedNucleotides" + }, + "metric": { + "type": "addedNucleotides" + }, + "agg": "Mean", + "normalizeByKey": false + }, { + "type": "individual", + "name": "Strength", + "preproc": { + "type": "chain", + "chain": [ { + "type": "filter", + "predicates": [ { + "type": "includesChains", + "chains": [ "IGH", "IGK", "IGL" ] + } ] + }, { + "type": "none" + } ] + }, + "weight": { + "type": "count" + }, + "key": { + "type": "named", + "name": "N2StrengthofCDR3" + }, + "metric": { + "type": "aaProperty", + "property": "N2Strength", + "geneFeature": "CDR3", + "adjustment": "LeadingCenter", + "nLetters": 5 + }, + "agg": "Mean", + "normalizeByKey": false + }, { + "type": "individual", + "name": "Hydrophobicity", + "preproc": { + 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13:50:58 +0300 Subject: [PATCH 122/282] P-Value correction algorithms --- .../postanalysis/stat/PValueCorrection.java | 293 ++++++++++++++++++ .../stat/PValueCorrectionTest.java | 123 ++++++++ 2 files changed, 416 insertions(+) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java new file mode 100644 index 000000000..8eff299b7 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java @@ -0,0 +1,293 @@ +package com.milaboratory.mixcr.postanalysis.stat; + +import java.util.Arrays; +import java.util.Comparator; + +public class PValueCorrection { + private static int[] seqLen(int start, int end) { + int[] result; + if (start == end) { + result = new int[end + 1]; + for (int i = 0; i < result.length; ++i) { + result[i] = i + 1; + } + } else if (start < end) { + result = new int[end - start + 1]; + for (int i = 0; i < result.length; ++i) { + result[i] = start + i; + } + } else { + result = new int[start - end + 1]; + for (int i = 0; i < result.length; ++i) { + result[i] = start - i; + } + } + return result; + } + + private static int[] order(double[] array, boolean decreasing) { + int size = array.length; + int[] idx = new int[size]; + double[] baseArr = new double[size]; + for (int i = 0; i < size; ++i) { + baseArr[i] = array[i]; + idx[i] = i; + } + + Comparator cmp; + if (!decreasing) { + cmp = Comparator.comparingDouble(a -> baseArr[a]); + } else { + cmp = (a, b) -> Double.compare(baseArr[b], baseArr[a]); + } + + return Arrays.stream(idx) + .boxed() + .sorted(cmp) + .mapToInt(a -> a) + .toArray(); + } + + private static double[] cummin(double[] array) { + if (array.length < 1) + throw new IllegalArgumentException("cummin requires at least one element"); + double[] output = new double[array.length]; + double cumulativeMin = array[0]; + for (int i = 0; i < array.length; ++i) { + if (array[i] < cumulativeMin) + cumulativeMin = array[i]; + output[i] = cumulativeMin; + } + return output; + } + + private static double[] cummax(double[] array) { + if (array.length < 1) + throw new IllegalArgumentException("cummax requires at least one element"); + double[] output = new double[array.length]; + double cumulativeMax = array[0]; + for (int i = 0; i < array.length; ++i) { + if (array[i] > cumulativeMax) + cumulativeMax = array[i]; + output[i] = cumulativeMax; + } + return output; + } + + private static double[] pminx(double[] array, double x) { + if (array.length < 1) + throw new IllegalArgumentException("pmin requires at least one element"); + double[] result = new double[array.length]; + for (int i = 0; i < array.length; ++i) { + result[i] = Math.min(array[i], x); + } + return result; + } + + private static double[] int2double(int[] array) { + double[] result = new double[array.length]; + for (int i = 0; i < array.length; i++) { + result[i] = array[i]; + } + return result; + } + + private static double doubleArrayMin(double[] array) { + if (array.length < 1) + throw new IllegalArgumentException("pAdjust requires at least one element"); + return Arrays.stream(array).min().orElse(Double.NaN); + } + + public static double[] Bonferoni(double[] pvalues) { + int size = pvalues.length; + if (size < 1) + throw new IllegalArgumentException("pAdjust requires at least one element"); + + double[] result = new double[size]; + for (int i = 0; i < size; ++i) { + double b = pvalues[i] * size; + if (b >= 1) { + result[i] = 1; + } else if (0 <= b) { + result[i] = b; + } else { + throw new RuntimeException("" + b + " is outside [0, 1)"); + } + } + return result; + } + + public static double[] Holm(double[] pvalues) { + int size = pvalues.length; + if (size < 1) + throw new IllegalArgumentException("pAdjust requires at least one element"); + + int[] o = order(pvalues, false); + double[] o2Double = int2double(o); + double[] cummaxInput = new double[size]; + for (int i = 0; i < size; ++i) { + cummaxInput[i] = (size - i) * pvalues[o[i]]; + } + int[] ro = order(o2Double, false); + double[] cummaxOutput = cummax(cummaxInput); + double[] pmin = pminx(cummaxOutput, 1.0); + double[] result = new double[size]; + for (int i = 0; i < size; ++i) { + result[i] = pmin[ro[i]]; + } + return result; + } + + public static double[] Hommel(double[] pvalues) { + int size = pvalues.length; + if (size < 1) + throw new IllegalArgumentException("pAdjust requires at least one element"); + int[] indices = seqLen(size, size); + int[] o = order(pvalues, false); + double[] p = new double[size]; + for (int i = 0; i < size; ++i) { + p[i] = pvalues[o[i]]; + } + double[] o2Double = int2double(o); + int[] ro = order(o2Double, false); + double[] q = new double[size]; + double[] pa = new double[size]; + double[] npi = new double[size]; + for (int i = 0; i < size; ++i) { + npi[i] = p[i] * size / indices[i]; + } + double min = doubleArrayMin(npi); + Arrays.fill(q, min); + Arrays.fill(pa, min); + for (int j = size; j >= 2; --j) { + int[] ij = seqLen(1, size - j + 1); + for (int i = 0; i < size - j + 1; ++i) { + ij[i]--; + } + int i2Length = j - 1; + int[] i2 = new int[i2Length]; + for (int i = 0; i < i2Length; ++i) { + i2[i] = size - j + 2 + i - 1; + } + double q1 = j * p[i2[0]] / 2.0; + for (int i = 1; i < i2Length; ++i) { + double temp_q1 = p[i2[i]] * j / (2.0 + i); + if (temp_q1 < q1) q1 = temp_q1; + } + for (int i = 0; i < size - j + 1; ++i) { + q[ij[i]] = Math.min(p[ij[i]] * j, q1); + } + for (int i = 0; i < i2Length; ++i) { + q[i2[i]] = q[size - j]; + } + for (int i = 0; i < size; ++i) { + if (pa[i] < q[i]) { + pa[i] = q[i]; + } + } + } + for (int i = 0; i < size; ++i) { + q[i] = pa[ro[i]]; + } + return q; + } + + private static final class IntermediateData { + final double[] ni; + final int[] o, ro; + + public IntermediateData(double[] ni, int[] o, int[] ro) { + this.ni = ni; + this.o = o; + this.ro = ro; + } + + double[] result(double[] cumminInput) { + double[] cumminArray = cummin(cumminInput); + double[] pmin = pminx(cumminArray, 1.0); + double[] result = new double[cumminInput.length]; + for (int i = 0; i < cumminInput.length; ++i) + result[i] = pmin[ro[i]]; + return result; + } + } + + private static IntermediateData computeIntermediateData(double[] pvalues) { + int size = pvalues.length; + double[] ni = new double[size]; + int[] o = order(pvalues, true); + double[] oDouble = int2double(o); + for (int i = 0; i < size; ++i) { + if (pvalues[i] < 0 || pvalues[i] > 1) { + throw new RuntimeException("array[" + i + "] = " + pvalues[i] + " is outside [0, 1]"); + } + ni[i] = (double) size / (size - i); + } + int[] ro = order(oDouble, false); + return new IntermediateData(ni, o, ro); + } + + public static double[] BenjaminiHochberg(double[] pvalues) { + int size = pvalues.length; + if (size < 1) + throw new IllegalArgumentException("pAdjust requires at least one element"); + + IntermediateData data = computeIntermediateData(pvalues); + double[] cumminInput = new double[size]; + for (int i = 0; i < size; ++i) + cumminInput[i] = data.ni[i] * pvalues[data.o[i]]; + return data.result(cumminInput); + } + + + public static double[] BenjaminiYekutieli(double[] pvalues) { + int size = pvalues.length; + if (size < 1) + throw new IllegalArgumentException("pAdjust requires at least one element"); + + IntermediateData data = computeIntermediateData(pvalues); + double[] cumminInput = new double[size]; + double q = 0; + for (int i = 1; i < size + 1; ++i) + q += 1.0 / i; + for (int i = 0; i < size; ++i) + cumminInput[i] = q * data.ni[i] * pvalues[data.o[i]]; + return data.result(cumminInput); + } + + public static double[] Hochberg(double[] pvalues) { + int size = pvalues.length; + if (size < 1) + throw new IllegalArgumentException("pAdjust requires at least one element"); + + IntermediateData data = computeIntermediateData(pvalues); + double[] cumminInput = new double[size]; + for (int i = 0; i < size; ++i) + cumminInput[i] = (i + 1) * pvalues[data.o[i]]; + return data.result(cumminInput); + } + + + public enum Method { + BenjaminiHochberg, + FDR, + BenjaminiYekutieli, + Bonferroni, + Hochberg, + Holm, + Hommel, + } + + public static double[] adjustPValues(double[] pValues, Method method) { + switch (method) { + case FDR: + case BenjaminiHochberg: return BenjaminiHochberg(pValues); + case BenjaminiYekutieli: return BenjaminiYekutieli(pValues); + case Bonferroni: return Bonferoni(pValues); + case Hochberg: return Hochberg(pValues); + case Holm: return Holm(pValues); + case Hommel: return Hommel(pValues); + default: throw new RuntimeException("not supported"); + } + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java new file mode 100644 index 000000000..ac18babbc --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java @@ -0,0 +1,123 @@ +package com.milaboratory.mixcr.postanalysis.stat; + +import org.junit.Assert; +import org.junit.Test; + +/** + * + */ +public class PValueCorrectionTest { + @Test + public void test1() { + double[] pvalues = new double[]{ + 4.533744e-01, 7.296024e-01, 9.936026e-02, 9.079658e-02, 1.801962e-01, + 8.752257e-01, 2.922222e-01, 9.115421e-01, 4.355806e-01, 5.324867e-01, + 4.926798e-01, 5.802978e-01, 3.485442e-01, 7.883130e-01, 2.729308e-01, + 8.502518e-01, 4.268138e-01, 6.442008e-01, 3.030266e-01, 5.001555e-02, + 3.194810e-01, 7.892933e-01, 9.991834e-01, 1.745691e-01, 9.037516e-01, + 1.198578e-01, 3.966083e-01, 1.403837e-02, 7.328671e-01, 6.793476e-02, + 4.040730e-03, 3.033349e-04, 1.125147e-02, 2.375072e-02, 5.818542e-04, + 3.075482e-04, 8.251272e-03, 1.356534e-03, 1.360696e-02, 3.764588e-04, + 1.801145e-05, 2.504456e-07, 3.310253e-02, 9.427839e-03, 8.791153e-04, + 2.177831e-04, 9.693054e-04, 6.610250e-05, 2.900813e-02, 5.735490e-03 + }; + + double[] bh = { // Benjamini-Hochberg + 6.126681e-01, 8.521710e-01, 1.987205e-01, 1.891595e-01, 3.217789e-01, + 9.301450e-01, 4.870370e-01, 9.301450e-01, 6.049731e-01, 6.826753e-01, + 6.482629e-01, 7.253722e-01, 5.280973e-01, 8.769926e-01, 4.705703e-01, + 9.241867e-01, 6.049731e-01, 7.856107e-01, 4.887526e-01, 1.136717e-01, + 4.991891e-01, 8.769926e-01, 9.991834e-01, 3.217789e-01, 9.301450e-01, + 2.304958e-01, 5.832475e-01, 3.899547e-02, 8.521710e-01, 1.476843e-01, + 1.683638e-02, 2.562902e-03, 3.516084e-02, 6.250189e-02, 3.636589e-03, + 2.562902e-03, 2.946883e-02, 6.166064e-03, 3.899547e-02, 2.688991e-03, + 4.502862e-04, 1.252228e-05, 7.881555e-02, 3.142613e-02, 4.846527e-03, + 2.562902e-03, 4.846527e-03, 1.101708e-03, 7.252032e-02, 2.205958e-02 + }; + + Assert.assertArrayEquals(bh, PValueCorrection.BenjaminiHochberg(pvalues), 1e-5); + + double[] by = { // Benjamini & Yekutieli + 1.000000e+00, 1.000000e+00, 8.940844e-01, 8.510676e-01, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 5.114323e-01, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.754486e-01, 1.000000e+00, 6.644618e-01, + 7.575031e-02, 1.153102e-02, 1.581959e-01, 2.812089e-01, 1.636176e-02, + 1.153102e-02, 1.325863e-01, 2.774239e-02, 1.754486e-01, 1.209832e-02, + 2.025930e-03, 5.634031e-05, 3.546073e-01, 1.413926e-01, 2.180552e-02, + 1.153102e-02, 2.180552e-02, 4.956812e-03, 3.262838e-01, 9.925057e-02 + }; + + Assert.assertArrayEquals(by, PValueCorrection.BenjaminiYekutieli(pvalues), 1e-5); + + double[] bonferoni = { // Bonferroni + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 7.019185e-01, 1.000000e+00, 1.000000e+00, + 2.020365e-01, 1.516674e-02, 5.625735e-01, 1.000000e+00, 2.909271e-02, + 1.537741e-02, 4.125636e-01, 6.782670e-02, 6.803480e-01, 1.882294e-02, + 9.005725e-04, 1.252228e-05, 1.000000e+00, 4.713920e-01, 4.395577e-02, + 1.088915e-02, 4.846527e-02, 3.305125e-03, 1.000000e+00, 2.867745e-01 + }; + + Assert.assertArrayEquals(bonferoni, PValueCorrection.Bonferoni(pvalues), 1e-5); + + double[] hochberg = { // Hochberg + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 4.632662e-01, 9.991834e-01, 9.991834e-01, + 1.575885e-01, 1.383967e-02, 3.938014e-01, 7.600230e-01, 2.501973e-02, + 1.383967e-02, 3.052971e-01, 5.426136e-02, 4.626366e-01, 1.656419e-02, + 8.825610e-04, 1.252228e-05, 9.930759e-01, 3.394022e-01, 3.692284e-02, + 1.023581e-02, 3.974152e-02, 3.172920e-03, 8.992520e-01, 2.179486e-01 + }; + + Assert.assertArrayEquals(hochberg, PValueCorrection.Hochberg(pvalues), 1e-5); + + double[] holm = { // Holm + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, 1.000000e+00, + 1.000000e+00, 1.000000e+00, 4.632662e-01, 1.000000e+00, 1.000000e+00, + 1.575885e-01, 1.395341e-02, 3.938014e-01, 7.600230e-01, 2.501973e-02, + 1.395341e-02, 3.052971e-01, 5.426136e-02, 4.626366e-01, 1.656419e-02, + 8.825610e-04, 1.252228e-05, 9.930759e-01, 3.394022e-01, 3.692284e-02, + 1.023581e-02, 3.974152e-02, 3.172920e-03, 8.992520e-01, 2.179486e-01 + }; + + Assert.assertArrayEquals(holm, PValueCorrection.Holm(pvalues), 1e-5); + + double[] hommel = { // Hommel + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.987624e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.595180e-01, + 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, 9.991834e-01, + 9.991834e-01, 9.991834e-01, 4.351895e-01, 9.991834e-01, 9.766522e-01, + 1.414256e-01, 1.304340e-02, 3.530937e-01, 6.887709e-01, 2.385602e-02, + 1.322457e-02, 2.722920e-01, 5.426136e-02, 4.218158e-01, 1.581127e-02, + 8.825610e-04, 1.252228e-05, 8.743649e-01, 3.016908e-01, 3.516461e-02, + 9.582456e-03, 3.877222e-02, 3.172920e-03, 8.122276e-01, 1.950067e-01 + }; + + Assert.assertArrayEquals(hommel, PValueCorrection.Hommel(pvalues), 1e-5); + } + + static double err(double[] expected, double[] actual) { + double error = 0.0; + for (int i = 0; i < expected.length; ++i) { + error += Math.abs(expected[i] - actual[i]); + } + return error; + } +} From c88263fadc13799e1a2ab135a7179e3218bbf8c1 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 21 Dec 2021 15:00:14 +0300 Subject: [PATCH 123/282] CompareMeans implementation (not really tested) --- .../dataframe/pubr/CompareMeans.kt | 151 +++++++++++++----- .../dataframe/pubr/CompareMeansTest.kt | 5 +- 2 files changed, 112 insertions(+), 44 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt index cd25fe23b..461351d22 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.postanalysis.dataframe.pubr import com.milaboratory.mixcr.postanalysis.dataframe.pubr.RefGroup.Companion.all +import com.milaboratory.mixcr.postanalysis.stat.PValueCorrection import org.apache.commons.math3.stat.inference.MannWhitneyUTest import org.apache.commons.math3.stat.inference.OneWayAnova import org.apache.commons.math3.stat.inference.TTest @@ -39,16 +40,18 @@ sealed interface RefGroup { override fun toString() = "all" } - /** */ + /** All dataset */ val all: RefGroup = All - data class RefGroupImpl(val colValues: List) : RefGroup { + internal data class RefGroupImpl(val colValues: List) : RefGroup { override fun toString() = colValues.joinToString("+") } - fun of(vararg columnValues: Any) = RefGroupImpl(columnValues.toList()) + /** Select part of dataset for specific values of columns */ + fun of(vararg columnValues: Any): RefGroup = RefGroupImpl(columnValues.toList()) - fun of(columnValues: List) = RefGroupImpl(columnValues) + /** Select part of dataset for specific values of columns */ + fun of(columnValues: List): RefGroup = RefGroupImpl(columnValues) } } @@ -56,75 +59,136 @@ sealed interface RefGroup { * */ class CompareMeans( + /** + * The formula + */ val formula: Formula, + /** + * A dataframe containing the variables in the formula. + */ val data: AnyFrame, - val groupBy: Factor? = null, + /** + * The type of test. Default is Wilcox + */ val method: TestMethod = TestMethod.Wilcox, - val pAdjustMethod: String? = null, + /** + * Variables used to group the data set before applying the test. + * When specified the mean comparisons will be performed in each + * subset of the data formed by the different levels of the groupBy variables. + */ + val groupBy: Factor? = null, + /** + * Method for adjusting p values. Default is Holm. + */ + val pAdjustMethod: PValueCorrection.Method? = PValueCorrection.Method.Holm, + /** + * The reference group. If specified, for a given grouping variable, each of the + * group levels will be compared to the reference group (i.e. control group). + * refGroup can be also “all”. In this case, each of the grouping variable levels + * is compared to all (i.e. base-mean). + */ val refGroup: RefGroup? = null ) { - /** dataframe for each group*/ - private val groups: List> = + /** all data array */ + private val allData by lazy { + data[formula.y].cast().toDoubleArray() + } + + /** data array for each group*/ + private val groups: List> = data.groupBy(*formula.factor.arr).groups.toList().map { - getGroupName(it, formula.factor.arr) to it + getRefGroup(it, formula.factor.arr) to it[formula.y].cast().toDoubleArray() } + /** Overall p-value computed with one way ANOVA */ + val anovaPValue by lazy { + OneWayAnova().anovaPValue(groups.map { it.second }) + } - val stat = run { + /** List of all "compare means" with no p-Value adjustment */ + private val compareMeansRaw: List = run { if (refGroup != null) { val groups = this.groups.toMap() // get reference data val refData = ( if (refGroup == all) - data + allData else groups[refGroup] ?: throw IllegalArgumentException("reference group not found") - )[formula.y].cast().toDoubleArray() + ) + + groups.map { (group, data) -> + if (group == refGroup) + return@map null - groups.map { (gr, df) -> - if (gr == refGroup) + if (refData.size < 2 || data.size < 2) return@map null - val data = df[formula.y].cast().toDoubleArray() - val pValue = calc(method, refData, data) + val pValue = pValue(method, refData, data) - CompareMeansRow(formula.y, method, refGroup, gr, pValue, -1.0, significance(pValue)); + CompareMeansRow( + formula.y, method, + refGroup, group, + pValue, -1.0, SignificanceLevel.of(pValue) + ); }.filterNotNull() - .toDataFrame() } else { - val comparisons = mutableListOf() + val cmpList = mutableListOf() - for (i in groupsList.indices) { + for (i in groups.indices) { for (j in 0 until i) { - val iGroup = groupsList[i] - val jGroup = groupsList[j] - val pValue = calc( + val iGroup = groups[i] + val jGroup = groups[j] + + if (iGroup.second.size < 2 || jGroup.second.size < 2) + continue + + val pValue = pValue( method, - iGroup.second[formula.y].cast().toDoubleArray(), - jGroup.second[formula.y].cast().toDoubleArray() + iGroup.second, + jGroup.second ) - comparisons += CompareMeansRow( + cmpList += CompareMeansRow( formula.y, method, iGroup.first, jGroup.first, - pValue, -1.0, significance(pValue) + pValue, -1.0, SignificanceLevel.of(pValue) ) } } - comparisons.toDataFrame() + cmpList } } - private fun getGroupName(df: AnyFrame, group: Array) = run { + /** Compare means with adjusted p-values and significance */ + private val compareMeansAdj = + if (pAdjustMethod == null || compareMeansRaw.isEmpty()) + compareMeansRaw + else { + val adjusted = + PValueCorrection.adjustPValues(compareMeansRaw.map { it.pValue }.toDoubleArray(), pAdjustMethod) + + compareMeansRaw.mapIndexed { i, cmp -> + cmp.copy( + pValueAdj = adjusted[i], + pSignif = SignificanceLevel.of(adjusted[i]) + ) + } + } + + /** Compare means statistics */ + val stat = compareMeansAdj.toDataFrame() + + private fun getRefGroup(df: AnyFrame, group: Array) = run { val f = df.first() RefGroup.Companion.RefGroupImpl(group.map { f[it] }) } - - private fun calc(method: TestMethod, a: DoubleArray, b: DoubleArray) = when (method) { + /** Compute p-value */ + private fun pValue(method: TestMethod, a: DoubleArray, b: DoubleArray) = when (method) { TestMethod.Wilcox -> if (a.size != b.size) MannWhitneyUTest().mannWhitneyUTest(a, b) @@ -138,21 +202,24 @@ class CompareMeans( TestMethod.ANOVA -> OneWayAnova().anovaPValue(listOf(a, b)) TestMethod.Kruskal -> throw RuntimeException("not supported yet") } -// -// private fun byGroups() = run { -// groupBy!! -// -// } +} + +enum class SignificanceLevel(val string: String) { + NS("ns"), + One("*"), + Two("**"), + Three("***"); companion object { - private fun significance(pValue: Double) = - if (pValue >= 0.05) "ns" - else if (pValue < 0.0001) "***" - else if (pValue < 0.001) "**" - else "*" + fun of(pValue: Double) = + if (pValue >= 0.05) NS + else if (pValue < 0.0001) Three + else if (pValue < 0.001) Two + else One } } +/** Method for calculation of p-value */ enum class TestMethod { TTest, Wilcox, @@ -185,5 +252,5 @@ data class CompareMeansRow( val pValueAdj: Double, /** The significance level */ - val pSignif: String + val pSignif: SignificanceLevel ) diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt index ec0e397eb..d409db6d0 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt @@ -33,13 +33,14 @@ internal class CompareMeansTest { "V" to Gaussian, "A" to Category(2), "C" to Category(2), - len = 100001 + len = 100000 ) val comp = CompareMeans( Formula("V", Factor("A", "C")), data, - refGroup = RefGroup.all + refGroup = RefGroup.all, + method = TestMethod.TTest ).stat comp.print() From 2877f0ef74a6dfea690921a9569df12ab7914283 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 22 Dec 2021 02:25:04 +0300 Subject: [PATCH 124/282] wip --- .../dataframe/SimpleStatistics.kt | 3 +- .../mixcr/postanalysis/dataframe/Util.kt | 7 +++ .../dataframe/pubr/CompareMeans.kt | 52 ++++++++++++---- .../dataframe/pubr/StatCompareMeans.kt | 59 +++++++++++++++++++ .../dataframe/pubr/CompareMeansTest.kt | 36 ++++++----- .../dataframe/pubr/StatCompareMeansTest.kt | 39 ++++++++++++ 6 files changed, 169 insertions(+), 27 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt index eb17afc93..e8e6abeae 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt @@ -8,6 +8,7 @@ import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.Pos import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.geom.geomPoint +import jetbrains.letsPlot.intern.Plot import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.label.ggtitle import jetbrains.letsPlot.label.labs @@ -135,7 +136,7 @@ object SimpleStatistics { if (filteredDf.isEmpty()) return@map null - var plt = letsPlot(filteredDf.toMap()) { + var plt: Plot = letsPlot(filteredDf.toMap()) { x = settings.primaryGroup y = SimpleMetricsRow.value.name() group = settings.secondaryGroup diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt index 4f49f0ce9..cebd9981a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt @@ -1,5 +1,8 @@ package com.milaboratory.mixcr.postanalysis.dataframe +import jetbrains.datalore.plot.PlotSvgExport +import jetbrains.letsPlot.intern.Plot +import jetbrains.letsPlot.intern.toSpec import org.apache.batik.transcoder.TranscoderInput import org.apache.batik.transcoder.TranscoderOutput import org.apache.fop.render.ps.EPSTranscoder @@ -12,6 +15,10 @@ import java.nio.file.Path import kotlin.io.path.absolutePathString import kotlin.io.path.writeBytes +fun Plot.toSvg() = PlotSvgExport.buildSvgImageFromRawSpecs(toSpec()) +fun Plot.toPDF() = toPdf(this.toSvg()) +fun Plot.toEPS() = toEPS(this.toSvg()) + fun toPdf(svg: String) = toVector(svg, ExportType.PDF) fun toEPS(svg: String) = toVector(svg, ExportType.EPS) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt index 461351d22..a8e0e8b54 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt @@ -55,38 +55,66 @@ sealed interface RefGroup { } } -/** - * - */ -class CompareMeans( +interface CompareMeansParameters { /** * The formula */ - val formula: Formula, + var formula: Formula? + /** * A dataframe containing the variables in the formula. */ - val data: AnyFrame, + var data: AnyFrame? + /** * The type of test. Default is Wilcox */ - val method: TestMethod = TestMethod.Wilcox, + val method: TestMethod + /** * Variables used to group the data set before applying the test. * When specified the mean comparisons will be performed in each * subset of the data formed by the different levels of the groupBy variables. */ - val groupBy: Factor? = null, + val groupBy: Factor? + /** * Method for adjusting p values. Default is Holm. */ - val pAdjustMethod: PValueCorrection.Method? = PValueCorrection.Method.Holm, + val pAdjustMethod: PValueCorrection.Method? + /** * The reference group. If specified, for a given grouping variable, each of the * group levels will be compared to the reference group (i.e. control group). * refGroup can be also “all”. In this case, each of the grouping variable levels * is compared to all (i.e. base-mean). */ + val refGroup: RefGroup? +} + +class CompareMeans( + override var formula: Formula? = null, + override var data: AnyFrame? = null, + override val method: TestMethod = TestMethod.Wilcox, + override val groupBy: Factor? = null, + override val pAdjustMethod: PValueCorrection.Method? = null, + override val refGroup: RefGroup? = null, +) : CompareMeansParameters { + + val statistics by lazy { + CompareMeansImpl(formula!!, data!!, method, groupBy, pAdjustMethod, refGroup) + } +} + +/** + * + */ +class CompareMeansImpl( + val formula: Formula, + val data: AnyFrame, + val method: TestMethod = TestMethod.Wilcox, + val groupBy: Factor? = null, + val pAdjustMethod: PValueCorrection.Method? = PValueCorrection.Method.Holm, val refGroup: RefGroup? = null ) { @@ -103,7 +131,11 @@ class CompareMeans( /** Overall p-value computed with one way ANOVA */ val anovaPValue by lazy { - OneWayAnova().anovaPValue(groups.map { it.second }) + val datum = groups.map { it.second }.filter { it.size > 2 } + if (datum.size < 2) + -1.0 + else + OneWayAnova().anovaPValue(datum) } /** List of all "compare means" with no p-Value adjustment */ diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt new file mode 100644 index 000000000..acbf4452f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt @@ -0,0 +1,59 @@ +package com.milaboratory.mixcr.postanalysis.dataframe.pubr + +import com.milaboratory.mixcr.postanalysis.stat.PValueCorrection +import jetbrains.letsPlot.geom.geomText +import jetbrains.letsPlot.intern.Plot +import org.jetbrains.kotlinx.dataframe.AnyFrame +import org.jetbrains.kotlinx.dataframe.api.cast +import org.jetbrains.kotlinx.dataframe.api.max +import org.jetbrains.kotlinx.dataframe.api.toDataFrame + +@Suppress("ClassName") +class statCompareMeans( + override var formula: Formula? = null, + override var data: AnyFrame? = null, + override val method: TestMethod = TestMethod.Wilcox, + override val groupBy: Factor? = null, + override val pAdjustMethod: PValueCorrection.Method? = null, + override val refGroup: RefGroup? = null, + + val pairs: List> = emptyList() +) : CompareMeansParameters { + val statistics by lazy { + CompareMeansImpl(formula!!, data!!, method, groupBy, pAdjustMethod, refGroup) + } +} + + +operator fun Plot.plus(cmp: statCompareMeans) = run { + if (cmp.data == null) { + @Suppress("UNCHECKED_CAST") + cmp.data = (this.data!! as Map>).toDataFrame() + } + + if (cmp.formula == null) { + val aes = this.mapping.map + val factor = + if (aes.containsKey("x") && aes.containsKey("group")) + Factor(aes["x"] as String, aes["group"] as String) + else if (aes.containsKey("x")) + Factor(aes["x"] as String) + else if (aes.containsKey("group")) + Factor(aes["group"] as String) + else + Factor() + + cmp.formula = Formula(aes["y"] as String, factor) + } + + if (cmp.pairs.isEmpty()) { + + val data = cmp.data!! + val y = cmp.formula!!.y + val maxY = data[y].cast().max() + + this + geomText(x = 0, y = maxY, label = "p-value " + cmp.statistics.anovaPValue) + } else { + this + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt index d409db6d0..4ce2865da 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt @@ -11,21 +11,6 @@ import kotlin.random.asJavaRandom */ internal class CompareMeansTest { - fun rndData( - vararg cols: Pair, - len: Int = 100, - random: Random = Random.Default - ) = run { - val datum = cols.map { - val d = it.second - it.first to when (d) { - Normal -> (0 until len).map { random.nextDouble() } - Gaussian -> (0 until len).map { random.asJavaRandom().nextGaussian() } - is Category -> (0 until len).map { random.nextInt(d.n).toString() } - } - } - datum.toMap().toDataFrame() - } @Test fun test1() { @@ -41,10 +26,29 @@ internal class CompareMeansTest { data, refGroup = RefGroup.all, method = TestMethod.TTest - ).stat + ).statistics.stat comp.print() } + + companion object { + + fun rndData( + vararg cols: Pair, + len: Int = 100, + random: Random = Random.Default + ) = run { + val datum = cols.map { + val d = it.second + it.first to when (d) { + Normal -> (0 until len).map { random.nextDouble() } + Gaussian -> (0 until len).map { random.asJavaRandom().nextGaussian() } + is Category -> (0 until len).map { random.nextInt(d.n).toString() } + } + } + datum.toMap().toDataFrame() + } + } } sealed interface Distribution diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt new file mode 100644 index 000000000..c3880d511 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt @@ -0,0 +1,39 @@ +package com.milaboratory.mixcr.postanalysis.dataframe.pubr + +import com.milaboratory.mixcr.postanalysis.dataframe.toPDF +import com.milaboratory.mixcr.postanalysis.dataframe.writePDF +import jetbrains.letsPlot.geom.geomBoxplot +import jetbrains.letsPlot.letsPlot +import org.jetbrains.kotlinx.dataframe.api.toMap +import org.junit.Test +import java.nio.file.Paths + +/** + * + */ +class StatCompareMeansTest { + + @Test + fun test1() { + val data = CompareMeansTest.rndData( + "V" to Gaussian, + "A" to Category(10), + "C" to Category(2), + len = 100000 + ) + + var plot = letsPlot(data.toMap()) { + x = "A" + y = "V" + fill = "A" + } + + plot += geomBoxplot() + plot += statCompareMeans() + + writePDF( + Paths.get("scratch/bp.pdf"), + plot.toPDF() + ) + } +} From 1e102c7758692d31f8a18c98c6250433ef59cf05 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 24 Dec 2021 16:18:30 +0300 Subject: [PATCH 125/282] save --- .../dataframe/pubr/CompareMeans.kt | 38 ++++++++++++------- .../dataframe/pubr/StatCompareMeans.kt | 33 +++++++++++++--- .../dataframe/pubr/StatCompareMeansTest.kt | 11 ++++-- 3 files changed, 60 insertions(+), 22 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt index a8e0e8b54..669116e41 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt @@ -95,7 +95,7 @@ interface CompareMeansParameters { class CompareMeans( override var formula: Formula? = null, override var data: AnyFrame? = null, - override val method: TestMethod = TestMethod.Wilcox, + override val method: TestMethod = TestMethod.Wilcoxon, override val groupBy: Factor? = null, override val pAdjustMethod: PValueCorrection.Method? = null, override val refGroup: RefGroup? = null, @@ -112,7 +112,7 @@ class CompareMeans( class CompareMeansImpl( val formula: Formula, val data: AnyFrame, - val method: TestMethod = TestMethod.Wilcox, + val method: TestMethod = TestMethod.Wilcoxon, val groupBy: Factor? = null, val pAdjustMethod: PValueCorrection.Method? = PValueCorrection.Method.Holm, val refGroup: RefGroup? = null @@ -124,13 +124,20 @@ class CompareMeansImpl( } /** data array for each group*/ - private val groups: List> = + private val groups: List> by lazy { data.groupBy(*formula.factor.arr).groups.toList().map { getRefGroup(it, formula.factor.arr) to it[formula.y].cast().toDoubleArray() } + } + + /** Method used to compute overall p-value */ + val overallPValueMethod = + if (method.pairedOnly) + TestMethod.ANOVA + else method /** Overall p-value computed with one way ANOVA */ - val anovaPValue by lazy { + val overallPValue by lazy { val datum = groups.map { it.second }.filter { it.size > 2 } if (datum.size < 2) -1.0 @@ -139,7 +146,7 @@ class CompareMeansImpl( } /** List of all "compare means" with no p-Value adjustment */ - private val compareMeansRaw: List = run { + private val compareMeansRaw: List by lazy { if (refGroup != null) { val groups = this.groups.toMap() @@ -196,7 +203,7 @@ class CompareMeansImpl( } /** Compare means with adjusted p-values and significance */ - private val compareMeansAdj = + private val compareMeansAdj by lazy { if (pAdjustMethod == null || compareMeansRaw.isEmpty()) compareMeansRaw else { @@ -210,9 +217,10 @@ class CompareMeansImpl( ) } } + } /** Compare means statistics */ - val stat = compareMeansAdj.toDataFrame() + val stat by lazy { compareMeansAdj.toDataFrame() } private fun getRefGroup(df: AnyFrame, group: Array) = run { val f = df.first() @@ -221,7 +229,7 @@ class CompareMeansImpl( /** Compute p-value */ private fun pValue(method: TestMethod, a: DoubleArray, b: DoubleArray) = when (method) { - TestMethod.Wilcox -> + TestMethod.Wilcoxon -> if (a.size != b.size) MannWhitneyUTest().mannWhitneyUTest(a, b) else @@ -252,11 +260,15 @@ enum class SignificanceLevel(val string: String) { } /** Method for calculation of p-value */ -enum class TestMethod { - TTest, - Wilcox, - ANOVA, - Kruskal +enum class TestMethod(val pairedOnly: Boolean, val str: String) { + TTest(true, "T-test"), + Wilcoxon(true, "Wilcoxon"), + ANOVA(false, "ANOVA"), + Kruskal(false, "Kruskal-Wallis"); + + override fun toString(): String { + return str; + } } /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt index acbf4452f..7035c3c30 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.postanalysis.dataframe.pubr import com.milaboratory.mixcr.postanalysis.stat.PValueCorrection +import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.geom.geomText import jetbrains.letsPlot.intern.Plot import org.jetbrains.kotlinx.dataframe.AnyFrame @@ -12,7 +13,7 @@ import org.jetbrains.kotlinx.dataframe.api.toDataFrame class statCompareMeans( override var formula: Formula? = null, override var data: AnyFrame? = null, - override val method: TestMethod = TestMethod.Wilcox, + override val method: TestMethod = TestMethod.Wilcoxon, override val groupBy: Factor? = null, override val pAdjustMethod: PValueCorrection.Method? = null, override val refGroup: RefGroup? = null, @@ -24,15 +25,31 @@ class statCompareMeans( } } +internal val Plot.boxPlotData + get() = this.data + ?: this.features.filterIsInstance().firstOrNull()?.data + ?: throw IllegalArgumentException("no data for statCompareMeans") + +internal val Plot.boxPlotMapping + get() = + if (!this.mapping.isEmpty()) + this.mapping + else { + val m = this.features.filterIsInstance().firstOrNull()?.mapping + ?: throw IllegalArgumentException("no mapping for statCompareMeans") + if (m.isEmpty() || !m.map.containsKey("y")) + throw IllegalArgumentException("no y found in mapping") + m + } operator fun Plot.plus(cmp: statCompareMeans) = run { if (cmp.data == null) { @Suppress("UNCHECKED_CAST") - cmp.data = (this.data!! as Map>).toDataFrame() + cmp.data = (this.boxPlotData as Map>).toDataFrame() } if (cmp.formula == null) { - val aes = this.mapping.map + val aes = this.boxPlotMapping.map val factor = if (aes.containsKey("x") && aes.containsKey("group")) Factor(aes["x"] as String, aes["group"] as String) @@ -48,11 +65,17 @@ operator fun Plot.plus(cmp: statCompareMeans) = run { if (cmp.pairs.isEmpty()) { + val stat = cmp.statistics val data = cmp.data!! val y = cmp.formula!!.y - val maxY = data[y].cast().max() + val yMax = data[y].cast().max() + - this + geomText(x = 0, y = maxY, label = "p-value " + cmp.statistics.anovaPValue) + this + geomText( + x = 0, + y = yMax * 1.1, + label = "${stat.overallPValueMethod} p-value ${stat.overallPValue}" + ) } else { this } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt index c3880d511..83ba95c53 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt @@ -2,8 +2,10 @@ package com.milaboratory.mixcr.postanalysis.dataframe.pubr import com.milaboratory.mixcr.postanalysis.dataframe.toPDF import com.milaboratory.mixcr.postanalysis.dataframe.writePDF +import jetbrains.letsPlot.elementRect import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.letsPlot +import jetbrains.letsPlot.theme import org.jetbrains.kotlinx.dataframe.api.toMap import org.junit.Test import java.nio.file.Paths @@ -17,18 +19,19 @@ class StatCompareMeansTest { fun test1() { val data = CompareMeansTest.rndData( "V" to Gaussian, - "A" to Category(10), + "A" to Category(2), "C" to Category(2), len = 100000 ) - var plot = letsPlot(data.toMap()) { + var plot = letsPlot() + + plot += geomBoxplot(data.toMap()) { x = "A" y = "V" fill = "A" - } + } + theme(panelGrid = "blank", panelBackground = elementRect(color = "black")) - plot += geomBoxplot() plot += statCompareMeans() writePDF( From 5cc18c23c773025b4588ece566aca0572c0975e8 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 24 Dec 2021 22:44:42 +0300 Subject: [PATCH 126/282] wip --- .../dataframe/pubr/CompareMeans.kt | 94 +++++++++---- .../dataframe/pubr/StatCompareMeans.kt | 66 +++++++--- .../dataframe/pubr/CompareMeansTest.kt | 8 +- .../dataframe/pubr/StatCompareMeansTest.kt | 123 ++++++++++++++++-- 4 files changed, 234 insertions(+), 57 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt index 669116e41..600119822 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt @@ -35,8 +35,11 @@ fun Factor(vararg columnNames: String) = Factor(columnNames.toList()) * Reference group **/ sealed interface RefGroup { + fun value(): Any + companion object { internal object All : RefGroup { + override fun value(): Any = "" override fun toString() = "all" } @@ -44,6 +47,7 @@ sealed interface RefGroup { val all: RefGroup = All internal data class RefGroupImpl(val colValues: List) : RefGroup { + override fun value(): Any = colValues.joinToString(",") override fun toString() = colValues.joinToString("+") } @@ -130,9 +134,15 @@ class CompareMeansImpl( } } + /** maximal y value */ + val yMax by lazy { allData.maxOrNull() ?: 0.0 } + + /** minimal y value */ + val yMin by lazy { allData.minOrNull() ?: 0.0 } + /** Method used to compute overall p-value */ val overallPValueMethod = - if (method.pairedOnly) + if (method.pairedOnly && groups.map { it.second }.filter { it.size > 2 }.size > 2) TestMethod.ANOVA else method @@ -142,7 +152,12 @@ class CompareMeansImpl( if (datum.size < 2) -1.0 else - OneWayAnova().anovaPValue(datum) + overallPValueMethod.pValue(*datum.toTypedArray()) + } + + /** Formatted [overallPValue] */ + val overallPValueFmt by lazy { + formatPValue(overallPValue) } /** List of all "compare means" with no p-Value adjustment */ @@ -165,7 +180,7 @@ class CompareMeansImpl( if (refData.size < 2 || data.size < 2) return@map null - val pValue = pValue(method, refData, data) + val pValue = method.pValue(refData, data) CompareMeansRow( formula.y, method, @@ -184,8 +199,7 @@ class CompareMeansImpl( if (iGroup.second.size < 2 || jGroup.second.size < 2) continue - val pValue = pValue( - method, + val pValue = method.pValue( iGroup.second, jGroup.second ) @@ -226,22 +240,6 @@ class CompareMeansImpl( val f = df.first() RefGroup.Companion.RefGroupImpl(group.map { f[it] }) } - - /** Compute p-value */ - private fun pValue(method: TestMethod, a: DoubleArray, b: DoubleArray) = when (method) { - TestMethod.Wilcoxon -> - if (a.size != b.size) - MannWhitneyUTest().mannWhitneyUTest(a, b) - else - WilcoxonSignedRankTest().wilcoxonSignedRankTest(a, b, false) - TestMethod.TTest -> - if (a.size != b.size) - TTest().tTest(a, b) - else - TTest().pairedTTest(a, b) - TestMethod.ANOVA -> OneWayAnova().anovaPValue(listOf(a, b)) - TestMethod.Kruskal -> throw RuntimeException("not supported yet") - } } enum class SignificanceLevel(val string: String) { @@ -259,16 +257,62 @@ enum class SignificanceLevel(val string: String) { } } +private fun formatPValue(pValue: Double, vararg oth: Double) = run { + val fn = (if (oth.isEmpty()) + listOf(pValue) + else + oth.toList()).map { d -> + d.toString() + .replace(".", "") + .toCharArray() + .indexOfFirst { it != '0' } + }.maxOrNull() ?: 3 + + "%.${fn}f".format(pValue) +} + /** Method for calculation of p-value */ enum class TestMethod(val pairedOnly: Boolean, val str: String) { - TTest(true, "T-test"), - Wilcoxon(true, "Wilcoxon"), - ANOVA(false, "ANOVA"), - Kruskal(false, "Kruskal-Wallis"); + TTest(true, "T-test") { + override fun pValue(vararg arr: DoubleArray): Double { + if (arr.size != 2) + throw IllegalArgumentException("more than 2 datasets passed") + val a = arr[0] + val b = arr[1] + return if (a.size != b.size) + TTest().tTest(a, b) + else + TTest().pairedTTest(a, b) + } + }, + Wilcoxon(true, "Wilcoxon") { + override fun pValue(vararg arr: DoubleArray): Double { + if (arr.size != 2) + throw IllegalArgumentException("more than 2 datasets passed") + val a = arr[0] + val b = arr[1] + return if (a.size != b.size) + MannWhitneyUTest().mannWhitneyUTest(a, b) + else + WilcoxonSignedRankTest().wilcoxonSignedRankTest(a, b, false) + } + }, + ANOVA(false, "ANOVA") { + override fun pValue(vararg arr: DoubleArray) = + OneWayAnova().anovaPValue(arr.toList()) + + }, + Kruskal(false, "Kruskal-Wallis") { + override fun pValue(vararg arr: DoubleArray): Double { + TODO("Not yet implemented") + } + }; override fun toString(): String { return str; } + + abstract fun pValue(vararg arr: DoubleArray): Double } /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt index 7035c3c30..02cd7f135 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt @@ -5,8 +5,6 @@ import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.geom.geomText import jetbrains.letsPlot.intern.Plot import org.jetbrains.kotlinx.dataframe.AnyFrame -import org.jetbrains.kotlinx.dataframe.api.cast -import org.jetbrains.kotlinx.dataframe.api.max import org.jetbrains.kotlinx.dataframe.api.toDataFrame @Suppress("ClassName") @@ -20,6 +18,9 @@ class statCompareMeans( val pairs: List> = emptyList() ) : CompareMeansParameters { + + internal var x: String? = null + val statistics by lazy { CompareMeansImpl(formula!!, data!!, method, groupBy, pAdjustMethod, refGroup) } @@ -42,14 +43,20 @@ internal val Plot.boxPlotMapping m } -operator fun Plot.plus(cmp: statCompareMeans) = run { +operator fun Plot.plus(cmp: statCompareMeans): Plot = run { if (cmp.data == null) { @Suppress("UNCHECKED_CAST") cmp.data = (this.boxPlotData as Map>).toDataFrame() } + val aes = this.boxPlotMapping.map + if (cmp.x == null) { + if (aes.containsKey("x")) + cmp.x = aes["x"] as String + else if (aes.containsKey("group")) + cmp.x = aes["пкщгз"] as String + } if (cmp.formula == null) { - val aes = this.boxPlotMapping.map val factor = if (aes.containsKey("x") && aes.containsKey("group")) Factor(aes["x"] as String, aes["group"] as String) @@ -59,24 +66,49 @@ operator fun Plot.plus(cmp: statCompareMeans) = run { Factor(aes["group"] as String) else Factor() - cmp.formula = Formula(aes["y"] as String, factor) } - if (cmp.pairs.isEmpty()) { + if (cmp.pairs.isEmpty() && cmp.refGroup == null) { + this.withOverallPValue(cmp) + } else if (cmp.refGroup != null) { + this.withSignificanceLevel(cmp) + } else + this +} + +private fun Plot.withOverallPValue(cmp: statCompareMeans) = run { + val stat = cmp.statistics - val stat = cmp.statistics - val data = cmp.data!! - val y = cmp.formula!!.y - val yMax = data[y].cast().max() + this + geomText( + x = 0, + y = stat.yMax * 1.1, + family = "Inter", + size = 8, + label = "${stat.overallPValueMethod}, p = ${stat.overallPValueFmt}" + ) +} +private fun Plot.withSignificanceLevel(cmp: statCompareMeans) = run { + val xVar = cmp.x!! + val stat = cmp.statistics - this + geomText( - x = 0, - y = yMax * 1.1, - label = "${stat.overallPValueMethod} p-value ${stat.overallPValue}" - ) - } else { - this + // group1 = refGroup + val statDf = stat.stat +// statDf[statDf.group2, statDf.pSignif].rename(statDf.group2.name() to x) +// listOf( +// stat.stat.group2, +// stat.stat.pSignif +// ).toDataFrame() + + this + geomText( + mapOf( + xVar to statDf.group2.toList().map { it.value() }, + "signif" to statDf.pSignif.toList().map { it.string } + ), + y = stat.yMax * 1.1 + ) { + x = xVar + label = "signif" } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt index 4ce2865da..a68906d2d 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt @@ -41,9 +41,10 @@ internal class CompareMeansTest { val datum = cols.map { val d = it.second it.first to when (d) { - Normal -> (0 until len).map { random.nextDouble() } - Gaussian -> (0 until len).map { random.asJavaRandom().nextGaussian() } - is Category -> (0 until len).map { random.nextInt(d.n).toString() } + Rnd -> (0 until len).map { if (it % 10 < 5) 1.0 * random.nextInt(1000) else 1000 * random.nextDouble() } + Normal -> (0 until len).map { 10 * random.nextDouble() } + Gaussian -> (0 until len).map { 10 * random.asJavaRandom().nextGaussian() } + is Category -> (0 until len).map { (65 + random.nextInt(d.n)).toChar().toString() } } } datum.toMap().toDataFrame() @@ -56,3 +57,4 @@ sealed interface Distribution data class Category(val n: Int) : Distribution object Gaussian : Distribution object Normal : Distribution +object Rnd : Distribution diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt index 83ba95c53..9a49979ea 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt @@ -2,41 +2,140 @@ package com.milaboratory.mixcr.postanalysis.dataframe.pubr import com.milaboratory.mixcr.postanalysis.dataframe.toPDF import com.milaboratory.mixcr.postanalysis.dataframe.writePDF +import jetbrains.datalore.plot.base.stat.math3.mean +import jetbrains.letsPlot.Pos import jetbrains.letsPlot.elementRect import jetbrains.letsPlot.geom.geomBoxplot +import jetbrains.letsPlot.geom.geomPoint +import jetbrains.letsPlot.geom.geomText import jetbrains.letsPlot.letsPlot import jetbrains.letsPlot.theme +import org.apache.commons.math3.distribution.BinomialDistribution +import org.apache.commons.math3.stat.StatUtils +import org.apache.commons.math3.stat.inference.TTest import org.jetbrains.kotlinx.dataframe.api.toMap import org.junit.Test import java.nio.file.Paths +import kotlin.random.Random +import kotlin.random.asJavaRandom /** * */ class StatCompareMeansTest { + @Test + fun name() { + val rnd = Random(100).asJavaRandom() + val d = BinomialDistribution(100, 0.1) +// val a = (0 until 111000).map { 1.0 * d.sample() }.toDoubleArray() +// val b = (0 until 111000).map { 1.0 * d.sample() }.toDoubleArray() + val a = (0 until 111000).map { it * 1.0 }.toDoubleArray() + val b = (0 until 111000).map { d.sample() * 1.0 }.toDoubleArray() + println(mean(a)) + println(mean(b)) + println(StatUtils.variance(a)) + println(StatUtils.variance(b)) + println(a.minOrNull()) + println(a.maxOrNull()) + println(b.minOrNull()) + println(b.maxOrNull()) + println(TTest().tTest(a, b)) + } + @Test fun test1() { + + val Y = "Y" + val X = "X" + val G = "G" + val data = CompareMeansTest.rndData( - "V" to Gaussian, - "A" to Category(2), - "C" to Category(2), - len = 100000 + "Y" to Rnd, + "X" to Category(10), + "G" to Category(2), + len = 100 + ) + + var plt = letsPlot(data.toMap()) { + x = X + y = Y + } + + plt += geomBoxplot { + fill = X + } + + plt += geomPoint( + position = Pos.jitterdodge, + shape = 21, + color = "black" + ) { + color = X + fill = X + } + + + plt += theme(panelGrid = "blank", panelBackground = elementRect(color = "black")) + .legendPositionTop() + + val overall = plt + statCompareMeans() + val refGroupAll = plt + statCompareMeans(method = TestMethod.TTest, refGroup = RefGroup.all) + val refGroupA = plt + statCompareMeans(method = TestMethod.TTest, refGroup = RefGroup.of("A")) + + + writePDF( + Paths.get("scratch/bp.pdf"), + overall.toPDF(), + refGroupAll.toPDF(), + refGroupA.toPDF() + ) + } + + @Test + fun test2() { + val data3 = mapOf( + "category" to listOf("1", "2", "3", "1", "2", "3", "1", "2", "3"), + "category2" to listOf("1", "2", "3", "1", "2", "3", "1", "2", "3"), + "value" to listOf(1, 2, 3, 4, 7, 8, 11, 0, 1) ) - var plot = letsPlot() + var p = letsPlot(data3) { + x = "category" + y = "value" + } + + p += geomBoxplot { + fill = "category" + } + + + p += geomPoint( + position = Pos.jitterdodge, + shape = 21, + color = "black" + ) { + color = "category" + fill = "category" + } + + + val sign = mapOf( + "category" to listOf("2", "1", "3"), + "z" to listOf("*", "**", "***") + ) - plot += geomBoxplot(data.toMap()) { - x = "A" - y = "V" - fill = "A" - } + theme(panelGrid = "blank", panelBackground = elementRect(color = "black")) + p += geomText(sign, y = 15) { + x = "category" + label = "z" + } - plot += statCompareMeans() + p += theme(panelGrid = "blank", panelBackground = elementRect(color = "black")) + .legendPositionTop() writePDF( Paths.get("scratch/bp.pdf"), - plot.toPDF() + p.toPDF() ) } } From 6a768a4fb2398b9b4ae9f3a97c8d5ac30b23908c Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Fri, 7 Jan 2022 00:07:04 +0300 Subject: [PATCH 127/282] Purification. No mixcr is a pure function in respect to data files. --- build.gradle.kts | 4 ++-- .../mixcr/assembler/CloneAssemblerRunner.java | 9 ++++----- .../mixcr/cli/CommandAssemble.java | 20 +++++++++---------- .../mixcr/cli/CommandAssembleContigs.java | 5 ++--- .../com/milaboratory/mixcr/util/RunMiXCR.java | 2 +- .../assembler/CloneAssemblerRunnerTest.java | 4 ++-- 6 files changed, 21 insertions(+), 23 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 76b522bdb..d2fda9c91 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -63,9 +63,9 @@ repositories { } } -val milibVersion = "1.14.1-18-f7ca543948" +val milibVersion = "0.0.1-4-eab6152014" val repseqioVersion = "1.3.5-5-2d9bf3f814" -val jacksonVersion = "2.12.4" +val jacksonVersion = "2.13.1" dependencies { api("com.milaboratory:milib:$milibVersion") diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index 7f32f9c62..d112210be 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -42,16 +42,15 @@ public class CloneAssemblerRunner implements CanReportProgressAndStage { final AlignmentsProvider alignmentsProvider; final CloneAssembler assembler; - final int threads; + final int threads = 1; volatile String stage = "Initialization"; volatile CanReportProgress innerProgress; volatile VDJCAlignmentsReader alignmentReader = null; volatile boolean isFinished = false; - public CloneAssemblerRunner(AlignmentsProvider alignmentsProvider, CloneAssembler assembler, int threads) { + public CloneAssemblerRunner(AlignmentsProvider alignmentsProvider, CloneAssembler assembler) { this.alignmentsProvider = alignmentsProvider; this.assembler = assembler; - this.threads = Math.min(threads, Runtime.getRuntime().availableProcessors()); } @Override @@ -104,8 +103,8 @@ public void run() { } try { CUtils.processAllInParallel(CUtils.buffered( - new FilteringPort<>(alignmentsPort, - assembler.getDeferredAlignmentsFilter()), 128), + new FilteringPort<>(alignmentsPort, + assembler.getDeferredAlignmentsFilter()), 128), assembler.getDeferredAlignmentsMapper(), threads); } catch (InterruptedException e) { throw new RuntimeException(e); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index f5710dc7b..083802b43 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -66,15 +66,15 @@ public class CommandAssemble extends ACommandWithSmartOverwriteWithSingleInputMi names = {"-p", "--preset"}) public String assemblerParametersName = "default"; - public int threads = Runtime.getRuntime().availableProcessors(); - - @Option(description = "Processing threads", - names = {"-t", "--threads"}) - public void setThreads(int threads) { - if (threads <= 0) - throwValidationException("-t / --threads must be positive"); - this.threads = threads; - } + // public int threads = Runtime.getRuntime().availableProcessors(); + // + // @Option(description = "Processing threads", + // names = {"-t", "--threads"}) + // public void setThreads(int threads) { + // if (threads <= 0) + // throwValidationException("-t / --threads must be positive"); + // this.threads = threads; + // } @Option(description = "Use higher compression for output file.", names = {"--high-compression"}) @@ -233,7 +233,7 @@ public void run1() throws Exception { // Running assembler CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner( alignmentsProvider, - assembler, threads); + assembler); SmartProgressReporter.startProgressReport(assemblerRunner); if (reportBuffers) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 0f2138986..3e33e03d8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -31,7 +31,6 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; -import cc.redberry.pipe.blocks.ParallelProcessor; import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; @@ -144,7 +143,7 @@ public void run1() throws Exception { ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments(); SmartProgressReporter.startProgressReport("Assembling contigs", cloneAlignmentsPort); - OutputPort parallelProcessor = new ParallelProcessor<>(cloneAlignmentsPort, cloneAlignments -> { + OutputPort parallelProcessor = CUtils.orderedParallelProcessor(cloneAlignmentsPort, cloneAlignments -> { Clone clone = cloneAlignments.clone; if (ignoreTags) @@ -242,7 +241,7 @@ public void run1() throws Exception { } catch (Throwable re) { throw new RuntimeException("While processing clone #" + clone.getId(), re); } - }, threads); + }, 1024, threads); for (Clone[] clones : CUtils.it(parallelProcessor)) { totalClonesCount += clones.length; diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 87616923e..25bc39035 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -102,7 +102,7 @@ public OutputPortCloseable create() { public long getTotalNumberOfReads() { return align.alignments.size(); } - }, assembler, parameters.threads); + }, assembler); //start progress reporting SmartProgressReporter.startProgressReport(assemblerRunner); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index e2b0cb66a..77656d724 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -121,7 +121,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException System.out.println(GlobalObjectMappers.toOneLine(assemblerParameters)); CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner(alignmentsProvider, - new CloneAssembler(assemblerParameters, true, aligner.getUsedGenes(), alignerParameters), 2); + new CloneAssembler(assemblerParameters, true, aligner.getUsedGenes(), alignerParameters)); SmartProgressReporter.startProgressReport(assemblerRunner); assemblerRunner.run(); @@ -157,4 +157,4 @@ private static void assertCSEquals(CloneSet expected, CloneSet actual) { for (int i = 0; i < expected.getClones().size(); ++i) Assert.assertEquals(expected.getClones().get(i), actual.getClones().get(i)); } -} \ No newline at end of file +} From f4ed1f7ddf8bd8dc9dfc8e3ea9bcf02c1b0ff2c9 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 19 Jan 2022 20:46:15 +0300 Subject: [PATCH 128/282] wip --- build.gradle.kts | 2 +- .../java/com/milaboratory/mixcr/cli/CommandAssemble.java | 2 +- .../postanalysis/dataframe/pubr/StatCompareMeans.kt | 7 ------- .../milaboratory/mixcr/assembler/AssemblerUtilsTest.java | 2 +- .../postanalysis/dataframe/pubr/CompareMeansTest.kt | 2 -- .../postanalysis/dataframe/pubr/StatCompareMeansTest.kt | 9 +++++++-- 6 files changed, 10 insertions(+), 14 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index a5e352fd7..1b5f411a6 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -5,7 +5,7 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile import java.net.InetAddress -val milibVersion = "1.14.1-16-774c60afab" +val milibVersion = "2.0.0" val repseqioVersion = "1.3.5-10-05b9291c5e" val jacksonVersion = "2.12.4" val letsPlotLibraryVersion = "2.1.0" diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index c8a4a15c1..4abab9b64 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -358,7 +358,7 @@ public void run1() throws Exception { } } else try (ClnsWriter writer = new ClnsWriter(out)) { - writer.writeCloneSet(getFullPipelineConfiguration(), cloneSet); + writer.writeCloneSet(pipelineConfiguration, cloneSet); } // Writing report diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt index 02cd7f135..4747759de 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt @@ -92,14 +92,7 @@ private fun Plot.withOverallPValue(cmp: statCompareMeans) = run { private fun Plot.withSignificanceLevel(cmp: statCompareMeans) = run { val xVar = cmp.x!! val stat = cmp.statistics - - // group1 = refGroup val statDf = stat.stat -// statDf[statDf.group2, statDf.pSignif].rename(statDf.group2.name() to x) -// listOf( -// stat.stat.group2, -// stat.stat.pSignif -// ).toDataFrame() this + geomText( mapOf( diff --git a/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java b/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java index 4f50266e7..5ead0d293 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java @@ -44,4 +44,4 @@ public void test1() throws Exception { Assert.assertEquals(1, mt.getThreshold(5)); Assert.assertEquals(0, mt.getThreshold(30)); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt index a68906d2d..62e7d593a 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt @@ -41,7 +41,6 @@ internal class CompareMeansTest { val datum = cols.map { val d = it.second it.first to when (d) { - Rnd -> (0 until len).map { if (it % 10 < 5) 1.0 * random.nextInt(1000) else 1000 * random.nextDouble() } Normal -> (0 until len).map { 10 * random.nextDouble() } Gaussian -> (0 until len).map { 10 * random.asJavaRandom().nextGaussian() } is Category -> (0 until len).map { (65 + random.nextInt(d.n)).toChar().toString() } @@ -57,4 +56,3 @@ sealed interface Distribution data class Category(val n: Int) : Distribution object Gaussian : Distribution object Normal : Distribution -object Rnd : Distribution diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt index 9a49979ea..56c1a1aea 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt @@ -9,6 +9,7 @@ import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.geom.geomPoint import jetbrains.letsPlot.geom.geomText import jetbrains.letsPlot.letsPlot +import jetbrains.letsPlot.scale.scaleColorManual import jetbrains.letsPlot.theme import org.apache.commons.math3.distribution.BinomialDistribution import org.apache.commons.math3.stat.StatUtils @@ -51,8 +52,8 @@ class StatCompareMeansTest { val G = "G" val data = CompareMeansTest.rndData( - "Y" to Rnd, - "X" to Category(10), + "Y" to Normal, + "X" to Category(5), "G" to Category(2), len = 100 ) @@ -75,6 +76,10 @@ class StatCompareMeansTest { fill = X } + plt += scaleColorManual( + listOf("#ffffff", "#aaaaaa") + ) + plt += theme(panelGrid = "blank", panelBackground = elementRect(color = "black")) .legendPositionTop() From e93c420e606f1e945238c7ce309ce46185acf0a5 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Thu, 10 Feb 2022 00:28:26 +0300 Subject: [PATCH 129/282] fix: fixes incorrect behaviour of amino acid mutations columns in the export for non-germline gene featires with frame shifts --- .../mixcr/export/FeatureExtractors.java | 26 ++++---- .../mixcr/export/FieldExtractors.java | 60 ++++++++++++------- 2 files changed, 52 insertions(+), 34 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java index 18c15c3f0..8fd0f6542 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java @@ -149,14 +149,15 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) { return "-"; GeneFeature alignedFeature = hit.getAlignedFeature(); -// if (!alignedFeature.contains(smallGeneFeature)) -// return "-"; + // if (!alignedFeature.contains(smallGeneFeature)) + // return "-"; VDJCGene gene = hit.getGene(); ReferencePoints germlinePartitioning = gene.getPartitioning(); if (!germlinePartitioning.isAvailable(bigGeneFeature)) return "-"; + Range bigTargetRage = germlinePartitioning.getRelativeRange(alignedFeature, bigGeneFeature); Range smallTargetRage = smallGeneFeature.isAlignmentAttached() ? null : @@ -203,21 +204,24 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) { mutations = mutations.move(shift); -// int shift = germlinePartitioning.getRelativePosition(bigGeneFeature, smallGeneFeature.getFirstPoint()); -// if (shift < 0) -// continue; -// mutations = mutations.move(shift); -// mutations = mutations.extractRelativeMutationsForRange(bigRange); -// if (mutations == null) -// continue; + // int shift = germlinePartitioning.getRelativePosition(bigGeneFeature, smallGeneFeature.getFirstPoint()); + // if (shift < 0) + // continue; + // mutations = mutations.move(shift); + // mutations = mutations.extractRelativeMutationsForRange(bigRange); + // if (mutations == null) + // continue; } else mutations = alignment.getAbsoluteMutations().extractRelativeMutationsForRange(smallTargetRage); - return convert(mutations, gene.getFeature(bigGeneFeature), object.getFeature(smallGeneFeature).getSequence(), germlinePartitioning.getTranslationParameters(bigGeneFeature)); + return convert(mutations, gene.getFeature(bigGeneFeature), + object.getFeature(smallGeneFeature).getSequence(), + bigTargetRage.getRelativeRangeOf(smallTargetRage), + germlinePartitioning.getTranslationParameters(bigGeneFeature)); } return "-"; } - abstract String convert(Mutations mutations, NucleotideSequence seq1, NucleotideSequence seq2, TranslationParameters tr); + abstract String convert(Mutations mutations, NucleotideSequence seq1, NucleotideSequence seq2, Range range, TranslationParameters tr); } } diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index e466626d0..cc45a6f83 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -36,6 +36,7 @@ import com.milaboratory.core.mutations.Mutations; import com.milaboratory.core.mutations.MutationsUtil; import com.milaboratory.core.sequence.AminoAcidSequence; +import com.milaboratory.core.sequence.AminoAcidSequence.AminoAcidSequencePosition; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.TranslationParameters; @@ -57,6 +58,7 @@ public final class FieldExtractors { static final String NULL = ""; private static final DecimalFormat SCORE_FORMAT = new DecimalFormat("#.#"); + private static final int MAX_SHIFTED_TRIPLETS = 3; static Field[] descriptors = null; @@ -321,23 +323,23 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) { }); -// descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromLeft", "Export amino acid sequence of " + -// "specified gene feature starting from the leftmost nucleotide (differs from -aaFeature only for " + -// "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") { -// @Override -// public String convert(NSequenceWithQuality seq) { -// return AminoAcidSequence.translate(seq.getSequence(), FromLeftWithoutIncompleteCodon).toString(); -// } -// }); -// -// descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromRight", "Export amino acid sequence of " + -// "specified gene feature starting from the rightmost nucleotide (differs from -aaFeature only for " + -// "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") { -// @Override -// public String convert(NSequenceWithQuality seq) { -// return AminoAcidSequence.translate(seq.getSequence(), FromRightWithoutIncompleteCodon).toString(); -// } -// }); + // descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromLeft", "Export amino acid sequence of " + + // "specified gene feature starting from the leftmost nucleotide (differs from -aaFeature only for " + + // "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") { + // @Override + // public String convert(NSequenceWithQuality seq) { + // return AminoAcidSequence.translate(seq.getSequence(), FromLeftWithoutIncompleteCodon).toString(); + // } + // }); + // + // descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromRight", "Export amino acid sequence of " + + // "specified gene feature starting from the rightmost nucleotide (differs from -aaFeature only for " + + // "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") { + // @Override + // public String convert(NSequenceWithQuality seq) { + // return AminoAcidSequence.translate(seq.getSequence(), FromRightWithoutIncompleteCodon).toString(); + // } + // }); descriptorsList.add(new FeatureExtractors.NSeqExtractor("-minFeatureQuality", "Export minimal quality of specified gene feature", "Min. qual. ", "minQual") { @Override @@ -365,7 +367,7 @@ public String convert(NSequenceWithQuality seq) { new String[]{"N. Mutations in "}, new String[]{"nMutations"}) { @Override String convert(Mutations mutations, NucleotideSequence seq1, - NucleotideSequence seq2, TranslationParameters tr) { + NucleotideSequence seq2, Range range, TranslationParameters tr) { return mutations.encode(","); } }); @@ -375,7 +377,7 @@ String convert(Mutations mutations, NucleotideSequence seq1, new String[]{"N. Mutations in ", " relative to "}, new String[]{"nMutationsIn", "Relative"}) { @Override String convert(Mutations mutations, NucleotideSequence seq1, - NucleotideSequence seq2, TranslationParameters tr) { + NucleotideSequence seq2, Range range, TranslationParameters tr) { return mutations.encode(","); } }); @@ -387,11 +389,23 @@ final class AAMutations extends FeatureExtractors.MutationsExtractor { @Override String convert(Mutations mutations, NucleotideSequence seq1, - NucleotideSequence seq2, TranslationParameters tr) { + NucleotideSequence seq2, Range range, TranslationParameters tr) { if (tr == null) return "-"; - Mutations aaMuts = MutationsUtil.nt2aa(seq1, mutations, tr); + Mutations aaMuts = MutationsUtil.nt2aa(seq1, mutations, tr, MAX_SHIFTED_TRIPLETS); if (aaMuts == null) return "-"; + + AminoAcidSequencePosition aaPos = AminoAcidSequence.convertNtPositionToAA(range.getFrom(), seq1.size(), tr); + if (aaPos == null) + return "-"; + int aaFromP1 = aaPos.floor(); + aaPos = AminoAcidSequence.convertNtPositionToAA(range.getTo(), seq1.size(), tr); + if (aaPos == null) + return "-"; + int aaToP1 = aaPos.ceil(); + + aaMuts = aaMuts.extractAbsoluteMutationsForRange(aaFromP1, aaToP1); + return aaMuts.encode(","); } } @@ -410,9 +424,9 @@ final class MutationsDetailed extends FeatureExtractors.MutationsExtractor { } @Override - String convert(Mutations mutations, NucleotideSequence seq1, NucleotideSequence seq2, TranslationParameters tr) { + String convert(Mutations mutations, NucleotideSequence seq1, NucleotideSequence seq2, Range range, TranslationParameters tr) { if (tr == null) return "-"; - MutationsUtil.MutationNt2AADescriptor[] descriptors = MutationsUtil.nt2aaDetailed(seq1, mutations, tr, 10); + MutationsUtil.MutationNt2AADescriptor[] descriptors = MutationsUtil.nt2aaDetailed(seq1, mutations, tr, MAX_SHIFTED_TRIPLETS); if (descriptors == null) return "-"; StringBuilder sb = new StringBuilder(); From 504fdaf2cde34f1e5bf9a447df27343e1ea33be9 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Thu, 10 Feb 2022 21:07:37 +0300 Subject: [PATCH 130/282] Micro cleanup. --- .../mixcr/export/FieldExtractors.java | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index cc45a6f83..df434879f 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -322,25 +322,6 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) { } }); - - // descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromLeft", "Export amino acid sequence of " + - // "specified gene feature starting from the leftmost nucleotide (differs from -aaFeature only for " + - // "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") { - // @Override - // public String convert(NSequenceWithQuality seq) { - // return AminoAcidSequence.translate(seq.getSequence(), FromLeftWithoutIncompleteCodon).toString(); - // } - // }); - // - // descriptorsList.add(new FeatureExtractorDescriptor("-aaFeatureFromRight", "Export amino acid sequence of " + - // "specified gene feature starting from the rightmost nucleotide (differs from -aaFeature only for " + - // "sequences which length are not multiple of 3)", "AA. Seq.", "aaSeq") { - // @Override - // public String convert(NSequenceWithQuality seq) { - // return AminoAcidSequence.translate(seq.getSequence(), FromRightWithoutIncompleteCodon).toString(); - // } - // }); - descriptorsList.add(new FeatureExtractors.NSeqExtractor("-minFeatureQuality", "Export minimal quality of specified gene feature", "Min. qual. ", "minQual") { @Override public String convert(NSequenceWithQuality seq) { From cb413f093d91a55946cb628521e48d2f8b1522c4 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 14 Feb 2022 14:49:35 +0300 Subject: [PATCH 131/282] feat: AIRR fomat exporter (exportAirr subcommand) (#38) * feat: Airr format export command 1.0 * Final airr export implementation. --- build.gradle.kts | 2 +- .../mixcr/cli/CommandExportAirr.java | 187 +++++++++ .../java/com/milaboratory/mixcr/cli/Main.java | 2 + .../mixcr/export/AirrColumns.java | 363 ++++++++++++++++++ .../milaboratory/mixcr/export/AirrUtil.java | 140 +++++++ .../mixcr/export/AirrVDJCObjectWrapper.java | 39 ++ 6 files changed, 732 insertions(+), 1 deletion(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java create mode 100644 src/main/java/com/milaboratory/mixcr/export/AirrColumns.java create mode 100644 src/main/java/com/milaboratory/mixcr/export/AirrUtil.java create mode 100644 src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java diff --git a/build.gradle.kts b/build.gradle.kts index 867392d42..fee26008f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -8,7 +8,7 @@ plugins { application `maven-publish` id("com.palantir.git-version") version "0.12.3" - id("com.github.johnrengelman.shadow") version "7.0.0" + id("com.github.johnrengelman.shadow") version "7.1.2" } val miRepoAccessKeyId: String by project diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java new file mode 100644 index 000000000..be079b00e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java @@ -0,0 +1,187 @@ +package com.milaboratory.mixcr.cli; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.export.AirrVDJCObjectWrapper; +import com.milaboratory.mixcr.export.FieldExtractor; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; + +import java.io.PrintStream; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import static com.milaboratory.mixcr.basictypes.IOUtil.*; +import static com.milaboratory.mixcr.export.AirrColumns.*; +import static picocli.CommandLine.*; + +@Command(name = "exportAirr", + separator = " ", + description = "Exports a clns, clna or vdjca file to Airr formatted tsv file.") +public class CommandExportAirr extends ACommandMiXCR { + @Option(description = "Target id (use -1 to export from the target containing CDR3).", + names = {"-t", "--target"}) + public int targetId = -1; + + @Parameters(index = "0", description = "input_file.[vdjca|clna|clns]") + public String in; + @Parameters(index = "1", description = "output.tsv") + public String out; + + private IOUtil.MiXCRFileInfo info0 = null; + + public String getType() { + if (info0 == null) + info0 = (IOUtil.MiXCRFileInfo) fileInfoExtractorInstance.getFileInfo(in); + return info0.fileType; + } + + private List> CommonExtractors() { + List> ret = new ArrayList<>(Arrays.asList( + new Sequence(targetId), + new RevComp(), + new Productive(), + + new VDJCCalls(GeneType.Variable), + new VDJCCalls(GeneType.Diversity), + new VDJCCalls(GeneType.Joining), + new VDJCCalls(GeneType.Constant), + + new SequenceAlignment(targetId), + new GermlineAlignment(targetId), + + new CompleteVDJ(targetId), + + new NFeature(GeneFeature.CDR3, "junction"), + new AAFeature(GeneFeature.CDR3, "junction_aa"), + + new NFeature(GeneFeature.CDR1, "cdr1"), + new AAFeature(GeneFeature.CDR1, "cdr1_aa"), + + new NFeature(GeneFeature.CDR2, "cdr2"), + new AAFeature(GeneFeature.CDR2, "cdr2_aa"), + + new NFeature(GeneFeature.ShortCDR3, "cdr3"), + new AAFeature(GeneFeature.ShortCDR3, "cdr3_aa"), + + new NFeature(GeneFeature.FR1, "fwr1"), + new AAFeature(GeneFeature.FR1, "fwr1_aa"), + + new NFeature(GeneFeature.FR2, "fwr2"), + new AAFeature(GeneFeature.FR2, "fwr2_aa"), + + new NFeature(GeneFeature.FR3, "fwr3"), + new AAFeature(GeneFeature.FR3, "fwr3_aa"), + + new NFeature(GeneFeature.FR4, "fwr4"), + new AAFeature(GeneFeature.FR4, "fwr4_aa"), + + new AlignmentScoring(targetId, GeneType.Variable), + new AlignmentCigar(targetId, GeneType.Variable), + + new AlignmentScoring(targetId, GeneType.Diversity), + new AlignmentCigar(targetId, GeneType.Diversity), + + new AlignmentScoring(targetId, GeneType.Joining), + new AlignmentCigar(targetId, GeneType.Joining), + + new AlignmentScoring(targetId, GeneType.Constant), + new AlignmentCigar(targetId, GeneType.Constant) + )); + + for (GeneType gt : GeneType.VDJC_REFERENCE) + for (boolean start : new boolean[]{true, false}) + for (boolean germline : new boolean[]{true, false}) + ret.add(new SequenceAlignmentBoundary(targetId, gt, start, germline)); + + for (GeneType gt : GeneType.VDJC_REFERENCE) + for (boolean start : new boolean[]{true, false}) + ret.add(new AirrAlignmentBoundary(targetId, gt, start)); + + return ret; + } + + private List> CloneExtractors() { + List> ret = new ArrayList<>(); + ret.add(new CloneId()); + ret.addAll(CommonExtractors()); + ret.add(new CloneCount()); + return ret; + } + + private List> AlignmentsExtractors() { + List> ret = new ArrayList<>(); + ret.add(new AlignmentId()); + ret.addAll(CommonExtractors()); + return ret; + } + + @Override + public void run0() throws Exception { + List> extractors; + AutoCloseable closeable; + OutputPortCloseable port; + + Path inPath = Paths.get(in); + VDJCLibraryRegistry libraryRegistry = VDJCLibraryRegistry.getDefault(); + + switch (getType()) { + case MAGIC_CLNA: + extractors = CloneExtractors(); + ClnAReader clnaReader = new ClnAReader(inPath, libraryRegistry, 4); + //noinspection unchecked,rawtypes + port = (OutputPortCloseable) clnaReader.readClones(); + closeable = clnaReader; + break; + case MAGIC_CLNS: + extractors = CloneExtractors(); + ClnsReader clnsReader = new ClnsReader(inPath, libraryRegistry); + //noinspection unchecked,rawtypes + port = (OutputPortCloseable) clnsReader.readClones(); + closeable = clnsReader; + break; + case MAGIC_VDJC: + extractors = AlignmentsExtractors(); + VDJCAlignmentsReader alignmentsReader = new VDJCAlignmentsReader(inPath, libraryRegistry); + //noinspection unchecked,rawtypes + port = (OutputPortCloseable) alignmentsReader; + closeable = alignmentsReader; + break; + default: + throwValidationException("Unexpected file type."); + return; + } + + try (PrintStream output = new PrintStream(out); + AutoCloseable c = closeable; OutputPortCloseable p = port) { + boolean first = true; + + for (FieldExtractor extractor : extractors) { + if (!first) + output.print("\t"); + first = false; + output.print(extractor.getHeader()); + } + output.println(); + + for (VDJCObject obj : CUtils.it(port)) { + first = true; + + AirrVDJCObjectWrapper wrapper = new AirrVDJCObjectWrapper(obj); + + for (FieldExtractor extractor : extractors) { + if (!first) + output.print("\t"); + first = false; + output.print(extractor.extractValue(wrapper)); + } + output.println(); + } + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 311b77646..9143fc696 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -163,6 +163,8 @@ public static CommandLine mkCmd() { .addSubcommand("exportClones", CommandExport.mkClonesSpec()) .addSubcommand("exportClonesPretty", CommandExportClonesPretty.class) + .addSubcommand("exportAirr", CommandExportAirr.class) + .addSubcommand("exportReadsForClones", CommandExportReadsForClones.class) .addSubcommand("exportAlignmentsForClones", CommandExportAlignmentsForClones.class) .addSubcommand("exportReads", CommandExportReads.class) diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java new file mode 100644 index 000000000..d8c3b4dfa --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java @@ -0,0 +1,363 @@ +package com.milaboratory.mixcr.export; + +import com.milaboratory.core.Range; +import com.milaboratory.core.alignment.Alignment; +import com.milaboratory.core.sequence.AminoAcidSequence; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence; +import com.milaboratory.mixcr.export.AirrUtil.AirrAlignment; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGene; + +import java.util.Arrays; +import java.util.stream.Collectors; + +public final class AirrColumns { + private AirrColumns() { + } + + public static final class CloneId implements FieldExtractor { + @Override + public String getHeader() { + return "sequence_id"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + return "clone." + object.asClone().getId(); + } + } + + public static final class AlignmentId implements FieldExtractor { + @Override + public String getHeader() { + return "sequence_id"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + return "read." + object.asAlignment().getMinReadId(); + } + } + + public static final class Sequence implements FieldExtractor { + private final int targetId; + + public Sequence(int targetId) { + this.targetId = targetId; + } + + @Override + public String getHeader() { + return "sequence"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + int resolvedTargetId = targetId == -1 ? object.getBestTarget() : targetId; + return object.object.getTarget(resolvedTargetId).getSequence().toString(); + } + } + + public static final class RevComp implements FieldExtractor { + @Override + public String getHeader() { + return "rev_comp"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + return "F"; + } + } + + public static class Productive implements FieldExtractor { + @Override + public String getHeader() { + return "productive"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + // TODO better implementation + return "T"; + } + } + + public static final class VDJCCalls implements FieldExtractor { + private final GeneType gt; + + public VDJCCalls(GeneType gt) { + this.gt = gt; + } + + @Override + public String getHeader() { + return gt.getLetterLowerCase() + "_call"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + return Arrays.stream(object.object.getHits(gt)) + .map(h -> h.getGene().getName()) + .collect(Collectors.joining(",")); + } + } + + public static final class BestVDJCCall implements FieldExtractor { + private final GeneType gt; + + public BestVDJCCall(GeneType gt) { + this.gt = gt; + } + + @Override + public String getHeader() { + return Character.toLowerCase(gt.getLetter()) + "_call"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + VDJCGene bestHitGene = object.object.getBestHitGene(gt); + return bestHitGene == null ? "" : bestHitGene.getGeneName(); + } + } + + public static abstract class AirrAlignmentExtractor implements FieldExtractor { + private final int targetId; + + public AirrAlignmentExtractor(int targetId) { + this.targetId = targetId; + } + + public abstract String extractValue(AirrAlignment object); + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + int resolvedTargetId = targetId == -1 ? object.getBestTarget() : targetId; + AirrAlignment alignment = object.getAirrAlignment(resolvedTargetId); + return extractValue(alignment); + } + } + + public static final class SequenceAlignment extends AirrAlignmentExtractor { + public SequenceAlignment(int targetId) { + super(targetId); + } + + @Override + public String getHeader() { + return "sequence_alignment"; + } + + @Override + public String extractValue(AirrAlignment object) { + return object.sequence; + } + } + + public static final class GermlineAlignment extends AirrAlignmentExtractor { + public GermlineAlignment(int targetId) { + super(targetId); + } + + @Override + public String getHeader() { + return "germline_alignment"; + } + + @Override + public String extractValue(AirrAlignment object) { + return object.germline; + } + } + + public static final class NFeature implements FieldExtractor { + private final GeneFeature feature; + private final String header; + + public NFeature(GeneFeature feature, String header) { + this.feature = feature; + this.header = header; + } + + @Override + public String getHeader() { + return header; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + NSequenceWithQuality feature = object.object.getFeature(this.feature); + if (feature == null) + return ""; + return feature.getSequence().toString(); + } + } + + public static final class AAFeature implements FieldExtractor { + private final GeneFeature feature; + private final String header; + + public AAFeature(GeneFeature feature, String header) { + this.feature = feature; + this.header = header; + } + + @Override + public String getHeader() { + return header; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + AminoAcidSequence feature = object.object.getAAFeature(this.feature); + if (feature == null) + return ""; + return feature.toString(); + } + } + + public static abstract class AlignmentColumn implements FieldExtractor { + protected final int targetId; + protected final GeneType geneType; + + public AlignmentColumn(int targetId, GeneType geneType) { + this.targetId = targetId; + this.geneType = geneType; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + int resolvedTargetId = targetId == -1 ? object.getBestTarget() : targetId; + VDJCHit bestHit = object.object.getBestHit(geneType); + if (bestHit == null) + return ""; + Alignment alignment = bestHit.getAlignment(resolvedTargetId); + if (alignment == null) + return ""; + return extractValue(alignment); + } + + public abstract String extractValue(Alignment alignment); + } + + /** + * Scoring for actual alignment in actual target, in contrast with normal MiXCR output where score shows the sum for + * all targets, or an aggregated value for clonotypes. + */ + public static final class AlignmentScoring extends AlignmentColumn { + public AlignmentScoring(int targetId, GeneType geneType) { + super(targetId, geneType); + } + + @Override + public String getHeader() { + return geneType.getLetterLowerCase() + "_score"; + } + + @Override + public String extractValue(Alignment alignment) { + return "" + alignment.getScore(); + } + } + + public static final class AlignmentCigar extends AlignmentColumn { + public AlignmentCigar(int targetId, GeneType geneType) { + super(targetId, geneType); + } + + @Override + public String getHeader() { + return geneType.getLetterLowerCase() + "_cigar"; + } + + @Override + public String extractValue(Alignment alignment) { + return alignment.getCigarString(true); + } + } + + public static final class SequenceAlignmentBoundary extends AlignmentColumn { + final boolean start, germline; + + public SequenceAlignmentBoundary(int targetId, GeneType geneType, boolean start, boolean germline) { + super(targetId, geneType); + this.start = start; + this.germline = germline; + } + + @Override + public String getHeader() { + return geneType.getLetterLowerCase() + "_" + + (germline ? "germline" : "sequence") + "_" + + (start ? "start" : "end"); + } + + @Override + public String extractValue(Alignment alignment) { + Range range = germline ? alignment.getSequence1Range() : alignment.getSequence2Range(); + return "" + (start ? range.getLower() + 1 : range.getUpper()); + } + } + + public static final class AirrAlignmentBoundary extends AirrAlignmentExtractor { + private final GeneType geneType; + private final boolean start; + + public AirrAlignmentBoundary(int targetId, GeneType geneType, boolean start) { + super(targetId); + this.geneType = geneType; + this.start = start; + } + + @Override + public String getHeader() { + return geneType.getLetterLowerCase() + "_alignment_" + + (start ? "start" : "end"); + } + + @Override + public String extractValue(AirrAlignment object) { + Range range = object.ranges.get(geneType); + if (range == null) + return ""; + return "" + (start ? range.getLower() + 1 : range.getUpper()); + } + } + + public static final class CloneCount implements FieldExtractor { + @Override + public String getHeader() { + return "duplicate_count"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + return "" + (int) Math.round(object.asClone().getCount()); + } + } + + public static final class CompleteVDJ implements FieldExtractor { + private final int targetId; + + public CompleteVDJ(int targetId) { + this.targetId = targetId; + } + + @Override + public String getHeader() { + return "complete_vdj"; + } + + @Override + public String extractValue(AirrVDJCObjectWrapper object) { + int resolvedTargetId = targetId == -1 ? object.getBestTarget() : targetId; + VDJCPartitionedSequence partitionedTarget = object.object.getPartitionedTarget(resolvedTargetId); + return partitionedTarget.getPartitioning().isAvailable(GeneFeature.VDJRegion) ? "T" : "F"; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java b/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java new file mode 100644 index 000000000..357ba3713 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java @@ -0,0 +1,140 @@ +package com.milaboratory.mixcr.export; + +import com.milaboratory.core.Range; +import com.milaboratory.core.alignment.Alignment; +import com.milaboratory.core.alignment.MultiAlignmentHelper; +import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.util.BitArray; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.EnumMap; +import java.util.List; + +public final class AirrUtil { + private AirrUtil() { + } + + public static AirrAlignment calculateAirAlignment(VDJCObject object, int targetId) { + NucleotideSequence target = object.getTarget(targetId).getSequence(); + MultiAlignmentHelper.Settings settings = new MultiAlignmentHelper.Settings( + false, false, false, ' ', ' '); + List> alignments = new ArrayList<>(); + List actualGeneTypes = new ArrayList<>(); + for (GeneType gt : GeneType.VDJC_REFERENCE) { + VDJCHit bestHit = object.getBestHit(gt); + if (bestHit == null) + continue; + Alignment alignment = bestHit.getAlignment(targetId); + if (alignment == null) + continue; + actualGeneTypes.add(gt); + alignments.add(alignment.invert(target)); + } + // noinspection unchecked + MultiAlignmentHelper helper = MultiAlignmentHelper.build(settings, new Range(0, target.size()), target, alignments.toArray(new Alignment[0])); + + // merging alignments + String sequence = helper.getSubject(); + StringBuilder germlineBuilder = new StringBuilder(); + GeneType[] geneType = new GeneType[helper.size()]; + int[] germlinePosition = new int[helper.size()]; + Arrays.fill(germlinePosition, -1); + BitArray match = new BitArray(helper.size()); + int firstAligned = -1, lastAligned = 0; + outer: + for (int i = 0; i < helper.size(); i++) { + for (int gti = 0; gti < actualGeneTypes.size(); gti++) { + if (helper.getQuery(gti).charAt(i) != ' ') { + GeneType gt = actualGeneTypes.get(gti); + germlineBuilder.append(helper.getQuery(gti).charAt(i)); + geneType[i] = gt; + germlinePosition[i] = helper.getAbsQueryPositionAt(gti, i); + match.set(i, helper.getMatch()[gti].get(i)); + + if (firstAligned == -1) + firstAligned = i; + lastAligned = i; + + continue outer; + } + } + germlineBuilder.append('N'); + } + + // trimming unaligned + sequence = sequence.substring(firstAligned, lastAligned + 1); + String germline = germlineBuilder.substring(firstAligned, lastAligned + 1); + + return new AirrAlignment(sequence, germline, geneType, germlinePosition, match); + } + + /** + * Selects the most appropriate target for export in multi-target cases. + * + * Selection criteria is the following: + * - target containing CDR3 wins + * - if no CDR3 target with the longest total alignment length over best hits wins + * - if no alignments are present 0 is returned + */ + public static int bestTarget(VDJCObject obj) { + for (int i = 0; i < obj.numberOfTargets(); i++) + if (obj.getPartitionedTarget(i).getPartitioning().isAvailable(GeneFeature.CDR3)) + return i; + int maxAlignmentLength = -1; + int targetWithMaxAlignmentLength = -1; + for (int i = 0; i < obj.numberOfTargets(); i++) { + int alignmentLength = 0; + for (GeneType gt : GeneType.VDJC_REFERENCE) { + VDJCHit bh = obj.getBestHit(gt); + if (bh == null) + continue; + Alignment al = bh.getAlignment(i); + if (al == null) + continue; + alignmentLength += al.getSequence2Range().length(); + } + if (alignmentLength > maxAlignmentLength) { + maxAlignmentLength = alignmentLength; + targetWithMaxAlignmentLength = i; + } + } + return targetWithMaxAlignmentLength; + } + + public static class AirrAlignment { + final String sequence, germline; + final GeneType[] geneType; + final int[] germlinePosition; + final BitArray match; + final EnumMap ranges; + + public AirrAlignment(String sequence, String germline, + GeneType[] geneType, int[] germlinePosition, + BitArray match) { + this.sequence = sequence; + this.germline = germline; + this.geneType = geneType; + this.germlinePosition = germlinePosition; + this.match = match; + EnumMap ranges = new EnumMap<>(GeneType.class); + for (GeneType gt : GeneType.VDJC_REFERENCE) { + int min = -1; + int max = -1; + for (int i = 0; i < geneType.length; i++) + if (geneType[i] == gt) { + if (min == -1) + min = i; + max = i; + } + if (min != -1) + ranges.put(gt, new Range(min, max + 1)); + } + this.ranges = ranges; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java b/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java new file mode 100644 index 000000000..beab6ad7c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java @@ -0,0 +1,39 @@ +package com.milaboratory.mixcr.export; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCObject; + +public final class AirrVDJCObjectWrapper { + public final VDJCObject object; + private int bestTarget = -1; + private int alignmentTarget = -1; + private AirrUtil.AirrAlignment alignment; + + public AirrVDJCObjectWrapper(VDJCObject object) { + this.object = object; + } + + public Clone asClone() { + return (Clone) object; + } + + public VDJCAlignments asAlignment() { + return (VDJCAlignments) object; + } + + public int getBestTarget() { + if (bestTarget != -1) + return bestTarget; + bestTarget = AirrUtil.bestTarget(object); + return bestTarget; + } + + public AirrUtil.AirrAlignment getAirrAlignment(int target) { + if (alignmentTarget == target) + return alignment; + alignmentTarget = target; + alignment = AirrUtil.calculateAirAlignment(object, target); + return alignment; + } +} From ab4697d0607cc08d56dc67ff47bd4884fc5ab312 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 14 Feb 2022 22:36:54 +0300 Subject: [PATCH 132/282] wip --- build.gradle.kts | 2 ++ 1 file changed, 2 insertions(+) diff --git a/build.gradle.kts b/build.gradle.kts index 1b5f411a6..62a4390f8 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -5,6 +5,7 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile import java.net.InetAddress +val miplotsVersion = "1.0.0" val milibVersion = "2.0.0" val repseqioVersion = "1.3.5-10-05b9291c5e" val jacksonVersion = "2.12.4" @@ -77,6 +78,7 @@ repositories { } dependencies { + api("com.milaboratory:miplots:$miplotsVersion") api("com.milaboratory:milib:$milibVersion") api("io.repseq:repseqio:$repseqioVersion") { exclude("com.milaboratory", "milib") From c5855599361f4fea7e59c74709e5daf2cb1802ce Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 16 Feb 2022 02:06:13 +0300 Subject: [PATCH 133/282] wip --- build.gradle.kts | 4 +- gradle/wrapper/gradle-wrapper.properties | 2 +- .../mixcr/cli/CommandExportPostanalysis.java | 130 ------- ...ommandPostanalysis.java => CommandPa.java} | 8 +- .../mixcr/cli/CommandPaExport.java | 176 +++++++++ .../java/com/milaboratory/mixcr/cli/Main.java | 14 +- .../postanalysis/dataframe/BasicStatistics.kt | 182 +++++++++ .../mixcr/postanalysis/dataframe/GeneUsage.kt | 87 ++--- .../mixcr/postanalysis/dataframe/Metadata.kt | 32 -- .../dataframe/SimpleStatistics.kt | 219 ----------- .../dataframe/SingleSpectratype.kt | 127 ++----- .../mixcr/postanalysis/dataframe/Util.kt | 109 +++--- .../dataframe/pubr/CompareMeans.kt | 344 ------------------ .../dataframe/pubr/StatCompareMeans.kt | 107 ------ .../mixcr/postanalysis/ui/GroupMelt.java | 2 +- ...stanalysisTest.java => CommandPaTest.java} | 2 +- .../dataframe/BasicStatisticsTest.kt | 48 +++ .../dataframe/SimpleStatisticsTest.kt | 37 -- .../dataframe/SingleSpectratypeTest.kt | 20 +- .../dataframe/pubr/CompareMeansTest.kt | 58 --- .../dataframe/pubr/StatCompareMeansTest.kt | 146 -------- 21 files changed, 545 insertions(+), 1309 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java rename src/main/java/com/milaboratory/mixcr/cli/{CommandPostanalysis.java => CommandPa.java} (98%) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt delete mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt rename src/test/java/com/milaboratory/mixcr/cli/{CommandPostanalysisTest.java => CommandPaTest.java} (78%) create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt delete mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt delete mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt delete mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt diff --git a/build.gradle.kts b/build.gradle.kts index a7a2a023e..4b0a02496 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -16,9 +16,9 @@ plugins { `java-library` application `maven-publish` - id("com.palantir.git-version") version "0.12.3" + id("com.palantir.git-version") version "0.13.0" id("com.github.johnrengelman.shadow") version "7.0.0" - kotlin("jvm") version "1.6.0-M1" + kotlin("jvm") version "1.6.10" id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-dev-808" } diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 05679dc3c..2e6e5897b 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java deleted file mode 100644 index cfb6b6797..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportPostanalysis.java +++ /dev/null @@ -1,130 +0,0 @@ -package com.milaboratory.mixcr.cli; - -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.cli.CommandPostanalysis.PaResult; -import com.milaboratory.mixcr.cli.CommandPostanalysis.PaResultByChain; -import com.milaboratory.mixcr.postanalysis.dataframe.SimpleStatistics; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; -import com.milaboratory.mixcr.postanalysis.ui.OutputTable; -import com.milaboratory.util.GlobalObjectMappers; -import io.repseq.core.Chains; -import picocli.CommandLine; -import picocli.CommandLine.Option; -import picocli.CommandLine.Parameters; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.Map; - -/** - * - */ -public abstract class CommandExportPostanalysis extends ACommandWithOutputMiXCR { - @Option(names = {"-m", "--metadata"}, description = "Metadata file") - public String metadata; - @Parameters(index = "0", description = "pa_result.json") - public String in; - @Parameters(index = "1", description = "output") - public String out; - - /** Check that directory */ - private void ensureChainsDirExists(Chains.NamedChains chains) { - try { - Files.createDirectories(Paths.get(out).resolve(chains.name)); - } catch (IOException e) { - throwExecutionException(e.getMessage()); - } - } - - Path outPath(Chains.NamedChains chains, String suffix) { - return Paths.get(out).resolve(chains.name).resolve(suffix); - } - - /** Cached PA result */ - private PaResult paResult = null; - - /** Get full PA result */ - PaResult getPaResult() { - try { - if (paResult != null) - return paResult; - return paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); - } catch (IOException e) { - throwValidationException("Broken input file: " + in); - return null; - } - } - - @Override - public void run0() throws Exception { - for (Map.Entry r : getPaResult().results.entrySet()) { - ensureChainsDirExists(r.getKey()); - run(r.getKey(), r.getValue()); - } - } - - abstract void run(Chains.NamedChains chains, PaResultByChain result); - - @CommandLine.Command(name = "tables", - sortOptions = false, - separator = " ", - description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") - public static final class ExportTables extends CommandExportPostanalysis { - @Override - void run(Chains.NamedChains chains, PaResultByChain result) { - for (CharacteristicGroup table : result.schema.tables) { - writeTables(chains, result.result.getTable(table)); - } - } - - void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { - for (CharacteristicGroupOutputExtractor view : tableResult.group.views) - for (OutputTable t : view.getTables(tableResult).values()) - t.writeTSV(Paths.get(chain.name).toAbsolutePath(), ""); - } - } - - @CommandLine.Command(name = "box-plots", - sortOptions = false, - separator = " ", - description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") - public static final class ExportBoxPlots extends CommandExportPostanalysis { - @Option(names = {"-p", "--primary-group"}, description = "Primary group") - public String primaryGroup; - @Option(names = {"-s", "--secondary-group"}, description = "Secondary group") - public String secondaryGroup; - - @Override - void run(Chains.NamedChains chains, PaResultByChain result) { - CharacteristicGroup biophysics = result.schema.getGroup(CommandPostanalysis.Biophysics); - - SimpleStatistics.INSTANCE.plotPDF(outPath(chains, "biophysics.pdf"), - result.result.forGroup(biophysics), - null, - SimpleStatistics.BoxPlotSettings.Companion.getDefault() - ); - - CharacteristicGroup diversity = result.schema.getGroup(CommandPostanalysis.Diversity); - SimpleStatistics.INSTANCE.plotPDF(outPath(chains, "diversity.pdf"), - result.result.forGroup(diversity), - null, - SimpleStatistics.BoxPlotSettings.Companion.getDefault() - ); - } - } - - - @CommandLine.Command(name = "exportPostanalysis", - separator = " ", - description = "Export postanalysis results.", - subcommands = { - CommandLine.HelpCommand.class - }) - public static class CommandExportPostanalysisMain { - } -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java similarity index 98% rename from src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java rename to src/main/java/com/milaboratory/mixcr/cli/CommandPa.java index e6888f51a..30b402195 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPostanalysis.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java @@ -49,7 +49,7 @@ /** * */ -public abstract class CommandPostanalysis extends ACommandWithOutputMiXCR { +public abstract class CommandPa extends ACommandWithOutputMiXCR { public static final NamedChains[] CHAINS = {TRAD_NAMED, TRB_NAMED, TRG_NAMED, IGH_NAMED, IGKL_NAMED}; @Parameters(description = "cloneset.{clns|clna}... result.json") @@ -216,7 +216,7 @@ public void run0() throws Exception { sortOptions = false, separator = " ", description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") - public static class CommandIndividual extends CommandPostanalysis { + public static class CommandIndividual extends CommandPa { public CommandIndividual() {} @Override @@ -307,7 +307,7 @@ PaResultByChain run(Chains chain) { sortOptions = false, separator = " ", description = "Overlap analysis") - public static class CommandOverlap extends CommandPostanalysis { + public static class CommandOverlap extends CommandPa { @Option(description = "Override downsampling for F2 umi|d[number]|f[number]", names = {"--f2-downsampling"}, required = false) @@ -352,7 +352,7 @@ PaResultByChain run(Chains chain) { .collect(Collectors.toList()); OverlapDataset overlapDataset = OverlapUtil.overlap( - getInputFiles().stream().map(CommandPostanalysis::getSampleId).collect(toList()), + getInputFiles().stream().map(CommandPa::getSampleId).collect(toList()), ordering, readers); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java new file mode 100644 index 000000000..6ffab2ba5 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -0,0 +1,176 @@ +package com.milaboratory.mixcr.cli; + +import com.milaboratory.miplots.ExportKt; +import com.milaboratory.miplots.stat.util.TestMethod; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.cli.CommandPa.PaResult; +import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; +import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatRow; +import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatistics; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; +import com.milaboratory.mixcr.postanalysis.ui.OutputTable; +import com.milaboratory.util.GlobalObjectMappers; +import io.repseq.core.Chains; +import jetbrains.letsPlot.intern.Plot; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import picocli.CommandLine; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; + +/** + * + */ +public abstract class CommandPaExport extends ACommandWithOutputMiXCR { + @Option(names = {"-m", "--meta", "--metadata"}, description = "Metadata file") + public String metadata; + @Parameters(index = "0", description = "pa_result.json") + public String in; + @Option(names = {"--chains"}, description = "Export for specific chains only") + public List chains; + + /** + * Cached PA result + */ + private PaResult paResult = null; + + /** + * Get full PA result + */ + PaResult getPaResult() { + try { + if (paResult != null) + return paResult; + return paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + } catch (IOException e) { + throwValidationException("Broken input file: " + in); + return null; + } + } + + @Override + public void run0() throws Exception { + Set set = chains == null + ? null + : chains.stream().map(Chains::getNamedChains).collect(Collectors.toSet()); + + for (Map.Entry r : getPaResult().results.entrySet()) { + if (set == null || set.stream().anyMatch(c -> c.chains.intersects(r.getKey().chains))) + run(r.getKey(), r.getValue()); + } + } + + abstract void run(Chains.NamedChains chains, PaResultByChain result); + + @CommandLine.Command(name = "tables", + sortOptions = false, + separator = " ", + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") + public static final class ExportTables extends CommandPaExport { + @Parameters(index = "1", description = "Output directory") + public String out; + + @Override + void run(Chains.NamedChains chains, PaResultByChain result) { + Path p = Path.of(out).toAbsolutePath(); + try { + Files.createDirectories(p); + } catch (IOException e) { + throw new RuntimeException(e); + } + for (CharacteristicGroup table : result.schema.tables) { + writeTables(chains, result.result.getTable(table)); + } + } + + void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { + for (CharacteristicGroupOutputExtractor view : tableResult.group.views) + for (OutputTable t : view.getTables(tableResult).values()) + t.writeCSV(Path.of(out).toAbsolutePath(), "", "\t", "." + chain.name + ".tsv"); + } + } + + static abstract class ExportBasicStatistics extends CommandPaExport { + abstract String group(); + + @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") + public String out; + + @Option(names = {"-p", "--primary-group"}, description = "Primary group") + public String primaryGroup; + @Option(names = {"-s", "--secondary-group"}, description = "Secondary group") + public String secondaryGroup; + @Option(names = {"--facet-by"}, description = "Facet by") + public String facetBy; + @Option(names = {"--metric"}, description = "Metrics to export") + public List metrics; + + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".pdf")) + throwValidationException("Output file must ends with .pdf extension"); + } + + @Override + void run(Chains.NamedChains chains, PaResultByChain result) { + CharacteristicGroup ch = result.schema.getGroup(group()); + + DataFrame df = BasicStatistics.INSTANCE.dataFrame( + result.result.forGroup(ch), + metrics, + metadata + ); + + List plots = BasicStatistics.INSTANCE.plots(df, + new BasicStatistics.PlotParameters( + primaryGroup, + secondaryGroup, + facetBy, + true, + true, + null, + false, + null, + null, + null, + false, + TestMethod.Wilcoxon, + TestMethod.KruskalWallis, + null + )); + + ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + } + } + + @CommandLine.Command(name = "biophysics", + sortOptions = false, + separator = " ", + description = "Export biophysical characteristics") + public static class ExportBiophysics extends ExportBasicStatistics { + @Override + String group() { + return CommandPa.Biophysics; + } + } + + @CommandLine.Command(name = "exportPostanalysis", + separator = " ", + description = "Export postanalysis results.", + subcommands = { + CommandLine.HelpCommand.class + }) + public static class CommandExportPostanalysisMain { + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 67dd885ea..a00b39ec2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -148,8 +148,8 @@ public static CommandLine mkCmd() { .setCommandName(command) .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) - .addSubcommand("postanalysis", CommandPostanalysis.CommandPostanalysisMain.class) - .addSubcommand("exportPostanalysis", CommandExportPostanalysis.CommandExportPostanalysisMain.class) + .addSubcommand("postanalysis", CommandPa.CommandPostanalysisMain.class) + .addSubcommand("exportPa", CommandPaExport.CommandExportPostanalysisMain.class) .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) @@ -191,13 +191,13 @@ public static CommandLine mkCmd() { cmd.getSubcommands() .get("postanalysis") - .addSubcommand("individual", CommandSpec.forAnnotatedObject(CommandPostanalysis.CommandIndividual.class)) - .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPostanalysis.CommandOverlap.class)); + .addSubcommand("individual", CommandSpec.forAnnotatedObject(CommandPa.CommandIndividual.class)) + .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPa.CommandOverlap.class)); cmd.getSubcommands() - .get("exportPostanalysis") - .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandExportPostanalysis.ExportBoxPlots.class)) - .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandExportPostanalysis.ExportTables.class)); + .get("exportPa") + .addSubcommand("biophysics", CommandSpec.forAnnotatedObject(CommandPaExport.ExportBiophysics.class)) + .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExport.ExportTables.class)); cmd.setSeparator(" "); return cmd; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt new file mode 100644 index 000000000..0e55e0dfc --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt @@ -0,0 +1,182 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.miplots.stat.util.PValueCorrection +import com.milaboratory.miplots.stat.util.RefGroup +import com.milaboratory.miplots.stat.util.TestMethod +import com.milaboratory.miplots.stat.xdiscrete.* +import com.milaboratory.miplots.writePDF +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import jetbrains.letsPlot.facet.facetWrap +import jetbrains.letsPlot.geom.geomBoxplot +import jetbrains.letsPlot.intern.Plot +import jetbrains.letsPlot.label.ggtitle +import jetbrains.letsPlot.label.xlab +import jetbrains.letsPlot.letsPlot +import org.jetbrains.kotlinx.dataframe.AnyFrame +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.* +import org.jetbrains.kotlinx.dataframe.io.read +import java.nio.file.Path + +/** + * DataFrame row for single statistical char group + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +data class BasicStatRow( + /** Sample ID */ + val sample: String, + + /** Metric name */ + val metric: String, + + /** Value */ + val value: Double, +) + +object BasicStatistics { + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paResult: PostanalysisResult, + metricsFilter: List?, + ): DataFrame = run { + val data = mutableListOf() + + val mf = metricsFilter?.toSet() + for ((_, charData) in paResult.data) { + for ((sampleId, keys) in charData.data) { + for (metric in keys.data) { + val key = metric.key.toString() + if (mf != null && !mf.contains(key)) { + continue + } + data += BasicStatRow(sampleId, key, metric.value) + } + } + } + + data.toDataFrame() + } + + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paResult: PostanalysisResult, + metricsFilter: List?, + metadataPath: String?, + ) = run { + var df = dataFrame(paResult, metricsFilter) + if (metadataPath != null) + df = df.withMetadata(DataFrame.read(metadataPath)) + df + } + + /** + * Attaches metadata to statistics + **/ + fun DataFrame.withMetadata(metadata: AnyFrame) = run { + attachMetadata(this, "sample", metadata, "sample").cast() + } + + data class PlotParameters( + val primaryGroup: String? = null, + val secondaryGroup: String? = null, + val facetBy: String? = null, + val showOverallPValue: Boolean = true, + val showPairwisePValue: Boolean = true, + val refGroup: RefGroup? = null, + val hideNS: Boolean = false, + val overallPValueFormat: LabelFormat? = null, + val refPValueFormat: LabelFormat? = null, + val comparisonsPValueFormat: LabelFormat? = null, + val paired: Boolean = false, + val method: TestMethod = TestMethod.Wilcoxon, + val multipleGroupsMethod: TestMethod = TestMethod.KruskalWallis, + val pAdjustMethod: PValueCorrection.Method? = PValueCorrection.Method.Bonferroni, + ) + + fun plots( + df: DataFrame, + pp: PlotParameters, + ) = df.metric.distinct().toList() + .map { mt -> plot(df.filter { metric == mt }, pp) + ggtitle(mt) } + + fun write(path: String, plots: List) { + writePDF(Path.of(path), plots) + } + + fun plot( + df: DataFrame, + pp: PlotParameters, + ) = + if (pp.primaryGroup == null) { + val data = df.add(List(df.rowsCount()) { "" }.toColumn("__x__")).toMap() + var plt = letsPlot(data) { + x = "__x__" + y = BasicStatRow::value.name + } + plt += geomBoxplot() + if (pp.facetBy != null) + plt += facetWrap(pp.facetBy) + + plt += xlab("") + plt + } else { + val plt = + if (df.isNumeric(pp.primaryGroup)) + GGLinePlot( + df, + x = pp.primaryGroup, + facetBy = pp.facetBy, + facetNRow = 1, + y = BasicStatRow::value.name + ) { + fill = pp.secondaryGroup ?: pp.primaryGroup + } + else + GGBoxPlot( + df, + x = pp.primaryGroup, + facetBy = pp.facetBy, + facetNRow = 1, + y = BasicStatRow::value.name + ) { + fill = pp.secondaryGroup ?: pp.primaryGroup + } + + if (pp.showPairwisePValue) + plt += statCompareMeans( + method = pp.method, + multipleGroupsMethod = pp.multipleGroupsMethod, + pAdjustMethod = pp.pAdjustMethod, + paired = pp.paired, + hideNS = pp.hideNS, + labelFormat = pp.comparisonsPValueFormat, + allComparisons = true + ) + + if (pp.refGroup != null) + plt += statCompareMeans( + method = pp.method, + multipleGroupsMethod = pp.multipleGroupsMethod, + pAdjustMethod = pp.pAdjustMethod, + paired = pp.paired, + hideNS = pp.hideNS, + labelFormat = pp.refPValueFormat, + refGroup = pp.refGroup + ) + + if (pp.showOverallPValue) + plt += statCompareMeans( + method = pp.method, + multipleGroupsMethod = pp.multipleGroupsMethod, + labelFormat = pp.overallPValueFormat, + ) + + plt.plot + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt index 3af1f0eb2..4c9c5cca4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt @@ -2,12 +2,10 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema -import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.coordCartesian import jetbrains.letsPlot.coordFixed import jetbrains.letsPlot.geom.geomTile import jetbrains.letsPlot.intern.Plot -import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.letsPlot import jetbrains.letsPlot.scale.scaleSizeIdentity import jetbrains.letsPlot.scale.scaleXDiscrete @@ -19,7 +17,6 @@ import org.jetbrains.kotlinx.dataframe.api.cast import org.jetbrains.kotlinx.dataframe.api.toDataFrame import org.jetbrains.kotlinx.dataframe.api.toMap import org.jetbrains.kotlinx.dataframe.io.writeCSV -import java.nio.file.Path /** @@ -67,33 +64,33 @@ object GeneUsage { data.toDataFrame().cast() } - - /** - * Create Plot - **/ - fun DataFrame.plot() = run { - var plt = letsPlot(toMap()) { - x = GeneUsageRow::gene.name - y = GeneUsageRow::sample.name - fill = GeneUsageRow::weight.name - } - - writeCSV("data.csv") - val xValues = this.gene.toList() - val yValues = this.sample.toList() - - plt += geomTile( -// sampling = samplingNone, -// size = 0.0, -// width = xValues.size * 40.0, -// height = yValues.size * 40.0 - ) - -// plt += scaleFillGradient() -// plt += ggsize(1024, 1024) - - addCommonParams(plt, xValues, yValues, true) - } +// +// /** +// * Create Plot +// **/ +// fun DataFrame.plot() = run { +// var plt = letsPlot(toMap()) { +// x = GeneUsageRow::gene.name +// y = GeneUsageRow::sample.name +// fill = GeneUsageRow::weight.name +// } +// +// writeCSV("data.csv") +// val xValues = this.gene.toList() +// val yValues = this.sample.toList() +// +// plt += geomTile( +//// sampling = samplingNone, +//// size = 0.0, +//// width = xValues.size * 40.0, +//// height = yValues.size * 40.0 +// ) +// +//// plt += scaleFillGradient() +//// plt += ggsize(1024, 1024) +// +// addCommonParams(plt, xValues, yValues, true) +// } /////// from CorrPlot private fun addCommonParams( @@ -127,34 +124,4 @@ object GeneUsage { } return plot } - - /** - * Export plot to PDF - * - * @param destination path to export PDF - */ - fun DataFrame.plotPDF( - destination: Path - ) = run { - writePDF( - destination, - toPdf(PlotSvgExport.buildSvgImageFromRawSpecs(plot().toSpec())) - ) - } - - /** - * Create and export plot into single PDF file - * - * @param destination path to export PDF - * @param paSett PA settings - * @param paResult PA results - * */ - fun plotPDF( - destination: Path, - paSett: PostanalysisSchema<*>, - paResult: PostanalysisResult, - group: String - ) { - dataFrame(paSett, paResult, group).plotPDF(destination) - } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt deleted file mode 100644 index 8b41ac3ff..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Metadata.kt +++ /dev/null @@ -1,32 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.dataframe - -import org.jetbrains.kotlinx.dataframe.DataColumn -import org.jetbrains.kotlinx.dataframe.DataFrame -import org.jetbrains.kotlinx.dataframe.DataRow -import org.jetbrains.kotlinx.dataframe.annotations.DataSchema -import org.jetbrains.kotlinx.dataframe.api.column - -/** - * DataFrame row for metadata - */ -@DataSchema -@Suppress("UNCHECKED_CAST") -interface MetadataRow { - /** Sample */ - val sample: String - - companion object { - ////// DSL - - val sample by column() - - val DataFrame.sample get() = this[MetadataRow::sample.name] as DataColumn - val DataRow.sample get() = this[MetadataRow::sample.name] as String - } -} - -object Metadata { - - - -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt deleted file mode 100644 index e8e6abeae..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatistics.kt +++ /dev/null @@ -1,219 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.dataframe - -import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.dataframe.SimpleMetricsRow.Companion.metric -import com.milaboratory.mixcr.postanalysis.dataframe.SimpleMetricsRow.Companion.value -import com.milaboratory.mixcr.postanalysis.stat.HolmBonferroni -import jetbrains.datalore.plot.PlotSvgExport -import jetbrains.letsPlot.Pos -import jetbrains.letsPlot.geom.geomBoxplot -import jetbrains.letsPlot.geom.geomPoint -import jetbrains.letsPlot.intern.Plot -import jetbrains.letsPlot.intern.toSpec -import jetbrains.letsPlot.label.ggtitle -import jetbrains.letsPlot.label.labs -import jetbrains.letsPlot.letsPlot -import jetbrains.letsPlot.stat.statBoxplot -import jetbrains.letsPlot.stat.statContour -import org.jetbrains.kotlinx.dataframe.* -import org.jetbrains.kotlinx.dataframe.annotations.DataSchema -import org.jetbrains.kotlinx.dataframe.api.* -import java.nio.file.Path - -/** - * DataFrame row for single statistical char group - */ -@DataSchema -@Suppress("UNCHECKED_CAST") -interface SimpleMetricsRow { - /** Sample ID */ - val sample: String - - /** Metric name */ - val metric: String - - /** Value */ - val value: Double - - companion object { - ////// DSL - - val sample by column() - - val DataFrame.sample get() = this[SimpleMetricsRow::sample.name] as DataColumn - val DataRow.sample get() = this[SimpleMetricsRow::sample.name] as String - - val metric by column() - - val DataFrame.metric get() = this[SimpleMetricsRow::metric.name] as DataColumn - val DataRow.metric get() = this[SimpleMetricsRow::metric.name] as String - - val value by column() - - val DataFrame.value get() = this[SimpleMetricsRow::value.name] as DataColumn - val DataRow.value get() = this[SimpleMetricsRow::value.name] as Double - } -} - -object SimpleStatistics { - - /** - * Box plot settings - * - * @param metrics metrics to export in plots (null for all available metrics) - * @param primaryGroup metadata field used for primary grouping - * @param secondaryGroup metadata field used for secondary grouping - * */ - data class BoxPlotSettings( - val metrics: List? = null, - val primaryGroup: String? = null, - val primaryGroupOrder: List? = null, - val secondaryGroup: String? = null, - val secondaryGroupOrder: List? = null, - val applyHolmBonferroni: Boolean = false, - val HolmBonferroniFWer: Double = 0.01 - ) { - companion object { - val Default = BoxPlotSettings() - } - } - - /** - * Imports data into DataFrame - **/ - fun dataFrame( - paResult: PostanalysisResult, - metricsFilter: Set?, - ) = run { - - val data = mutableMapOf>( - SimpleMetricsRow::sample.name to mutableListOf(), - SimpleMetricsRow::metric.name to mutableListOf(), - SimpleMetricsRow::value.name to mutableListOf(), - ) - - for ((_, charData) in paResult.data) { - for ((sampleId, keys) in charData.data) { - for (metric in keys.data) { - val key = metric.key.toString() - if (metricsFilter != null && !metricsFilter.contains(key)) { - continue - } - data[SimpleMetricsRow::sample.name]!! += sampleId - data[SimpleMetricsRow::metric.name]!! += key - data[SimpleMetricsRow::value.name]!! += metric.value - } - } - } - - data.toDataFrame().cast() - } - - /** - * Attaches metadata to statistics - **/ - fun DataFrame.withMetadata(metadata: AnyFrame) = run { - this.leftJoin(metadata) { SimpleMetricsRow.sample } - } - - /** - * Create Plots for all metrics - **/ - fun DataFrame.plots( - settings: BoxPlotSettings, - ) = groupBy { SimpleMetricsRow.metric }.groups.map { df -> - - val filteredDf = - if (settings.applyHolmBonferroni) - HolmBonferroni.run( - df.rows().toList(), - { it.value }, - settings.HolmBonferroniFWer - ).toDataFrame() - else - df - - if (filteredDf.isEmpty()) - return@map null - - var plt: Plot = letsPlot(filteredDf.toMap()) { - x = settings.primaryGroup - y = SimpleMetricsRow.value.name() - group = settings.secondaryGroup - fill = settings.secondaryGroup ?: settings.primaryGroup - } - - - plt += geomBoxplot( - fatten = 2, - outlierShape = null, - outlierColor = null, - outlierSize = 0, -// position = positionDodge(0.1) - ) { -// color = settings.secondaryGroup -// fill = settings.secondaryGroup - } - - - plt += geomPoint( - position = Pos.jitterdodge, - shape = 21, - color = "black" - ) { - color = settings.secondaryGroup - fill = settings.secondaryGroup - } - - val metricName = if (!df.isEmpty()) { - df.first().metric - } else { - "" - } - - plt += ggtitle(metricName) - plt += labs(x = settings.primaryGroup, y = metricName) - -// plt += theme().axisTitleXBlank() -// plt += theme().axisTextXBlank() -// plt += theme().axisTicksXBlank() - - metricName to plt - }.filter { it != null }.map { it!! }.toList().toMap() - - - /** - * Export plot into single PDF file - * - * @param destination path to export PDF - * @param settings plot settings - * */ - fun DataFrame.plotPDF( - destination: Path, - settings: BoxPlotSettings, - ) = run { - writePDF(destination, - plots(settings).values.map { metric -> - PlotSvgExport.buildSvgImageFromRawSpecs( - metric.toSpec() - ) - }.toList().map { toPdf(it) } - ) - } - - /** - * Create and export all plots into single PDF file - * - * @param destination path to export PDF - * @param paResult PA results - * @param settings plot settings - * */ - fun plotPDF( - destination: Path, - paResult: PostanalysisResult, - metricsFilter: Set?, - settings: BoxPlotSettings - ) { - dataFrame(paResult, metricsFilter).plotPDF(destination, settings) - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt index f3f235b82..1dce57bf3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt @@ -1,73 +1,35 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.length -import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.payload -import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.sample -import com.milaboratory.mixcr.postanalysis.dataframe.SpectratypeRow.Companion.weight import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema -import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.* import jetbrains.letsPlot.geom.geomBar -import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.label.ggtitle import jetbrains.letsPlot.label.labs import jetbrains.letsPlot.scale.scaleXDiscrete -import org.jetbrains.kotlinx.dataframe.DataColumn import org.jetbrains.kotlinx.dataframe.DataFrame -import org.jetbrains.kotlinx.dataframe.DataRow import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.* -import java.nio.file.Path /** * DataFrame row for single (V/J/CDR3) spectratype */ @DataSchema @Suppress("UNCHECKED_CAST") -interface SpectratypeRow { +data class SpectratypeRow( /** Sample ID */ - val sample: String + val sample: String, /** Gene feature length */ - val length: Int + val length: Int, /** Payload (gene name / gene feature aa) */ - val payload: String + val payload: String, /** Payload weight */ - val weight: Double - - companion object { - ////// DSL - - val sample by column() - val length by column() - val payload by column() - val weight by column() - - val DataFrame.sample get() = this[SpectratypeRow::sample.name] as DataColumn - val DataRow.sample get() = this[SpectratypeRow::sample.name] as String - - val DataFrame.length get() = this[SpectratypeRow::length.name] as DataColumn - val DataRow.length get() = this[SpectratypeRow::length.name] as Int - - val DataFrame.payload get() = this[SpectratypeRow::payload.name] as DataColumn - val DataRow.payload get() = this[SpectratypeRow::payload.name] as String - - val DataFrame.weight get() = this[SpectratypeRow::weight.name] as DataColumn - val DataRow.weight get() = this[SpectratypeRow::weight.name] as Double - } -} - -data class SpectratypeRowImp( - override val sample: String, - override val length: Int, - override val weight: Double, - override val payload: String -) : SpectratypeRow - + val weight: Double, +) object SingleSpectratype { private const val OtherPayload = "Other" @@ -80,27 +42,19 @@ object SingleSpectratype { paResult: PostanalysisResult, group: String ): DataFrame { - val data = mutableMapOf>( - SpectratypeRow::sample.name to mutableListOf(), - SpectratypeRow::length.name to mutableListOf(), - SpectratypeRow::weight.name to mutableListOf(), - SpectratypeRow::payload.name to mutableListOf() - ) + val data = mutableListOf() for ((_, charData) in paResult.forGroup(paSett.getGroup>(group)).data) { for ((sampleId, keys) in charData.data) { for (metric in keys.data) { @Suppress("UNCHECKED_CAST") val key = metric.key as SpectratypeKey - data[SpectratypeRow::sample.name]!! += sampleId - data[SpectratypeRow::length.name]!! += key.length - data[SpectratypeRow::payload.name]!! += (key.payload ?: OtherPayload).toString() - data[SpectratypeRow::weight.name]!! += metric.value + data += SpectratypeRow(sampleId, key.length, (key.payload ?: OtherPayload).toString(), metric.value) } } } - return data.toDataFrame().cast() + return data.toDataFrame() } /** @@ -130,19 +84,19 @@ object SingleSpectratype { /** * Creates Plot for sample * - * @param sample sample + * @param smpl sample * @param settings plot settings * */ fun DataFrame.plot( - sample: String, + smpl: String, settings: SpectratypePlotSettings = SpectratypePlotSettings.Default, ) = run { var df = this // for sample - df = df.filter { SpectratypeRow.sample.eq(sample) } + df = df.filter { sample == smpl } // sort by weight - df = df.sortByDesc(SpectratypeRow.weight) + df = df.sortByDesc { weight } // select top val top = df.payload @@ -151,7 +105,7 @@ object SingleSpectratype { .toSet() // replace non top payloads with "Other" - df = df.update { SpectratypeRow.payload } + df = df.update { payload } .where { !top.contains(it) } .with { OtherPayload } @@ -162,19 +116,19 @@ object SingleSpectratype { // add auxiliary points for each cdr3 length df = df.concat( (min..max) - .map { SpectratypeRowImp(sample, it, 0.0, OtherPayload) } + .map { SpectratypeRow(smpl, it, OtherPayload, 0.0) } .toDataFrame() ) // collapse all "Other" into a single row df = df - .groupBy { SpectratypeRow.length and SpectratypeRow.payload } + .groupBy { length and payload } .aggregate { sumOf { it.weight } into SpectratypeRow::weight.name } // sort so that "Other" will be at the bottom when it is big - df = df.sortByDesc(SpectratypeRow.weight) + df = df.sortByDesc { weight } if (settings.normalize) df.add(SpectratypeRow::weight.name) { df.weight / df.weight.sum() } @@ -185,14 +139,14 @@ object SingleSpectratype { stat = Stat.identity, width = 0.6 ) { - x = asDiscrete(SpectratypeRow.length.name(), order = 1) - y = SpectratypeRow.weight.name() + x = asDiscrete(SpectratypeRow::length.name, order = 1) + y = SpectratypeRow::weight.name fill = asDiscrete( - SpectratypeRow.payload.name(), + SpectratypeRow::payload.name, orderBy = SpectratypeRow::weight.name, order = -1 ) } - plt += ggtitle(sample) + plt += ggtitle(smpl) plt += labs(y = "", x = "CDR3 length, bp") // adjust breaks @@ -210,43 +164,4 @@ object SingleSpectratype { plt } - - /** - * Export all plots into single PDF file - * - * @param destination path to export PDF - * @param settings plot settings - * */ - fun DataFrame.plotPDF( - destination: Path, - settings: SpectratypePlotSettings = SpectratypePlotSettings.Default, - ) = run { - writePDF(destination, - this.sample - .distinct().map { sample -> - PlotSvgExport.buildSvgImageFromRawSpecs( - plot(sample, settings).toSpec() - ) - }.toList() - .map { toPdf(it) } - ) - } - - /** - * Create and export all plots into single PDF file - * - * @param destination path to export PDF - * @param paSett PA settings - * @param paResult PA results - * @param settings plot settings - * */ - fun plotPDF( - destination: Path, - paSett: PostanalysisSchema<*>, - paResult: PostanalysisResult, - group: String, - settings: SpectratypePlotSettings = SpectratypePlotSettings.Default - ) { - dataFrame(paSett, paResult, group).plotPDF(destination, settings) - } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt index cebd9981a..1c0d8be64 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt @@ -1,54 +1,75 @@ package com.milaboratory.mixcr.postanalysis.dataframe -import jetbrains.datalore.plot.PlotSvgExport -import jetbrains.letsPlot.intern.Plot -import jetbrains.letsPlot.intern.toSpec -import org.apache.batik.transcoder.TranscoderInput -import org.apache.batik.transcoder.TranscoderOutput -import org.apache.fop.render.ps.EPSTranscoder -import org.apache.fop.svg.PDFTranscoder -import org.apache.pdfbox.io.MemoryUsageSetting -import org.apache.pdfbox.multipdf.PDFMergerUtility -import java.io.ByteArrayInputStream -import java.io.ByteArrayOutputStream -import java.nio.file.Path -import kotlin.io.path.absolutePathString -import kotlin.io.path.writeBytes - -fun Plot.toSvg() = PlotSvgExport.buildSvgImageFromRawSpecs(toSpec()) -fun Plot.toPDF() = toPdf(this.toSvg()) -fun Plot.toEPS() = toEPS(this.toSvg()) - -fun toPdf(svg: String) = toVector(svg, ExportType.PDF) -fun toEPS(svg: String) = toVector(svg, ExportType.EPS) - -enum class ExportType { PDF, EPS } - -private fun toVector(svg: String, type: ExportType) = run { - val pdfTranscoder = if (type == ExportType.PDF) PDFTranscoder() else EPSTranscoder() - val input = TranscoderInput(ByteArrayInputStream(svg.toByteArray())) - ByteArrayOutputStream().use { byteArrayOutputStream -> - val output = TranscoderOutput(byteArrayOutputStream) - pdfTranscoder.transcode(input, output) - byteArrayOutputStream.toByteArray() +import com.milaboratory.util.StringUtil +import org.jetbrains.kotlinx.dataframe.AnyFrame +import org.jetbrains.kotlinx.dataframe.api.add +import org.jetbrains.kotlinx.dataframe.api.all +import org.jetbrains.kotlinx.dataframe.api.cast +import org.jetbrains.kotlinx.dataframe.api.leftJoin +import java.util.* + + +fun AnyFrame.isNumeric(col: String) = this[col].all { it == null || it is Number } +fun AnyFrame.isCategorial(col: String) = !isNumeric(col) + +fun attachMetadata( + data: AnyFrame, + dataCol: String, + meta: AnyFrame, + metaCol: String +) = run { + val m = matchLists( + data[dataCol].distinct().cast().toList(), + meta[metaCol].distinct().cast().toList(), + ) + + m.filter { it.value == null }.apply { + if (!isEmpty()) + throw IllegalArgumentException("can't unambiguously match metadata for the following rows: $keys") } -} -fun writeEPS(destination: Path, image: ByteArray) { - destination.writeBytes(image) + data + .add("_meta_join_") { m[it[dataCol]] } + .leftJoin(meta) { "_meta_join_" match metaCol } } -fun writePDF(destination: Path, vararg images: ByteArray) { - writePDF(destination, images.toList()) -} +fun matchLists(target: List, query: List): Map { + val matched: MutableMap>> = HashMap() + for (t in target) { + val matchedForKey = PriorityQueue>( + Comparator.comparing { -it.second } + ) -fun writePDF(destination: Path, images: List) { - val merger = PDFMergerUtility() - merger.destinationFileName = destination.absolutePathString() + for (q in query) { + val a = t.lowercase(Locale.getDefault()) + val b = q.lowercase(Locale.getDefault()) + val match = StringUtil.longestCommonSubstring(a, b) + val score = 2.0 * (0.5 + match) / (1 + a.length + b.length) + matchedForKey.add(q to score) + } - for (image in images) { - merger.addSource(ByteArrayInputStream(image)) + matched[t] = matchedForKey } - merger.mergeDocuments(MemoryUsageSetting.setupMainMemoryOnly()) -} + val unmatchedQ = query.toMutableSet() + val r = mutableMapOf() + + for ((t, q) in matched.toList().sortedBy { kv -> -kv.second.maxOf { it.second } }) { + if (q.isEmpty()) { + r[t] = null + continue + } + var m: String? = null + while (!q.isEmpty()) { + val candidate = q.poll() + val wasUnmatched = unmatchedQ.remove(candidate.first) + if (wasUnmatched) { + m = candidate.first + break + } + } + r[t] = m + } + + return r +} \ No newline at end of file diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt deleted file mode 100644 index 600119822..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeans.kt +++ /dev/null @@ -1,344 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.dataframe.pubr - -import com.milaboratory.mixcr.postanalysis.dataframe.pubr.RefGroup.Companion.all -import com.milaboratory.mixcr.postanalysis.stat.PValueCorrection -import org.apache.commons.math3.stat.inference.MannWhitneyUTest -import org.apache.commons.math3.stat.inference.OneWayAnova -import org.apache.commons.math3.stat.inference.TTest -import org.apache.commons.math3.stat.inference.WilcoxonSignedRankTest -import org.jetbrains.kotlinx.dataframe.AnyFrame -import org.jetbrains.kotlinx.dataframe.annotations.DataSchema -import org.jetbrains.kotlinx.dataframe.api.* - -/** - * A formula containing - * y - a numeric variable - * factor - a factor with one or multiple levels - */ -data class Formula( - /** A numeric variable */ - val y: String, - /** A factor */ - val factor: Factor -) - -/** - * A group of columns representing a factor for grouping - */ -data class Factor(val columnNames: List) { - internal val arr = columnNames.toTypedArray() -} - -fun Factor(vararg columnNames: String) = Factor(columnNames.toList()) - -/** - * Reference group - **/ -sealed interface RefGroup { - fun value(): Any - - companion object { - internal object All : RefGroup { - override fun value(): Any = "" - override fun toString() = "all" - } - - /** All dataset */ - val all: RefGroup = All - - internal data class RefGroupImpl(val colValues: List) : RefGroup { - override fun value(): Any = colValues.joinToString(",") - override fun toString() = colValues.joinToString("+") - } - - /** Select part of dataset for specific values of columns */ - fun of(vararg columnValues: Any): RefGroup = RefGroupImpl(columnValues.toList()) - - /** Select part of dataset for specific values of columns */ - fun of(columnValues: List): RefGroup = RefGroupImpl(columnValues) - } -} - -interface CompareMeansParameters { - /** - * The formula - */ - var formula: Formula? - - /** - * A dataframe containing the variables in the formula. - */ - var data: AnyFrame? - - /** - * The type of test. Default is Wilcox - */ - val method: TestMethod - - /** - * Variables used to group the data set before applying the test. - * When specified the mean comparisons will be performed in each - * subset of the data formed by the different levels of the groupBy variables. - */ - val groupBy: Factor? - - /** - * Method for adjusting p values. Default is Holm. - */ - val pAdjustMethod: PValueCorrection.Method? - - /** - * The reference group. If specified, for a given grouping variable, each of the - * group levels will be compared to the reference group (i.e. control group). - * refGroup can be also “all”. In this case, each of the grouping variable levels - * is compared to all (i.e. base-mean). - */ - val refGroup: RefGroup? -} - -class CompareMeans( - override var formula: Formula? = null, - override var data: AnyFrame? = null, - override val method: TestMethod = TestMethod.Wilcoxon, - override val groupBy: Factor? = null, - override val pAdjustMethod: PValueCorrection.Method? = null, - override val refGroup: RefGroup? = null, -) : CompareMeansParameters { - - val statistics by lazy { - CompareMeansImpl(formula!!, data!!, method, groupBy, pAdjustMethod, refGroup) - } -} - -/** - * - */ -class CompareMeansImpl( - val formula: Formula, - val data: AnyFrame, - val method: TestMethod = TestMethod.Wilcoxon, - val groupBy: Factor? = null, - val pAdjustMethod: PValueCorrection.Method? = PValueCorrection.Method.Holm, - val refGroup: RefGroup? = null -) { - - /** all data array */ - private val allData by lazy { - data[formula.y].cast().toDoubleArray() - } - - /** data array for each group*/ - private val groups: List> by lazy { - data.groupBy(*formula.factor.arr).groups.toList().map { - getRefGroup(it, formula.factor.arr) to it[formula.y].cast().toDoubleArray() - } - } - - /** maximal y value */ - val yMax by lazy { allData.maxOrNull() ?: 0.0 } - - /** minimal y value */ - val yMin by lazy { allData.minOrNull() ?: 0.0 } - - /** Method used to compute overall p-value */ - val overallPValueMethod = - if (method.pairedOnly && groups.map { it.second }.filter { it.size > 2 }.size > 2) - TestMethod.ANOVA - else method - - /** Overall p-value computed with one way ANOVA */ - val overallPValue by lazy { - val datum = groups.map { it.second }.filter { it.size > 2 } - if (datum.size < 2) - -1.0 - else - overallPValueMethod.pValue(*datum.toTypedArray()) - } - - /** Formatted [overallPValue] */ - val overallPValueFmt by lazy { - formatPValue(overallPValue) - } - - /** List of all "compare means" with no p-Value adjustment */ - private val compareMeansRaw: List by lazy { - if (refGroup != null) { - val groups = this.groups.toMap() - - // get reference data - val refData = ( - if (refGroup == all) - allData - else - groups[refGroup] ?: throw IllegalArgumentException("reference group not found") - ) - - groups.map { (group, data) -> - if (group == refGroup) - return@map null - - if (refData.size < 2 || data.size < 2) - return@map null - - val pValue = method.pValue(refData, data) - - CompareMeansRow( - formula.y, method, - refGroup, group, - pValue, -1.0, SignificanceLevel.of(pValue) - ); - }.filterNotNull() - } else { - val cmpList = mutableListOf() - - for (i in groups.indices) { - for (j in 0 until i) { - val iGroup = groups[i] - val jGroup = groups[j] - - if (iGroup.second.size < 2 || jGroup.second.size < 2) - continue - - val pValue = method.pValue( - iGroup.second, - jGroup.second - ) - - cmpList += CompareMeansRow( - formula.y, method, - iGroup.first, jGroup.first, - pValue, -1.0, SignificanceLevel.of(pValue) - ) - } - } - - cmpList - } - } - - /** Compare means with adjusted p-values and significance */ - private val compareMeansAdj by lazy { - if (pAdjustMethod == null || compareMeansRaw.isEmpty()) - compareMeansRaw - else { - val adjusted = - PValueCorrection.adjustPValues(compareMeansRaw.map { it.pValue }.toDoubleArray(), pAdjustMethod) - - compareMeansRaw.mapIndexed { i, cmp -> - cmp.copy( - pValueAdj = adjusted[i], - pSignif = SignificanceLevel.of(adjusted[i]) - ) - } - } - } - - /** Compare means statistics */ - val stat by lazy { compareMeansAdj.toDataFrame() } - - private fun getRefGroup(df: AnyFrame, group: Array) = run { - val f = df.first() - RefGroup.Companion.RefGroupImpl(group.map { f[it] }) - } -} - -enum class SignificanceLevel(val string: String) { - NS("ns"), - One("*"), - Two("**"), - Three("***"); - - companion object { - fun of(pValue: Double) = - if (pValue >= 0.05) NS - else if (pValue < 0.0001) Three - else if (pValue < 0.001) Two - else One - } -} - -private fun formatPValue(pValue: Double, vararg oth: Double) = run { - val fn = (if (oth.isEmpty()) - listOf(pValue) - else - oth.toList()).map { d -> - d.toString() - .replace(".", "") - .toCharArray() - .indexOfFirst { it != '0' } - }.maxOrNull() ?: 3 - - "%.${fn}f".format(pValue) -} - -/** Method for calculation of p-value */ -enum class TestMethod(val pairedOnly: Boolean, val str: String) { - TTest(true, "T-test") { - override fun pValue(vararg arr: DoubleArray): Double { - if (arr.size != 2) - throw IllegalArgumentException("more than 2 datasets passed") - val a = arr[0] - val b = arr[1] - return if (a.size != b.size) - TTest().tTest(a, b) - else - TTest().pairedTTest(a, b) - } - }, - Wilcoxon(true, "Wilcoxon") { - override fun pValue(vararg arr: DoubleArray): Double { - if (arr.size != 2) - throw IllegalArgumentException("more than 2 datasets passed") - val a = arr[0] - val b = arr[1] - return if (a.size != b.size) - MannWhitneyUTest().mannWhitneyUTest(a, b) - else - WilcoxonSignedRankTest().wilcoxonSignedRankTest(a, b, false) - } - }, - ANOVA(false, "ANOVA") { - override fun pValue(vararg arr: DoubleArray) = - OneWayAnova().anovaPValue(arr.toList()) - - }, - Kruskal(false, "Kruskal-Wallis") { - override fun pValue(vararg arr: DoubleArray): Double { - TODO("Not yet implemented") - } - }; - - override fun toString(): String { - return str; - } - - abstract fun pValue(vararg arr: DoubleArray): Double -} - -/** - * DataFrame row for CompareMeans result - */ -@DataSchema -@Suppress("UNCHECKED_CAST") -data class CompareMeansRow( - /** The variable used in test */ - val y: String, - - /** Method used */ - val method: TestMethod, - - /** First group */ - val group1: RefGroup, - - /** Second group */ - val group2: RefGroup, - - /** The p-value */ - val pValue: Double, - - /** The adjusted p-value */ - val pValueAdj: Double, - - /** The significance level */ - val pSignif: SignificanceLevel -) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt deleted file mode 100644 index 4747759de..000000000 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeans.kt +++ /dev/null @@ -1,107 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.dataframe.pubr - -import com.milaboratory.mixcr.postanalysis.stat.PValueCorrection -import jetbrains.letsPlot.geom.geomBoxplot -import jetbrains.letsPlot.geom.geomText -import jetbrains.letsPlot.intern.Plot -import org.jetbrains.kotlinx.dataframe.AnyFrame -import org.jetbrains.kotlinx.dataframe.api.toDataFrame - -@Suppress("ClassName") -class statCompareMeans( - override var formula: Formula? = null, - override var data: AnyFrame? = null, - override val method: TestMethod = TestMethod.Wilcoxon, - override val groupBy: Factor? = null, - override val pAdjustMethod: PValueCorrection.Method? = null, - override val refGroup: RefGroup? = null, - - val pairs: List> = emptyList() -) : CompareMeansParameters { - - internal var x: String? = null - - val statistics by lazy { - CompareMeansImpl(formula!!, data!!, method, groupBy, pAdjustMethod, refGroup) - } -} - -internal val Plot.boxPlotData - get() = this.data - ?: this.features.filterIsInstance().firstOrNull()?.data - ?: throw IllegalArgumentException("no data for statCompareMeans") - -internal val Plot.boxPlotMapping - get() = - if (!this.mapping.isEmpty()) - this.mapping - else { - val m = this.features.filterIsInstance().firstOrNull()?.mapping - ?: throw IllegalArgumentException("no mapping for statCompareMeans") - if (m.isEmpty() || !m.map.containsKey("y")) - throw IllegalArgumentException("no y found in mapping") - m - } - -operator fun Plot.plus(cmp: statCompareMeans): Plot = run { - if (cmp.data == null) { - @Suppress("UNCHECKED_CAST") - cmp.data = (this.boxPlotData as Map>).toDataFrame() - } - - val aes = this.boxPlotMapping.map - if (cmp.x == null) { - if (aes.containsKey("x")) - cmp.x = aes["x"] as String - else if (aes.containsKey("group")) - cmp.x = aes["пкщгз"] as String - } - if (cmp.formula == null) { - val factor = - if (aes.containsKey("x") && aes.containsKey("group")) - Factor(aes["x"] as String, aes["group"] as String) - else if (aes.containsKey("x")) - Factor(aes["x"] as String) - else if (aes.containsKey("group")) - Factor(aes["group"] as String) - else - Factor() - cmp.formula = Formula(aes["y"] as String, factor) - } - - if (cmp.pairs.isEmpty() && cmp.refGroup == null) { - this.withOverallPValue(cmp) - } else if (cmp.refGroup != null) { - this.withSignificanceLevel(cmp) - } else - this -} - -private fun Plot.withOverallPValue(cmp: statCompareMeans) = run { - val stat = cmp.statistics - - this + geomText( - x = 0, - y = stat.yMax * 1.1, - family = "Inter", - size = 8, - label = "${stat.overallPValueMethod}, p = ${stat.overallPValueFmt}" - ) -} - -private fun Plot.withSignificanceLevel(cmp: statCompareMeans) = run { - val xVar = cmp.x!! - val stat = cmp.statistics - val statDf = stat.stat - - this + geomText( - mapOf( - xVar to statDf.group2.toList().map { it.value() }, - "signif" to statDf.pSignif.toList().map { it.string } - ), - y = stat.yMax * 1.1 - ) { - x = xVar - label = "signif" - } -} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java index be9652e23..728094c2b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java @@ -49,7 +49,7 @@ interface CoordinatesProvider { public static final class VJUsageMelt extends GroupMelt> { public VJUsageMelt() { - super("vjUsage_", + super("vjUsage.", (result, cell) -> cell.datasetId, () -> key -> new Coordinates(key.key.vGene, key.key.jJene)); } diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPostanalysisTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java similarity index 78% rename from src/test/java/com/milaboratory/mixcr/cli/CommandPostanalysisTest.java rename to src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java index f746fb6d4..1da372348 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPostanalysisTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java @@ -6,7 +6,7 @@ /** * */ -public class CommandPostanalysisTest extends TestCase { +public class CommandPaTest extends TestCase { @Test public void test1() { Main.main("postanalysis", "help", "overlap"); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt new file mode 100644 index 000000000..6e2e78d1e --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt @@ -0,0 +1,48 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.miplots.writePDF +import com.milaboratory.mixcr.cli.CommandPa +import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatistics.withMetadata +import com.milaboratory.util.GlobalObjectMappers +import io.repseq.core.Chains +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.api.filter +import org.jetbrains.kotlinx.dataframe.io.read +import org.junit.Test +import java.nio.file.Paths + + +/** + * + */ +internal class BasicStatisticsTest { + @Test + fun test1() { + val meta = DataFrame.read(javaClass.getResource("/postanalysis/metadata.csv")!!) + val pa = GlobalObjectMappers.PRETTY.readValue( + javaClass.getResource("/postanalysis/sample_pa.json"), + CommandPa.PaResult::class.java + ) + + val igh = pa.results[Chains.IGH_NAMED]!! + + + var df = BasicStatistics.dataFrame(igh.result.forGroup(igh.schema.getGroup("biophysics")), null) + df = df.withMetadata(meta) + + df = df.filter { metric == "ntLengthOfCDR3" } + + val plt = BasicStatistics.plot( + df, BasicStatistics.PlotParameters( + primaryGroup = "Cat3", + secondaryGroup = "Cat2", + facetBy = null + ) + ) + + writePDF( + Paths.get("scratch/pa/diversity.pdf"), + plt + ) + } +} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt deleted file mode 100644 index 57e00dea1..000000000 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SimpleStatisticsTest.kt +++ /dev/null @@ -1,37 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.dataframe - -import com.milaboratory.mixcr.cli.CommandPostanalysis -import com.milaboratory.mixcr.postanalysis.dataframe.SimpleStatistics.plotPDF -import com.milaboratory.mixcr.postanalysis.dataframe.SimpleStatistics.withMetadata -import com.milaboratory.util.GlobalObjectMappers -import io.repseq.core.Chains -import org.jetbrains.kotlinx.dataframe.DataFrame -import org.jetbrains.kotlinx.dataframe.io.read -import org.junit.Test -import java.nio.file.Paths - - -/** - * - */ -internal class SimpleStatisticsTest { - @Test - fun test1() { - val meta = DataFrame.read(javaClass.getResource("/postanalysis/metadata.csv")!!) - val pa = GlobalObjectMappers.PRETTY.readValue( - javaClass.getResource("/postanalysis/sample_pa.json"), - CommandPostanalysis.PaResult::class.java - ) - - val igh = pa.results[Chains.IGH_NAMED]!! - - var df = SimpleStatistics.dataFrame(igh.result.forGroup(igh.schema.getGroup("biophysics")), null) - - df = df.withMetadata(meta) - - df.plotPDF( - Paths.get("scratch/pa/diversity.pdf"), - SimpleStatistics.BoxPlotSettings(primaryGroup = "Cat3", applyHolmBonferroni = true) - ) - } -} diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt index 04880c05b..7f0e7c4f2 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt @@ -31,11 +31,11 @@ internal class SingleSpectratypeTest { fill = "weight" } + geomTile(color = "white") + coordFixed() - writePDF( - Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( - PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) - ) - ) +// writePDF( +// Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( +// PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) +// ) +// ) } @Test @@ -61,10 +61,10 @@ internal class SingleSpectratypeTest { ggsize(xs * f + 5 * f, 3 * ys * f / 5) - writePDF( - Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( - PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) - ) - ) +// writePDF( +// Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( +// PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) +// ) +// ) } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt deleted file mode 100644 index 62e7d593a..000000000 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/CompareMeansTest.kt +++ /dev/null @@ -1,58 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.dataframe.pubr - -import org.jetbrains.kotlinx.dataframe.api.print -import org.jetbrains.kotlinx.dataframe.api.toDataFrame -import org.junit.Test -import kotlin.random.Random -import kotlin.random.asJavaRandom - -/** - * - */ -internal class CompareMeansTest { - - - @Test - fun test1() { - val data = rndData( - "V" to Gaussian, - "A" to Category(2), - "C" to Category(2), - len = 100000 - ) - - val comp = CompareMeans( - Formula("V", Factor("A", "C")), - data, - refGroup = RefGroup.all, - method = TestMethod.TTest - ).statistics.stat - - comp.print() - } - - companion object { - - fun rndData( - vararg cols: Pair, - len: Int = 100, - random: Random = Random.Default - ) = run { - val datum = cols.map { - val d = it.second - it.first to when (d) { - Normal -> (0 until len).map { 10 * random.nextDouble() } - Gaussian -> (0 until len).map { 10 * random.asJavaRandom().nextGaussian() } - is Category -> (0 until len).map { (65 + random.nextInt(d.n)).toChar().toString() } - } - } - datum.toMap().toDataFrame() - } - } -} - -sealed interface Distribution - -data class Category(val n: Int) : Distribution -object Gaussian : Distribution -object Normal : Distribution diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt deleted file mode 100644 index 56c1a1aea..000000000 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/pubr/StatCompareMeansTest.kt +++ /dev/null @@ -1,146 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.dataframe.pubr - -import com.milaboratory.mixcr.postanalysis.dataframe.toPDF -import com.milaboratory.mixcr.postanalysis.dataframe.writePDF -import jetbrains.datalore.plot.base.stat.math3.mean -import jetbrains.letsPlot.Pos -import jetbrains.letsPlot.elementRect -import jetbrains.letsPlot.geom.geomBoxplot -import jetbrains.letsPlot.geom.geomPoint -import jetbrains.letsPlot.geom.geomText -import jetbrains.letsPlot.letsPlot -import jetbrains.letsPlot.scale.scaleColorManual -import jetbrains.letsPlot.theme -import org.apache.commons.math3.distribution.BinomialDistribution -import org.apache.commons.math3.stat.StatUtils -import org.apache.commons.math3.stat.inference.TTest -import org.jetbrains.kotlinx.dataframe.api.toMap -import org.junit.Test -import java.nio.file.Paths -import kotlin.random.Random -import kotlin.random.asJavaRandom - -/** - * - */ -class StatCompareMeansTest { - @Test - fun name() { - val rnd = Random(100).asJavaRandom() - val d = BinomialDistribution(100, 0.1) -// val a = (0 until 111000).map { 1.0 * d.sample() }.toDoubleArray() -// val b = (0 until 111000).map { 1.0 * d.sample() }.toDoubleArray() - val a = (0 until 111000).map { it * 1.0 }.toDoubleArray() - val b = (0 until 111000).map { d.sample() * 1.0 }.toDoubleArray() - println(mean(a)) - println(mean(b)) - println(StatUtils.variance(a)) - println(StatUtils.variance(b)) - println(a.minOrNull()) - println(a.maxOrNull()) - println(b.minOrNull()) - println(b.maxOrNull()) - println(TTest().tTest(a, b)) - } - - - @Test - fun test1() { - - val Y = "Y" - val X = "X" - val G = "G" - - val data = CompareMeansTest.rndData( - "Y" to Normal, - "X" to Category(5), - "G" to Category(2), - len = 100 - ) - - var plt = letsPlot(data.toMap()) { - x = X - y = Y - } - - plt += geomBoxplot { - fill = X - } - - plt += geomPoint( - position = Pos.jitterdodge, - shape = 21, - color = "black" - ) { - color = X - fill = X - } - - plt += scaleColorManual( - listOf("#ffffff", "#aaaaaa") - ) - - - plt += theme(panelGrid = "blank", panelBackground = elementRect(color = "black")) - .legendPositionTop() - - val overall = plt + statCompareMeans() - val refGroupAll = plt + statCompareMeans(method = TestMethod.TTest, refGroup = RefGroup.all) - val refGroupA = plt + statCompareMeans(method = TestMethod.TTest, refGroup = RefGroup.of("A")) - - - writePDF( - Paths.get("scratch/bp.pdf"), - overall.toPDF(), - refGroupAll.toPDF(), - refGroupA.toPDF() - ) - } - - @Test - fun test2() { - val data3 = mapOf( - "category" to listOf("1", "2", "3", "1", "2", "3", "1", "2", "3"), - "category2" to listOf("1", "2", "3", "1", "2", "3", "1", "2", "3"), - "value" to listOf(1, 2, 3, 4, 7, 8, 11, 0, 1) - ) - - var p = letsPlot(data3) { - x = "category" - y = "value" - } - - p += geomBoxplot { - fill = "category" - } - - - p += geomPoint( - position = Pos.jitterdodge, - shape = 21, - color = "black" - ) { - color = "category" - fill = "category" - } - - - val sign = mapOf( - "category" to listOf("2", "1", "3"), - "z" to listOf("*", "**", "***") - ) - - p += geomText(sign, y = 15) { - x = "category" - label = "z" - } - - p += theme(panelGrid = "blank", panelBackground = elementRect(color = "black")) - .legendPositionTop() - - writePDF( - Paths.get("scratch/bp.pdf"), - p.toPDF() - ) - } -} From fcc7e1c1ed1b801db4a871136d184a49c1352487 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 16 Feb 2022 23:58:05 +0300 Subject: [PATCH 134/282] feat: new fields in AIRR export feat: AIRR export added to integration tests feat: minor gradle script upgrades. --- build.gradle.kts | 2 +- gradle/wrapper/gradle-wrapper.jar | Bin 59203 -> 59536 bytes gradle/wrapper/gradle-wrapper.properties | 2 +- gradlew | 2 +- itests/case1.sh | 2 + itests/case4.sh | 4 + .../mixcr/cli/CommandExportAirr.java | 107 ++++++---- .../mixcr/export/AirrColumns.java | 184 ++++++++++++++++-- 8 files changed, 256 insertions(+), 47 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 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b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.4-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index 4f906e0c8..744e882ed 100755 --- a/gradlew +++ b/gradlew @@ -72,7 +72,7 @@ case "`uname`" in Darwin* ) darwin=true ;; - MINGW* ) + MSYS* | MINGW* ) msys=true ;; NONSTOP* ) diff --git a/itests/case1.sh b/itests/case1.sh index f33e082f6..b234f3fb3 100755 --- a/itests/case1.sh +++ b/itests/case1.sh @@ -3,4 +3,6 @@ set -euxo pipefail mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP -OsaveOriginalReads=true test_R1.fastq test_R2.fastq case1.vdjca +mixcr exportAirr case1.vdjca case1.vdjca.airr.tsv mixcr assemble case1.vdjca case1.clns +mixcr exportAirr case1.clns case1.clns.airr.tsv diff --git a/itests/case4.sh b/itests/case4.sh index f7e3bfcfd..217bc5abd 100755 --- a/itests/case4.sh +++ b/itests/case4.sh @@ -5,5 +5,9 @@ set -euxo pipefail # Checking generic pipeline with relatively big input files mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case4 +# Checking AIRR export on big files +mixcr exportAirr case4.vdjca case4.vdjca.airr.tsv +mixcr exportAirr case4.clna case4.clna.airr.tsv + # Checking skip steps behaviour mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case4 diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java index be079b00e..748644438 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java @@ -2,10 +2,12 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; +import cc.redberry.pipe.util.CountingOutputPort; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.export.AirrVDJCObjectWrapper; import com.milaboratory.mixcr.export.FieldExtractor; -import io.repseq.core.GeneFeature; +import com.milaboratory.util.CanReportProgress; +import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; @@ -18,6 +20,9 @@ import static com.milaboratory.mixcr.basictypes.IOUtil.*; import static com.milaboratory.mixcr.export.AirrColumns.*; +import static io.repseq.core.GeneFeature.*; +import static io.repseq.core.GeneType.*; +import static io.repseq.core.ReferencePoint.*; import static picocli.CommandLine.*; @Command(name = "exportAirr", @@ -41,65 +46,84 @@ public String getType() { return info0.fileType; } + @SuppressWarnings("UnnecessaryLocalVariable") private List> CommonExtractors() { + ComplexReferencePoint vnpEnd = new Leftmost(VEndTrimmed, VEnd); + ComplexReferencePoint dnpBegin = new Rightmost(DBegin, DBeginTrimmed); + ComplexReferencePoint dnpEnd = new Leftmost(DEnd, DEndTrimmed); + ComplexReferencePoint jnpBegin = new Rightmost(JBegin, JBeginTrimmed); + + ComplexReferencePoint np1Begin = vnpEnd; + ComplexReferencePoint np1End = new Leftmost(dnpBegin, jnpBegin); + + ComplexReferencePoint np2Begin = dnpEnd; + ComplexReferencePoint np2End = jnpBegin; + List> ret = new ArrayList<>(Arrays.asList( new Sequence(targetId), new RevComp(), new Productive(), - new VDJCCalls(GeneType.Variable), - new VDJCCalls(GeneType.Diversity), - new VDJCCalls(GeneType.Joining), - new VDJCCalls(GeneType.Constant), + new VDJCCalls(Variable), + new VDJCCalls(Diversity), + new VDJCCalls(Joining), + new VDJCCalls(Constant), new SequenceAlignment(targetId), new GermlineAlignment(targetId), new CompleteVDJ(targetId), - new NFeature(GeneFeature.CDR3, "junction"), - new AAFeature(GeneFeature.CDR3, "junction_aa"), + new NFeature(CDR3, "junction"), + new AAFeature(CDR3, "junction_aa"), + + new NFeature(targetId, np1Begin, np1End, "np1"), + new NFeature(targetId, np2Begin, np2End, "np2"), + + new NFeature(CDR1, "cdr1"), + new AAFeature(CDR1, "cdr1_aa"), - new NFeature(GeneFeature.CDR1, "cdr1"), - new AAFeature(GeneFeature.CDR1, "cdr1_aa"), + new NFeature(CDR2, "cdr2"), + new AAFeature(CDR2, "cdr2_aa"), - new NFeature(GeneFeature.CDR2, "cdr2"), - new AAFeature(GeneFeature.CDR2, "cdr2_aa"), + new NFeature(ShortCDR3, "cdr3"), + new AAFeature(ShortCDR3, "cdr3_aa"), - new NFeature(GeneFeature.ShortCDR3, "cdr3"), - new AAFeature(GeneFeature.ShortCDR3, "cdr3_aa"), + new NFeature(FR1, "fwr1"), + new AAFeature(FR1, "fwr1_aa"), - new NFeature(GeneFeature.FR1, "fwr1"), - new AAFeature(GeneFeature.FR1, "fwr1_aa"), + new NFeature(FR2, "fwr2"), + new AAFeature(FR2, "fwr2_aa"), - new NFeature(GeneFeature.FR2, "fwr2"), - new AAFeature(GeneFeature.FR2, "fwr2_aa"), + new NFeature(FR3, "fwr3"), + new AAFeature(FR3, "fwr3_aa"), - new NFeature(GeneFeature.FR3, "fwr3"), - new AAFeature(GeneFeature.FR3, "fwr3_aa"), + new NFeature(FR4, "fwr4"), + new AAFeature(FR4, "fwr4_aa"), - new NFeature(GeneFeature.FR4, "fwr4"), - new AAFeature(GeneFeature.FR4, "fwr4_aa"), + new AlignmentScoring(targetId, Variable), + new AlignmentCigar(targetId, Variable), - new AlignmentScoring(targetId, GeneType.Variable), - new AlignmentCigar(targetId, GeneType.Variable), + new AlignmentScoring(targetId, Diversity), + new AlignmentCigar(targetId, Diversity), - new AlignmentScoring(targetId, GeneType.Diversity), - new AlignmentCigar(targetId, GeneType.Diversity), + new AlignmentScoring(targetId, Joining), + new AlignmentCigar(targetId, Joining), - new AlignmentScoring(targetId, GeneType.Joining), - new AlignmentCigar(targetId, GeneType.Joining), + new AlignmentScoring(targetId, Constant), + new AlignmentCigar(targetId, Constant), - new AlignmentScoring(targetId, GeneType.Constant), - new AlignmentCigar(targetId, GeneType.Constant) + new NFeatureLength(CDR3, "junction_length"), + new NFeatureLength(targetId, np1Begin, np1End, "np1_length"), + new NFeatureLength(targetId, np2Begin, np2End, "np2_length") )); - for (GeneType gt : GeneType.VDJC_REFERENCE) + for (GeneType gt : VDJC_REFERENCE) for (boolean start : new boolean[]{true, false}) for (boolean germline : new boolean[]{true, false}) ret.add(new SequenceAlignmentBoundary(targetId, gt, start, germline)); - for (GeneType gt : GeneType.VDJC_REFERENCE) + for (GeneType gt : VDJC_REFERENCE) for (boolean start : new boolean[]{true, false}) ret.add(new AirrAlignmentBoundary(targetId, gt, start)); @@ -129,21 +153,35 @@ public void run0() throws Exception { Path inPath = Paths.get(in); VDJCLibraryRegistry libraryRegistry = VDJCLibraryRegistry.getDefault(); + CountingOutputPort cPort; + CanReportProgress progressReporter = null; switch (getType()) { case MAGIC_CLNA: extractors = CloneExtractors(); ClnAReader clnaReader = new ClnAReader(inPath, libraryRegistry, 4); //noinspection unchecked,rawtypes - port = (OutputPortCloseable) clnaReader.readClones(); + cPort = new CountingOutputPort<>((OutputPortCloseable) clnaReader.readClones()); + port = cPort; closeable = clnaReader; + progressReporter = SmartProgressReporter.extractProgress(cPort, clnaReader.numberOfClones()); break; case MAGIC_CLNS: extractors = CloneExtractors(); ClnsReader clnsReader = new ClnsReader(inPath, libraryRegistry); + + // I know, still writing airr is much slower... + int maxCount = 0; + try (OutputPortCloseable p = clnsReader.readClones()) { + for (Clone ignore : CUtils.it(p)) + ++maxCount; + } + //noinspection unchecked,rawtypes - port = (OutputPortCloseable) clnsReader.readClones(); + cPort = new CountingOutputPort<>((OutputPortCloseable) clnsReader.readClones()); + port = cPort; closeable = clnsReader; + progressReporter = SmartProgressReporter.extractProgress(cPort, maxCount); break; case MAGIC_VDJC: extractors = AlignmentsExtractors(); @@ -151,12 +189,15 @@ public void run0() throws Exception { //noinspection unchecked,rawtypes port = (OutputPortCloseable) alignmentsReader; closeable = alignmentsReader; + progressReporter = alignmentsReader; break; default: throwValidationException("Unexpected file type."); return; } + SmartProgressReporter.startProgressReport("Exporting to AIRR format", progressReporter); + try (PrintStream output = new PrintStream(out); AutoCloseable c = closeable; OutputPortCloseable p = port) { boolean first = true; diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java index d8c3b4dfa..370a6968b 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java +++ b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java @@ -8,9 +8,7 @@ import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence; import com.milaboratory.mixcr.export.AirrUtil.AirrAlignment; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; -import io.repseq.core.VDJCGene; +import io.repseq.core.*; import java.util.Arrays; import java.util.stream.Collectors; @@ -175,12 +173,120 @@ public String extractValue(AirrAlignment object) { } } - public static final class NFeature implements FieldExtractor { - private final GeneFeature feature; - private final String header; + public interface ComplexReferencePoint { + int getPosition(SequencePartitioning partitioning); + } - public NFeature(GeneFeature feature, String header) { + public static final class Single implements ComplexReferencePoint { + private final ReferencePoint point; + + public Single(ReferencePoint refPoint) { + this.point = refPoint; + } + + @Override + public int getPosition(SequencePartitioning partitioning) { + return partitioning.getPosition(point); + } + + @Override + public String toString() { + return point.toString(); + } + } + + public static final class Rightmost implements ComplexReferencePoint { + private final ComplexReferencePoint[] points; + + public Rightmost(ReferencePoint... points) { + this.points = new ComplexReferencePoint[points.length]; + for (int i = 0; i < points.length; i++) + this.points[i] = new Single(points[i]); + } + + public Rightmost(ComplexReferencePoint... points) { + this.points = points; + } + + @Override + public int getPosition(SequencePartitioning partitioning) { + int result = -1; + for (ComplexReferencePoint rp : points) { + int position = rp.getPosition(partitioning); + if (position < 0) + continue; + result = Math.max(result, position); + } + return result; + } + + @Override + public String toString() { + return "Rightmost{" + Arrays.toString(points) + '}'; + } + } + + public static final class Leftmost implements ComplexReferencePoint { + private final ComplexReferencePoint[] points; + + public Leftmost(ReferencePoint... points) { + this.points = new ComplexReferencePoint[points.length]; + for (int i = 0; i < points.length; i++) + this.points[i] = new Single(points[i]); + } + + public Leftmost(ComplexReferencePoint... points) { + this.points = points; + } + + @Override + public int getPosition(SequencePartitioning partitioning) { + int result = Integer.MAX_VALUE; + for (ComplexReferencePoint rp : points) { + int position = rp.getPosition(partitioning); + if (position < 0) + continue; + result = Math.min(result, position); + } + return result == Integer.MAX_VALUE ? -1 : result; + } + + @Override + public String toString() { + return "Leftmost{" + Arrays.toString(points) + '}'; + } + } + + public abstract static class NFeatureAbstract implements FieldExtractor { + /** + * Used only for complex features + */ + protected final int targetId; + /** + * Not null for simple gene features + */ + protected final GeneFeature feature; + /** + * Not null for complex gene features. + */ + protected final ComplexReferencePoint from, to; + protected final String header; + + public NFeatureAbstract(int targetId, + ComplexReferencePoint from, ComplexReferencePoint to, + String header) { + this.targetId = targetId; + this.feature = null; + this.from = from; + this.to = to; + this.header = header; + } + + public NFeatureAbstract(GeneFeature feature, String header) { + this.targetId = -1; // will not be used this.feature = feature; + this.from = null; + this.to = null; this.header = header; } @@ -191,10 +297,66 @@ public String getHeader() { @Override public String extractValue(AirrVDJCObjectWrapper object) { - NSequenceWithQuality feature = object.object.getFeature(this.feature); - if (feature == null) - return ""; - return feature.getSequence().toString(); + if (feature != null) { + NSequenceWithQuality feature = object.object.getFeature(this.feature); + if (feature == null) + return ""; + return extractValue(feature.getSequence()); + } else { + int resolvedTargetId = targetId == -1 ? object.getBestTarget() : targetId; + + assert from != null && to != null; + SequencePartitioning partitioning = object.object.getPartitionedTarget(resolvedTargetId).getPartitioning(); + + int fromPosition = from.getPosition(partitioning); + if (fromPosition < 0) + return ""; + + int toPosition = to.getPosition(partitioning); + if (toPosition < 0) + return ""; + + if (fromPosition < toPosition) + return extractValue(object.object.getTarget(resolvedTargetId).getSequence().getRange(fromPosition, toPosition)); + else + return extractValue(NucleotideSequence.EMPTY); + } + } + + protected abstract String extractValue(NucleotideSequence feature); + } + + public static final class NFeature extends NFeatureAbstract { + public NFeature(int targetId, + ComplexReferencePoint from, ComplexReferencePoint to, + String header) { + super(targetId, from, to, header); + } + + public NFeature(GeneFeature feature, String header) { + super(feature, header); + } + + @Override + public String extractValue(NucleotideSequence feature) { + return feature.toString(); + } + } + + public static final class NFeatureLength extends NFeatureAbstract { + public NFeatureLength(int targetId, + ComplexReferencePoint from, ComplexReferencePoint to, + String header) { + super(targetId, from, to, header); + } + + public NFeatureLength(GeneFeature feature, String header) { + super(feature, header); + } + + @Override + public String extractValue(NucleotideSequence feature) { + return "" + feature.size(); } } From ff11bea367b1da706e518656f4c2cca281c51500 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 17 Feb 2022 01:40:26 +0300 Subject: [PATCH 135/282] wip --- .../mixcr/cli/CommandPaExport.java | 60 +++++++++++++- .../java/com/milaboratory/mixcr/cli/Main.java | 4 +- .../postanalysis/dataframe/BasicStatistics.kt | 56 ++++++++----- .../mixcr/cli/CommandPaExportTest.java | 21 +++++ src/test/resources/postanalysis/metadata.csv | 80 +++++++++---------- 5 files changed, 156 insertions(+), 65 deletions(-) create mode 100644 src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 6ffab2ba5..0a7b6c6fa 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -2,6 +2,7 @@ import com.milaboratory.miplots.ExportKt; import com.milaboratory.miplots.stat.util.TestMethod; +import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.CommandPa.PaResult; import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; @@ -23,6 +24,7 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.Arrays; import java.util.List; import java.util.Map; import java.util.Set; @@ -100,6 +102,47 @@ void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tabl } } + @CommandLine.Command(name = "listMetrics", + sortOptions = false, + separator = " ", + description = "List available metrics") + static class ListMetrics extends ACommandMiXCR { + @Parameters(index = "0", description = "pa_result.json") + public String in; + + @Override + public void run0() { + PaResult paResult; + try { + paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + } catch (IOException e) { + throwValidationException("Corrupted PA file."); + throw new RuntimeException(); + } + + PaResultByChain result = paResult.results.values().stream().findAny().orElseThrow(); + CharacteristicGroup + biophys = result.schema.getGroup(CommandPa.Biophysics), + diversity = result.schema.getGroup(CommandPa.Diversity); + + for (int i = 0; i < 2; i++) { + System.out.println(); + CharacteristicGroup gr = i == 0 ? biophys : diversity; + if (i == 0) + System.out.println("Biophysics metrics:"); + else + System.out.println("Diversity metrics:"); + result.result.forGroup(gr) + .data.values().stream() + .flatMap(d -> d.data.values() + .stream().flatMap(ma -> Arrays.stream(ma.data))) + .map(m -> m.key) + .distinct() + .forEach(metric -> System.out.println(" " + metric)); + } + } + } + static abstract class ExportBasicStatistics extends CommandPaExport { abstract String group(); @@ -112,9 +155,10 @@ static abstract class ExportBasicStatistics extends CommandPaExport { public String secondaryGroup; @Option(names = {"--facet-by"}, description = "Facet by") public String facetBy; - @Option(names = {"--metric"}, description = "Metrics to export") + @Option(names = {"--metric"}, description = "Select specific metrics to export.") public List metrics; + @Override public void validate() { super.validate(); @@ -147,7 +191,8 @@ void run(Chains.NamedChains chains, PaResultByChain result) { false, TestMethod.Wilcoxon, TestMethod.KruskalWallis, - null + null, + CorrelationMethod.Pearson )); ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); @@ -165,6 +210,17 @@ String group() { } } + @CommandLine.Command(name = "diversity", + sortOptions = false, + separator = " ", + description = "Export diversity characteristics") + public static class ExportDiversity extends ExportBasicStatistics { + @Override + String group() { + return CommandPa.Diversity; + } + } + @CommandLine.Command(name = "exportPostanalysis", separator = " ", description = "Export postanalysis results.", diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index a00b39ec2..b546a1ef2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -196,8 +196,10 @@ public static CommandLine mkCmd() { cmd.getSubcommands() .get("exportPa") + .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExport.ExportTables.class)) + .addSubcommand("listMetrics", CommandSpec.forAnnotatedObject(CommandPaExport.ListMetrics.class)) .addSubcommand("biophysics", CommandSpec.forAnnotatedObject(CommandPaExport.ExportBiophysics.class)) - .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExport.ExportTables.class)); + .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandPaExport.ExportBiophysics.class)); cmd.setSeparator(" "); return cmd; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt index 0e55e0dfc..870091dbe 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt @@ -3,7 +3,14 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.miplots.stat.util.PValueCorrection import com.milaboratory.miplots.stat.util.RefGroup import com.milaboratory.miplots.stat.util.TestMethod -import com.milaboratory.miplots.stat.xdiscrete.* +import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod +import com.milaboratory.miplots.stat.xcontinious.GGScatter +import com.milaboratory.miplots.stat.xcontinious.plusAssign +import com.milaboratory.miplots.stat.xcontinious.statCor +import com.milaboratory.miplots.stat.xdiscrete.GGBoxPlot +import com.milaboratory.miplots.stat.xdiscrete.LabelFormat +import com.milaboratory.miplots.stat.xdiscrete.plusAssign +import com.milaboratory.miplots.stat.xdiscrete.statCompareMeans import com.milaboratory.miplots.writePDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult import jetbrains.letsPlot.facet.facetWrap @@ -97,6 +104,7 @@ object BasicStatistics { val method: TestMethod = TestMethod.Wilcoxon, val multipleGroupsMethod: TestMethod = TestMethod.KruskalWallis, val pAdjustMethod: PValueCorrection.Method? = PValueCorrection.Method.Bonferroni, + val correlationMethod: CorrelationMethod = CorrelationMethod.Pearson, ) fun plots( @@ -125,28 +133,32 @@ object BasicStatistics { plt += xlab("") plt + } else if (df.isNumeric(pp.primaryGroup)) { + val plt = GGScatter( + df, + x = pp.primaryGroup, + y = BasicStatRow::value.name, + facetBy = pp.facetBy, + facetNRow = 1, + ) { + shape = pp.secondaryGroup + color = pp.secondaryGroup + linetype = pp.secondaryGroup + } + + plt += statCor(method = pp.correlationMethod) + + plt.plot } else { - val plt = - if (df.isNumeric(pp.primaryGroup)) - GGLinePlot( - df, - x = pp.primaryGroup, - facetBy = pp.facetBy, - facetNRow = 1, - y = BasicStatRow::value.name - ) { - fill = pp.secondaryGroup ?: pp.primaryGroup - } - else - GGBoxPlot( - df, - x = pp.primaryGroup, - facetBy = pp.facetBy, - facetNRow = 1, - y = BasicStatRow::value.name - ) { - fill = pp.secondaryGroup ?: pp.primaryGroup - } + val plt = GGBoxPlot( + df, + x = pp.primaryGroup, + y = BasicStatRow::value.name, + facetBy = pp.facetBy, + facetNRow = 1, + ) { + fill = pp.secondaryGroup ?: pp.primaryGroup + } if (pp.showPairwisePValue) plt += statCompareMeans( diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java new file mode 100644 index 000000000..f6eedf992 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -0,0 +1,21 @@ +package com.milaboratory.mixcr.cli; + +import org.junit.Ignore; +import org.junit.Test; + +public class CommandPaExportTest { + @Ignore + @Test + public void test1() { + Main.main( + "exportPa", + "biophysics", + "--meta", + "scratch/metadata.csv", + "--primary-group", + "Cat2", + "scratch/pa/pa.json", + "scratch/pa/bio.pdf" + ); + } +} \ No newline at end of file diff --git a/src/test/resources/postanalysis/metadata.csv b/src/test/resources/postanalysis/metadata.csv index c01010266..bf51457a7 100644 --- a/src/test/resources/postanalysis/metadata.csv +++ b/src/test/resources/postanalysis/metadata.csv @@ -1,40 +1,40 @@ -sample,Cat3,Cat2 -d50_1-N-U023765_S1_L001.clns,B,X -d50_10-N-U022019_S1_L001.clns,A,Y -d50_11-B-U022019_S2_L001.clns,C,X -d50_12-D-U022019_S3_L001.clns,A,Y -d50_12782B_S12_L001.clns,B,X -d50_12782D_S11_L001.clns,A,Y -d50_12782N_S10_L001.clns,C,X -d50_13-N-U024230_S4_L001.clns,B,Y -d50_13457B_S3_L001.clns,B,X -d50_13457D_S2_L001.clns,A,Y -d50_13457N_S1_L001.clns,C,X -d50_13489D_S5_L001.clns,C,Y -d50_13489B_S6_L001.clns,B,X -d50_13489N_S4_L001.clns,A,Y -d50_13641B_S9_L001.clns,C,X -d50_13641D_S8_L001.clns,A,Y -d50_13641N_S7_L001.clns,B,X -d50_14-B-U024230_S5_L001.clns,A,X -d50_15-D-U024230_S6_L001.clns,C,Y -d50_16-N-U026467_S7_L001.clns,B,X -d50_17-B-U026467_S8_L001.clns,B,Y -d50_18-D-U026467_S9_L001.clns,A,X -d50_19-N-U027135_S1_L001.clns,C,Y -d50_2-B-U023765_S2_L001.clns,C,X -d50_20-B-U027135_S2_L001.clns,B,X -d50_21-D-U027135_S3_L001.clns,A,Y -d50_22-N-U029238_S4_L001.clns,C,X -d50_24-D-U029238_S6_L001.clns,A,Y -d50_23-B-U029238_S5_L001.clns,B,X -d50_25-N-U030739_S7_L001.clns,A,Y -d50_26-B-U030739_S8_L001.clns,C,X -d50_27-D-U030739_S9_L001.clns,B,Y -d50_3-D-U023765_S3_L001.clns,C,X -d50_5-B-U025238_S5_L001.clns,C,Y -d50_4-N-U025238_S4_L001.clns,B,X -d50_6-D-U025238_S6_L001.clns,A,Y -d50_7-N-U028710_S7_L001.clns,C,X -d50_8-B-U028710_S8_L001.clns,B,Y -d50_9-D-U028710_S9_L001.clns,A,X +sample,Cat3,Cat2,Num1 +d50_1-N-U023765_S1_L001.clns,B,X,12 +d50_10-N-U022019_S1_L001.clns,A,Y,23 +d50_11-B-U022019_S2_L001.clns,C,X,43 +d50_12-D-U022019_S3_L001.clns,A,Y,2 +d50_12782B_S12_L001.clns,B,X,4 +d50_12782D_S11_L001.clns,A,Y,5 +d50_12782N_S10_L001.clns,C,X,34 +d50_13-N-U024230_S4_L001.clns,B,Y,1 +d50_13457B_S3_L001.clns,B,X,43 +d50_13457D_S2_L001.clns,A,Y,5 +d50_13457N_S1_L001.clns,C,X,2 +d50_13489D_S5_L001.clns,C,Y,7 +d50_13489B_S6_L001.clns,B,X,8 +d50_13489N_S4_L001.clns,A,Y,2 +d50_13641B_S9_L001.clns,C,X,4 +d50_13641D_S8_L001.clns,A,Y,9 +d50_13641N_S7_L001.clns,B,X,7 +d50_14-B-U024230_S5_L001.clns,A,X,1 +d50_15-D-U024230_S6_L001.clns,C,Y,3 +d50_16-N-U026467_S7_L001.clns,B,X,6 +d50_17-B-U026467_S8_L001.clns,B,Y,9 +d50_18-D-U026467_S9_L001.clns,A,X,4 +d50_19-N-U027135_S1_L001.clns,C,Y,5 +d50_2-B-U023765_S2_L001.clns,C,X,8 +d50_20-B-U027135_S2_L001.clns,B,X,4 +d50_21-D-U027135_S3_L001.clns,A,Y,2 +d50_22-N-U029238_S4_L001.clns,C,X,4 +d50_24-D-U029238_S6_L001.clns,A,Y,8 +d50_23-B-U029238_S5_L001.clns,B,X,0 +d50_25-N-U030739_S7_L001.clns,A,Y,6 +d50_26-B-U030739_S8_L001.clns,C,X,12 +d50_27-D-U030739_S9_L001.clns,B,Y,3 +d50_3-D-U023765_S3_L001.clns,C,X,34 +d50_5-B-U025238_S5_L001.clns,C,Y,5 +d50_4-N-U025238_S4_L001.clns,B,X,89 +d50_6-D-U025238_S6_L001.clns,A,Y,8 +d50_7-N-U028710_S7_L001.clns,C,X,67 +d50_8-B-U028710_S8_L001.clns,B,Y,3 +d50_9-D-U028710_S9_L001.clns,A,X,2 From ce61080817f043d47c02a0ee2f768846650ced03 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 18 Feb 2022 01:42:32 +0300 Subject: [PATCH 136/282] wip --- .../mixcr/cli/CommandPaExport.java | 80 +++++++++- .../java/com/milaboratory/mixcr/cli/Main.java | 6 +- .../postanalysis/dataframe/BasicStatistics.kt | 15 -- .../mixcr/postanalysis/dataframe/GeneUsage.kt | 145 +++++++----------- .../dataframe/SingleSpectratype.kt | 4 +- .../mixcr/postanalysis/dataframe/Util.kt | 11 ++ .../mixcr/cli/CommandPaExportTest.java | 15 ++ .../dataframe/BasicStatisticsTest.kt | 1 - 8 files changed, 169 insertions(+), 108 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 0a7b6c6fa..530934cbb 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -8,6 +8,8 @@ import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatRow; import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatistics; +import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsage; +import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; @@ -158,7 +160,6 @@ static abstract class ExportBasicStatistics extends CommandPaExport { @Option(names = {"--metric"}, description = "Select specific metrics to export.") public List metrics; - @Override public void validate() { super.validate(); @@ -221,7 +222,82 @@ String group() { } } - @CommandLine.Command(name = "exportPostanalysis", + static abstract class ExportGeneUsage extends CommandPaExport { + abstract String group(); + + @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") + public String out; + @Option(names = {"--no-dendro-samples"}, description = "Plot dendrogram for hierarchical clusterization of samples.") + public boolean noSamplesDendro; + @Option(names = {"--no-dendro-genes"}, description = "Plot dendrogram for hierarchical clusterization of genes.") + public boolean noGenesDendro; + @Option(names = {"--color-key"}, description = "Add color key layer.") + public List colorKey; + + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".pdf")) + throwValidationException("Output file must ends with .pdf extension"); + } + + @Override + void run(Chains.NamedChains chains, PaResultByChain result) { + CharacteristicGroup ch = result.schema.getGroup(group()); + + DataFrame df = GeneUsage.INSTANCE.dataFrame( + result.result.forGroup(ch), + metadata + ); + + if (df.rowsCount() == 0) + return; + + Plot plots = GeneUsage.INSTANCE.plot(df, + new GeneUsage.PlotParameters( + colorKey, + !noSamplesDendro, + !noGenesDendro + )); + + ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + } + } + + @CommandLine.Command(name = "vUsage", + sortOptions = false, + separator = " ", + description = "Export V gene usage heatmap") + public static class ExportVUsage extends ExportGeneUsage { + @Override + String group() { + return CommandPa.VUsage; + } + } + + @CommandLine.Command(name = "jUsage", + sortOptions = false, + separator = " ", + description = "Export J gene usage heatmap") + public static class ExportJUsage extends ExportGeneUsage { + @Override + String group() { + return CommandPa.JUsage; + } + } + + @CommandLine.Command(name = "isotypeUsage", + sortOptions = false, + separator = " ", + description = "Export isotype usage heatmap") + public static class ExportIsotypeUsage extends ExportGeneUsage { + @Override + String group() { + return CommandPa.IsotypeUsage; + } + } + + @CommandLine.Command(name = "exportPa", separator = " ", description = "Export postanalysis results.", subcommands = { diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index b546a1ef2..0d24caf37 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -199,7 +199,11 @@ public static CommandLine mkCmd() { .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExport.ExportTables.class)) .addSubcommand("listMetrics", CommandSpec.forAnnotatedObject(CommandPaExport.ListMetrics.class)) .addSubcommand("biophysics", CommandSpec.forAnnotatedObject(CommandPaExport.ExportBiophysics.class)) - .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandPaExport.ExportBiophysics.class)); + .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandPaExport.ExportDiversity.class)) + + .addSubcommand("vUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVUsage.class)) + .addSubcommand("jUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportJUsage.class)) + .addSubcommand("isotypeUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportIsotypeUsage.class)); cmd.setSeparator(" "); return cmd; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt index 870091dbe..45d9c6d9a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt @@ -11,20 +11,16 @@ import com.milaboratory.miplots.stat.xdiscrete.GGBoxPlot import com.milaboratory.miplots.stat.xdiscrete.LabelFormat import com.milaboratory.miplots.stat.xdiscrete.plusAssign import com.milaboratory.miplots.stat.xdiscrete.statCompareMeans -import com.milaboratory.miplots.writePDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult import jetbrains.letsPlot.facet.facetWrap import jetbrains.letsPlot.geom.geomBoxplot -import jetbrains.letsPlot.intern.Plot import jetbrains.letsPlot.label.ggtitle import jetbrains.letsPlot.label.xlab import jetbrains.letsPlot.letsPlot -import org.jetbrains.kotlinx.dataframe.AnyFrame import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.* import org.jetbrains.kotlinx.dataframe.io.read -import java.nio.file.Path /** * DataFrame row for single statistical char group @@ -82,13 +78,6 @@ object BasicStatistics { df } - /** - * Attaches metadata to statistics - **/ - fun DataFrame.withMetadata(metadata: AnyFrame) = run { - attachMetadata(this, "sample", metadata, "sample").cast() - } - data class PlotParameters( val primaryGroup: String? = null, val secondaryGroup: String? = null, @@ -113,10 +102,6 @@ object BasicStatistics { ) = df.metric.distinct().toList() .map { mt -> plot(df.filter { metric == mt }, pp) + ggtitle(mt) } - fun write(path: String, plots: List) { - writePDF(Path.of(path), plots) - } - fun plot( df: DataFrame, pp: PlotParameters, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt index 4c9c5cca4..f898336e5 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt @@ -1,22 +1,12 @@ package com.milaboratory.mixcr.postanalysis.dataframe +import com.milaboratory.miplots.Position +import com.milaboratory.miplots.heatmap.* import com.milaboratory.mixcr.postanalysis.PostanalysisResult -import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema -import jetbrains.letsPlot.coordCartesian -import jetbrains.letsPlot.coordFixed -import jetbrains.letsPlot.geom.geomTile -import jetbrains.letsPlot.intern.Plot -import jetbrains.letsPlot.letsPlot -import jetbrains.letsPlot.scale.scaleSizeIdentity -import jetbrains.letsPlot.scale.scaleXDiscrete -import jetbrains.letsPlot.scale.scaleYDiscrete -import jetbrains.letsPlot.theme import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema -import org.jetbrains.kotlinx.dataframe.api.cast import org.jetbrains.kotlinx.dataframe.api.toDataFrame -import org.jetbrains.kotlinx.dataframe.api.toMap -import org.jetbrains.kotlinx.dataframe.io.writeCSV +import org.jetbrains.kotlinx.dataframe.io.read /** @@ -24,104 +14,85 @@ import org.jetbrains.kotlinx.dataframe.io.writeCSV */ @DataSchema @Suppress("UNCHECKED_CAST") -interface GeneUsageRow { +data class GeneUsageRow( /** Sample ID */ - val sample: String + val sample: String, /** Payload (Gene) */ - val gene: String + val gene: String, /** Payload weight */ - val weight: Double -} + val weight: Double, +) object GeneUsage { /** * Imports data into DataFrame **/ - fun dataFrame( - paSett: PostanalysisSchema<*>, - paResult: PostanalysisResult, - group: String - ) = run { + fun dataFrame(paResult: PostanalysisResult) = run { + val data = mutableListOf() - val data = mutableMapOf>( - GeneUsageRow::sample.name to mutableListOf(), - GeneUsageRow::gene.name to mutableListOf(), - GeneUsageRow::weight.name to mutableListOf(), - ) - - for ((_, charData) in paResult.forGroup(paSett.getGroup(group)).data) { + for ((_, charData) in paResult.data) { for ((sampleId, keys) in charData.data) { for (metric in keys.data) { val key = metric.key.toString() - data[GeneUsageRow::sample.name]!! += sampleId - data[GeneUsageRow::gene.name]!! += key - data[GeneUsageRow::weight.name]!! += metric.value + data += GeneUsageRow(sampleId, key, metric.value) } } } - data.toDataFrame().cast() + data.toDataFrame() } -// -// /** -// * Create Plot -// **/ -// fun DataFrame.plot() = run { -// var plt = letsPlot(toMap()) { -// x = GeneUsageRow::gene.name -// y = GeneUsageRow::sample.name -// fill = GeneUsageRow::weight.name -// } -// -// writeCSV("data.csv") -// val xValues = this.gene.toList() -// val yValues = this.sample.toList() -// -// plt += geomTile( -//// sampling = samplingNone, -//// size = 0.0, -//// width = xValues.size * 40.0, -//// height = yValues.size * 40.0 -// ) -// -//// plt += scaleFillGradient() -//// plt += ggsize(1024, 1024) -// -// addCommonParams(plt, xValues, yValues, true) -// } - /////// from CorrPlot - private fun addCommonParams( - plot: Plot, - xValues: List, - yValues: List, - onlyTiles: Boolean - ): Plot { - @Suppress("NAME_SHADOWING") - var plot = plot - plot += theme() - .axisTitleBlank() - .axisLineBlank() + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paResult: PostanalysisResult, + metadataPath: String?, + ) = run { + var df = dataFrame(paResult) + if (metadataPath != null) + df = df.withMetadata(DataFrame.read(metadataPath)) + df + } - plot += scaleSizeIdentity(naValue = 0, guide = "none") + data class PlotParameters( + val colorKey: List? = null, + val clusterSamples: Boolean = true, + val clusterGenes: Boolean = true + ) - val expand = listOf(0.0, 0.0) - plot += scaleXDiscrete(breaks = xValues, limits = xValues, expand = expand) - plot += scaleYDiscrete( - breaks = yValues, - limits = yValues, - expand = expand + fun plot( + df: DataFrame, + pp: PlotParameters, + ) = run { + var plt = Heatmap( + df, + x = GeneUsageRow::sample.name, + y = GeneUsageRow::gene.name, + z = GeneUsageRow::weight.name, + xOrder = if (pp.clusterSamples) Hierarchical() else null, + yOrder = if (pp.clusterGenes) Hierarchical() else null ) - val xLim = Pair(-0.6, xValues.size - 1 + 0.6) - val yLim = Pair(-0.6, yValues.size - 1 + 0.6) - if (onlyTiles) { - plot += coordCartesian(xlim = xLim, ylim = yLim) - } else { - plot += coordFixed(xlim = xLim, ylim = yLim) + pp.colorKey?.let { + var first = false + for (key in it) { + plt.withColorKey(key, pos = Position.Bottom, sep = if (first) 0.1 else 0.0) + first = true + } } - return plot + + if (pp.clusterSamples) + plt = plt.withDendrogram(pos = Position.Top, 0.1) + if (pp.clusterGenes) + plt = plt.withDendrogram(pos = Position.Right, 0.1) + + plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) + plt = plt.withLabels(Position.Left, sep = 0.1, width = 7.0) + plt = plt.withFillLegend(Position.Left) + plt = plt.withColorKeyLegend(Position.Left) + plt.plot } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt index 1dce57bf3..670e31058 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt @@ -110,8 +110,8 @@ object SingleSpectratype { .with { OtherPayload } // find min max - val min = df.length.min() ?: 0 - val max = df.length.max() ?: 0 + val min = df.length.min() + val max = df.length.max() // add auxiliary points for each cdr3 length df = df.concat( diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt index 1c0d8be64..d4d95068c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt @@ -2,6 +2,7 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.util.StringUtil import org.jetbrains.kotlinx.dataframe.AnyFrame +import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.api.add import org.jetbrains.kotlinx.dataframe.api.all import org.jetbrains.kotlinx.dataframe.api.cast @@ -12,6 +13,16 @@ import java.util.* fun AnyFrame.isNumeric(col: String) = this[col].all { it == null || it is Number } fun AnyFrame.isCategorial(col: String) = !isNumeric(col) +/** + * Attaches metadata to statistics + **/ +fun DataFrame.withMetadata(metadata: AnyFrame) = run { + attachMetadata(this, "sample", metadata, "sample").cast() +} + +/** + * Attaches metadata to statistics + **/ fun attachMetadata( data: AnyFrame, dataCol: String, diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index f6eedf992..20b343908 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -18,4 +18,19 @@ public void test1() { "scratch/pa/bio.pdf" ); } + + @Ignore + @Test + public void test2() { + Main.main( + "exportPa", + "vUsage", + "--chains", + "TRB", + "--meta", + "scratch/metadata.csv", + "scratch/pa/pa.json", + "scratch/pa/vUsage.pdf" + ); + } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt index 6e2e78d1e..8b89422e4 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt @@ -2,7 +2,6 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.miplots.writePDF import com.milaboratory.mixcr.cli.CommandPa -import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatistics.withMetadata import com.milaboratory.util.GlobalObjectMappers import io.repseq.core.Chains import org.jetbrains.kotlinx.dataframe.DataFrame From 571d4ff3976f45439979438737d7504e749a7348 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Fri, 18 Feb 2022 11:20:40 +0300 Subject: [PATCH 137/282] Now should compile without composite build. fix: fixes all snapshot dependencies --- build.gradle.kts | 23 ++++++----------------- 1 file changed, 6 insertions(+), 17 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 26830f929..f3cbaa400 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -1,6 +1,6 @@ +import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar import com.palantir.gradle.gitversion.VersionDetails import groovy.lang.Closure -import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar import java.net.InetAddress plugins { @@ -20,10 +20,7 @@ val gitDetails = versionDetails() val longTests: String? by project group = "com.milaboratory" -val gitLastTag = gitDetails.lastTag.removePrefix("v") -version = - if (gitDetails.commitDistance == 0) gitLastTag - else "${gitLastTag}-${gitDetails.commitDistance}-${gitDetails.gitHash}" +version = if (version != "unspecified") version else "SNAPSHOT" description = "MiXCR" java { @@ -36,7 +33,7 @@ application { mainClass.set("com.milaboratory.mixcr.cli.Main") } -tasks.withType() { +tasks.withType { options.encoding = "UTF-8" } @@ -44,25 +41,17 @@ tasks.withType { (options as StandardJavadocDocletOptions).addStringOption("Xdoclint:none", "-quiet") } -tasks.register("createInfoFile") { - doLast { - projectDir - .resolve("build_info.json") - .writeText("""{"version":"$version"}""") - } -} - repositories { mavenCentral() - // Snapshot versions of milib and repseqio distributed via this repo + // Snapshot versions of redberry-pipe, milib and repseqio distributed via this repo maven { url = uri("https://pub.maven.milaboratory.com") } } -val milibVersion = "1.14.1-16-774c60afab" -val repseqioVersion = "1.3.5-4-f7170dd23b" +val milibVersion = "1.14.1-47-master" +val repseqioVersion = "1.3.5-18-master" val jacksonVersion = "2.12.4" dependencies { From 44ceeb3cc39ca28da63771cc6c5e23428162fcf9 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 21 Feb 2022 03:44:47 +0300 Subject: [PATCH 138/282] wip --- .../com/milaboratory/mixcr/cli/CommandPa.java | 15 ++- .../mixcr/cli/CommandPaExport.java | 96 +++++++++++++- .../java/com/milaboratory/mixcr/cli/Main.java | 3 +- .../postanalysis/dataframe/BasicStatistics.kt | 5 +- .../mixcr/postanalysis/dataframe/GeneUsage.kt | 27 +++- .../mixcr/postanalysis/dataframe/Overlap.kt | 120 +++++++++++++++++ .../mixcr/postanalysis/dataframe/VJUsage.kt | 122 ++++++++++++++++++ .../postanalysis/overlap/OverlapKey.java | 2 +- .../mixcr/cli/CommandPaExportTest.java | 4 +- 9 files changed, 372 insertions(+), 22 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Overlap.kt create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/VJUsage.kt diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java index 30b402195..47c315325 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java @@ -150,7 +150,9 @@ SetPreprocessorFactory downsampling(String downsamplingStr) { */ @JsonAutoDetect public static final class PaResult { - /** Results for individual chains */ + /** + * Results for individual chains + */ @JsonProperty("results") @JsonSerialize(keyUsing = KnownChainsKeySerializer.class) @JsonDeserialize(keyUsing = KnownChainsKeyDeserializer.class) @@ -209,7 +211,8 @@ public void run0() throws Exception { IsotypeUsage = "IsotypeUsage", CDR3Spectratype = "CDR3Spectratype", VSpectratype = "VSpectratype", - VSpectratypeMean = "VSpectratypeMean"; + VSpectratypeMean = "VSpectratypeMean", + Overlap = "overlap"; @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") @CommandLine.Command(name = "individual", @@ -217,7 +220,8 @@ public void run0() throws Exception { separator = " ", description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") public static class CommandIndividual extends CommandPa { - public CommandIndividual() {} + public CommandIndividual() { + } @Override @SuppressWarnings({"unchecked", "rawtypes"}) @@ -313,7 +317,8 @@ public static class CommandOverlap extends CommandPa { required = false) public String f2downsampling; - public CommandOverlap() {} + public CommandOverlap() { + } @Override @SuppressWarnings("unchecked") @@ -437,7 +442,7 @@ public PostanalysisSchema> getSchema(int nSamples, Chains ch overlaps.addAll(getCharacteristics(i, j, chain)); return new PostanalysisSchema<>(Collections.singletonList( - new CharacteristicGroup<>("overlap", + new CharacteristicGroup<>(Overlap, overlaps, Arrays.asList(new OverlapSummary<>()) ))); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 530934cbb..7515669bd 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -6,10 +6,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.CommandPa.PaResult; import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; -import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatRow; -import com.milaboratory.mixcr.postanalysis.dataframe.BasicStatistics; -import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsage; -import com.milaboratory.mixcr.postanalysis.dataframe.GeneUsageRow; +import com.milaboratory.mixcr.postanalysis.dataframe.*; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; @@ -227,9 +224,9 @@ static abstract class ExportGeneUsage extends CommandPaExport { @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") public String out; - @Option(names = {"--no-dendro-samples"}, description = "Plot dendrogram for hierarchical clusterization of samples.") + @Option(names = {"--no-samples-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of samples.") public boolean noSamplesDendro; - @Option(names = {"--no-dendro-genes"}, description = "Plot dendrogram for hierarchical clusterization of genes.") + @Option(names = {"--no-genes-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of genes.") public boolean noGenesDendro; @Option(names = {"--color-key"}, description = "Add color key layer.") public List colorKey; @@ -297,6 +294,93 @@ String group() { } } + @CommandLine.Command(name = "vjUsage", + sortOptions = false, + separator = " ", + description = "Export V-J usage heatmap") + static class ExportVJUsage extends CommandPaExport { + @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") + public String out; + @Option(names = {"--no-v-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") + public boolean noVDendro; + @Option(names = {"--no-j-dendro"}, description = "Plot dendrogram for hierarchical clusterization of genes.") + public boolean noJDendro; + @Option(names = {"--color-key"}, description = "Add color key layer.") + public List colorKey; + + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".pdf")) + throwValidationException("Output file must ends with .pdf extension"); + } + + @Override + void run(Chains.NamedChains chains, PaResultByChain result) { + CharacteristicGroup ch = result.schema.getGroup(CommandPa.VJUsage); + + DataFrame df = VJUsage.INSTANCE.dataFrame( + result.result.forGroup(ch), + metadata + ); + + if (df.rowsCount() == 0) + return; + + Plot plots = VJUsage.INSTANCE.plot(df, + new VJUsage.PlotParameters( + colorKey, + !noVDendro, + !noJDendro + )); + + ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + } + } + + @CommandLine.Command(name = "overlap", + sortOptions = false, + separator = " ", + description = "Export overlap heatmap") + static class ExportOverlap extends CommandPaExport { + @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") + public String out; + @Option(names = {"--no-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") + public boolean noDendro; + @Option(names = {"--color-key"}, description = "Add color key layer.") + public List colorKey; + @Option(names = {"--metric"}, description = "Select specific metrics to export.") + public List metrics; + + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".pdf")) + throwValidationException("Output file must ends with .pdf extension"); + } + + @Override + void run(Chains.NamedChains chains, PaResultByChain result) { + CharacteristicGroup ch = result.schema.getGroup(CommandPa.Overlap); + + DataFrame df = Overlap.INSTANCE.dataFrame( + result.result.forGroup(ch), + metadata + ); + + if (df.rowsCount() == 0) + return; + + Plot plots = Overlap.INSTANCE.plot(df, + new Overlap.PlotParameters( + colorKey, + !noDendro, + )); + + ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + } + } + @CommandLine.Command(name = "exportPa", separator = " ", description = "Export postanalysis results.", diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 0d24caf37..451d7cb9e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -203,7 +203,8 @@ public static CommandLine mkCmd() { .addSubcommand("vUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVUsage.class)) .addSubcommand("jUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportJUsage.class)) - .addSubcommand("isotypeUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportIsotypeUsage.class)); + .addSubcommand("isotypeUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportIsotypeUsage.class)) + .addSubcommand("vjUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVJUsage.class)); cmd.setSeparator(" "); return cmd; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt index 45d9c6d9a..a5e4d3818 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt @@ -99,8 +99,9 @@ object BasicStatistics { fun plots( df: DataFrame, pp: PlotParameters, - ) = df.metric.distinct().toList() - .map { mt -> plot(df.filter { metric == mt }, pp) + ggtitle(mt) } + ) = df.groupBy { metric }.groups.toList() + .filter { !it.isEmpty() } + .map { mdf -> plot(mdf, pp) + ggtitle(mdf.first()[BasicStatRow::metric.name]!!.toString()) } fun plot( df: DataFrame, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt index f898336e5..ff0b0b88a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.postanalysis.dataframe import com.milaboratory.miplots.Position +import com.milaboratory.miplots.color.Palletes import com.milaboratory.miplots.heatmap.* import com.milaboratory.mixcr.postanalysis.PostanalysisResult import org.jetbrains.kotlinx.dataframe.DataFrame @@ -73,14 +74,28 @@ object GeneUsage { y = GeneUsageRow::gene.name, z = GeneUsageRow::weight.name, xOrder = if (pp.clusterSamples) Hierarchical() else null, - yOrder = if (pp.clusterGenes) Hierarchical() else null + yOrder = if (pp.clusterGenes) Hierarchical() else null, + fillPallette = Palletes.Diverging.lime90rose130 ) + plt = plt.withBorder() + + val ncats = pp.colorKey?.map { df[it].distinct().size() }?.sum() ?: 0 + var pallete = Palletes.Categorical.auto(ncats) pp.colorKey?.let { - var first = false + var first = true for (key in it) { - plt.withColorKey(key, pos = Position.Bottom, sep = if (first) 0.1 else 0.0) - first = true + val nColors = df[key].distinct().size() + plt.withColorKey( + key, + pos = Position.Bottom, + sep = if (first) 0.1 else 0.0, + labelPos = Position.Left, + labelSep = 0.1, + pallete = pallete + ) + pallete = pallete.shift(nColors) + first = false } } @@ -90,8 +105,8 @@ object GeneUsage { plt = plt.withDendrogram(pos = Position.Right, 0.1) plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) - plt = plt.withLabels(Position.Left, sep = 0.1, width = 7.0) - plt = plt.withFillLegend(Position.Left) + plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) + plt = plt.withFillLegend(Position.Left, size = 0.5) plt = plt.withColorKeyLegend(Position.Left) plt.plot } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Overlap.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Overlap.kt new file mode 100644 index 000000000..24b92698b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Overlap.kt @@ -0,0 +1,120 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.miplots.Position +import com.milaboratory.miplots.color.Palletes +import com.milaboratory.miplots.heatmap.* +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey +import com.milaboratory.mixcr.postanalysis.overlap.OverlapType +import jetbrains.letsPlot.label.ggtitle +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.cast +import org.jetbrains.kotlinx.dataframe.api.first +import org.jetbrains.kotlinx.dataframe.api.groupBy +import org.jetbrains.kotlinx.dataframe.api.toDataFrame +import org.jetbrains.kotlinx.dataframe.io.read + +/** + * DataFrame row for V or J usage data + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +data class OverlapRow( + val sample1: String, + val sample2: String, + val metric: OverlapType, + val weight: Double, +) + +object Overlap { + /** + * Imports data into DataFrame + **/ + @Suppress("UNCHECKED_CAST") + fun dataFrame(paResult: PostanalysisResult) = run { + val data = mutableListOf() + + for ((_, charData) in paResult.data) { + for ((_, keys) in charData.data) { + for (metric in keys.data) { + val key = metric.key as? OverlapKey ?: throw RuntimeException() + data += OverlapRow(key.id1, key.id2, key.key, metric.value) + } + } + } + + data.toDataFrame() + } + + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paResult: PostanalysisResult, + metadataPath: String?, + ) = run { + var df = dataFrame(paResult) + if (metadataPath != null) + df = attachMetadata(df, "sample1", DataFrame.read(metadataPath), "sample").cast() + df + } + + data class PlotParameters( + val colorKey: List? = null, + val cluster: Boolean = true + ) + + fun plots( + df: DataFrame, + pp: PlotParameters, + ) = df.groupBy { "metric"() }.groups.toList() + .map { sdf -> plot(df, pp) + ggtitle(sdf.first()[VJUsageRow::sample.name]!!.toString()) } + + fun plot( + df: DataFrame, + pp: PlotParameters, + ) = run { + var plt = Heatmap( + df, + x = OverlapRow::sample1.name, + y = OverlapRow::sample2.name, + z = GeneUsageRow::weight.name, + xOrder = if (pp.cluster) Hierarchical() else null, + yOrder = if (pp.cluster) Hierarchical() else null, + fillPallette = Palletes.Diverging.lime90rose130 + ) + + plt = plt.withBorder() + + val ncats = pp.colorKey?.map { df[it].distinct().size() }?.sum() ?: 0 + var pallete = Palletes.Categorical.auto(ncats) + pp.colorKey?.let { + var first = true + for (key in it) { + val nColors = df[key].distinct().size() + plt.withColorKey( + key, + pos = Position.Bottom, + sep = if (first) 0.1 else 0.0, + labelPos = Position.Left, + labelSep = 0.1, + pallete = pallete + ) + pallete = pallete.shift(nColors) + first = false + } + } + + if (pp.cluster) { + plt = plt.withDendrogram(pos = Position.Top, 0.1) + plt = plt.withDendrogram(pos = Position.Right, 0.1) + } + + plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) + plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) + plt = plt.withFillLegend(Position.Left, size = 0.5) + plt = plt.withColorKeyLegend(Position.Left) + plt.plot + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/VJUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/VJUsage.kt new file mode 100644 index 000000000..c0fc71a3c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/VJUsage.kt @@ -0,0 +1,122 @@ +package com.milaboratory.mixcr.postanalysis.dataframe + +import com.milaboratory.miplots.Position +import com.milaboratory.miplots.color.Palletes +import com.milaboratory.miplots.heatmap.* +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions +import jetbrains.letsPlot.label.ggtitle +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.first +import org.jetbrains.kotlinx.dataframe.api.groupBy +import org.jetbrains.kotlinx.dataframe.api.toDataFrame +import org.jetbrains.kotlinx.dataframe.io.read + +/** + * DataFrame row for V or J usage data + */ +@DataSchema +@Suppress("UNCHECKED_CAST") +data class VJUsageRow( + /** Sample ID */ + val sample: String, + + val vGene: String, + val jGene: String, + /** Payload weight */ + val weight: Double, +) + +object VJUsage { + /** + * Imports data into DataFrame + **/ + @Suppress("UNCHECKED_CAST") + fun dataFrame(paResult: PostanalysisResult) = run { + val data = mutableListOf() + + for ((_, charData) in paResult.data) { + for ((sampleId, keys) in charData.data) { + for (metric in keys.data) { + val key = metric.key as? KeyFunctions.VJGenes ?: throw RuntimeException() + data += VJUsageRow(sampleId, key.vGene, key.jJene, metric.value) + } + } + } + + data.toDataFrame() + } + + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paResult: PostanalysisResult, + metadataPath: String?, + ) = run { + var df = dataFrame(paResult) + if (metadataPath != null) + df = df.withMetadata(DataFrame.read(metadataPath)) + df + } + + data class PlotParameters( + val colorKey: List? = null, + val clusterV: Boolean = true, + val clusterJ: Boolean = true + ) + + fun plots( + df: DataFrame, + pp: PlotParameters, + ) = df.groupBy { "sample"() }.groups.toList() + .map { sdf -> plot(df, pp) + ggtitle(sdf.first()[VJUsageRow::sample.name]!!.toString()) } + + fun plot( + df: DataFrame, + pp: PlotParameters, + ) = run { + var plt = Heatmap( + df, + x = VJUsageRow::jGene.name, + y = VJUsageRow::vGene.name, + z = GeneUsageRow::weight.name, + xOrder = if (pp.clusterV) Hierarchical() else null, + yOrder = if (pp.clusterJ) Hierarchical() else null, + fillPallette = Palletes.Diverging.lime90rose130 + ) + + plt = plt.withBorder() + + val ncats = pp.colorKey?.map { df[it].distinct().size() }?.sum() ?: 0 + var pallete = Palletes.Categorical.auto(ncats) + pp.colorKey?.let { + var first = true + for (key in it) { + val nColors = df[key].distinct().size() + plt.withColorKey( + key, + pos = Position.Bottom, + sep = if (first) 0.1 else 0.0, + labelPos = Position.Left, + labelSep = 0.1, + pallete = pallete + ) + pallete = pallete.shift(nColors) + first = false + } + } + + if (pp.clusterV) + plt = plt.withDendrogram(pos = Position.Top, 0.1) + if (pp.clusterJ) + plt = plt.withDendrogram(pos = Position.Right, 0.1) + + plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) + plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) + plt = plt.withFillLegend(Position.Left, size = 0.5) + plt = plt.withColorKeyLegend(Position.Left) + plt.plot + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java index b95e61642..f9f618281 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java @@ -15,7 +15,7 @@ getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE ) -public final class OverlapKey { +public final class OverlapKey { @JsonProperty("key") @JsonTypeInfo(use = JsonTypeInfo.Id.CLASS, property = "type") public final K key; diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index 20b343908..c904e7696 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -26,7 +26,9 @@ public void test2() { "exportPa", "vUsage", "--chains", - "TRB", + "IGH", + "--color-key", + "Cat2", "--meta", "scratch/metadata.csv", "scratch/pa/pa.json", From 7f19b971813b5b5b736d8f69b8d93955bcfbe918 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Mon, 21 Feb 2022 13:39:58 +0300 Subject: [PATCH 139/282] build script --- build.gradle.kts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index f3cbaa400..cae89ff79 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -50,8 +50,8 @@ repositories { } } -val milibVersion = "1.14.1-47-master" -val repseqioVersion = "1.3.5-18-master" +val milibVersion = "1.15.0" +val repseqioVersion = "1.3.5-19-master" val jacksonVersion = "2.12.4" dependencies { From 03a593607c8ef971153ebdcad227322e6ac57bfa Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 23 Feb 2022 23:38:04 +0300 Subject: [PATCH 140/282] Add number of clonotypes to CLN readers --- .../com/milaboratory/mixcr/basictypes/ClnAReader.java | 1 + .../com/milaboratory/mixcr/basictypes/ClnsReader.java | 8 ++++++++ .../com/milaboratory/mixcr/basictypes/ClnsWriter.java | 10 +++++----- .../com/milaboratory/mixcr/basictypes/CloneReader.java | 2 ++ 4 files changed, 16 insertions(+), 5 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index fc4963075..3647141dc 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -207,6 +207,7 @@ public GeneFeature[] getAssemblingFeatures() { /** * Returns number of clones in the file */ + @Override public int numberOfClones() { return numberOfClones; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index d99493c36..74b691b7b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -62,6 +62,7 @@ public class ClnsReader extends PipelineConfigurationReaderMiXCR implements Clon private final VDJCSProperties.CloneOrdering ordering; private final String versionInfo; private final List genes; + private final int numberOfClones; private final long clonesPosition; @@ -106,12 +107,14 @@ private ClnsReader(PrimitivIHybrid input, VDJCLibraryRegistry libraryRegistry) { throw new RuntimeException("Corrupted file."); } + // read header try (PrimitivI i = input.beginPrimitivI(true)) { versionInfo = i.readUTF(); pipelineConfiguration = i.readObject(PipelineConfiguration.class); alignerParameters = i.readObject(VDJCAlignerParameters.class); assemblerParameters = i.readObject(CloneAssemblerParameters.class); ordering = i.readObject(VDJCSProperties.CloneOrdering.class); + numberOfClones = i.readInt(); genes = IOUtil.stdVDJCPrimitivIStateInit(i, alignerParameters, libraryRegistry); } @@ -151,6 +154,11 @@ public VDJCSProperties.CloneOrdering ordering() { return ordering; } + @Override + public int numberOfClones() { + return numberOfClones; + } + @Override public void close() throws IOException { input.close(); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index 614f1b0f3..8bd5831be 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -55,11 +55,8 @@ public final class ClnsWriter implements PipelineConfigurationWriter, AutoClosea static final int MAGIC_LENGTH = 14; static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII); - final String stage = "Writing clones"; final PrimitivOHybrid output; - private volatile int current; - public ClnsWriter(String fileName) throws IOException { this(new PrimitivOHybrid(Paths.get(fileName))); } @@ -80,7 +77,8 @@ public void writeHeaderFromCloneSet( cloneSet.getAssemblerParameters(), cloneSet.getOrdering(), cloneSet.getUsedGenes(), - cloneSet); + cloneSet, + cloneSet.size()); } public void writeHeader( @@ -89,7 +87,8 @@ public void writeHeader( CloneAssemblerParameters assemblerParameters, VDJCSProperties.CloneOrdering ordering, List genes, - HasFeatureToAlign featureToAlign + HasFeatureToAlign featureToAlign, + int numberOfClones ) { try (PrimitivO o = output.beginPrimitivO(true)) { // Writing magic bytes @@ -105,6 +104,7 @@ public void writeHeader( o.writeObject(alignmentParameters); o.writeObject(assemblerParameters); o.writeObject(ordering); + o.writeInt(numberOfClones); IOUtil.stdVDJCPrimitivOStateInit(o, genes, featureToAlign); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java index f608122b5..22af042ec 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -40,4 +40,6 @@ public interface CloneReader extends AutoCloseable { VDJCSProperties.CloneOrdering ordering(); OutputPortCloseable readClones(); + + int numberOfClones(); } From a576e566ae9da0b8151683725938abd9c0e87d25 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 23 Feb 2022 23:39:46 +0300 Subject: [PATCH 141/282] Many fixes to PA overlap & other things --- .../mixcr/basictypes/CloneSetOverlap.java | 54 ++++++++++- .../com/milaboratory/mixcr/cli/CommandPa.java | 11 +++ .../mixcr/cli/CommandPaExport.java | 2 +- .../mixcr/cli/CommandSortAlignments.java | 4 +- .../mixcr/cli/CommandSortClones.java | 92 +++++++++++++++++++ .../java/com/milaboratory/mixcr/cli/Main.java | 1 + .../mixcr/postanalysis/Dataset.java | 34 +++++-- .../postanalysis/PostanalysisRunner.java | 44 ++++++--- .../postanalysis/SetPreprocessorFactory.java | 22 ++++- .../overlap/OverlapAggregator.java | 5 +- .../postanalysis/overlap/OverlapGroup.java | 10 +- .../postanalysis/overlap/OverlapUtil.java | 38 +++++++- .../preproc/OverlapPreprocessorAdapter.java | 4 +- .../postanalysis/ui/ClonotypeDataset.java | 8 +- .../mixcr/util/OutputPortWithProgress.java | 51 ++++++++++ .../milaboratory/mixcr/cli/CommandPaTest.java | 12 ++- .../mixcr/postanalysis/TestDataset.java | 10 +- .../overlap/OverlapCharacteristicTest.java | 35 ++++++- 18 files changed, 382 insertions(+), 55 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java create mode 100644 src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java index ef3fc1f35..618284edd 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java @@ -30,15 +30,19 @@ package com.milaboratory.mixcr.basictypes; import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.util.sorting.MergeStrategy; import java.util.List; +import java.util.concurrent.atomic.AtomicBoolean; +import java.util.concurrent.atomic.AtomicLong; import java.util.stream.Collectors; public final class CloneSetOverlap { - private CloneSetOverlap() {} + private CloneSetOverlap() { + } - public static OutputPortCloseable>> overlap( + public static OutputPortWithProgress>> overlap( List> by, List readers) { VDJCSProperties.CloneOrdering ordering = readers.get(0).ordering(); @@ -48,8 +52,48 @@ public static OutputPortCloseable>> overlap( MergeStrategy strategy = MergeStrategy.calculateStrategy(ordering.getProperties(), by); if (!strategy.usesStreamOrdering()) throw new RuntimeException("Clone sorting is incompatible with overlap criteria."); - return strategy.join(readers.stream() - .map(CloneReader::readClones) - .collect(Collectors.toList())); + + List> individualPorts = readers + .stream() + .map(r -> OutputPortWithProgress.wrap(r.numberOfClones(), r.readClones())) + .collect(Collectors.toList()); + + OutputPortCloseable>> joinedPort = strategy.join(individualPorts); + + AtomicLong index = new AtomicLong(0); + AtomicBoolean isFinished = new AtomicBoolean(false); + long totalClones = readers.stream().mapToLong(CloneReader::numberOfClones).sum(); + return new OutputPortWithProgress<>() { + @Override + public long index() { + return index.get(); + } + + @Override + public void close() { + joinedPort.close(); + } + + @Override + public List> take() { + List> t = joinedPort.take(); + if (t == null) { + isFinished.set(true); + return null; + } + index.incrementAndGet(); + return t; + } + + @Override + public double getProgress() { + return 1.0 * individualPorts.stream().mapToLong(OutputPortWithProgress::index).sum() / totalClones; + } + + @Override + public boolean isFinished() { + return isFinished.get(); + } + }; } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java index 47c315325..1165dd63b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java @@ -25,6 +25,7 @@ import com.milaboratory.mixcr.postanalysis.ui.*; import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.LambdaSemaphore; +import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.Chains; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -301,6 +302,8 @@ PaResultByChain run(Chains chain) { new ClonotypeDataset(getSampleId(file), file, VDJCLibraryRegistry.getDefault()) ).collect(Collectors.toList()); + System.out.println("Running for " + chain); + SmartProgressReporter.startProgressReport(runner); return new PaResultByChain(schema, runner.run(datasets)); } } @@ -363,6 +366,9 @@ PaResultByChain run(Chains chain) { PostanalysisRunner> runner = new PostanalysisRunner<>(); runner.addCharacteristics(schema.getAllCharacterisitcs()); + + System.out.println("Running for " + chain); + SmartProgressReporter.startProgressReport(runner); PostanalysisResult result = runner.run(overlapDataset); return new PaResultByChain(schema, result); @@ -405,6 +411,11 @@ public Clone take() { public void close() throws Exception { inner.close(); } + + @Override + public int numberOfClones() { + return inner.numberOfClones(); + } }; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 7515669bd..71bf7c277 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -374,7 +374,7 @@ void run(Chains.NamedChains chains, PaResultByChain result) { Plot plots = Overlap.INSTANCE.plot(df, new Overlap.PlotParameters( colorKey, - !noDendro, + !noDendro )); ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java index c65c6f2f5..d0d75a9e3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java @@ -67,7 +67,7 @@ public class CommandSortAlignments extends ACommandWithSmartOverwriteWithSingleI static final String SORT_ALIGNMENTS_COMMAND_NAME = "sortAlignments"; @Override - public ActionConfiguration getConfiguration() { + public ActionConfiguration getConfiguration() { return new SortConfiguration(); } @@ -142,7 +142,7 @@ protected void init() { use = JsonTypeInfo.Id.CLASS, include = JsonTypeInfo.As.PROPERTY, property = "type") - public static class SortConfiguration implements ActionConfiguration { + public static class SortConfiguration implements ActionConfiguration { @Override public String actionName() { return "sortAlignments"; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java new file mode 100644 index 000000000..423bad628 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java @@ -0,0 +1,92 @@ +package com.milaboratory.mixcr.cli; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonTypeInfo; +import com.milaboratory.cli.ActionConfiguration; +import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.util.ArraysUtils; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; +import picocli.CommandLine; + +import java.io.File; +import java.nio.file.Path; +import java.util.Objects; + +import static com.milaboratory.mixcr.basictypes.IOUtil.MAGIC_CLNA; +import static com.milaboratory.mixcr.basictypes.IOUtil.MAGIC_CLNS; +import static com.milaboratory.mixcr.cli.CommandSortClones.SORT_CLONES_COMMAND_NAME; + + +@CommandLine.Command(name = SORT_CLONES_COMMAND_NAME, + sortOptions = true, + separator = " ", + description = "Sort clones by sequence. Clones in the output file will be sorted by clonal sequence, which allows to build overlaps between clonesets.") +public class CommandSortClones extends ACommandWithSmartOverwriteWithSingleInputMiXCR { + static final String SORT_CLONES_COMMAND_NAME = "sortClones"; + + @Override + public ActionConfiguration getConfiguration() { + return new SortConfiguration(); + } + + @Override + public void run1() throws Exception { + switch (Objects.requireNonNull(IOUtil.fileInfoExtractorInstance.getFileInfo(new File(in))).fileType) { + case MAGIC_CLNS: + try (ClnsReader reader = new ClnsReader(Path.of(in), VDJCLibraryRegistry.getDefault()); + ClnsWriter writer = new ClnsWriter(out)) { + + GeneFeature[] assemblingFeatures = reader.getAssemblerParameters().getAssemblingFeatures(); + + // Any CDR3 containing feature will become first + for (int i = 0; i < assemblingFeatures.length; i++) + if (assemblingFeatures[i].contains(GeneFeature.CDR3)) { + if (i != 0) + ArraysUtils.swap(assemblingFeatures, 0, i); + break; + } + + VDJCSProperties.CloneOrdering ordering = VDJCSProperties.cloneOrderingByNucleotide(assemblingFeatures, + GeneType.Variable, GeneType.Joining); + + writer.writeCloneSet(reader.getPipelineConfiguration(), CloneSet.reorder(reader.getCloneSet(), ordering)); + } + return; + + case MAGIC_CLNA: + throw new RuntimeException(); + + } + + } + + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) + @JsonTypeInfo( + use = JsonTypeInfo.Id.CLASS, + include = JsonTypeInfo.As.PROPERTY, + property = "type") + public static class SortConfiguration implements ActionConfiguration { + @Override + public String actionName() { + return "sortClones"; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return Objects.hash(CommandSortAlignments.SortConfiguration.class); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 451d7cb9e..4f07b6493 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -173,6 +173,7 @@ public static CommandLine mkCmd() { .addSubcommand("mergeAlignments", CommandMergeAlignments.class) .addSubcommand("filterAlignments", CommandFilterAlignments.class) .addSubcommand("sortAlignments", CommandSortAlignments.class) + .addSubcommand("sortClones", CommandSortClones.class) .addSubcommand("alignmentsDiff", CommandAlignmentsDiff.class) .addSubcommand("clonesDiff", CommandClonesDiff.class) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java index 729e08a35..c59ab7e5b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java @@ -1,16 +1,20 @@ package com.milaboratory.mixcr.postanalysis; -import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.util.OutputPortWithProgress; /** * */ public interface Dataset { - /** Unique dataset identifier */ + /** + * Unique dataset identifier + */ String id(); - /** Closeable port of dataset elements */ - OutputPortCloseable mkElementsPort(); + /** + * Closeable port of dataset elements + */ + OutputPortWithProgress mkElementsPort(); static Dataset empty(String id) { return new Dataset() { @@ -20,10 +24,26 @@ public String id() { } @Override - public OutputPortCloseable mkElementsPort() { - return new OutputPortCloseable() { + public OutputPortWithProgress mkElementsPort() { + return new OutputPortWithProgress<>() { @Override - public void close() {} + public long index() { + return 0; + } + + @Override + public double getProgress() { + return 0.0; + } + + @Override + public boolean isFinished() { + return true; + } + + @Override + public void close() { + } @Override public K take() { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index fba00ae0f..0a3ef16dd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -4,7 +4,9 @@ import cc.redberry.pipe.InputPort; import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.util.CanReportProgressAndStage; +import gnu.trove.list.array.TIntArrayList; import java.util.*; import java.util.stream.Collectors; @@ -16,13 +18,15 @@ public class PostanalysisRunner implements CanReportProgressAndStage { private final List> characteristics = new ArrayList<>(); - public void addCharacteristics(CharacteristicGroup... groups) { + @SafeVarargs + public final void addCharacteristics(CharacteristicGroup... groups) { for (CharacteristicGroup g : groups) { addCharacteristics(g.characteristics); } } - public void addCharacteristics(Characteristic... chs) { + @SafeVarargs + public final void addCharacteristics(Characteristic... chs) { addCharacteristics(Arrays.asList(chs)); } @@ -30,7 +34,7 @@ public void addCharacteristics(List> chs) { characteristics.addAll(chs); } - private volatile String stage; + private volatile String stage = "Initializing"; private volatile double progress = 0.0; private volatile boolean isFinished = false; @@ -54,21 +58,27 @@ public PostanalysisResult run(List> datasets) { return run(datasets.toArray(new Dataset[0])); } - /** Run PA for a given datasets */ + /** + * Run PA for a given datasets + */ @SuppressWarnings("unchecked") public PostanalysisResult run(Dataset... datasets) { - stage = "Preparing"; - progress = 0.0; + stage = "Preprocessing datasets"; + progress = Double.NaN; isFinished = false; + // save char indices in array for faster access + Map, Integer> char2idx = new HashMap<>(); + for (int i = 0; i < characteristics.size(); i++) + char2idx.put(characteristics.get(i), i); // charID -> proc (deduplicated) Map> id2proc = new HashMap<>(); Map, SetPreprocessor> distinctProcs = new HashMap<>(); - Map, List>> proc2char = new HashMap<>(); + Map, TIntArrayList> proc2char = new IdentityHashMap<>(); for (Characteristic ch : characteristics) { id2proc.put(ch.name, distinctProcs.computeIfAbsent(ch.preprocessor, __ -> ch.preprocessor.getInstance())); SetPreprocessor proc = distinctProcs.get(ch.preprocessor); - proc2char.computeIfAbsent(proc, __ -> new ArrayList<>()).add(ch); + proc2char.computeIfAbsent(proc, __ -> new TIntArrayList()).add(char2idx.get(ch)); } List> procs = id2proc.values().stream().distinct().collect(Collectors.toList()); @@ -121,19 +131,23 @@ public PostanalysisResult run(Dataset... datasets) { Map, Map[]>> result = new IdentityHashMap<>(); for (int i = 0; i < datasets.length; i++) { Dataset dataset = datasets[i]; + if (datasets.length == 1) + stage = "Processing"; + else + stage = "Processing: " + dataset.id(); - Map, Aggregator> aggregators = characteristics.stream() - .collect(Collectors.toMap(c -> c, c -> c.createAggregator(dataset))); + Aggregator[] aggregators = characteristics.stream() + .map(c -> c.createAggregator(dataset)).toArray(Aggregator[]::new); - try (OutputPortCloseable port = dataset.mkElementsPort()) { + try (OutputPortWithProgress port = dataset.mkElementsPort()) { for (T o : CUtils.it(port)) { + progress = port.getProgress(); for (Map.Entry, MappingFunction> e : mappingFunctions[i].entrySet()) { MappingFunction mapper = e.getValue(); T oMapped = mapper.apply(o); if (oMapped != null) - for (Characteristic ch : proc2char.get(e.getKey())) { - aggregators.get(ch).consume(oMapped); - } + for (int ch : proc2char.get(e.getKey()).toArray()) + aggregators[ch].consume(oMapped); } } } @@ -144,7 +158,7 @@ public PostanalysisResult run(Dataset... datasets) { __ -> new HashMap<>()); if (charValues.containsKey(dataset.id())) throw new IllegalArgumentException("Dataset occurred twice."); - charValues.put(dataset.id(), aggregators.get(characteristic).result()); + charValues.put(dataset.id(), aggregators[char2idx.get(characteristic)].result()); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java index 949a10159..81c4e6011 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java @@ -9,6 +9,7 @@ import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; import com.milaboratory.mixcr.postanalysis.preproc.*; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import java.util.ArrayList; import java.util.Arrays; @@ -95,9 +96,24 @@ public String id() { } @Override - public OutputPortCloseable mkElementsPort() { - OutputPortCloseable inner = initial[datasetIdx].mkElementsPort(); - return new OutputPortCloseable() { + public OutputPortWithProgress mkElementsPort() { + OutputPortWithProgress inner = initial[datasetIdx].mkElementsPort(); + return new OutputPortWithProgress() { + @Override + public double getProgress() { + return inner.getProgress(); + } + + @Override + public boolean isFinished() { + return inner.isFinished(); + } + + @Override + public long index() { + return inner.index(); + } + @Override public void close() { inner.close(); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java index 186c34d8f..91c357550 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java @@ -37,8 +37,9 @@ public OverlapAggregator(WeightFunction weight, int i1, int i2, String id1, S public void consume(OverlapGroup obj) { List s1 = obj.getBySample(i1); List s2 = obj.getBySample(i2); - double ss1 = s1.stream().mapToDouble(weight::weight).sum(); - double ss2 = s2.stream().mapToDouble(weight::weight).sum(); + double ss1 = s1.isEmpty() ? 0.0 : s1.stream().mapToDouble(weight::weight).sum(); + double ss2 = s2.isEmpty() ? 0.0 : s2.stream().mapToDouble(weight::weight).sum(); + regressionAll.addData(ss1, ss2); sumS1 += ss1; sumS2 += ss2; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java index 9478e263c..244ada9b6 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java @@ -35,7 +35,9 @@ import java.util.stream.Stream; public final class OverlapGroup implements Iterable> { - /** Elements in group separated by sample */ + /** + * Elements in group separated by sample + */ final List> elements; public OverlapGroup(List> elements) { @@ -50,8 +52,12 @@ public List getBySample(int sampleIndex) { return elements.get(sampleIndex); } + public boolean isEmpty() { + return elements.stream().allMatch(List::isEmpty); + } + public boolean notEmpty() { - return !elements.stream().allMatch(List::isEmpty); + return !isEmpty(); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java index d98a8b62d..4b52f0d53 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java @@ -29,26 +29,54 @@ */ package com.milaboratory.mixcr.postanalysis.overlap; -import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.SimpleProcessorWrapper; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneReader; import com.milaboratory.mixcr.basictypes.CloneSetOverlap; import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import java.util.List; public final class OverlapUtil { - private OverlapUtil() {} + private OverlapUtil() { + } public static OverlapDataset overlap( List datasetIds, List> by, List readers) { - return new OverlapDataset(datasetIds) { + return new OverlapDataset<>(datasetIds) { @Override - public OutputPortCloseable> mkElementsPort() { - return new SimpleProcessorWrapper<>(CloneSetOverlap.overlap(by, readers), OverlapGroup::new); + public OutputPortWithProgress> mkElementsPort() { + OutputPortWithProgress>> port = CloneSetOverlap.overlap(by, readers); + SimpleProcessorWrapper>, OverlapGroup> processor = new SimpleProcessorWrapper<>(port, OverlapGroup::new); + return new OutputPortWithProgress<>() { + @Override + public long index() { + return port.index(); + } + + @Override + public void close() { + processor.close(); + } + + @Override + public OverlapGroup take() { + return processor.take(); + } + + @Override + public double getProgress() { + return port.getProgress(); + } + + @Override + public boolean isFinished() { + return port.isFinished(); + } + }; } }; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java index 3462e4556..39f4853fc 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java @@ -27,7 +27,7 @@ public SetPreprocessorSetup> nextSetupStep() { SetPreprocessorSetup innerStep = inner.nextSetupStep(); if (innerStep == null) return null; - return new SetPreprocessorSetup>() { + return new SetPreprocessorSetup<>() { boolean initialized = false; @Override @@ -92,6 +92,8 @@ public MappingFunction> getMapper(int iOverlap) { result.add(gr); } + if (result.stream().allMatch(List::isEmpty)) + return null; return new OverlapGroup<>(result); }; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java index 96f0a9316..51db885f7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java @@ -1,9 +1,10 @@ package com.milaboratory.mixcr.postanalysis.ui; -import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneReader; import com.milaboratory.mixcr.basictypes.CloneSetIO; import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.util.LambdaSemaphore; import io.repseq.core.VDJCLibraryRegistry; @@ -45,9 +46,10 @@ public String id() { } @Override - public OutputPortCloseable mkElementsPort() { + public OutputPortWithProgress mkElementsPort() { try { - return CloneSetIO.mkReader(path, registry, concurrencyLimiter).readClones(); + CloneReader reader = CloneSetIO.mkReader(path, registry, concurrencyLimiter); + return OutputPortWithProgress.wrap(reader.numberOfClones(), reader.readClones()); } catch (IOException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java new file mode 100644 index 000000000..331e1f9a6 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java @@ -0,0 +1,51 @@ +package com.milaboratory.mixcr.util; + +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.util.CanReportProgress; + +import java.util.concurrent.atomic.AtomicBoolean; +import java.util.concurrent.atomic.AtomicLong; + +public interface OutputPortWithProgress extends OutputPortCloseable, CanReportProgress { + /** + * @return number of returned elemens so far + */ + long index(); + + static OutputPortWithProgress wrap(int size, OutputPortCloseable inner) { + final AtomicBoolean isFinished = new AtomicBoolean(false); + final AtomicLong index = new AtomicLong(0); + return new OutputPortWithProgress<>() { + @Override + public long index() { + return index.get(); + } + + @Override + public T take() { + T t = inner.take(); + if (t == null) { + isFinished.set(true); + return null; + } + index.incrementAndGet(); + return t; + } + + @Override + public double getProgress() { + return (index.get() + 1.0) / size; + } + + @Override + public boolean isFinished() { + return isFinished.get(); + } + + @Override + public void close() { + inner.close(); + } + }; + } +} diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java index 1da372348..6d6747ccb 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java @@ -1,14 +1,22 @@ package com.milaboratory.mixcr.cli; -import junit.framework.TestCase; +import org.junit.Ignore; import org.junit.Test; /** * */ -public class CommandPaTest extends TestCase { +public class CommandPaTest { @Test public void test1() { Main.main("postanalysis", "help", "overlap"); } + + @Ignore + @Test + public void test2() { + Main.main("postanalysis", "overlap", + "--chains", "IGH", "-f", + "--only-productive", "-d", "umi-count-auto", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_a.clns", 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"/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json"); + } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java index 4fe4a2e60..c542f3274 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java @@ -3,6 +3,7 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.IteratorOutputPortAdapter; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import java.util.ArrayList; import java.util.Iterator; @@ -47,16 +48,17 @@ public String id() { } @Override - public OutputPortCloseable mkElementsPort() { + public OutputPortWithProgress mkElementsPort() { final IteratorOutputPortAdapter adapter = new IteratorOutputPortAdapter<>(data); - return new OutputPortCloseable() { + return OutputPortWithProgress.wrap(data.size(), new OutputPortCloseable() { @Override - public void close() { } + public void close() { + } @Override public T take() { return adapter.take(); } - }; + }); } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java index 139c60143..1b9504eb2 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -13,6 +13,7 @@ import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; import com.milaboratory.mixcr.postanalysis.ui.OutputTable; import com.milaboratory.mixcr.postanalysis.ui.OverlapSummary; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.util.sorting.MergeStrategy; import com.milaboratory.util.sorting.SortingProperty; import com.milaboratory.util.sorting.SortingPropertyRelation; @@ -132,11 +133,38 @@ public void testOverlapCharacteristic1() { PostanalysisResult paResult = runner.run(new OverlapDataset(datasetIds) { @Override - public OutputPortCloseable> mkElementsPort() { - return new SimpleProcessorWrapper<>(strategy + public OutputPortWithProgress> mkElementsPort() { + OutputPortCloseable> inner = new SimpleProcessorWrapper<>(strategy .join(Arrays.stream(ovp.datasets) .map(TestDataset::mkElementsPort) .collect(Collectors.toList())), OverlapGroup::new); + + return new OutputPortWithProgress>() { + @Override + public long index() { + return 0; + } + + @Override + public void close() { + inner.close(); + } + + @Override + public OverlapGroup take() { + return inner.take(); + } + + @Override + public double getProgress() { + return 0; + } + + @Override + public boolean isFinished() { + return false; + } + }; } }); @@ -226,7 +254,8 @@ private static OutputPortCloseable asOutputPort(List l) { OutputPort p = CUtils.asOutputPort(l); return new OutputPortCloseable() { @Override - public void close() {} + public void close() { + } @Override public T take() { From d7c4c8751a5895e3381e546106d84b145150d446 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 24 Feb 2022 02:42:48 +0300 Subject: [PATCH 142/282] Sort CLNA --- .../mixcr/cli/CommandSortClones.java | 23 +++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java index 423bad628..936ffebc3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java @@ -5,6 +5,7 @@ import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.util.ArraysUtils; +import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; @@ -56,10 +57,28 @@ public void run1() throws Exception { return; case MAGIC_CLNA: - throw new RuntimeException(); + try (ClnAReader reader = new ClnAReader(Path.of(in), VDJCLibraryRegistry.getDefault(), Runtime.getRuntime().availableProcessors()); + ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { + SmartProgressReporter.startProgressReport(writer); - } + GeneFeature[] assemblingFeatures = reader.getAssemblerParameters().getAssemblingFeatures(); + // Any CDR3 containing feature will become first + for (int i = 0; i < assemblingFeatures.length; i++) + if (assemblingFeatures[i].contains(GeneFeature.CDR3)) { + if (i != 0) + ArraysUtils.swap(assemblingFeatures, 0, i); + break; + } + + VDJCSProperties.CloneOrdering ordering = VDJCSProperties.cloneOrderingByNucleotide(assemblingFeatures, + GeneType.Variable, GeneType.Joining); + + writer.writeClones(CloneSet.reorder(reader.readCloneSet(), ordering)); + writer.collateAlignments(reader.readAllAlignments(), reader.numberOfAlignments()); + writer.writeAlignmentsAndIndex(); + } + } } From b10274a2296b6d58e29e43632e6d9278b4fc65fb Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Fri, 4 Mar 2022 16:01:16 +0300 Subject: [PATCH 143/282] feat: build app with GitHub Actions. Read MiCI gradle properties --- .github/workflows/build.yaml | 53 ++++++++++++++++++++++++++++++++++++ build.gradle.kts | 16 +++++++++-- 2 files changed, 66 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/build.yaml diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml new file mode 100644 index 000000000..7cea5fa29 --- /dev/null +++ b/.github/workflows/build.yaml @@ -0,0 +1,53 @@ +name: "Build" + +on: + push: + tags: [ '*' ] + branches: [ 'master' ] + + workflow_dispatch: {} + +jobs: + init: + runs-on: ubuntu-latest + steps: + - id: context + uses: milaboratory/github-ci/actions/context/init@v2 + + outputs: + is-release: ${{ steps.context.outputs.is-release }} + + run: + needs: + - init + + uses: milaboratory/github-ci/.github/workflows/java-gradle-app.yaml@v2 + with: + # Environment + java-version: '11' + app-name: MiXCR + app-name-slug: 'mixcr' + + # Distribution + dist-archive-tasks: 'distributionZip' + dist-archive-paths: './distributions/*.zip' + + # Release to S3 + release-to-s3: true + release-s3-add-version: true + release-s3-add-sha: ${{ fromJSON(needs.init.outputs.is-release) && 'false' || '8' }} + + # Send notifications + notify-telegram: true + + secrets: + GRADLE_PROPERTIES: | + miRepoAccessKeyId=${{ secrets.AWS_CI_ACCESS_KEY_ID }} + miRepoSecretAccessKey= ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }} + + AWS_KEY_ID: ${{ secrets.AWS_CI_ACCESS_KEY_ID }} + AWS_KEY_SECRET: ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }} + + TELEGRAM_NOTIFICATION_TARGET: ${{ secrets.TG_CHANNEL_MIBUILDS }} + TELEGRAM_API_TOKEN: ${{ secrets.TG_CI_BOT_TOKEN }} + diff --git a/build.gradle.kts b/build.gradle.kts index cae89ff79..4efe2c34d 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -17,10 +17,15 @@ val miRepoSecretAccessKey: String by project val versionDetails: Closure by extra val gitDetails = versionDetails() -val longTests: String? by project +fun boolProperty(name: String): Boolean { + return ((properties[name] as String?) ?: "false").toBoolean() +} -group = "com.milaboratory" -version = if (version != "unspecified") version else "SNAPSHOT" +val isMiCi = boolProperty("mi-ci") +val isRelease = boolProperty("mi-release") + +val longTests: String? by project +val miCiStage = properties["mi-ci-stage"] as String? description = "MiXCR" java { @@ -136,5 +141,10 @@ tasks.test { minHeapSize = "1024m" maxHeapSize = "2048m" +// miCiStage?.let { +// if (it == "test") { +// systemProperty("longTests", "true"); +// } +// } longTests?.let { systemProperty("longTests", it) } } From a069926a1556f23a05811442364b2139ec6649b9 Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Fri, 4 Mar 2022 16:10:52 +0300 Subject: [PATCH 144/282] fix: don't try to canonize version numbers in version detection --- .github/workflows/build.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 7cea5fa29..3063c43e5 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -13,6 +13,8 @@ jobs: steps: - id: context uses: milaboratory/github-ci/actions/context/init@v2 + with: + version-canonize: false outputs: is-release: ${{ steps.context.outputs.is-release }} From 344c5391f1ca531e830124e615677efdba15c4d0 Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Fri, 4 Mar 2022 16:12:00 +0300 Subject: [PATCH 145/282] feat: autobuild on changes in 'pmaster' instead of 'master' --- .github/workflows/build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 3063c43e5..d11428c53 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -3,7 +3,7 @@ name: "Build" on: push: tags: [ '*' ] - branches: [ 'master' ] + branches: [ 'pmaster' ] workflow_dispatch: {} From 55d880c28371358c96358a75aa91fdea540e0147 Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Fri, 4 Mar 2022 16:20:36 +0300 Subject: [PATCH 146/282] fix: get 'is-release' from context after initialization --- .github/workflows/build.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index d11428c53..82b313b5a 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -11,10 +11,11 @@ jobs: init: runs-on: ubuntu-latest steps: - - id: context - uses: milaboratory/github-ci/actions/context/init@v2 + - uses: milaboratory/github-ci/actions/context/init@v2 with: version-canonize: false + - id: context + uses: milaboratory/github-ci/actions/context@v2 outputs: is-release: ${{ steps.context.outputs.is-release }} From e7f034bf0dd474a531cbb752757338f04ed8ed37 Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Fri, 4 Mar 2022 23:10:35 +0300 Subject: [PATCH 147/282] feat: disable docker app distribution with gradle --- .github/workflows/build.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 82b313b5a..d59fa0e07 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -32,6 +32,8 @@ jobs: app-name-slug: 'mixcr' # Distribution + dist-docker: false + dist-archive: true dist-archive-tasks: 'distributionZip' dist-archive-paths: './distributions/*.zip' From ce13e7bb906845e0dddde68650fb8819ba180f93 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sun, 6 Mar 2022 22:40:00 +0200 Subject: [PATCH 148/282] wip --- build.gradle.kts | 10 +++---- gradle/wrapper/gradle-wrapper.properties | 2 +- .../mixcr/cli/CommandPaExport.java | 30 +++++++++++++------ .../java/com/milaboratory/mixcr/cli/Main.java | 6 ++-- .../{dataframe => plots}/BasicStatistics.kt | 2 +- .../{dataframe => plots}/GeneUsage.kt | 2 +- .../{dataframe => plots}/Overlap.kt | 27 ++++++++++------- .../postanalysis/plots/PlotParameters.kt | 6 ++++ .../{dataframe => plots}/SingleSpectratype.kt | 2 +- .../postanalysis/{dataframe => plots}/Util.kt | 6 ++-- .../{dataframe => plots}/VJUsage.kt | 2 +- .../mixcr/cli/CommandPaExportTest.java | 9 ++++++ .../BasicStatisticsTest.kt | 2 +- .../SingleSpectratypeTest.kt | 5 +--- 14 files changed, 71 insertions(+), 40 deletions(-) rename src/main/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/BasicStatistics.kt (99%) rename src/main/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/GeneUsage.kt (98%) rename src/main/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/Overlap.kt (83%) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt rename src/main/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/SingleSpectratype.kt (98%) rename src/main/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/Util.kt (95%) rename src/main/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/VJUsage.kt (98%) rename src/test/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/BasicStatisticsTest.kt (95%) rename src/test/java/com/milaboratory/mixcr/postanalysis/{dataframe => plots}/SingleSpectratypeTest.kt (92%) diff --git a/build.gradle.kts b/build.gradle.kts index 4b0a02496..3b94c1757 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -9,8 +9,7 @@ val miplotsVersion = "1.0.0" val milibVersion = "2.0.0" val repseqioVersion = "1.3.5-10-05b9291c5e" val jacksonVersion = "2.12.4" -val letsPlotLibraryVersion = "2.1.0" -val letsPlotKotlinApiVersion = "3.1.1" +val dataframeVersion = "0.8.0-rc-7" plugins { `java-library` @@ -18,8 +17,8 @@ plugins { `maven-publish` id("com.palantir.git-version") version "0.13.0" id("com.github.johnrengelman.shadow") version "7.0.0" - kotlin("jvm") version "1.6.10" - id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-dev-808" + kotlin("jvm") version "1.6.20-M1" + id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-rc-7" } // Make IDE aware of the generated code: @@ -95,9 +94,8 @@ dependencies { implementation(testFixtures("com.milaboratory:milib:$milibVersion")) testImplementation("org.mockito:mockito-all:1.9.5") - // plots implementation(kotlin("stdlib")) - + implementation("org.jetbrains.kotlinx:dataframe:$dataframeVersion") implementation("org.apache.xmlgraphics:fop-transcoder:2.6") implementation("org.apache.pdfbox:pdfbox:2.0.21") diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 2e6e5897b..41dfb8790 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.4-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 71bf7c277..972520035 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -6,7 +6,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.CommandPa.PaResult; import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; -import com.milaboratory.mixcr.postanalysis.dataframe.*; +import com.milaboratory.mixcr.postanalysis.plots.*; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; @@ -142,7 +142,14 @@ public void run0() { } } - static abstract class ExportBasicStatistics extends CommandPaExport { + static abstract class CommandPaExportPlots extends CommandPaExport { + @Option(names = {"--width"}, description = "Plot width") + public int width = 0; + @Option(names = {"--height"}, description = "Plot height") + public int height = 0; + } + + static abstract class ExportBasicStatistics extends CommandPaExportPlots { abstract String group(); @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") @@ -219,7 +226,7 @@ String group() { } } - static abstract class ExportGeneUsage extends CommandPaExport { + static abstract class ExportGeneUsage extends CommandPaExportPlots { abstract String group(); @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") @@ -298,7 +305,7 @@ String group() { sortOptions = false, separator = " ", description = "Export V-J usage heatmap") - static class ExportVJUsage extends CommandPaExport { + static class ExportVJUsage extends CommandPaExportPlots { @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") public String out; @Option(names = {"--no-v-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") @@ -342,7 +349,7 @@ void run(Chains.NamedChains chains, PaResultByChain result) { sortOptions = false, separator = " ", description = "Export overlap heatmap") - static class ExportOverlap extends CommandPaExport { + static class ExportOverlap extends CommandPaExportPlots { @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") public String out; @Option(names = {"--no-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") @@ -371,13 +378,18 @@ void run(Chains.NamedChains chains, PaResultByChain result) { if (df.rowsCount() == 0) return; - Plot plots = Overlap.INSTANCE.plot(df, - new Overlap.PlotParameters( + if (df.get("weight").distinct().toList().size() <= 1) + return; + + List plots = Overlap.INSTANCE.plots(df, + new Overlap.OverlapParameters( colorKey, - !noDendro + !noDendro, + width, + height )); - ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 4f07b6493..b0b60044e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -205,7 +205,9 @@ public static CommandLine mkCmd() { .addSubcommand("vUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVUsage.class)) .addSubcommand("jUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportJUsage.class)) .addSubcommand("isotypeUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportIsotypeUsage.class)) - .addSubcommand("vjUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVJUsage.class)); + .addSubcommand("vjUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVJUsage.class)) + + .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPaExport.ExportOverlap.class)); cmd.setSeparator(" "); return cmd; @@ -214,7 +216,7 @@ public static CommandLine mkCmd() { public static CommandLine parseArgs(String... args) { if (args.length == 0) args = new String[]{"help"}; - ExceptionHandler exHandler = new ExceptionHandler(); + ExceptionHandler exHandler = new ExceptionHandler<>(); exHandler.andExit(1); CommandLine cmd = mkCmd(); try { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt similarity index 99% rename from src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt rename to src/main/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt index a5e4d3818..8b2b29188 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatistics.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.stat.util.PValueCorrection import com.milaboratory.miplots.stat.util.RefGroup diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt similarity index 98% rename from src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt rename to src/main/java/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt index ff0b0b88a..924aa4cba 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/GeneUsage.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.Position import com.milaboratory.miplots.color.Palletes diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Overlap.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt similarity index 83% rename from src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Overlap.kt rename to src/main/java/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index 24b92698b..d80f41efc 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Overlap.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.Position import com.milaboratory.miplots.color.Palletes @@ -6,6 +6,7 @@ import com.milaboratory.miplots.heatmap.* import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey import com.milaboratory.mixcr.postanalysis.overlap.OverlapType +import jetbrains.letsPlot.ggsize import jetbrains.letsPlot.label.ggtitle import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema @@ -19,7 +20,6 @@ import org.jetbrains.kotlinx.dataframe.io.read * DataFrame row for V or J usage data */ @DataSchema -@Suppress("UNCHECKED_CAST") data class OverlapRow( val sample1: String, val sample2: String, @@ -31,7 +31,6 @@ object Overlap { /** * Imports data into DataFrame **/ - @Suppress("UNCHECKED_CAST") fun dataFrame(paResult: PostanalysisResult) = run { val data = mutableListOf() @@ -54,26 +53,28 @@ object Overlap { paResult: PostanalysisResult, metadataPath: String?, ) = run { - var df = dataFrame(paResult) + var df: DataFrame = dataFrame(paResult) if (metadataPath != null) df = attachMetadata(df, "sample1", DataFrame.read(metadataPath), "sample").cast() df } - data class PlotParameters( + data class OverlapParameters( val colorKey: List? = null, - val cluster: Boolean = true - ) + val cluster: Boolean = true, + override val width: Int, + override val height: Int + ) : PlotParameters fun plots( df: DataFrame, - pp: PlotParameters, + pp: OverlapParameters, ) = df.groupBy { "metric"() }.groups.toList() - .map { sdf -> plot(df, pp) + ggtitle(sdf.first()[VJUsageRow::sample.name]!!.toString()) } + .map { sdf -> plot(df, pp) + ggtitle(sdf.first()[OverlapRow::metric.name]!!.toString()) } fun plot( df: DataFrame, - pp: PlotParameters, + pp: OverlapParameters, ) = run { var plt = Heatmap( df, @@ -82,7 +83,9 @@ object Overlap { z = GeneUsageRow::weight.name, xOrder = if (pp.cluster) Hierarchical() else null, yOrder = if (pp.cluster) Hierarchical() else null, - fillPallette = Palletes.Diverging.lime90rose130 + fillPallette = Palletes.Diverging.lime90rose130, + fillNoValue = true, + noValue = 0.0 ) plt = plt.withBorder() @@ -115,6 +118,8 @@ object Overlap { plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) plt = plt.withFillLegend(Position.Left, size = 0.5) plt = plt.withColorKeyLegend(Position.Left) + if (pp.width > 0 && pp.height > 0) + plt.plusAssign(ggsize(pp.width, pp.height)) plt.plot } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt new file mode 100644 index 000000000..c5d3b85ac --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt @@ -0,0 +1,6 @@ +package com.milaboratory.mixcr.postanalysis.plots + +interface PlotParameters { + val width: Int + val height: Int +} \ No newline at end of file diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt similarity index 98% rename from src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt rename to src/main/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt index 670e31058..3d2b0e1d2 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratype.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt similarity index 95% rename from src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt rename to src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt index d4d95068c..147d1007e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/Util.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.util.StringUtil import org.jetbrains.kotlinx.dataframe.AnyFrame @@ -83,4 +83,6 @@ fun matchLists(target: List, query: List): Map } return r -} \ No newline at end of file +} + +data class Filter(val column: String, val value: Any) \ No newline at end of file diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/VJUsage.kt b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt similarity index 98% rename from src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/VJUsage.kt rename to src/main/java/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt index c0fc71a3c..01a59fe73 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/dataframe/VJUsage.kt +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.Position import com.milaboratory.miplots.color.Palletes diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index c904e7696..c40c9c413 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -35,4 +35,13 @@ public void test2() { "scratch/pa/vUsage.pdf" ); } + + @Test + public void test3() { + Main.main("exportPa", "overlap", + "--width", "1000", + "--height", "3000", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap.pdf"); + } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatisticsTest.kt similarity index 95% rename from src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt rename to src/test/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatisticsTest.kt index 8b89422e4..387ab8f2e 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/BasicStatisticsTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatisticsTest.kt @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.writePDF import com.milaboratory.mixcr.cli.CommandPa diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratypeTest.kt similarity index 92% rename from src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt rename to src/test/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratypeTest.kt index 7f0e7c4f2..887de789b 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/dataframe/SingleSpectratypeTest.kt +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratypeTest.kt @@ -1,10 +1,8 @@ -package com.milaboratory.mixcr.postanalysis.dataframe +package com.milaboratory.mixcr.postanalysis.plots -import jetbrains.datalore.plot.PlotSvgExport import jetbrains.letsPlot.coordFixed import jetbrains.letsPlot.geom.geomTile import jetbrains.letsPlot.ggsize -import jetbrains.letsPlot.intern.toSpec import jetbrains.letsPlot.letsPlot import jetbrains.letsPlot.scale.scaleXContinuous import jetbrains.letsPlot.scale.scaleYContinuous @@ -13,7 +11,6 @@ import org.jetbrains.kotlinx.dataframe.api.head import org.jetbrains.kotlinx.dataframe.api.toMap import org.jetbrains.kotlinx.dataframe.io.read import org.junit.Test -import java.nio.file.Path /** From 679c1794af9279672a231d709d662f4ed7e8694c Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sun, 6 Mar 2022 22:49:28 +0200 Subject: [PATCH 149/282] fix --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 3b94c1757..a0c0bbf8a 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -17,7 +17,7 @@ plugins { `maven-publish` id("com.palantir.git-version") version "0.13.0" id("com.github.johnrengelman.shadow") version "7.0.0" - kotlin("jvm") version "1.6.20-M1" + kotlin("jvm") version "1.6.10" id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-rc-7" } From fa7c6047e568ee992da6b4acfa6724cbd06e415e Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 7 Mar 2022 00:32:18 +0200 Subject: [PATCH 150/282] wip --- build.gradle.kts | 8 +++----- .../mixcr/postanalysis/plots/BasicStatistics.kt | 0 .../milaboratory/mixcr/postanalysis/plots/GeneUsage.kt | 1 - .../com/milaboratory/mixcr/postanalysis/plots/Overlap.kt | 2 +- .../mixcr/postanalysis/plots/PlotParameters.kt | 0 .../mixcr/postanalysis/plots/SingleSpectratype.kt | 1 - .../com/milaboratory/mixcr/postanalysis/plots/Util.kt | 0 .../com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt | 1 - 8 files changed, 4 insertions(+), 9 deletions(-) rename src/main/{java => kotlin}/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt (100%) rename src/main/{java => kotlin}/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt (99%) rename src/main/{java => kotlin}/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt (98%) rename src/main/{java => kotlin}/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt (100%) rename src/main/{java => kotlin}/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt (99%) rename src/main/{java => kotlin}/com/milaboratory/mixcr/postanalysis/plots/Util.kt (100%) rename src/main/{java => kotlin}/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt (99%) diff --git a/build.gradle.kts b/build.gradle.kts index a0c0bbf8a..5f651bb57 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -49,7 +49,7 @@ application { mainClass.set("com.milaboratory.mixcr.cli.Main") } -tasks.withType() { +tasks.withType { options.encoding = "UTF-8" } @@ -96,10 +96,8 @@ dependencies { implementation(kotlin("stdlib")) implementation("org.jetbrains.kotlinx:dataframe:$dataframeVersion") - implementation("org.apache.xmlgraphics:fop-transcoder:2.6") - implementation("org.apache.pdfbox:pdfbox:2.0.21") - - implementation("org.apache.commons:commons-csv:1.9.0") + implementation("org.jetbrains.lets-plot:lets-plot-common:$letsPlotLibraryVersion") + implementation("org.jetbrains.lets-plot:lets-plot-kotlin-jvm:$letsPlotKotlinApiVersion") } val writeBuildProperties by tasks.registering(WriteProperties::class) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt similarity index 100% rename from src/main/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt similarity index 99% rename from src/main/java/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt index 924aa4cba..f56af216c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt @@ -14,7 +14,6 @@ import org.jetbrains.kotlinx.dataframe.io.read * DataFrame row for V or J usage data */ @DataSchema -@Suppress("UNCHECKED_CAST") data class GeneUsageRow( /** Sample ID */ val sample: String, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt similarity index 98% rename from src/main/java/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index d80f41efc..167ed495c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -31,7 +31,7 @@ object Overlap { /** * Imports data into DataFrame **/ - fun dataFrame(paResult: PostanalysisResult) = run { + fun dataFrame(paResult: PostanalysisResult) = run { val data = mutableListOf() for ((_, charData) in paResult.data) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt similarity index 100% rename from src/main/java/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt similarity index 99% rename from src/main/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt index 3d2b0e1d2..9eaf6cb4d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt @@ -16,7 +16,6 @@ import org.jetbrains.kotlinx.dataframe.api.* * DataFrame row for single (V/J/CDR3) spectratype */ @DataSchema -@Suppress("UNCHECKED_CAST") data class SpectratypeRow( /** Sample ID */ val sample: String, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Util.kt similarity index 100% rename from src/main/java/com/milaboratory/mixcr/postanalysis/plots/Util.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Util.kt diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt similarity index 99% rename from src/main/java/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt index 01a59fe73..40e49d9f9 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt @@ -17,7 +17,6 @@ import org.jetbrains.kotlinx.dataframe.io.read * DataFrame row for V or J usage data */ @DataSchema -@Suppress("UNCHECKED_CAST") data class VJUsageRow( /** Sample ID */ val sample: String, From a7070b4697043a90b2854c3bd2e46de625050313 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 7 Mar 2022 00:57:22 +0200 Subject: [PATCH 151/282] fix --- build.gradle.kts | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 5f651bb57..2e785b74f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -94,10 +94,6 @@ dependencies { implementation(testFixtures("com.milaboratory:milib:$milibVersion")) testImplementation("org.mockito:mockito-all:1.9.5") - implementation(kotlin("stdlib")) - implementation("org.jetbrains.kotlinx:dataframe:$dataframeVersion") - implementation("org.jetbrains.lets-plot:lets-plot-common:$letsPlotLibraryVersion") - implementation("org.jetbrains.lets-plot:lets-plot-kotlin-jvm:$letsPlotKotlinApiVersion") } val writeBuildProperties by tasks.registering(WriteProperties::class) { @@ -126,6 +122,8 @@ val shadowJar = tasks.withType { exclude(dependency("commons-logging:commons-logging")) exclude(dependency("ch.qos.logback:logback-core")) exclude(dependency("ch.qos.logback:logback-classic")) + + exclude(dependency("org.jetbrains.kotlin:.*")) } } From 16c34683be84fd4b9cd8570d1cc4b10ac3482897 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 7 Mar 2022 16:44:16 +0200 Subject: [PATCH 152/282] fixes --- build.gradle.kts | 32 +++++++++++-------- .../clustering/HierarchicalClustering.java | 4 +-- .../mixcr/postanalysis/plots/Overlap.kt | 3 +- .../mixcr/cli/CommandPaExportTest.java | 5 +-- 4 files changed, 24 insertions(+), 20 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 2e785b74f..69d676c78 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -111,20 +111,24 @@ tasks.processResources { } val shadowJar = tasks.withType { - minimize { - exclude(dependency("io.repseq:repseqio")) - exclude(dependency("com.milaboratory:milib")) - exclude(dependency("org.lz4:lz4-java")) - exclude(dependency("com.fasterxml.jackson.core:jackson-databind")) - - exclude(dependency("log4j:log4j")) - exclude(dependency("org.slf4j:slf4j-api")) - exclude(dependency("commons-logging:commons-logging")) - exclude(dependency("ch.qos.logback:logback-core")) - exclude(dependency("ch.qos.logback:logback-classic")) - - exclude(dependency("org.jetbrains.kotlin:.*")) - } +// minimize { +// exclude(dependency("io.repseq:repseqio")) +// exclude(dependency("com.milaboratory:milib")) +// exclude(dependency("org.lz4:lz4-java")) +// exclude(dependency("com.fasterxml.jackson.core:jackson-databind")) +// +// exclude(dependency("log4j:log4j")) +// exclude(dependency("org.slf4j:slf4j-api")) +// exclude(dependency("commons-logging:commons-logging")) +// exclude(dependency("ch.qos.logback:logback-core")) +// exclude(dependency("ch.qos.logback:logback-classic")) +// +// exclude("org.apache.xmlgraphics:.*") +// exclude("org.apache.pdfbox:pdfbox:2.0.24") +// exclude("org.apache.commons:commons-csv:1.9.0") +// exclude(dependency("org.jetbrains.kotlin:.*")) +// exclude(dependency("org.apache.batik:.*")) +// } } val distributionZip by tasks.registering(Zip::class) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java index 45ea3a03f..d84001528 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java @@ -12,9 +12,7 @@ import java.util.function.ToDoubleBiFunction; public final class HierarchicalClustering { - - private HierarchicalClustering() { - } + private HierarchicalClustering() {} public static double EuclideanDistance(double[] vectori, double[] vectorj) { double diff_square_sum = 0.0; diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index 167ed495c..845e59eed 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -31,12 +31,13 @@ object Overlap { /** * Imports data into DataFrame **/ - fun dataFrame(paResult: PostanalysisResult) = run { + fun dataFrame(paResult: PostanalysisResult) = run { val data = mutableListOf() for ((_, charData) in paResult.data) { for ((_, keys) in charData.data) { for (metric in keys.data) { + @Suppress("UNCHECKED_CAST") val key = metric.key as? OverlapKey ?: throw RuntimeException() data += OverlapRow(key.id1, key.id2, key.key, metric.value) } diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index c40c9c413..b69a5a641 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -36,11 +36,12 @@ public void test2() { ); } + // @Ignore @Test public void test3() { Main.main("exportPa", "overlap", - "--width", "1000", - "--height", "3000", +// "--width", "2000", +// "--height", "5000", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap.pdf"); } From c8e019277fde686553c81bd7d9f804d7115dd9a5 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Thu, 10 Mar 2022 13:33:27 +0400 Subject: [PATCH 153/282] fix: better error reporting for malformed files --- .../java/com/milaboratory/mixcr/basictypes/CloneSetIO.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java index edf2bbf7d..fe468318b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java @@ -29,6 +29,7 @@ */ package com.milaboratory.mixcr.basictypes; +import com.milaboratory.cli.BinaryFileInfo; import com.milaboratory.util.LambdaSemaphore; import io.repseq.core.VDJCLibraryRegistry; @@ -53,7 +54,10 @@ public static CloneSet read(String file, VDJCLibraryRegistry libraryRegistry) th } public static CloneSet read(File file, VDJCLibraryRegistry libraryRegistry) throws IOException { - switch (Objects.requireNonNull(fileInfoExtractorInstance.getFileInfo(file)).fileType) { + BinaryFileInfo fileInfo = fileInfoExtractorInstance.getFileInfo(file); + if (fileInfo == null) + throw new RuntimeException("Unsupported file type"); + switch (Objects.requireNonNull(fileInfo).fileType) { case MAGIC_CLNA: try (ClnAReader r = new ClnAReader(file.toPath(), libraryRegistry, 1)) { return r.readCloneSet(); From 4ba29e0217cda72d057fc14a547c191a19d8ce50 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 11 Mar 2022 03:12:57 +0200 Subject: [PATCH 154/282] wip --- .../mixcr/cli/CommandPaExport.java | 90 +++++----- .../java/com/milaboratory/mixcr/cli/Main.java | 2 +- .../postanalysis/plots/BasicStatistics.kt | 16 +- .../mixcr/postanalysis/plots/GeneUsage.kt | 21 +-- .../mixcr/postanalysis/plots/Metadata.kt | 170 ++++++++++++++++++ .../mixcr/postanalysis/plots/Overlap.kt | 30 +++- .../mixcr/postanalysis/plots/Util.kt | 88 --------- .../mixcr/postanalysis/plots/VJUsage.kt | 36 +--- .../mixcr/cli/CommandPaExportTest.java | 3 + 9 files changed, 276 insertions(+), 180 deletions(-) create mode 100644 src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt delete mode 100644 src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Util.kt diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 972520035..7e4a49225 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -147,14 +147,41 @@ static abstract class CommandPaExportPlots extends CommandPaExport { public int width = 0; @Option(names = {"--height"}, description = "Plot height") public int height = 0; + @Option(names = {"--filter"}, description = "Filter by metadata. Possible filters column=value, column>=value etc.") + public String filterByMetadata; + + @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") + public String out; + + DataFrame filter(DataFrame df) { + if (filterByMetadata != null) { + return MetadataKt.parseFilter(metadata(), filterByMetadata).apply(df); + } else + return df; + } + + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".pdf")) + throwValidationException("Output file must ends with .pdf extension"); + + if (filterByMetadata != null && metadata == null) + throwValidationException("Filter is specified by metadata is not."); + } + + private DataFrame metadataDf; + + DataFrame metadata() { + return metadataDf != null + ? metadataDf + : (metadata == null ? null : (metadataDf = MetadataKt.readMetadata(metadata))); + } } static abstract class ExportBasicStatistics extends CommandPaExportPlots { abstract String group(); - @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") - public String out; - @Option(names = {"-p", "--primary-group"}, description = "Primary group") public String primaryGroup; @Option(names = {"-s", "--secondary-group"}, description = "Secondary group") @@ -164,23 +191,20 @@ static abstract class ExportBasicStatistics extends CommandPaExportPlots { @Option(names = {"--metric"}, description = "Select specific metrics to export.") public List metrics; - @Override - public void validate() { - super.validate(); - if (!out.endsWith(".pdf")) - throwValidationException("Output file must ends with .pdf extension"); - } - @Override void run(Chains.NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(group()); + DataFrame metadata = metadata(); + DataFrame df = BasicStatistics.INSTANCE.dataFrame( result.result.forGroup(ch), metrics, metadata ); + df = filter(df); + List plots = BasicStatistics.INSTANCE.plots(df, new BasicStatistics.PlotParameters( primaryGroup, @@ -229,8 +253,6 @@ String group() { static abstract class ExportGeneUsage extends CommandPaExportPlots { abstract String group(); - @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") - public String out; @Option(names = {"--no-samples-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of samples.") public boolean noSamplesDendro; @Option(names = {"--no-genes-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of genes.") @@ -238,21 +260,16 @@ static abstract class ExportGeneUsage extends CommandPaExportPlots { @Option(names = {"--color-key"}, description = "Add color key layer.") public List colorKey; - @Override - public void validate() { - super.validate(); - if (!out.endsWith(".pdf")) - throwValidationException("Output file must ends with .pdf extension"); - } - @Override void run(Chains.NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(group()); + DataFrame metadata = metadata(); DataFrame df = GeneUsage.INSTANCE.dataFrame( result.result.forGroup(ch), metadata ); + df = filter(df); if (df.rowsCount() == 0) return; @@ -306,42 +323,32 @@ String group() { separator = " ", description = "Export V-J usage heatmap") static class ExportVJUsage extends CommandPaExportPlots { - @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") - public String out; @Option(names = {"--no-v-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") public boolean noVDendro; @Option(names = {"--no-j-dendro"}, description = "Plot dendrogram for hierarchical clusterization of genes.") public boolean noJDendro; - @Option(names = {"--color-key"}, description = "Add color key layer.") - public List colorKey; - - @Override - public void validate() { - super.validate(); - if (!out.endsWith(".pdf")) - throwValidationException("Output file must ends with .pdf extension"); - } @Override void run(Chains.NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(CommandPa.VJUsage); + DataFrame metadata = metadata(); DataFrame df = VJUsage.INSTANCE.dataFrame( result.result.forGroup(ch), metadata ); + df = filter(df); if (df.rowsCount() == 0) return; - Plot plots = VJUsage.INSTANCE.plot(df, + List plots = VJUsage.INSTANCE.plots(df, new VJUsage.PlotParameters( - colorKey, !noVDendro, !noJDendro )); - ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); } } @@ -350,8 +357,6 @@ void run(Chains.NamedChains chains, PaResultByChain result) { separator = " ", description = "Export overlap heatmap") static class ExportOverlap extends CommandPaExportPlots { - @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") - public String out; @Option(names = {"--no-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") public boolean noDendro; @Option(names = {"--color-key"}, description = "Add color key layer.") @@ -359,21 +364,24 @@ static class ExportOverlap extends CommandPaExportPlots { @Option(names = {"--metric"}, description = "Select specific metrics to export.") public List metrics; - @Override - public void validate() { - super.validate(); - if (!out.endsWith(".pdf")) - throwValidationException("Output file must ends with .pdf extension"); + DataFrame filterOverlap(DataFrame df) { + if (filterByMetadata != null) { + Filter filter = MetadataKt.parseFilter(metadata(), filterByMetadata); + return Overlap.INSTANCE.filterOverlap(filter, df); + } else + return df; } @Override void run(Chains.NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(CommandPa.Overlap); + DataFrame metadata = metadata(); DataFrame df = Overlap.INSTANCE.dataFrame( result.result.forGroup(ch), metadata ); + df = filterOverlap(df); if (df.rowsCount() == 0) return; @@ -399,6 +407,6 @@ void run(Chains.NamedChains chains, PaResultByChain result) { subcommands = { CommandLine.HelpCommand.class }) - public static class CommandExportPostanalysisMain { + public static class CommandExportPaMain { } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index b0b60044e..847154157 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -149,7 +149,7 @@ public static CommandLine mkCmd() { .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) .addSubcommand("postanalysis", CommandPa.CommandPostanalysisMain.class) - .addSubcommand("exportPa", CommandPaExport.CommandExportPostanalysisMain.class) + .addSubcommand("exportPa", CommandPaExport.CommandExportPaMain.class) .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt index 8b2b29188..15ebe2f29 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt @@ -20,7 +20,6 @@ import jetbrains.letsPlot.letsPlot import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.* -import org.jetbrains.kotlinx.dataframe.io.read /** * DataFrame row for single statistical char group @@ -70,14 +69,23 @@ object BasicStatistics { fun dataFrame( paResult: PostanalysisResult, metricsFilter: List?, - metadataPath: String?, + metadata: Metadata?, ) = run { var df = dataFrame(paResult, metricsFilter) - if (metadataPath != null) - df = df.withMetadata(DataFrame.read(metadataPath)) + if (metadata != null) + df = df.withMetadata(metadata) df } + /** + * Imports data into DataFrame + **/ + fun dataFrame( + paResult: PostanalysisResult, + metricsFilter: List?, + metadataPath: String?, + ) = dataFrame(paResult, metricsFilter, readMetadata(metadataPath)) + data class PlotParameters( val primaryGroup: String? = null, val secondaryGroup: String? = null, diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt index f56af216c..599ed293a 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt @@ -7,7 +7,6 @@ import com.milaboratory.mixcr.postanalysis.PostanalysisResult import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.toDataFrame -import org.jetbrains.kotlinx.dataframe.io.read /** @@ -49,11 +48,11 @@ object GeneUsage { **/ fun dataFrame( paResult: PostanalysisResult, - metadataPath: String?, + metadata: Metadata?, ) = run { var df = dataFrame(paResult) - if (metadataPath != null) - df = df.withMetadata(DataFrame.read(metadataPath)) + if (metadata != null) + df = df.withMetadata(metadata) df } @@ -77,8 +76,6 @@ object GeneUsage { fillPallette = Palletes.Diverging.lime90rose130 ) - plt = plt.withBorder() - val ncats = pp.colorKey?.map { df[it].distinct().size() }?.sum() ?: 0 var pallete = Palletes.Categorical.auto(ncats) pp.colorKey?.let { @@ -98,15 +95,19 @@ object GeneUsage { } } + plt = plt.withBorder() + if (pp.clusterSamples) plt = plt.withDendrogram(pos = Position.Top, 0.1) if (pp.clusterGenes) plt = plt.withDendrogram(pos = Position.Right, 0.1) - plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) - plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) - plt = plt.withFillLegend(Position.Left, size = 0.5) - plt = plt.withColorKeyLegend(Position.Left) + plt = plt + .withLabels(Position.Bottom, angle = 45, sep = 0.1) + .withLabels(Position.Left, sep = 0.1, width = 4.0) + .withFillLegend(Position.Left, size = 0.5) + .withColorKeyLegend(Position.Left) + plt.plot } } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt new file mode 100644 index 000000000..994789255 --- /dev/null +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt @@ -0,0 +1,170 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.milaboratory.util.StringUtil +import org.jetbrains.kotlinx.dataframe.AnyFrame +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.RowFilter +import org.jetbrains.kotlinx.dataframe.api.* +import org.jetbrains.kotlinx.dataframe.io.read +import org.jetbrains.kotlinx.dataframe.io.readTSV +import java.util.* + +fun AnyFrame.isNumeric(col: String) = this[col].all { it == null || it is Number } +fun AnyFrame.isCategorial(col: String) = !isNumeric(col) + +typealias Metadata = AnyFrame + +@JvmName("readMetadataNullable") +fun readMetadata(path: String?): Metadata? = if (path == null) null else readMetadata(path) + +/** + * Read metadata from file + */ +fun readMetadata(path: String): Metadata = + if (path.endsWith(".tsv")) + DataFrame.readTSV(path) + else + DataFrame.read(path) + +/** + * Attaches metadata to statistics + **/ +fun DataFrame.withMetadata(metadataPath: String) = withMetadata(readMetadata(metadataPath)) + +/** + * Attaches metadata to statistics + **/ +fun DataFrame.withMetadata(metadata: Metadata) = run { + attachMetadata(this, "sample", metadata, "sample").cast() +} + +/** + * Attaches metadata to statistics + **/ +fun attachMetadata( + data: AnyFrame, + dataCol: String, + meta: Metadata, + metaCol: String +) = run { + val m = matchLists( + data[dataCol].distinct().cast().toList(), + meta[metaCol].distinct().cast().toList(), + ) + + m.filter { it.value == null }.apply { + if (!isEmpty()) + throw IllegalArgumentException("can't unambiguously match metadata for the following rows: $keys") + } + + data.add("_meta_join_") { m[it[dataCol]] } + .leftJoin(meta) { "_meta_join_" match metaCol } + .remove("_meta_join_") +} + +fun matchLists(target: List, query: List): Map { + val matched: MutableMap>> = HashMap() + for (t in target) { + val matchedForKey = PriorityQueue>( + Comparator.comparing { -it.second } + ) + + for (q in query) { + val a = t.lowercase(Locale.getDefault()) + val b = q.lowercase(Locale.getDefault()) + val match = StringUtil.longestCommonSubstring(a, b) + val score = 2.0 * (0.5 + match) / (1 + a.length + b.length) + matchedForKey.add(q to score) + } + + matched[t] = matchedForKey + } + + val unmatchedQ = query.toMutableSet() + val r = mutableMapOf() + + for ((t, q) in matched.toList().sortedBy { kv -> -kv.second.maxOf { it.second } }) { + if (q.isEmpty()) { + r[t] = null + continue + } + var m: String? = null + while (!q.isEmpty()) { + val candidate = q.poll() + val wasUnmatched = unmatchedQ.remove(candidate.first) + if (wasUnmatched) { + m = candidate.first + break + } + } + r[t] = m + } + + return r +} + + +fun Metadata.parseFilter(expr: String) = + // equality + if (expr.contains("=")) { + val (column, value) = expr.split("=") + if (isNumeric(column)) + Eq(column, value.toDouble()) + else + Eq(column, value) + } else if (expr.contains(">=")) { + val (column, value) = expr.split(">=") + Geq(column, value.toDouble()) + } else if (expr.contains("<=")) { + val (column, value) = expr.split("<=") + Leq(column, value.toDouble()) + } else if (expr.contains(">")) { + val (column, value) = expr.split(">=") + Ge(column, value.toDouble()) + } else if (expr.contains("<")) { + val (column, value) = expr.split("<=") + Le(column, value.toDouble()) + } else throw IllegalArgumentException("incorrect filter string") + + +sealed interface Filter { + val column: String + + fun apply(df: DataFrame): DataFrame = df.filter(predicate()) + + fun predicate(): RowFilter + + fun rename(newColumn: String): Filter + + fun rename(mapping: (String) -> String): Filter = rename(mapping(column)) +} + +/** = */ +data class Eq(override val column: String, val value: Any) : Filter { + override fun predicate(): RowFilter = { it[column] == value } + override fun rename(newColumn: String) = copy(column = newColumn) +} + +/** <= */ +data class Leq(override val column: String, val value: Double) : Filter { + override fun predicate(): RowFilter = { column() <= value } + override fun rename(newColumn: String) = copy(column = newColumn) +} + +/** >= */ +data class Geq(override val column: String, val value: Double) : Filter { + override fun predicate(): RowFilter = { column() >= value } + override fun rename(newColumn: String) = copy(column = newColumn) +} + +/** < */ +data class Le(override val column: String, val value: Double) : Filter { + override fun predicate(): RowFilter = { column() < value } + override fun rename(newColumn: String) = copy(column = newColumn) +} + +/** > */ +data class Ge(override val column: String, val value: Double) : Filter { + override fun predicate(): RowFilter = { column() > value } + override fun rename(newColumn: String) = copy(column = newColumn) +} diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index 845e59eed..bfda53879 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -10,11 +10,7 @@ import jetbrains.letsPlot.ggsize import jetbrains.letsPlot.label.ggtitle import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema -import org.jetbrains.kotlinx.dataframe.api.cast -import org.jetbrains.kotlinx.dataframe.api.first -import org.jetbrains.kotlinx.dataframe.api.groupBy -import org.jetbrains.kotlinx.dataframe.api.toDataFrame -import org.jetbrains.kotlinx.dataframe.io.read +import org.jetbrains.kotlinx.dataframe.api.* /** * DataFrame row for V or J usage data @@ -40,6 +36,7 @@ object Overlap { @Suppress("UNCHECKED_CAST") val key = metric.key as? OverlapKey ?: throw RuntimeException() data += OverlapRow(key.id1, key.id2, key.key, metric.value) + data += OverlapRow(key.id2, key.id1, key.key, metric.value) } } } @@ -52,14 +49,30 @@ object Overlap { **/ fun dataFrame( paResult: PostanalysisResult, - metadataPath: String?, + metadata: Metadata?, ) = run { var df: DataFrame = dataFrame(paResult) - if (metadataPath != null) - df = attachMetadata(df, "sample1", DataFrame.read(metadataPath), "sample").cast() + if (metadata != null) + df = df.withMetadata(metadata) df } + private fun DataFrame.withMetadata(meta: Metadata) = run { + var df = this + val metaX = meta.rename { all() }.into { "x_" + it.name() } + val metaY = meta.rename { all() }.into { "y_" + it.name() } + df = attachMetadata(df, "sample1", metaX, "x_sample").cast() + df = attachMetadata(df, "sample2", metaY, "y_sample").cast() + df + } + + fun filterOverlap(filter: Filter, df: DataFrame) = run { + var ndf = df + ndf = filter.rename { "x_$it" }.apply(ndf) + ndf = filter.rename { "y_$it" }.apply(ndf) + ndf + } + data class OverlapParameters( val colorKey: List? = null, val cluster: Boolean = true, @@ -115,6 +128,7 @@ object Overlap { plt = plt.withDendrogram(pos = Position.Right, 0.1) } + // TRAV14D-3-DV8*00 plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) plt = plt.withFillLegend(Position.Left, size = 0.5) diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Util.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Util.kt deleted file mode 100644 index 147d1007e..000000000 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Util.kt +++ /dev/null @@ -1,88 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import com.milaboratory.util.StringUtil -import org.jetbrains.kotlinx.dataframe.AnyFrame -import org.jetbrains.kotlinx.dataframe.DataFrame -import org.jetbrains.kotlinx.dataframe.api.add -import org.jetbrains.kotlinx.dataframe.api.all -import org.jetbrains.kotlinx.dataframe.api.cast -import org.jetbrains.kotlinx.dataframe.api.leftJoin -import java.util.* - - -fun AnyFrame.isNumeric(col: String) = this[col].all { it == null || it is Number } -fun AnyFrame.isCategorial(col: String) = !isNumeric(col) - -/** - * Attaches metadata to statistics - **/ -fun DataFrame.withMetadata(metadata: AnyFrame) = run { - attachMetadata(this, "sample", metadata, "sample").cast() -} - -/** - * Attaches metadata to statistics - **/ -fun attachMetadata( - data: AnyFrame, - dataCol: String, - meta: AnyFrame, - metaCol: String -) = run { - val m = matchLists( - data[dataCol].distinct().cast().toList(), - meta[metaCol].distinct().cast().toList(), - ) - - m.filter { it.value == null }.apply { - if (!isEmpty()) - throw IllegalArgumentException("can't unambiguously match metadata for the following rows: $keys") - } - - data - .add("_meta_join_") { m[it[dataCol]] } - .leftJoin(meta) { "_meta_join_" match metaCol } -} - -fun matchLists(target: List, query: List): Map { - val matched: MutableMap>> = HashMap() - for (t in target) { - val matchedForKey = PriorityQueue>( - Comparator.comparing { -it.second } - ) - - for (q in query) { - val a = t.lowercase(Locale.getDefault()) - val b = q.lowercase(Locale.getDefault()) - val match = StringUtil.longestCommonSubstring(a, b) - val score = 2.0 * (0.5 + match) / (1 + a.length + b.length) - matchedForKey.add(q to score) - } - - matched[t] = matchedForKey - } - - val unmatchedQ = query.toMutableSet() - val r = mutableMapOf() - - for ((t, q) in matched.toList().sortedBy { kv -> -kv.second.maxOf { it.second } }) { - if (q.isEmpty()) { - r[t] = null - continue - } - var m: String? = null - while (!q.isEmpty()) { - val candidate = q.poll() - val wasUnmatched = unmatchedQ.remove(candidate.first) - if (wasUnmatched) { - m = candidate.first - break - } - } - r[t] = m - } - - return r -} - -data class Filter(val column: String, val value: Any) \ No newline at end of file diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt index 40e49d9f9..cf41d727f 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt @@ -11,7 +11,6 @@ import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.first import org.jetbrains.kotlinx.dataframe.api.groupBy import org.jetbrains.kotlinx.dataframe.api.toDataFrame -import org.jetbrains.kotlinx.dataframe.io.read /** * DataFrame row for V or J usage data @@ -52,16 +51,15 @@ object VJUsage { **/ fun dataFrame( paResult: PostanalysisResult, - metadataPath: String?, + metadata: Metadata?, ) = run { var df = dataFrame(paResult) - if (metadataPath != null) - df = df.withMetadata(DataFrame.read(metadataPath)) + if (metadata != null) + df = df.withMetadata(metadata) df } data class PlotParameters( - val colorKey: List? = null, val clusterV: Boolean = true, val clusterJ: Boolean = true ) @@ -88,34 +86,16 @@ object VJUsage { plt = plt.withBorder() - val ncats = pp.colorKey?.map { df[it].distinct().size() }?.sum() ?: 0 - var pallete = Palletes.Categorical.auto(ncats) - pp.colorKey?.let { - var first = true - for (key in it) { - val nColors = df[key].distinct().size() - plt.withColorKey( - key, - pos = Position.Bottom, - sep = if (first) 0.1 else 0.0, - labelPos = Position.Left, - labelSep = 0.1, - pallete = pallete - ) - pallete = pallete.shift(nColors) - first = false - } - } - if (pp.clusterV) plt = plt.withDendrogram(pos = Position.Top, 0.1) if (pp.clusterJ) plt = plt.withDendrogram(pos = Position.Right, 0.1) - plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) - plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) - plt = plt.withFillLegend(Position.Left, size = 0.5) - plt = plt.withColorKeyLegend(Position.Left) + plt = plt + .withLabels(Position.Bottom, angle = 45, sep = 0.1) + .withLabels(Position.Left, sep = 0.1, width = 4.0) + .withFillLegend(Position.Left, size = 0.5) + plt.plot } } diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index b69a5a641..8a34ef563 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -42,6 +42,9 @@ public void test3() { Main.main("exportPa", "overlap", // "--width", "2000", // "--height", "5000", + "--chains", "TRA", + "--filter", "Chain=TRA", + "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap.pdf"); } From d0e97b1d622cba35dcf8c81021db23bc07faaa6b Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Fri, 11 Mar 2022 12:14:42 +0400 Subject: [PATCH 155/282] micro corrections --- .../mixcr/assembler/CloneAssembler.java | 36 +++++++------------ .../milaboratory/mixcr/cli/CommandAlign.java | 1 + 2 files changed, 13 insertions(+), 24 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index 679e34ed7..d8ef7cca9 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -35,7 +35,6 @@ import com.milaboratory.core.Range; import com.milaboratory.core.clustering.Cluster; import com.milaboratory.core.clustering.Clustering; -import com.milaboratory.core.clustering.SequenceExtractor; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.SequenceQuality; @@ -298,15 +297,10 @@ public void runClustering() { if (!preClusteringDone) throw new IllegalStateException("No pre-clustering is done."); - @SuppressWarnings("unchecked") - Clustering clustering = new Clustering(cloneList, - new SequenceExtractor() { - @Override - public NucleotideSequence getSequence(CloneAccumulator object) { - return object.getSequence().getConcatenated().getSequence(); - } - }, new CloneClusteringStrategy(parameters.getCloneClusteringParameters(), - this)); + Clustering clustering = new Clustering<>(cloneList, + object -> object.getSequence().getConcatenated().getSequence(), + new CloneClusteringStrategy(parameters.getCloneClusteringParameters(), this)); + this.progressReporter = clustering; List> clusters = clustering.performClustering(); clusteredClonesAccumulators = new ArrayList<>(clusters.size()); @@ -319,15 +313,12 @@ public NucleotideSequence getSequence(CloneAccumulator object) { head.setCloneIndex(i); // k - index to be set for all child clonotypes final int k = ~i; - cluster.processAllChildren(new TObjectProcedure>() { - @Override - public boolean execute(Cluster object) { - onClustered(head, object.getHead()); - if (parameters.isAddReadsCountOnClustering()) - head.mergeCounts(object.getHead()); - idMapping.put(object.getHead().getCloneIndex(), k); - return true; - } + cluster.processAllChildren(object -> { + onClustered(head, object.getHead()); + if (parameters.isAddReadsCountOnClustering()) + head.mergeCounts(object.getHead()); + idMapping.put(object.getHead().getCloneIndex(), k); + return true; }); clusteredClonesAccumulators.add(head); } @@ -518,6 +509,7 @@ else if (minMismatches < iterator.getMismatches()) return; } + // Selecting a random clone if mapping is ambiguous count = (count == 1 ? 1 : RandomUtil.getThreadLocalRandomData().nextLong(1, count)); CloneAccumulator accumulator = null; for (CloneAccumulator acc : candidates) @@ -694,10 +686,6 @@ public List build() { if (mappedClones == null) reversePreClustered.put(accs[i].getCloneIndex(), mappedClones = new TIntArrayList()); mappedClones.add(accs[j].getCloneIndex()); - // Also adding nested clones (clones that were previously clustered to current minor clone) - TIntArrayList subClones = reversePreClustered.get(accs[j].getCloneIndex()); - if (subClones != null) - mappedClones.addAll(subClones); accs[j] = null; ++deleted; @@ -755,7 +743,7 @@ public List build() { } } - // Filtering low quality clonotypes + // Filtering low quality clonotypes (has nothing to do with clustering) List result = new ArrayList<>(accs.length - deleted); for (CloneAccumulator acc : accs) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 06573b8d4..6baf35c62 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -570,6 +570,7 @@ else if (featureSequence.containsWildcards()) Merger> mainInputReads = CUtils.buffered((OutputPort) chunked(sReads, 64), Math.max(16, threads)); OutputPort> mainInputReadsPreprocessed = mainInputReads; + // TODO do this after barcode extraction if (trimmingQualityThreshold > 0) { ReadTrimmerReport rep = new ReadTrimmerReport(); mainInputReadsPreprocessed = CUtils.wrap( From 5b9c910606cf598f813201d3b4a98b29542c81f0 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sat, 12 Mar 2022 01:33:58 +0200 Subject: [PATCH 156/282] Wip --- .../mixcr/cli/CommandPaExport.java | 73 ++++++++--- .../mixcr/postanalysis/plots/GeneUsage.kt | 63 ++------- .../mixcr/postanalysis/plots/Heatmap.kt | 123 ++++++++++++++++++ .../mixcr/postanalysis/plots/Overlap.kt | 82 +++--------- .../mixcr/postanalysis/plots/VJUsage.kt | 44 ++----- .../{PlotParameters.kt => WithPlotSize.kt} | 2 +- .../mixcr/cli/CommandPaExportTest.java | 1 + 7 files changed, 213 insertions(+), 175 deletions(-) create mode 100644 src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt rename src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/{PlotParameters.kt => WithPlotSize.kt} (77%) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 7e4a49225..7acd52620 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.cli; import com.milaboratory.miplots.ExportKt; +import com.milaboratory.miplots.Position; import com.milaboratory.miplots.stat.util.TestMethod; import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod; import com.milaboratory.mixcr.basictypes.Clone; @@ -23,10 +24,7 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.Arrays; -import java.util.List; -import java.util.Map; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; /** @@ -177,6 +175,14 @@ DataFrame metadata() { ? metadataDf : (metadata == null ? null : (metadataDf = MetadataKt.readMetadata(metadata))); } + + void writePlots(Chains.NamedChains chains, List plots) { + ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + } + + void writePlots(Chains.NamedChains chains, Plot plot) { + ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plot); + } } static abstract class ExportBasicStatistics extends CommandPaExportPlots { @@ -224,7 +230,7 @@ void run(Chains.NamedChains chains, PaResultByChain result) { CorrelationMethod.Pearson )); - ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + writePlots(chains, plots); } } @@ -250,7 +256,14 @@ String group() { } } - static abstract class ExportGeneUsage extends CommandPaExportPlots { + static abstract class ExportHeatmap extends CommandPaExportPlots { + @Option(names = {"--h-labels-size"}, description = "Width of horizontal labels. One unit corresponds to the width of one tile.") + public double hLabelsSize = -1.0; + @Option(names = {"--v-labels-size"}, description = "Height of vertical labels. One unit corresponds to the height of one tile.") + public double vLabelsSize = -1.0; + } + + static abstract class ExportGeneUsage extends ExportHeatmap { abstract String group(); @Option(names = {"--no-samples-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of samples.") @@ -258,7 +271,7 @@ static abstract class ExportGeneUsage extends CommandPaExportPlots { @Option(names = {"--no-genes-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of genes.") public boolean noGenesDendro; @Option(names = {"--color-key"}, description = "Add color key layer.") - public List colorKey; + public List colorKey = new ArrayList<>(); @Override void run(Chains.NamedChains chains, PaResultByChain result) { @@ -274,14 +287,19 @@ void run(Chains.NamedChains chains, PaResultByChain result) { if (df.rowsCount() == 0) return; - Plot plots = GeneUsage.INSTANCE.plot(df, - new GeneUsage.PlotParameters( - colorKey, + Plot plot = GeneUsage.INSTANCE.plot(df, + new HeatmapParameters( !noSamplesDendro, - !noGenesDendro + !noGenesDendro, + colorKey.stream().map(it -> new ColorKey(it, Position.Bottom)).collect(Collectors.toList()), + hLabelsSize, + vLabelsSize, + false, + width, + height )); - ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + writePlots(chains, plot); } } @@ -322,7 +340,7 @@ String group() { sortOptions = false, separator = " ", description = "Export V-J usage heatmap") - static class ExportVJUsage extends CommandPaExportPlots { + static class ExportVJUsage extends ExportHeatmap { @Option(names = {"--no-v-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") public boolean noVDendro; @Option(names = {"--no-j-dendro"}, description = "Plot dendrogram for hierarchical clusterization of genes.") @@ -343,12 +361,18 @@ void run(Chains.NamedChains chains, PaResultByChain result) { return; List plots = VJUsage.INSTANCE.plots(df, - new VJUsage.PlotParameters( + new HeatmapParameters( + !noJDendro, !noVDendro, - !noJDendro + Collections.emptyList(), + hLabelsSize, + vLabelsSize, + false, + width, + height )); - ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + writePlots(chains, plots); } } @@ -356,11 +380,11 @@ void run(Chains.NamedChains chains, PaResultByChain result) { sortOptions = false, separator = " ", description = "Export overlap heatmap") - static class ExportOverlap extends CommandPaExportPlots { + static class ExportOverlap extends ExportHeatmap { @Option(names = {"--no-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") public boolean noDendro; @Option(names = {"--color-key"}, description = "Add color key layer.") - public List colorKey; + public List colorKey = new ArrayList<>(); @Option(names = {"--metric"}, description = "Select specific metrics to export.") public List metrics; @@ -379,6 +403,7 @@ void run(Chains.NamedChains chains, PaResultByChain result) { DataFrame metadata = metadata(); DataFrame df = Overlap.INSTANCE.dataFrame( result.result.forGroup(ch), + metrics, metadata ); df = filterOverlap(df); @@ -390,14 +415,20 @@ void run(Chains.NamedChains chains, PaResultByChain result) { return; List plots = Overlap.INSTANCE.plots(df, - new Overlap.OverlapParameters( - colorKey, + new HeatmapParameters( + !noDendro, !noDendro, + colorKey.stream() + .map(it -> new ColorKey(it, it.startsWith("x") ? Position.Bottom : Position.Left)) + .collect(Collectors.toList()), + hLabelsSize, + vLabelsSize, + true, width, height )); - ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + writePlots(chains, plots); } } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt index 599ed293a..cc04b1cf4 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt @@ -1,8 +1,5 @@ package com.milaboratory.mixcr.postanalysis.plots -import com.milaboratory.miplots.Position -import com.milaboratory.miplots.color.Palletes -import com.milaboratory.miplots.heatmap.* import com.milaboratory.mixcr.postanalysis.PostanalysisResult import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema @@ -56,58 +53,14 @@ object GeneUsage { df } - data class PlotParameters( - val colorKey: List? = null, - val clusterSamples: Boolean = true, - val clusterGenes: Boolean = true - ) - fun plot( df: DataFrame, - pp: PlotParameters, - ) = run { - var plt = Heatmap( - df, - x = GeneUsageRow::sample.name, - y = GeneUsageRow::gene.name, - z = GeneUsageRow::weight.name, - xOrder = if (pp.clusterSamples) Hierarchical() else null, - yOrder = if (pp.clusterGenes) Hierarchical() else null, - fillPallette = Palletes.Diverging.lime90rose130 - ) - - val ncats = pp.colorKey?.map { df[it].distinct().size() }?.sum() ?: 0 - var pallete = Palletes.Categorical.auto(ncats) - pp.colorKey?.let { - var first = true - for (key in it) { - val nColors = df[key].distinct().size() - plt.withColorKey( - key, - pos = Position.Bottom, - sep = if (first) 0.1 else 0.0, - labelPos = Position.Left, - labelSep = 0.1, - pallete = pallete - ) - pallete = pallete.shift(nColors) - first = false - } - } - - plt = plt.withBorder() - - if (pp.clusterSamples) - plt = plt.withDendrogram(pos = Position.Top, 0.1) - if (pp.clusterGenes) - plt = plt.withDendrogram(pos = Position.Right, 0.1) - - plt = plt - .withLabels(Position.Bottom, angle = 45, sep = 0.1) - .withLabels(Position.Left, sep = 0.1, width = 4.0) - .withFillLegend(Position.Left, size = 0.5) - .withColorKeyLegend(Position.Left) - - plt.plot - } + params: HeatmapParameters, + ) = mkHeatmap( + df, + x = GeneUsageRow::sample.name, + y = GeneUsageRow::gene.name, + z = GeneUsageRow::weight.name, + params = params + ) } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt new file mode 100644 index 000000000..028463880 --- /dev/null +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt @@ -0,0 +1,123 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.milaboratory.miplots.Position +import com.milaboratory.miplots.Position.* +import com.milaboratory.miplots.color.Palletes +import com.milaboratory.miplots.heatmap.* +import com.milaboratory.mixcr.postanalysis.plots.HeatmapParameters.Companion.hLabelSize +import com.milaboratory.mixcr.postanalysis.plots.HeatmapParameters.Companion.vLabelSize +import jetbrains.letsPlot.ggsize +import org.jetbrains.kotlinx.dataframe.AnyFrame +import kotlin.math.sqrt + +data class ColorKey( + val key: String, + val pos: Position +) + +data class HeatmapParameters( + val clusterX: Boolean, + val clusterY: Boolean, + val colorKey: List? = null, + val hLabelsSize: Double, + val vLabelsSize: Double, + val fillNaZeroes: Boolean, + override val width: Int, + override val height: Int, +) : WithPlotSize { + + companion object { + fun defaultHLabelSize(labels: List) = run { + val l = labels.maxOfOrNull { it.length } ?: 0 + (0.9 * l / 3) + } + + fun defaultVLabelSize(labels: List) = defaultHLabelSize(labels) + + private fun AnyFrame.labels(col: String) = this[col].distinct().toList().map { it?.toString() }.filterNotNull() + + fun AnyFrame.hLabelSize(w: Double, col: String) = if (w < 0.0) defaultHLabelSize(labels(col)) else w + fun AnyFrame.vLabelSize(h: Double, col: String) = if (h < 0.0) defaultVLabelSize(labels(col)) else h + } +} + +fun mkHeatmap( + df: AnyFrame, + x: String, y: String, z: String, + params: HeatmapParameters, +) = run { + var plt = Heatmap( + df, + x = x, + y = y, + z = z, + xOrder = if (params.clusterX) Hierarchical() else null, + yOrder = if (params.clusterY) Hierarchical() else null, + fillNoValue = params.fillNaZeroes, + noValue = 0.0, + fillPalette = Palletes.Diverging.lime90rose130 + ) + + plt = plt.withBorder() + + val ncats = params.colorKey?.map { df[it.key].distinct().size() }?.sum() ?: 0 + var pallete = Palletes.Categorical.auto(ncats) + params.colorKey?.let { + val first = Position.values().map { p -> p to true }.toMap().toMutableMap() + for (key in it) { + val keyCol = key.key + val nColors = df[keyCol].distinct().size() + plt.withColorKey( + keyCol, + pos = key.pos, + sep = if (first[key.pos]!!) 0.1 else 0.0, + labelPos = when (key.pos) { + Bottom -> Left + Left -> Top + Top -> Right + Right -> Bottom + }, + labelAngle = when (key.pos) { + Bottom, Top -> 0 + Left, Right -> 90 + }, + label = if (keyCol.startsWith("x_") || keyCol.startsWith("y_")) + keyCol + .replaceFirst("_x", "") + .replaceFirst("_y", "") + else + null, + labelSep = 0.1, + pallete = pallete + ) + pallete = pallete.shift(nColors) + first[key.pos] = false + } + } + + if (params.clusterX) + plt = plt.withDendrogram(pos = Position.Top, 0.1) + if (params.clusterY) + plt = plt.withDendrogram(pos = Position.Right, 0.1) + + plt = plt.withLabels( + Bottom, + angle = 45, + sep = 0.1, + height = df.vLabelSize(params.vLabelsSize, x) * sqrt(2.0) / 2 + ) + + plt = plt.withLabels( + Left, + sep = 0.1, + width = df.hLabelSize(params.hLabelsSize, y) + ) + + plt = plt.withFillLegend(Left, size = 0.5) + plt = plt.withColorKeyLegend(Left) + + if (params.width > 0 && params.height > 0) + plt.plusAssign(ggsize(params.width, params.height)) + + plt.plot +} \ No newline at end of file diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index bfda53879..e65f4c49a 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -1,12 +1,8 @@ package com.milaboratory.mixcr.postanalysis.plots -import com.milaboratory.miplots.Position -import com.milaboratory.miplots.color.Palletes -import com.milaboratory.miplots.heatmap.* import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey import com.milaboratory.mixcr.postanalysis.overlap.OverlapType -import jetbrains.letsPlot.ggsize import jetbrains.letsPlot.label.ggtitle import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema @@ -27,14 +23,21 @@ object Overlap { /** * Imports data into DataFrame **/ - fun dataFrame(paResult: PostanalysisResult) = run { + fun dataFrame( + paResult: PostanalysisResult, + metricsFilter: List? + ) = run { val data = mutableListOf() + val mf = metricsFilter?.map { it.lowercase() }?.toSet() for ((_, charData) in paResult.data) { for ((_, keys) in charData.data) { for (metric in keys.data) { @Suppress("UNCHECKED_CAST") val key = metric.key as? OverlapKey ?: throw RuntimeException() + if (mf != null && !mf.contains(key.key.toString().lowercase())) { + continue + } data += OverlapRow(key.id1, key.id2, key.key, metric.value) data += OverlapRow(key.id2, key.id1, key.key, metric.value) } @@ -49,9 +52,10 @@ object Overlap { **/ fun dataFrame( paResult: PostanalysisResult, + metricsFilter: List?, metadata: Metadata?, ) = run { - var df: DataFrame = dataFrame(paResult) + var df: DataFrame = dataFrame(paResult, metricsFilter) if (metadata != null) df = df.withMetadata(metadata) df @@ -73,68 +77,20 @@ object Overlap { ndf } - data class OverlapParameters( - val colorKey: List? = null, - val cluster: Boolean = true, - override val width: Int, - override val height: Int - ) : PlotParameters - fun plots( df: DataFrame, - pp: OverlapParameters, + pp: HeatmapParameters, ) = df.groupBy { "metric"() }.groups.toList() .map { sdf -> plot(df, pp) + ggtitle(sdf.first()[OverlapRow::metric.name]!!.toString()) } fun plot( df: DataFrame, - pp: OverlapParameters, - ) = run { - var plt = Heatmap( - df, - x = OverlapRow::sample1.name, - y = OverlapRow::sample2.name, - z = GeneUsageRow::weight.name, - xOrder = if (pp.cluster) Hierarchical() else null, - yOrder = if (pp.cluster) Hierarchical() else null, - fillPallette = Palletes.Diverging.lime90rose130, - fillNoValue = true, - noValue = 0.0 - ) - - plt = plt.withBorder() - - val ncats = pp.colorKey?.map { df[it].distinct().size() }?.sum() ?: 0 - var pallete = Palletes.Categorical.auto(ncats) - pp.colorKey?.let { - var first = true - for (key in it) { - val nColors = df[key].distinct().size() - plt.withColorKey( - key, - pos = Position.Bottom, - sep = if (first) 0.1 else 0.0, - labelPos = Position.Left, - labelSep = 0.1, - pallete = pallete - ) - pallete = pallete.shift(nColors) - first = false - } - } - - if (pp.cluster) { - plt = plt.withDendrogram(pos = Position.Top, 0.1) - plt = plt.withDendrogram(pos = Position.Right, 0.1) - } - - // TRAV14D-3-DV8*00 - plt = plt.withLabels(Position.Bottom, angle = 45, sep = 0.1) - plt = plt.withLabels(Position.Left, sep = 0.1, width = 4.0) - plt = plt.withFillLegend(Position.Left, size = 0.5) - plt = plt.withColorKeyLegend(Position.Left) - if (pp.width > 0 && pp.height > 0) - plt.plusAssign(ggsize(pp.width, pp.height)) - plt.plot - } + params: HeatmapParameters, + ) = mkHeatmap( + df, + x = OverlapRow::sample1.name, + y = OverlapRow::sample2.name, + z = GeneUsageRow::weight.name, + params = params + ) } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt index cf41d727f..6b43c0545 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt @@ -1,8 +1,5 @@ package com.milaboratory.mixcr.postanalysis.plots -import com.milaboratory.miplots.Position -import com.milaboratory.miplots.color.Palletes -import com.milaboratory.miplots.heatmap.* import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions import jetbrains.letsPlot.label.ggtitle @@ -59,43 +56,20 @@ object VJUsage { df } - data class PlotParameters( - val clusterV: Boolean = true, - val clusterJ: Boolean = true - ) - fun plots( df: DataFrame, - pp: PlotParameters, + pp: HeatmapParameters, ) = df.groupBy { "sample"() }.groups.toList() .map { sdf -> plot(df, pp) + ggtitle(sdf.first()[VJUsageRow::sample.name]!!.toString()) } fun plot( df: DataFrame, - pp: PlotParameters, - ) = run { - var plt = Heatmap( - df, - x = VJUsageRow::jGene.name, - y = VJUsageRow::vGene.name, - z = GeneUsageRow::weight.name, - xOrder = if (pp.clusterV) Hierarchical() else null, - yOrder = if (pp.clusterJ) Hierarchical() else null, - fillPallette = Palletes.Diverging.lime90rose130 - ) - - plt = plt.withBorder() - - if (pp.clusterV) - plt = plt.withDendrogram(pos = Position.Top, 0.1) - if (pp.clusterJ) - plt = plt.withDendrogram(pos = Position.Right, 0.1) - - plt = plt - .withLabels(Position.Bottom, angle = 45, sep = 0.1) - .withLabels(Position.Left, sep = 0.1, width = 4.0) - .withFillLegend(Position.Left, size = 0.5) - - plt.plot - } + params: HeatmapParameters, + ) = mkHeatmap( + df, + x = VJUsageRow::jGene.name, + y = VJUsageRow::vGene.name, + z = GeneUsageRow::weight.name, + params = params + ) } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/WithPlotSize.kt similarity index 77% rename from src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt rename to src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/WithPlotSize.kt index c5d3b85ac..cd33cc57c 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/PlotParameters.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/WithPlotSize.kt @@ -1,6 +1,6 @@ package com.milaboratory.mixcr.postanalysis.plots -interface PlotParameters { +interface WithPlotSize { val width: Int val height: Int } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index 8a34ef563..c7f8500f4 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -45,6 +45,7 @@ public void test3() { "--chains", "TRA", "--filter", "Chain=TRA", "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", + "--color-key", "x_Tissue", "--color-key", "x_CellPopulation", "--color-key", "y_MouseID", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap.pdf"); } From 655a5c39480bb9b68050af25f04a00b8711f2e1e Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Tue, 15 Mar 2022 18:11:08 +0400 Subject: [PATCH 157/282] wip --- build.gradle.kts | 4 +- gradle/wrapper/gradle-wrapper.properties | 2 +- gradlew | 257 +++++++++++------- .../mixcr/assembler/CloneAccumulator.java | 2 +- .../assembler/CloneClusteringStrategy.java | 2 +- .../mixcr/assembler/CloneFactory.java | 2 +- .../milaboratory/mixcr/basictypes/Clone.java | 3 + .../mixcr/basictypes/CloneSet.java | 2 + .../com/milaboratory/mixcr/basictypes/IO.java | 39 +-- .../mixcr/basictypes/TagTuple.java | 36 --- .../mixcr/basictypes/VDJCAlignments.java | 1 + .../mixcr/basictypes/VDJCObject.java | 1 + .../milaboratory/mixcr/basictypes/tag/IO.java | 51 ++++ .../basictypes/{ => tag}/TagCounter.java | 3 +- .../{ => tag}/TagCounterBuilder.java | 2 +- .../mixcr/basictypes/tag/TagTuple.java | 62 +++++ .../milaboratory/mixcr/cli/CommandAlign.java | 7 +- .../mixcr/cli/CommandAssemble.java | 2 + .../milaboratory/mixcr/cli/CommandExport.java | 1 + .../mixcr/cli/CommandGroupCells.java | 4 +- .../mixcr/export/FieldExtractors.java | 2 + .../PartialAlignmentsAssembler.java | 2 + .../PartialAlignmentsAssemblerAligner.java | 2 +- .../mixcr/partialassembler/TargetMerger.java | 2 +- .../mixcr/tags/DropletCloneGraph.java | 2 +- .../mixcr/vdjaligners/VDJCAlignerPVFirst.java | 1 + .../mixcr/vdjaligners/VDJCAlignerS.java | 2 +- .../mixcr/cli/CommandAlignTest.java | 2 +- 28 files changed, 305 insertions(+), 193 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java rename src/main/java/com/milaboratory/mixcr/basictypes/{ => tag}/TagCounter.java (98%) rename src/main/java/com/milaboratory/mixcr/basictypes/{ => tag}/TagCounterBuilder.java (98%) create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java diff --git a/build.gradle.kts b/build.gradle.kts index 6eca6d033..b00927d60 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -59,7 +59,7 @@ repositories { val milibVersion = "1.15.0" val repseqioVersion = "1.3.5-23-master" -val jacksonVersion = "2.13.1" +val jacksonVersion = "2.13.2" dependencies { api("com.milaboratory:milib:$milibVersion") @@ -72,7 +72,7 @@ dependencies { implementation("org.lz4:lz4-java:1.4.1") implementation("net.sf.trove4j:trove4j:3.0.3") implementation("info.picocli:picocli:4.1.1") - implementation("com.google.guava:guava:30.1.1-jre") + implementation("com.google.guava:guava:31.1-jre") testImplementation("junit:junit:4.13.2") implementation(testFixtures("com.milaboratory:milib:$milibVersion")) diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 41dfb8790..00e33edef 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.4-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.1-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index 744e882ed..1b6c78733 100755 --- a/gradlew +++ b/gradlew @@ -1,7 +1,7 @@ -#!/usr/bin/env sh +#!/bin/sh # -# Copyright 2015 the original author or authors. +# Copyright © 2015-2021 the original authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -17,67 +17,101 @@ # ############################################################################## -## -## Gradle start up script for UN*X -## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# ############################################################################## # Attempt to set APP_HOME + # Resolve links: $0 may be a link -PRG="$0" -# Need this for relative symlinks. -while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac done -SAVED="`pwd`" -cd "`dirname \"$PRG\"`/" >/dev/null -APP_HOME="`pwd -P`" -cd "$SAVED" >/dev/null + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit APP_NAME="Gradle" -APP_BASE_NAME=`basename "$0"` +APP_BASE_NAME=${0##*/} # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' # Use the maximum available, or set MAX_FD != -1 to use that value. -MAX_FD="maximum" +MAX_FD=maximum warn () { echo "$*" -} +} >&2 die () { echo echo "$*" echo exit 1 -} +} >&2 # OS specific support (must be 'true' or 'false'). cygwin=false msys=false darwin=false nonstop=false -case "`uname`" in - CYGWIN* ) - cygwin=true - ;; - Darwin* ) - darwin=true - ;; - MSYS* | MINGW* ) - msys=true - ;; - NONSTOP* ) - nonstop=true - ;; +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; esac CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar @@ -87,9 +121,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar if [ -n "$JAVA_HOME" ] ; then if [ -x "$JAVA_HOME/jre/sh/java" ] ; then # IBM's JDK on AIX uses strange locations for the executables - JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACMD=$JAVA_HOME/jre/sh/java else - JAVACMD="$JAVA_HOME/bin/java" + JAVACMD=$JAVA_HOME/bin/java fi if [ ! -x "$JAVACMD" ] ; then die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME @@ -98,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the location of your Java installation." fi else - JAVACMD="java" + JAVACMD=java which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the @@ -106,80 +140,95 @@ location of your Java installation." fi # Increase the maximum file descriptors if we can. -if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then - MAX_FD_LIMIT=`ulimit -H -n` - if [ $? -eq 0 ] ; then - if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then - MAX_FD="$MAX_FD_LIMIT" - fi - ulimit -n $MAX_FD - if [ $? -ne 0 ] ; then - warn "Could not set maximum file descriptor limit: $MAX_FD" - fi - else - warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" - fi +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac fi -# For Darwin, add options to specify how the application appears in the dock -if $darwin; then - GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" -fi +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. # For Cygwin or MSYS, switch paths to Windows format before running java -if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then - APP_HOME=`cygpath --path --mixed "$APP_HOME"` - CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` - - JAVACMD=`cygpath --unix "$JAVACMD"` - - # We build the pattern for arguments to be converted via cygpath - ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` - SEP="" - for dir in $ROOTDIRSRAW ; do - ROOTDIRS="$ROOTDIRS$SEP$dir" - SEP="|" - done - OURCYGPATTERN="(^($ROOTDIRS))" - # Add a user-defined pattern to the cygpath arguments - if [ "$GRADLE_CYGPATTERN" != "" ] ; then - OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" - fi +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + # Now convert the arguments - kludge to limit ourselves to /bin/sh - i=0 - for arg in "$@" ; do - CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` - CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option - - if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition - eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` - else - eval `echo args$i`="\"$arg\"" + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) fi - i=`expr $i + 1` + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg done - case $i in - 0) set -- ;; - 1) set -- "$args0" ;; - 2) set -- "$args0" "$args1" ;; - 3) set -- "$args0" "$args1" "$args2" ;; - 4) set -- "$args0" "$args1" "$args2" "$args3" ;; - 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; - 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; - 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; - 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; - 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; - esac fi -# Escape application args -save () { - for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done - echo " " -} -APP_ARGS=`save "$@"` +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# -# Collect all arguments for the java command, following the shell quoting and substitution rules -eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' exec "$JAVACMD" "$@" diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index 57f4ea3a1..a2fdcca69 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -37,7 +37,7 @@ import com.milaboratory.core.sequence.quality.QualityAggregationType; import com.milaboratory.core.sequence.quality.QualityAggregator; import com.milaboratory.mixcr.basictypes.ClonalSequence; -import com.milaboratory.mixcr.basictypes.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import gnu.trove.iterator.TObjectFloatIterator; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java index 06cdd90c7..4e8d3230d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java @@ -36,7 +36,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.tree.NeighborhoodIterator; import com.milaboratory.core.tree.TreeSearchParameters; -import com.milaboratory.mixcr.basictypes.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; public class CloneClusteringStrategy implements ClusteringStrategy { final CloneClusteringParameters parameters; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index 7c0191193..db3255196 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -34,7 +34,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.vdjaligners.SingleDAligner; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index 39fe529f4..ac79fe1d4 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -30,6 +30,9 @@ package com.milaboratory.mixcr.basictypes; import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.primitivio.annotations.Serializable; import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.GeneType; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index 9d19ff604..1130b345e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -31,6 +31,8 @@ import cc.redberry.primitives.Filter; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index e2891d45f..7bc51f49a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -34,6 +34,8 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.Serializer; @@ -82,43 +84,6 @@ public boolean handlesReference() { } } - public static class TagCounterSerializer implements Serializer { - @Override - public void write(PrimitivO output, TagCounter object) { - output.writeInt(object.tags.size()); - TObjectDoubleIterator it = object.tags.iterator(); - while (it.hasNext()) { - it.advance(); - output.writeObject(it.key().tags); - output.writeDouble(it.value()); - } - } - - @Override - public TagCounter read(PrimitivI input) { - int len = input.readInt(); - if (len == 0) - return TagCounter.EMPTY; - TObjectDoubleHashMap r = new TObjectDoubleHashMap<>(len, Constants.DEFAULT_LOAD_FACTOR, 0.0); - for (int i = 0; i < len; ++i) { - String[] tags = input.readObject(String[].class); - double count = input.readDouble(); - r.put(new TagTuple(tags), count); - } - return new TagCounter(r); - } - - @Override - public boolean isReference() { - return true; - } - - @Override - public boolean handlesReference() { - return false; - } - } - public static class VDJCAlignmentsSerializer implements Serializer { @Override public void write(PrimitivO output, VDJCAlignments object) { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java deleted file mode 100644 index b6e1e3409..000000000 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagTuple.java +++ /dev/null @@ -1,36 +0,0 @@ -package com.milaboratory.mixcr.basictypes; - -import java.util.Arrays; - -/** - * - */ -public final class TagTuple { - public final String[] tags; - private final int hash; - - public TagTuple(String... tags) { - if (tags.length == 0) - throw new IllegalArgumentException(); - this.tags = tags; - this.hash = Arrays.hashCode(tags); - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - TagTuple tagTuple = (TagTuple) o; - return hash == tagTuple.hash && Arrays.equals(tags, tagTuple.tags); - } - - @Override - public int hashCode() { - return hash; - } - - @Override - public String toString() { - return String.join("+", tags); - } -} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index d94159829..b86d23810 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -36,6 +36,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.primitivio.annotations.Serializable; import com.milaboratory.util.ArraysUtils; import gnu.trove.map.hash.TLongObjectHashMap; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 60988431b..d895d8f15 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -32,6 +32,7 @@ import com.milaboratory.core.Range; import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.sequence.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.util.Cache; import io.repseq.core.*; import io.repseq.gen.VDJCGenes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java new file mode 100644 index 000000000..9b994abc8 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java @@ -0,0 +1,51 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.primitivio.Serializer; +import com.milaboratory.util.ByteString; +import gnu.trove.impl.Constants; +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.map.hash.TObjectDoubleHashMap; + +public final class IO { + private IO() { + } + + public static class TagCounterSerializer implements Serializer { + @Override + public void write(PrimitivO output, TagCounter object) { + output.writeInt(object.tags.size()); + TObjectDoubleIterator it = object.tags.iterator(); + while (it.hasNext()) { + it.advance(); + output.writeObject(it.key().tags); + output.writeDouble(it.value()); + } + } + + @Override + public TagCounter read(PrimitivI input) { + int len = input.readInt(); + if (len == 0) + return TagCounter.EMPTY; + TObjectDoubleHashMap r = new TObjectDoubleHashMap<>(len, Constants.DEFAULT_LOAD_FACTOR, 0.0); + for (int i = 0; i < len; ++i) { + ByteString[] tags = input.readObject(String[].class); + double count = input.readDouble(); + r.put(new TagTuple(tags), count); + } + return new TagCounter(r); + } + + @Override + public boolean isReference() { + return true; + } + + @Override + public boolean handlesReference() { + return false; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java similarity index 98% rename from src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java rename to src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java index 11b5eab4e..6a4a43726 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java @@ -1,5 +1,6 @@ -package com.milaboratory.mixcr.basictypes; +package com.milaboratory.mixcr.basictypes.tag; +import com.milaboratory.mixcr.basictypes.IO; import com.milaboratory.primitivio.annotations.Serializable; import gnu.trove.TDoubleCollection; import gnu.trove.iterator.TDoubleIterator; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounterBuilder.java similarity index 98% rename from src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java rename to src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounterBuilder.java index 140fedfd5..49f065339 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TagCounterBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounterBuilder.java @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.basictypes; +package com.milaboratory.mixcr.basictypes.tag; import gnu.trove.impl.Constants; import gnu.trove.iterator.TObjectDoubleIterator; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java new file mode 100644 index 000000000..af48e1756 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -0,0 +1,62 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.google.common.hash.Hasher; +import com.google.common.hash.Hashing; +import com.milaboratory.util.ByteString; + +import java.util.Arrays; + +/** + * Class represents a tuple of tags associated with a sequence, alignment, clone or other entity. + * + * Tag may be a sample name, cell marker or unique molecular identifier. + */ +public final class TagTuple implements Comparable { + public final ByteString[] tags; + private final int hash; + + @SuppressWarnings("UnstableApiUsage") + public TagTuple(ByteString... tags) { + if (tags.length == 0) + throw new IllegalArgumentException(); + this.tags = tags; + Hasher hasher = Hashing.murmur3_32_fixed().newHasher(); + for (ByteString tag : tags) + hasher.putInt(tag.hashCode()); + this.hash = hasher.hash().hashCode(); + } + + @Override + public int compareTo(TagTuple o) { + int l = Math.min(tags.length, o.tags.length); + int c; + for (int i = 0; i < l; i++) + if ((c = tags[i].compareTo(o.tags[i])) != 0) + return c; + return Integer.compare(tags.length, o.tags.length); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagTuple tagTuple = (TagTuple) o; + return hash == tagTuple.hash && Arrays.equals(tags, tagTuple.tags); + } + + @Override + public int hashCode() { + return hash; + } + + @Override + public String toString() { + StringBuilder sb = new StringBuilder(); + for (ByteString tag : tags) { + if (sb.length() != 0) + sb.append('+'); + sb.append(tag.toString()); + } + return sb.toString(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 6baf35c62..a668b8d4f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -62,7 +62,12 @@ import com.milaboratory.core.sequence.quality.QualityTrimmerParameters; import com.milaboratory.core.sequence.quality.ReadTrimmerProcessor; import com.milaboratory.core.sequence.quality.ReadTrimmerReport; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.SequenceHistory; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.tags.WhitelistReader; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.mixcr.vdjaligners.*; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 083802b43..fabc33308 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -39,6 +39,8 @@ import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.*; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.ArraysUtils; import com.milaboratory.util.SmartProgressReporter; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 8cee9f4be..ac232dc31 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -34,6 +34,7 @@ import cc.redberry.pipe.blocks.FilteringPort; import cc.redberry.primitives.Filter; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.export.*; import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.util.CanReportProgress; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 3a304e9e1..064913c03 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -7,6 +7,8 @@ import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.tags.CloneGroup; import com.milaboratory.mixcr.tags.DropletCloneGraph; import com.milaboratory.mixcr.tags.DropletCloneGraphParameters; @@ -14,8 +16,6 @@ import com.milaboratory.util.ProgressAndStage; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.impl.Constants; -import gnu.trove.iterator.TObjectIntIterator; -import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; import gnu.trove.map.hash.TObjectIntHashMap; import io.repseq.core.VDJCLibraryRegistry; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index df434879f..207f57c1f 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -42,6 +42,8 @@ import com.milaboratory.core.sequence.TranslationParameters; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.util.GlobalObjectMappers; import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.iterator.TObjectFloatIterator; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 291e979fd..1a6323e50 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -36,6 +36,8 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.cli.Report; import com.milaboratory.mixcr.cli.ReportHelper; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java index ede4b30a9..b6787d40a 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java @@ -38,7 +38,7 @@ import com.milaboratory.core.alignment.kaligner2.KAlignerParameters2; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.basictypes.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerAbstract; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java index 528e3562d..1b6924694 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java @@ -44,7 +44,7 @@ import com.milaboratory.core.sequence.SequencesUtils; import com.milaboratory.mixcr.basictypes.SequenceHistory; import com.milaboratory.mixcr.basictypes.SequenceHistory.OverlapType; -import com.milaboratory.mixcr.basictypes.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.vdjaligners.KGeneAlignmentParameters; diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java index f42df7c68..80b9bd040 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java @@ -31,7 +31,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; -import com.milaboratory.mixcr.basictypes.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.util.AdjacencyMatrix; import com.milaboratory.mixcr.util.BitArrayInt; import com.milaboratory.util.ProgressAndStage; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java index da13cf693..340243645 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java @@ -46,6 +46,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.partialassembler.AlignedTarget; import com.milaboratory.mixcr.partialassembler.TargetMerger; import com.milaboratory.util.BitArray; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java index 055e817a2..3be123fe8 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java @@ -40,7 +40,7 @@ import com.milaboratory.core.io.sequence.SingleRead; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.SequenceHistory; -import com.milaboratory.mixcr.basictypes.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.util.BitArray; diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java index a7dc108ff..ab1244314 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java @@ -32,7 +32,7 @@ import com.milaboratory.core.io.sequence.SequenceRead; import com.milaboratory.core.io.sequence.SingleReadImpl; import com.milaboratory.core.sequence.NSequenceWithQuality; -import com.milaboratory.mixcr.basictypes.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import org.junit.*; import picocli.CommandLine; From 89ed7e4ecc57eaff5e22da8e6a207603d10bb436 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Tue, 15 Mar 2022 23:15:22 +0400 Subject: [PATCH 158/282] feat: gradle script now supports building without miRepo credentials --- build.gradle.kts | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 4efe2c34d..d385c1127 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -11,8 +11,8 @@ plugins { id("com.github.johnrengelman.shadow") version "7.1.2" } -val miRepoAccessKeyId: String by project -val miRepoSecretAccessKey: String by project +val miRepoAccessKeyId: String? by project +val miRepoSecretAccessKey: String? by project val versionDetails: Closure by extra val gitDetails = versionDetails() @@ -118,14 +118,16 @@ val distributionZip by tasks.registering(Zip::class) { publishing { repositories { - maven { - name = "mipriv" - url = uri("s3://milaboratory-artefacts-private-files.s3.eu-central-1.amazonaws.com/maven") - - authentication { - credentials(AwsCredentials::class) { - accessKey = miRepoAccessKeyId - secretKey = miRepoSecretAccessKey + if (miRepoAccessKeyId != null) { + maven { + name = "mipriv" + url = uri("s3://milaboratory-artefacts-private-files.s3.eu-central-1.amazonaws.com/maven") + + authentication { + credentials(AwsCredentials::class) { + accessKey = miRepoAccessKeyId!! + secretKey = miRepoSecretAccessKey!! + } } } } @@ -141,10 +143,10 @@ tasks.test { minHeapSize = "1024m" maxHeapSize = "2048m" -// miCiStage?.let { -// if (it == "test") { -// systemProperty("longTests", "true"); -// } -// } + // miCiStage?.let { + // if (it == "test") { + // systemProperty("longTests", "true"); + // } + // } longTests?.let { systemProperty("longTests", it) } } From bb8a8820d3d18a5a77ce031ee5665cd6329691d8 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 16 Mar 2022 01:13:58 +0400 Subject: [PATCH 159/282] feat: Fixes and enhanceents for AIRR exporter (#40) * WIP * Nearly done. Not thuroughly tested. FR4 problem not fixed. * fix: correct behaviour for FR4 in exportAirr * alignment based nucleotide features, multiple important fixes * Migration to new repseqio. * repseqio upgrade * fix: array size error in AirrUtils * fix: corner case in airr exporter --- build.gradle.kts | 6 +- gradle/wrapper/gradle-wrapper.properties | 2 +- gradlew | 257 +++++++------ itests/case1.sh | 2 + itests/case4.sh | 5 + .../mixcr/cli/CommandExportAirr.java | 39 +- .../mixcr/export/AirrColumns.java | 92 +++-- .../milaboratory/mixcr/export/AirrUtil.java | 351 ++++++++++++++++-- .../mixcr/export/AirrVDJCObjectWrapper.java | 10 +- 9 files changed, 591 insertions(+), 173 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index d385c1127..c3a169bef 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -56,8 +56,8 @@ repositories { } val milibVersion = "1.15.0" -val repseqioVersion = "1.3.5-19-master" -val jacksonVersion = "2.12.4" +val repseqioVersion = "1.3.5-24-master" +val jacksonVersion = "2.13.2" dependencies { api("com.milaboratory:milib:$milibVersion") @@ -70,7 +70,7 @@ dependencies { implementation("org.lz4:lz4-java:1.4.1") implementation("net.sf.trove4j:trove4j:3.0.3") implementation("info.picocli:picocli:4.1.1") - implementation("com.google.guava:guava:30.1.1-jre") + implementation("com.google.guava:guava:31.1-jre") testImplementation("junit:junit:4.13.2") implementation(testFixtures("com.milaboratory:milib:$milibVersion")) diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 41dfb8790..00e33edef 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.4-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.1-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index 744e882ed..1b6c78733 100755 --- a/gradlew +++ b/gradlew @@ -1,7 +1,7 @@ -#!/usr/bin/env sh +#!/bin/sh # -# Copyright 2015 the original author or authors. +# Copyright © 2015-2021 the original authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -17,67 +17,101 @@ # ############################################################################## -## -## Gradle start up script for UN*X -## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# ############################################################################## # Attempt to set APP_HOME + # Resolve links: $0 may be a link -PRG="$0" -# Need this for relative symlinks. -while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac done -SAVED="`pwd`" -cd "`dirname \"$PRG\"`/" >/dev/null -APP_HOME="`pwd -P`" -cd "$SAVED" >/dev/null + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit APP_NAME="Gradle" -APP_BASE_NAME=`basename "$0"` +APP_BASE_NAME=${0##*/} # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' # Use the maximum available, or set MAX_FD != -1 to use that value. -MAX_FD="maximum" +MAX_FD=maximum warn () { echo "$*" -} +} >&2 die () { echo echo "$*" echo exit 1 -} +} >&2 # OS specific support (must be 'true' or 'false'). cygwin=false msys=false darwin=false nonstop=false -case "`uname`" in - CYGWIN* ) - cygwin=true - ;; - Darwin* ) - darwin=true - ;; - MSYS* | MINGW* ) - msys=true - ;; - NONSTOP* ) - nonstop=true - ;; +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; esac CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar @@ -87,9 +121,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar if [ -n "$JAVA_HOME" ] ; then if [ -x "$JAVA_HOME/jre/sh/java" ] ; then # IBM's JDK on AIX uses strange locations for the executables - JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACMD=$JAVA_HOME/jre/sh/java else - JAVACMD="$JAVA_HOME/bin/java" + JAVACMD=$JAVA_HOME/bin/java fi if [ ! -x "$JAVACMD" ] ; then die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME @@ -98,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the location of your Java installation." fi else - JAVACMD="java" + JAVACMD=java which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the @@ -106,80 +140,95 @@ location of your Java installation." fi # Increase the maximum file descriptors if we can. -if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then - MAX_FD_LIMIT=`ulimit -H -n` - if [ $? -eq 0 ] ; then - if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then - MAX_FD="$MAX_FD_LIMIT" - fi - ulimit -n $MAX_FD - if [ $? -ne 0 ] ; then - warn "Could not set maximum file descriptor limit: $MAX_FD" - fi - else - warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" - fi +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac fi -# For Darwin, add options to specify how the application appears in the dock -if $darwin; then - GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" -fi +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. # For Cygwin or MSYS, switch paths to Windows format before running java -if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then - APP_HOME=`cygpath --path --mixed "$APP_HOME"` - CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` - - JAVACMD=`cygpath --unix "$JAVACMD"` - - # We build the pattern for arguments to be converted via cygpath - ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` - SEP="" - for dir in $ROOTDIRSRAW ; do - ROOTDIRS="$ROOTDIRS$SEP$dir" - SEP="|" - done - OURCYGPATTERN="(^($ROOTDIRS))" - # Add a user-defined pattern to the cygpath arguments - if [ "$GRADLE_CYGPATTERN" != "" ] ; then - OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" - fi +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + # Now convert the arguments - kludge to limit ourselves to /bin/sh - i=0 - for arg in "$@" ; do - CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` - CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option - - if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition - eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` - else - eval `echo args$i`="\"$arg\"" + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) fi - i=`expr $i + 1` + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg done - case $i in - 0) set -- ;; - 1) set -- "$args0" ;; - 2) set -- "$args0" "$args1" ;; - 3) set -- "$args0" "$args1" "$args2" ;; - 4) set -- "$args0" "$args1" "$args2" "$args3" ;; - 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; - 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; - 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; - 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; - 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; - esac fi -# Escape application args -save () { - for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done - echo " " -} -APP_ARGS=`save "$@"` +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# -# Collect all arguments for the java command, following the shell quoting and substitution rules -eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' exec "$JAVACMD" "$@" diff --git a/itests/case1.sh b/itests/case1.sh index b234f3fb3..b7202a2b5 100755 --- a/itests/case1.sh +++ b/itests/case1.sh @@ -3,6 +3,8 @@ set -euxo pipefail mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP -OsaveOriginalReads=true test_R1.fastq test_R2.fastq case1.vdjca +mixcr exportAirr --imgt-gaps case1.vdjca case1.vdjca.imgt.airr.tsv mixcr exportAirr case1.vdjca case1.vdjca.airr.tsv mixcr assemble case1.vdjca case1.clns +mixcr exportAirr --imgt-gaps case1.clns case1.clns.imgt.airr.tsv mixcr exportAirr case1.clns case1.clns.airr.tsv diff --git a/itests/case4.sh b/itests/case4.sh index 217bc5abd..46252cca4 100755 --- a/itests/case4.sh +++ b/itests/case4.sh @@ -6,7 +6,12 @@ set -euxo pipefail mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case4 # Checking AIRR export on big files +mixcr exportAirr --imgt-gaps case4.vdjca case4.vdjca.imgt.airr.tsv +mixcr exportAirr --imgt-gaps --from-alignment case4.vdjca case4.vdjca.imgta.airr.tsv mixcr exportAirr case4.vdjca case4.vdjca.airr.tsv + +mixcr exportAirr --imgt-gaps case4.clna case4.clna.imgt.airr.tsv +mixcr exportAirr --imgt-gaps --from-alignment case4.clna case4.clna.imgta.airr.tsv mixcr exportAirr case4.clna case4.clna.airr.tsv # Checking skip steps behaviour diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java index 748644438..42ffff6d9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java @@ -8,6 +8,7 @@ import com.milaboratory.mixcr.export.FieldExtractor; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.SmartProgressReporter; +import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; @@ -33,6 +34,14 @@ public class CommandExportAirr extends ACommandMiXCR { names = {"-t", "--target"}) public int targetId = -1; + @Option(description = "If this option alignment fields will be padded with IMGT-style gaps.", + names = {"-g", "--imgt-gaps"}) + public boolean withPadding = false; + + @Option(description = "Get fields like fwr1, cdr2, etc.. from alignment.", + names = {"-a", "--from-alignment"}) + public boolean fromAlignment = false; + @Parameters(index = "0", description = "input_file.[vdjca|clna|clns]") public String in; @Parameters(index = "1", description = "output.tsv") @@ -46,6 +55,16 @@ public String getType() { return info0.fileType; } + private FieldExtractor nFeature(GeneFeature gf, String header) { + if (gf.isComposite()) + throw new IllegalArgumentException(); + return fromAlignment + ? new NFeatureFromAlign(targetId, withPadding, + new Single(gf.getFirstPoint()), new Single(gf.getLastPoint()), + header) + : new NFeature(gf, header); + } + @SuppressWarnings("UnnecessaryLocalVariable") private List> CommonExtractors() { ComplexReferencePoint vnpEnd = new Leftmost(VEndTrimmed, VEnd); @@ -69,8 +88,8 @@ private List> CommonExtractors() { new VDJCCalls(Joining), new VDJCCalls(Constant), - new SequenceAlignment(targetId), - new GermlineAlignment(targetId), + new SequenceAlignment(targetId, withPadding), + new GermlineAlignment(targetId, withPadding), new CompleteVDJ(targetId), @@ -80,25 +99,25 @@ private List> CommonExtractors() { new NFeature(targetId, np1Begin, np1End, "np1"), new NFeature(targetId, np2Begin, np2End, "np2"), - new NFeature(CDR1, "cdr1"), + nFeature(CDR1, "cdr1"), new AAFeature(CDR1, "cdr1_aa"), - new NFeature(CDR2, "cdr2"), + nFeature(CDR2, "cdr2"), new AAFeature(CDR2, "cdr2_aa"), - new NFeature(ShortCDR3, "cdr3"), + nFeature(ShortCDR3, "cdr3"), new AAFeature(ShortCDR3, "cdr3_aa"), - new NFeature(FR1, "fwr1"), + nFeature(FR1, "fwr1"), new AAFeature(FR1, "fwr1_aa"), - new NFeature(FR2, "fwr2"), + nFeature(FR2, "fwr2"), new AAFeature(FR2, "fwr2_aa"), - new NFeature(FR3, "fwr3"), + nFeature(FR3, "fwr3"), new AAFeature(FR3, "fwr3_aa"), - new NFeature(FR4, "fwr4"), + nFeature(FR4, "fwr4"), new AAFeature(FR4, "fwr4_aa"), new AlignmentScoring(targetId, Variable), @@ -125,7 +144,7 @@ private List> CommonExtractors() { for (GeneType gt : VDJC_REFERENCE) for (boolean start : new boolean[]{true, false}) - ret.add(new AirrAlignmentBoundary(targetId, gt, start)); + ret.add(new AirrAlignmentBoundary(targetId, withPadding, gt, start)); return ret; } diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java index 370a6968b..a9ab5c7e0 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java +++ b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java @@ -17,6 +17,14 @@ public final class AirrColumns { private AirrColumns() { } + private static String airrStr(String str) { + return str == null ? "" : str; + } + + private static String airrBoolean(Boolean value) { + return value == null ? "" : value ? "T" : "F"; + } + public static final class CloneId implements FieldExtractor { @Override public String getHeader() { @@ -80,8 +88,14 @@ public String getHeader() { @Override public String extractValue(AirrVDJCObjectWrapper object) { - // TODO better implementation - return "T"; + NSequenceWithQuality cdr3nt = object.object.getFeature(GeneFeature.CDR3); + AminoAcidSequence cdr3aa = object.object.getAAFeature(GeneFeature.CDR3); + return airrBoolean( + cdr3nt != null + && cdr3aa != null + && cdr3nt.size() % 3 == 0 + && !cdr3aa.containStops() + ); } } @@ -126,9 +140,11 @@ public String extractValue(AirrVDJCObjectWrapper object) { public static abstract class AirrAlignmentExtractor implements FieldExtractor { private final int targetId; + protected final boolean withPadding; - public AirrAlignmentExtractor(int targetId) { + public AirrAlignmentExtractor(int targetId, boolean withPadding) { this.targetId = targetId; + this.withPadding = withPadding; } public abstract String extractValue(AirrAlignment object); @@ -136,14 +152,16 @@ public AirrAlignmentExtractor(int targetId) { @Override public String extractValue(AirrVDJCObjectWrapper object) { int resolvedTargetId = targetId == -1 ? object.getBestTarget() : targetId; - AirrAlignment alignment = object.getAirrAlignment(resolvedTargetId); - return extractValue(alignment); + AirrAlignment alignment = object.getAirrAlignment(resolvedTargetId, withPadding); + if (alignment == null) + return ""; + return airrStr(extractValue(alignment)); } } public static final class SequenceAlignment extends AirrAlignmentExtractor { - public SequenceAlignment(int targetId) { - super(targetId); + public SequenceAlignment(int targetId, boolean withPadding) { + super(targetId, withPadding); } @Override @@ -153,13 +171,13 @@ public String getHeader() { @Override public String extractValue(AirrAlignment object) { - return object.sequence; + return airrStr(object.getSequence(withPadding)); } } public static final class GermlineAlignment extends AirrAlignmentExtractor { - public GermlineAlignment(int targetId) { - super(targetId); + public GermlineAlignment(int targetId, boolean withPadding) { + super(targetId, withPadding); } @Override @@ -169,12 +187,12 @@ public String getHeader() { @Override public String extractValue(AirrAlignment object) { - return object.germline; + return airrStr(object.getGermline(withPadding)); } } public interface ComplexReferencePoint { - int getPosition(SequencePartitioning partitioning); + int getPosition(SequencePartitioning partitioning, GeneFeature referenceFeature); } public static final class Single implements ComplexReferencePoint { @@ -185,8 +203,10 @@ public Single(ReferencePoint refPoint) { } @Override - public int getPosition(SequencePartitioning partitioning) { - return partitioning.getPosition(point); + public int getPosition(SequencePartitioning partitioning, GeneFeature referenceFeature) { + return referenceFeature == null + ? partitioning.getPosition(point) + : partitioning.getRelativePosition(referenceFeature, point); } @Override @@ -209,10 +229,10 @@ public Rightmost(ComplexReferencePoint... points) { } @Override - public int getPosition(SequencePartitioning partitioning) { + public int getPosition(SequencePartitioning partitioning, GeneFeature referenceFeature) { int result = -1; for (ComplexReferencePoint rp : points) { - int position = rp.getPosition(partitioning); + int position = rp.getPosition(partitioning, referenceFeature); if (position < 0) continue; result = Math.max(result, position); @@ -240,10 +260,10 @@ public Leftmost(ComplexReferencePoint... points) { } @Override - public int getPosition(SequencePartitioning partitioning) { + public int getPosition(SequencePartitioning partitioning, GeneFeature referenceFeature) { int result = Integer.MAX_VALUE; for (ComplexReferencePoint rp : points) { - int position = rp.getPosition(partitioning); + int position = rp.getPosition(partitioning, referenceFeature); if (position < 0) continue; result = Math.min(result, position); @@ -257,6 +277,30 @@ public String toString() { } } + public final static class NFeatureFromAlign extends AirrAlignmentExtractor { + private final ComplexReferencePoint from, to; + private final String header; + + public NFeatureFromAlign(int targetId, boolean withPadding, + ComplexReferencePoint from, ComplexReferencePoint to, + String header) { + super(targetId, withPadding); + this.from = from; + this.to = to; + this.header = header; + } + + @Override + public String getHeader() { + return header; + } + + @Override + public String extractValue(AirrAlignment object) { + return object.getSequence(from, to, withPadding); + } + } + public abstract static class NFeatureAbstract implements FieldExtractor { /** * Used only for complex features @@ -308,11 +352,11 @@ public String extractValue(AirrVDJCObjectWrapper object) { assert from != null && to != null; SequencePartitioning partitioning = object.object.getPartitionedTarget(resolvedTargetId).getPartitioning(); - int fromPosition = from.getPosition(partitioning); + int fromPosition = from.getPosition(partitioning, null); if (fromPosition < 0) return ""; - int toPosition = to.getPosition(partitioning); + int toPosition = to.getPosition(partitioning, null); if (toPosition < 0) return ""; @@ -470,8 +514,8 @@ public static final class AirrAlignmentBoundary extends AirrAlignmentExtractor { private final GeneType geneType; private final boolean start; - public AirrAlignmentBoundary(int targetId, GeneType geneType, boolean start) { - super(targetId); + public AirrAlignmentBoundary(int targetId, boolean withPadding, GeneType geneType, boolean start) { + super(targetId, withPadding); this.geneType = geneType; this.start = start; } @@ -484,7 +528,7 @@ public String getHeader() { @Override public String extractValue(AirrAlignment object) { - Range range = object.ranges.get(geneType); + Range range = object.getRange(geneType, withPadding); if (range == null) return ""; return "" + (start ? range.getLower() + 1 : range.getUpper()); @@ -519,7 +563,7 @@ public String getHeader() { public String extractValue(AirrVDJCObjectWrapper object) { int resolvedTargetId = targetId == -1 ? object.getBestTarget() : targetId; VDJCPartitionedSequence partitionedTarget = object.object.getPartitionedTarget(resolvedTargetId); - return partitionedTarget.getPartitioning().isAvailable(GeneFeature.VDJRegion) ? "T" : "F"; + return airrBoolean(partitionedTarget.getPartitioning().isAvailable(GeneFeature.VDJRegion)); } } } diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java b/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java index 357ba3713..e42e91a9e 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java +++ b/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java @@ -6,55 +6,145 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.export.AirrColumns.ComplexReferencePoint; import com.milaboratory.util.BitArray; -import io.repseq.core.GeneFeature; +import com.milaboratory.util.StringUtil; import io.repseq.core.GeneType; +import io.repseq.util.IMGTPadding; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.EnumMap; -import java.util.List; +import java.util.*; + +import static io.repseq.core.GeneFeature.CDR3; +import static io.repseq.core.GeneType.*; +import static io.repseq.core.ReferencePoint.*; public final class AirrUtil { + public static final char PADDING_CHARACTER = '.'; + private AirrUtil() { } - public static AirrAlignment calculateAirAlignment(VDJCObject object, int targetId) { + // /** Germline FR4 end position rounded down to the triplet boundary relative to aligned feature */ + // private static int imgtFR4End(VDJCHit jHit) { + // ReferencePoints partitioning = jHit.getGene().getPartitioning(); + // GeneFeature af = jHit.getAlignedFeature(); + // int fr4End = partitioning.getRelativePosition(af, FR4End); + // if (fr4End < 0) // in case gene has no anchor point for the position + // return -1; + // int cdr3End = partitioning.getRelativePosition(af, CDR3End); + // if (cdr3End < 0) // in case gene has no anchor point for the position + // return -1; + // return cdr3End + (fr4End - cdr3End) / 3 * 3; + // } + + private static final int NULL_PADDING_LENGTH = Integer.MIN_VALUE; + + /** + * Pre-calculates AIRR style alignment data + * + * @param object source data + * @param targetId target to build alignment from (AIRR format has no support for multi target sequence structures) + * @param vdjRegion if true alignment will be forced to the boundaries of VDJRegion (in IMGT's sense, with FR4End bound to the reading frame) + * @return pre-calculated alignment data + */ + public static AirrAlignment calculateAirrAlignment(VDJCObject object, int targetId, boolean vdjRegion) { NucleotideSequence target = object.getTarget(targetId).getSequence(); MultiAlignmentHelper.Settings settings = new MultiAlignmentHelper.Settings( false, false, false, ' ', ' '); List> alignments = new ArrayList<>(); List actualGeneTypes = new ArrayList<>(); - for (GeneType gt : GeneType.VDJC_REFERENCE) { + + boolean validPaddings = true; + // padding insertion positions are in germline coordinates + EnumMap> paddingsByGeneType = new EnumMap<>(GeneType.class); + + // positive numbers means imgt gaps must be added, negative - letters must be removed from the + // corresponding side, compared to IMGT's VDJRegion + // these numbers represent number of nucleotides in the germline sequence to fill up the sequence, + // IMGTPadding's calculated must additionally be added + int leftVDJPadding = NULL_PADDING_LENGTH, rightVDJPadding = NULL_PADDING_LENGTH; + // for positive values above these sequences represent a germline sequence ranges to be appended to tha alignment + Range leftVDJExtraRange = null, rightVDJExtraRange = null; + // and the sequences themselves + NucleotideSequence leftVDJExtra = null, rightVDJExtra = null; + // these positions are initially in germline coordinates, conversion to alignment position happens below + int cdr3Begin = -1, cdr3End = -1; + + EnumMap bestHits = new EnumMap<>(GeneType.class); + + for (GeneType gt : vdjRegion ? VDJ_REFERENCE : VDJC_REFERENCE) { VDJCHit bestHit = object.getBestHit(gt); if (bestHit == null) continue; - Alignment alignment = bestHit.getAlignment(targetId); - if (alignment == null) + Alignment al = bestHit.getAlignment(targetId); + if (al == null) continue; actualGeneTypes.add(gt); - alignments.add(alignment.invert(target)); + bestHits.put(gt, bestHit); + alignments.add(al.invert(target)); + + // IMGT related code below + + if (gt == Variable) { + cdr3Begin = bestHit.getGene().getPartitioning().getRelativePosition(bestHit.getAlignedFeature(), CDR3Begin); + int fr1Begin = bestHit.getGene().getPartitioning().getRelativePosition(bestHit.getAlignedFeature(), FR1Begin); + if (fr1Begin >= 0) { // in case gene has no anchor point for the position + leftVDJPadding = al.getSequence1Range().getFrom() - fr1Begin; + if (leftVDJPadding > 0) { + leftVDJExtraRange = new Range(fr1Begin, al.getSequence1Range().getFrom()); + leftVDJExtra = al.getSequence1().getRange(leftVDJExtraRange); + } + } + } + if (gt == Joining) { + cdr3End = bestHit.getGene().getPartitioning().getRelativePosition(bestHit.getAlignedFeature(), CDR3End); + int fr4End = bestHit.getGene().getPartitioning().getRelativePosition(bestHit.getAlignedFeature(), FR4End); + if (fr4End >= 0) { // in case gene has no anchor point for the position + rightVDJPadding = fr4End - al.getSequence1Range().getTo(); + if (rightVDJPadding > 0) { + rightVDJExtraRange = new Range(al.getSequence1Range().getTo(), fr4End); + rightVDJExtra = al.getSequence1().getRange(al.getSequence1Range().getTo(), fr4End); + } + } + } + + if (!validPaddings) + continue; + + List germlinePaddings = IMGTPadding.calculateForSequence(bestHit.getGene().getPartitioning(), + bestHit.getAlignedFeature()); + if (germlinePaddings == null) + validPaddings = false; + + paddingsByGeneType.put(gt, germlinePaddings); } + // noinspection unchecked MultiAlignmentHelper helper = MultiAlignmentHelper.build(settings, new Range(0, target.size()), target, alignments.toArray(new Alignment[0])); // merging alignments + // output data String sequence = helper.getSubject(); + // output data StringBuilder germlineBuilder = new StringBuilder(); - GeneType[] geneType = new GeneType[helper.size()]; - int[] germlinePosition = new int[helper.size()]; + int size = helper.size(); + // output data + int[] germlinePosition = new int[size]; Arrays.fill(germlinePosition, -1); - BitArray match = new BitArray(helper.size()); + // output data + GeneType[] geneType = new GeneType[size]; + // output data + boolean[] match = new boolean[size]; int firstAligned = -1, lastAligned = 0; outer: - for (int i = 0; i < helper.size(); i++) { + for (int i = 0; i < size; i++) { for (int gti = 0; gti < actualGeneTypes.size(); gti++) { if (helper.getQuery(gti).charAt(i) != ' ') { GeneType gt = actualGeneTypes.get(gti); germlineBuilder.append(helper.getQuery(gti).charAt(i)); - geneType[i] = gt; germlinePosition[i] = helper.getAbsQueryPositionAt(gti, i); - match.set(i, helper.getMatch()[gti].get(i)); + geneType[i] = gt; + match[i] = helper.getMatch()[gti].get(i); if (firstAligned == -1) firstAligned = i; @@ -69,8 +159,132 @@ public static AirrAlignment calculateAirAlignment(VDJCObject object, int targetI // trimming unaligned sequence = sequence.substring(firstAligned, lastAligned + 1); String germline = germlineBuilder.substring(firstAligned, lastAligned + 1); + germlinePosition = Arrays.copyOfRange(germlinePosition, firstAligned, lastAligned + 1); + geneType = Arrays.copyOfRange(geneType, firstAligned, lastAligned + 1); + match = Arrays.copyOfRange(match, firstAligned, lastAligned + 1); + size = lastAligned - firstAligned + 1; + + assert sequence.length() == size; + + if (vdjRegion) { + if (leftVDJPadding == NULL_PADDING_LENGTH || rightVDJPadding == NULL_PADDING_LENGTH) { + // impossible to construct VDJRegion-bound AIRR alignment + return null; + } else { + // Processing left side + if (leftVDJPadding > 0) { + assert leftVDJPadding == leftVDJExtra.size(); + assert leftVDJPadding == leftVDJExtraRange.length(); + + sequence = StringUtil.chars(PADDING_CHARACTER, leftVDJPadding) + sequence; + germline = leftVDJExtra + germline; + + int[] newGermlinePosition = new int[leftVDJPadding + size]; + System.arraycopy(germlinePosition, 0, newGermlinePosition, + leftVDJPadding, size); + GeneType[] newGeneType = new GeneType[leftVDJPadding + size]; + System.arraycopy(geneType, 0, newGeneType, + leftVDJPadding, size); + boolean[] newMatch = new boolean[leftVDJPadding + size]; + System.arraycopy(match, 0, newMatch, + leftVDJPadding, size); + for (int p = leftVDJExtraRange.getFrom(), i = 0; p < leftVDJExtraRange.getTo(); ++p, ++i) { + newGermlinePosition[i] = p; + newGeneType[i] = Variable; + newMatch[i] = true; + } + germlinePosition = newGermlinePosition; + geneType = newGeneType; + match = newMatch; + } else if (leftVDJPadding != 0) { + sequence = sequence.substring(-leftVDJPadding); + germline = germline.substring(-leftVDJPadding); + germlinePosition = Arrays.copyOfRange(germlinePosition, -leftVDJPadding, germlinePosition.length); + geneType = Arrays.copyOfRange(geneType, -leftVDJPadding, geneType.length); + match = Arrays.copyOfRange(match, -leftVDJPadding, match.length); + } + size += leftVDJPadding; + assert sequence.length() == size; + + if (rightVDJPadding > 0) { + assert rightVDJPadding == rightVDJExtra.size(); + assert rightVDJPadding == rightVDJExtraRange.length(); + + sequence = sequence + StringUtil.chars(PADDING_CHARACTER, rightVDJPadding); + germline = germline + rightVDJExtra; + germlinePosition = Arrays.copyOf(germlinePosition, size + rightVDJPadding); + geneType = Arrays.copyOf(geneType, size + rightVDJPadding); + match = Arrays.copyOf(match, size + rightVDJPadding); + // size here is "previous size" + for (int p = rightVDJExtraRange.getFrom(), i = size; p < rightVDJExtraRange.getTo(); ++p, ++i) { + germlinePosition[i] = p; + geneType[i] = Joining; + match[i] = true; + } + } else if (rightVDJPadding != 0) { + sequence = sequence.substring(0, size + rightVDJPadding); // note that rightVDJPadding < 0 + germline = germline.substring(0, size + rightVDJPadding); + germlinePosition = Arrays.copyOf(germlinePosition, size + rightVDJPadding); + geneType = Arrays.copyOf(geneType, size + rightVDJPadding); + match = Arrays.copyOf(match, size + rightVDJPadding); + } + size += rightVDJPadding; + assert germline.length() == size; + } + } + + int cdr3Length = object.ntLengthOf(CDR3); + + List paddings = null; + if (validPaddings) { + paddings = new ArrayList<>(); + outer: + for (Map.Entry> e : paddingsByGeneType.entrySet()) { + GeneType gt = e.getKey(); + List germlinePaddings = e.getValue(); + for (IMGTPadding germlinePadding : germlinePaddings) { + int pos = projectPosition(germlinePosition, geneType, + germlinePadding.getInsertionPosition(), gt); + if (pos == -1) { + paddings = null; + break outer; + } + paddings.add(new IMGTPadding(pos, germlinePadding.getPaddingLength())); + } + } + + if (paddings == null || cdr3Begin == -1 || cdr3End == -1 || cdr3Length < 0) + paddings = null; + else { + cdr3Begin = projectPosition(germlinePosition, geneType, cdr3Begin, Variable); + cdr3End = projectPosition(germlinePosition, geneType, cdr3End, Joining); + int paddedLength = IMGTPadding.getPaddedLengthNt(CDR3, cdr3Length); + if (cdr3Begin == -1 || cdr3End == -1 || paddedLength == -1) + paddings = null; + else { + int position = cdr3Begin + IMGTPadding.insertPosition(cdr3End - cdr3Begin); + paddings.add(new IMGTPadding(position, paddedLength - cdr3Length)); + } + } + } + + if (paddings != null) + Collections.sort(paddings); - return new AirrAlignment(sequence, germline, geneType, germlinePosition, match); + return new AirrAlignment(bestHits, sequence, germline, geneType, germlinePosition, new BitArray(match), paddings); + } + + private static int projectPosition(int[] germlinePositions, GeneType[] geneTypes, + int position, GeneType geneType) { + boolean onLeft = false; + for (int i = 0; i < germlinePositions.length; i++) + if (geneTypes[i] == geneType) { + if (germlinePositions[i] < position) + onLeft = true; + if (onLeft && germlinePositions[i] >= position) + return i; + } + return -1; } /** @@ -83,13 +297,13 @@ public static AirrAlignment calculateAirAlignment(VDJCObject object, int targetI */ public static int bestTarget(VDJCObject obj) { for (int i = 0; i < obj.numberOfTargets(); i++) - if (obj.getPartitionedTarget(i).getPartitioning().isAvailable(GeneFeature.CDR3)) + if (obj.getPartitionedTarget(i).getPartitioning().isAvailable(CDR3)) return i; int maxAlignmentLength = -1; int targetWithMaxAlignmentLength = -1; for (int i = 0; i < obj.numberOfTargets(); i++) { int alignmentLength = 0; - for (GeneType gt : GeneType.VDJC_REFERENCE) { + for (GeneType gt : VDJC_REFERENCE) { VDJCHit bh = obj.getBestHit(gt); if (bh == null) continue; @@ -107,22 +321,35 @@ public static int bestTarget(VDJCObject obj) { } public static class AirrAlignment { - final String sequence, germline; - final GeneType[] geneType; - final int[] germlinePosition; - final BitArray match; - final EnumMap ranges; + private final EnumMap bestHits; + private final String sequence, germline; + private final GeneType[] geneType; + private final int[] germlinePosition; + private final BitArray match; + private final EnumMap ranges; + private final List paddings; - public AirrAlignment(String sequence, String germline, + public AirrAlignment(EnumMap bestHits, + String sequence, String germline, GeneType[] geneType, int[] germlinePosition, - BitArray match) { + BitArray match, List paddings) { + if (sequence.length() != germline.length()) + throw new IllegalArgumentException(); + if (germline.length() != geneType.length) + throw new IllegalArgumentException(); + if (geneType.length != germlinePosition.length) + throw new IllegalArgumentException(); + if (germlinePosition.length != match.size()) + throw new IllegalArgumentException(); + + this.bestHits = bestHits; this.sequence = sequence; this.germline = germline; this.geneType = geneType; this.germlinePosition = germlinePosition; this.match = match; EnumMap ranges = new EnumMap<>(GeneType.class); - for (GeneType gt : GeneType.VDJC_REFERENCE) { + for (GeneType gt : VDJC_REFERENCE) { int min = -1; int max = -1; for (int i = 0; i < geneType.length; i++) @@ -135,6 +362,76 @@ public AirrAlignment(String sequence, String germline, ranges.put(gt, new Range(min, max + 1)); } this.ranges = ranges; + this.paddings = paddings; + } + + private String padded(String input) { + if (paddings == null) + return null; + return IMGTPadding.applyPadding(paddings, PADDING_CHARACTER, input); + } + + private int projectToPadded(int unpaddedPosition) { + if (paddings == null) + return -1; + int result = unpaddedPosition; + for (IMGTPadding p : paddings) + if (p.getInsertionPosition() >= unpaddedPosition) + return result; + else + result += p.getPaddingLength(); + return result; + } + + public String getSequence(boolean withPadding) { + return withPadding ? padded(sequence) : sequence; + } + + public String getGermline(boolean withPadding) { + return withPadding ? padded(germline) : germline; + } + + public int projectGermlinePosition(GeneType gt, int position, boolean withPadding) { + position = projectPosition(germlinePosition, geneType, position, gt); + if (position == -1) + return -1; + return withPadding ? projectToPadded(position) : position; + } + + public int getPosition(ComplexReferencePoint point, boolean withPadding) { + for (GeneType gt : VDJC_REFERENCE) { + VDJCHit hit = bestHits.get(gt); + if (hit == null) + continue; + int position = point.getPosition(hit.getGene().getPartitioning(), hit.getAlignedFeature()); + if (position == -1) + continue; + return projectGermlinePosition(gt, position, withPadding); + } + return -1; + } + + public String getSequence(ComplexReferencePoint from, ComplexReferencePoint to, boolean withPadding) { + int fromPosition = getPosition(from, withPadding); + int toPosition = getPosition(to, withPadding); + if (fromPosition == -1 || toPosition == -1) + return null; + return getSequence(withPadding).substring(fromPosition, toPosition); + } + + public Range getRange(GeneType gt, boolean withPadding) { + Range range = ranges.get(gt); + if (range == null) + return null; + + if (withPadding) { + return paddings == null + ? null + : new Range( + projectToPadded(range.getLower()), + projectToPadded(range.getUpper())); + } else + return range; } } } diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java b/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java index beab6ad7c..4ab0c462f 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java +++ b/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java @@ -7,7 +7,8 @@ public final class AirrVDJCObjectWrapper { public final VDJCObject object; private int bestTarget = -1; - private int alignmentTarget = -1; + private int alignmentTarget = -2; + private boolean alignmentVDJ = false; private AirrUtil.AirrAlignment alignment; public AirrVDJCObjectWrapper(VDJCObject object) { @@ -29,11 +30,12 @@ public int getBestTarget() { return bestTarget; } - public AirrUtil.AirrAlignment getAirrAlignment(int target) { - if (alignmentTarget == target) + public AirrUtil.AirrAlignment getAirrAlignment(int target, boolean vdj) { + if (alignmentTarget == target && alignmentVDJ == vdj) return alignment; alignmentTarget = target; - alignment = AirrUtil.calculateAirAlignment(object, target); + alignmentVDJ = vdj; + alignment = AirrUtil.calculateAirrAlignment(object, target, vdj); return alignment; } } From 060dbab37fe20d3e72aa38f85aa0783d9c3ee050 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 16 Mar 2022 01:16:40 +0400 Subject: [PATCH 160/282] chore: disable drone and old circleci --- .circleci/config.yml | 85 ---------- .drone.yml | 303 ----------------------------------- .github/workflows/build.yaml | 2 +- 3 files changed, 1 insertion(+), 389 deletions(-) delete mode 100644 .circleci/config.yml delete mode 100644 .drone.yml diff --git a/.circleci/config.yml b/.circleci/config.yml deleted file mode 100644 index 134d38737..000000000 --- a/.circleci/config.yml +++ /dev/null @@ -1,85 +0,0 @@ -version: 2.1 -jobs: - build: - docker: - - image: circleci/openjdk:8-jdk - - working_directory: ~/mixcr - - environment: - MAX_MEMORY_OVERRIDE: 3500 - MAVEN_OPTS: -Xmx3g - - steps: - - checkout - - - run: - name: Installing moreutils - command: | - sudo apt-get update - sudo apt-get install -y moreutils parallel - - - run: - name: Downloading git submodules - command: git submodule update --init --recursive - - - restore_cache: - keys: - - v1-dependencies-{{ checksum "pom.xml" }}-{{ checksum "milib/pom.xml" }}-{{ checksum "repseqio/pom.xml" }} - - v1-dependencies- - - - run: - name: Building MiLib - working_directory: milib - command: mvn clean install -DskipTests --batch-mode - - - restore_cache: - keys: - - v1-repseqio-cache-{{ checksum "repseqio/.gitmodules" }} - - v1-repseqio-cache- - - - run: - name: Building RepseqIO - working_directory: repseqio - command: mvn clean install -DskipTests --batch-mode - - - save_cache: - paths: - - repseqio/.cache - key: v1-repseqio-cache-{{ checksum "repseqio/.gitmodules" }} - - - restore_cache: - key: v1-test-data-{{ checksum "ensure-test-data.sh" }} - - - run: - name: Downloading test data - command: ./ensure-test-data.sh - - - save_cache: - paths: - - src/test/resources/sequences/big/ - key: v1-test-data-{{ checksum "ensure-test-data.sh" }} - - - run: - name: Building and testing MiXCR - command: mvn clean install - - - store_test_results: - path: target/surefire-reports - - - save_cache: - paths: - - ~/.m2 - key: v1-dependencies-{{ checksum "pom.xml" }}-{{ checksum "milib/pom.xml" }}-{{ checksum "repseqio/pom.xml" }} - - - run: - name: Prepare Integration Test Data - command: ./prepare-test-data.sh - - - run: - name: Running Maven Integration tests - command: mvn test -DintegrationTests - - - run: - name: Running Script Integration and Regression tests - command: ./itests.sh test | ts diff --git a/.drone.yml b/.drone.yml deleted file mode 100644 index 327c2a654..000000000 --- a/.drone.yml +++ /dev/null @@ -1,303 +0,0 @@ ---- -kind: pipeline -type: docker -name: build - -platform: - os: linux - arch: amd64 - -trigger: - event: - - push - - tag - -image_pull_secrets: - - docker-dockerconfig - - quay-dockerconfig - -anchors: - aws_credentials: &aws_credentials - AWS_DEFAULT_REGION: - from_secret: aws-region - AWS_ACCESS_KEY_ID: - from_secret: aws-key-id - AWS_SECRET_ACCESS_KEY: - from_secret: aws-secret-key - DEPLOY_S3_CDN_BUCKET: - from_secret: cdn-s3-bucket - DEPLOY_S3_CDN_PREFIX: - from_secret: cdn-s3-prefix - - gradle_task: &gradle_task - image: gradle:7.0.2-jdk8-hotspot - environment: - # Gradle folder - GRADLE_USER_HOME: "/drone/src/.gradle" - - # MiLab repository credentials - ORG_GRADLE_PROJECT_miRepoAccessKeyId: - from_secret: aws-key-id - ORG_GRADLE_PROJECT_miRepoSecretAccessKey: - from_secret: aws-secret-key - - # For Maven Central release - ORG_GRADLE_PROJECT_sonatypeUsername: - from_secret: sonatype-username - ORG_GRADLE_PROJECT_sonatypePassword: - from_secret: sonatype-password - ORG_GRADLE_PROJECT_signingKey: - from_secret: signing-key - - cache_settings: &cache_settings - # debug: true - access_key: - from_secret: aws-key-id - secret_key: - from_secret: aws-secret-key - bucket: - from_secret: aws-cache-bucket - region: - from_secret: aws-region - local_root: /drone/src - -steps: - - name: fetch - image: alpine/git - commands: - - git fetch --tags - - - name: restore_gradle_cache - image: meltwater/drone-cache - pull: true - settings: - restore: true - cache_key: '{{ .Commit.Branch }}' - mount: - - .gradle - <<: *cache_settings - - - <<: *gradle_task - name: initialization - commands: - - echo "{}" > build_info.json - - gradle -i --no-daemon CreateInfoFile - - - <<: *gradle_task - name: create_zip_and_publish_artefact - commands: - - gradle --no-daemon -i -x test PublishAllPublicationsToMiPrivRepository distributionZip - - - name: publish_zip_to_cdn - image: alpine - when: - event: - - push - commands: - - apk add jq aws-cli - - | - aws s3 cp \ - "build/distributions/mixcr.zip" \ - "s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/software/mixcr/mixcr-$(jq -r .version build_info.json).zip" - environment: - <<: *aws_credentials - - - name: telegram_mipub_published - when: - event: - - push - image: appleboy/drone-telegram - settings: - token: - from_secret: telegram-token - to: - from_secret: telegram-chat-id-micore - format: markdown - template_vars_file: build_info.json - disable_web_page_preview: true - message: | - 🧩 build {{build.number}} on `{{commit.branch}}` published ```com.milaboratory:mixcr:{{tpl.version}}``` - - 📦 https://cdn.milaboratory.com/software/mixcr/mixcr-{{tpl.version}}.zip - ---- - -kind: pipeline -type: docker -name: integration_tests - -platform: - os: linux - arch: amd64 - -node: - type: highcpu - -trigger: - event: - - push - -image_pull_secrets: - - docker-dockerconfig - - quay-dockerconfig - -anchors: - aws_credentials: &aws_credentials - AWS_DEFAULT_REGION: - from_secret: aws-region - AWS_ACCESS_KEY_ID: - from_secret: aws-key-id - AWS_SECRET_ACCESS_KEY: - from_secret: aws-secret-key - DEPLOY_S3_CDN_BUCKET: - from_secret: cdn-s3-bucket - DEPLOY_S3_CDN_PREFIX: - from_secret: cdn-s3-prefix - - gradle_task: &gradle_task - image: gradle:7.0.2-jdk8-hotspot - environment: - # Gradle folder - GRADLE_USER_HOME: "/drone/src/.gradle" - - # MiLab repository credentials - ORG_GRADLE_PROJECT_miRepoAccessKeyId: - from_secret: aws-key-id - ORG_GRADLE_PROJECT_miRepoSecretAccessKey: - from_secret: aws-secret-key - - # For Maven Central release - ORG_GRADLE_PROJECT_sonatypeUsername: - from_secret: sonatype-username - ORG_GRADLE_PROJECT_sonatypePassword: - from_secret: sonatype-password - ORG_GRADLE_PROJECT_signingKey: - from_secret: signing-key - - cache_settings: &cache_settings - # debug: true - access_key: - from_secret: aws-key-id - secret_key: - from_secret: aws-secret-key - bucket: - from_secret: aws-cache-bucket - region: - from_secret: aws-region - local_root: /drone/src - -steps: - - name: restore_gradle_cache - image: meltwater/drone-cache - pull: true - settings: - restore: true - cache_key: '{{ .Commit.Branch }}' - mount: - - .gradle - <<: *cache_settings - - - name: restore_test_resource_cache - image: meltwater/drone-cache - pull: true - settings: - restore: true - cache_key: mixcr_test_resource - mount: - - src/test/resources/sequences/big - <<: *cache_settings - - - <<: *gradle_task - name: initialization - commands: - - apt-get update - - apt-get install -y moreutils parallel - - ./ensure-test-data.sh - - find src/test/resources/sequences/big -type f - - echo "{}" > build_info.json - - gradle -i --no-daemon CreateInfoFile - - gradle -i --no-daemon -x test build - - ./prepare-test-data.sh - - - name: rebuild_test_resource_cache - image: meltwater/drone-cache - pull: true - settings: - rebuild: true - cache_key: mixcr_test_resource - mount: - - src/test/resources/sequences/big - <<: *cache_settings - - - name: add_url_secret - image: alpine - commands: - - apk add jq - - jq ".urlsecret=\"$${URL_SECRET}\"" build_info.json > build_info.json.1 - - mv build_info.json.1 build_info.json - environment: - URL_SECRET: - from_secret: url-secret - - - <<: *gradle_task - name: build - commands: - - gradle -i --no-daemon -PlongTests=true test build - - - name: test_report_upload - image: amazon/aws-cli - when: - status: - - success - - failure - commands: - - aws s3 cp --recursive build/reports/tests/test s3://$${DEPLOY_S3_CDN_BUCKET}/$${DEPLOY_S3_CDN_PREFIX}/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-$${URL_SECRET}/tests/ - environment: - <<: *aws_credentials - DEPLOY_S3_CDN_BUCKET: - from_secret: cdn-s3-bucket - DEPLOY_S3_CDN_PREFIX: - from_secret: cdn-s3-prefix - URL_SECRET: - from_secret: url-secret - - - <<: *gradle_task - name: integration_tests - commands: - - apt-get update - - apt-get install -y jq - - ./itests.sh test - - - name: telegram_tests - image: appleboy/drone-telegram - when: - status: - - success - - failure - settings: - token: - from_secret: telegram-token - to: - from_secret: telegram-chat-id-micore - format: markdown - template_vars_file: build_info.json - message: | - {{#success build.status}} - ✅ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` tests and integration tests success. - {{else}} - ❌ 🗜 MiXCR build {{build.number}} by {{commit.author}} on `{{commit.branch}}` tests or integration tests failure. - {{/success}} - - 🌐 {{build.link}} - - [📊 Test Report](https://cdn.milaboratory.com/internal/ci/${DRONE_REPO}/${DRONE_COMMIT}-${DRONE_BUILD_NUMBER}-{{tpl.urlsecret}}/tests/index.html) - - - name: rebuild_gradle_cache - image: meltwater/drone-cache - pull: true - settings: - rebuild: true - cache_key: '{{ .Commit.Branch }}' - mount: - - .gradle - <<: *cache_settings diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index d59fa0e07..b17ff8872 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -3,7 +3,7 @@ name: "Build" on: push: tags: [ '*' ] - branches: [ 'pmaster' ] + branches: [ '*' ] workflow_dispatch: {} From d49dc871093c7fc41949c59d2457d7d395c90b79 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 16 Mar 2022 02:24:01 +0200 Subject: [PATCH 161/282] Tracking preprocessors performance. --- .../com/milaboratory/mixcr/cli/CommandPa.java | 6 +- .../mixcr/cli/CommandPaExport.java | 65 ++++++- .../java/com/milaboratory/mixcr/cli/Main.java | 5 +- .../postanalysis/PostanalysisResult.java | 20 +- .../postanalysis/PostanalysisRunner.java | 28 ++- .../mixcr/postanalysis/SetPreprocessor.java | 14 +- .../postanalysis/SetPreprocessorFactory.java | 7 +- .../postanalysis/SetPreprocessorSetup.java | 2 +- .../postanalysis/SetPreprocessorStat.java | 176 +++++++++++++++++- .../postanalysis/SetPreprocessorSummary.java | 121 ++++++++++++ .../mixcr/postanalysis/WeightFunction.java | 1 + .../mixcr/postanalysis/WeightFunctions.java | 25 +++ ...ClonesDownsamplingPreprocessorFactory.java | 11 +- .../downsampling/DownsampleValueChooser.java | 19 +- .../DownsamplingPreprocessor.java | 30 ++- .../overlap/OverlapAggregator.java | 12 +- .../postanalysis/overlap/OverlapDataset.java | 2 +- .../preproc/ElementPredicate.java | 17 +- .../preproc/FilterPreprocessor.java | 47 +++-- .../postanalysis/preproc/NoPreprocessing.java | 34 +++- .../preproc/OverlapPreprocessorAdapter.java | 24 ++- .../preproc/PreprocessorChain.java | 62 ++++-- .../mixcr/postanalysis/preproc/SelectTop.java | 49 +++-- .../mixcr/cli/CommandPaExportTest.java | 9 + .../DownsamplingPreprocessorTest.java | 3 +- .../OverlapDownsamplingPreprocessorTest.java | 3 +- .../preproc/PreprocessorChainTest.java | 24 ++- .../postanalysis/preproc/SelectTopTest.java | 6 +- 28 files changed, 687 insertions(+), 135 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java index 1165dd63b..3b1b678d5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java @@ -221,8 +221,7 @@ public void run0() throws Exception { separator = " ", description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") public static class CommandIndividual extends CommandPa { - public CommandIndividual() { - } + public CommandIndividual() {} @Override @SuppressWarnings({"unchecked", "rawtypes"}) @@ -439,8 +438,9 @@ private SetPreprocessorFactory> getPreprocessor(OverlapType return new OverlapPreprocessorAdapter.Factory<>(preprocessors.get(type).filterFirst(new ElementPredicate.IncludeChains(chain))); } + //fixme only productive?? public List> getCharacteristics(int i, int j, Chains chain) { - return groupped.entrySet().stream().map(e -> new OverlapCharacteristic<>("overlap_" + i + "_" + j + e.getValue().stream().map(t -> t.name).collect(Collectors.joining("_")), weight, + return groupped.entrySet().stream().map(e -> new OverlapCharacteristic<>("overlap_" + i + "_" + j + " / " + e.getValue().stream().map(t -> t.name).collect(Collectors.joining(" / ")), weight, new OverlapPreprocessorAdapter.Factory<>(e.getKey().filterFirst(new ElementPredicate.IncludeChains(chain))), e.getValue().toArray(new OverlapType[0]), i, j)).collect(toList()); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 7acd52620..de883ca21 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -7,6 +7,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.CommandPa.PaResult; import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; import com.milaboratory.mixcr.postanalysis.plots.*; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; @@ -71,22 +72,54 @@ public void run0() throws Exception { abstract void run(Chains.NamedChains chains, PaResultByChain result); - @CommandLine.Command(name = "tables", - sortOptions = false, - separator = " ", - description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") - public static final class ExportTables extends CommandPaExport { - @Parameters(index = "1", description = "Output directory") + private abstract static class ExportTablesBase extends CommandPaExport { + @Parameters(index = "1", description = "Output path") public String out; + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".tsv") && !out.endsWith(".csv")) + throwValidationException("Output file must have .tsv or .csv extension"); + } + + Path outDir() { + return Path.of(out).toAbsolutePath().getParent(); + } + + String outPrefix() { + String fName = Path.of(out).getFileName().toString(); + return fName.substring(0, fName.length() - 4); + } + + String outExtension(Chains.NamedChains chains) { + return "." + chains.name + "." + out.substring(out.length() - 3); + } + + String separator() { + return out.endsWith("tsv") ? "\t" : ","; + } + @Override void run(Chains.NamedChains chains, PaResultByChain result) { - Path p = Path.of(out).toAbsolutePath(); try { - Files.createDirectories(p); + Files.createDirectories(outDir()); } catch (IOException e) { throw new RuntimeException(e); } + run1(chains, result); + } + + abstract void run1(Chains.NamedChains chains, PaResultByChain result); + } + + @CommandLine.Command(name = "tables", + sortOptions = false, + separator = " ", + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") + public static final class ExportTables extends ExportTablesBase { + @Override + void run1(Chains.NamedChains chains, PaResultByChain result) { for (CharacteristicGroup table : result.schema.tables) { writeTables(chains, result.result.getTable(table)); } @@ -94,8 +127,20 @@ void run(Chains.NamedChains chains, PaResultByChain result) { void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { for (CharacteristicGroupOutputExtractor view : tableResult.group.views) - for (OutputTable t : view.getTables(tableResult).values()) - t.writeCSV(Path.of(out).toAbsolutePath(), "", "\t", "." + chain.name + ".tsv"); + for (OutputTable t : view.getTables(tableResult).values()) { + t.writeCSV(outDir(), outPrefix() + ".", separator(), outExtension(chain)); + } + } + } + + @CommandLine.Command(name = "preprocSummary", + sortOptions = false, + separator = " ", + description = "Export preprocessing summary tables.") + public static final class ExportPreprocessingSummary extends ExportTablesBase { + @Override + void run1(Chains.NamedChains chains, PaResultByChain result) { + SetPreprocessorSummary.writeToCSV(outDir().resolve(outPrefix() + outExtension(chains)), result.result.preprocSummary, "\t"); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 847154157..b858afa8b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -74,9 +74,7 @@ protected List handle(ParseResult parseResult) throws CommandLine.Execut return new ArrayList<>(); } return super.handle(parseResult); - } catch (ParameterException ex) { - throw ex; - } catch (CommandLine.ExecutionException ex) { + } catch (ParameterException | CommandLine.ExecutionException ex) { throw ex; } catch (Exception ex) { throw new CommandLine.ExecutionException(commandLine, @@ -198,6 +196,7 @@ public static CommandLine mkCmd() { cmd.getSubcommands() .get("exportPa") .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExport.ExportTables.class)) + .addSubcommand("preprocSummary", CommandSpec.forAnnotatedObject(CommandPaExport.ExportPreprocessingSummary.class)) .addSubcommand("listMetrics", CommandSpec.forAnnotatedObject(CommandPaExport.ListMetrics.class)) .addSubcommand("biophysics", CommandSpec.forAnnotatedObject(CommandPaExport.ExportBiophysics.class)) .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandPaExport.ExportDiversity.class)) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index 7184d8bf8..3e72eccc8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -26,20 +26,26 @@ public class PostanalysisResult { /** Characteristic Id -> characteristic data */ @JsonProperty("data") public final Map data; + /** Preprocessor Id -> Preprocessors summary */ + @JsonProperty("preprocSummary") + public final Map preprocSummary; @JsonCreator public PostanalysisResult(@JsonProperty("datasetIds") Set datasetIds, - @JsonProperty("data") Map data) { + @JsonProperty("data") Map data, + @JsonProperty("preprocSummary") Map preprocSummary) { this.datasetIds = datasetIds; this.data = data; + this.preprocSummary = preprocSummary; } static PostanalysisResult create(Set datasetIds, - Map, Map[]>> data) { + Map, Map[]>> data, + Map preprocSummary) { Map d = new HashMap<>(); for (Map.Entry, Map[]>> e : data.entrySet()) d.put(e.getKey().name, new Array2d(e.getValue())); - return new PostanalysisResult(datasetIds, d); + return new PostanalysisResult(datasetIds, d, preprocSummary); } /** cached results for char groups */ @@ -47,10 +53,14 @@ static PostanalysisResult create(Set datasetIds, /** project result on a specific char group */ public PostanalysisResult forGroup(CharacteristicGroup group) { - return new PostanalysisResult(datasetIds, + return new PostanalysisResult( + datasetIds, group.characteristics.stream() .map(c -> c.name) - .collect(Collectors.toMap(c -> c, data::get))); + .collect(Collectors.toMap(c -> c, data::get)), + group.characteristics.stream() + .map(c -> c.name) + .collect(Collectors.toMap(c -> c, preprocSummary::get))); } /** project result on a specific char group */ diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index 0a3ef16dd..d6d230978 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -3,10 +3,13 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.InputPort; import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapDataset; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.util.CanReportProgressAndStage; +import gnu.trove.iterator.TIntObjectIterator; import gnu.trove.list.array.TIntArrayList; +import gnu.trove.map.hash.TIntObjectHashMap; import java.util.*; import java.util.stream.Collectors; @@ -76,7 +79,7 @@ public PostanalysisResult run(Dataset... datasets) { Map, SetPreprocessor> distinctProcs = new HashMap<>(); Map, TIntArrayList> proc2char = new IdentityHashMap<>(); for (Characteristic ch : characteristics) { - id2proc.put(ch.name, distinctProcs.computeIfAbsent(ch.preprocessor, __ -> ch.preprocessor.getInstance())); + id2proc.put(ch.name, distinctProcs.computeIfAbsent(ch.preprocessor, __ -> ch.preprocessor.newInstance())); SetPreprocessor proc = distinctProcs.get(ch.preprocessor); proc2char.computeIfAbsent(proc, __ -> new TIntArrayList()).add(char2idx.get(ch)); } @@ -166,6 +169,27 @@ public PostanalysisResult run(Dataset... datasets) { Set datasetIds = Arrays.stream(datasets) .map(Dataset::id) .collect(Collectors.toCollection(LinkedHashSet::new)); - return PostanalysisResult.create(datasetIds, result); + + // collect summary by preprocessor + Map preprocResult = procs.stream().collect(Collectors.toMap(SetPreprocessor::id, p -> { + TIntObjectHashMap> stat = p.getStat(); + List datasetIdsActual; + if (datasets.length == 1 && datasets[0] instanceof OverlapDataset) { + datasetIdsActual = ((OverlapDataset) datasets[0]).datasetIds; + } else { + datasetIdsActual = Arrays + .stream(datasets) + .map(Dataset::id) + .collect(Collectors.toList()); + } + Map> r = new HashMap<>(); + TIntObjectIterator> it = stat.iterator(); + while (it.hasNext()) { + it.advance(); + r.put(datasetIdsActual.get(it.key()), it.value()); + } + return new SetPreprocessorSummary(r); + })); + return PostanalysisResult.create(datasetIds, result, preprocResult); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index 7381e525c..fdf469bfc 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -1,5 +1,9 @@ package com.milaboratory.mixcr.postanalysis; +import gnu.trove.map.hash.TIntObjectHashMap; + +import java.util.List; + /** * */ @@ -8,7 +12,11 @@ public interface SetPreprocessor { MappingFunction getMapper(int iDataset); - default SetPreprocessorStat getStat() { - return null; - } + /** + * Returns statistics per dataset or null if the dataset was excluded as result of preprocessing + */ + TIntObjectHashMap> getStat(); + + /** Id from {@link SetPreprocessorFactory#id()} */ + String id(); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java index 81c4e6011..fd674f415 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java @@ -36,11 +36,10 @@ }) @JsonIgnoreProperties(ignoreUnknown = true) public interface SetPreprocessorFactory { - SetPreprocessor getInstance(); + SetPreprocessor newInstance(); - default String[] description() { - return new String[0]; - } + /** Descriptive unique identifier */ + String id(); @SuppressWarnings("unchecked") default SetPreprocessorFactory filter(boolean before, ElementPredicate... predicates) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java index 9c48d95ed..8ae36078a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java @@ -8,5 +8,5 @@ public interface SetPreprocessorSetup { void initialize(int nDatasets); - InputPort consumer(int i); + InputPort consumer(int iDataset); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java index aa2a62bc1..fe298466b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java @@ -1,6 +1,174 @@ package com.milaboratory.mixcr.postanalysis; -/** - * - */ -public interface SetPreprocessorStat {} +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.google.common.util.concurrent.AtomicDouble; +import gnu.trove.iterator.TIntObjectIterator; +import gnu.trove.map.hash.TIntObjectHashMap; + +import java.util.Collections; +import java.util.List; +import java.util.Objects; +import java.util.concurrent.atomic.AtomicBoolean; +import java.util.concurrent.atomic.AtomicLong; +import java.util.stream.Collectors; + +public class SetPreprocessorStat { + @JsonProperty("preprocId") + public final String preprocId; + @JsonProperty("dropped") + public final boolean dropped; + @JsonProperty("nElementsBefore") + public final long nElementsBefore; + @JsonProperty("nElementsAfter") + public final long nElementsAfter; + @JsonProperty("sumWeightBefore") + public final double sumWeightBefore; + @JsonProperty("sumWeightAfter") + public final double sumWeightAfter; + + @JsonCreator + public SetPreprocessorStat(@JsonProperty("preprocId") String preprocId, + @JsonProperty("dropped") boolean dropped, + @JsonProperty("nElementsBefore") long nElementsBefore, + @JsonProperty("nElementsAfter") long nElementsAfter, + @JsonProperty("sumWeightBefore") double sumWeightBefore, + @JsonProperty("sumWeightAfter") double sumWeightAfter) { + this.preprocId = preprocId; + this.dropped = dropped; + this.nElementsBefore = nElementsBefore; + this.nElementsAfter = nElementsAfter; + this.sumWeightBefore = sumWeightBefore; + this.sumWeightAfter = sumWeightAfter; + } + + public SetPreprocessorStat(String preprocId, + long nElementsBefore, + long nElementsAfter, + double sumWeightBefore, + double sumWeightAfter) { + this.preprocId = preprocId; + this.dropped = false; + this.nElementsBefore = nElementsBefore; + this.nElementsAfter = nElementsAfter; + this.sumWeightBefore = sumWeightBefore; + this.sumWeightAfter = sumWeightAfter; + } + + public SetPreprocessorStat(String preprocId) { + this(preprocId, true, -1, -1, Double.NaN, Double.NaN); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SetPreprocessorStat that = (SetPreprocessorStat) o; + return dropped == that.dropped && nElementsBefore == that.nElementsBefore && nElementsAfter == that.nElementsAfter && Double.compare(that.sumWeightBefore, sumWeightBefore) == 0 && Double.compare(that.sumWeightAfter, sumWeightAfter) == 0 && Objects.equals(preprocId, that.preprocId); + } + + @Override + public int hashCode() { + return Objects.hash(preprocId, dropped, nElementsBefore, nElementsAfter, sumWeightBefore, sumWeightAfter); + } + + public static SetPreprocessorStat cumulative(List stats) { + SetPreprocessorStat first = stats.get(0); + SetPreprocessorStat last = stats.get(stats.size() - 1); + return new SetPreprocessorStat( + stats.stream().map(s -> s.preprocId).collect(Collectors.joining("_")), + first.nElementsBefore, + last.nElementsAfter, + first.sumWeightBefore, + last.sumWeightAfter); + } + + private static final class BuilderForSample { + final String preprocId; + final AtomicBoolean dropped = new AtomicBoolean(false); + final AtomicLong nElementsBefore = new AtomicLong(0); + final AtomicLong nElementsAfter = new AtomicLong(0); + final AtomicDouble sumWeightBefore = new AtomicDouble(0); + final AtomicDouble sumWeightAfter = new AtomicDouble(0); + final WeightFunction wtFunc; + + public BuilderForSample(String preprocId, WeightFunction wtFunc) { + this.preprocId = preprocId; + this.wtFunc = wtFunc; + } + + public void before(T t) { + nElementsBefore.incrementAndGet(); + sumWeightBefore.addAndGet(wtFunc.weight(t)); + } + + public void after(T t) { + nElementsAfter.incrementAndGet(); + sumWeightAfter.addAndGet(wtFunc.weight(t)); + } + + public void drop() { + dropped.set(true); + } + + public SetPreprocessorStat build() { + return new SetPreprocessorStat( + preprocId, + dropped.get(), + nElementsBefore.get(), + nElementsAfter.get(), + sumWeightBefore.get(), + sumWeightAfter.get() + ); + } + } + + public static final class Builder { + final String preprocId; + final TIntObjectHashMap> map = new TIntObjectHashMap<>(); + final WeightFunction wtFunc; + + public Builder(String preprocId, + WeightFunction wtFunc) { + this.preprocId = preprocId; + this.wtFunc = wtFunc; + } + + private BuilderForSample builder(int iDataset) { + BuilderForSample b = map.get(iDataset); + if (b == null) + map.put(iDataset, b = new BuilderForSample<>(preprocId, wtFunc)); + return b; + } + + public void drop(int iDataset) { + builder(iDataset).drop(); + } + + public void before(int iDataset, T t) { + builder(iDataset).before(t); + } + + public void after(int iDataset, T t) { + builder(iDataset).after(t); + } + + public SetPreprocessorStat getStat(int iDataset) { + BuilderForSample b = map.get(iDataset); + if (b == null) + return new SetPreprocessorStat(preprocId); + return b.build(); + } + + public TIntObjectHashMap> getStatMap() { + TIntObjectHashMap> r = new TIntObjectHashMap<>(); + TIntObjectIterator> it = map.iterator(); + while (it.hasNext()) { + it.advance(); + r.put(it.key(), Collections.singletonList(it.value().build())); + } + return r; + } + } +} + diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java new file mode 100644 index 000000000..ab969a1e6 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java @@ -0,0 +1,121 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + +import java.io.BufferedWriter; +import java.io.FileWriter; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.StandardOpenOption; +import java.util.*; + + +public class SetPreprocessorSummary { + /** SampleId -> (Preproc -> Stat) */ + @JsonProperty("result") + public final Map> result; + + @JsonCreator + public SetPreprocessorSummary(@JsonProperty("result") Map> result) { + this.result = result; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SetPreprocessorSummary that = (SetPreprocessorSummary) o; + return Objects.equals(result, that.result); + } + + @Override + public int hashCode() { + return Objects.hash(result); + } + + public static void writeToCSV(Path file, + Map preprocSummary, + String sep) { + List> rows = new ArrayList<>(); + for (Map.Entry e : preprocSummary.entrySet()) { + String preprocId = e.getKey(); + SetPreprocessorSummary chSummay = e.getValue(); + for (Map.Entry> ee : chSummay.result.entrySet()) { + String sample = ee.getKey(); + List stats = ee.getValue(); + if (stats == null) + continue; + List row = new ArrayList<>(); + row.add(sample); + row.add(preprocId); + addStat(row, SetPreprocessorStat.cumulative(stats)); + for (SetPreprocessorStat stat : stats) { + row.add(stat.preprocId); + addStat(row, stat); + } + rows.add(row); + } + } + + int nCols = rows.stream().mapToInt(List::size).max().orElse(0); + for (List row : rows) { + if (row.size() < nCols) + row.addAll(Collections.nCopies(nCols - row.size(), "")); + } + + List header = new ArrayList<>(); + header.add("sample"); + for (int i = 0; i < (nCols - 1) / 5; i++) { + String suff; + if (i == 0) + suff = ""; + else + suff = "#" + i; + + header.add("preprocessor" + suff); + header.add("nElementsBefore" + suff); + header.add("sumWeightBefore" + suff); + header.add("nElementsAfter" + suff); + header.add("sumWeightAfter" + suff); + } + + try (BufferedWriter writer = Files.newBufferedWriter(file, StandardOpenOption.CREATE)) { + for (int i = 0; ; i++) { + writer.write(header.get(i)); + if (i == header.size() - 1) + break; + writer.write(sep); + } + writer.write("\n"); + + for (int i = 0; ; i++) { + for (int j = 0; ; j++) { + writer.write(rows.get(i).get(j).toString()); + if (j == rows.get(i).size() - 1) + break; + writer.write(sep); + } + if (i == rows.size() - 1) + break; + writer.write("\n"); + } + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + private static void addStat(List row, SetPreprocessorStat stat) { + if (stat.dropped) { + for (int i = 0; i < 4; i++) { + row.add("na"); + } + } else { + row.add(stat.nElementsBefore); + row.add(stat.sumWeightBefore); + row.add(stat.nElementsAfter); + row.add(stat.sumWeightAfter); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java index a9a918c74..98f7ea973 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java @@ -15,6 +15,7 @@ @JsonSubTypes({ @JsonSubTypes.Type(value = WeightFunctions.Count.class, name = "count"), @JsonSubTypes.Type(value = WeightFunctions.NoWeight.class, name = "none"), + @JsonSubTypes.Type(value = WeightFunctions.DefaultWtFunction.class, name = "default"), }) public interface WeightFunction { double weight(T t); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java index 1a85de5cf..7c19db35e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java @@ -29,6 +29,7 @@ public int hashCode() { } } + @SuppressWarnings("rawtypes") public static final NoWeight NoWeight = new NoWeight(); public static final class NoWeight implements WeightFunction { @@ -49,4 +50,28 @@ public int hashCode() { return 11; } } + + public static WeightFunction Default() {return new DefaultWtFunction();} + + public static class DefaultWtFunction implements WeightFunction { + @Override + public double weight(T o) { + if (o instanceof Clone) + return ((Clone) o).getCount(); + else + throw new RuntimeException(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + return true; + } + + @Override + public int hashCode() { + return 12; + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java index 4465e4090..57e976446 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java @@ -31,18 +31,15 @@ public ClonesDownsamplingPreprocessorFactory(@JsonProperty("downsampleValueChoos } @Override - public String[] description() { - String ch = downsampleValueChooser.description(); - if (ch == null || ch.isEmpty()) - return new String[0]; - return new String[]{ch}; + public String id() { + return "Downsample " + downsampleValueChooser.id(); } @Override - public SetPreprocessor getInstance() { + public SetPreprocessor newInstance() { return new DownsamplingPreprocessor<>( c -> Math.round(c.getCount()), - Clone::setCount, downsampleValueChooser, seed); + Clone::setCount, downsampleValueChooser, seed, id()); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java index 01f3c1e52..73fd16dcc 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java @@ -3,6 +3,7 @@ import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonSubTypes; import com.fasterxml.jackson.annotation.JsonTypeInfo; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; import org.apache.commons.math3.stat.descriptive.rank.Percentile; import java.util.Arrays; @@ -26,9 +27,8 @@ public interface DownsampleValueChooser { long compute(long[] totalCounts); - default String description() { - return ""; - } + /** Used for {@link SetPreprocessorFactory#id()} */ + default String id() {return "";} class Fixed implements DownsampleValueChooser { public long value; @@ -40,8 +40,8 @@ public Fixed(long value) { } @Override - public String description() { - return "Downsample to a fixed count = " + value; + public String id() { + return "to count " + value; } @Override @@ -65,8 +65,8 @@ public int hashCode() { class Minimal implements DownsampleValueChooser { @Override - public String description() { - return "Downsample to the minimal dataset"; + public String id() { + return "to minimal count"; } @Override @@ -101,8 +101,9 @@ public Auto(double quantile, double scale, long threshold) { } @Override - public String description() { - return String.format("Downsample to the min(%s * percentile(%s), %s))", scale, quantile, threshold); + public String id() { +// return String.format("min(%s*percentile(%s),%s))", scale, quantile, threshold); + return "automatic"; } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index 7f41e7d63..5a6299edb 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -6,10 +6,14 @@ import com.milaboratory.mixcr.postanalysis.MappingFunction; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat; import gnu.trove.list.array.TLongArrayList; +import gnu.trove.map.hash.TIntObjectHashMap; import org.apache.commons.math3.random.RandomGenerator; import org.apache.commons.math3.random.Well19937c; +import java.util.Collections; +import java.util.List; import java.util.concurrent.atomic.AtomicInteger; import java.util.function.BiFunction; import java.util.function.ToLongFunction; @@ -26,18 +30,24 @@ public class DownsamplingPreprocessor implements SetPreprocessor { public final DownsampleValueChooser downsampleValueChooser; @JsonProperty("seed") public final long seed; + final String id; + private final SetPreprocessorStat.Builder stats; public DownsamplingPreprocessor(ToLongFunction getCount, BiFunction setCount, - DownsampleValueChooser downsampleValueChooser, long seed) { + DownsampleValueChooser downsampleValueChooser, + long seed, + String id) { this.getCount = getCount; this.setCount = setCount; this.downsampleValueChooser = downsampleValueChooser; this.seed = seed; + this.id = id; + this.stats = new SetPreprocessorStat.Builder<>(id, getCount::applyAsLong); } public String[] description() { - String ch = downsampleValueChooser.description(); + String ch = downsampleValueChooser.id(); if (ch == null || ch.isEmpty()) return new String[0]; return new String[]{ch}; @@ -59,8 +69,10 @@ public MappingFunction getMapper(int iDataset) { if (downsampling == -1) downsampling = downsampleValueChooser.compute(setup.counts); - if (downsampling > setup.counts[iDataset]) + if (downsampling > setup.counts[iDataset]) { + stats.drop(iDataset); return t -> null; + } long[] counts = setup.countLists[iDataset].toArray(); RandomGenerator rnd = new Well19937c(seed); @@ -68,13 +80,25 @@ public MappingFunction getMapper(int iDataset) { AtomicInteger idx = new AtomicInteger(0); return t -> { + stats.before(iDataset, t); int i = idx.getAndIncrement(); if (countsDownsampled[i] == 0) return null; + stats.after(iDataset, t); return setCount.apply(t, countsDownsampled[i]); }; } + @Override + public TIntObjectHashMap> getStat() { + return stats.getStatMap(); + } + + @Override + public String id() { + return id; + } + class ComputeCountsStep implements SetPreprocessorSetup { long[] counts; TLongArrayList[] countLists; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java index 91c357550..a63b06887 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java @@ -60,15 +60,15 @@ public void consume(OverlapGroup obj) { public MetricValue>[] result() { List>> result = new ArrayList<>(); if (types.contains(OverlapType.D)) - result.add(new MetricValue<>(key(OverlapType.D, id1, id2), 1.0 * diversityIntersection / diversity1 / diversity2)); + result.add(new MetricValue<>(key(OverlapType.D, id1, id2), safeDiv(diversityIntersection, diversity1 * diversity2))); if (types.contains(OverlapType.SharedClonotypes)) result.add(new MetricValue<>(key(OverlapType.SharedClonotypes, id1, id2), 1.0 * diversityIntersection)); if (types.contains(OverlapType.F1)) - result.add(new MetricValue<>(key(OverlapType.F1, id1, id2), Math.sqrt(sumS1Intersection * sumS2Intersection / sumS1 / sumS2))); + result.add(new MetricValue<>(key(OverlapType.F1, id1, id2), Math.sqrt(safeDiv(sumS1Intersection * sumS2Intersection, sumS1 * sumS2)))); if (types.contains(OverlapType.F2)) - result.add(new MetricValue<>(key(OverlapType.F2, id1, id2), sumSqProduct / Math.sqrt(sumS1 * sumS2))); + result.add(new MetricValue<>(key(OverlapType.F2, id1, id2), safeDiv(sumSqProduct, Math.sqrt(sumS1 * sumS2)))); if (types.contains(OverlapType.Jaccard)) - result.add(new MetricValue<>(key(OverlapType.Jaccard, id1, id2), 1.0 * diversityIntersection / (diversity1 + diversity2 - diversityIntersection))); + result.add(new MetricValue<>(key(OverlapType.Jaccard, id1, id2), safeDiv(diversityIntersection, (diversity1 + diversity2 - diversityIntersection)))); if (types.contains(OverlapType.R_Intersection)) result.add(new MetricValue<>(key(OverlapType.R_Intersection, id1, id2), regressionIntersection.getR())); if (types.contains(OverlapType.R_All)) @@ -77,6 +77,10 @@ public MetricValue>[] result() { return result.toArray(new MetricValue[0]); } + private static double safeDiv(double num, double den) { + return num == 0.0 ? 0.0 : num / den; + } + private static OverlapKey key(OverlapType type, String i, String j) { return new OverlapKey<>(type, i, j); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java index 67de7246b..9a5a544d0 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java @@ -16,6 +16,6 @@ public OverlapDataset(List datasetIds) { @Override public String id() { - return String.join("_", datasetIds); + return "overlap"; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java index 1c7b21011..51b86c9da 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java @@ -19,9 +19,7 @@ @JsonSubTypes.Type(value = ElementPredicate.IncludeChains.class, name = "includesChains"), }) public interface ElementPredicate extends Predicate { - default String description() { - return ""; - } + String id(); @JsonAutoDetect final class NoOutOfFrames implements ElementPredicate { @@ -34,8 +32,8 @@ public NoOutOfFrames(@JsonProperty("feature") GeneFeature feature) { } @Override - public String description() { - return "Exclude out-of-frames"; + public String id() { + return "OOF in " + GeneFeature.encode(feature); } @Override @@ -68,11 +66,10 @@ public NoStops(@JsonProperty("feature") GeneFeature feature) { } @Override - public String description() { - return "Exclude stop-codons in " + GeneFeature.encode(feature); + public String id() { + return "stops in " + GeneFeature.encode(feature); } - @Override public boolean test(Clone clone) { return !clone.containsStops(feature); @@ -102,8 +99,8 @@ public IncludeChains(@JsonProperty("chains") Chains chains) { } @Override - public String description() { - return "Select chains: " + chains; + public String id() { + return chains + " chains"; } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index 27fc55445..79e83f09a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -2,23 +2,26 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.MappingFunction; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; +import com.milaboratory.mixcr.postanalysis.*; +import gnu.trove.map.hash.TIntObjectHashMap; import java.util.Arrays; import java.util.List; import java.util.Objects; +import java.util.stream.Collectors; /** * */ public class FilterPreprocessor implements SetPreprocessor { final List> predicates; + final String id; + final SetPreprocessorStat.Builder stats; - FilterPreprocessor(@JsonProperty("predicates") List> predicates) { + public FilterPreprocessor(List> predicates, String id) { this.predicates = predicates; + this.id = id; + this.stats = new SetPreprocessorStat.Builder<>(id, WeightFunctions.Default()); } @Override @@ -28,7 +31,23 @@ public SetPreprocessorSetup nextSetupStep() { @Override public MappingFunction getMapper(int iDataset) { - return t -> predicates.stream().allMatch(p -> p.test(t)) ? t : null; + return t -> { + stats.before(iDataset, t); + if (!predicates.stream().allMatch(p -> p.test(t))) + return null; + stats.after(iDataset, t); + return t; + }; + } + + @Override + public TIntObjectHashMap> getStat() { + return stats.getStatMap(); + } + + @Override + public String id() { + return id; } public static final class Factory implements SetPreprocessorFactory { @@ -40,23 +59,21 @@ public Factory(@JsonProperty("predicates") List> predicates) this.predicates = predicates; } + @SafeVarargs public Factory(ElementPredicate... predicates) { this(Arrays.asList(predicates)); } @Override - public String[] description() { - return predicates.stream() - .map(ElementPredicate::description) - .filter(Objects::nonNull) - .filter(s -> !s.isEmpty()) - .map(f -> "Filter: " + f) - .toArray(String[]::new); + public String id() { + return "Filter " + predicates.stream() + .map(ElementPredicate::id) + .collect(Collectors.joining(", ")); } @Override - public SetPreprocessor getInstance() { - return new FilterPreprocessor<>(predicates); + public SetPreprocessor newInstance() { + return new FilterPreprocessor<>(predicates, id()); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java index 1bf65091f..56429b816 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java @@ -1,10 +1,11 @@ package com.milaboratory.mixcr.postanalysis.preproc; -import com.milaboratory.mixcr.postanalysis.MappingFunction; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; +import com.milaboratory.mixcr.postanalysis.*; +import gnu.trove.map.hash.TIntObjectHashMap; + +import java.util.Collections; +import java.util.List; /** * @@ -24,18 +25,39 @@ public MappingFunction getMapper(int iDataset) { return MappingFunction.identity(); } + @Override + public TIntObjectHashMap> getStat() { + //noinspection ExternalizableWithoutPublicNoArgConstructor + return new TIntObjectHashMap<>() { + @Override + public List get(int key) { + return Collections.emptyList(); + } + }; + } + + @Override + public String id() { + return factory().id(); + } + public static final Factory factory = new Factory<>(); @SuppressWarnings("unchecked") - public static Factory factory() { return (Factory) factory; } + public static Factory factory() {return (Factory) factory;} public static final class Factory implements SetPreprocessorFactory { @SuppressWarnings("unchecked") @Override - public SetPreprocessor getInstance() { + public SetPreprocessor newInstance() { return (SetPreprocessor) NoPreprocessing.instance; } + @Override + public String id() { + return "NoPreprocessing"; + } + @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java index 39f4853fc..2e5c00e7a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java @@ -2,11 +2,9 @@ import cc.redberry.pipe.InputPort; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.MappingFunction; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; +import com.milaboratory.mixcr.postanalysis.*; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import gnu.trove.map.hash.TIntObjectHashMap; import java.util.ArrayList; import java.util.List; @@ -98,6 +96,16 @@ public MappingFunction> getMapper(int iOverlap) { }; } + @Override + public TIntObjectHashMap> getStat() { + return inner.getStat(); + } + + @Override + public String id() { + return inner.id(); + } + public static final class Factory implements SetPreprocessorFactory> { @JsonProperty("inner") public final SetPreprocessorFactory inner; @@ -107,13 +115,13 @@ public Factory(@JsonProperty("inner") SetPreprocessorFactory inner) { } @Override - public String[] description() { - return inner.description(); + public String id() { + return inner.id(); } @Override - public SetPreprocessor> getInstance() { - return new OverlapPreprocessorAdapter<>(inner.getInstance()); + public SetPreprocessor> newInstance() { + return new OverlapPreprocessorAdapter<>(inner.newInstance()); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index 6eac6c0d8..29eb9d497 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -3,26 +3,33 @@ import cc.redberry.pipe.InputPort; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.postanalysis.MappingFunction; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; +import com.milaboratory.mixcr.postanalysis.*; +import gnu.trove.iterator.TIntObjectIterator; +import gnu.trove.map.hash.TIntObjectHashMap; +import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Objects; import java.util.concurrent.atomic.AtomicReference; import java.util.function.Function; import java.util.stream.Collectors; +import java.util.stream.Stream; /** * */ public class PreprocessorChain implements SetPreprocessor { final List> chain; - - public PreprocessorChain(List> chain) { - this.chain = chain; + final String id; + + public PreprocessorChain(List> chain, String id) { + this.chain = chain.stream().flatMap(c -> + c instanceof PreprocessorChain + ? ((PreprocessorChain) c).chain.stream() + : Stream.of(c)) + .collect(Collectors.toList()); + this.id = id; } private final AtomicReference>> mapperRef = new AtomicReference<>(i -> t -> t); @@ -104,6 +111,31 @@ public MappingFunction getMapper(int iDataset) { return mapper.apply(iDataset); } + @Override + public TIntObjectHashMap> getStat() { + TIntObjectHashMap> r = new TIntObjectHashMap<>(); + for (TIntObjectHashMap> stat : + chain.stream().map(SetPreprocessor::getStat).collect(Collectors.toList())) { + + TIntObjectIterator> it = stat.iterator(); + while (it.hasNext()) { + it.advance(); + List l = r.get(it.key()); + if (l == null) { + r.put(it.key(), l = new ArrayList<>()); + } + l.addAll(it.value()); + } + } + + return r; + } + + @Override + public String id() { + return id; + } + public static final class Factory implements SetPreprocessorFactory { @JsonProperty("chain") public final List> chain; @@ -113,25 +145,23 @@ public Factory(@JsonProperty("chain") List> chain) { this.chain = chain; } + @SafeVarargs public Factory(SetPreprocessorFactory... chain) { this(Arrays.asList(chain)); } @Override - public String[] description() { + public String id() { return chain.stream() - .map(SetPreprocessorFactory::description) - .filter(Objects::nonNull) - .flatMap(Arrays::stream) - .filter(s -> !s.isEmpty()) - .toArray(String[]::new); + .map(SetPreprocessorFactory::id) + .collect(Collectors.joining(" | ")); } @Override - public SetPreprocessor getInstance() { + public SetPreprocessor newInstance() { return new PreprocessorChain<>(chain.stream() - .map(SetPreprocessorFactory::getInstance) - .collect(Collectors.toList())); + .map(SetPreprocessorFactory::newInstance) + .collect(Collectors.toList()), id()); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java index b1cf1387d..454de29de 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java @@ -4,9 +4,11 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.postanalysis.*; import gnu.trove.impl.Constants; +import gnu.trove.map.hash.TIntObjectHashMap; import gnu.trove.map.hash.TLongLongHashMap; import java.util.Arrays; +import java.util.List; import java.util.Objects; import static java.lang.Math.round; @@ -18,10 +20,13 @@ public class SelectTop implements SetPreprocessor { final WeightFunction weight; final double abundanceFraction; final int numberOfTop; + final String id; + final SetPreprocessorStat.Builder stats; SelectTop(WeightFunction weight, double abundanceFraction, - int numberOfTop) { + int numberOfTop, + String id) { if (!Double.isNaN(abundanceFraction) && (abundanceFraction <= 0 || abundanceFraction > 1.0)) throw new IllegalArgumentException(); if (numberOfTop != -1 && numberOfTop <= 0) @@ -30,6 +35,8 @@ public class SelectTop implements SetPreprocessor { this.weight = weight; this.abundanceFraction = abundanceFraction; this.numberOfTop = numberOfTop; + this.id = id; + this.stats = new SetPreprocessorStat.Builder<>(id, WeightFunctions.Default()); } private boolean computeCumulativeTop() { @@ -53,10 +60,13 @@ public SetPreprocessorSetup nextSetupStep() { @Override public MappingFunction getMapper(int iDataset) { TLongLongHashMap hist = computeHists.downsampledHist(iDataset); - return t -> { - if (hist.isEmpty()) - return null; + if (hist.isEmpty()) { + stats.drop(iDataset); + return t -> null; + } + return t -> { + stats.before(iDataset, t); long wt = Math.round(this.weight.weight(t)); long n = hist.get(wt); if (n == -1) @@ -67,10 +77,21 @@ public MappingFunction getMapper(int iDataset) { else hist.adjustValue(wt, -1); + stats.after(iDataset, t); return t; }; } + @Override + public TIntObjectHashMap> getStat() { + return stats.getStatMap(); + } + + @Override + public String id() { + return id; + } + private class ComputeHists2 implements SetPreprocessorSetup { // weight -> n elements private TLongLongHashMap[] hists; @@ -173,19 +194,19 @@ public Factory(WeightFunction weight, int numberOfTop) { } @Override - public SetPreprocessor getInstance() { - return new SelectTop<>(weight, abundanceFraction, numberOfTop); + public SetPreprocessor newInstance() { + return new SelectTop<>(weight, abundanceFraction, numberOfTop, id()); } @Override - public String[] description() { - String s1 = Double.isNaN(abundanceFraction) ? null : "Select top clonotypes constituting " + (abundanceFraction * 100) + "% of reads"; - String s2 = numberOfTop == -1 ? null : "Select top " + numberOfTop + " clonotypes"; - if (s1 == null) - return new String[]{s2}; - else if (s2 == null) - return new String[]{s1}; - return new String[]{s1, s2,}; + public String id() { + String topAbundance = Double.isNaN(abundanceFraction) ? null : "Cumulative top " + (abundanceFraction * 100); + String topCount = numberOfTop == -1 ? null : "Top " + numberOfTop; + if (topAbundance == null) + return topCount; + else if (topCount == null) + return topAbundance; + return topAbundance + " | " + topCount; } @Override diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index c7f8500f4..07f39f6ef 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -49,4 +49,13 @@ public void test3() { "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap.pdf"); } + + @Test + public void test4() { + Main.main("exportPa", "preprocSummary", +// "--width", "2000", +// "--height", "5000", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/tables/preproc/overlap.tsv"); + } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index 515242a5c..ef6137fdc 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -102,7 +102,8 @@ public void test3() { t -> Math.round(t.weight), (t, w) -> new TestObject(t.value, 1d * w), dsChooser, - rng.nextLong(0, Long.MAX_VALUE / 2) + rng.nextLong(0, Long.MAX_VALUE / 2), + "" ); int nDatasets = 10; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index 6a8f89c6e..33051de1d 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -39,7 +39,8 @@ public void test1() { t -> Math.round(t.weight), (t, newW) -> new TestObject(t.value, newW), chooser, - System.currentTimeMillis() + System.currentTimeMillis(), + "" ); Dataset>[] downsampled = SetPreprocessorFactory.processDatasets(new OverlapPreprocessorAdapter<>(proc), datasets); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java index a4fab2289..6a88cd220 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java @@ -3,6 +3,7 @@ import cc.redberry.pipe.InputPort; import com.milaboratory.mixcr.postanalysis.*; import gnu.trove.list.array.TLongArrayList; +import gnu.trove.map.hash.TIntObjectHashMap; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; import org.junit.Assert; @@ -10,6 +11,7 @@ import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.Stream; @@ -37,7 +39,7 @@ public void test1() { RandomDataGenerator rng = new RandomDataGenerator(new Well512a(System.currentTimeMillis())); TestDataset ds = rndDataset(rng, 10000); - TestDataset r = new TestDataset<>(SetPreprocessorFactory.processDatasets(preproc.getInstance(), ds)[0]); + TestDataset r = new TestDataset<>(SetPreprocessorFactory.processDatasets(preproc.newInstance(), ds)[0]); List expected = new ArrayList<>(); for (TestObject c : ds) { @@ -56,9 +58,14 @@ public TestPreprocFactory(long modulus) { } @Override - public SetPreprocessor getInstance() { + public SetPreprocessor newInstance() { return new TestPreproc(modulus); } + + @Override + public String id() { + return ""; + } } public static final class TestPreproc implements SetPreprocessor { @@ -93,16 +100,29 @@ public InputPort consumer(int i) { } + private final SetPreprocessorStat.Builder stats = new SetPreprocessorStat.Builder<>("", t -> t.weight); + @Override public MappingFunction getMapper(int iDataset) { AtomicInteger idx = new AtomicInteger(0); return element -> { + stats.before(iDataset, element); if (l.get(idx.getAndIncrement()) % modulus == 0) return null; + stats.after(iDataset, element); return element; }; } + @Override + public TIntObjectHashMap> getStat() { + return stats.getStatMap(); + } + + @Override + public String id() { + return ""; + } } public static TestDataset rndDataset(RandomDataGenerator rng, int size) { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java index dd0170659..7c09f9f7d 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java @@ -55,7 +55,7 @@ public void test1() { break; } - SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1); + SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1, ""); Dataset topCumulative = SetPreprocessorFactory.processDatasets(cumulativeTopProc, dataset)[0]; double actualCum = 0; @@ -64,7 +64,7 @@ public void test1() { } Assert.assertEquals(expectedSumCum, actualCum, 1e-5); - SelectTop fixedTopProc = new SelectTop<>(o -> o.weight, Double.NaN, nTop); + SelectTop fixedTopProc = new SelectTop<>(o -> o.weight, Double.NaN, nTop, ""); Dataset topFixed = SetPreprocessorFactory.processDatasets(fixedTopProc, dataset)[0]; double actualFixed = 0; int actualNTop = 0; @@ -129,7 +129,7 @@ private void assertFraction(double topFraction, TestDataset dataset, ArrayList list = new ArrayList<>(dataset.data); list.sort(Comparator.comparing(t -> -t.weight)); - SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1); + SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1, ""); Dataset topCumulative = SetPreprocessorFactory.processDatasets(cumulativeTopProc, dataset)[0]; double actualCum = 0; From f031fdcc9112608a239b668756a3c5c9b026586d Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Thu, 17 Mar 2022 23:52:55 +0300 Subject: [PATCH 162/282] feat: add unit tests preparation hook --- .github/workflows/build.yaml | 8 ++++++++ .mi-ci/hooks/test-unit-before.sh | 9 +++++++++ 2 files changed, 17 insertions(+) create mode 100755 .mi-ci/hooks/test-unit-before.sh diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index b17ff8872..dc265e6ef 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -31,6 +31,14 @@ jobs: app-name: MiXCR app-name-slug: 'mixcr' + # Tests + test-unit: true + test-unit-before-tasks: shadowJar + + test-integration: true + test-integration-before-tasks: shadowJar + test-integration-tasks: '' + # Distribution dist-docker: false dist-archive: true diff --git a/.mi-ci/hooks/test-unit-before.sh b/.mi-ci/hooks/test-unit-before.sh new file mode 100755 index 000000000..297e183a6 --- /dev/null +++ b/.mi-ci/hooks/test-unit-before.sh @@ -0,0 +1,9 @@ +#!/usr/bin/env bash + +script_dir=$(dirname "${0}") + +# downloadable test data +"${script_dir}/../../ensure-test-data.sh" + +# builds predprocessed test data +"${script_dir}/../../prepare-test-data.sh" From 37da35fa67f4dff1dce5e3a62d167b38cf7e8eb4 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 18 Mar 2022 12:37:48 +0200 Subject: [PATCH 163/282] preprocessing summary --- build.gradle.kts | 6 +- .../mixcr/cli/CommandPaExport.java | 98 ++++++++++------ .../postanalysis/PostanalysisResult.java | 3 +- .../mixcr/postanalysis/plots/Overlap.kt | 43 +++++-- .../mixcr/postanalysis/plots/Preprocessing.kt | 107 ++++++++++++++++++ 5 files changed, 207 insertions(+), 50 deletions(-) create mode 100644 src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt diff --git a/build.gradle.kts b/build.gradle.kts index 69d676c78..ecfc05e78 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -76,7 +76,6 @@ repositories { } dependencies { - api("com.milaboratory:miplots:$miplotsVersion") api("com.milaboratory:milib:$milibVersion") api("io.repseq:repseqio:$repseqioVersion") { exclude("com.milaboratory", "milib") @@ -90,10 +89,13 @@ dependencies { implementation("info.picocli:picocli:4.1.1") implementation("com.google.guava:guava:30.1.1-jre") + api("com.milaboratory:miplots:$miplotsVersion") + implementation("com.itextpdf:itext7-core:7.2.1") + implementation("com.itextpdf:layout:7.2.1") + testImplementation("junit:junit:4.13.2") implementation(testFixtures("com.milaboratory:milib:$milibVersion")) testImplementation("org.mockito:mockito-all:1.9.5") - } val writeBuildProperties by tasks.registering(WriteProperties::class) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index de883ca21..085a5a7e1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -7,6 +7,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.CommandPa.PaResult; import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; import com.milaboratory.mixcr.postanalysis.plots.*; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; @@ -15,6 +16,7 @@ import com.milaboratory.mixcr.postanalysis.ui.OutputTable; import com.milaboratory.util.GlobalObjectMappers; import io.repseq.core.Chains; +import io.repseq.core.Chains.NamedChains; import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; @@ -60,17 +62,17 @@ PaResult getPaResult() { @Override public void run0() throws Exception { - Set set = chains == null + Set set = chains == null ? null : chains.stream().map(Chains::getNamedChains).collect(Collectors.toSet()); - for (Map.Entry r : getPaResult().results.entrySet()) { + for (Map.Entry r : getPaResult().results.entrySet()) { if (set == null || set.stream().anyMatch(c -> c.chains.intersects(r.getKey().chains))) run(r.getKey(), r.getValue()); } } - abstract void run(Chains.NamedChains chains, PaResultByChain result); + abstract void run(NamedChains chains, PaResultByChain result); private abstract static class ExportTablesBase extends CommandPaExport { @Parameters(index = "1", description = "Output path") @@ -92,7 +94,7 @@ String outPrefix() { return fName.substring(0, fName.length() - 4); } - String outExtension(Chains.NamedChains chains) { + String outExtension(NamedChains chains) { return "." + chains.name + "." + out.substring(out.length() - 3); } @@ -101,7 +103,7 @@ String separator() { } @Override - void run(Chains.NamedChains chains, PaResultByChain result) { + void run(NamedChains chains, PaResultByChain result) { try { Files.createDirectories(outDir()); } catch (IOException e) { @@ -110,22 +112,22 @@ void run(Chains.NamedChains chains, PaResultByChain result) { run1(chains, result); } - abstract void run1(Chains.NamedChains chains, PaResultByChain result); + abstract void run1(NamedChains chains, PaResultByChain result); } @CommandLine.Command(name = "tables", sortOptions = false, separator = " ", - description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype, Overlap") public static final class ExportTables extends ExportTablesBase { @Override - void run1(Chains.NamedChains chains, PaResultByChain result) { + void run1(NamedChains chains, PaResultByChain result) { for (CharacteristicGroup table : result.schema.tables) { writeTables(chains, result.result.getTable(table)); } } - void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tableResult) { + void writeTables(NamedChains chain, CharacteristicGroupResult tableResult) { for (CharacteristicGroupOutputExtractor view : tableResult.group.views) for (OutputTable t : view.getTables(tableResult).values()) { t.writeCSV(outDir(), outPrefix() + ".", separator(), outExtension(chain)); @@ -139,7 +141,7 @@ void writeTables(Chains.NamedChains chain, CharacteristicGroupResult tabl description = "Export preprocessing summary tables.") public static final class ExportPreprocessingSummary extends ExportTablesBase { @Override - void run1(Chains.NamedChains chains, PaResultByChain result) { + void run1(NamedChains chains, PaResultByChain result) { SetPreprocessorSummary.writeToCSV(outDir().resolve(outPrefix() + outExtension(chains)), result.result.preprocSummary, "\t"); } } @@ -192,7 +194,6 @@ static abstract class CommandPaExportPlots extends CommandPaExport { public int height = 0; @Option(names = {"--filter"}, description = "Filter by metadata. Possible filters column=value, column>=value etc.") public String filterByMetadata; - @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") public String out; @@ -221,12 +222,32 @@ DataFrame metadata() { : (metadata == null ? null : (metadataDf = MetadataKt.readMetadata(metadata))); } - void writePlots(Chains.NamedChains chains, List plots) { - ExportKt.writePDFFigure(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plots); + String plotDestStr(NamedChains chains) { + return out.substring(0, out.length() - 3) + chains.name + ".pdf"; + } + + Path plotDestPath(NamedChains chains) { + return Path.of(plotDestStr(chains)); + } + + String tablesDestStr(NamedChains chains) { + return out.substring(0, out.length() - 3) + "preproc." + chains.name + ".pdf"; + } + + Path tablesDestPath(NamedChains chains) { + return Path.of(tablesDestStr(chains)); + } + + void writeTables(NamedChains chains, List tables) { + ExportKt.writePDF(tablesDestPath(chains), tables); } - void writePlots(Chains.NamedChains chains, Plot plot) { - ExportKt.writePDF(Path.of(out.substring(0, out.length() - 3) + chains.name + ".pdf"), plot); + void writePlots(NamedChains chains, List plots) { + ExportKt.writePDFFigure(plotDestPath(chains), plots); + } + + void writePlots(NamedChains chains, Plot plot) { + ExportKt.writePDF(tablesDestPath(chains), plot); } } @@ -243,7 +264,7 @@ static abstract class ExportBasicStatistics extends CommandPaExportPlots { public List metrics; @Override - void run(Chains.NamedChains chains, PaResultByChain result) { + void run(NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(group()); DataFrame metadata = metadata(); @@ -319,7 +340,7 @@ static abstract class ExportGeneUsage extends ExportHeatmap { public List colorKey = new ArrayList<>(); @Override - void run(Chains.NamedChains chains, PaResultByChain result) { + void run(NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(group()); DataFrame metadata = metadata(); @@ -392,7 +413,7 @@ static class ExportVJUsage extends ExportHeatmap { public boolean noJDendro; @Override - void run(Chains.NamedChains chains, PaResultByChain result) { + void run(NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(CommandPa.VJUsage); DataFrame metadata = metadata(); @@ -442,12 +463,14 @@ DataFrame filterOverlap(DataFrame df) { } @Override - void run(Chains.NamedChains chains, PaResultByChain result) { + void run(NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(CommandPa.Overlap); - + PostanalysisResult paResult = result.result.forGroup(ch); DataFrame metadata = metadata(); + DataFrame df = Overlap.INSTANCE.dataFrame( - result.result.forGroup(ch), + ch, + paResult, metrics, metadata ); @@ -459,21 +482,25 @@ void run(Chains.NamedChains chains, PaResultByChain result) { if (df.get("weight").distinct().toList().size() <= 1) return; - List plots = Overlap.INSTANCE.plots(df, - new HeatmapParameters( - !noDendro, - !noDendro, - colorKey.stream() - .map(it -> new ColorKey(it, it.startsWith("x") ? Position.Bottom : Position.Left)) - .collect(Collectors.toList()), - hLabelsSize, - vLabelsSize, - true, - width, - height - )); + DataFrame pp = Preprocessing.INSTANCE.dataFrame(paResult, null); + + HeatmapParameters par = new HeatmapParameters( + !noDendro, + !noDendro, + colorKey.stream() + .map(it -> new ColorKey(it, it.startsWith("x") ? Position.Bottom : Position.Left)) + .collect(Collectors.toList()), + hLabelsSize, + vLabelsSize, + true, + width, + height + ); + List plots = Overlap.INSTANCE.plots(df, par); + List tables = Overlap.INSTANCE.tables(df, pp); writePlots(chains, plots); + writeTables(chains, tables); } } @@ -483,6 +510,5 @@ void run(Chains.NamedChains chains, PaResultByChain result) { subcommands = { CommandLine.HelpCommand.class }) - public static class CommandExportPaMain { - } + public static class CommandExportPaMain {} } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index 3e72eccc8..6f5d4c781 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -59,7 +59,8 @@ public PostanalysisResult forGroup(CharacteristicGroup group) { .map(c -> c.name) .collect(Collectors.toMap(c -> c, data::get)), group.characteristics.stream() - .map(c -> c.name) + .map(c -> c.preprocessor.id()) + .distinct() .collect(Collectors.toMap(c -> c, preprocSummary::get))); } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index e65f4c49a..cc8faf58c 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -3,6 +3,8 @@ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey import com.milaboratory.mixcr.postanalysis.overlap.OverlapType +import com.milaboratory.mixcr.postanalysis.plots.Preprocessing.pdfTable +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup import jetbrains.letsPlot.label.ggtitle import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema @@ -13,6 +15,7 @@ import org.jetbrains.kotlinx.dataframe.api.* */ @DataSchema data class OverlapRow( + val preproc: String, val sample1: String, val sample2: String, val metric: OverlapType, @@ -24,13 +27,17 @@ object Overlap { * Imports data into DataFrame **/ fun dataFrame( + ch: CharacteristicGroup<*, *>, paResult: PostanalysisResult, metricsFilter: List? ) = run { val data = mutableListOf() + val ch2preproc = ch.characteristics.associate { it.name to it.preprocessor.id() } + val projectedResult = paResult.forGroup(ch) val mf = metricsFilter?.map { it.lowercase() }?.toSet() - for ((_, charData) in paResult.data) { + for ((char, charData) in projectedResult.data) { + val preproc = ch2preproc[char]!! for ((_, keys) in charData.data) { for (metric in keys.data) { @Suppress("UNCHECKED_CAST") @@ -38,8 +45,8 @@ object Overlap { if (mf != null && !mf.contains(key.key.toString().lowercase())) { continue } - data += OverlapRow(key.id1, key.id2, key.key, metric.value) - data += OverlapRow(key.id2, key.id1, key.key, metric.value) + data += OverlapRow(preproc, key.id1, key.id2, key.key, metric.value) + data += OverlapRow(preproc, key.id2, key.id1, key.key, metric.value) } } } @@ -51,11 +58,12 @@ object Overlap { * Imports data into DataFrame **/ fun dataFrame( + ch: CharacteristicGroup<*, *>, paResult: PostanalysisResult, metricsFilter: List?, metadata: Metadata?, ) = run { - var df: DataFrame = dataFrame(paResult, metricsFilter) + var df: DataFrame = dataFrame(ch, paResult, metricsFilter) if (metadata != null) df = df.withMetadata(metadata) df @@ -77,13 +85,7 @@ object Overlap { ndf } - fun plots( - df: DataFrame, - pp: HeatmapParameters, - ) = df.groupBy { "metric"() }.groups.toList() - .map { sdf -> plot(df, pp) + ggtitle(sdf.first()[OverlapRow::metric.name]!!.toString()) } - - fun plot( + private fun plot( df: DataFrame, params: HeatmapParameters, ) = mkHeatmap( @@ -93,4 +95,23 @@ object Overlap { z = GeneUsageRow::weight.name, params = params ) + + fun plots( + df: DataFrame, + par: HeatmapParameters, + ) = df.groupBy { metric }.groups.toList() + .map { sdf -> plot(df, par) + ggtitle(sdf.first()[OverlapRow::metric.name]!!.toString()) } + + fun tables( + df: DataFrame, + pp: DataFrame + ) = df + .groupBy { preproc } + .groups.toList().map { byChar -> + val metrics = byChar.metric.distinct().toList() + val preprocId = byChar.first()[OverlapRow::preproc.name] as String + pp + .filter { preproc == preprocId } + .pdfTable(header = metrics.joinToString(",") { it.toString() }) + } } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt new file mode 100644 index 000000000..f939dce1d --- /dev/null +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt @@ -0,0 +1,107 @@ +package com.milaboratory.mixcr.postanalysis.plots + +import com.itextpdf.kernel.geom.PageSize +import com.itextpdf.kernel.geom.Rectangle +import com.itextpdf.kernel.pdf.PdfDocument +import com.itextpdf.kernel.pdf.PdfWriter +import com.itextpdf.layout.Document +import com.itextpdf.layout.element.Paragraph +import com.itextpdf.layout.element.Table +import com.itextpdf.layout.layout.LayoutArea +import com.itextpdf.layout.layout.LayoutContext +import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.maxOfOrNull +import org.jetbrains.kotlinx.dataframe.api.rows +import org.jetbrains.kotlinx.dataframe.api.toDataFrame +import java.io.ByteArrayOutputStream +import java.io.OutputStream + + +@DataSchema +data class PreprocSummaryRow( + val preproc: String, + val sample: String, + val stat: SetPreprocessorStat, + val chain: List, +) + +object Preprocessing { + /** Imports data into DataFrame **/ + fun dataFrame(paResult: PostanalysisResult, preprocFilter: Set?) = run { + val rows = mutableListOf() + for ((preproc, summary) in paResult.preprocSummary) { + if (preprocFilter == null || preprocFilter.contains(preproc)) + for ((sample, stat) in summary.result) { + rows += PreprocSummaryRow( + preproc, sample, + SetPreprocessorStat.cumulative(stat), + stat + ) + } + } + rows.toDataFrame() + } + + fun DataFrame.pdfTable(header: String = "") = run { + val nCols = 1 + (this.maxOfOrNull { it.chain.size } ?: 0) + + val table = Table(1 + nCols * 5) + table.setFixedLayout() + + // header + table.addCell("sample") + for (i in 0 until nCols) { + val suff: String = if (i == 0) "" else "#$i" + table.addCell("preprocessor$suff") + table.addCell("nElementsBefore$suff") + table.addCell("sumWeightBefore$suff") + table.addCell("nElementsAfter$suff") + table.addCell("sumWeightAfter$suff") + } + + for (row in rows()) { + table.addCell(row.sample) + table.writeStat(row.stat) + for (cs in row.chain) { + table.writeStat(cs) + } + if (row.chain.size < (nCols - 1)) { + table.writeDummyStat(nCols - 1 - row.chain.size) + } + } + + val bs = ByteArrayOutputStream() + val pdfDoc = PdfDocument(PdfWriter(bs)) + + val dummyDoc = Document(PdfDocument(PdfWriter(OutputStream.nullOutputStream()))) + val renderer = table.createRendererSubTree().setParent(dummyDoc.renderer) + val layout = + renderer.layout(LayoutContext(LayoutArea(0, Rectangle(1000.0f, 1000.0f)))) + dummyDoc.close() + + val document = Document(pdfDoc, PageSize(layout.occupiedArea.bBox.width, layout.occupiedArea.bBox.height)) + document.use { + document.add(Paragraph(header)) + document.add(table) + document.close() + bs.toByteArray() + } + } + + private fun Table.writeStat(stat: SetPreprocessorStat) { + addCell(stat.preprocId) + addCell(stat.nElementsBefore.toString()) + addCell(stat.sumWeightBefore.toString()) + addCell(stat.nElementsAfter.toString()) + addCell(stat.sumWeightAfter.toString()) + } + + private fun Table.writeDummyStat(n: Int) { + for (j in 0 until n) + for (i in 0 until 5) + addCell("") + } +} \ No newline at end of file From 0183acd3089121e953fc4d5dd3bc74269f7557c4 Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Mon, 21 Mar 2022 19:42:12 +0300 Subject: [PATCH 164/282] feat: add integration test hooks --- .mi-ci/hooks/test-integration-after.sh | 6 ++++++ .mi-ci/hooks/test-integration-before.sh | 5 +++++ 2 files changed, 11 insertions(+) create mode 100644 .mi-ci/hooks/test-integration-after.sh create mode 100644 .mi-ci/hooks/test-integration-before.sh diff --git a/.mi-ci/hooks/test-integration-after.sh b/.mi-ci/hooks/test-integration-after.sh new file mode 100644 index 000000000..2002a3815 --- /dev/null +++ b/.mi-ci/hooks/test-integration-after.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash + +script_dir=$(dirname "${0}") + +# Run integration tests +"${script_dir}/../../itests.sh" diff --git a/.mi-ci/hooks/test-integration-before.sh b/.mi-ci/hooks/test-integration-before.sh new file mode 100644 index 000000000..f222132eb --- /dev/null +++ b/.mi-ci/hooks/test-integration-before.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +script_dir=$(dirname "${0}") + +# Do nothing for now From 8bf84f4304879d452804477d771cb3874a71795a Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Mon, 21 Mar 2022 19:49:41 +0300 Subject: [PATCH 165/282] fix: make hooks executable --- .mi-ci/hooks/test-integration-after.sh | 0 .mi-ci/hooks/test-integration-before.sh | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 .mi-ci/hooks/test-integration-after.sh mode change 100644 => 100755 .mi-ci/hooks/test-integration-before.sh diff --git a/.mi-ci/hooks/test-integration-after.sh b/.mi-ci/hooks/test-integration-after.sh old mode 100644 new mode 100755 diff --git a/.mi-ci/hooks/test-integration-before.sh b/.mi-ci/hooks/test-integration-before.sh old mode 100644 new mode 100755 From 3eae111f2eba75cdd5130627bf614dc14c3f5e74 Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Mon, 21 Mar 2022 19:58:44 +0300 Subject: [PATCH 166/282] feat: download test data before running integration tests --- .mi-ci/hooks/test-integration-before.sh | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.mi-ci/hooks/test-integration-before.sh b/.mi-ci/hooks/test-integration-before.sh index f222132eb..297e183a6 100755 --- a/.mi-ci/hooks/test-integration-before.sh +++ b/.mi-ci/hooks/test-integration-before.sh @@ -2,4 +2,8 @@ script_dir=$(dirname "${0}") -# Do nothing for now +# downloadable test data +"${script_dir}/../../ensure-test-data.sh" + +# builds predprocessed test data +"${script_dir}/../../prepare-test-data.sh" From 6e92631064969ab50b9e1acb49175044ba748d46 Mon Sep 17 00:00:00 2001 From: Korenevskiy Denis Date: Tue, 22 Mar 2022 17:48:30 +0300 Subject: [PATCH 167/282] feat: support Mi CI long tests run style, enable cache for big sequences --- .github/workflows/build.yaml | 8 ++++++++ build.gradle.kts | 10 +++++----- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index dc265e6ef..d75c6e330 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -34,10 +34,18 @@ jobs: # Tests test-unit: true test-unit-before-tasks: shadowJar + test-unit-cache: true + test-unit-cache-paths: | + ./src/test/resources/sequences/big/** + test-unit-cache-key: 'tests-sequences-v1' test-integration: true test-integration-before-tasks: shadowJar test-integration-tasks: '' + test-integration-cache: true + test-integration-cache-paths: | + ./src/test/resources/sequences/big/** + test-integration-cache-key: 'tests-sequences-v1' # Distribution dist-docker: false diff --git a/build.gradle.kts b/build.gradle.kts index c3a169bef..04bbd2c7f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -143,10 +143,10 @@ tasks.test { minHeapSize = "1024m" maxHeapSize = "2048m" - // miCiStage?.let { - // if (it == "test") { - // systemProperty("longTests", "true"); - // } - // } + miCiStage?.let { + if (it == "test") { + systemProperty("longTests", "true"); + } + } longTests?.let { systemProperty("longTests", it) } } From bc0c556a2367538fa2f49329c7385b41ed7c6b2d Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 23 Mar 2022 23:20:48 +0400 Subject: [PATCH 168/282] feat: slight adjustment for assembleContig parameters feat: limit number of output rows in exportAirr --- .../mixcr/cli/CommandExportAirr.java | 23 ++++++++++++++++--- .../full_seq_assembler_parameters.json | 4 ++-- 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java index 42ffff6d9..10950d59e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java @@ -2,6 +2,7 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; +import cc.redberry.pipe.util.CountLimitingOutputPort; import cc.redberry.pipe.util.CountingOutputPort; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.export.AirrVDJCObjectWrapper; @@ -11,6 +12,7 @@ import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; +import org.apache.commons.io.output.CloseShieldOutputStream; import java.io.PrintStream; import java.nio.file.Path; @@ -42,10 +44,15 @@ public class CommandExportAirr extends ACommandMiXCR { names = {"-a", "--from-alignment"}) public boolean fromAlignment = false; + @Option(description = "Limit number of filtered alignments; no more " + + "than N alignments will be outputted", + names = {"-n", "--limit"}) + public Integer limit = null; + @Parameters(index = "0", description = "input_file.[vdjca|clna|clns]") public String in; - @Parameters(index = "1", description = "output.tsv") - public String out; + @Parameters(index = "1", description = "output.tsv", arity = "0..1") + public String out = null; private IOUtil.MiXCRFileInfo info0 = null; @@ -164,6 +171,7 @@ private List> AlignmentsExtractors() { return ret; } + @SuppressWarnings("rawtypes") @Override public void run0() throws Exception { List> extractors; @@ -215,9 +223,18 @@ public void run0() throws Exception { return; } + + if (limit != null) { + CountLimitingOutputPort clop = new CountLimitingOutputPort(port, limit); + port = clop; + progressReporter = SmartProgressReporter.extractProgress(clop); + } + SmartProgressReporter.startProgressReport("Exporting to AIRR format", progressReporter); - try (PrintStream output = new PrintStream(out); + try (PrintStream output = out == null + ? new PrintStream(new CloseShieldOutputStream(System.out)) + : new PrintStream(out); AutoCloseable c = closeable; OutputPortCloseable p = port) { boolean first = true; diff --git a/src/main/resources/parameters/full_seq_assembler_parameters.json b/src/main/resources/parameters/full_seq_assembler_parameters.json index 41d5f44c9..37ffec86b 100644 --- a/src/main/resources/parameters/full_seq_assembler_parameters.json +++ b/src/main/resources/parameters/full_seq_assembler_parameters.json @@ -3,7 +3,7 @@ "branchingMinimalQualityShare": 0.1, "branchingMinimalSumQuality": 60, "decisiveBranchingSumQualityThreshold": 120, - "outputMinimalQualityShare": 0.8, + "outputMinimalQualityShare": 0.75, "outputMinimalSumQuality": 0, "alignedSequenceEdgeDelta": 3, "minimalMeanNormalizedQuality": 5.0, @@ -17,4 +17,4 @@ "minimalContigLength": 20, "alignedRegionsOnly": false } -} \ No newline at end of file +} From d73c99c6d84d8e624d6a23f2533c57c41c68f9f8 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sat, 26 Mar 2022 04:12:38 +0400 Subject: [PATCH 169/282] fix: shifting of indels in homopolymers now is performed only for alignments built with linear gap scoring --- .../mixcr/basictypes/VDJCAlignments.java | 6 ++++-- .../com/milaboratory/mixcr/cli/CommandAlign.java | 8 +++++++- .../milaboratory/mixcr/cli/CommandExtend.java | 13 ++++++++----- .../PartialAlignmentsAssembler.java | 2 +- .../mixcr/vdjaligners/VDJCAlignerParameters.java | 16 ++++++++++++---- .../mixcr/vdjaligners/VDJCAlignmentResult.java | 7 +++++-- 6 files changed, 37 insertions(+), 15 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 270e38999..af7502cba 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -107,8 +107,10 @@ public VDJCAlignments(VDJCHit[] vHits, VDJCHit[] dHits, VDJCHit[] jHits, VDJCHit this(-1, createHits(vHits, dHits, jHits, cHits), tagCounter, targets, history, originalReads); } - public VDJCAlignments shiftIndelsAtHomopolymers() { - return mapHits(h -> h.mapAlignments(AlignmentUtils::shiftIndelsAtHomopolymers)); + public VDJCAlignments shiftIndelsAtHomopolymers(Set gts) { + return mapHits(h -> gts.contains(h.getGeneType()) + ? h.mapAlignments(AlignmentUtils::shiftIndelsAtHomopolymers) + : h); } public VDJCAlignments mapHits(Function mapper) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 655c6e2d8..8ef25cee1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -551,6 +551,11 @@ else if (featureSequence.containsWildcards()) progress = SmartProgressReporter.extractProgress((CountLimitingOutputPort) sReads); } + // Shifting indels in homopolymers is effective only for alignments build with linear gap scoring, + // consolidating some gaps, on the contrary, for alignments obtained with affine scoring such procedure + // may break the alignment (gaps there are already consolidated as much as possible) + Set gtRequiringIndelShifts = alignerParameters.getGeneTypesWithLinearScoring(); + EnumMap emptyHits = new EnumMap<>(GeneType.class); for (GeneType gt : GeneType.values()) if (alignerParameters.getGeneAlignerParameters(gt) != null) @@ -597,9 +602,10 @@ public String getStatus() { }); reporter.start(); } + OutputPort alignments = unchunked( CUtils.wrap(alignedChunks, - CUtils.chunked(VDJCAlignmentResult::shiftIndelsAtHomopolymers))); + CUtils.chunked(al -> al.shiftIndelsAtHomopolymers(gtRequiringIndelShifts)))); for (VDJCAlignmentResult result : CUtils.it(new OrderedOutputPort<>(alignments, o -> o.read.getId()))) { VDJCAlignments alignment = result.alignment; SequenceRead read = result.read; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index b4c7f2f7e..02ec57d8c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -45,15 +45,13 @@ import com.milaboratory.mixcr.util.VDJCObjectExtender; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.Chains; +import io.repseq.core.GeneType; import io.repseq.core.ReferencePoint; import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.io.IOException; -import java.util.ArrayList; -import java.util.Comparator; -import java.util.List; -import java.util.Objects; +import java.util.*; import static com.milaboratory.mixcr.basictypes.IOUtil.*; import static com.milaboratory.mixcr.cli.CommandExtend.EXTEND_COMMAND_NAME; @@ -176,8 +174,13 @@ void processVDJCA() throws IOException { reader.getParameters().getVAlignerParameters().getParameters().getScoring(), reader.getParameters().getJAlignerParameters().getParameters().getScoring()); + // Shifting indels in homopolymers is effective only for alignments build with linear gap scoring, + // consolidating some gaps, on the contrary, for alignments obtained with affine scoring such procedure + // may break the alignment (gaps there are already consolidated as much as possible) + Set gtRequiringIndelShifts = reader.getParameters().getGeneTypesWithLinearScoring(); + for (VDJCAlignments alignments : CUtils.it(new OrderedOutputPort<>(process.getOutput(), VDJCAlignments::getAlignmentsIndex))) - writer.write(alignments.shiftIndelsAtHomopolymers()); + writer.write(alignments.shiftIndelsAtHomopolymers(gtRequiringIndelShifts)); writer.setNumberOfProcessedReads(reader.getNumberOfReads()); process.finish(); diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index c87ec065b..43d8977b9 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -240,7 +240,7 @@ public void run() { overlapped.incrementAndGet(); totalWritten.incrementAndGet(); - writer.write(mAlignment.shiftIndelsAtHomopolymers()); + writer.write(mAlignment); // Saving alignment that where merge to prevent it's use as left part alreadyMergedIds.add(alignment.getAlignmentsIndex()); diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java index a2107234f..822f8362a 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java @@ -30,8 +30,8 @@ package com.milaboratory.mixcr.vdjaligners; import com.fasterxml.jackson.annotation.*; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; import com.milaboratory.core.PairedEndReadsLayout; +import com.milaboratory.core.alignment.LinearGapAlignmentScoring; import com.milaboratory.core.merger.MergerParameters; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.HasFeatureToAlign; @@ -40,9 +40,7 @@ import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; -import java.util.EnumMap; -import java.util.Map; -import java.util.Objects; +import java.util.*; @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE) @@ -368,6 +366,16 @@ public VDJCAlignerParameters setSaveOriginalReads(boolean saveOriginalReads) { return this; } + public Set getGeneTypesWithLinearScoring() { + final Set gtRequiringIndelShifts = new HashSet<>(); + for (GeneType gt : GeneType.values()) { + GeneAlignmentParameters p = getGeneAlignerParameters(gt); + if (p != null && p.getScoring() instanceof LinearGapAlignmentScoring) + gtRequiringIndelShifts.add(gt); + } + return Collections.unmodifiableSet(gtRequiringIndelShifts); + } + @Override public String toString() { return "VDJCAlignerParameters{" + diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java index b0a2dbe98..a5411f90e 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java @@ -31,6 +31,9 @@ import com.milaboratory.core.io.sequence.SequenceRead; import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import io.repseq.core.GeneType; + +import java.util.Set; public final class VDJCAlignmentResult { public final R read; @@ -46,9 +49,9 @@ public VDJCAlignmentResult(R read) { this.alignment = null; } - public VDJCAlignmentResult shiftIndelsAtHomopolymers() { + public VDJCAlignmentResult shiftIndelsAtHomopolymers(Set gts) { if (alignment == null) return this; - return new VDJCAlignmentResult<>(read, alignment.shiftIndelsAtHomopolymers()); + return new VDJCAlignmentResult<>(read, alignment.shiftIndelsAtHomopolymers(gts)); } } From 67ec2c7309d9296a2a4eb5c55e71b978ef0f2836 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 29 Mar 2022 00:06:35 +0300 Subject: [PATCH 170/282] wip --- .../com/milaboratory/mixcr/cli/CommandPa.java | 2 +- .../mixcr/cli/CommandPaExport.java | 47 ++++-- .../postanalysis/SetPreprocessorStat.java | 16 +- .../postanalysis/SetPreprocessorSummary.java | 41 ++++- .../DownsamplingPreprocessor.java | 6 +- .../mixcr/postanalysis/plots/Heatmap.kt | 1 + .../mixcr/postanalysis/plots/Metadata.kt | 5 +- .../mixcr/postanalysis/plots/Overlap.kt | 48 +++++- .../mixcr/postanalysis/plots/Preprocessing.kt | 158 ++++++++++++------ .../mixcr/cli/CommandPaExportTest.java | 1 + .../DownsamplingPreprocessorTest.java | 21 ++- .../OverlapDownsamplingPreprocessorTest.java | 21 ++- .../overlap/OverlapCharacteristicTest.java | 6 +- 13 files changed, 273 insertions(+), 100 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java index 3b1b678d5..ea65a07d0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java @@ -449,7 +449,7 @@ public List> getCharacteristics(int i, int j, Chain public PostanalysisSchema> getSchema(int nSamples, Chains chain) { List> overlaps = new ArrayList<>(); for (int i = 0; i < nSamples; ++i) - for (int j = i + 1; j < nSamples; ++j) + for (int j = i; j < nSamples; ++j) // j=i to include diagonal elements overlaps.addAll(getCharacteristics(i, j, chain)); return new PostanalysisSchema<>(Collections.singletonList( diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java index 085a5a7e1..172ff57a5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java @@ -142,7 +142,7 @@ void writeTables(NamedChains chain, CharacteristicGroupResult tableResult public static final class ExportPreprocessingSummary extends ExportTablesBase { @Override void run1(NamedChains chains, PaResultByChain result) { - SetPreprocessorSummary.writeToCSV(outDir().resolve(outPrefix() + outExtension(chains)), result.result.preprocSummary, "\t"); + SetPreprocessorSummary.writeToCSV(outDir().resolve(outPrefix() + outExtension(chains)), result.result.preprocSummary, null, "\t"); } } @@ -193,13 +193,16 @@ static abstract class CommandPaExportPlots extends CommandPaExport { @Option(names = {"--height"}, description = "Plot height") public int height = 0; @Option(names = {"--filter"}, description = "Filter by metadata. Possible filters column=value, column>=value etc.") - public String filterByMetadata; + public List filterByMetadata; @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") public String out; DataFrame filter(DataFrame df) { if (filterByMetadata != null) { - return MetadataKt.parseFilter(metadata(), filterByMetadata).apply(df); + for (Filter f : filterByMetadata.stream().map(f -> MetadataKt.parseFilter(metadata(), f)).collect(Collectors.toList())) { + df = f.apply(df); + } + return df; } else return df; } @@ -231,7 +234,7 @@ Path plotDestPath(NamedChains chains) { } String tablesDestStr(NamedChains chains) { - return out.substring(0, out.length() - 3) + "preproc." + chains.name + ".pdf"; + return out.substring(0, out.length() - 3) + "preproc." + chains.name + ".tsv"; } Path tablesDestPath(NamedChains chains) { @@ -329,7 +332,12 @@ static abstract class ExportHeatmap extends CommandPaExportPlots { public double vLabelsSize = -1.0; } - static abstract class ExportGeneUsage extends ExportHeatmap { + static abstract class ExportHeatmapWithGroupBy extends ExportHeatmap { + @Option(names = {"--group-by"}, description = "Group heatmaps by specific metadata properties.") + public List groupBy; + } + + static abstract class ExportGeneUsage extends ExportHeatmapWithGroupBy { abstract String group(); @Option(names = {"--no-samples-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of samples.") @@ -358,6 +366,7 @@ void run(NamedChains chains, PaResultByChain result) { !noSamplesDendro, !noGenesDendro, colorKey.stream().map(it -> new ColorKey(it, Position.Bottom)).collect(Collectors.toList()), + groupBy, hLabelsSize, vLabelsSize, false, @@ -431,6 +440,7 @@ void run(NamedChains chains, PaResultByChain result) { !noJDendro, !noVDendro, Collections.emptyList(), + null, hLabelsSize, vLabelsSize, false, @@ -446,7 +456,7 @@ void run(NamedChains chains, PaResultByChain result) { sortOptions = false, separator = " ", description = "Export overlap heatmap") - static class ExportOverlap extends ExportHeatmap { + static class ExportOverlap extends ExportHeatmapWithGroupBy { @Option(names = {"--no-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") public boolean noDendro; @Option(names = {"--color-key"}, description = "Add color key layer.") @@ -456,16 +466,19 @@ static class ExportOverlap extends ExportHeatmap { DataFrame filterOverlap(DataFrame df) { if (filterByMetadata != null) { - Filter filter = MetadataKt.parseFilter(metadata(), filterByMetadata); - return Overlap.INSTANCE.filterOverlap(filter, df); - } else - return df; + for (String f : filterByMetadata) { + Filter filter = MetadataKt.parseFilter(metadata(), f); + df = Overlap.INSTANCE.filterOverlap(filter, df); + } + } + return df; } @Override void run(NamedChains chains, PaResultByChain result) { CharacteristicGroup ch = result.schema.getGroup(CommandPa.Overlap); PostanalysisResult paResult = result.result.forGroup(ch); + Map preprocSummary = paResult.preprocSummary; DataFrame metadata = metadata(); DataFrame df = Overlap.INSTANCE.dataFrame( @@ -483,6 +496,8 @@ void run(NamedChains chains, PaResultByChain result) { return; DataFrame pp = Preprocessing.INSTANCE.dataFrame(paResult, null); + pp = MetadataKt.attachMetadata(pp, "sample", metadata, "sample"); + pp = filter(pp); HeatmapParameters par = new HeatmapParameters( !noDendro, @@ -490,17 +505,19 @@ void run(NamedChains chains, PaResultByChain result) { colorKey.stream() .map(it -> new ColorKey(it, it.startsWith("x") ? Position.Bottom : Position.Left)) .collect(Collectors.toList()), + groupBy, hLabelsSize, vLabelsSize, - true, + false, width, height ); - List plots = Overlap.INSTANCE.plots(df, par); - List tables = Overlap.INSTANCE.tables(df, pp); - writePlots(chains, plots); - writeTables(chains, tables); + List plotsAndSummary = Overlap.INSTANCE.plotsAndSummary(df, pp, par); + ExportKt.writePDF(plotDestPath(chains), plotsAndSummary); + SetPreprocessorSummary.writeCSV(tablesDestPath(chains), + ch, preprocSummary, + "\t"); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java index fe298466b..53dcaf80d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java @@ -48,7 +48,7 @@ public SetPreprocessorStat(String preprocId, double sumWeightBefore, double sumWeightAfter) { this.preprocId = preprocId; - this.dropped = false; + this.dropped = nElementsAfter == 0; this.nElementsBefore = nElementsBefore; this.nElementsAfter = nElementsAfter; this.sumWeightBefore = sumWeightBefore; @@ -72,11 +72,23 @@ public int hashCode() { return Objects.hash(preprocId, dropped, nElementsBefore, nElementsAfter, sumWeightBefore, sumWeightAfter); } + @Override + public String toString() { + return "SetPreprocessorStat{" + + "preprocId='" + preprocId + '\'' + + ", dropped=" + dropped + + ", nElementsBefore=" + nElementsBefore + + ", nElementsAfter=" + nElementsAfter + + ", sumWeightBefore=" + sumWeightBefore + + ", sumWeightAfter=" + sumWeightAfter + + '}'; + } + public static SetPreprocessorStat cumulative(List stats) { SetPreprocessorStat first = stats.get(0); SetPreprocessorStat last = stats.get(stats.size() - 1); return new SetPreprocessorStat( - stats.stream().map(s -> s.preprocId).collect(Collectors.joining("_")), + stats.stream().map(s -> s.preprocId).collect(Collectors.joining(" | ")), first.nElementsBefore, last.nElementsAfter, first.sumWeightBefore, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java index ab969a1e6..3065b7c61 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java @@ -2,14 +2,16 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import java.io.BufferedWriter; -import java.io.FileWriter; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.StandardOpenOption; import java.util.*; +import java.util.stream.Collectors; public class SetPreprocessorSummary { @@ -35,8 +37,37 @@ public int hashCode() { return Objects.hash(result); } - public static void writeToCSV(Path file, + public static void writeCSV(Path path, + CharacteristicGroup chGroup, + Map preprocSummary, + String sep + ) { + Set preprocs = chGroup.characteristics + .stream() + .map(ch -> ch.preprocessor.id()) + .collect(Collectors.toSet()); + preprocSummary = preprocSummary.entrySet().stream() + .filter(e -> preprocs.contains(e.getKey())) + .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue)); + Map> pp2ch = chGroup.characteristics.stream().collect(Collectors.toMap( + ch -> ch.preprocessor.id(), + ch -> Collections.singletonList(ch.name), + (a, b) -> { + List c = new ArrayList<>(a); + c.addAll(b); + return c; + } + )); + writeToCSV( + path, + preprocSummary, + pp2ch, + sep); + } + + public static void writeToCSV(Path path, Map preprocSummary, + Map> pp2ch, String sep) { List> rows = new ArrayList<>(); for (Map.Entry e : preprocSummary.entrySet()) { @@ -49,6 +80,8 @@ public static void writeToCSV(Path file, continue; List row = new ArrayList<>(); row.add(sample); + if (pp2ch != null) + row.add(String.join(",", pp2ch.get(preprocId))); row.add(preprocId); addStat(row, SetPreprocessorStat.cumulative(stats)); for (SetPreprocessorStat stat : stats) { @@ -67,6 +100,8 @@ public static void writeToCSV(Path file, List header = new ArrayList<>(); header.add("sample"); + if (pp2ch != null) + header.add("characteristics"); for (int i = 0; i < (nCols - 1) / 5; i++) { String suff; if (i == 0) @@ -81,7 +116,7 @@ public static void writeToCSV(Path file, header.add("sumWeightAfter" + suff); } - try (BufferedWriter writer = Files.newBufferedWriter(file, StandardOpenOption.CREATE)) { + try (BufferedWriter writer = Files.newBufferedWriter(path, StandardOpenOption.CREATE)) { for (int i = 0; ; i++) { writer.write(header.get(i)); if (i == header.size() - 1) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index 5a6299edb..17e4d2188 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -12,7 +12,6 @@ import org.apache.commons.math3.random.RandomGenerator; import org.apache.commons.math3.random.Well19937c; -import java.util.Collections; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; import java.util.function.BiFunction; @@ -84,8 +83,9 @@ public MappingFunction getMapper(int iDataset) { int i = idx.getAndIncrement(); if (countsDownsampled[i] == 0) return null; - stats.after(iDataset, t); - return setCount.apply(t, countsDownsampled[i]); + T tNew = setCount.apply(t, countsDownsampled[i]); + stats.after(iDataset, tNew); + return tNew; }; } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt index 028463880..3be0eb633 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt @@ -19,6 +19,7 @@ data class HeatmapParameters( val clusterX: Boolean, val clusterY: Boolean, val colorKey: List? = null, + val groupBy: List? = null, val hLabelsSize: Double, val vLabelsSize: Double, val fillNaZeroes: Boolean, diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt index 994789255..b6d98d929 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt @@ -8,6 +8,7 @@ import org.jetbrains.kotlinx.dataframe.api.* import org.jetbrains.kotlinx.dataframe.io.read import org.jetbrains.kotlinx.dataframe.io.readTSV import java.util.* +import javax.xml.crypto.Data fun AnyFrame.isNumeric(col: String) = this[col].all { it == null || it is Number } fun AnyFrame.isCategorial(col: String) = !isNumeric(col) @@ -41,8 +42,8 @@ fun DataFrame.withMetadata(metadata: Metadata) = run { /** * Attaches metadata to statistics **/ -fun attachMetadata( - data: AnyFrame, +fun attachMetadata( + data: DataFrame, dataCol: String, meta: Metadata, metaCol: String diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index cc8faf58c..f70470878 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -1,9 +1,10 @@ package com.milaboratory.mixcr.postanalysis.plots +import com.milaboratory.miplots.toPDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey import com.milaboratory.mixcr.postanalysis.overlap.OverlapType -import com.milaboratory.mixcr.postanalysis.plots.Preprocessing.pdfTable +import com.milaboratory.mixcr.postanalysis.plots.Preprocessing.pdfSummary import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup import jetbrains.letsPlot.label.ggtitle import org.jetbrains.kotlinx.dataframe.DataFrame @@ -102,16 +103,45 @@ object Overlap { ) = df.groupBy { metric }.groups.toList() .map { sdf -> plot(df, par) + ggtitle(sdf.first()[OverlapRow::metric.name]!!.toString()) } - fun tables( +// fun tables( +// df: DataFrame, +// pp: DataFrame +// ) = df +// .groupBy { preproc } +// .groups.toList().map { byPreproc -> +// val metrics = byPreproc.metric.distinct().toList() +// val preprocId = byPreproc.first()[OverlapRow::preproc.name] as String +// pp +// .filter { preproc == preprocId } +// .pdfTable(header = metrics.joinToString(",") { it.toString() }) +// } + + fun plotsAndSummary( df: DataFrame, - pp: DataFrame + pp: DataFrame, + par: HeatmapParameters, ) = df .groupBy { preproc } - .groups.toList().map { byChar -> - val metrics = byChar.metric.distinct().toList() - val preprocId = byChar.first()[OverlapRow::preproc.name] as String - pp - .filter { preproc == preprocId } - .pdfTable(header = metrics.joinToString(",") { it.toString() }) + .groups.toList().flatMap { byPreproc -> + val metrics = byPreproc.metric.distinct().toList() + val preprocId = byPreproc.first()[OverlapRow::preproc.name] as String + + val ppFiltered = pp.filter { preproc == preprocId } + val droppedSamples = + ppFiltered.filter { stat.dropped || stat.nElementsAfter == 0L } + .sample.distinct().toSet() + + val summary = ppFiltered.pdfSummary(metrics.joinToString(", ")) + val plots = byPreproc + .filter { !droppedSamples.contains(it.sample1) && !droppedSamples.contains(it.sample2) } + .groupBy { metric }.groups.toList() + .map { byMetric -> + plot(byMetric, par) + ggtitle(byMetric.first()[OverlapRow::metric.name]!!.toString()) + }.map { it.toPDF() } + + if (summary == null) + plots + else + listOf(summary) + plots } } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt index f939dce1d..c8459a5e0 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt @@ -1,23 +1,18 @@ package com.milaboratory.mixcr.postanalysis.plots -import com.itextpdf.kernel.geom.PageSize -import com.itextpdf.kernel.geom.Rectangle import com.itextpdf.kernel.pdf.PdfDocument import com.itextpdf.kernel.pdf.PdfWriter import com.itextpdf.layout.Document import com.itextpdf.layout.element.Paragraph -import com.itextpdf.layout.element.Table -import com.itextpdf.layout.layout.LayoutArea -import com.itextpdf.layout.layout.LayoutContext +import com.itextpdf.layout.element.Text import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema -import org.jetbrains.kotlinx.dataframe.api.maxOfOrNull +import org.jetbrains.kotlinx.dataframe.api.filter import org.jetbrains.kotlinx.dataframe.api.rows import org.jetbrains.kotlinx.dataframe.api.toDataFrame import java.io.ByteArrayOutputStream -import java.io.OutputStream @DataSchema @@ -45,63 +40,118 @@ object Preprocessing { rows.toDataFrame() } - fun DataFrame.pdfTable(header: String = "") = run { - val nCols = 1 + (this.maxOfOrNull { it.chain.size } ?: 0) + fun DataFrame.pdfSummary( + preprocId: String?, + header: String = "" + ): ByteArray? = run { + val pp = if (preprocId == null) + this + else + this.filter { preproc == preprocId } - val table = Table(1 + nCols * 5) - table.setFixedLayout() - - // header - table.addCell("sample") - for (i in 0 until nCols) { - val suff: String = if (i == 0) "" else "#$i" - table.addCell("preprocessor$suff") - table.addCell("nElementsBefore$suff") - table.addCell("sumWeightBefore$suff") - table.addCell("nElementsAfter$suff") - table.addCell("sumWeightAfter$suff") + val downsampling = pp.filter { + stat.nElementsAfter > 0 + && preproc.lowercase().contains("downsampling") } + val elementsAfter = downsampling.rows().map { it.stat.nElementsAfter }.distinct() + val weightAfter = downsampling.rows().map { it.stat.sumWeightAfter }.distinct() - for (row in rows()) { - table.addCell(row.sample) - table.writeStat(row.stat) - for (cs in row.chain) { - table.writeStat(cs) - } - if (row.chain.size < (nCols - 1)) { - table.writeDummyStat(nCols - 1 - row.chain.size) - } - } + val downsamplingText1 = + if (elementsAfter.size == 1) + "Downsampled to $elementsAfter clonotypes" + else + null + + val downsamplingText2 = + if (weightAfter.size == 1) + "Downsampled to $weightAfter reads" + else + null + + // dropped samples: + val dropped = pp.filter { stat.dropped || stat.nElementsAfter == 0L }.sample.toList().distinct() + + if (downsamplingText1 == null && downsamplingText2 == null && dropped.isEmpty()) + return@run null val bs = ByteArrayOutputStream() val pdfDoc = PdfDocument(PdfWriter(bs)) - val dummyDoc = Document(PdfDocument(PdfWriter(OutputStream.nullOutputStream()))) - val renderer = table.createRendererSubTree().setParent(dummyDoc.renderer) - val layout = - renderer.layout(LayoutContext(LayoutArea(0, Rectangle(1000.0f, 1000.0f)))) - dummyDoc.close() - - val document = Document(pdfDoc, PageSize(layout.occupiedArea.bBox.width, layout.occupiedArea.bBox.height)) + val document = Document(pdfDoc) document.use { - document.add(Paragraph(header)) - document.add(table) + document.add(Paragraph(header).setBold()) + if (downsamplingText1 != null) + document.add(Paragraph(downsamplingText1)) + if (downsamplingText2 != null) + document.add(Paragraph(downsamplingText2)) + if (dropped.isNotEmpty()) { + document.add( + Paragraph("Dropped samples (" + dropped.size + "):\n") + .add(Text(dropped.joinToString(", ")).setFontSize(8.0f)) + ) + } document.close() bs.toByteArray() } } - - private fun Table.writeStat(stat: SetPreprocessorStat) { - addCell(stat.preprocId) - addCell(stat.nElementsBefore.toString()) - addCell(stat.sumWeightBefore.toString()) - addCell(stat.nElementsAfter.toString()) - addCell(stat.sumWeightAfter.toString()) - } - - private fun Table.writeDummyStat(n: Int) { - for (j in 0 until n) - for (i in 0 until 5) - addCell("") - } +// +// fun DataFrame.pdfTable(header: String = "") = run { +// val nCols = 1 + (this.maxOfOrNull { it.chain.size } ?: 0) +// +// val table = Table(1 + nCols * 5) +// table.setFixedLayout() +// +// // header +// table.addCell("sample") +// for (i in 0 until nCols) { +// val suff: String = if (i == 0) "" else "#$i" +// table.addCell("preprocessor$suff") +// table.addCell("nElementsBefore$suff") +// table.addCell("sumWeightBefore$suff") +// table.addCell("nElementsAfter$suff") +// table.addCell("sumWeightAfter$suff") +// } +// +// for (row in rows()) { +// table.addCell(row.sample) +// table.writeStat(row.stat) +// for (cs in row.chain) { +// table.writeStat(cs) +// } +// if (row.chain.size < (nCols - 1)) { +// table.writeDummyStat(nCols - 1 - row.chain.size) +// } +// } +// +// val bs = ByteArrayOutputStream() +// val pdfDoc = PdfDocument(PdfWriter(bs)) +// +// val dummyDoc = Document(PdfDocument(PdfWriter(OutputStream.nullOutputStream()))) +// val renderer = table.createRendererSubTree().setParent(dummyDoc.renderer) +// val layout = +// renderer.layout(LayoutContext(LayoutArea(0, Rectangle(1000.0f, 1000.0f)))) +// dummyDoc.close() +// +// val document = Document(pdfDoc, PageSize(layout.occupiedArea.bBox.width, layout.occupiedArea.bBox.height)) +// document.use { +// document.add(Paragraph(header)) +// document.add(table) +// document.close() +// bs.toByteArray() +// } +// } +// +// private fun Table.writeStat(stat: SetPreprocessorStat) { +// addCell(stat.preprocId) +// addCell(stat.nElementsBefore.toString()) +// addCell(stat.sumWeightBefore.toString()) +// addCell(stat.nElementsAfter.toString()) +// addCell(stat.sumWeightAfter.toString()) +// } +// +// private fun Table.writeDummyStat(n: Int) { +// for (j in 0 until n) +// for (i in 0 until 5) +// addCell("") +// } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java index 07f39f6ef..d05896703 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java @@ -44,6 +44,7 @@ public void test3() { // "--height", "5000", "--chains", "TRA", "--filter", "Chain=TRA", + "--filter", "CellPopulation=CD4mem", "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", "--color-key", "x_Tissue", "--color-key", "x_CellPopulation", "--color-key", "y_MouseID", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index ef6137fdc..ed920d405 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -1,10 +1,9 @@ package com.milaboratory.mixcr.postanalysis.downsampling; import cc.redberry.pipe.CUtils; -import com.milaboratory.mixcr.postanalysis.Dataset; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.TestDataset; -import com.milaboratory.mixcr.postanalysis.TestObject; +import com.milaboratory.mixcr.postanalysis.*; +import gnu.trove.iterator.TIntObjectIterator; +import gnu.trove.map.hash.TIntObjectHashMap; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; @@ -124,6 +123,20 @@ public void test3() { Assert.assertTrue(in.set.containsAll(dw.set)); Assert.assertEquals(dsValue, dw.count); } + + TIntObjectHashMap> stat = proc.getStat(); + Assert.assertEquals(nDatasets, stat.size()); + TIntObjectIterator> it = stat.iterator(); + double wtAfter = -1; + while (it.hasNext()) { + it.advance(); + Assert.assertEquals(1, it.value().size()); + SetPreprocessorStat istat = it.value().get(0); + if (wtAfter == -1) + wtAfter = istat.sumWeightAfter; + else + Assert.assertEquals(wtAfter, istat.sumWeightAfter, 1e-5); + } } static List toList(Iterable it) { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index 33051de1d..8ba26fc41 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -1,12 +1,11 @@ package com.milaboratory.mixcr.postanalysis.downsampling; import cc.redberry.pipe.CUtils; -import com.milaboratory.mixcr.postanalysis.Dataset; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.TestDataset; -import com.milaboratory.mixcr.postanalysis.TestObject; +import com.milaboratory.mixcr.postanalysis.*; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; +import gnu.trove.iterator.TIntObjectIterator; +import gnu.trove.map.hash.TIntObjectHashMap; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; import org.junit.Assert; @@ -63,6 +62,20 @@ public void test1() { } } } + + TIntObjectHashMap> stat = proc.getStat(); + Assert.assertEquals(dataset.sets.length, stat.size()); + TIntObjectIterator> it = stat.iterator(); + double wtAfter = -1; + while (it.hasNext()) { + it.advance(); + Assert.assertEquals(1, it.value().size()); + SetPreprocessorStat istat = it.value().get(0); + if (wtAfter == -1) + wtAfter = istat.sumWeightAfter; + else + Assert.assertEquals(wtAfter, istat.sumWeightAfter, 1e-5); + } } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java index 1b9504eb2..bba4191f8 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -125,13 +125,13 @@ public void testOverlapCharacteristic1() { } CharacteristicGroup, OverlapGroup> chGroup = - new CharacteristicGroup<>("overlap", chars, Arrays.asList(new OverlapSummary<>())); + new CharacteristicGroup<>("overlap", chars, List.of(new OverlapSummary<>())); PostanalysisRunner> runner = new PostanalysisRunner<>(); runner.addCharacteristics(chGroup); List datasetIds = Arrays.stream(ovp.datasets).map(d -> d.id).collect(Collectors.toList()); - PostanalysisResult paResult = runner.run(new OverlapDataset(datasetIds) { + PostanalysisResult paResult = runner.run(new OverlapDataset<>(datasetIds) { @Override public OutputPortWithProgress> mkElementsPort() { OutputPortCloseable> inner = new SimpleProcessorWrapper<>(strategy @@ -139,7 +139,7 @@ public OutputPortWithProgress> mkElementsPort() { .map(TestDataset::mkElementsPort) .collect(Collectors.toList())), OverlapGroup::new); - return new OutputPortWithProgress>() { + return new OutputPortWithProgress<>() { @Override public long index() { return 0; From 5dd48f320bd1f81fe1ec2eb1ba840da28059e90a Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 30 Mar 2022 04:00:11 +0300 Subject: [PATCH 171/282] Refactoring --- .../mixcr/cli/CommandMergeAlignments.java | 4 +- .../com/milaboratory/mixcr/cli/CommandPa.java | 472 ---------------- .../mixcr/cli/CommandPaExport.java | 531 ------------------ .../java/com/milaboratory/mixcr/cli/Main.java | 29 +- .../mixcr/cli/postanalysis/CommandPa.java | 259 +++++++++ .../cli/postanalysis/CommandPaExport.java | 76 +++ .../postanalysis/CommandPaExportPlots.java | 83 +++ .../CommandPaExportPlotsBasicStatistics.java | 85 +++ .../CommandPaExportPlotsGeneUsage.java | 94 ++++ .../CommandPaExportPlotsHeatmap.java | 12 + ...ommandPaExportPlotsHeatmapWithGroupBy.java | 11 + .../CommandPaExportPlotsOverlap.java | 89 +++ .../CommandPaExportPlotsVJUsage.java | 55 ++ .../postanalysis/CommandPaExportTables.java | 27 + .../CommandPaExportTablesBase.java | 48 ++ .../CommandPaExportTablesPreprocSummary.java | 17 + .../cli/postanalysis/CommandPaIndividual.java | 132 +++++ .../postanalysis/CommandPaListMetrics.java | 53 ++ .../cli/postanalysis/CommandPaOverlap.java | 178 ++++++ .../cli/postanalysis/IsolationGroup.java | 76 +++ .../mixcr/cli/postanalysis/PaResult.java | 74 +++ .../cli/postanalysis/PaResultByGroup.java | 29 + .../mixcr/postanalysis/plots/Metadata.kt | 46 +- .../CommandPaExportTest.java | 5 +- .../cli/{ => postanalysis}/CommandPaTest.java | 3 +- .../cli/postanalysis/IsolationGroupTest.java | 20 + .../postanalysis/plots/BasicStatisticsTest.kt | 47 -- 27 files changed, 1441 insertions(+), 1114 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandPa.java delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java rename src/test/java/com/milaboratory/mixcr/cli/{ => postanalysis}/CommandPaExportTest.java (92%) rename src/test/java/com/milaboratory/mixcr/cli/{ => postanalysis}/CommandPaTest.java (99%) create mode 100644 src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java delete mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatisticsTest.kt diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java index 088f89187..62d2f46e2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java @@ -73,7 +73,7 @@ protected List getOutputFiles() { private MergeConfiguration configuration = null; @Override - public ActionConfiguration getConfiguration() { + public ActionConfiguration getConfiguration() { return configuration != null ? configuration : (configuration = new MergeConfiguration(getInputFiles().stream() @@ -107,7 +107,7 @@ public void run1() throws Exception { use = JsonTypeInfo.Id.CLASS, include = JsonTypeInfo.As.PROPERTY, property = "type") - public static class MergeConfiguration implements ActionConfiguration { + public static class MergeConfiguration implements ActionConfiguration { final PipelineConfiguration[] sources; @JsonCreator diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java deleted file mode 100644 index ea65a07d0..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPa.java +++ /dev/null @@ -1,472 +0,0 @@ -package com.milaboratory.mixcr.cli; - -import cc.redberry.pipe.OutputPortCloseable; -import com.fasterxml.jackson.annotation.JsonAutoDetect; -import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonProperty; -import com.fasterxml.jackson.databind.annotation.JsonDeserialize; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; -import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.postanalysis.*; -import com.milaboratory.mixcr.postanalysis.additive.AAProperties; -import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; -import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; -import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; -import com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure; -import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; -import com.milaboratory.mixcr.postanalysis.overlap.*; -import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; -import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; -import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; -import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; -import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; -import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; -import com.milaboratory.mixcr.postanalysis.ui.*; -import com.milaboratory.util.GlobalObjectMappers; -import com.milaboratory.util.LambdaSemaphore; -import com.milaboratory.util.SmartProgressReporter; -import io.repseq.core.Chains; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; -import io.repseq.core.VDJCLibraryRegistry; -import picocli.CommandLine; -import picocli.CommandLine.Option; -import picocli.CommandLine.Parameters; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.*; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; -import static io.repseq.core.Chains.*; -import static java.util.stream.Collectors.*; - -/** - * - */ -public abstract class CommandPa extends ACommandWithOutputMiXCR { - public static final NamedChains[] CHAINS = {TRAD_NAMED, TRB_NAMED, TRG_NAMED, IGH_NAMED, IGKL_NAMED}; - - @Parameters(description = "cloneset.{clns|clna}... result.json") - public List inOut; - - @Option(description = "Use only productive sequences in postanalysis.", - names = {"--only-productive"}) - public boolean onlyProductive = false; // FIXME - not used - - @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", - names = {"-d", "--downsampling"}, - required = true) - public String downsampling; - - @Option(description = "Chains", - names = {"-c", "--chains"}) - public String chains = "ALL"; - - @Override - protected List getInputFiles() { - return inOut.subList(0, inOut.size() - 1) - .stream() - .flatMap(f -> { - if (Files.isDirectory(Paths.get(f))) { - try { - return Files - .list(Paths.get(f)) - .map(Path::toString); - } catch (IOException ignored) { - } - } - return Stream.of(f); - }) - .collect(toList()); - } - - @Override - protected List getOutputFiles() { - return Collections.singletonList(outputFile()); - } - - String outputFile() { - return inOut.get(inOut.size() - 1); - } - - private static int downsamplingValue(String downsampling) { - return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); - } - - /** - * Get sample id from file name - */ - static String getSampleId(String file) { - return Paths.get(file).getFileName().toString(); - } - - private static SetPreprocessorFactory parseDownsampling(String downsampling) { - if (downsampling.equalsIgnoreCase("no-downsampling")) { - return new NoPreprocessing.Factory<>(); - } else if (downsampling.startsWith("umi-count")) { - if (downsampling.endsWith("auto")) - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); - else { - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), 314); - } - } else { - int value = downsamplingValue(downsampling); - if (downsampling.startsWith("cumulative-top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); - } else if (downsampling.startsWith("top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, value); - } else { - throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); - } - } - } - - SetPreprocessorFactory downsampling() { - return downsampling(this.downsampling); - } - - SetPreprocessorFactory downsampling(String downsamplingStr) { - SetPreprocessorFactory downsampling = - parseDownsampling(downsamplingStr); - - if (onlyProductive) { - List> filters = new ArrayList<>(); - filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); - filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); - downsampling = downsampling.filterFirst(filters); - } - - return downsampling; - } - - /** - * Resulting data written to disk - */ - @JsonAutoDetect - public static final class PaResult { - /** - * Results for individual chains - */ - @JsonProperty("results") - @JsonSerialize(keyUsing = KnownChainsKeySerializer.class) - @JsonDeserialize(keyUsing = KnownChainsKeyDeserializer.class) - public final Map results; - - @JsonCreator - public PaResult(@JsonProperty("results") Map results) { - this.results = results; - } - } - - /** - * Resulting data written to disk - */ - @JsonAutoDetect - public static final class PaResultByChain { - @JsonProperty("schema") - public final PostanalysisSchema schema; - @JsonProperty("result") - public final PostanalysisResult result; - - @JsonCreator - public PaResultByChain(@JsonProperty("schema") PostanalysisSchema schema, - @JsonProperty("result") PostanalysisResult result) { - this.schema = schema; - this.result = result; - } - } - - @Override - public void run0() throws Exception { - Map resultsMap = new HashMap<>(); - Chains c = Chains.parse(chains); - for (NamedChains knownChains : CHAINS) { - if (c.intersects(knownChains.chains)) - resultsMap.put(knownChains, run(knownChains.chains)); - } - PaResult result = new PaResult(resultsMap); - try { - GlobalObjectMappers.PRETTY.writeValue(new File(outputFile()), result); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - - abstract PaResultByChain run(Chains chain); - - ///////////////////////////////////////////// Individual ///////////////////////////////////////////// - - static final String - Biophysics = "biophysics", - Diversity = "diversity", - VUsage = "vUsage", - JUsage = "JUsage", - VJUsage = "VJUsage", - IsotypeUsage = "IsotypeUsage", - CDR3Spectratype = "CDR3Spectratype", - VSpectratype = "VSpectratype", - VSpectratypeMean = "VSpectratypeMean", - Overlap = "overlap"; - - @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") - @CommandLine.Command(name = "individual", - sortOptions = false, - separator = " ", - description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") - public static class CommandIndividual extends CommandPa { - public CommandIndividual() {} - - @Override - @SuppressWarnings({"unchecked", "rawtypes"}) - PaResultByChain run(Chains chain) { - List> groups = new ArrayList<>(); - - SetPreprocessorFactory downsampling = downsampling() - .filterFirst(new ElementPredicate.IncludeChains(chain)); - - groups.add(new CharacteristicGroup<>(Biophysics, - Arrays.asList( - weightedLengthOf(downsampling, GeneFeature.CDR3, false).setName("CDR3 length, nt"), - weightedLengthOf(downsampling, GeneFeature.CDR3, true).setName("CDR3 length, aa"), - weightedLengthOf(downsampling, GeneFeature.VJJunction, false).setName("NDN length, nt"), - weightedAddedNucleotides(downsampling).setName("Added N, nt"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Strength"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Hydrophobicity"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Surface"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), - weightedBiophysics(downsampling, AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") - ), - Arrays.asList(new GroupSummary<>()) - )); - - groups.add(new CharacteristicGroup<>(Diversity, - Arrays.asList(new DiversityCharacteristic<>("Diversity", new WeightFunctions.Count(), - downsampling, - new DiversityMeasure[]{ - DiversityMeasure.Observed, - DiversityMeasure.Clonality, - DiversityMeasure.ShannonWeiner, - DiversityMeasure.InverseSimpson, - DiversityMeasure.Chao1, - DiversityMeasure.Gini - })), - Arrays.asList(new GroupSummary<>()) - )); - - groups.add(new CharacteristicGroup<>(VUsage, - Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Variable)), - Arrays.asList(new GroupSummary<>()) - )); - groups.add(new CharacteristicGroup<>(JUsage, - Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Joining)), - Arrays.asList(new GroupSummary<>()) - )); - groups.add(new CharacteristicGroup<>(VJUsage, - Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(downsampling)), - Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) - )); - - groups.add(new CharacteristicGroup<>(IsotypeUsage, - Arrays.asList(AdditiveCharacteristics.isotypeUsage(downsampling)), - Arrays.asList(new GroupSummary<>()) - )); - - groups.add(new CharacteristicGroup<>(CDR3Spectratype, - Arrays.asList(new SpectratypeCharacteristic("CDR3 spectratype", - downsampling, 10, - new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), - Collections.singletonList(new GroupSummary<>()))); - - groups.add(new CharacteristicGroup<>(VSpectratype, - Arrays.asList(AdditiveCharacteristics.VSpectratype(downsampling)), - Collections.singletonList(new GroupSummary<>()))); - - groups.add(new CharacteristicGroup<>(VSpectratypeMean, - Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(downsampling)), - Collections.singletonList(new GroupSummary<>()))); - - PostanalysisSchema schema = new PostanalysisSchema<>(groups); - PostanalysisRunner runner = new PostanalysisRunner<>(); - runner.addCharacteristics(schema.getAllCharacterisitcs()); - - List datasets = getInputFiles().stream() - .map(file -> - new ClonotypeDataset(getSampleId(file), file, VDJCLibraryRegistry.getDefault()) - ).collect(Collectors.toList()); - - System.out.println("Running for " + chain); - SmartProgressReporter.startProgressReport(runner); - return new PaResultByChain(schema, runner.run(datasets)); - } - } - - ///////////////////////////////////////////// Overlap ///////////////////////////////////////////// - - @CommandLine.Command(name = "overlap", - sortOptions = false, - separator = " ", - description = "Overlap analysis") - public static class CommandOverlap extends CommandPa { - @Option(description = "Override downsampling for F2 umi|d[number]|f[number]", - names = {"--f2-downsampling"}, - required = false) - public String f2downsampling; - - public CommandOverlap() { - } - - @Override - @SuppressWarnings("unchecked") - PaResultByChain run(Chains chain) { - SetPreprocessorFactory downsampling = downsampling(); - - Map> downsamplingByType = new HashMap<>(); - downsamplingByType.put(OverlapType.D, downsampling); - downsamplingByType.put(OverlapType.F2, f2downsampling == null - ? downsampling - : downsampling(f2downsampling)); - downsamplingByType.put(OverlapType.R_Intersection, downsampling); - - List> ordering = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); - OverlapPostanalysisSettings overlapPA = new OverlapPostanalysisSettings( - ordering, - new WeightFunctions.Count(), - downsamplingByType - ); - - PostanalysisSchema> schema = overlapPA.getSchema(getInputFiles().size(), chain); - - // Limits concurrency across all readers - LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(32); - List readers = getInputFiles() - .stream() - .map(s -> { - try { - return mkCheckedReader( - Paths.get(s).toAbsolutePath(), - concurrencyLimiter); - } catch (IOException e) { - throw new RuntimeException(e); - } - }) - .collect(Collectors.toList()); - - OverlapDataset overlapDataset = OverlapUtil.overlap( - getInputFiles().stream().map(CommandPa::getSampleId).collect(toList()), - ordering, - readers); - - PostanalysisRunner> runner = new PostanalysisRunner<>(); - runner.addCharacteristics(schema.getAllCharacterisitcs()); - - System.out.println("Running for " + chain); - SmartProgressReporter.startProgressReport(runner); - PostanalysisResult result = runner.run(overlapDataset); - - return new PaResultByChain(schema, result); - } - - public static CloneReader mkCheckedReader(Path path, - LambdaSemaphore concurrencyLimiter) throws IOException { - ClnsReader inner = new ClnsReader( - path, - VDJCLibraryRegistry.getDefault(), - concurrencyLimiter); - return new CloneReader() { - @Override - public VDJCSProperties.CloneOrdering ordering() { - return inner.ordering(); - } - - @Override - public OutputPortCloseable readClones() { - OutputPortCloseable in = inner.readClones(); - return new OutputPortCloseable() { - @Override - public void close() { - in.close(); - } - - @Override - public Clone take() { - Clone t = in.take(); - if (t == null) - return null; - if (t.getFeature(GeneFeature.CDR3) == null) - return take(); - return t; - } - }; - } - - @Override - public void close() throws Exception { - inner.close(); - } - - @Override - public int numberOfClones() { - return inner.numberOfClones(); - } - }; - } - - @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") - static final class OverlapPostanalysisSettings { - final List> ordering; - final WeightFunction weight; - final Map> preprocessors; - final Map, List> groupped; - - OverlapPostanalysisSettings(List> ordering, - WeightFunction weight, - Map> preprocessors) { - this.ordering = ordering; - this.weight = weight; - this.preprocessors = preprocessors; - this.groupped = preprocessors.entrySet().stream().collect(groupingBy(Map.Entry::getValue, mapping(Map.Entry::getKey, toList()))); - } - - private SetPreprocessorFactory> getPreprocessor(OverlapType type, Chains chain) { - return new OverlapPreprocessorAdapter.Factory<>(preprocessors.get(type).filterFirst(new ElementPredicate.IncludeChains(chain))); - } - - //fixme only productive?? - public List> getCharacteristics(int i, int j, Chains chain) { - return groupped.entrySet().stream().map(e -> new OverlapCharacteristic<>("overlap_" + i + "_" + j + " / " + e.getValue().stream().map(t -> t.name).collect(Collectors.joining(" / ")), weight, - new OverlapPreprocessorAdapter.Factory<>(e.getKey().filterFirst(new ElementPredicate.IncludeChains(chain))), - e.getValue().toArray(new OverlapType[0]), - i, j)).collect(toList()); - } - - public PostanalysisSchema> getSchema(int nSamples, Chains chain) { - List> overlaps = new ArrayList<>(); - for (int i = 0; i < nSamples; ++i) - for (int j = i; j < nSamples; ++j) // j=i to include diagonal elements - overlaps.addAll(getCharacteristics(i, j, chain)); - - return new PostanalysisSchema<>(Collections.singletonList( - new CharacteristicGroup<>(Overlap, - overlaps, - Arrays.asList(new OverlapSummary<>()) - ))); - } - } - } - - @CommandLine.Command(name = "postanalysis", - separator = " ", - description = "Run postanalysis routines.", - subcommands = { - CommandLine.HelpCommand.class - }) - public static class CommandPostanalysisMain { - } -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java deleted file mode 100644 index 172ff57a5..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPaExport.java +++ /dev/null @@ -1,531 +0,0 @@ -package com.milaboratory.mixcr.cli; - -import com.milaboratory.miplots.ExportKt; -import com.milaboratory.miplots.Position; -import com.milaboratory.miplots.stat.util.TestMethod; -import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod; -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.cli.CommandPa.PaResult; -import com.milaboratory.mixcr.cli.CommandPa.PaResultByChain; -import com.milaboratory.mixcr.postanalysis.PostanalysisResult; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; -import com.milaboratory.mixcr.postanalysis.plots.*; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; -import com.milaboratory.mixcr.postanalysis.ui.OutputTable; -import com.milaboratory.util.GlobalObjectMappers; -import io.repseq.core.Chains; -import io.repseq.core.Chains.NamedChains; -import jetbrains.letsPlot.intern.Plot; -import org.jetbrains.kotlinx.dataframe.DataFrame; -import picocli.CommandLine; -import picocli.CommandLine.Option; -import picocli.CommandLine.Parameters; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.*; -import java.util.stream.Collectors; - -/** - * - */ -public abstract class CommandPaExport extends ACommandWithOutputMiXCR { - @Option(names = {"-m", "--meta", "--metadata"}, description = "Metadata file") - public String metadata; - @Parameters(index = "0", description = "pa_result.json") - public String in; - @Option(names = {"--chains"}, description = "Export for specific chains only") - public List chains; - - /** - * Cached PA result - */ - private PaResult paResult = null; - - /** - * Get full PA result - */ - PaResult getPaResult() { - try { - if (paResult != null) - return paResult; - return paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); - } catch (IOException e) { - throwValidationException("Broken input file: " + in); - return null; - } - } - - @Override - public void run0() throws Exception { - Set set = chains == null - ? null - : chains.stream().map(Chains::getNamedChains).collect(Collectors.toSet()); - - for (Map.Entry r : getPaResult().results.entrySet()) { - if (set == null || set.stream().anyMatch(c -> c.chains.intersects(r.getKey().chains))) - run(r.getKey(), r.getValue()); - } - } - - abstract void run(NamedChains chains, PaResultByChain result); - - private abstract static class ExportTablesBase extends CommandPaExport { - @Parameters(index = "1", description = "Output path") - public String out; - - @Override - public void validate() { - super.validate(); - if (!out.endsWith(".tsv") && !out.endsWith(".csv")) - throwValidationException("Output file must have .tsv or .csv extension"); - } - - Path outDir() { - return Path.of(out).toAbsolutePath().getParent(); - } - - String outPrefix() { - String fName = Path.of(out).getFileName().toString(); - return fName.substring(0, fName.length() - 4); - } - - String outExtension(NamedChains chains) { - return "." + chains.name + "." + out.substring(out.length() - 3); - } - - String separator() { - return out.endsWith("tsv") ? "\t" : ","; - } - - @Override - void run(NamedChains chains, PaResultByChain result) { - try { - Files.createDirectories(outDir()); - } catch (IOException e) { - throw new RuntimeException(e); - } - run1(chains, result); - } - - abstract void run1(NamedChains chains, PaResultByChain result); - } - - @CommandLine.Command(name = "tables", - sortOptions = false, - separator = " ", - description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype, Overlap") - public static final class ExportTables extends ExportTablesBase { - @Override - void run1(NamedChains chains, PaResultByChain result) { - for (CharacteristicGroup table : result.schema.tables) { - writeTables(chains, result.result.getTable(table)); - } - } - - void writeTables(NamedChains chain, CharacteristicGroupResult tableResult) { - for (CharacteristicGroupOutputExtractor view : tableResult.group.views) - for (OutputTable t : view.getTables(tableResult).values()) { - t.writeCSV(outDir(), outPrefix() + ".", separator(), outExtension(chain)); - } - } - } - - @CommandLine.Command(name = "preprocSummary", - sortOptions = false, - separator = " ", - description = "Export preprocessing summary tables.") - public static final class ExportPreprocessingSummary extends ExportTablesBase { - @Override - void run1(NamedChains chains, PaResultByChain result) { - SetPreprocessorSummary.writeToCSV(outDir().resolve(outPrefix() + outExtension(chains)), result.result.preprocSummary, null, "\t"); - } - } - - @CommandLine.Command(name = "listMetrics", - sortOptions = false, - separator = " ", - description = "List available metrics") - static class ListMetrics extends ACommandMiXCR { - @Parameters(index = "0", description = "pa_result.json") - public String in; - - @Override - public void run0() { - PaResult paResult; - try { - paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); - } catch (IOException e) { - throwValidationException("Corrupted PA file."); - throw new RuntimeException(); - } - - PaResultByChain result = paResult.results.values().stream().findAny().orElseThrow(); - CharacteristicGroup - biophys = result.schema.getGroup(CommandPa.Biophysics), - diversity = result.schema.getGroup(CommandPa.Diversity); - - for (int i = 0; i < 2; i++) { - System.out.println(); - CharacteristicGroup gr = i == 0 ? biophys : diversity; - if (i == 0) - System.out.println("Biophysics metrics:"); - else - System.out.println("Diversity metrics:"); - result.result.forGroup(gr) - .data.values().stream() - .flatMap(d -> d.data.values() - .stream().flatMap(ma -> Arrays.stream(ma.data))) - .map(m -> m.key) - .distinct() - .forEach(metric -> System.out.println(" " + metric)); - } - } - } - - static abstract class CommandPaExportPlots extends CommandPaExport { - @Option(names = {"--width"}, description = "Plot width") - public int width = 0; - @Option(names = {"--height"}, description = "Plot height") - public int height = 0; - @Option(names = {"--filter"}, description = "Filter by metadata. Possible filters column=value, column>=value etc.") - public List filterByMetadata; - @Parameters(index = "1", description = "Output PDF file name", defaultValue = "plot.pdf") - public String out; - - DataFrame filter(DataFrame df) { - if (filterByMetadata != null) { - for (Filter f : filterByMetadata.stream().map(f -> MetadataKt.parseFilter(metadata(), f)).collect(Collectors.toList())) { - df = f.apply(df); - } - return df; - } else - return df; - } - - @Override - public void validate() { - super.validate(); - if (!out.endsWith(".pdf")) - throwValidationException("Output file must ends with .pdf extension"); - - if (filterByMetadata != null && metadata == null) - throwValidationException("Filter is specified by metadata is not."); - } - - private DataFrame metadataDf; - - DataFrame metadata() { - return metadataDf != null - ? metadataDf - : (metadata == null ? null : (metadataDf = MetadataKt.readMetadata(metadata))); - } - - String plotDestStr(NamedChains chains) { - return out.substring(0, out.length() - 3) + chains.name + ".pdf"; - } - - Path plotDestPath(NamedChains chains) { - return Path.of(plotDestStr(chains)); - } - - String tablesDestStr(NamedChains chains) { - return out.substring(0, out.length() - 3) + "preproc." + chains.name + ".tsv"; - } - - Path tablesDestPath(NamedChains chains) { - return Path.of(tablesDestStr(chains)); - } - - void writeTables(NamedChains chains, List tables) { - ExportKt.writePDF(tablesDestPath(chains), tables); - } - - void writePlots(NamedChains chains, List plots) { - ExportKt.writePDFFigure(plotDestPath(chains), plots); - } - - void writePlots(NamedChains chains, Plot plot) { - ExportKt.writePDF(tablesDestPath(chains), plot); - } - } - - static abstract class ExportBasicStatistics extends CommandPaExportPlots { - abstract String group(); - - @Option(names = {"-p", "--primary-group"}, description = "Primary group") - public String primaryGroup; - @Option(names = {"-s", "--secondary-group"}, description = "Secondary group") - public String secondaryGroup; - @Option(names = {"--facet-by"}, description = "Facet by") - public String facetBy; - @Option(names = {"--metric"}, description = "Select specific metrics to export.") - public List metrics; - - @Override - void run(NamedChains chains, PaResultByChain result) { - CharacteristicGroup ch = result.schema.getGroup(group()); - - DataFrame metadata = metadata(); - - DataFrame df = BasicStatistics.INSTANCE.dataFrame( - result.result.forGroup(ch), - metrics, - metadata - ); - - df = filter(df); - - List plots = BasicStatistics.INSTANCE.plots(df, - new BasicStatistics.PlotParameters( - primaryGroup, - secondaryGroup, - facetBy, - true, - true, - null, - false, - null, - null, - null, - false, - TestMethod.Wilcoxon, - TestMethod.KruskalWallis, - null, - CorrelationMethod.Pearson - )); - - writePlots(chains, plots); - } - } - - @CommandLine.Command(name = "biophysics", - sortOptions = false, - separator = " ", - description = "Export biophysical characteristics") - public static class ExportBiophysics extends ExportBasicStatistics { - @Override - String group() { - return CommandPa.Biophysics; - } - } - - @CommandLine.Command(name = "diversity", - sortOptions = false, - separator = " ", - description = "Export diversity characteristics") - public static class ExportDiversity extends ExportBasicStatistics { - @Override - String group() { - return CommandPa.Diversity; - } - } - - static abstract class ExportHeatmap extends CommandPaExportPlots { - @Option(names = {"--h-labels-size"}, description = "Width of horizontal labels. One unit corresponds to the width of one tile.") - public double hLabelsSize = -1.0; - @Option(names = {"--v-labels-size"}, description = "Height of vertical labels. One unit corresponds to the height of one tile.") - public double vLabelsSize = -1.0; - } - - static abstract class ExportHeatmapWithGroupBy extends ExportHeatmap { - @Option(names = {"--group-by"}, description = "Group heatmaps by specific metadata properties.") - public List groupBy; - } - - static abstract class ExportGeneUsage extends ExportHeatmapWithGroupBy { - abstract String group(); - - @Option(names = {"--no-samples-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of samples.") - public boolean noSamplesDendro; - @Option(names = {"--no-genes-dendro"}, description = "Do not plot dendrogram for hierarchical clusterization of genes.") - public boolean noGenesDendro; - @Option(names = {"--color-key"}, description = "Add color key layer.") - public List colorKey = new ArrayList<>(); - - @Override - void run(NamedChains chains, PaResultByChain result) { - CharacteristicGroup ch = result.schema.getGroup(group()); - - DataFrame metadata = metadata(); - DataFrame df = GeneUsage.INSTANCE.dataFrame( - result.result.forGroup(ch), - metadata - ); - df = filter(df); - - if (df.rowsCount() == 0) - return; - - Plot plot = GeneUsage.INSTANCE.plot(df, - new HeatmapParameters( - !noSamplesDendro, - !noGenesDendro, - colorKey.stream().map(it -> new ColorKey(it, Position.Bottom)).collect(Collectors.toList()), - groupBy, - hLabelsSize, - vLabelsSize, - false, - width, - height - )); - - writePlots(chains, plot); - } - } - - @CommandLine.Command(name = "vUsage", - sortOptions = false, - separator = " ", - description = "Export V gene usage heatmap") - public static class ExportVUsage extends ExportGeneUsage { - @Override - String group() { - return CommandPa.VUsage; - } - } - - @CommandLine.Command(name = "jUsage", - sortOptions = false, - separator = " ", - description = "Export J gene usage heatmap") - public static class ExportJUsage extends ExportGeneUsage { - @Override - String group() { - return CommandPa.JUsage; - } - } - - @CommandLine.Command(name = "isotypeUsage", - sortOptions = false, - separator = " ", - description = "Export isotype usage heatmap") - public static class ExportIsotypeUsage extends ExportGeneUsage { - @Override - String group() { - return CommandPa.IsotypeUsage; - } - } - - @CommandLine.Command(name = "vjUsage", - sortOptions = false, - separator = " ", - description = "Export V-J usage heatmap") - static class ExportVJUsage extends ExportHeatmap { - @Option(names = {"--no-v-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") - public boolean noVDendro; - @Option(names = {"--no-j-dendro"}, description = "Plot dendrogram for hierarchical clusterization of genes.") - public boolean noJDendro; - - @Override - void run(NamedChains chains, PaResultByChain result) { - CharacteristicGroup ch = result.schema.getGroup(CommandPa.VJUsage); - - DataFrame metadata = metadata(); - DataFrame df = VJUsage.INSTANCE.dataFrame( - result.result.forGroup(ch), - metadata - ); - df = filter(df); - - if (df.rowsCount() == 0) - return; - - List plots = VJUsage.INSTANCE.plots(df, - new HeatmapParameters( - !noJDendro, - !noVDendro, - Collections.emptyList(), - null, - hLabelsSize, - vLabelsSize, - false, - width, - height - )); - - writePlots(chains, plots); - } - } - - @CommandLine.Command(name = "overlap", - sortOptions = false, - separator = " ", - description = "Export overlap heatmap") - static class ExportOverlap extends ExportHeatmapWithGroupBy { - @Option(names = {"--no-dendro"}, description = "Plot dendrogram for hierarchical clusterization of V genes.") - public boolean noDendro; - @Option(names = {"--color-key"}, description = "Add color key layer.") - public List colorKey = new ArrayList<>(); - @Option(names = {"--metric"}, description = "Select specific metrics to export.") - public List metrics; - - DataFrame filterOverlap(DataFrame df) { - if (filterByMetadata != null) { - for (String f : filterByMetadata) { - Filter filter = MetadataKt.parseFilter(metadata(), f); - df = Overlap.INSTANCE.filterOverlap(filter, df); - } - } - return df; - } - - @Override - void run(NamedChains chains, PaResultByChain result) { - CharacteristicGroup ch = result.schema.getGroup(CommandPa.Overlap); - PostanalysisResult paResult = result.result.forGroup(ch); - Map preprocSummary = paResult.preprocSummary; - DataFrame metadata = metadata(); - - DataFrame df = Overlap.INSTANCE.dataFrame( - ch, - paResult, - metrics, - metadata - ); - df = filterOverlap(df); - - if (df.rowsCount() == 0) - return; - - if (df.get("weight").distinct().toList().size() <= 1) - return; - - DataFrame pp = Preprocessing.INSTANCE.dataFrame(paResult, null); - pp = MetadataKt.attachMetadata(pp, "sample", metadata, "sample"); - pp = filter(pp); - - HeatmapParameters par = new HeatmapParameters( - !noDendro, - !noDendro, - colorKey.stream() - .map(it -> new ColorKey(it, it.startsWith("x") ? Position.Bottom : Position.Left)) - .collect(Collectors.toList()), - groupBy, - hLabelsSize, - vLabelsSize, - false, - width, - height - ); - - List plotsAndSummary = Overlap.INSTANCE.plotsAndSummary(df, pp, par); - ExportKt.writePDF(plotDestPath(chains), plotsAndSummary); - SetPreprocessorSummary.writeCSV(tablesDestPath(chains), - ch, preprocSummary, - "\t"); - } - } - - @CommandLine.Command(name = "exportPa", - separator = " ", - description = "Export postanalysis results.", - subcommands = { - CommandLine.HelpCommand.class - }) - public static class CommandExportPaMain {} -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index b858afa8b..788e65037 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -30,6 +30,7 @@ package com.milaboratory.mixcr.cli; import com.milaboratory.cli.ValidationException; +import com.milaboratory.mixcr.cli.postanalysis.*; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.VersionInfo; import io.repseq.core.VDJCLibraryRegistry; @@ -190,23 +191,23 @@ public static CommandLine mkCmd() { cmd.getSubcommands() .get("postanalysis") - .addSubcommand("individual", CommandSpec.forAnnotatedObject(CommandPa.CommandIndividual.class)) - .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPa.CommandOverlap.class)); + .addSubcommand("individual", CommandSpec.forAnnotatedObject(CommandPaIndividual.class)) + .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPaOverlap.class)); cmd.getSubcommands() .get("exportPa") - .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExport.ExportTables.class)) - .addSubcommand("preprocSummary", CommandSpec.forAnnotatedObject(CommandPaExport.ExportPreprocessingSummary.class)) - .addSubcommand("listMetrics", CommandSpec.forAnnotatedObject(CommandPaExport.ListMetrics.class)) - .addSubcommand("biophysics", CommandSpec.forAnnotatedObject(CommandPaExport.ExportBiophysics.class)) - .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandPaExport.ExportDiversity.class)) - - .addSubcommand("vUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVUsage.class)) - .addSubcommand("jUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportJUsage.class)) - .addSubcommand("isotypeUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportIsotypeUsage.class)) - .addSubcommand("vjUsage", CommandSpec.forAnnotatedObject(CommandPaExport.ExportVJUsage.class)) - - .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPaExport.ExportOverlap.class)); + .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExportTables.class)) + .addSubcommand("preprocSummary", CommandSpec.forAnnotatedObject(CommandPaExportTablesPreprocSummary.class)) + .addSubcommand("listMetrics", CommandSpec.forAnnotatedObject(CommandPaListMetrics.class)) + .addSubcommand("biophysics", CommandSpec.forAnnotatedObject(CommandPaExportPlotsBasicStatistics.ExportBiophysics.class)) + .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandPaExportPlotsBasicStatistics.ExportDiversity.class)) + + .addSubcommand("vUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsGeneUsage.ExportVUsage.class)) + .addSubcommand("jUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsGeneUsage.ExportJUsage.class)) + .addSubcommand("isotypeUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsGeneUsage.ExportIsotypeUsage.class)) + .addSubcommand("vjUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsVJUsage.class)) + + .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPaExportPlotsOverlap.class)); cmd.setSeparator(" "); return cmd; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java new file mode 100644 index 000000000..4e6d21c4f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -0,0 +1,259 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; +import com.milaboratory.util.StringUtil; +import io.repseq.core.Chains; +import io.repseq.core.GeneFeature; +import picocli.CommandLine; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Stream; + +import static io.repseq.core.Chains.*; +import static java.util.stream.Collectors.toList; + +/** + * + */ +public abstract class CommandPa extends ACommandWithOutputMiXCR { + public static final NamedChains[] CHAINS = {TRAD_NAMED, TRB_NAMED, TRG_NAMED, IGH_NAMED, IGKL_NAMED}; + + @Parameters(description = "cloneset.{clns|clna}... result.json.gz|result.json") + public List inOut; + + @Option(description = "Use only productive CDR3s.", + names = {"--only-productive"}) + public boolean onlyProductive = false; + + @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", + names = {"-d", "--downsampling"}, + required = true) + public String downsampling; + + @Option(description = "Filter specific chains", + names = {"-c", "--chains"}) + public String chains = "ALL"; + + @Option(description = "Metadata file (csv/tsv). Must have \"sample\" column.", + names = {"-m", "--meta", "--metadata"}) + public String metadata; + + @Option(description = "Metadata categories used to isolate samples into separate groups", + names = {"-g", "--group"}) + public List isolationGroups; + + @Override + protected List getInputFiles() { + return inOut.subList(0, inOut.size() - 1) + .stream() + .flatMap(f -> { + if (Files.isDirectory(Paths.get(f))) { + try { + return Files + .list(Paths.get(f)) + .map(Path::toString); + } catch (IOException ignored) { + } + } + return Stream.of(f); + }) + .collect(toList()); + } + + @Override + protected List getOutputFiles() { + return Collections.singletonList(outputFile()); + } + + @Override + public void validate() { + super.validate(); + if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) + throwValidationException("Metadata should be .csv or .tsv"); + if (!outputFile().endsWith(".json") && !outputFile().endsWith(".json.gz")) + throwValidationException("Output file name should ends with .json.gz or .json"); + } + + private String outputFile() { + return inOut.get(inOut.size() - 1); + } + + private Path outputPath() { + return Paths.get(outputFile()).toAbsolutePath(); + } + + /** Get sample id from file name */ + static String getSampleId(String file) { + return Paths.get(file).getFileName().toString(); + } + + private static int downsamplingValue(String downsampling) { + return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); + } + + private static SetPreprocessorFactory parseDownsampling(String downsampling) { + if (downsampling.equalsIgnoreCase("no-downsampling")) { + return new NoPreprocessing.Factory<>(); + } else if (downsampling.startsWith("umi-count")) { + if (downsampling.endsWith("auto")) + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); + else { + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), 314); + } + } else { + int value = downsamplingValue(downsampling); + if (downsampling.startsWith("cumulative-top")) { + return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); + } else if (downsampling.startsWith("top")) { + return new SelectTop.Factory<>(WeightFunctions.Count, value); + } else { + throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); + } + } + } + + protected SetPreprocessorFactory downsampling() { + return downsampling(this.downsampling); + } + + protected SetPreprocessorFactory downsampling(String downsamplingStr) { + SetPreprocessorFactory downsampling = + parseDownsampling(downsamplingStr); + + if (onlyProductive) { + List> filters = new ArrayList<>(); + filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); + filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); + downsampling = downsampling.filterFirst(filters); + } + + return downsampling; + } + + private Map> _metadata = null; + + protected Map> readMetadata() { + if (metadata == null) + return null; + if (_metadata != null) + return _metadata; + List content; + try { + content = Files.readAllLines(Path.of(metadata).toAbsolutePath()); + } catch (IOException e) { + throw new RuntimeException(e); + } + if (content.isEmpty()) + return null; + String sep = metadata.endsWith(".csv") ? "," : "\t"; + + Map> result = new HashMap<>(); + String[] header = content.get(0).split(sep); + for (int iRow = 1; iRow < content.size(); iRow++) { + String[] row = content.get(iRow).split(sep); + for (int iCol = 0; iCol < row.length; iCol++) { + result.computeIfAbsent(header[iCol], __ -> new ArrayList<>()).add(row[iCol]); + } + } + + for (Map.Entry> e : result.entrySet()) { + if (e.getValue().stream().anyMatch(n -> !StringUtil.isNumber((String) n))) + continue; + + // set to double + e.setValue(e.getValue().stream().map(s -> Double.parseDouble((String) s)).collect(toList())); + } + + return _metadata = result; + } + + private static class SamplesGroup { + /** sample names */ + final List samples; + /** metadata category = value */ + final Map group; + + public SamplesGroup(List samples, Map group) { + this.samples = samples; + this.group = group; + } + } + + /** group samples into isolated groups */ + protected List groupSamples() { + if (isolationGroups == null || isolationGroups.isEmpty()) { + return Collections.singletonList(new SamplesGroup(getInputFiles(), Collections.emptyMap())); + } + + Map> metadata = readMetadata(); + @SuppressWarnings({"unchecked", "rawtypes"}) + List mSamples = (List) metadata.get("sample"); + List qSamples = getInputFiles(); + + Map sample2meta = StringUtil.matchLists(qSamples, mSamples); + for (Map.Entry e : sample2meta.entrySet()) { + if (e.getValue() == null) + throw new IllegalArgumentException("Malformed metadata: can't find metadata row for sample " + e.getKey()); + } + Map meta2sample = new HashMap<>(); + for (Map.Entry e : sample2meta.entrySet()) { + meta2sample.put(e.getValue(), e.getKey()); + } + + int nRows = metadata.entrySet().iterator().next().getValue().size(); + Map, List> samplesByGroup = new HashMap<>(); + for (int i = 0; i < nRows; i++) { + Map group = new HashMap<>(); + for (String igr : isolationGroups) { + group.put(igr, metadata.get(igr).get(i)); + } + String sample = (String) metadata.get("sample").get(i); + samplesByGroup.computeIfAbsent(group, __ -> new ArrayList<>()) + .add(meta2sample.get(sample)); + } + + return samplesByGroup.entrySet().stream().map(e -> + new SamplesGroup(e.getValue(), e.getKey())) + .collect(toList()); + } + + @Override + public void run0() throws Exception { + List results = new ArrayList<>(); + for (SamplesGroup group : groupSamples()) { + Chains c = Chains.parse(chains); + for (NamedChains knownChains : CHAINS) { + if (c.intersects(knownChains.chains)) { + results.add(run(new IsolationGroup(knownChains, group.group), group.samples)); + } + } + } + PaResult result = new PaResult(readMetadata(), isolationGroups, results); + PaResult.writeJson(outputPath(), result); + } + + abstract PaResultByGroup run(IsolationGroup group, List samples); + + + @CommandLine.Command(name = "postanalysis", + separator = " ", + description = "Run postanalysis routines.", + subcommands = { + CommandLine.HelpCommand.class + }) + public static class CommandPostanalysisMain {} +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java new file mode 100644 index 000000000..63d67b4cd --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java @@ -0,0 +1,76 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import io.repseq.core.Chains; +import io.repseq.core.Chains.NamedChains; +import picocli.CommandLine; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.nio.file.Path; +import java.util.Collections; +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +/** + * + */ +public abstract class CommandPaExport extends ACommandWithOutputMiXCR { + @Parameters(description = "Input file with PA results", index = "0", defaultValue = "pa.json.gz") + public String in; + @Option(description = "Metadata file (csv/tsv).", + names = {"-m", "--meta", "--metadata"}) + public String metadata; + @Option(description = "Export for specific chains only", + names = {"--chains"}) + public List chains; + + @Override + protected List getInputFiles() { + return Collections.singletonList(in); + } + + @Override + public void validateInfo(String inputFile) { + super.validateInfo(inputFile); + if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) + throwValidationException("Metadata should be .csv or .tsv"); + } + + /** + * Cached PA result + */ + private PaResult paResult = null; + + /** + * Get full PA result + */ + protected PaResult getPaResult() { + if (paResult != null) + return paResult; + return paResult = PaResult.readJson(Path.of(in).toAbsolutePath()); + } + + @Override + public void run0() throws Exception { + Set set = chains == null + ? null + : chains.stream().map(Chains::getNamedChains).collect(Collectors.toSet()); + + for (PaResultByGroup r : getPaResult().results) { + if (set == null || set.stream().anyMatch(c -> c.chains.intersects(r.group.chains.chains))) + run(r); + } + } + + abstract void run(PaResultByGroup result); + + @CommandLine.Command(name = "exportPa", + separator = " ", + description = "Export postanalysis results.", + subcommands = { + CommandLine.HelpCommand.class + }) + public static class CommandExportPaMain {} +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java new file mode 100644 index 000000000..35268fa63 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java @@ -0,0 +1,83 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.miplots.ExportKt; +import com.milaboratory.mixcr.postanalysis.plots.Filter; +import com.milaboratory.mixcr.postanalysis.plots.MetadataKt; +import jetbrains.letsPlot.intern.Plot; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import org.jetbrains.kotlinx.dataframe.api.DataFrameIterableKt; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.nio.file.Path; +import java.util.List; +import java.util.stream.Collectors; + +abstract class CommandPaExportPlots extends CommandPaExport { + @Option(description = "Plot width", names = {"--width"}) + public int width = 0; + @Option(description = "Plot height", names = {"--height"}) + public int height = 0; + @Option(description = "Filter by metadata. Possible filters column=value, column>=value etc.", + names = {"--filter"}) + public List filterByMetadata; + @Parameters(description = "Output PDF file name", index = "1", defaultValue = "plot.pdf") + public String out; + + protected DataFrame filter(DataFrame df) { + if (filterByMetadata != null) + for (Filter f : filterByMetadata.stream().map(f -> MetadataKt.parseFilter(metadata(), f)).collect(Collectors.toList())) + df = f.apply(df); + return df; + } + + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".pdf")) + throwValidationException("Output file must ends with .pdf extension"); + if (filterByMetadata != null && metadata == null) + throwValidationException("Filter is specified by metadata is not."); + } + + private DataFrame metadataDf; + + /** Get metadata from file */ + protected DataFrame metadata() { + if (metadataDf != null) + return metadataDf; + if (metadata != null) + return metadataDf = MetadataKt.readMetadata(metadata); + if (getPaResult().metadata != null) + return metadataDf = DataFrameIterableKt.toDataFrame(getPaResult().metadata); + return null; + } + + String plotDestStr(IsolationGroup group) { + return out.substring(0, out.length() - 4) + group.extension() + ".pdf"; + } + + Path plotDestPath(IsolationGroup group) { + return Path.of(plotDestStr(group)); + } + + String tablesDestStr(IsolationGroup group) { + return out.substring(0, out.length() - 3) + "preproc" + group.extension() + ".tsv"; + } + + Path tablesDestPath(IsolationGroup group) { + return Path.of(tablesDestStr(group)); + } + + void writeTables(IsolationGroup group, List tables) { + ExportKt.writePDF(tablesDestPath(group), tables); + } + + void writePlots(IsolationGroup group, List plots) { + ExportKt.writePDFFigure(plotDestPath(group), plots); + } + + void writePlots(IsolationGroup group, Plot plot) { + ExportKt.writePDF(tablesDestPath(group), plot); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java new file mode 100644 index 000000000..76adbe168 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -0,0 +1,85 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.miplots.stat.util.TestMethod; +import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.plots.BasicStatRow; +import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import jetbrains.letsPlot.intern.Plot; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import picocli.CommandLine; +import picocli.CommandLine.Option; + +import java.util.List; + +public abstract class CommandPaExportPlotsBasicStatistics extends CommandPaExportPlots { + abstract String group(); + + @Option(description = "Primary group", names = {"-p", "--primary-group"}) + public String primaryGroup; + @Option(description = "Secondary group", names = {"-s", "--secondary-group"}) + public String secondaryGroup; + @Option(description = "Facet by", names = {"--facet-by"}) + public String facetBy; + @Option(description = "Select specific metrics to export.", names = {"--metric"}) + public List metrics; + + @Override + void run(PaResultByGroup result) { + CharacteristicGroup ch = result.schema.getGroup(group()); + + DataFrame metadata = metadata(); + + DataFrame df = BasicStatistics.INSTANCE.dataFrame( + result.result.forGroup(ch), + metrics, + metadata + ); + + df = filter(df); + + List plots = BasicStatistics.INSTANCE.plots(df, + new BasicStatistics.PlotParameters( + primaryGroup, + secondaryGroup, + facetBy, + true, + true, + null, + false, + null, + null, + null, + false, + TestMethod.Wilcoxon, + TestMethod.KruskalWallis, + null, + CorrelationMethod.Pearson + )); + + writePlots(result.group, plots); + } + + @CommandLine.Command(name = "biophysics", + sortOptions = false, + separator = " ", + description = "Export biophysical characteristics") + public static class ExportBiophysics extends CommandPaExportPlotsBasicStatistics { + @Override + String group() { + return CommandPaIndividual.Biophysics; + } + } + + @CommandLine.Command(name = "diversity", + sortOptions = false, + separator = " ", + description = "Export diversity characteristics") + public static class ExportDiversity extends CommandPaExportPlotsBasicStatistics { + @Override + String group() { + return CommandPaIndividual.Diversity; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java new file mode 100644 index 000000000..ddd5555c5 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java @@ -0,0 +1,94 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.miplots.Position; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.plots.ColorKey; +import com.milaboratory.mixcr.postanalysis.plots.GeneUsage; +import com.milaboratory.mixcr.postanalysis.plots.GeneUsageRow; +import com.milaboratory.mixcr.postanalysis.plots.HeatmapParameters; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import jetbrains.letsPlot.intern.Plot; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import picocli.CommandLine; +import picocli.CommandLine.Option; + +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; + +public abstract class CommandPaExportPlotsGeneUsage extends CommandPaExportPlotsHeatmapWithGroupBy { + abstract String group(); + + @Option(description = "Do not plot dendrogram for hierarchical clusterization of samples.", + names = {"--no-samples-dendro"}) + public boolean noSamplesDendro; + @Option(description = "Do not plot dendrogram for hierarchical clusterization of genes.", + names = {"--no-genes-dendro"}) + public boolean noGenesDendro; + @Option(description = "Add color key layer.", + names = {"--color-key"}) + public List colorKey = new ArrayList<>(); + + @Override + void run(PaResultByGroup result) { + CharacteristicGroup ch = result.schema.getGroup(group()); + + DataFrame metadata = metadata(); + DataFrame df = GeneUsage.INSTANCE.dataFrame( + result.result.forGroup(ch), + metadata + ); + df = filter(df); + + if (df.rowsCount() == 0) + return; + + Plot plot = GeneUsage.INSTANCE.plot(df, + new HeatmapParameters( + !noSamplesDendro, + !noGenesDendro, + colorKey.stream().map(it -> new ColorKey(it, Position.Bottom)).collect(Collectors.toList()), + groupBy, + hLabelsSize, + vLabelsSize, + false, + width, + height + )); + + writePlots(result.group, plot); + } + + @CommandLine.Command(name = "vUsage", + sortOptions = false, + separator = " ", + description = "Export V gene usage heatmap") + public static class ExportVUsage extends CommandPaExportPlotsGeneUsage { + @Override + String group() { + return CommandPaIndividual.VUsage; + } + } + + @CommandLine.Command(name = "jUsage", + sortOptions = false, + separator = " ", + description = "Export J gene usage heatmap") + public static class ExportJUsage extends CommandPaExportPlotsGeneUsage { + @Override + String group() { + return CommandPaIndividual.JUsage; + } + } + + @CommandLine.Command(name = "isotypeUsage", + sortOptions = false, + separator = " ", + description = "Export isotype usage heatmap") + public static class ExportIsotypeUsage extends CommandPaExportPlotsGeneUsage { + @Override + String group() { + return CommandPaIndividual.IsotypeUsage; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java new file mode 100644 index 000000000..535115d63 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java @@ -0,0 +1,12 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import picocli.CommandLine.Option; + +public abstract class CommandPaExportPlotsHeatmap extends CommandPaExportPlots { + @Option(description = "Width of horizontal labels. One unit corresponds to the width of one tile.", + names = {"--h-labels-size"}) + public double hLabelsSize = -1.0; + @Option(description = "Height of vertical labels. One unit corresponds to the height of one tile.", + names = {"--v-labels-size"}) + public double vLabelsSize = -1.0; +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java new file mode 100644 index 000000000..89a88ca05 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java @@ -0,0 +1,11 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import picocli.CommandLine.Option; + +import java.util.List; + +public abstract class CommandPaExportPlotsHeatmapWithGroupBy extends CommandPaExportPlotsHeatmap { + @Option(description = "Group heatmaps by specific metadata properties.", + names = {"--group-by"}) + public List groupBy; +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java new file mode 100644 index 000000000..d8d74ef58 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -0,0 +1,89 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.miplots.ExportKt; +import com.milaboratory.miplots.Position; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; +import com.milaboratory.mixcr.postanalysis.plots.*; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import picocli.CommandLine; +import picocli.CommandLine.Option; + +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +@CommandLine.Command(name = "overlap", + sortOptions = false, + separator = " ", + description = "Export overlap heatmap") +public class CommandPaExportPlotsOverlap extends CommandPaExportPlotsHeatmapWithGroupBy { + @Option(description = "Plot dendrogram for hierarchical clusterization of V genes.", + names = {"--no-dendro"}) + public boolean noDendro; + @Option(description = "Add color key layer.", + names = {"--color-key"}) + public List colorKey = new ArrayList<>(); + @Option(description = "Select specific metrics to export.", + names = {"--metric"}) + public List metrics; + + DataFrame filterOverlap(DataFrame df) { + if (filterByMetadata != null) { + for (String f : filterByMetadata) { + Filter filter = MetadataKt.parseFilter(metadata(), f); + df = Overlap.INSTANCE.filterOverlap(filter, df); + } + } + return df; + } + + @Override + void run(PaResultByGroup result) { + CharacteristicGroup ch = result.schema.getGroup(CommandPaOverlap.Overlap); + PostanalysisResult paResult = result.result.forGroup(ch); + Map preprocSummary = paResult.preprocSummary; + DataFrame metadata = metadata(); + + DataFrame df = Overlap.INSTANCE.dataFrame( + ch, + paResult, + metrics, + metadata + ); + df = filterOverlap(df); + + if (df.rowsCount() == 0) + return; + + if (df.get("weight").distinct().toList().size() <= 1) + return; + + DataFrame pp = Preprocessing.INSTANCE.dataFrame(paResult, null); + pp = MetadataKt.attachMetadata(pp, "sample", metadata, "sample"); + pp = filter(pp); + + HeatmapParameters par = new HeatmapParameters( + !noDendro, + !noDendro, + colorKey.stream() + .map(it -> new ColorKey(it, it.startsWith("x") ? Position.Bottom : Position.Left)) + .collect(Collectors.toList()), + groupBy, + hLabelsSize, + vLabelsSize, + false, + width, + height + ); + + List plotsAndSummary = Overlap.INSTANCE.plotsAndSummary(df, pp, par); + ExportKt.writePDF(plotDestPath(result.group), plotsAndSummary); + SetPreprocessorSummary.writeCSV(tablesDestPath(result.group), + ch, preprocSummary, + "\t"); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java new file mode 100644 index 000000000..d172817c1 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java @@ -0,0 +1,55 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.plots.HeatmapParameters; +import com.milaboratory.mixcr.postanalysis.plots.VJUsage; +import com.milaboratory.mixcr.postanalysis.plots.VJUsageRow; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import jetbrains.letsPlot.intern.Plot; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import picocli.CommandLine; +import picocli.CommandLine.Option; + +import java.util.Collections; +import java.util.List; + +@CommandLine.Command(name = "vjUsage", + sortOptions = false, + separator = " ", + description = "Export V-J usage heatmap") +public class CommandPaExportPlotsVJUsage extends CommandPaExportPlotsHeatmap { + @Option(description = "Plot dendrogram for hierarchical clusterization of V genes.", names = {"--no-v-dendro"}) + public boolean noVDendro; + @Option(description = "Plot dendrogram for hierarchical clusterization of genes.", names = {"--no-j-dendro"}) + public boolean noJDendro; + + @Override + void run(PaResultByGroup result) { + CharacteristicGroup ch = result.schema.getGroup(CommandPaIndividual.VJUsage); + + DataFrame metadata = metadata(); + DataFrame df = VJUsage.INSTANCE.dataFrame( + result.result.forGroup(ch), + metadata + ); + df = filter(df); + + if (df.rowsCount() == 0) + return; + + List plots = VJUsage.INSTANCE.plots(df, + new HeatmapParameters( + !noJDendro, + !noVDendro, + Collections.emptyList(), + null, + hLabelsSize, + vLabelsSize, + false, + width, + height + )); + + writePlots(result.group, plots); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java new file mode 100644 index 000000000..15bd50e12 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java @@ -0,0 +1,27 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupOutputExtractor; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; +import com.milaboratory.mixcr.postanalysis.ui.OutputTable; +import picocli.CommandLine; + +@CommandLine.Command(name = "tables", + sortOptions = false, + separator = " ", + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype, Overlap") +public final class CommandPaExportTables extends CommandPaExportTablesBase { + @Override + void run1(PaResultByGroup result) { + for (CharacteristicGroup table : result.schema.tables) { + writeTables(outExtension(result.group), result.result.getTable(table)); + } + } + + void writeTables(String extension, CharacteristicGroupResult tableResult) { + for (CharacteristicGroupOutputExtractor view : tableResult.group.views) + for (OutputTable t : view.getTables(tableResult).values()) { + t.writeCSV(outDir(), outPrefix() + ".", separator(), extension); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java new file mode 100644 index 000000000..905d59cf2 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java @@ -0,0 +1,48 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import picocli.CommandLine.Parameters; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +abstract class CommandPaExportTablesBase extends CommandPaExport { + @Parameters(description = "Path for output files", index = "1", defaultValue = "path/table.tsv") + public String out; + + @Override + public void validate() { + super.validate(); + if (!out.endsWith(".tsv") && !out.endsWith(".csv")) + throwValidationException("Output file must have .tsv or .csv extension"); + } + + protected Path outDir() { + return Path.of(out).toAbsolutePath().getParent(); + } + + protected String outPrefix() { + String fName = Path.of(out).getFileName().toString(); + return fName.substring(0, fName.length() - 4); + } + + protected String outExtension(IsolationGroup group) { + return group.extension() + "." + out.substring(out.length() - 3); + } + + protected String separator() { + return out.endsWith("tsv") ? "\t" : ","; + } + + @Override + void run(PaResultByGroup result) { + try { + Files.createDirectories(outDir()); + } catch (IOException e) { + throw new RuntimeException(e); + } + run1(result); + } + + abstract void run1(PaResultByGroup result); +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java new file mode 100644 index 000000000..3e3c7fe1b --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java @@ -0,0 +1,17 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; +import picocli.CommandLine; + +@CommandLine.Command(name = "preprocSummary", + sortOptions = false, + separator = " ", + description = "Export preprocessing summary tables.") +public final class CommandPaExportTablesPreprocSummary extends CommandPaExportTablesBase { + @Override + void run1(PaResultByGroup result) { + SetPreprocessorSummary.writeToCSV( + outDir().resolve(outPrefix() + outExtension(result.group)), + result.result.preprocSummary, null, separator()); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java new file mode 100644 index 000000000..166b53d78 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -0,0 +1,132 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.additive.AAProperties; +import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; +import com.milaboratory.mixcr.postanalysis.ui.*; +import com.milaboratory.util.SmartProgressReporter; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; +import picocli.CommandLine; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.stream.Collectors; + +import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; + +@SuppressWarnings("ArraysAsListWithZeroOrOneArgument") +@CommandLine.Command(name = "individual", + sortOptions = false, + separator = " ", + description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") +public class CommandPaIndividual extends CommandPa { + static final String + Biophysics = "biophysics", + Diversity = "diversity", + VUsage = "vUsage", + JUsage = "JUsage", + VJUsage = "VJUsage", + IsotypeUsage = "IsotypeUsage", + CDR3Spectratype = "CDR3Spectratype", + VSpectratype = "VSpectratype", + VSpectratypeMean = "VSpectratypeMean"; + + public CommandPaIndividual() {} + + @Override + @SuppressWarnings({"unchecked", "rawtypes"}) + PaResultByGroup run(IsolationGroup group, List samples) { + List> groups = new ArrayList<>(); + + SetPreprocessorFactory downsampling = downsampling() + .filterFirst(new ElementPredicate.IncludeChains(group.chains.chains)); + + groups.add(new CharacteristicGroup<>(Biophysics, + Arrays.asList( + weightedLengthOf(downsampling, GeneFeature.CDR3, false).setName("CDR3 length, nt"), + weightedLengthOf(downsampling, GeneFeature.CDR3, true).setName("CDR3 length, aa"), + weightedLengthOf(downsampling, GeneFeature.VJJunction, false).setName("NDN length, nt"), + weightedAddedNucleotides(downsampling).setName("Added N, nt"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Strength"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Hydrophobicity"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Surface"), + weightedBiophysics(downsampling, AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), + weightedBiophysics(downsampling, AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") + ), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>(Diversity, + Arrays.asList(new DiversityCharacteristic<>("Diversity", new WeightFunctions.Count(), + downsampling, + new DiversityMeasure[]{ + DiversityMeasure.Observed, + DiversityMeasure.Clonality, + DiversityMeasure.ShannonWeiner, + DiversityMeasure.InverseSimpson, + DiversityMeasure.Chao1, + DiversityMeasure.Gini + })), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>(VUsage, + Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Variable)), + Arrays.asList(new GroupSummary<>()) + )); + groups.add(new CharacteristicGroup<>(JUsage, + Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Joining)), + Arrays.asList(new GroupSummary<>()) + )); + groups.add(new CharacteristicGroup<>(VJUsage, + Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(downsampling)), + Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) + )); + + groups.add(new CharacteristicGroup<>(IsotypeUsage, + Arrays.asList(AdditiveCharacteristics.isotypeUsage(downsampling)), + Arrays.asList(new GroupSummary<>()) + )); + + groups.add(new CharacteristicGroup<>(CDR3Spectratype, + Arrays.asList(new SpectratypeCharacteristic("CDR3 spectratype", + downsampling, 10, + new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), + Collections.singletonList(new GroupSummary<>()))); + + groups.add(new CharacteristicGroup<>(VSpectratype, + Arrays.asList(AdditiveCharacteristics.VSpectratype(downsampling)), + Collections.singletonList(new GroupSummary<>()))); + + groups.add(new CharacteristicGroup<>(VSpectratypeMean, + Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(downsampling)), + Collections.singletonList(new GroupSummary<>()))); + + PostanalysisSchema schema = new PostanalysisSchema<>(groups); + PostanalysisRunner runner = new PostanalysisRunner<>(); + runner.addCharacteristics(schema.getAllCharacterisitcs()); + + List datasets = samples.stream() + .map(file -> + new ClonotypeDataset(getSampleId(file), file, VDJCLibraryRegistry.getDefault()) + ).collect(Collectors.toList()); + + System.out.println("Running for " + group); + SmartProgressReporter.startProgressReport(runner); + return new PaResultByGroup(group, schema, runner.run(datasets)); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java new file mode 100644 index 000000000..311d2c538 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java @@ -0,0 +1,53 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.cli.ACommandMiXCR; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.util.GlobalObjectMappers; +import picocli.CommandLine; +import picocli.CommandLine.Parameters; + +import java.io.File; +import java.io.IOException; +import java.util.Arrays; + +@CommandLine.Command(name = "listMetrics", + sortOptions = false, + separator = " ", + description = "List available metrics") +public class CommandPaListMetrics extends ACommandMiXCR { + @Parameters(description = "Input file with PA results", index = "0") + public String in; + + @Override + public void run0() { + PaResult paResult; + try { + paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + } catch (IOException e) { + throwValidationException("Corrupted PA file."); + throw new RuntimeException(); + } + + PaResultByGroup result = paResult.results.get(0); + CharacteristicGroup + biophys = result.schema.getGroup(CommandPaIndividual.Biophysics), + diversity = result.schema.getGroup(CommandPaIndividual.Diversity); + + for (int i = 0; i < 2; i++) { + System.out.println(); + CharacteristicGroup gr = i == 0 ? biophys : diversity; + if (i == 0) + System.out.println("Biophysics metrics:"); + else + System.out.println("Diversity metrics:"); + result.result.forGroup(gr) + .data.values().stream() + .flatMap(d -> d.data.values() + .stream().flatMap(ma -> Arrays.stream(ma.data))) + .map(m -> m.key) + .distinct() + .forEach(metric -> System.out.println(" " + metric)); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java new file mode 100644 index 000000000..fc940d41f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -0,0 +1,178 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.postanalysis.*; +import com.milaboratory.mixcr.postanalysis.overlap.*; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.OverlapSummary; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema; +import com.milaboratory.util.LambdaSemaphore; +import com.milaboratory.util.SmartProgressReporter; +import io.repseq.core.Chains; +import io.repseq.core.GeneFeature; +import io.repseq.core.VDJCLibraryRegistry; +import picocli.CommandLine; +import picocli.CommandLine.Option; + +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; + +import static java.util.stream.Collectors.*; + +@CommandLine.Command(name = "overlap", + sortOptions = false, + separator = " ", + description = "Overlap analysis") +public class CommandPaOverlap extends CommandPa { + public static String Overlap = "overlap"; + + @Option(description = "Override downsampling for F2 umi|d[number]|f[number]", + names = {"--f2-downsampling"}) + public String f2downsampling; + + public CommandPaOverlap() {} + + @Override + @SuppressWarnings("unchecked") + PaResultByGroup run(IsolationGroup group, List samples) { + SetPreprocessorFactory downsampling = downsampling(); + + Map> downsamplingByType = new HashMap<>(); + downsamplingByType.put(OverlapType.D, downsampling); + downsamplingByType.put(OverlapType.F2, f2downsampling == null + ? downsampling + : downsampling(f2downsampling)); + downsamplingByType.put(OverlapType.R_Intersection, downsampling); + + List> ordering = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); + OverlapPostanalysisSettings overlapPA = new OverlapPostanalysisSettings( + ordering, + new WeightFunctions.Count(), + downsamplingByType + ); + + PostanalysisSchema> schema = overlapPA.getSchema(samples.size(), group.chains.chains); + + // Limits concurrency across all readers + LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(32); + List readers = samples + .stream() + .map(s -> { + try { + return mkCheckedReader( + Paths.get(s).toAbsolutePath(), + concurrencyLimiter); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); + + OverlapDataset overlapDataset = OverlapUtil.overlap( + samples.stream().map(CommandPa::getSampleId).collect(toList()), + ordering, + readers); + + PostanalysisRunner> runner = new PostanalysisRunner<>(); + runner.addCharacteristics(schema.getAllCharacterisitcs()); + + System.out.println("Running for " + group); + SmartProgressReporter.startProgressReport(runner); + PostanalysisResult result = runner.run(overlapDataset); + + return new PaResultByGroup(group, schema, result); + } + + public static CloneReader mkCheckedReader(Path path, + LambdaSemaphore concurrencyLimiter) throws IOException { + ClnsReader inner = new ClnsReader( + path, + VDJCLibraryRegistry.getDefault(), + concurrencyLimiter); + return new CloneReader() { + @Override + public VDJCSProperties.CloneOrdering ordering() { + return inner.ordering(); + } + + @Override + public OutputPortCloseable readClones() { + OutputPortCloseable in = inner.readClones(); + return new OutputPortCloseable() { + @Override + public void close() { + in.close(); + } + + @Override + public Clone take() { + Clone t = in.take(); + if (t == null) + return null; + if (t.getFeature(GeneFeature.CDR3) == null) + return take(); + return t; + } + }; + } + + @Override + public void close() throws Exception { + inner.close(); + } + + @Override + public int numberOfClones() { + return inner.numberOfClones(); + } + }; + } + + @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") + static final class OverlapPostanalysisSettings { + final List> ordering; + final WeightFunction weight; + final Map> preprocessors; + final Map, List> groupped; + + OverlapPostanalysisSettings(List> ordering, + WeightFunction weight, + Map> preprocessors) { + this.ordering = ordering; + this.weight = weight; + this.preprocessors = preprocessors; + this.groupped = preprocessors.entrySet().stream().collect(groupingBy(Map.Entry::getValue, mapping(Map.Entry::getKey, toList()))); + } + + private SetPreprocessorFactory> getPreprocessor(OverlapType type, Chains chain) { + return new OverlapPreprocessorAdapter.Factory<>(preprocessors.get(type).filterFirst(new ElementPredicate.IncludeChains(chain))); + } + + //fixme only productive?? + public List> getCharacteristics(int i, int j, Chains chain) { + return groupped.entrySet().stream().map(e -> new OverlapCharacteristic<>("overlap_" + i + "_" + j + " / " + e.getValue().stream().map(t -> t.name).collect(Collectors.joining(" / ")), weight, + new OverlapPreprocessorAdapter.Factory<>(e.getKey().filterFirst(new ElementPredicate.IncludeChains(chain))), + e.getValue().toArray(new OverlapType[0]), + i, j)).collect(toList()); + } + + public PostanalysisSchema> getSchema(int nSamples, Chains chain) { + List> overlaps = new ArrayList<>(); + for (int i = 0; i < nSamples; ++i) + for (int j = i; j < nSamples; ++j) // j=i to include diagonal elements + overlaps.addAll(getCharacteristics(i, j, chain)); + + return new PostanalysisSchema<>(Collections.singletonList( + new CharacteristicGroup<>(Overlap, + overlaps, + Arrays.asList(new OverlapSummary<>()) + ))); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java new file mode 100644 index 000000000..e4e60bb44 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java @@ -0,0 +1,76 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; +import com.fasterxml.jackson.databind.annotation.JsonSerialize; +import io.repseq.core.Chains; +import io.repseq.core.Chains.NamedChains; + +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Objects; +import java.util.stream.Collectors; + +/** + * Group of samples with specific metadata properties projected onto specific chains. Common downsampling is applied for + * all samples in the group. + */ +public class IsolationGroup { + /** Chains */ + @JsonProperty("chains") + @JsonSerialize(using = Chains.KnownChainsSerializer.class) + @JsonDeserialize(using = Chains.KnownChainsDeserializer.class) + final NamedChains chains; + /** Metadata field=value; always sorted by key */ + @JsonProperty("groups") + final Map group; + + @JsonCreator + public IsolationGroup(@JsonProperty("chains") NamedChains chains, + @JsonProperty("groups") Map group) { + this.chains = chains; + this.group = group == null ? null : sortByKey(group); + } + + private static LinkedHashMap sortByKey(Map group) { + return group.entrySet().stream().sorted(Map.Entry.comparingByKey()).collect(Collectors.toMap( + Map.Entry::getKey, Map.Entry::getValue, (a, __) -> a, LinkedHashMap::new + )); + } + + @Override + public String toString() { + StringBuilder sb = new StringBuilder(); + sb.append("chains=").append(chains.name); + for (Map.Entry e : group.entrySet()) { + sb.append(",").append(e.getKey()).append("=").append(e.getValue()); + } + return sb.toString(); + } + + /** + * Generate file extension for specific group + */ + public String extension() { + StringBuilder sb = new StringBuilder(); + sb.append(".").append(chains.name); + for (Object v : group.values()) { + sb.append(".").append(v); + } + return sb.toString(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + IsolationGroup that = (IsolationGroup) o; + return Objects.equals(chains, that.chains) && Objects.equals(group, that.group); + } + + @Override + public int hashCode() { + return Objects.hash(chains, group); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java new file mode 100644 index 000000000..c0685032e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java @@ -0,0 +1,74 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.util.GlobalObjectMappers; + +import java.io.*; +import java.nio.file.Path; +import java.util.List; +import java.util.Map; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; + +/** + * PA results (written to disk) + */ +@JsonAutoDetect +public final class PaResult { + /** Metadata. Null if was not specified */ + @JsonProperty("metadata") + public final Map> metadata; + /** Metadata categories used to isolate samples into groups */ + @JsonProperty("isolatedGroups") + public final List isolationGroups; + /** Results for groups */ + @JsonProperty("results") + public final List results; + + @JsonCreator + public PaResult(@JsonProperty("metadata") Map> metadata, + @JsonProperty("isolationGroups") List isolationGroups, + @JsonProperty("results") List results) { + this.metadata = metadata; + this.isolationGroups = isolationGroups; + this.results = results; + } + + public static void writeJson(Path path, PaResult paResult) { + if (path.getFileName().toString().endsWith(".json")) { + try { + GlobalObjectMappers.PRETTY.writeValue(path.toFile(), paResult); + } catch (IOException e) { + throw new RuntimeException(e); + } + } else if (path.getFileName().toString().endsWith(".json.gz")) { + try (FileOutputStream fs = new FileOutputStream(path.toFile()); + GZIPOutputStream zs = new GZIPOutputStream(new BufferedOutputStream(fs))) { + GlobalObjectMappers.ONE_LINE.writeValue(zs, paResult); + } catch (IOException e) { + throw new RuntimeException(e); + } + } else + throw new IllegalArgumentException("path should ends with .json.gz or .json but was " + path); + } + + public static PaResult readJson(Path path) { + if (path.getFileName().toString().endsWith(".json")) { + try { + return GlobalObjectMappers.PRETTY.readValue(path.toFile(), PaResult.class); + } catch (IOException e) { + throw new RuntimeException(e); + } + } else if (path.getFileName().toString().endsWith(".json.gz")) + try (FileInputStream fs = new FileInputStream(path.toFile()); + GZIPInputStream zs = new GZIPInputStream(new BufferedInputStream(fs))) { + return GlobalObjectMappers.ONE_LINE.readValue(zs, PaResult.class); + } catch (IOException e) { + throw new RuntimeException(e); + } + else + throw new IllegalArgumentException("path should ends with .json.gz or .json"); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java new file mode 100644 index 000000000..e990addc9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java @@ -0,0 +1,29 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema; + +/** + * PA results for isolation group. + */ +@JsonAutoDetect +public final class PaResultByGroup { + @JsonProperty("isolationGroup") + public final IsolationGroup group; + @JsonProperty("schema") + public final PostanalysisSchema schema; + @JsonProperty("result") + public final PostanalysisResult result; + + @JsonCreator + public PaResultByGroup(@JsonProperty("isolationGroup") IsolationGroup group, + @JsonProperty("schema") PostanalysisSchema schema, + @JsonProperty("result") PostanalysisResult result) { + this.group = group; + this.schema = schema; + this.result = result; + } +} diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt index b6d98d929..ea6618505 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt @@ -7,8 +7,6 @@ import org.jetbrains.kotlinx.dataframe.RowFilter import org.jetbrains.kotlinx.dataframe.api.* import org.jetbrains.kotlinx.dataframe.io.read import org.jetbrains.kotlinx.dataframe.io.readTSV -import java.util.* -import javax.xml.crypto.Data fun AnyFrame.isNumeric(col: String) = this[col].all { it == null || it is Number } fun AnyFrame.isCategorial(col: String) = !isNumeric(col) @@ -48,7 +46,7 @@ fun attachMetadata( meta: Metadata, metaCol: String ) = run { - val m = matchLists( + val m = StringUtil.matchLists( data[dataCol].distinct().cast().toList(), meta[metaCol].distinct().cast().toList(), ) @@ -63,48 +61,6 @@ fun attachMetadata( .remove("_meta_join_") } -fun matchLists(target: List, query: List): Map { - val matched: MutableMap>> = HashMap() - for (t in target) { - val matchedForKey = PriorityQueue>( - Comparator.comparing { -it.second } - ) - - for (q in query) { - val a = t.lowercase(Locale.getDefault()) - val b = q.lowercase(Locale.getDefault()) - val match = StringUtil.longestCommonSubstring(a, b) - val score = 2.0 * (0.5 + match) / (1 + a.length + b.length) - matchedForKey.add(q to score) - } - - matched[t] = matchedForKey - } - - val unmatchedQ = query.toMutableSet() - val r = mutableMapOf() - - for ((t, q) in matched.toList().sortedBy { kv -> -kv.second.maxOf { it.second } }) { - if (q.isEmpty()) { - r[t] = null - continue - } - var m: String? = null - while (!q.isEmpty()) { - val candidate = q.poll() - val wasUnmatched = unmatchedQ.remove(candidate.first) - if (wasUnmatched) { - m = candidate.first - break - } - } - r[t] = m - } - - return r -} - - fun Metadata.parseFilter(expr: String) = // equality if (expr.contains("=")) { diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java similarity index 92% rename from src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java rename to src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java index d05896703..3e29cae68 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java @@ -1,5 +1,6 @@ -package com.milaboratory.mixcr.cli; +package com.milaboratory.mixcr.cli.postanalysis; +import com.milaboratory.mixcr.cli.Main; import org.junit.Ignore; import org.junit.Test; @@ -44,7 +45,7 @@ public void test3() { // "--height", "5000", "--chains", "TRA", "--filter", "Chain=TRA", - "--filter", "CellPopulation=CD4mem", +// "--filter", "CellPopulation=CD4mem", "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", "--color-key", "x_Tissue", "--color-key", "x_CellPopulation", "--color-key", "y_MouseID", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java similarity index 99% rename from src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java rename to src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java index 6d6747ccb..064f6102f 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandPaTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java @@ -1,5 +1,6 @@ -package com.milaboratory.mixcr.cli; +package com.milaboratory.mixcr.cli.postanalysis; +import com.milaboratory.mixcr.cli.Main; import org.junit.Ignore; import org.junit.Test; diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java new file mode 100644 index 000000000..fe7635df4 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java @@ -0,0 +1,20 @@ +package com.milaboratory.mixcr.cli.postanalysis; + + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.milaboratory.util.GlobalObjectMappers; +import io.repseq.core.Chains; +import org.junit.Assert; +import org.junit.Test; + +import java.util.HashMap; + +public class IsolationGroupTest { + @Test + public void test1() throws JsonProcessingException { + IsolationGroup expected = new IsolationGroup(Chains.TRA_NAMED, new HashMap<>()); + String str = GlobalObjectMappers.PRETTY.writeValueAsString(expected); + IsolationGroup actual = GlobalObjectMappers.PRETTY.readValue(str, IsolationGroup.class); + Assert.assertEquals(expected, actual); + } +} \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatisticsTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatisticsTest.kt deleted file mode 100644 index 387ab8f2e..000000000 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/plots/BasicStatisticsTest.kt +++ /dev/null @@ -1,47 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import com.milaboratory.miplots.writePDF -import com.milaboratory.mixcr.cli.CommandPa -import com.milaboratory.util.GlobalObjectMappers -import io.repseq.core.Chains -import org.jetbrains.kotlinx.dataframe.DataFrame -import org.jetbrains.kotlinx.dataframe.api.filter -import org.jetbrains.kotlinx.dataframe.io.read -import org.junit.Test -import java.nio.file.Paths - - -/** - * - */ -internal class BasicStatisticsTest { - @Test - fun test1() { - val meta = DataFrame.read(javaClass.getResource("/postanalysis/metadata.csv")!!) - val pa = GlobalObjectMappers.PRETTY.readValue( - javaClass.getResource("/postanalysis/sample_pa.json"), - CommandPa.PaResult::class.java - ) - - val igh = pa.results[Chains.IGH_NAMED]!! - - - var df = BasicStatistics.dataFrame(igh.result.forGroup(igh.schema.getGroup("biophysics")), null) - df = df.withMetadata(meta) - - df = df.filter { metric == "ntLengthOfCDR3" } - - val plt = BasicStatistics.plot( - df, BasicStatistics.PlotParameters( - primaryGroup = "Cat3", - secondaryGroup = "Cat2", - facetBy = null - ) - ) - - writePDF( - Paths.get("scratch/pa/diversity.pdf"), - plt - ) - } -} From 0094cab7902dca6461cbfe7088df3831ebffdfca Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Sun, 3 Apr 2022 04:13:36 +0400 Subject: [PATCH 172/282] chore: minor cleanup for gradle build script --- build.gradle.kts | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 04bbd2c7f..3b73715c7 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -3,6 +3,8 @@ import com.palantir.gradle.gitversion.VersionDetails import groovy.lang.Closure import java.net.InetAddress +gradle.startParameter.excludedTaskNames += listOf("assembleDist", "assembleShadowDist", "distTar", "distZip", "installDist", "installShadowDist", "shadowDistTar", "shadowDistZip") + plugins { `java-library` application @@ -107,6 +109,7 @@ val shadowJar = tasks.withType { } val distributionZip by tasks.registering(Zip::class) { + group = "distribution" archiveFileName.set("${project.name}.zip") destinationDirectory.set(file("$buildDir/distributions")) from(shadowJar) { @@ -143,10 +146,10 @@ tasks.test { minHeapSize = "1024m" maxHeapSize = "2048m" - miCiStage?.let { - if (it == "test") { - systemProperty("longTests", "true"); - } - } + miCiStage?.let { + if (it == "test") { + systemProperty("longTests", "true"); + } + } longTests?.let { systemProperty("longTests", it) } } From 27a68769ab00d1805ac8967f66a40b81d05d9073 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Mon, 11 Apr 2022 02:34:48 +0400 Subject: [PATCH 173/282] feat: milib upgrade --- build.gradle.kts | 12 ++++++------ .../mixcr/export/FieldExtractorsTest.java | 2 +- .../mixcr/vdjaligners/VDJCAlignerWithMergeTest.java | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 3b73715c7..71653b429 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -57,9 +57,9 @@ repositories { } } -val milibVersion = "1.15.0" +val milibVersion = "1.15.0-16-master" val repseqioVersion = "1.3.5-24-master" -val jacksonVersion = "2.13.2" +val jacksonVersion = "2.13.2.2" dependencies { api("com.milaboratory:milib:$milibVersion") @@ -68,15 +68,15 @@ dependencies { } implementation("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion") - implementation("commons-io:commons-io:2.7") - implementation("org.lz4:lz4-java:1.4.1") + implementation("commons-io:commons-io:2.11.0") + implementation("org.lz4:lz4-java:1.8.0") implementation("net.sf.trove4j:trove4j:3.0.3") implementation("info.picocli:picocli:4.1.1") implementation("com.google.guava:guava:31.1-jre") testImplementation("junit:junit:4.13.2") implementation(testFixtures("com.milaboratory:milib:$milibVersion")) - testImplementation("org.mockito:mockito-all:1.9.5") + testImplementation("org.mockito:mockito-all:1.10.19") } val writeBuildProperties by tasks.registering(WriteProperties::class) { @@ -148,7 +148,7 @@ tasks.test { miCiStage?.let { if (it == "test") { - systemProperty("longTests", "true"); + systemProperty("longTests", "true") } } longTests?.let { systemProperty("longTests", it) } diff --git a/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java b/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java index fa62d340a..ad2c5a131 100644 --- a/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java +++ b/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java @@ -124,7 +124,7 @@ public Integer[][] go(String seq, int len, int offset1, int offset2, int offset3 Integer[][] r = goAssert.go("{CDR3Begin(-250):VEnd(-3)} 'CCAAA' {DBegin(0):DEnd(0)} 'AAA' {JBegin(2):FR4End} " + "{CBegin}C*100 N*100", - 100, 240, 307, 450, ""); + 100, 230, 307, 450, ""); assertExportPoint(r[0], ReferencePoint.VEnd, -3); assertExportPoint(r[0], ReferencePoint.DBegin, 0); assertExportPoint(r[0], ReferencePoint.DEnd, 0); diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java index f897e6de3..379506a6e 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java @@ -84,7 +84,7 @@ public void test1() throws Exception { if (result.alignment != null) { alignemntsList.add(result.alignment); for (VDJCHit hit : result.alignment.getHits(GeneType.Variable)) - if (hit.getAlignment(0) != null && hit.getAlignment(1) != null) + if (hit.getAlignment(0) != null && hit.numberOfTargets() > 1 && hit.getAlignment(1) != null) ++leftHit; } } From 7fc179f2cd0401c2bbba4342490bfc9cc75ef52e Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 13 Apr 2022 01:23:35 +0400 Subject: [PATCH 174/282] feat: JsonOverrider moved to milib --- build.gradle.kts | 2 +- .../milaboratory/mixcr/cli/CommandAlign.java | 1 + .../mixcr/cli/CommandAnalyze.java | 1 + .../mixcr/cli/CommandAssemble.java | 1 + .../mixcr/cli/CommandAssembleContigs.java | 1 + .../cli/CommandAssemblePartialAlignments.java | 1 + .../mixcr/cli/CommandGroupCells.java | 3 +- .../milaboratory/mixcr/cli/JsonOverrider.java | 225 ------------------ .../mixcr/cli/JsonOverriderTest.java | 1 + 9 files changed, 8 insertions(+), 228 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java diff --git a/build.gradle.kts b/build.gradle.kts index 71653b429..87537506d 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -57,7 +57,7 @@ repositories { } } -val milibVersion = "1.15.0-16-master" +val milibVersion = "1.15.0-18-master" val repseqioVersion = "1.3.5-24-master" val jacksonVersion = "2.13.2.2" diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 8ef25cee1..1745fe531 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -67,6 +67,7 @@ import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.GlobalObjectMappers; +import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.*; import picocli.CommandLine; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index a4135d6b1..b1c424e80 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -33,6 +33,7 @@ import com.milaboratory.cli.ACommandWithSmartOverwrite; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.util.JsonOverrider; import io.repseq.core.Chains; import io.repseq.core.GeneFeature; import picocli.CommandLine; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index c8a4a15c1..50ccd7c8b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -41,6 +41,7 @@ import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.ArraysUtils; +import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.*; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 25ee8d32d..1c7fced65 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -49,6 +49,7 @@ import com.milaboratory.primitivio.PipeDataInputReader; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index f773e9422..65b3cd823 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -35,6 +35,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssembler; import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssemblerParameters; +import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.SmartProgressReporter; import picocli.CommandLine.Command; import picocli.CommandLine.Option; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 82a12ca19..44193b324 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -11,11 +11,10 @@ import com.milaboratory.mixcr.tags.DropletCloneGraph; import com.milaboratory.mixcr.tags.DropletCloneGraphParameters; import com.milaboratory.mixcr.tags.DropletCloneGraphReport; +import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.ProgressAndStage; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.impl.Constants; -import gnu.trove.iterator.TObjectIntIterator; -import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; import gnu.trove.map.hash.TObjectIntHashMap; import io.repseq.core.VDJCLibraryRegistry; diff --git a/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java b/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java deleted file mode 100644 index 410f12680..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java +++ /dev/null @@ -1,225 +0,0 @@ -/* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. - */ -package com.milaboratory.mixcr.cli; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.NullNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import com.milaboratory.util.GlobalObjectMappers; -import com.milaboratory.util.ParseUtil; - -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; -import java.util.Map; - -public class JsonOverrider { - static boolean suppressSameValueOverride = false; - - public static T override(T object, Class clazz, String... commands) { - JsonNode node = GlobalObjectMappers.ONE_LINE.valueToTree(object); - for (String command : commands) - if (!override(node, command)) - return null; - try { - return (T) GlobalObjectMappers.ONE_LINE.treeToValue(node, clazz); - } catch (JsonProcessingException e) { - throw new IllegalArgumentException(); - } - } - - public static T override(T object, Class clazz, Map overrideMap) { - JsonNode node = GlobalObjectMappers.ONE_LINE.valueToTree(object); - for (Map.Entry entry : overrideMap.entrySet()) - if (!override(node, entry.getKey(), entry.getValue())) - return null; - try { - return (T) GlobalObjectMappers.ONE_LINE.treeToValue(node, clazz); - } catch (JsonProcessingException e) { - throw new IllegalArgumentException(e); - } - } - - public static boolean override(JsonNode node, String command) { - String[] split = command.split("=", 2); - String path = split[0]; - String value = split[1]; - return override(node, path, value); - } - - public static boolean override(JsonNode node, String path, String value) { - return override1(node, path, value, false); - } - - private static boolean override1(JsonNode node, String path, String value, boolean v) { - if (node == null) - return false; - value = value.replaceAll("^[\'\"]", "").replaceAll("[\'\"]$", ""); - boolean b = false; - if (override0(node, path, value)) - b = true; - else { - Iterator iterator = node.iterator(); - while (iterator.hasNext()) - if (override1(iterator.next(), path, value, b || v)) - b = true; - } - if (v && b) - throw new IllegalArgumentException("Multiple matches of parameter " + path); - return b; - } - - private static void overrideWarn(String fieldName, String newValue) { - if (!suppressSameValueOverride) - System.out.printf("WARNING: unnecessary override -O%s=%s with the same value.\n", fieldName, newValue); - } - - public static boolean override0(JsonNode node, String path, String value) { - String[] pathArray = path.split("\\."); - for (int i = 0; i < pathArray.length - 1; ++i) - if ((node = node.get(pathArray[i])) == null) - return false; - - String fieldName = pathArray[pathArray.length - 1]; - - boolean setToNull = value.equalsIgnoreCase("null"); - - if (!(node instanceof ObjectNode)) - return false; - - ObjectNode oNode = (ObjectNode) node; - - JsonNode valueNode = oNode.get(fieldName); - if (valueNode == null) { - if (setToNull) - overrideWarn(fieldName, value); - return setToNull; - } - - JsonNode valueTree = null; - if (value.startsWith("{") && value.endsWith("}")) { - try { - valueTree = GlobalObjectMappers.ONE_LINE.readTree(value); - } catch (Throwable ignored) {} - } - - if (valueNode instanceof ArrayNode) { - ArrayNode arrayNode = (ArrayNode) valueNode; - List oldValues = new ArrayList<>(); - final Iterator it = arrayNode.elements(); - while (it.hasNext()) - oldValues.add(it.next().asText()); - - arrayNode.removeAll(); - - boolean settingTheSame; - if (!value.startsWith("[") || !value.endsWith("]")) { - arrayNode.add(value); - settingTheSame = oldValues.size() == 1 && oldValues.get(0).equalsIgnoreCase(value); - } else { - value = value.substring(1, value.length() - 1); - String[] values = ParseUtil.splitWithBrackets(value, ',', "(){}[]"); - settingTheSame = true; - for (int i = 0; i < values.length; i++) { - arrayNode.add(values[i]); - if (settingTheSame && oldValues.size() > i) - settingTheSame = oldValues.get(i).equalsIgnoreCase(values[i]); - } - } - if (settingTheSame) - overrideWarn(fieldName, value); - return true; - } else if (valueTree != null) { - oNode.set(fieldName, valueTree); - return true; - } else if (valueNode.isTextual()) { - if (valueNode.asText().equals(value)) - overrideWarn(fieldName, value); - oNode.put(fieldName, value); - return true; - } else if (valueNode.isBoolean()) { - boolean v; - if (value.equalsIgnoreCase("true")) - v = true; - else if (value.equalsIgnoreCase("false")) - v = false; - else - return false; - if (v == valueNode.asBoolean()) - overrideWarn(fieldName, value); - oNode.put(fieldName, v); - return true; - } else if (valueNode.isIntegralNumber()) { - long v; - try { - v = Long.parseLong(value); - } catch (NumberFormatException e) { - return false; - } - if (v == valueNode.asLong()) - overrideWarn(fieldName, value); - oNode.put(fieldName, v); - return true; - } else if (valueNode.isFloatingPointNumber()) { - double v; - try { - v = Double.parseDouble(value); - } catch (NumberFormatException e) { - return false; - } - if (v == valueNode.asDouble()) - overrideWarn(fieldName, value); - oNode.put(fieldName, v); - return true; - } else if (valueNode.isObject() && setToNull) { - if (valueNode.isNull()) - overrideWarn(fieldName, value); - oNode.set(fieldName, NullNode.getInstance()); - return true; - } else if (valueNode.isNull()) { - oNode.put(fieldName, value); - return true; - } - return false; - } - - public static JsonNode getNodeByPath(JsonNode node, String path) { - return getNodeByPath(node, path.split("\\.")); - } - - public static JsonNode getNodeByPath(JsonNode node, String[] pathArray) { - for (int i = 0; i < pathArray.length; ++i) - if ((node = node.get(pathArray[i])) == null) - return null; - return node; - } -} diff --git a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java index aad2e9766..e6c5a8880 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java @@ -38,6 +38,7 @@ import com.milaboratory.mixcr.assembler.*; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; +import com.milaboratory.util.JsonOverrider; import io.repseq.core.GeneFeature; import org.junit.Assert; import org.junit.Test; From 638fe403ad1ab942a9ce4441748b2ac35bd169f5 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Tue, 19 Apr 2022 18:44:17 +0400 Subject: [PATCH 175/282] feat: Warning message for overrides of xParameters.parameters.relativeMinScore parameters, inviting to change xParameters.relativeMinScore instead. --- .../java/com/milaboratory/mixcr/cli/CommandAlign.java | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 1745fe531..7d0c7d295 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -245,6 +245,14 @@ public VDJCAlignerParameters getAlignerParameters() { throwValidationException("Unknown aligner parameters: " + alignerParametersName); if (!overrides.isEmpty()) { + // Printing warning message for some common mistakes in parameter overrides + for (Map.Entry o : overrides.entrySet()) + if ("Parameters.parameters.relativeMinScore".equals(o.getKey().substring(1))) + warn("WARNING: most probably you want to change \"" + o.getKey().charAt(0) + + "Parameters.relativeMinScore\" instead of \"" + o.getKey().charAt(0) + + "Parameters.parameters.relativeMinScore\". " + + "The latter should be touched only in a very specific cases."); + // Perform parameters overriding alignerParameters = JsonOverrider.override(alignerParameters, VDJCAlignerParameters.class, overrides); if (alignerParameters == null) From fa444dc4a108e670f69cd9e9a93465b8e1584141 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Wed, 20 Apr 2022 16:13:13 +0400 Subject: [PATCH 176/282] feat: ReportHelper moved to milib --- build.gradle.kts | 2 +- .../fullseq/FullSeqAssemblerReport.java | 2 +- .../mixcr/cli/AbstractCommandReport.java | 1 + .../milaboratory/mixcr/cli/AlignerReport.java | 1 + .../mixcr/cli/ChainUsageStats.java | 1 + .../mixcr/cli/CloneAssemblerReport.java | 3 +- .../milaboratory/mixcr/cli/CommandAlign.java | 7 +- .../mixcr/cli/CommandAlignmentsDiff.java | 5 +- .../mixcr/cli/CommandClonesDiff.java | 9 +- .../milaboratory/mixcr/cli/CommandExport.java | 5 +- .../com/milaboratory/mixcr/cli/Report.java | 2 +- .../milaboratory/mixcr/cli/ReportHelper.java | 112 ------------------ .../milaboratory/mixcr/cli/ReportWrapper.java | 1 + .../java/com/milaboratory/mixcr/cli/Util.java | 12 +- .../info/GeneFeatureCoverageCollector.java | 4 +- .../info/ReferencePointCoverageCollector.java | 6 +- .../PartialAlignmentsAssembler.java | 2 +- .../mixcr/tags/DropletCloneGraphReport.java | 9 +- .../mixcr/util/VDJCObjectExtender.java | 2 +- .../mixcr/tags/DropletCloneGraphTest.java | 6 +- 20 files changed, 35 insertions(+), 157 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java diff --git a/build.gradle.kts b/build.gradle.kts index 87537506d..bf3265b4a 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -57,7 +57,7 @@ repositories { } } -val milibVersion = "1.15.0-18-master" +val milibVersion = "1.15.0-23-master" val repseqioVersion = "1.3.5-24-master" val jacksonVersion = "2.13.2.2" diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java index 24b17fb16..0b9b4fea8 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java @@ -36,7 +36,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.VDJCObject; import com.milaboratory.mixcr.cli.Report; -import com.milaboratory.mixcr.cli.ReportHelper; +import com.milaboratory.util.ReportHelper; import io.repseq.core.GeneFeature; import java.util.Arrays; diff --git a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java index a068133d0..159b274a4 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java @@ -32,6 +32,7 @@ import com.fasterxml.jackson.annotation.JsonFormat; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.util.MiXCRVersionInfo; +import com.milaboratory.util.ReportHelper; import java.util.Collection; import java.util.Date; diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 179a3c20d..f5917f220 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -35,6 +35,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerEventListener; import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentFailCause; +import com.milaboratory.util.ReportHelper; import io.repseq.core.GeneType; import java.util.HashMap; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java index c3f9ff7bd..82e39db2f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java @@ -35,6 +35,7 @@ import com.fasterxml.jackson.databind.SerializerProvider; import com.fasterxml.jackson.databind.annotation.JsonSerialize; import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.util.ReportHelper; import io.repseq.core.Chains; import java.io.IOException; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index 3007c2d0a..cc8ea27aa 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -35,6 +35,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.util.ReportHelper; import java.util.concurrent.atomic.AtomicInteger; import java.util.concurrent.atomic.AtomicLong; @@ -279,7 +280,7 @@ public void writeReport(ReportHelper helper) { long clusterizationBase = getReadsInClonesBeforeClustering(); helper.writeField("Final clonotype count", clonesCount) - .writeField("Average number of reads per clonotype", Util.PERCENT_FORMAT.format(1.0 * alignmentsInClones / clonesCount)) + .writeField("Average number of reads per clonotype", ReportHelper.PERCENT_FORMAT.format(1.0 * alignmentsInClones / clonesCount)) .writePercentAndAbsoluteField("Reads used in clonotypes, percent of total", alignmentsInClones, totalReads) .writePercentAndAbsoluteField("Reads used in clonotypes before clustering, percent of total", clusterizationBase, totalReads) .writePercentAndAbsoluteField("Number of reads used as a core, percent of used", coreAlignments.get(), clusterizationBase) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 7d0c7d295..34511d4f5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -65,10 +65,7 @@ import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult; import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; -import com.milaboratory.util.CanReportProgress; -import com.milaboratory.util.GlobalObjectMappers; -import com.milaboratory.util.JsonOverrider; -import com.milaboratory.util.SmartProgressReporter; +import com.milaboratory.util.*; import io.repseq.core.*; import picocli.CommandLine; import picocli.CommandLine.Command; @@ -283,7 +280,7 @@ public VDJCAlignerParameters getAlignerParameters() { if (totalVErrors > totalV * 0.9 && hasVRegion > totalVErrors * 0.8) { warn("WARNING: forcing -OvParameters.geneFeatureToAlign=" + GeneFeature.encode(correctingFeature) + " since current gene feature (" + GeneFeature.encode(alignerParameters.getVAlignerParameters().getGeneFeatureToAlign()) + ") is absent in " + - Util.PERCENT_FORMAT.format(100.0 * totalVErrors / totalV) + "% of V genes."); + ReportHelper.PERCENT_FORMAT.format(100.0 * totalVErrors / totalV) + "% of V genes."); alignerParameters.getVAlignerParameters().setGeneFeatureToAlign(correctingFeature); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java index c7e4d9e18..777942707 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java @@ -34,6 +34,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriterI; import com.milaboratory.mixcr.util.VDJCAlignmentsDifferenceReader; +import com.milaboratory.util.ReportHelper; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -153,8 +154,8 @@ public void run0() throws Exception { report.println("First file: " + in1); report.println("Second file: " + in2); report.println("Completely same reads: " + same); - report.println("Aligned reads present only in the FIRST file: " + onlyIn1 + " (" + Util.PERCENT_FORMAT.format(100. * onlyIn1 / reader1.getNumberOfReads()) + ")%"); - report.println("Aligned reads present only in the SECOND file: " + onlyIn2 + " (" + Util.PERCENT_FORMAT.format(100. * onlyIn2 / reader2.getNumberOfReads()) + ")%"); + report.println("Aligned reads present only in the FIRST file: " + onlyIn1 + " (" + ReportHelper.PERCENT_FORMAT.format(100. * onlyIn1 / reader1.getNumberOfReads()) + ")%"); + report.println("Aligned reads present only in the SECOND file: " + onlyIn2 + " (" + ReportHelper.PERCENT_FORMAT.format(100. * onlyIn2 / reader2.getNumberOfReads()) + ")%"); report.println("Total number of different reads: " + justDiff); report.println("Reads with not same " + geneFeatureToMatch + ": " + diffFeature); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java b/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java index 53ed2660c..ba2e85810 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java @@ -33,6 +33,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.mixcr.basictypes.CloneSetIO; +import com.milaboratory.util.ReportHelper; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; import picocli.CommandLine.Command; @@ -125,11 +126,11 @@ public void run0() throws Exception { } } - report.println("Unique clones in cloneset 1: " + newClones1 + " (" + Util.PERCENT_FORMAT.format(100.0 * newClones1 / cs1.size()) + "%)"); - report.println("Reads in unique clones in cloneset 1: " + newClones1Reads + " (" + Util.PERCENT_FORMAT.format(100.0 * newClones1Reads / cs1.getTotalCount()) + "%)"); + report.println("Unique clones in cloneset 1: " + newClones1 + " (" + ReportHelper.PERCENT_FORMAT.format(100.0 * newClones1 / cs1.size()) + "%)"); + report.println("Reads in unique clones in cloneset 1: " + newClones1Reads + " (" + ReportHelper.PERCENT_FORMAT.format(100.0 * newClones1Reads / cs1.getTotalCount()) + "%)"); - report.println("Unique clones in cloneset 2: " + newClones2 + " (" + Util.PERCENT_FORMAT.format(100.0 * newClones2 / cs2.size()) + "%)"); - report.println("Reads in unique clones in cloneset 2: " + newClones2Reads + " (" + Util.PERCENT_FORMAT.format(100.0 * newClones2Reads / cs2.getTotalCount()) + "%)"); + report.println("Unique clones in cloneset 2: " + newClones2 + " (" + ReportHelper.PERCENT_FORMAT.format(100.0 * newClones2 / cs2.size()) + "%)"); + report.println("Reads in unique clones in cloneset 2: " + newClones2Reads + " (" + ReportHelper.PERCENT_FORMAT.format(100.0 * newClones2Reads / cs2.getTotalCount()) + "%)"); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 8cee9f4be..1c647ccfd 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -38,6 +38,7 @@ import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.CanReportProgressAndStage; +import com.milaboratory.util.ReportHelper; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.Chains; import io.repseq.core.GeneFeature; @@ -259,8 +260,8 @@ void run1(List> exporters) throws Exception { count = set.getClones().stream().mapToDouble(Clone::getCount).sum(); int di = initialSet.size() - set.size(); double cdi = initialCount - count; - warn("Filtered " + set.size() + " of " + initialSet.size() + " clones (" + Util.PERCENT_FORMAT.format(100.0 * di / initialSet.size()) + "%)."); - warn("Filtered " + count + " of " + initialCount + " reads (" + Util.PERCENT_FORMAT.format(100.0 * cdi / initialCount) + "%)."); + warn("Filtered " + set.size() + " of " + initialSet.size() + " clones (" + ReportHelper.PERCENT_FORMAT.format(100.0 * di / initialSet.size()) + "%)."); + warn("Filtered " + count + " of " + initialCount + " reads (" + ReportHelper.PERCENT_FORMAT.format(100.0 * cdi / initialCount) + "%)."); } } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Report.java b/src/main/java/com/milaboratory/mixcr/cli/Report.java index a8ded1b2d..d6a8b8958 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Report.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Report.java @@ -30,7 +30,7 @@ package com.milaboratory.mixcr.cli; import com.fasterxml.jackson.annotation.JsonAutoDetect; -import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.util.ReportHelper; @JsonAutoDetect( getterVisibility = JsonAutoDetect.Visibility.NONE, diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java deleted file mode 100644 index 58a170806..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java +++ /dev/null @@ -1,112 +0,0 @@ -/* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. - */ -package com.milaboratory.mixcr.cli; - -import java.io.FileNotFoundException; -import java.io.OutputStream; -import java.io.PrintStream; -import java.util.concurrent.atomic.AtomicLong; - -public final class ReportHelper { - public static final ReportHelper STDOUT = new ReportHelper(System.out, true); - public static final ReportHelper STDERR = new ReportHelper(System.err, true); - - private final PrintStream printStream; - private final boolean stdout; - - public ReportHelper(String fileName) { - try { - this.printStream = new PrintStream(fileName); - this.stdout = false; - } catch (FileNotFoundException e) { - throw new RuntimeException(e); - } - } - - public ReportHelper(OutputStream outputStream, boolean stdout) { - this.printStream = new PrintStream(outputStream); - this.stdout = stdout; - } - - public ReportHelper(PrintStream printStream, boolean stdout) { - this.printStream = printStream; - this.stdout = stdout; - } - - public boolean isStdout() { - return stdout; - } - - public ReportHelper writeField(String fieldName, Object value) { - printStream.println(fieldName + ": " + value); - return this; - } - - public ReportHelper writePercentField(String fieldName, long value, long total) { - double percent = 100.0 * value / total; - printStream.println(fieldName + ": " + Util.PERCENT_FORMAT.format(percent) + "%"); - return this; - } - - public ReportHelper writePercentAndAbsoluteField(String fieldName, long value, long total) { - double percent = 100.0 * value / total; - printStream.println(fieldName + ": " + value + " (" + Util.PERCENT_FORMAT.format(percent) + "%)"); - return this; - } - - public ReportHelper writePercentAndAbsoluteFieldNonZero(String fieldName, long value, long total) { - if (value == 0) - return this; - double percent = 100.0 * value / total; - printStream.println(fieldName + ": " + value + " (" + Util.PERCENT_FORMAT.format(percent) + "%)"); - return this; - } - - public ReportHelper writePercentAndAbsoluteField(String fieldName, double value, double total) { - double percent = 100.0 * value / total; - printStream.println(fieldName + ": " + value + " (" + Util.PERCENT_FORMAT.format(percent) + "%)"); - return this; - } - - public ReportHelper writePercentField(String fieldName, AtomicLong value, long total) { - writePercentField(fieldName, value.get(), total); - return this; - } - - public ReportHelper writePercentAndAbsoluteField(String fieldName, AtomicLong value, long total) { - writePercentAndAbsoluteField(fieldName, value.get(), total); - return this; - } - - public ReportHelper end() { - printStream.println("======================================"); - return this; - } -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java index 6bf3d4a9d..681327d3c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java @@ -30,6 +30,7 @@ package com.milaboratory.mixcr.cli; import com.fasterxml.jackson.annotation.JsonUnwrapped; +import com.milaboratory.util.ReportHelper; public final class ReportWrapper extends AbstractCommandReport { private final String action; diff --git a/src/main/java/com/milaboratory/mixcr/cli/Util.java b/src/main/java/com/milaboratory/mixcr/cli/Util.java index ed3fdb999..25b9c8cce 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Util.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Util.java @@ -31,6 +31,7 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.milaboratory.util.GlobalObjectMappers; +import com.milaboratory.util.ReportHelper; import gnu.trove.map.hash.TIntObjectHashMap; import java.io.ByteArrayOutputStream; @@ -52,17 +53,6 @@ public final class Util { private Util() { } - private static final DecimalFormatSymbols DFS; - - public static final DecimalFormat PERCENT_FORMAT; - - static { - DFS = new DecimalFormatSymbols(); - DFS.setNaN("NaN"); - DFS.setInfinity("Inf"); - PERCENT_FORMAT = new DecimalFormat("#.##", DFS); - } - public static void writeReportToStdout(Report report) { report.writeReport(new ReportHelper(System.out, true)); } diff --git a/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java b/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java index 2035010f0..228d3282d 100644 --- a/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java @@ -30,7 +30,7 @@ package com.milaboratory.mixcr.info; import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.cli.Util; +import com.milaboratory.util.ReportHelper; import io.repseq.core.GeneFeature; import java.io.PrintStream; @@ -51,7 +51,7 @@ public GeneFeatureCoverageCollector(GeneFeature feature) { @Override public void writeResult(PrintStream writer) { writer.println("" + GeneFeature.encode(feature) + "\t" + covered.get() + - "\t" + Util.PERCENT_FORMAT.format(100.0 * covered.get() / total.get()) + "%"); + "\t" + ReportHelper.PERCENT_FORMAT.format(100.0 * covered.get() / total.get()) + "%"); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java b/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java index ff5a70ffc..5e61d372c 100644 --- a/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java @@ -32,7 +32,7 @@ import com.milaboratory.core.Range; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.cli.Util; +import com.milaboratory.util.ReportHelper; import io.repseq.core.ReferencePoint; import java.io.PrintStream; @@ -62,9 +62,9 @@ public void writeResult(PrintStream writer) { writer.println(); writer.println("Coverage of " + refPoint + ":"); for (int i = leftHist.length() - 1; i > 0; --i) - writer.println("-" + i + "\t" + leftHist.get(i) + "\t" + Util.PERCENT_FORMAT.format(100.0 * leftHist.get(i) / totalCount.get()) + "%"); + writer.println("-" + i + "\t" + leftHist.get(i) + "\t" + ReportHelper.PERCENT_FORMAT.format(100.0 * leftHist.get(i) / totalCount.get()) + "%"); for (int i = 0; i < rightHist.length(); ++i) - writer.println(i + "\t" + rightHist.get(i) + "\t" + Util.PERCENT_FORMAT.format(100.0 * rightHist.get(i) / totalCount.get()) + "%"); + writer.println(i + "\t" + rightHist.get(i) + "\t" + ReportHelper.PERCENT_FORMAT.format(100.0 * rightHist.get(i) / totalCount.get()) + "%"); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 43d8977b9..63bc32999 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -37,7 +37,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.cli.Report; -import com.milaboratory.mixcr.cli.ReportHelper; +import com.milaboratory.util.ReportHelper; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TLongObjectHashMap; diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java index 84e27b387..301bdde32 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java @@ -34,8 +34,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.mixcr.cli.Report; -import com.milaboratory.mixcr.cli.ReportHelper; -import com.milaboratory.mixcr.cli.Util; +import com.milaboratory.util.ReportHelper; import gnu.trove.map.hash.TIntObjectHashMap; import java.util.List; @@ -368,12 +367,12 @@ public void writeReport(ReportHelper helper) { .writeField("Groups", numberOfGroups.get() - groupsClustered.get()) .writeField("Groups before clustering", numberOfGroups.get()) .writeField("Max clones per group", maxClonesPerGroup.get()) - .writeField("Mean clones per group", Util.PERCENT_FORMAT.format(1.0 * sumClonesPerGroup.get() / numberOfGroups.get())) + .writeField("Mean clones per group", ReportHelper.PERCENT_FORMAT.format(1.0 * sumClonesPerGroup.get() / numberOfGroups.get())) .writeField("Max tags per group", maxTagsPerGroup.get()) - .writeField("Mean tags per group", Util.PERCENT_FORMAT.format(1.0 * sumTagsPerGroup.get() / numberOfGroups.get())) + .writeField("Mean tags per group", ReportHelper.PERCENT_FORMAT.format(1.0 * sumTagsPerGroup.get() / numberOfGroups.get())) .writeField("Max tags clique", maxTagsClique.get()) .writeField("Max tags clique delta", maxTagsCliqueDelta.get()) - .writeField("Mean tags clique delta", Util.PERCENT_FORMAT.format(1.0 * sumTagsCliqueDelta.get() / numberOfGroups.get())); + .writeField("Mean tags clique delta", ReportHelper.PERCENT_FORMAT.format(1.0 * sumTagsCliqueDelta.get() / numberOfGroups.get())); helper .writePercentAndAbsoluteField("Groups clustered", groupsClustered.get(), numberOfGroups.get()) diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java index 622f644d3..d2c0357f4 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java @@ -42,7 +42,7 @@ import com.milaboratory.core.sequence.SequenceQuality; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.cli.Report; -import com.milaboratory.mixcr.cli.ReportHelper; +import com.milaboratory.util.ReportHelper; import io.repseq.core.*; import java.util.Arrays; diff --git a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java index 0bb43598a..06998f661 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java @@ -2,18 +2,14 @@ import com.milaboratory.mixcr.basictypes.ClnAReader; import com.milaboratory.mixcr.basictypes.CloneSet; -import com.milaboratory.mixcr.cli.ReportHelper; +import com.milaboratory.util.ReportHelper; import com.milaboratory.util.ProgressAndStage; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.VDJCLibraryRegistry; -import org.apache.commons.math3.stat.descriptive.rank.Percentile; import org.junit.Ignore; import org.junit.Test; import java.nio.file.Paths; -import java.util.Collection; -import java.util.List; -import java.util.stream.Collectors; /** * From 65fcee54c09e1bcfa4593300d1dec47722484b80 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 20 Apr 2022 21:30:02 +0200 Subject: [PATCH 177/282] wip --- .../cli/postanalysis/CommandPaExportPlots.java | 13 +++++++++++++ .../postanalysis/CommandPaExportPlotsOverlap.java | 1 + .../mixcr/cli/postanalysis/CommandPaExportTest.java | 4 ++-- 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java index 35268fa63..24a3f7688 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java @@ -9,6 +9,8 @@ import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; +import java.io.IOException; +import java.nio.file.Files; import java.nio.file.Path; import java.util.List; import java.util.stream.Collectors; @@ -69,15 +71,26 @@ Path tablesDestPath(IsolationGroup group) { return Path.of(tablesDestStr(group)); } + protected void ensureOutputPathExists() { + try { + Files.createDirectories(Path.of(out).toAbsolutePath().getParent()); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + void writeTables(IsolationGroup group, List tables) { + ensureOutputPathExists(); ExportKt.writePDF(tablesDestPath(group), tables); } void writePlots(IsolationGroup group, List plots) { + ensureOutputPathExists(); ExportKt.writePDFFigure(plotDestPath(group), plots); } void writePlots(IsolationGroup group, Plot plot) { + ensureOutputPathExists(); ExportKt.writePDF(tablesDestPath(group), plot); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java index d8d74ef58..0dcbabe05 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -80,6 +80,7 @@ void run(PaResultByGroup result) { height ); + ensureOutputPathExists(); List plotsAndSummary = Overlap.INSTANCE.plotsAndSummary(df, pp, par); ExportKt.writePDF(plotDestPath(result.group), plotsAndSummary); SetPreprocessorSummary.writeCSV(tablesDestPath(result.group), diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java index 3e29cae68..b5e1ce9b6 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java @@ -47,9 +47,9 @@ public void test3() { "--filter", "Chain=TRA", // "--filter", "CellPopulation=CD4mem", "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", - "--color-key", "x_Tissue", "--color-key", "x_CellPopulation", "--color-key", "y_MouseID", + "--color-key", "x_Tissue", "--color-key", "x_Age(months)", "--color-key", "y_MouseID", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", - "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap.pdf"); + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap/overlap.pdf"); } @Test From 833b2d42975865b471d1349b850622dd2e200d64 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 20 Apr 2022 21:53:42 +0200 Subject: [PATCH 178/282] wip --- .../com/milaboratory/mixcr/postanalysis/WeightFunctions.java | 2 +- .../com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java index 7c19db35e..6dd26e6ed 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java @@ -59,7 +59,7 @@ public double weight(T o) { if (o instanceof Clone) return ((Clone) o).getCount(); else - throw new RuntimeException(); + throw new RuntimeException("Unsupported for class: " + o.getClass()); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java index 454de29de..39315fc16 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java @@ -36,7 +36,7 @@ public class SelectTop implements SetPreprocessor { this.abundanceFraction = abundanceFraction; this.numberOfTop = numberOfTop; this.id = id; - this.stats = new SetPreprocessorStat.Builder<>(id, WeightFunctions.Default()); + this.stats = new SetPreprocessorStat.Builder<>(id, weight); } private boolean computeCumulativeTop() { From beff53311d35667955dc4bb897f83d5d79c8c1b1 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 20 Apr 2022 23:30:08 +0200 Subject: [PATCH 179/282] wip --- .../cli/postanalysis/CommandPaExportTest.java | 3 +- .../plots/SingleSpectratypeTest.kt | 67 ------------------- .../VDJCAlignmentsDifferenceReaderTest.java | 3 - 3 files changed, 2 insertions(+), 71 deletions(-) delete mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratypeTest.kt diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java index b5e1ce9b6..f050e4cff 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java @@ -37,7 +37,7 @@ public void test2() { ); } - // @Ignore + @Ignore @Test public void test3() { Main.main("exportPa", "overlap", @@ -52,6 +52,7 @@ public void test3() { "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlap/overlap.pdf"); } + @Ignore @Test public void test4() { Main.main("exportPa", "preprocSummary", diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratypeTest.kt b/src/test/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratypeTest.kt deleted file mode 100644 index 887de789b..000000000 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratypeTest.kt +++ /dev/null @@ -1,67 +0,0 @@ -package com.milaboratory.mixcr.postanalysis.plots - -import jetbrains.letsPlot.coordFixed -import jetbrains.letsPlot.geom.geomTile -import jetbrains.letsPlot.ggsize -import jetbrains.letsPlot.letsPlot -import jetbrains.letsPlot.scale.scaleXContinuous -import jetbrains.letsPlot.scale.scaleYContinuous -import org.jetbrains.kotlinx.dataframe.DataFrame -import org.jetbrains.kotlinx.dataframe.api.head -import org.jetbrains.kotlinx.dataframe.api.toMap -import org.jetbrains.kotlinx.dataframe.io.read -import org.junit.Test - - -/** - * - */ -internal class SingleSpectratypeTest { - @Test - fun name1() { - val data = - DataFrame.read("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") - val mData = data.head(1000).toMap() - val plot = letsPlot(mData) { - x = "sample" - y = "gene" - fill = "weight" - } + geomTile(color = "white") + coordFixed() - -// writePDF( -// Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( -// PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) -// ) -// ) - } - - @Test - fun name() { - val data = - DataFrame.read("https://raw.githubusercontent.com/PoslavskySV/scratch/master/lets-plot-heatmap/data1.csv") - - val mData = data.head(1000).toMap() - val xs = mData["sample"]!!.toList().distinct().size - val ys = mData["gene"]!!.toList().distinct().size - val f = 25 - - println(xs * f + 5 * f) - println(ys * f) - val plot = letsPlot(mData) { - x = "sample" - y = "gene" - fill = "weight" - } + geomTile(color = "white") + - scaleXContinuous(expand = listOf(0.0, 0.0)) + - scaleYContinuous(expand = listOf(0.0, 0.0)) + - coordFixed() + - ggsize(xs * f + 5 * f, 3 * ys * f / 5) - - -// writePDF( -// Path.of("/Users/poslavskysv/Downloads/letsplot.pdf"), toPdf( -// PlotSvgExport.buildSvgImageFromRawSpecs(plot.toSpec()) -// ) -// ) - } -} diff --git a/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java b/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java index 5d1e1e373..a3a292c28 100644 --- a/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java @@ -43,9 +43,6 @@ public class VDJCAlignmentsDifferenceReaderTest { @Test public void test1() throws Exception { -// "/Users/poslavsky/Projects/milab/temp/al_1.vdjca", -// "/Users/poslavsky/Projects/milab/temp/al_2.vdjca" - RunMiXCR.RunMiXCRAnalysis params = new RunMiXCR.RunMiXCRAnalysis( RunMiXCR.class.getResource("/sequences/test_R1.fastq").getFile(), RunMiXCR.class.getResource("/sequences/test_R2.fastq").getFile() From 482cb35cedd1fc28d18a1efe8fad265b6771726a Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 21 Apr 2022 23:50:55 +0200 Subject: [PATCH 180/282] minor --- .../com/milaboratory/mixcr/cli/postanalysis/CommandPa.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 4e6d21c4f..64b6d7554 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -243,6 +243,11 @@ public void run0() throws Exception { } } PaResult result = new PaResult(readMetadata(), isolationGroups, results); + try { + Files.createDirectories(outputPath().getParent()); + } catch (IOException e) { + throw new RuntimeException(e); + } PaResult.writeJson(outputPath(), result); } From 73622cd94e02953eb7386497965435c06a8be68d Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 25 Apr 2022 01:23:19 +0200 Subject: [PATCH 181/282] wip --- .../mixcr/cli/postanalysis/CommandPa.java | 27 +++-- .../postanalysis/CommandPaExportPlots.java | 23 +++- .../CommandPaExportPlotsBasicStatistics.java | 45 ++++--- .../CommandPaExportPlotsGeneUsage.java | 10 +- .../CommandPaExportPlotsOverlap.java | 16 +-- .../cli/postanalysis/CommandPaOverlap.java | 15 +++ .../cli/postanalysis/IsolationGroup.java | 3 +- .../postanalysis/PostanalysisResult.java | 28 +++-- .../postanalysis/SetPreprocessorStat.java | 4 + .../postanalysis/plots/BasicStatistics.kt | 111 ++++++++++++------ .../mixcr/postanalysis/plots/GeneUsage.kt | 39 +++++- .../mixcr/postanalysis/plots/Overlap.kt | 37 +++--- .../mixcr/postanalysis/plots/Preprocessing.kt | 61 +++++----- .../cli/postanalysis/CommandPaExportTest.java | 4 +- .../mixcr/cli/postanalysis/CommandPaTest.java | 10 +- 15 files changed, 280 insertions(+), 153 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 64b6d7554..222718837 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -52,6 +52,10 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { names = {"-m", "--meta", "--metadata"}) public String metadata; + @Option(description = "Metadata column for chains.", + names = {"--chains-column"}) + public String chainsColumn; + @Option(description = "Metadata categories used to isolate samples into separate groups", names = {"-g", "--group"}) public List isolationGroups; @@ -153,7 +157,7 @@ protected Map> readMetadata() { return _metadata; List content; try { - content = Files.readAllLines(Path.of(metadata).toAbsolutePath()); + content = Files.readAllLines(Paths.get(metadata).toAbsolutePath()); } catch (IOException e) { throw new RuntimeException(e); } @@ -195,7 +199,7 @@ public SamplesGroup(List samples, Map group) { /** group samples into isolated groups */ protected List groupSamples() { - if (isolationGroups == null || isolationGroups.isEmpty()) { + if ((isolationGroups == null || isolationGroups.isEmpty()) && chainsColumn == null) { return Collections.singletonList(new SamplesGroup(getInputFiles(), Collections.emptyMap())); } @@ -218,9 +222,12 @@ protected List groupSamples() { Map, List> samplesByGroup = new HashMap<>(); for (int i = 0; i < nRows; i++) { Map group = new HashMap<>(); - for (String igr : isolationGroups) { + for (String igr : isolationGroups == null ? Collections.singletonList(chainsColumn) : isolationGroups) { group.put(igr, metadata.get(igr).get(i)); } + if (chainsColumn != null) + group.put(chainsColumn, metadata.get(chainsColumn).get(i)); + String sample = (String) metadata.get("sample").get(i); samplesByGroup.computeIfAbsent(group, __ -> new ArrayList<>()) .add(meta2sample.get(sample)); @@ -234,13 +241,17 @@ protected List groupSamples() { @Override public void run0() throws Exception { List results = new ArrayList<>(); + Chains c = Chains.parse(chains); for (SamplesGroup group : groupSamples()) { - Chains c = Chains.parse(chains); - for (NamedChains knownChains : CHAINS) { - if (c.intersects(knownChains.chains)) { - results.add(run(new IsolationGroup(knownChains, group.group), group.samples)); + if (chainsColumn != null) + results.add(run(new IsolationGroup( + Chains.getNamedChains(group.group.get(chainsColumn).toString()), group.group), group.samples)); + else + for (NamedChains knownChains : CHAINS) { + if (c.intersects(knownChains.chains)) { + results.add(run(new IsolationGroup(knownChains, group.group), group.samples)); + } } - } } PaResult result = new PaResult(readMetadata(), isolationGroups, results); try { diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java index 24a3f7688..f1136b3fe 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java @@ -1,8 +1,11 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.miplots.ExportKt; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; import com.milaboratory.mixcr.postanalysis.plots.Filter; import com.milaboratory.mixcr.postanalysis.plots.MetadataKt; +import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; import org.jetbrains.kotlinx.dataframe.api.DataFrameIterableKt; @@ -12,7 +15,9 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.nio.file.Paths; import java.util.List; +import java.util.Map; import java.util.stream.Collectors; abstract class CommandPaExportPlots extends CommandPaExport { @@ -60,7 +65,7 @@ String plotDestStr(IsolationGroup group) { } Path plotDestPath(IsolationGroup group) { - return Path.of(plotDestStr(group)); + return Paths.get(plotDestStr(group)); } String tablesDestStr(IsolationGroup group) { @@ -68,12 +73,12 @@ String tablesDestStr(IsolationGroup group) { } Path tablesDestPath(IsolationGroup group) { - return Path.of(tablesDestStr(group)); + return Paths.get(tablesDestStr(group)); } protected void ensureOutputPathExists() { try { - Files.createDirectories(Path.of(out).toAbsolutePath().getParent()); + Files.createDirectories(Paths.get(out).toAbsolutePath().getParent()); } catch (IOException e) { throw new RuntimeException(e); } @@ -93,4 +98,16 @@ void writePlots(IsolationGroup group, Plot plot) { ensureOutputPathExists(); ExportKt.writePDF(tablesDestPath(group), plot); } + + void writePlotsAndSummary(CharacteristicGroup ch, + IsolationGroup group, + List plotsAndSummary, + Map preprocSummary + ) { + ensureOutputPathExists(); + ExportKt.writePDF(plotDestPath(group), plotsAndSummary); + SetPreprocessorSummary.writeCSV(tablesDestPath(group), + ch, preprocSummary, + "\t"); + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index 76adbe168..5e2a224c4 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -3,10 +3,10 @@ import com.milaboratory.miplots.stat.util.TestMethod; import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.plots.BasicStatRow; import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; -import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; import picocli.CommandLine.Option; @@ -28,37 +28,36 @@ public abstract class CommandPaExportPlotsBasicStatistics extends CommandPaExpor @Override void run(PaResultByGroup result) { CharacteristicGroup ch = result.schema.getGroup(group()); - + PostanalysisResult paResult = result.result.forGroup(ch); DataFrame metadata = metadata(); - DataFrame df = BasicStatistics.INSTANCE.dataFrame( - result.result.forGroup(ch), + paResult, metrics, metadata ); df = filter(df); - List plots = BasicStatistics.INSTANCE.plots(df, - new BasicStatistics.PlotParameters( - primaryGroup, - secondaryGroup, - facetBy, - true, - true, - null, - false, - null, - null, - null, - false, - TestMethod.Wilcoxon, - TestMethod.KruskalWallis, - null, - CorrelationMethod.Pearson - )); + BasicStatistics.PlotParameters par = new BasicStatistics.PlotParameters( + primaryGroup, + secondaryGroup, + facetBy, + true, + true, + null, + false, + null, + null, + null, + false, + TestMethod.Wilcoxon, + TestMethod.KruskalWallis, + null, + CorrelationMethod.Pearson + ); - writePlots(result.group, plots); + List plots = BasicStatistics.INSTANCE.plotsAndSummary(df, par); + writePlotsAndSummary(ch, result.group, plots, paResult.preprocSummary); } @CommandLine.Command(name = "biophysics", diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java index ddd5555c5..9c956f220 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java @@ -2,12 +2,12 @@ import com.milaboratory.miplots.Position; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.plots.ColorKey; import com.milaboratory.mixcr.postanalysis.plots.GeneUsage; import com.milaboratory.mixcr.postanalysis.plots.GeneUsageRow; import com.milaboratory.mixcr.postanalysis.plots.HeatmapParameters; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; -import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; import picocli.CommandLine.Option; @@ -32,10 +32,10 @@ public abstract class CommandPaExportPlotsGeneUsage extends CommandPaExportPlots @Override void run(PaResultByGroup result) { CharacteristicGroup ch = result.schema.getGroup(group()); - + PostanalysisResult paResult = result.result.forGroup(ch); DataFrame metadata = metadata(); DataFrame df = GeneUsage.INSTANCE.dataFrame( - result.result.forGroup(ch), + paResult, metadata ); df = filter(df); @@ -43,7 +43,7 @@ void run(PaResultByGroup result) { if (df.rowsCount() == 0) return; - Plot plot = GeneUsage.INSTANCE.plot(df, + List plot = GeneUsage.INSTANCE.plotAndSummary(df, new HeatmapParameters( !noSamplesDendro, !noGenesDendro, @@ -56,7 +56,7 @@ void run(PaResultByGroup result) { height )); - writePlots(result.group, plot); + writePlotsAndSummary(ch, result.group, plot, paResult.preprocSummary); } @CommandLine.Command(name = "vUsage", diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java index 0dcbabe05..d7ee390ac 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -1,6 +1,5 @@ package com.milaboratory.mixcr.cli.postanalysis; -import com.milaboratory.miplots.ExportKt; import com.milaboratory.miplots.Position; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; @@ -49,7 +48,6 @@ void run(PaResultByGroup result) { DataFrame metadata = metadata(); DataFrame df = Overlap.INSTANCE.dataFrame( - ch, paResult, metrics, metadata @@ -62,10 +60,6 @@ void run(PaResultByGroup result) { if (df.get("weight").distinct().toList().size() <= 1) return; - DataFrame pp = Preprocessing.INSTANCE.dataFrame(paResult, null); - pp = MetadataKt.attachMetadata(pp, "sample", metadata, "sample"); - pp = filter(pp); - HeatmapParameters par = new HeatmapParameters( !noDendro, !noDendro, @@ -80,11 +74,7 @@ void run(PaResultByGroup result) { height ); - ensureOutputPathExists(); - List plotsAndSummary = Overlap.INSTANCE.plotsAndSummary(df, pp, par); - ExportKt.writePDF(plotDestPath(result.group), plotsAndSummary); - SetPreprocessorSummary.writeCSV(tablesDestPath(result.group), - ch, preprocSummary, - "\t"); + List plotsAndSummary = Overlap.INSTANCE.plotsAndSummary(df, par); + writePlotsAndSummary(ch, result.group, plotsAndSummary, preprocSummary); } -} +} \ No newline at end of file diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index fc940d41f..6597305a2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -86,9 +86,24 @@ PaResultByGroup run(IsolationGroup group, List samples) { SmartProgressReporter.startProgressReport(runner); PostanalysisResult result = runner.run(overlapDataset); + result = updatePreprocSummary(result); + return new PaResultByGroup(group, schema, result); } + private static PostanalysisResult updatePreprocSummary(PostanalysisResult r) { + return new PostanalysisResult(r.datasetIds, r.data, + r.preprocSummary.entrySet().stream() + .map(e -> new AbstractMap.SimpleEntry<>(e.getKey(), + new SetPreprocessorSummary(e.getValue().result.entrySet().stream() + .map(e2 -> new AbstractMap.SimpleEntry<>(e2.getKey(), + e2.getValue().stream() + .map(l -> l.setPreprocId("overlap")) + .collect(toList()))).collect(toMap(Map.Entry::getKey, Map.Entry::getValue))) + ) + ).collect(toMap(Map.Entry::getKey, Map.Entry::getValue))); + } + public static CloneReader mkCheckedReader(Path path, LambdaSemaphore concurrencyLimiter) throws IOException { ClnsReader inner = new ClnsReader( diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java index e4e60bb44..4d87a8461 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java @@ -56,7 +56,8 @@ public String extension() { StringBuilder sb = new StringBuilder(); sb.append(".").append(chains.name); for (Object v : group.values()) { - sb.append(".").append(v); + if (!v.toString().equalsIgnoreCase(chains.name)) + sb.append(".").append(v); } return sb.toString(); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index 6f5d4c781..442b4e874 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -25,14 +25,14 @@ public class PostanalysisResult { public final Set datasetIds; /** Characteristic Id -> characteristic data */ @JsonProperty("data") - public final Map data; + public final Map data; /** Preprocessor Id -> Preprocessors summary */ @JsonProperty("preprocSummary") public final Map preprocSummary; @JsonCreator public PostanalysisResult(@JsonProperty("datasetIds") Set datasetIds, - @JsonProperty("data") Map data, + @JsonProperty("data") Map data, @JsonProperty("preprocSummary") Map preprocSummary) { this.datasetIds = datasetIds; this.data = data; @@ -42,9 +42,9 @@ public PostanalysisResult(@JsonProperty("datasetIds") Set datasetIds, static PostanalysisResult create(Set datasetIds, Map, Map[]>> data, Map preprocSummary) { - Map d = new HashMap<>(); + Map d = new HashMap<>(); for (Map.Entry, Map[]>> e : data.entrySet()) - d.put(e.getKey().name, new Array2d(e.getValue())); + d.put(e.getKey().name, new ChData(e.getKey().preprocessor.id(), e.getValue())); return new PostanalysisResult(datasetIds, d, preprocSummary); } @@ -64,6 +64,13 @@ public PostanalysisResult forGroup(CharacteristicGroup group) { .collect(Collectors.toMap(c -> c, preprocSummary::get))); } + /** + * Get preprocessor statistics for specified characteristic for spaecified sample + */ + public SetPreprocessorStat getPreprocStat(String charId, String sampleId) { + return SetPreprocessorStat.cumulative(preprocSummary.get(data.get(charId).preproc).result.get(sampleId)); + } + /** project result on a specific char group */ @SuppressWarnings({"unchecked"}) public CharacteristicGroupResult getTable(CharacteristicGroup group) { @@ -107,13 +114,18 @@ public String toString() { getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE ) - public static final class Array2d { + public static final class ChData { + /** Preprocessor Id */ + @JsonProperty("preproc") + public final String preproc; /** Dataset Id -> Metric values */ @JsonProperty("2darray") public final Map data; @JsonCreator - Array2d(@JsonProperty("2darray") Map[]> data) { + ChData(@JsonProperty("preproc") String preproc, + @JsonProperty("2darray") Map[]> data) { + this.preproc = preproc; this.data = data.entrySet().stream().collect(Collectors.toMap(Map.Entry::getKey, e -> new MetricsArray(e.getValue()))); } @@ -121,8 +133,8 @@ public static final class Array2d { public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; - Array2d array2d = (Array2d) o; - return Objects.equals(data, array2d.data); + ChData chData = (ChData) o; + return Objects.equals(data, chData.data); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java index 53dcaf80d..3d4c78ab1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java @@ -59,6 +59,10 @@ public SetPreprocessorStat(String preprocId) { this(preprocId, true, -1, -1, Double.NaN, Double.NaN); } + public SetPreprocessorStat setPreprocId(String newId) { + return new SetPreprocessorStat(newId, dropped, nElementsBefore, nElementsAfter, sumWeightBefore, sumWeightAfter); + } + @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt index 15ebe2f29..fb6f7c4e9 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt @@ -11,7 +11,9 @@ import com.milaboratory.miplots.stat.xdiscrete.GGBoxPlot import com.milaboratory.miplots.stat.xdiscrete.LabelFormat import com.milaboratory.miplots.stat.xdiscrete.plusAssign import com.milaboratory.miplots.stat.xdiscrete.statCompareMeans +import com.milaboratory.miplots.toPDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat import jetbrains.letsPlot.facet.facetWrap import jetbrains.letsPlot.geom.geomBoxplot import jetbrains.letsPlot.label.ggtitle @@ -27,12 +29,14 @@ import org.jetbrains.kotlinx.dataframe.api.* @DataSchema @Suppress("UNCHECKED_CAST") data class BasicStatRow( + /** Preprocessor */ + val preproc: String, + /** Preprocessor statistics for the sample */ + val preprocStat: SetPreprocessorStat, /** Sample ID */ val sample: String, - /** Metric name */ val metric: String, - /** Value */ val value: Double, ) @@ -48,14 +52,18 @@ object BasicStatistics { val data = mutableListOf() val mf = metricsFilter?.toSet() - for ((_, charData) in paResult.data) { + for ((ch, charData) in paResult.data) { for ((sampleId, keys) in charData.data) { for (metric in keys.data) { val key = metric.key.toString() if (mf != null && !mf.contains(key)) { continue } - data += BasicStatRow(sampleId, key, metric.value) + data += BasicStatRow( + charData.preproc, + paResult.getPreprocStat(ch, sampleId), + sampleId, key, metric.value + ) } } } @@ -111,76 +119,105 @@ object BasicStatistics { .filter { !it.isEmpty() } .map { mdf -> plot(mdf, pp) + ggtitle(mdf.first()[BasicStatRow::metric.name]!!.toString()) } + fun plotsAndSummary( + df: DataFrame, + par: PlotParameters, + ): List = df.groupBy { preproc }.groups.toList().flatMap { byPreproc -> + val metrics = byPreproc.metric.distinct().toList() + + val droppedSamples = + df.filter { preprocStat.dropped || preprocStat.nElementsAfter == 0L } + .sample.distinct().toSet() + + val summary = Preprocessing.pdfSummary( + byPreproc.rows().associate { it.sample to it.preprocStat }, + metrics.joinToString(", ") + ) + + val plots = byPreproc + .filter { !droppedSamples.contains(it.sample) } + .groupBy { metric }.groups.toList() + .filter { !it.isEmpty() } + .map { mdf -> plot(mdf, par) + ggtitle(mdf.first()[BasicStatRow::metric.name]!!.toString()) } + .map { it.toPDF() } + .toList() + + if (summary == null) + plots + else + listOf(summary) + plots + } + fun plot( df: DataFrame, - pp: PlotParameters, + par: PlotParameters, ) = - if (pp.primaryGroup == null) { + if (par.primaryGroup == null) { val data = df.add(List(df.rowsCount()) { "" }.toColumn("__x__")).toMap() var plt = letsPlot(data) { x = "__x__" y = BasicStatRow::value.name } plt += geomBoxplot() - if (pp.facetBy != null) - plt += facetWrap(pp.facetBy) + if (par.facetBy != null) + plt += facetWrap(par.facetBy) plt += xlab("") plt - } else if (df.isNumeric(pp.primaryGroup)) { + } else if (df.isNumeric(par.primaryGroup)) { val plt = GGScatter( df, - x = pp.primaryGroup, + x = par.primaryGroup, y = BasicStatRow::value.name, - facetBy = pp.facetBy, + facetBy = par.facetBy, facetNRow = 1, ) { - shape = pp.secondaryGroup - color = pp.secondaryGroup - linetype = pp.secondaryGroup + shape = par.secondaryGroup + color = par.secondaryGroup + linetype = par.secondaryGroup } - plt += statCor(method = pp.correlationMethod) + plt += statCor(method = par.correlationMethod) plt.plot } else { val plt = GGBoxPlot( df, - x = pp.primaryGroup, + x = par.primaryGroup, y = BasicStatRow::value.name, - facetBy = pp.facetBy, + facetBy = par.facetBy, facetNRow = 1, ) { - fill = pp.secondaryGroup ?: pp.primaryGroup + fill = par.secondaryGroup ?: par.primaryGroup } - if (pp.showPairwisePValue) + if (par.showPairwisePValue) plt += statCompareMeans( - method = pp.method, - multipleGroupsMethod = pp.multipleGroupsMethod, - pAdjustMethod = pp.pAdjustMethod, - paired = pp.paired, - hideNS = pp.hideNS, - labelFormat = pp.comparisonsPValueFormat, + method = par.method, + multipleGroupsMethod = par.multipleGroupsMethod, + pAdjustMethod = par.pAdjustMethod, + paired = par.paired, + hideNS = par.hideNS, + labelFormat = par.comparisonsPValueFormat, allComparisons = true ) - if (pp.refGroup != null) + if (par.refGroup != null) plt += statCompareMeans( - method = pp.method, - multipleGroupsMethod = pp.multipleGroupsMethod, - pAdjustMethod = pp.pAdjustMethod, - paired = pp.paired, - hideNS = pp.hideNS, - labelFormat = pp.refPValueFormat, - refGroup = pp.refGroup + method = par.method, + multipleGroupsMethod = par.multipleGroupsMethod, + pAdjustMethod = par.pAdjustMethod, + paired = par.paired, + hideNS = par.hideNS, + labelFormat = par.refPValueFormat, + refGroup = par.refGroup ) - if (pp.showOverallPValue) + if (par.showOverallPValue && par.secondaryGroup == null) plt += statCompareMeans( - method = pp.method, - multipleGroupsMethod = pp.multipleGroupsMethod, - labelFormat = pp.overallPValueFormat, + method = par.method, + multipleGroupsMethod = par.multipleGroupsMethod, + labelFormat = par.overallPValueFormat, ) plt.plot diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt index cc04b1cf4..8b23b71fc 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt @@ -1,8 +1,11 @@ package com.milaboratory.mixcr.postanalysis.plots +import com.milaboratory.miplots.toPDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.rows import org.jetbrains.kotlinx.dataframe.api.toDataFrame @@ -13,10 +16,10 @@ import org.jetbrains.kotlinx.dataframe.api.toDataFrame data class GeneUsageRow( /** Sample ID */ val sample: String, - + /** Preprocessor statistics for the sample */ + val preprocStat: SetPreprocessorStat, /** Payload (Gene) */ val gene: String, - /** Payload weight */ val weight: Double, ) @@ -28,11 +31,16 @@ object GeneUsage { fun dataFrame(paResult: PostanalysisResult) = run { val data = mutableListOf() - for ((_, charData) in paResult.data) { + for ((ch, charData) in paResult.data) { for ((sampleId, keys) in charData.data) { for (metric in keys.data) { val key = metric.key.toString() - data += GeneUsageRow(sampleId, key, metric.value) + data += GeneUsageRow( + sampleId, + paResult.getPreprocStat(ch, sampleId), + key, + metric.value + ) } } } @@ -53,6 +61,29 @@ object GeneUsage { df } + fun plotAndSummary( + df: DataFrame, + params: HeatmapParameters, + ) = run { + val summary = Preprocessing.pdfSummary( + df.rows().associate { it.sample to it.preprocStat }, + "" + ) + + val plt = mkHeatmap( + df, + x = GeneUsageRow::sample.name, + y = GeneUsageRow::gene.name, + z = GeneUsageRow::weight.name, + params = params + ).toPDF() + + if (summary == null) + listOf(plt) + else + listOf(summary, plt) + } + fun plot( df: DataFrame, params: HeatmapParameters, diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index f70470878..71681d707 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -2,10 +2,9 @@ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.toPDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult +import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey import com.milaboratory.mixcr.postanalysis.overlap.OverlapType -import com.milaboratory.mixcr.postanalysis.plots.Preprocessing.pdfSummary -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup import jetbrains.letsPlot.label.ggtitle import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema @@ -17,6 +16,8 @@ import org.jetbrains.kotlinx.dataframe.api.* @DataSchema data class OverlapRow( val preproc: String, + val preprocStat1: SetPreprocessorStat, + val preprocStat2: SetPreprocessorStat, val sample1: String, val sample2: String, val metric: OverlapType, @@ -28,17 +29,13 @@ object Overlap { * Imports data into DataFrame **/ fun dataFrame( - ch: CharacteristicGroup<*, *>, paResult: PostanalysisResult, metricsFilter: List? ) = run { val data = mutableListOf() - - val ch2preproc = ch.characteristics.associate { it.name to it.preprocessor.id() } - val projectedResult = paResult.forGroup(ch) val mf = metricsFilter?.map { it.lowercase() }?.toSet() - for ((char, charData) in projectedResult.data) { - val preproc = ch2preproc[char]!! + for ((ch, charData) in paResult.data) { + val preproc = charData.preproc for ((_, keys) in charData.data) { for (metric in keys.data) { @Suppress("UNCHECKED_CAST") @@ -46,8 +43,12 @@ object Overlap { if (mf != null && !mf.contains(key.key.toString().lowercase())) { continue } - data += OverlapRow(preproc, key.id1, key.id2, key.key, metric.value) - data += OverlapRow(preproc, key.id2, key.id1, key.key, metric.value) + val sample1 = key.id1 + val sample2 = key.id2 + val preprocStat1 = paResult.getPreprocStat(ch, sample1) + val preprocStat2 = paResult.getPreprocStat(ch, sample2) + data += OverlapRow(preproc, preprocStat1, preprocStat2, sample1, sample2, key.key, metric.value) + data += OverlapRow(preproc, preprocStat2, preprocStat1, sample2, sample1, key.key, metric.value) } } } @@ -59,12 +60,11 @@ object Overlap { * Imports data into DataFrame **/ fun dataFrame( - ch: CharacteristicGroup<*, *>, paResult: PostanalysisResult, metricsFilter: List?, metadata: Metadata?, ) = run { - var df: DataFrame = dataFrame(ch, paResult, metricsFilter) + var df: DataFrame = dataFrame(paResult, metricsFilter) if (metadata != null) df = df.withMetadata(metadata) df @@ -118,20 +118,21 @@ object Overlap { fun plotsAndSummary( df: DataFrame, - pp: DataFrame, par: HeatmapParameters, ) = df .groupBy { preproc } .groups.toList().flatMap { byPreproc -> val metrics = byPreproc.metric.distinct().toList() - val preprocId = byPreproc.first()[OverlapRow::preproc.name] as String - val ppFiltered = pp.filter { preproc == preprocId } val droppedSamples = - ppFiltered.filter { stat.dropped || stat.nElementsAfter == 0L } - .sample.distinct().toSet() + byPreproc.filter { preprocStat1.dropped || preprocStat1.nElementsAfter == 0L } + .sample1.distinct().toSet() + + val summary = Preprocessing.pdfSummary( + byPreproc.rows().associate { it.sample1 to it.preprocStat1 }, + metrics.joinToString(", ") + ) - val summary = ppFiltered.pdfSummary(metrics.joinToString(", ")) val plots = byPreproc .filter { !droppedSamples.contains(it.sample1) && !droppedSamples.contains(it.sample2) } .groupBy { metric }.groups.toList() diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt index c8459a5e0..9956e4076 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt @@ -7,10 +7,7 @@ import com.itextpdf.layout.element.Paragraph import com.itextpdf.layout.element.Text import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat -import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema -import org.jetbrains.kotlinx.dataframe.api.filter -import org.jetbrains.kotlinx.dataframe.api.rows import org.jetbrains.kotlinx.dataframe.api.toDataFrame import java.io.ByteArrayOutputStream @@ -40,60 +37,66 @@ object Preprocessing { rows.toDataFrame() } - fun DataFrame.pdfSummary( - preprocId: String?, - header: String = "" + fun pdfSummary( + stat: Map, + headerText: String ): ByteArray? = run { - val pp = if (preprocId == null) - this - else - this.filter { preproc == preprocId } - - val downsampling = pp.filter { - stat.nElementsAfter > 0 - && preproc.lowercase().contains("downsampling") + val statFiltered = stat.filter { + it.value.nElementsAfter > 0 // && preproc.lowercase().contains("downsampl") } - val elementsAfter = downsampling.rows().map { it.stat.nElementsAfter }.distinct() - val weightAfter = downsampling.rows().map { it.stat.sumWeightAfter }.distinct() + val elementsAfter = statFiltered.values.map { it.nElementsAfter }.distinct() + val weightAfter = statFiltered.values.map { it.sumWeightAfter }.distinct() val downsamplingText1 = if (elementsAfter.size == 1) - "Downsampled to $elementsAfter clonotypes" + "Downsampled to ${elementsAfter[0]} clonotypes" else null val downsamplingText2 = if (weightAfter.size == 1) - "Downsampled to $weightAfter reads" + "Downsampled to ${weightAfter[0]} reads" else null // dropped samples: - val dropped = pp.filter { stat.dropped || stat.nElementsAfter == 0L }.sample.toList().distinct() + val dropped = stat.filter { it.value.dropped || it.value.nElementsAfter == 0L }.keys.distinct() if (downsamplingText1 == null && downsamplingText2 == null && dropped.isEmpty()) return@run null - val bs = ByteArrayOutputStream() - val pdfDoc = PdfDocument(PdfWriter(bs)) - - val document = Document(pdfDoc) - document.use { - document.add(Paragraph(header).setBold()) + document { + add(Paragraph(headerText).setBold()) if (downsamplingText1 != null) - document.add(Paragraph(downsamplingText1)) + add(Paragraph(downsamplingText1)) if (downsamplingText2 != null) - document.add(Paragraph(downsamplingText2)) + add(Paragraph(downsamplingText2)) if (dropped.isNotEmpty()) { - document.add( + add( Paragraph("Dropped samples (" + dropped.size + "):\n") .add(Text(dropped.joinToString(", ")).setFontSize(8.0f)) ) } - document.close() + } + } + + private fun document(content: Document.() -> Unit) = run { +// val dummyDoc = Document(PdfDocument(PdfWriter(OutputStream.nullOutputStream()))) +// dummyDoc.content() +// val renderer = dummyDoc.renderer//.setParent(dummyDoc2.renderer) +// val layout = +// renderer.layout(LayoutContext(LayoutArea(0, Rectangle(1000.0f, 1000.0f)))) + + val bs = ByteArrayOutputStream() + val pdfDoc = PdfDocument(PdfWriter(bs)) + val document = Document(pdfDoc) //, PageSize(layout.occupiedArea.bBox.width, layout.occupiedArea.bBox.height)) + document.use { + it.content() + it.close() bs.toByteArray() } } + // // fun DataFrame.pdfTable(header: String = "") = run { // val nCols = 1 + (this.maxOfOrNull { it.chain.size } ?: 0) diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java index f050e4cff..2e406b9a0 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java @@ -43,8 +43,8 @@ public void test3() { Main.main("exportPa", "overlap", // "--width", "2000", // "--height", "5000", - "--chains", "TRA", - "--filter", "Chain=TRA", + // "--chains", "TRA", +// "--filter", "Chain=TRA", // "--filter", "CellPopulation=CD4mem", "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", "--color-key", "x_Tissue", "--color-key", "x_Age(months)", "--color-key", "y_MouseID", diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java index 064f6102f..70e9b1c55 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java @@ -17,7 +17,13 @@ public void test1() { @Test public void test2() { Main.main("postanalysis", "overlap", - "--chains", "IGH", "-f", - "--only-productive", "-d", "umi-count-auto", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m11_ct_spl_CD4mem_a.clns", 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"/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m2_young_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4m_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_dp_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_dp_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json"); +// "--chains", "IGH", + "-f", + "--only-productive", "-d", "umi-count-auto", + "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", + "--chains-column", "Chain", + "--group", "CellPopulation", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD8naive_a.sorted.clns", 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"/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4naiv_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4naiv_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_Cd8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_Cd8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_DP_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_DP_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4naiv_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4naiv_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_Cd8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4m_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_dp_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_dp_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_DP_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_DP_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_b.sorted.clns", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json"); } } From 4f1ab88ceef9316be9f41377d8fe79e9fa089112 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 26 Apr 2022 01:11:18 +0200 Subject: [PATCH 182/282] wip --- .../CommandPaExportPlotsBasicStatistics.java | 41 +++++++++++++++---- .../cli/postanalysis/CommandPaExportTest.java | 2 +- 2 files changed, 34 insertions(+), 9 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index 5e2a224c4..24a1d2bce 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -1,5 +1,7 @@ package com.milaboratory.mixcr.cli.postanalysis; +import com.milaboratory.miplots.stat.util.PValueCorrection; +import com.milaboratory.miplots.stat.util.RefGroup; import com.milaboratory.miplots.stat.util.TestMethod; import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod; import com.milaboratory.mixcr.basictypes.Clone; @@ -12,6 +14,7 @@ import picocli.CommandLine.Option; import java.util.List; +import java.util.Objects; public abstract class CommandPaExportPlotsBasicStatistics extends CommandPaExportPlots { abstract String group(); @@ -24,6 +27,22 @@ public abstract class CommandPaExportPlotsBasicStatistics extends CommandPaExpor public String facetBy; @Option(description = "Select specific metrics to export.", names = {"--metric"}) public List metrics; + @Option(description = "Hide overall p-value.", names = {"--hide-overall-p-value"}) + public boolean hideOverallPValue; + @Option(description = "Hide pairwise p-values.", names = {"--hide-pairwise-p-value"}) + public boolean hidePairwisePValue; + @Option(description = "Reference group. Can be \"all\" or some specific value.", names = {"--ref-group"}) + public String refGroup; + @Option(description = "Hide non-significant observations.", names = {"--hide-ns"}) + public boolean hideNS; + @Option(description = "Do paired analysis.", names = {"--paired"}) + public boolean paired; + @Option(description = "Test method. Default is Wilcoxon. Available methods: Wilcoxon, ANOVA, TTest, KruskalWallis, KolmogorovSmirnov", names = {"--method"}) + public String method = "Wilcoxon"; + @Option(description = "Test method for multiple groups comparison. Default is KruskalWallis. Available methods: ANOVA, KruskalWallis, KolmogorovSmirnov", names = {"--method-multiple-groups"}) + public String methodForMultipleGroups = "KruskalWallis"; + @Option(description = "Test method for multiple groups comparison. Default is KruskalWallis. Available methods: none, BenjaminiHochberg, BenjaminiYekutieli, Bonferroni, Hochberg, Holm, Hommel", names = {"--p-adjust-method"}) + public String pAdjustMethod = "Holm"; @Override void run(PaResultByGroup result) { @@ -38,21 +57,27 @@ void run(PaResultByGroup result) { df = filter(df); + RefGroup rg = null; + if (Objects.equals(refGroup, "all")) + rg = RefGroup.Companion.getAll(); + else if (refGroup != null) + rg = RefGroup.Companion.of(refGroup); + BasicStatistics.PlotParameters par = new BasicStatistics.PlotParameters( primaryGroup, secondaryGroup, facetBy, - true, - true, - null, - false, - null, + !hideOverallPValue, + !hidePairwisePValue, + rg, + hideNS, null, null, - false, - TestMethod.Wilcoxon, - TestMethod.KruskalWallis, null, + paired, + TestMethod.valueOf(method), + TestMethod.valueOf(methodForMultipleGroups), + pAdjustMethod.equals("none") ? null : PValueCorrection.Method.valueOf(pAdjustMethod), CorrelationMethod.Pearson ); diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java index 2e406b9a0..1e032d79b 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java @@ -43,7 +43,7 @@ public void test3() { Main.main("exportPa", "overlap", // "--width", "2000", // "--height", "5000", - // "--chains", "TRA", + // "--chains", "TRA", // "--filter", "Chain=TRA", // "--filter", "CellPopulation=CD4mem", "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", From 860b9419f625fec43b82ad181ee6ceb2aaf1da2f Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 26 Apr 2022 02:07:13 +0200 Subject: [PATCH 183/282] Non-enum diversity. --- .../cli/postanalysis/CommandPaIndividual.java | 24 ++++-- .../postanalysis/SetPreprocessorFactory.java | 12 ++- .../diversity/DiversityAggregator.java | 56 +++++++------ .../diversity/DiversityCharacteristic.java | 2 +- .../diversity/DiversityMeasure.java | 82 ++++++++++++++++--- 5 files changed, 129 insertions(+), 47 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index 166b53d78..9d1fd13cb 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -11,6 +11,7 @@ import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; import com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure; import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; import com.milaboratory.mixcr.postanalysis.ui.*; @@ -72,15 +73,20 @@ PaResultByGroup run(IsolationGroup group, List samples) { groups.add(new CharacteristicGroup<>(Diversity, Arrays.asList(new DiversityCharacteristic<>("Diversity", new WeightFunctions.Count(), - downsampling, - new DiversityMeasure[]{ - DiversityMeasure.Observed, - DiversityMeasure.Clonality, - DiversityMeasure.ShannonWeiner, - DiversityMeasure.InverseSimpson, - DiversityMeasure.Chao1, - DiversityMeasure.Gini - })), + downsampling, + new DiversityMeasure[]{ + DiversityMeasure.Observed, + DiversityMeasure.Clonality, + DiversityMeasure.ShannonWeiner, + DiversityMeasure.InverseSimpson, + DiversityMeasure.Chao1, + DiversityMeasure.Gini + }), + new DiversityCharacteristic<>("D50", new WeightFunctions.Count(), + downsampling.then(new SelectTop.Factory<>(WeightFunctions.Default(), 0.5)), + new DiversityMeasure[]{ + DiversityMeasure.Observed.overrideName("d50") + })), Arrays.asList(new GroupSummary<>()) )); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java index fd674f415..ca5582a1c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java @@ -56,9 +56,15 @@ default SetPreprocessorFactory filter(boolean before, ElementPredicate... } return new PreprocessorChain.Factory<>(list); } else - return before - ? new PreprocessorChain.Factory<>(filter, this) - : new PreprocessorChain.Factory<>(this, filter); + return before ? before(filter) : then(filter); + } + + default SetPreprocessorFactory then(SetPreprocessorFactory then) { + return new PreprocessorChain.Factory(this, then); + } + + default SetPreprocessorFactory before(SetPreprocessorFactory before) { + return new PreprocessorChain.Factory(before, this); } default SetPreprocessorFactory filterAfter(ElementPredicate... predicates) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java index dcdf9a1b5..0f639f7d3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -11,13 +11,13 @@ import java.util.function.ToLongFunction; import java.util.stream.IntStream; -import static com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure.*; +import static com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure.Measure.*; /** * */ public class DiversityAggregator implements Aggregator { - private final Set measures; + private final Map measures; /** number of clonotypes */ private int diversity = 0; /** total count across all clonotypes */ @@ -29,8 +29,10 @@ public class DiversityAggregator implements Aggregator { /** @param count returns count of element */ public DiversityAggregator(ToLongFunction count, DiversityMeasure[] measures) { this.count = count; - this.measures = EnumSet.noneOf(DiversityMeasure.class); - this.measures.addAll(Arrays.asList(measures)); + this.measures = new HashMap<>(); + for (DiversityMeasure m : measures) { + this.measures.put(m.measure, m); + } } @Override @@ -43,26 +45,32 @@ public void consume(T obj) { /** Chao1 */ private List> computeChao1() { - if (!measures.contains(Chao1) && !measures.contains(Chao1Std)) + if (!measures.containsKey(Chao1) && !measures.containsKey(Chao1Std)) return Collections.emptyList(); int sobs = diversity; double f1 = freqTable.get(1); // singletons double f2 = freqTable.get(2); // doubletons double f0 = f1 * (f1 - 1) / 2 / (f2 + 1); double chao1 = sobs + f0; - if (!measures.contains(Chao1Std)) - return Collections.singletonList(new MetricValue<>(Chao1, chao1)); + if (!measures.containsKey(Chao1Std)) + return Collections.singletonList(new MetricValue<>(measures.get(Chao1), chao1)); double chao1std = Math.sqrt( f0 + f1 * (2 * f1 - 1) * (2 * f1 - 1) / 4 / (f2 + 1) / (f2 + 1) + f1 * f1 * f2 * (f1 - 1) * (f1 - 1) / 4 / (f2 + 1) / (f2 + 1) / (f2 + 1) / (f2 + 1)); - return Arrays.asList(new MetricValue<>(Chao1, chao1), new MetricValue<>(Chao1Std, chao1std)); + return Arrays.asList( + new MetricValue<>(measures.get(Chao1), chao1), + new MetricValue<>(measures.get(Chao1Std), chao1std) + ); } /** Clonality, Gini and Shannon-Weiner */ private List> computeClonality() { - if (!(measures.contains(ShannonWeiner) || measures.contains(Clonality) || measures.contains(InverseSimpson) || measures.contains(Gini))) + if (!(measures.containsKey(ShannonWeiner) + || measures.containsKey(Clonality) + || measures.containsKey(InverseSimpson) + || measures.containsKey(Gini))) return Collections.emptyList(); double shannonWeiner = 0; double gini = 0; @@ -80,14 +88,14 @@ private List> computeClonality() { } List> result = new ArrayList<>(); - if (measures.contains(ShannonWeiner)) - result.add(new MetricValue<>(ShannonWeiner, shannonWeiner)); - if (measures.contains(Clonality)) - result.add(new MetricValue<>(Clonality, 1 - shannonWeiner / Math.log(diversity))); - if (measures.contains(InverseSimpson)) - result.add(new MetricValue<>(InverseSimpson, -1 / gini)); - if (measures.contains(Gini)) - result.add(new MetricValue<>(Gini, 1 - gini)); + if (measures.containsKey(ShannonWeiner)) + result.add(new MetricValue<>(measures.get(ShannonWeiner), shannonWeiner)); + if (measures.containsKey(Clonality)) + result.add(new MetricValue<>(measures.get(Clonality), 1 - shannonWeiner / Math.log(diversity))); + if (measures.containsKey(InverseSimpson)) + result.add(new MetricValue<>(measures.get(InverseSimpson), -1 / gini)); + if (measures.containsKey(Gini)) + result.add(new MetricValue<>(measures.get(Gini), 1 - gini)); return result; } @@ -100,7 +108,7 @@ private List> computeEfronThisted() { /** Efron-Thisted */ private List> computeEfronThisted(int maxDepth, double cvThreshold) { - if (!measures.contains(EfronThisted) && !measures.contains(EfronThistedStd)) + if (!measures.containsKey(EfronThisted) && !measures.containsKey(EfronThistedStd)) return Collections.emptyList(); double S = -1, D = -1, CV; @@ -130,17 +138,17 @@ private List> computeEfronThisted(int maxDepth, do } List> result = new ArrayList<>(); - if (measures.contains(EfronThisted)) - result.add(new MetricValue<>(EfronThisted, S)); - if (measures.contains(EfronThistedStd)) - result.add(new MetricValue<>(EfronThistedStd, D)); + if (measures.containsKey(EfronThisted)) + result.add(new MetricValue<>(measures.get(EfronThisted), S)); + if (measures.containsKey(EfronThistedStd)) + result.add(new MetricValue<>(measures.get(EfronThistedStd), D)); return result; } private List> computeObserved() { - if (!measures.contains(Observed)) + if (!measures.containsKey(Observed)) return Collections.emptyList(); - return Collections.singletonList(new MetricValue<>(Observed, diversity)); + return Collections.singletonList(new MetricValue<>(measures.get(Observed), diversity)); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java index bb82c09aa..6e4591679 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java @@ -29,7 +29,7 @@ public DiversityCharacteristic(@JsonProperty("name") String name, public DiversityCharacteristic(@JsonProperty("name") String name, @JsonProperty("weight") WeightFunction weight, @JsonProperty("preproc") SetPreprocessorFactory preprocessor) { - this(name, weight, preprocessor, DiversityMeasure.values()); + this(name, weight, preprocessor, DiversityMeasure.basic()); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java index 4a4f8eb51..03bdde643 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java @@ -1,16 +1,78 @@ package com.milaboratory.mixcr.postanalysis.diversity; +import java.util.Objects; + /** * */ -public enum DiversityMeasure { - Observed, - Chao1, - Chao1Std, - ShannonWeiner, - Clonality, - Gini, - InverseSimpson, - EfronThisted, - EfronThistedStd; +public final class DiversityMeasure { + public final Measure measure; + public final String name; + + public DiversityMeasure(Measure measure, String name) { + this.measure = measure; + this.name = name; + } + + public DiversityMeasure overrideName(String newName) { + return new DiversityMeasure(measure, newName); + } + + @Override + public String toString() { + return name; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + DiversityMeasure that = (DiversityMeasure) o; + return measure == that.measure && Objects.equals(name, that.name); + } + + @Override + public int hashCode() { + return Objects.hash(measure, name); + } + + public static DiversityMeasure[] basic() { + return new DiversityMeasure[]{ + Observed, + Chao1, + Chao1Std, + ShannonWeiner, + Clonality, + Gini, + InverseSimpson, + EfronThisted, + EfronThistedStd, + }; + } + + public static final DiversityMeasure Observed = Measure.Observed.toDiversityMeasure(); + public static final DiversityMeasure Chao1 = Measure.Chao1.toDiversityMeasure(); + public static final DiversityMeasure Chao1Std = Measure.Chao1Std.toDiversityMeasure(); + public static final DiversityMeasure ShannonWeiner = Measure.ShannonWeiner.toDiversityMeasure(); + public static final DiversityMeasure Clonality = Measure.Clonality.toDiversityMeasure(); + public static final DiversityMeasure Gini = Measure.Gini.toDiversityMeasure(); + public static final DiversityMeasure InverseSimpson = Measure.InverseSimpson.toDiversityMeasure(); + public static final DiversityMeasure EfronThisted = Measure.EfronThisted.toDiversityMeasure(); + public static final DiversityMeasure EfronThistedStd = Measure.EfronThistedStd.toDiversityMeasure(); + + enum Measure { + Observed, + Chao1, + Chao1Std, + ShannonWeiner, + Clonality, + Gini, + InverseSimpson, + EfronThisted, + EfronThistedStd; + + public DiversityMeasure toDiversityMeasure() { + return new DiversityMeasure(this, this.name()); + } + } } From a431e8c1cce3d1de75cbf32289af0dd9ba7b1ca5 Mon Sep 17 00:00:00 2001 From: Dmitriy Bolotin Date: Thu, 28 Apr 2022 01:38:43 +0400 Subject: [PATCH 184/282] fix: repeated creation of clone port for clna reader now correctly works (cherry picked from commit 22a1456ead618a687e2a59b15b3d813d9334016f) --- src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index fc4963075..e237664c5 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -260,7 +260,7 @@ public CloneSet readCloneSet() throws IOException { */ @Override public OutputPortCloseable readClones() { - return input.beginPrimitivIBlocks(Clone.class); + return input.beginRandomAccessPrimitivIBlocks(Clone.class, firstClonePosition); } /** From 88e307eb56a22f40369dc4e6c05b8339d73f7ced Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 29 Apr 2022 12:44:33 +0200 Subject: [PATCH 185/282] wip --- .../mixcr/cli/postanalysis/CommandPaIndividual.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index 9d1fd13cb..2c0be17b0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -82,7 +82,7 @@ PaResultByGroup run(IsolationGroup group, List samples) { DiversityMeasure.Chao1, DiversityMeasure.Gini }), - new DiversityCharacteristic<>("D50", new WeightFunctions.Count(), + new DiversityCharacteristic<>("d50", new WeightFunctions.Count(), downsampling.then(new SelectTop.Factory<>(WeightFunctions.Default(), 0.5)), new DiversityMeasure[]{ DiversityMeasure.Observed.overrideName("d50") From 5c851640dae0d7c8630efb3bfa28174cc2e3f52c Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 7 May 2022 15:38:49 +0400 Subject: [PATCH 186/282] MiLM2 Integration (#43) --- .github/workflows/build.yaml | 14 +++- .gitignore | 2 + .mi-ci/hooks/test-integration-after.sh | 6 +- .mi-ci/hooks/test-integration-before.sh | 12 ++- .mi-ci/hooks/test-unit-before.sh | 12 ++- build.gradle.kts | 28 ++++++- itests/case8.sh | 10 +-- itests/case9.sh | 10 +-- mixcr | 2 +- .../java/com/milaboratory/mixcr/cli/Main.java | 74 ++++++++++++++++++- 10 files changed, 144 insertions(+), 26 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index d75c6e330..94ebcc1b1 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -4,8 +4,10 @@ on: push: tags: [ '*' ] branches: [ '*' ] + schedule: + - cron: '10 1 * * *' - workflow_dispatch: {} + workflow_dispatch: { } jobs: init: @@ -49,12 +51,12 @@ jobs: # Distribution dist-docker: false - dist-archive: true + dist-archive: ${{ github.event_name != 'schedule' }} dist-archive-tasks: 'distributionZip' dist-archive-paths: './distributions/*.zip' # Release to S3 - release-to-s3: true + release-to-s3: ${{ github.event_name != 'schedule' }} release-s3-add-version: true release-s3-add-sha: ${{ fromJSON(needs.init.outputs.is-release) && 'false' || '8' }} @@ -62,10 +64,16 @@ jobs: notify-telegram: true secrets: + env: | + { "MI_LICENSE": ${{ toJSON(secrets.MI_LICENSE) }} } + GRADLE_PROPERTIES: | miRepoAccessKeyId=${{ secrets.AWS_CI_ACCESS_KEY_ID }} miRepoSecretAccessKey= ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }} + miGitHubMavenUser=${{ github.actor }} + miGitHubMavenToken=${{ secrets.GITHUB_TOKEN }} + AWS_KEY_ID: ${{ secrets.AWS_CI_ACCESS_KEY_ID }} AWS_KEY_SECRET: ${{ secrets.AWS_CI_SECRET_ACCESS_KEY }} diff --git a/.gitignore b/.gitignore index 6be4cea72..53d6f4be9 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,5 @@ test_target src/test/resources/sequences/big tmp pack +build +.gradle diff --git a/.mi-ci/hooks/test-integration-after.sh b/.mi-ci/hooks/test-integration-after.sh index 2002a3815..5522e9bf2 100755 --- a/.mi-ci/hooks/test-integration-after.sh +++ b/.mi-ci/hooks/test-integration-after.sh @@ -2,5 +2,9 @@ script_dir=$(dirname "${0}") +cd "${script_dir}/../.." || exit + +#export MI_LICENSE_DEBUG=MI_LICENSE_DEBUG + # Run integration tests -"${script_dir}/../../itests.sh" +./itests.sh test diff --git a/.mi-ci/hooks/test-integration-before.sh b/.mi-ci/hooks/test-integration-before.sh index 297e183a6..e3651b05a 100755 --- a/.mi-ci/hooks/test-integration-before.sh +++ b/.mi-ci/hooks/test-integration-before.sh @@ -2,8 +2,12 @@ script_dir=$(dirname "${0}") -# downloadable test data -"${script_dir}/../../ensure-test-data.sh" +cd "${script_dir}/../.." || exit -# builds predprocessed test data -"${script_dir}/../../prepare-test-data.sh" +#export MI_LICENSE_DEBUG=MI_LICENSE_DEBUG + +# Downloadable test data +./ensure-test-data.sh + +# Builds pre-processed test data +./prepare-test-data.sh diff --git a/.mi-ci/hooks/test-unit-before.sh b/.mi-ci/hooks/test-unit-before.sh index 297e183a6..e3651b05a 100755 --- a/.mi-ci/hooks/test-unit-before.sh +++ b/.mi-ci/hooks/test-unit-before.sh @@ -2,8 +2,12 @@ script_dir=$(dirname "${0}") -# downloadable test data -"${script_dir}/../../ensure-test-data.sh" +cd "${script_dir}/../.." || exit -# builds predprocessed test data -"${script_dir}/../../prepare-test-data.sh" +#export MI_LICENSE_DEBUG=MI_LICENSE_DEBUG + +# Downloadable test data +./ensure-test-data.sh + +# Builds pre-processed test data +./prepare-test-data.sh diff --git a/build.gradle.kts b/build.gradle.kts index bf3265b4a..ca60addf0 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -3,7 +3,16 @@ import com.palantir.gradle.gitversion.VersionDetails import groovy.lang.Closure import java.net.InetAddress -gradle.startParameter.excludedTaskNames += listOf("assembleDist", "assembleShadowDist", "distTar", "distZip", "installDist", "installShadowDist", "shadowDistTar", "shadowDistZip") +gradle.startParameter.excludedTaskNames += listOf( + "assembleDist", + "assembleShadowDist", + "distTar", + "distZip", + "installDist", + "installShadowDist", + "shadowDistTar", + "shadowDistZip" +) plugins { `java-library` @@ -13,6 +22,9 @@ plugins { id("com.github.johnrengelman.shadow") version "7.1.2" } +// val miGitHubMavenUser: String by project +// val miGitHubMavenToken: String by project + val miRepoAccessKeyId: String? by project val miRepoSecretAccessKey: String? by project @@ -45,10 +57,15 @@ tasks.withType { } tasks.withType { - (options as StandardJavadocDocletOptions).addStringOption("Xdoclint:none", "-quiet") + options { + this as StandardJavadocDocletOptions + addStringOption("Xdoclint:none", "-quiet") + } } repositories { + // mavenLocal() + mavenCentral() // Snapshot versions of redberry-pipe, milib and repseqio distributed via this repo @@ -67,6 +84,9 @@ dependencies { exclude("com.milaboratory", "milib") } + // implementation("com.milaboratory:milm2-jvm:0.2.0-test-2") { isChanging = true } + implementation("com.milaboratory:milm2-jvm:1.1.0") + implementation("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion") implementation("commons-io:commons-io:2.11.0") implementation("org.lz4:lz4-java:1.8.0") @@ -146,6 +166,10 @@ tasks.test { minHeapSize = "1024m" maxHeapSize = "2048m" + testLogging { + showStandardStreams = true + } + miCiStage?.let { if (it == "test") { systemProperty("longTests", "true") diff --git a/itests/case8.sh b/itests/case8.sh index caf1f62ce..3f767f33d 100755 --- a/itests/case8.sh +++ b/itests/case8.sh @@ -23,9 +23,9 @@ mixcr analyze amplicon \ --impute-germline-on-export --json-report case8 \ CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case8 -assert "cat case8.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197562" -assert "cat case8.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161627" -assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "223" -assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "1378" +assert "cat case8.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197642" +assert "cat case8.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161771" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "227" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "978" assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" -assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22402" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22384" diff --git a/itests/case9.sh b/itests/case9.sh index e67d08e26..b650f934a 100755 --- a/itests/case9.sh +++ b/itests/case9.sh @@ -24,9 +24,9 @@ mixcr analyze amplicon \ --impute-germline-on-export --json-report case9 \ CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case9 -assert "cat case9.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197562" -assert "cat case9.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161627" -assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "223" -assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "1378" +assert "cat case9.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197642" +assert "cat case9.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161771" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "227" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "978" assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" -assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22402" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22384" diff --git a/mixcr b/mixcr index dee31eef3..64d0045fa 100755 --- a/mixcr +++ b/mixcr @@ -193,6 +193,6 @@ if [[ "$jar" == "" ]]; then exit 1 fi -$java -D${app}.path="$dir" -D${app}.command=${app} "${javaArgs[@]}" -jar "$jar" "${appArgs[@]}" +$java -Dmi.license.file="$dir/mi.license" -D${app}.path="$dir" -D${app}.command=${app} "${javaArgs[@]}" -jar "$jar" "${appArgs[@]}" exit $? diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 9143fc696..c4715dc4f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -30,6 +30,9 @@ package com.milaboratory.mixcr.cli; import com.milaboratory.cli.ValidationException; +import com.milaboratory.milm.LM; +import com.milaboratory.milm.LicenseError; +import com.milaboratory.milm.LicenseErrorType; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.VersionInfo; import io.repseq.core.VDJCLibraryRegistry; @@ -45,17 +48,86 @@ import java.nio.file.Paths; import java.util.ArrayList; import java.util.List; - +import java.util.Scanner; +import java.util.function.Consumer; +import java.util.prefs.Preferences; public final class Main { private static boolean initialized = false; + public static final LM lm = new LM(Main.class); + + public static final String MI_LICENSE_PREFERENCES_KEY = "mi_license"; public static void main(String... args) { + Preferences prefs = Preferences.userNodeForPackage(Main.class); + if (args.length > 0 && "activate-license".equals(args[0])) { + try (Scanner reader = new Scanner(System.in)) { + System.out.println("Please enter the license:"); + String envelope = reader.nextLine(); + System.out.println("Checking the license..."); + lm.addStringLicenseSource(envelope); + lm.setWarningHandler(warning -> System.err.println("License Warning:\n" + warning)); + Consumer errorHandler = err -> System.err.println("License Error:\n" + err.getType() + "\n" + err.getMessage()); + lm.setAsyncErrorHandler(errorHandler); + LicenseError err = lm.init(); + if (err != null) { + errorHandler.accept(err); + System.exit(LM.LicenseErrorExitCode); + } + System.out.println("Ok"); + prefs.put(MI_LICENSE_PREFERENCES_KEY, envelope); + System.out.println("License activated successfully."); + System.exit(0); + } + } + + if (args.length > 0 && "deactivate-license".equals(args[0])) { + prefs.remove(MI_LICENSE_PREFERENCES_KEY); + System.out.println("License successfully deactivated."); + System.exit(0); + } + + lm.addPreferenceLicenseSource(prefs, MI_LICENSE_PREFERENCES_KEY); + lm.addDefaultSources(); + + Consumer licenseErrorHandler = licenseError -> { + if (licenseError.getType() == LicenseErrorType.NoLicense) { + System.err.println("=== No License ==="); + System.err.println(); + System.err.println("To use MiXCR, please, provide a valid license."); + System.err.println(); + System.err.println("If you already have a license, activate it by calling:"); + System.err.println(" mixcr activate-license"); + System.err.println(); + System.err.println("You can also activate the license via a special file, environment"); + System.err.println("variable or other means, please check the docs."); // TODO provide a link + System.err.println(); + System.err.println("If you don't have a license check https://licensing.milaboratories.com/."); + System.err.println("Free license is provided for academic users and non-profit organisations."); + } else + System.err.println("License error: " + licenseError); + System.exit(LM.LicenseErrorExitCode); + }; + + lm.setAsyncErrorHandler(licenseErrorHandler); + lm.setWarningHandler(warning -> System.err.println("License Warning: " + warning)); + LicenseError lmError = lm.init(); + if (lmError != null) licenseErrorHandler.accept(lmError); + + VersionInfo versionInfo = VersionInfo.getVersionInfoForArtifact("mixcr"); + lm.sendGenericStats("mixcr." + + versionInfo.getVersion() + "." + + versionInfo.getBranch() + "." + + versionInfo.getRevision() + "." + + versionInfo.getTimestamp().toInstant().getEpochSecond(), + args); + Thread.setDefaultUncaughtExceptionHandler((t, e) -> { e.printStackTrace(); System.exit(2); }); + handleParseResult(parseArgs(args).getParseResult(), args); } From e332558a87d579c602921274c3676ef7c3611570 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 7 May 2022 15:48:58 +0400 Subject: [PATCH 187/282] chore: gradle upgrade, milib upgrade --- build.gradle.kts | 7 ++----- gradle/wrapper/gradle-wrapper.jar | Bin 59536 -> 59821 bytes gradle/wrapper/gradle-wrapper.properties | 3 ++- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index ca60addf0..9c5446a23 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -18,13 +18,10 @@ plugins { `java-library` application `maven-publish` - id("com.palantir.git-version") version "0.13.0" + id("com.palantir.git-version") version "0.15.0" id("com.github.johnrengelman.shadow") version "7.1.2" } -// val miGitHubMavenUser: String by project -// val miGitHubMavenToken: String by project - val miRepoAccessKeyId: String? by project val miRepoSecretAccessKey: String? by project @@ -74,7 +71,7 @@ repositories { } } -val milibVersion = "1.15.0-23-master" +val milibVersion = "1.15.0-26-master" val repseqioVersion = "1.3.5-24-master" val jacksonVersion = "2.13.2.2" diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index 7454180f2ae8848c63b8b4dea2cb829da983f2fa..41d9927a4d4fb3f96a785543079b8df6723c946b 100644 GIT binary patch delta 8958 zcmY+KWl$VIlZIh&f(Hri?gR<$?iyT!TL`X;1^2~W7YVSq1qtqM!JWlDxLm%}UESUM zndj}Uny%^UnjhVhFb!8V3s(a#fIy>`VW15{5nuy;_V&a5O#0S&!a4dSkUMz_VHu3S zGA@p9Q$T|Sj}tYGWdjH;Mpp8m&yu&YURcrt{K;R|kM~(*{v%QwrBJIUF+K1kX5ZmF zty3i{d`y0;DgE+de>vN@yYqFPe1Ud{!&G*Q?iUc^V=|H%4~2|N zW+DM)W!`b&V2mQ0Y4u_)uB=P@-2`v|Wm{>CxER1P^ z>c}ZPZ)xxdOCDu59{X^~2id7+6l6x)U}C4Em?H~F`uOxS1?}xMxTV|5@}PlN%Cg$( zwY6c}r60=z5ZA1L zTMe;84rLtYvcm?M(H~ZqU;6F7Evo{P7!LGcdwO|qf1w+)MsnvK5^c@Uzj<{ zUoej1>95tuSvDJ|5K6k%&UF*uE6kBn47QJw^yE&#G;u^Z9oYWrK(+oL97hBsUMc_^ 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z`P}zfQ6l^AO8ehZ=l^ZR;R%uu4;BK*=?W9t|0{+-at(MQZ(CtG=EJFNaFMlKCMXu30(gJUqj5+ z`GM|!keqcj;FKTa_qq;{*dHRXAq157hlB@kL#8%yAm2AgfU|*rDKX@FLlp=HL8ddv zAWLCHe@DcDeB2}fl7#=0+#<05c3=VqM*O3bkr@9X4nO|)q0hU;Gye{L8ZN*NH8Id@mP-u;Fmb8YuorjLrW&ndip8CN%_qp982r w1WEnz9^$&s1hkp_3#lPJQ~!HI7WYYjA7>z!`?f%npAh2%rB@vD|Lau$2O)#1n*aa+ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 00e33edef..5c51a4acc 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,6 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.1-bin.zip +distributionSha256Sum=29e49b10984e585d8118b7d0bc452f944e386458df27371b49b4ac1dec4b7fda +distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists From e7692249704cedb8ad995e6a0acf3d9d16a0988a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 7 May 2022 15:57:03 +0400 Subject: [PATCH 188/282] feat: mi.license in gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 53d6f4be9..3bc827c7b 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,5 @@ tmp pack build .gradle +mi.license +.mi.license From d02e12f64fd659c6ad8c8cd7df259a32d8dc5a85 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sun, 8 May 2022 02:03:38 +0200 Subject: [PATCH 189/282] fixes after discussions with Dima --- .../java/com/milaboratory/mixcr/cli/Main.java | 11 +- .../mixcr/cli/postanalysis/CommandPa.java | 68 ++++++-- .../cli/postanalysis/CommandPaExport.java | 28 ++-- .../postanalysis/CommandPaExportPlots.java | 44 ++--- .../CommandPaExportPlotsBasicStatistics.java | 2 +- .../CommandPaExportPlotsGeneUsage.java | 2 +- .../CommandPaExportPlotsOverlap.java | 2 +- .../postanalysis/CommandPaExportTables.java | 8 +- .../CommandPaExportTablesBase.java | 12 +- .../CommandPaExportTablesPreprocSummary.java | 16 +- .../cli/postanalysis/CommandPaIndividual.java | 4 +- .../postanalysis/CommandPaListMetrics.java | 4 +- .../cli/postanalysis/CommandPaOverlap.java | 19 +-- .../postanalysis/PostanalysisResult.java | 5 + .../postanalysis/SetPreprocessorSummary.java | 153 ++++++++++++++++-- 15 files changed, 276 insertions(+), 102 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 788e65037..cbc9d91ac 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -148,7 +148,10 @@ public static CommandLine mkCmd() { .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) .addSubcommand("postanalysis", CommandPa.CommandPostanalysisMain.class) - .addSubcommand("exportPa", CommandPaExport.CommandExportPaMain.class) + .addSubcommand("exportPlots", CommandPaExportPlots.CommandExportPlotsMain.class) + .addSubcommand("exportTables", CommandPaExportTables.class) + .addSubcommand("exportPreprocTables", CommandPaExportTablesPreprocSummary.class) + .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) @@ -195,18 +198,14 @@ public static CommandLine mkCmd() { .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPaOverlap.class)); cmd.getSubcommands() - .get("exportPa") - .addSubcommand("tables", CommandSpec.forAnnotatedObject(CommandPaExportTables.class)) - .addSubcommand("preprocSummary", CommandSpec.forAnnotatedObject(CommandPaExportTablesPreprocSummary.class)) + .get("exportPlots") .addSubcommand("listMetrics", CommandSpec.forAnnotatedObject(CommandPaListMetrics.class)) .addSubcommand("biophysics", CommandSpec.forAnnotatedObject(CommandPaExportPlotsBasicStatistics.ExportBiophysics.class)) .addSubcommand("diversity", CommandSpec.forAnnotatedObject(CommandPaExportPlotsBasicStatistics.ExportDiversity.class)) - .addSubcommand("vUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsGeneUsage.ExportVUsage.class)) .addSubcommand("jUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsGeneUsage.ExportJUsage.class)) .addSubcommand("isotypeUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsGeneUsage.ExportIsotypeUsage.class)) .addSubcommand("vjUsage", CommandSpec.forAnnotatedObject(CommandPaExportPlotsVJUsage.class)) - .addSubcommand("overlap", CommandSpec.forAnnotatedObject(CommandPaExportPlotsOverlap.class)); cmd.setSeparator(" "); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 222718837..b78f46547 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -40,7 +40,7 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { public boolean onlyProductive = false; @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", - names = {"-d", "--downsampling"}, + names = {"--downsampling"}, required = true) public String downsampling; @@ -51,15 +51,23 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { @Option(description = "Metadata file (csv/tsv). Must have \"sample\" column.", names = {"-m", "--meta", "--metadata"}) public String metadata; - - @Option(description = "Metadata column for chains.", - names = {"--chains-column"}) - public String chainsColumn; +// +// @Option(description = "Metadata column for chains.", +// names = {"--chains-column"}) +// public String chainsColumn; @Option(description = "Metadata categories used to isolate samples into separate groups", names = {"-g", "--group"}) public List isolationGroups; + @Option(description = "Tabular results output path.", + names = {"--tables"}) + public String tablesOut; + + @Option(description = "Preprocessor summary output path.", + names = {"--preproc-tables"}) + public String preprocOut; + @Override protected List getInputFiles() { return inOut.subList(0, inOut.size() - 1) @@ -80,7 +88,7 @@ protected List getInputFiles() { @Override protected List getOutputFiles() { - return Collections.singletonList(outputFile()); + return Collections.singletonList(out()); } @Override @@ -88,16 +96,34 @@ public void validate() { super.validate(); if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) throwValidationException("Metadata should be .csv or .tsv"); - if (!outputFile().endsWith(".json") && !outputFile().endsWith(".json.gz")) + if (!out().endsWith(".json") && !out().endsWith(".json.gz")) throwValidationException("Output file name should ends with .json.gz or .json"); } - private String outputFile() { + private String outBase() { + String out = out(); + if (out.endsWith(".json.gz")) + return out.substring(0, out.length() - 8); + else if (out.endsWith(".json")) + return out.substring(0, out.length() - 5); + else + throw new IllegalArgumentException("output extension is illegal"); + } + + private String out() { return inOut.get(inOut.size() - 1); } + private String tablesOut() { + return tablesOut == null ? outBase() + ".tsv" : tablesOut; + } + + private String preprocOut() { + return preprocOut == null ? outBase() + ".preproc.tsv" : preprocOut; + } + private Path outputPath() { - return Paths.get(outputFile()).toAbsolutePath(); + return Paths.get(out()).toAbsolutePath(); } /** Get sample id from file name */ @@ -150,7 +176,7 @@ protected SetPreprocessorFactory downsampling(String downsamplingStr) { private Map> _metadata = null; - protected Map> readMetadata() { + protected Map> metadata() { if (metadata == null) return null; if (_metadata != null) @@ -197,13 +223,25 @@ public SamplesGroup(List samples, Map group) { } } + private static final String[] CHAINS_COLUMN_NAMES = {"chain", "chains"}; + + private String chainsColumn() { + Map> metadata = metadata(); + if (metadata == null) + return null; + return metadata.keySet().stream().filter( + col -> Arrays.stream(CHAINS_COLUMN_NAMES).anyMatch(col::equalsIgnoreCase) + ).findFirst().orElse(null); + } + /** group samples into isolated groups */ protected List groupSamples() { + String chainsColumn = chainsColumn(); if ((isolationGroups == null || isolationGroups.isEmpty()) && chainsColumn == null) { return Collections.singletonList(new SamplesGroup(getInputFiles(), Collections.emptyMap())); } - Map> metadata = readMetadata(); + Map> metadata = metadata(); @SuppressWarnings({"unchecked", "rawtypes"}) List mSamples = (List) metadata.get("sample"); List qSamples = getInputFiles(); @@ -242,6 +280,7 @@ protected List groupSamples() { public void run0() throws Exception { List results = new ArrayList<>(); Chains c = Chains.parse(chains); + String chainsColumn = chainsColumn(); for (SamplesGroup group : groupSamples()) { if (chainsColumn != null) results.add(run(new IsolationGroup( @@ -253,18 +292,21 @@ public void run0() throws Exception { } } } - PaResult result = new PaResult(readMetadata(), isolationGroups, results); + PaResult result = new PaResult(metadata(), isolationGroups, results); try { Files.createDirectories(outputPath().getParent()); } catch (IOException e) { throw new RuntimeException(e); } PaResult.writeJson(outputPath(), result); + + // export tables & preprocessing summary + new CommandPaExportTables(result, tablesOut()).run0(); + new CommandPaExportTablesPreprocSummary(result, preprocOut()).run0(); } abstract PaResultByGroup run(IsolationGroup group, List samples); - @CommandLine.Command(name = "postanalysis", separator = " ", description = "Run postanalysis routines.", diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java index 63d67b4cd..69c29646c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java @@ -3,11 +3,10 @@ import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; import io.repseq.core.Chains; import io.repseq.core.Chains.NamedChains; -import picocli.CommandLine; import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; -import java.nio.file.Path; +import java.nio.file.Paths; import java.util.Collections; import java.util.List; import java.util.Set; @@ -25,6 +24,17 @@ public abstract class CommandPaExport extends ACommandWithOutputMiXCR { @Option(description = "Export for specific chains only", names = {"--chains"}) public List chains; + /** + * Cached PA result + */ + private PaResult paResult = null; + + public CommandPaExport() {} + + /** Constructor used to export tables from code */ + CommandPaExport(PaResult paResult) { + this.paResult = paResult; + } @Override protected List getInputFiles() { @@ -38,10 +48,6 @@ public void validateInfo(String inputFile) { throwValidationException("Metadata should be .csv or .tsv"); } - /** - * Cached PA result - */ - private PaResult paResult = null; /** * Get full PA result @@ -49,7 +55,7 @@ public void validateInfo(String inputFile) { protected PaResult getPaResult() { if (paResult != null) return paResult; - return paResult = PaResult.readJson(Path.of(in).toAbsolutePath()); + return paResult = PaResult.readJson(Paths.get(in).toAbsolutePath()); } @Override @@ -65,12 +71,4 @@ public void run0() throws Exception { } abstract void run(PaResultByGroup result); - - @CommandLine.Command(name = "exportPa", - separator = " ", - description = "Export postanalysis results.", - subcommands = { - CommandLine.HelpCommand.class - }) - public static class CommandExportPaMain {} } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java index f1136b3fe..c39a42047 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java @@ -1,14 +1,13 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.miplots.ExportKt; -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; import com.milaboratory.mixcr.postanalysis.plots.Filter; import com.milaboratory.mixcr.postanalysis.plots.MetadataKt; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; import org.jetbrains.kotlinx.dataframe.api.DataFrameIterableKt; +import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; @@ -17,10 +16,12 @@ import java.nio.file.Path; import java.nio.file.Paths; import java.util.List; -import java.util.Map; import java.util.stream.Collectors; -abstract class CommandPaExportPlots extends CommandPaExport { +@Command(name = "exportPlots", + separator = " ", + description = "Export postanalysis plots.") +public abstract class CommandPaExportPlots extends CommandPaExport { @Option(description = "Plot width", names = {"--width"}) public int width = 0; @Option(description = "Plot height", names = {"--height"}) @@ -68,14 +69,6 @@ Path plotDestPath(IsolationGroup group) { return Paths.get(plotDestStr(group)); } - String tablesDestStr(IsolationGroup group) { - return out.substring(0, out.length() - 3) + "preproc" + group.extension() + ".tsv"; - } - - Path tablesDestPath(IsolationGroup group) { - return Paths.get(tablesDestStr(group)); - } - protected void ensureOutputPathExists() { try { Files.createDirectories(Paths.get(out).toAbsolutePath().getParent()); @@ -84,9 +77,9 @@ protected void ensureOutputPathExists() { } } - void writeTables(IsolationGroup group, List tables) { + void writePlotsAndSummary(IsolationGroup group, List plots) { ensureOutputPathExists(); - ExportKt.writePDF(tablesDestPath(group), tables); + ExportKt.writePDF(plotDestPath(group), plots); } void writePlots(IsolationGroup group, List plots) { @@ -96,18 +89,15 @@ void writePlots(IsolationGroup group, List plots) { void writePlots(IsolationGroup group, Plot plot) { ensureOutputPathExists(); - ExportKt.writePDF(tablesDestPath(group), plot); + ExportKt.writePDF(plotDestPath(group), plot); } - void writePlotsAndSummary(CharacteristicGroup ch, - IsolationGroup group, - List plotsAndSummary, - Map preprocSummary - ) { - ensureOutputPathExists(); - ExportKt.writePDF(plotDestPath(group), plotsAndSummary); - SetPreprocessorSummary.writeCSV(tablesDestPath(group), - ch, preprocSummary, - "\t"); - } + + @CommandLine.Command(name = "exportPlots", + separator = " ", + description = "Export postanalysis results.", + subcommands = { + CommandLine.HelpCommand.class + }) + public static class CommandExportPlotsMain {} } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index 24a1d2bce..39e744354 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -82,7 +82,7 @@ else if (refGroup != null) ); List plots = BasicStatistics.INSTANCE.plotsAndSummary(df, par); - writePlotsAndSummary(ch, result.group, plots, paResult.preprocSummary); + writePlotsAndSummary(result.group, plots); } @CommandLine.Command(name = "biophysics", diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java index 9c956f220..ae134eda8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java @@ -56,7 +56,7 @@ void run(PaResultByGroup result) { height )); - writePlotsAndSummary(ch, result.group, plot, paResult.preprocSummary); + writePlotsAndSummary(result.group, plot); } @CommandLine.Command(name = "vUsage", diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java index d7ee390ac..63d2d5529 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -75,6 +75,6 @@ void run(PaResultByGroup result) { ); List plotsAndSummary = Overlap.INSTANCE.plotsAndSummary(df, par); - writePlotsAndSummary(ch, result.group, plotsAndSummary, preprocSummary); + writePlotsAndSummary(result.group, plotsAndSummary); } } \ No newline at end of file diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java index 15bd50e12..ae1ce481e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java @@ -6,11 +6,17 @@ import com.milaboratory.mixcr.postanalysis.ui.OutputTable; import picocli.CommandLine; -@CommandLine.Command(name = "tables", +@CommandLine.Command(name = "exportTables", sortOptions = false, separator = " ", description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype, Overlap") public final class CommandPaExportTables extends CommandPaExportTablesBase { + public CommandPaExportTables() {} + + public CommandPaExportTables(PaResult paResult, String out) { + super(paResult, out); + } + @Override void run1(PaResultByGroup result) { for (CharacteristicGroup table : result.schema.tables) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java index 905d59cf2..70946dbff 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java @@ -5,11 +5,19 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.nio.file.Paths; abstract class CommandPaExportTablesBase extends CommandPaExport { @Parameters(description = "Path for output files", index = "1", defaultValue = "path/table.tsv") public String out; + public CommandPaExportTablesBase() {} + + CommandPaExportTablesBase(PaResult paResult, String out) { + super(paResult); + this.out = out; + } + @Override public void validate() { super.validate(); @@ -18,11 +26,11 @@ public void validate() { } protected Path outDir() { - return Path.of(out).toAbsolutePath().getParent(); + return Paths.get(out).toAbsolutePath().getParent(); } protected String outPrefix() { - String fName = Path.of(out).getFileName().toString(); + String fName = Paths.get(out).getFileName().toString(); return fName.substring(0, fName.length() - 4); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java index 3e3c7fe1b..6291e7948 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java @@ -1,17 +1,25 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; -import picocli.CommandLine; +import picocli.CommandLine.Command; -@CommandLine.Command(name = "preprocSummary", +@Command(name = "preprocSummary", sortOptions = false, separator = " ", description = "Export preprocessing summary tables.") public final class CommandPaExportTablesPreprocSummary extends CommandPaExportTablesBase { + public CommandPaExportTablesPreprocSummary() {} + + public CommandPaExportTablesPreprocSummary(PaResult paResult, String out) { + super(paResult, out); + } + @Override void run1(PaResultByGroup result) { - SetPreprocessorSummary.writeToCSV( + SetPreprocessorSummary.byCharToCSV( outDir().resolve(outPrefix() + outExtension(result.group)), - result.result.preprocSummary, null, separator()); + result.schema, + result.result, + separator()); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index 2c0be17b0..edce0b9ee 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -19,7 +19,7 @@ import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; -import picocli.CommandLine; +import picocli.CommandLine.Command; import java.util.ArrayList; import java.util.Arrays; @@ -30,7 +30,7 @@ import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") -@CommandLine.Command(name = "individual", +@Command(name = "individual", sortOptions = false, separator = " ", description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java index 311d2c538..604215448 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java @@ -4,14 +4,14 @@ import com.milaboratory.mixcr.cli.ACommandMiXCR; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.util.GlobalObjectMappers; -import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Parameters; import java.io.File; import java.io.IOException; import java.util.Arrays; -@CommandLine.Command(name = "listMetrics", +@Command(name = "listMetrics", sortOptions = false, separator = " ", description = "List available metrics") diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index 6597305a2..84c3a5e74 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -14,7 +14,7 @@ import io.repseq.core.Chains; import io.repseq.core.GeneFeature; import io.repseq.core.VDJCLibraryRegistry; -import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.io.IOException; @@ -25,7 +25,7 @@ import static java.util.stream.Collectors.*; -@CommandLine.Command(name = "overlap", +@Command(name = "overlap", sortOptions = false, separator = " ", description = "Overlap analysis") @@ -86,24 +86,9 @@ PaResultByGroup run(IsolationGroup group, List samples) { SmartProgressReporter.startProgressReport(runner); PostanalysisResult result = runner.run(overlapDataset); - result = updatePreprocSummary(result); - return new PaResultByGroup(group, schema, result); } - private static PostanalysisResult updatePreprocSummary(PostanalysisResult r) { - return new PostanalysisResult(r.datasetIds, r.data, - r.preprocSummary.entrySet().stream() - .map(e -> new AbstractMap.SimpleEntry<>(e.getKey(), - new SetPreprocessorSummary(e.getValue().result.entrySet().stream() - .map(e2 -> new AbstractMap.SimpleEntry<>(e2.getKey(), - e2.getValue().stream() - .map(l -> l.setPreprocId("overlap")) - .collect(toList()))).collect(toMap(Map.Entry::getKey, Map.Entry::getValue))) - ) - ).collect(toMap(Map.Entry::getKey, Map.Entry::getValue))); - } - public static CloneReader mkCheckedReader(Path path, LambdaSemaphore concurrencyLimiter) throws IOException { ClnsReader inner = new ClnsReader( diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index 442b4e874..2034aace8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -71,6 +71,11 @@ public SetPreprocessorStat getPreprocStat(String charId, String sampleId) { return SetPreprocessorStat.cumulative(preprocSummary.get(data.get(charId).preproc).result.get(sampleId)); } + /** Returns a set of characteristics */ + public Set getCharacteristics() { + return data.keySet(); + } + /** project result on a specific char group */ @SuppressWarnings({"unchecked"}) public CharacteristicGroupResult getTable(CharacteristicGroup group) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java index 3065b7c61..fc8c595ab 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java @@ -3,7 +3,10 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapCharacteristic; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapType; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema; import java.io.BufferedWriter; import java.io.IOException; @@ -37,10 +40,11 @@ public int hashCode() { return Objects.hash(result); } - public static void writeCSV(Path path, - CharacteristicGroup chGroup, - Map preprocSummary, - String sep +/* + public static void byPreprocToCSV(Path path, + CharacteristicGroup chGroup, + Map preprocSummary, + String sep ) { Set preprocs = chGroup.characteristics .stream() @@ -58,17 +62,17 @@ public static void writeCSV(Path path, return c; } )); - writeToCSV( + byPreprocToCSV( path, preprocSummary, pp2ch, sep); } - public static void writeToCSV(Path path, - Map preprocSummary, - Map> pp2ch, - String sep) { + public static void byPreprocToCSV(Path path, + Map preprocSummary, + Map> pp2ch, + String sep) { List> rows = new ArrayList<>(); for (Map.Entry e : preprocSummary.entrySet()) { String preprocId = e.getKey(); @@ -140,6 +144,135 @@ public static void writeToCSV(Path path, throw new RuntimeException(e); } } +*/ + + /** + * Write preprocessing summary data to CSV file with columns characteristic | samples | .... + */ + @SuppressWarnings("unchecked") + public static void byCharToCSV(Path path, + PostanalysisSchema schema, + PostanalysisResult result, + String sep) { + if (schema.getAllCharacterisitcs().get(0) instanceof OverlapCharacteristic) + overlapByCharToCSV(path, (PostanalysisSchema>) schema, result, sep); + else + individualByCharToCSV(path, result, sep); + } + + /** + * Write preprocessing summary data to CSV file with columns characteristic | samples | .... + */ + @SuppressWarnings("unchecked") + public static void overlapByCharToCSV(Path path, + PostanalysisSchema> schema, + PostanalysisResult result, + String sep) { + Map, OverlapCharacteristic> m = + schema.getAllCharacterisitcs() + .stream() + .map(it -> (OverlapCharacteristic) it) + .collect(Collectors.toMap( + it -> new HashSet<>(Arrays.asList(it.overlapTypes)), + it -> it, + (a, b) -> a)); + + List> rows = new ArrayList<>(); + for (Map.Entry, OverlapCharacteristic> eCh : m.entrySet()) { + String ch = eCh.getKey().stream().map(it -> it.name).collect(Collectors.joining("/")); + String preproc = eCh.getValue().preprocessor.id(); + SetPreprocessorSummary preprocSummary = result.preprocSummary.get(preproc); + addRows(rows, ch, preproc, preprocSummary); + } + writeTable(rows, path, sep); + } + + + /** + * Write preprocessing summary data to CSV file with columns characteristic | samples | .... + */ + public static void individualByCharToCSV(Path path, + PostanalysisResult result, + String sep) { + List> rows = new ArrayList<>(); + for (Map.Entry eCh : result.data.entrySet()) { + String ch = eCh.getKey(); + String preproc = eCh.getValue().preproc; + SetPreprocessorSummary preprocSummary = result.preprocSummary.get(preproc); + addRows(rows, ch, preproc, preprocSummary); + } + writeTable(rows, path, sep); + } + + private static void addRows(List> rows, String ch, String preproc, SetPreprocessorSummary preprocSummary) { + for (Map.Entry> ee : preprocSummary.result.entrySet()) { + String sample = ee.getKey(); + List stats = ee.getValue(); + if (stats == null) + continue; + List row = new ArrayList<>(); + row.add(ch); + row.add(sample); + row.add(preproc); + addStat(row, SetPreprocessorStat.cumulative(stats)); + for (SetPreprocessorStat stat : stats) { + row.add(stat.preprocId); + addStat(row, stat); + } + rows.add(row); + } + } + + private static void writeTable(List> rows, + Path path, + String sep) { + int nCols = rows.stream().mapToInt(List::size).max().orElse(0); + for (List row : rows) { + if (row.size() < nCols) + row.addAll(Collections.nCopies(nCols - row.size(), "")); + } + + List header = new ArrayList<>(); + header.add("characteristic"); + header.add("sample"); + for (int i = 0; i < (nCols - 1) / 5; i++) { + String suff; + if (i == 0) + suff = ""; + else + suff = "#" + i; + + header.add("preprocessor" + suff); + header.add("nElementsBefore" + suff); + header.add("sumWeightBefore" + suff); + header.add("nElementsAfter" + suff); + header.add("sumWeightAfter" + suff); + } + + try (BufferedWriter writer = Files.newBufferedWriter(path, StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING)) { + for (int i = 0; ; i++) { + writer.write(header.get(i)); + if (i == header.size() - 1) + break; + writer.write(sep); + } + writer.write("\n"); + + for (int i = 0; ; i++) { + for (int j = 0; ; j++) { + writer.write(rows.get(i).get(j).toString()); + if (j == rows.get(i).size() - 1) + break; + writer.write(sep); + } + if (i == rows.size() - 1) + break; + writer.write("\n"); + } + } catch (IOException e) { + throw new RuntimeException(e); + } + } private static void addStat(List row, SetPreprocessorStat stat) { if (stat.dropped) { From d594e65aa55725a42779a8c3651dc4b8e785bbf4 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sun, 8 May 2022 15:30:29 +0200 Subject: [PATCH 190/282] test fix --- .../mixcr/postanalysis/diversity/DiversityMeasure.java | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java index 03bdde643..b39463d16 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java @@ -1,15 +1,22 @@ package com.milaboratory.mixcr.postanalysis.diversity; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; + import java.util.Objects; /** * */ public final class DiversityMeasure { + @JsonProperty("measure") public final Measure measure; + @JsonProperty("name") public final String name; - public DiversityMeasure(Measure measure, String name) { + @JsonCreator + public DiversityMeasure(@JsonProperty("measure") Measure measure, + @JsonProperty("name") String name) { this.measure = measure; this.name = name; } From 58b28e4d6ca37d58f4ca8ea9184b2ea0cfc9e65e Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 11 May 2022 15:33:35 +0200 Subject: [PATCH 191/282] Bug fixes in postanalysis (#45) * Fix bug in preprocessor chain caused wrong results --- .../postanalysis/PostanalysisRunner.java | 74 ++++++++-------- .../mixcr/postanalysis/SetPreprocessor.java | 83 ++++++++++++++++++ .../postanalysis/SetPreprocessorFactory.java | 84 +----------------- .../postanalysis/SetPreprocessorStat.java | 7 +- .../diversity/DiversityCharacteristic.java | 18 ++++ ...ClonesDownsamplingPreprocessorFactory.java | 25 +----- .../DownsamplingPreprocessor.java | 1 + .../DownsamplingPreprocessorFactory.java | 56 ++++++++++++ .../preproc/FilterPreprocessor.java | 24 +++-- .../preproc/PreprocessorChain.java | 9 +- .../mixcr/postanalysis/preproc/SelectTop.java | 22 ++--- .../postanalysis/PostanalysisRunnerTest.java | 87 +++++++++++++++++++ .../mixcr/postanalysis/TestDataset.java | 49 ++++++++++- .../mixcr/postanalysis/TestObject.java | 43 ++------- .../additive/AdditiveCharacteristicsTest.java | 2 +- .../DiversityCharacteristicTest.java | 3 +- .../DownsamplingPreprocessorTest.java | 2 +- .../OverlapDownsamplingPreprocessorTest.java | 2 +- .../preproc/PreprocessorChainTest.java | 56 +++++++++++- .../postanalysis/preproc/SelectTopTest.java | 45 +++++----- 20 files changed, 461 insertions(+), 231 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index d6d230978..ecc655cc8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -75,19 +75,22 @@ public PostanalysisResult run(Dataset... datasets) { for (int i = 0; i < characteristics.size(); i++) char2idx.put(characteristics.get(i), i); // charID -> proc (deduplicated) - Map> id2proc = new HashMap<>(); + Map, SetPreprocessor> char2proc = new HashMap<>(); Map, SetPreprocessor> distinctProcs = new HashMap<>(); - Map, TIntArrayList> proc2char = new IdentityHashMap<>(); + IdentityHashMap, TIntArrayList> proc2char = new IdentityHashMap<>(); for (Characteristic ch : characteristics) { - id2proc.put(ch.name, distinctProcs.computeIfAbsent(ch.preprocessor, __ -> ch.preprocessor.newInstance())); - SetPreprocessor proc = distinctProcs.get(ch.preprocessor); + SetPreprocessor proc = distinctProcs.computeIfAbsent(ch.preprocessor, SetPreprocessorFactory::newInstance); + if (char2proc.containsKey(ch)) + throw new IllegalArgumentException("Characteristics with the same name illegal"); + char2proc.put(ch, proc); proc2char.computeIfAbsent(proc, __ -> new TIntArrayList()).add(char2idx.get(ch)); } - List> procs = id2proc.values().stream().distinct().collect(Collectors.toList()); + // distinct processors + List> procs = new ArrayList<>(distinctProcs.values()); while (true) { // next setup iterations - List> setupSteps = procs.stream() + Collection> setupSteps = procs.stream() .map(SetPreprocessor::nextSetupStep) .filter(Objects::nonNull) .collect(Collectors.toList()); @@ -100,10 +103,10 @@ public PostanalysisResult run(Dataset... datasets) { s.initialize(datasets.length); } // inputConsumers[datasetIndex] - all consumers for i-th dataset - List>> inputConsumers = IntStream + List>> inputConsumers = IntStream .range(0, datasets.length) - .mapToObj(i -> setupSteps.stream() - .map(s -> s.consumer(i)) + .mapToObj(iDataset -> setupSteps.stream() + .map(setup -> setup.consumer(iDataset)) .collect(Collectors.toList()) ).collect(Collectors.toList()); @@ -123,15 +126,15 @@ public PostanalysisResult run(Dataset... datasets) { } // mapper functions - Map, MappingFunction>[] mappingFunctions = new Map[datasets.length]; + IdentityHashMap, MappingFunction>[] mappingFunctions = new IdentityHashMap[datasets.length]; for (int i = 0; i < datasets.length; i++) { - mappingFunctions[i] = new HashMap<>(); + mappingFunctions[i] = new IdentityHashMap<>(); for (SetPreprocessor p : procs) { mappingFunctions[i].put(p, p.getMapper(i)); } } - Map, Map[]>> result = new IdentityHashMap<>(); + Map, Map[]>> result = new HashMap<>(); for (int i = 0; i < datasets.length; i++) { Dataset dataset = datasets[i]; if (datasets.length == 1) @@ -140,7 +143,8 @@ public PostanalysisResult run(Dataset... datasets) { stage = "Processing: " + dataset.id(); Aggregator[] aggregators = characteristics.stream() - .map(c -> c.createAggregator(dataset)).toArray(Aggregator[]::new); + .map(c -> c.createAggregator(dataset)) + .toArray(Aggregator[]::new); try (OutputPortWithProgress port = dataset.mkElementsPort()) { for (T o : CUtils.it(port)) { @@ -149,8 +153,8 @@ public PostanalysisResult run(Dataset... datasets) { MappingFunction mapper = e.getValue(); T oMapped = mapper.apply(o); if (oMapped != null) - for (int ch : proc2char.get(e.getKey()).toArray()) - aggregators[ch].consume(oMapped); + for (int chIdx : proc2char.get(e.getKey()).toArray()) + aggregators[chIdx].consume(oMapped); } } } @@ -171,25 +175,27 @@ public PostanalysisResult run(Dataset... datasets) { .collect(Collectors.toCollection(LinkedHashSet::new)); // collect summary by preprocessor - Map preprocResult = procs.stream().collect(Collectors.toMap(SetPreprocessor::id, p -> { - TIntObjectHashMap> stat = p.getStat(); - List datasetIdsActual; - if (datasets.length == 1 && datasets[0] instanceof OverlapDataset) { - datasetIdsActual = ((OverlapDataset) datasets[0]).datasetIds; - } else { - datasetIdsActual = Arrays - .stream(datasets) - .map(Dataset::id) - .collect(Collectors.toList()); - } - Map> r = new HashMap<>(); - TIntObjectIterator> it = stat.iterator(); - while (it.hasNext()) { - it.advance(); - r.put(datasetIdsActual.get(it.key()), it.value()); - } - return new SetPreprocessorSummary(r); - })); + Map preprocResult = procs.stream() + .collect(Collectors.toMap(SetPreprocessor::id, + p -> { + TIntObjectHashMap> stat = p.getStat(); + List datasetIdsActual; + if (datasets.length == 1 && datasets[0] instanceof OverlapDataset) { + datasetIdsActual = ((OverlapDataset) datasets[0]).datasetIds; + } else { + datasetIdsActual = Arrays + .stream(datasets) + .map(Dataset::id) + .collect(Collectors.toList()); + } + Map> r = new HashMap<>(); + TIntObjectIterator> it = stat.iterator(); + while (it.hasNext()) { + it.advance(); + r.put(datasetIdsActual.get(it.key()), it.value()); + } + return new SetPreprocessorSummary(r); + })); return PostanalysisResult.create(datasetIds, result, preprocResult); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index fdf469bfc..0a3cd07ba 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -1,8 +1,14 @@ package com.milaboratory.mixcr.postanalysis; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.InputPort; +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import gnu.trove.map.hash.TIntObjectHashMap; import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.IntStream; /** * @@ -19,4 +25,81 @@ public interface SetPreprocessor { /** Id from {@link SetPreprocessorFactory#id()} */ String id(); + + @SuppressWarnings("unchecked") + static Dataset[] processDatasets(SetPreprocessor proc, Dataset... initial) { + while (true) { + SetPreprocessorSetup setup = proc.nextSetupStep(); + if (setup == null) { + Dataset[] result = new Dataset[initial.length]; + for (int i = 0; i < initial.length; i++) { + int datasetIdx = i; + MappingFunction mapper = proc.getMapper(datasetIdx); + result[i] = new Dataset() { + @Override + public String id() { + return initial[datasetIdx].id(); + } + + @Override + public OutputPortWithProgress mkElementsPort() { + OutputPortWithProgress inner = initial[datasetIdx].mkElementsPort(); + return new OutputPortWithProgress() { + @Override + public double getProgress() { + return inner.getProgress(); + } + + @Override + public boolean isFinished() { + return inner.isFinished(); + } + + @Override + public long index() { + return inner.index(); + } + + @Override + public void close() { + inner.close(); + } + + @Override + public T take() { + while (true) { + T t = inner.take(); + if (t == null) + return null; + + T r = mapper.apply(t); + if (r == null) + continue; + return r; + } + } + }; + } + }; + } + return result; + } + setup.initialize(initial.length); + + List> consumers = IntStream.range(0, initial.length) + .mapToObj(setup::consumer) + .collect(Collectors.toList()); + + for (int i = 0; i < initial.length; i++) { + try (OutputPortCloseable port = initial[i].mkElementsPort()) { + for (T t : CUtils.it(port)) { + consumers.get(i).put(t); + } + } + } + for (InputPort c : consumers) { + c.put(null); + } + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java index ca5582a1c..bda4dc354 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java @@ -1,21 +1,15 @@ package com.milaboratory.mixcr.postanalysis; -import cc.redberry.pipe.CUtils; -import cc.redberry.pipe.InputPort; -import cc.redberry.pipe.OutputPortCloseable; import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonSubTypes; import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; import com.milaboratory.mixcr.postanalysis.preproc.*; -import com.milaboratory.mixcr.util.OutputPortWithProgress; import java.util.ArrayList; import java.util.Arrays; import java.util.List; -import java.util.stream.Collectors; -import java.util.stream.IntStream; /** * @@ -43,7 +37,7 @@ public interface SetPreprocessorFactory { @SuppressWarnings("unchecked") default SetPreprocessorFactory filter(boolean before, ElementPredicate... predicates) { - FilterPreprocessor.Factory filter = new FilterPreprocessor.Factory<>(Arrays.asList(predicates)); + FilterPreprocessor.Factory filter = new FilterPreprocessor.Factory<>(Arrays.asList(predicates), WeightFunctions.Default()); if (this instanceof PreprocessorChain.Factory) { PreprocessorChain.Factory p = (PreprocessorChain.Factory) this; List> list = new ArrayList<>(); @@ -85,80 +79,4 @@ default SetPreprocessorFactory filterFirst(List> predicat return filter(true, predicates.toArray(new ElementPredicate[0])); } - @SuppressWarnings("unchecked") - static Dataset[] processDatasets(SetPreprocessor proc, Dataset... initial) { - while (true) { - SetPreprocessorSetup setup = proc.nextSetupStep(); - if (setup == null) { - Dataset[] result = new Dataset[initial.length]; - for (int i = 0; i < initial.length; i++) { - int datasetIdx = i; - MappingFunction mapper = proc.getMapper(datasetIdx); - result[i] = new Dataset() { - @Override - public String id() { - return initial[datasetIdx].id(); - } - - @Override - public OutputPortWithProgress mkElementsPort() { - OutputPortWithProgress inner = initial[datasetIdx].mkElementsPort(); - return new OutputPortWithProgress() { - @Override - public double getProgress() { - return inner.getProgress(); - } - - @Override - public boolean isFinished() { - return inner.isFinished(); - } - - @Override - public long index() { - return inner.index(); - } - - @Override - public void close() { - inner.close(); - } - - @Override - public T take() { - while (true) { - T t = inner.take(); - if (t == null) - return null; - - T r = mapper.apply(t); - if (r == null) - continue; - return r; - } - } - }; - } - }; - } - return result; - } - setup.initialize(initial.length); - - List> consumers = IntStream.range(0, initial.length) - .mapToObj(setup::consumer) - .collect(Collectors.toList()); - - for (int i = 0; i < initial.length; i++) { - try (OutputPortCloseable port = initial[i].mkElementsPort()) { - for (T t : CUtils.it(port)) { - consumers.get(i).put(t); - } - } - } - for (InputPort c : consumers) { - c.put(null); - } - } - } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java index 3d4c78ab1..db56196cd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java @@ -3,6 +3,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.google.common.util.concurrent.AtomicDouble; +import gnu.trove.impl.Constants; import gnu.trove.iterator.TIntObjectIterator; import gnu.trove.map.hash.TIntObjectHashMap; @@ -141,7 +142,7 @@ public SetPreprocessorStat build() { public static final class Builder { final String preprocId; - final TIntObjectHashMap> map = new TIntObjectHashMap<>(); + final TIntObjectHashMap> map = new TIntObjectHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); final WeightFunction wtFunc; public Builder(String preprocId, @@ -161,6 +162,10 @@ public void drop(int iDataset) { builder(iDataset).drop(); } + public void clear(int iDataset) { + map.remove(iDataset); + } + public void before(int iDataset, T t) { builder(iDataset).before(t); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java index 6e4591679..0255e477b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java @@ -5,6 +5,8 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.postanalysis.*; +import java.util.Arrays; + /** * */ @@ -36,4 +38,20 @@ public DiversityCharacteristic(@JsonProperty("name") String name, protected Aggregator createAggregator(Dataset dataset) { return new DiversityAggregator<>(c -> Math.round(weight.weight(c)), measures); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + DiversityCharacteristic that = (DiversityCharacteristic) o; + return Arrays.equals(measures, that.measures); + } + + @Override + public int hashCode() { + int result = super.hashCode(); + result = 31 * result + Arrays.hashCode(measures); + return result; + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java index 57e976446..f0100f550 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java @@ -4,8 +4,6 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.postanalysis.SetPreprocessor; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; import java.util.Objects; @@ -17,29 +15,12 @@ getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE ) -public class ClonesDownsamplingPreprocessorFactory implements SetPreprocessorFactory { - @JsonProperty("downsampleValueChooser") - public final DownsampleValueChooser downsampleValueChooser; - @JsonProperty("seed") - public final long seed; - +public class ClonesDownsamplingPreprocessorFactory extends DownsamplingPreprocessorFactory { @JsonCreator public ClonesDownsamplingPreprocessorFactory(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, @JsonProperty("seed") long seed) { - this.downsampleValueChooser = downsampleValueChooser; - this.seed = seed; - } - - @Override - public String id() { - return "Downsample " + downsampleValueChooser.id(); - } - - @Override - public SetPreprocessor newInstance() { - return new DownsamplingPreprocessor<>( - c -> Math.round(c.getCount()), - Clone::setCount, downsampleValueChooser, seed, id()); + super(downsampleValueChooser, seed, c -> Math.round(c.getCount()), + Clone::setCount); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index 17e4d2188..58554a911 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -78,6 +78,7 @@ public MappingFunction getMapper(int iDataset) { long[] countsDownsampled = downsample_mvhg(counts, downsampling, rnd); AtomicInteger idx = new AtomicInteger(0); + stats.clear(iDataset); return t -> { stats.before(iDataset, t); int i = idx.getAndIncrement(); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java new file mode 100644 index 000000000..c72d92678 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java @@ -0,0 +1,56 @@ +package com.milaboratory.mixcr.postanalysis.downsampling; + +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; + +import java.util.Objects; +import java.util.function.BiFunction; +import java.util.function.ToLongFunction; + +/** + * + */ +public class DownsamplingPreprocessorFactory implements SetPreprocessorFactory { + @JsonProperty("downsampleValueChooser") + public final DownsampleValueChooser downsampleValueChooser; + @JsonProperty("seed") + public final long seed; + public final ToLongFunction getCount; + public final BiFunction setCount; + + public DownsamplingPreprocessorFactory(DownsampleValueChooser downsampleValueChooser, + long seed, + ToLongFunction getCount, + BiFunction setCount) { + this.downsampleValueChooser = downsampleValueChooser; + this.seed = seed; + this.getCount = getCount; + this.setCount = setCount; + } + + @Override + public String id() { + return "Downsample " + downsampleValueChooser.id(); + } + + @Override + public SetPreprocessor newInstance() { + return new DownsamplingPreprocessor<>( + getCount, + setCount, downsampleValueChooser, seed, id()); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + DownsamplingPreprocessorFactory that = (DownsamplingPreprocessorFactory) o; + return seed == that.seed && Objects.equals(downsampleValueChooser, that.downsampleValueChooser) && Objects.equals(getCount, that.getCount) && Objects.equals(setCount, that.setCount); + } + + @Override + public int hashCode() { + return Objects.hash(downsampleValueChooser, seed, getCount, setCount); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index 79e83f09a..bd88b6e44 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -18,10 +18,12 @@ public class FilterPreprocessor implements SetPreprocessor { final String id; final SetPreprocessorStat.Builder stats; - public FilterPreprocessor(List> predicates, String id) { + public FilterPreprocessor(List> predicates, + WeightFunction weightFunction, + String id) { this.predicates = predicates; this.id = id; - this.stats = new SetPreprocessorStat.Builder<>(id, WeightFunctions.Default()); + this.stats = new SetPreprocessorStat.Builder<>(id, weightFunction); } @Override @@ -53,15 +55,19 @@ public String id() { public static final class Factory implements SetPreprocessorFactory { @JsonProperty("predicates") public final List> predicates; + @JsonProperty("weightFunction") + public final WeightFunction weightFunction; @JsonCreator - public Factory(@JsonProperty("predicates") List> predicates) { + public Factory(@JsonProperty("predicates") List> predicates, + @JsonProperty("weightFunction") WeightFunction weightFunction) { this.predicates = predicates; + this.weightFunction = weightFunction; } @SafeVarargs - public Factory(ElementPredicate... predicates) { - this(Arrays.asList(predicates)); + public Factory(WeightFunction weightFunction, ElementPredicate... predicates) { + this(Arrays.asList(predicates), weightFunction); } @Override @@ -73,20 +79,20 @@ public String id() { @Override public SetPreprocessor newInstance() { - return new FilterPreprocessor<>(predicates, id()); + return new FilterPreprocessor<>(predicates, weightFunction, id()); } @Override public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; - Factory that = (Factory) o; - return Objects.equals(predicates, that.predicates); + Factory factory = (Factory) o; + return Objects.equals(predicates, factory.predicates) && Objects.equals(weightFunction, factory.weightFunction); } @Override public int hashCode() { - return Objects.hash(predicates); + return Objects.hash(predicates, weightFunction); } } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index 29eb9d497..b8b34a0e9 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -34,11 +34,15 @@ public PreprocessorChain(List> chain, String id) { private final AtomicReference>> mapperRef = new AtomicReference<>(i -> t -> t); private int lastActive = 0; + private boolean setupDone; @Override public SetPreprocessorSetup nextSetupStep() { + if (setupDone) + return null; SetPreprocessorSetup innerStep = null; - for (int i = lastActive; i < chain.size(); i++) { + int i = lastActive; + for (; i < chain.size(); i++) { SetPreprocessor p = chain.get(i); SetPreprocessorSetup step = p.nextSetupStep(); if (step != null) { @@ -67,6 +71,7 @@ public SetPreprocessorSetup nextSetupStep() { } } } + assert innerStep != null || i == chain.size(); Function> mapper = mapperRef.get(); if (innerStep != null) { @@ -100,6 +105,8 @@ public InputPort consumer(int i) { } }; } + + setupDone = true; return null; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java index 39315fc16..90f8d895c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java @@ -11,8 +11,6 @@ import java.util.List; import java.util.Objects; -import static java.lang.Math.round; - /** * */ @@ -67,15 +65,15 @@ public MappingFunction getMapper(int iDataset) { return t -> { stats.before(iDataset, t); - long wt = Math.round(this.weight.weight(t)); - long n = hist.get(wt); + long lwt = round(weight.weight(t)); + long n = hist.get(lwt); if (n == -1) return null; assert n != 0; if (n == 1) - hist.remove(wt); + hist.remove(lwt); else - hist.adjustValue(wt, -1); + hist.adjustValue(lwt, -1); stats.after(iDataset, t); return t; @@ -123,8 +121,6 @@ public InputPort consumer(int i) { return; totals[i] += dwt; long lwt = round(dwt); - if (lwt == 0) - lwt = 1; hists[i].adjustOrPutValue(lwt, 1, 1); }; } @@ -160,10 +156,9 @@ TLongLongHashMap downsampledHist(int iDataset) { downHist.put(wt, nToLeave); break; } - assert nToLeave == n; + assert nToLeave == n; // this case will be processed below } - nTotal += n; sumTotal += n * wt; downHist.put(wt, n); @@ -173,6 +168,13 @@ TLongLongHashMap downsampledHist(int iDataset) { } } + static long round(double wt) { + long lwt = Math.round(wt); + if (lwt == 0) + lwt = 1; + return lwt; + } + public static final class Factory implements SetPreprocessorFactory { @JsonProperty("weight") private WeightFunction weight; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java new file mode 100644 index 000000000..e13780bfe --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java @@ -0,0 +1,87 @@ +package com.milaboratory.mixcr.postanalysis; + +import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.FilterPreprocessor; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; +import org.apache.commons.math3.random.RandomDataGenerator; +import org.apache.commons.math3.random.Well512a; +import org.junit.Test; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +public class PostanalysisRunnerTest { + @Test + public void test1() { + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + int nDatasets = 50; + TestDataset[] datasets = TestDataset.generateDatasets(nDatasets, rng, + r -> r.nextInt(10, 1000), + r -> r.nextUniform(10, 1000), + r -> r.nextUniform(300, 1000)); + + int downsampling = 500; + + FilterPreprocessor.Factory filter = new FilterPreprocessor.Factory<>(c -> c.weight, + new ElementPredicate() { + @Override + public String id() { + return "filter"; + } + + @Override + public boolean test(TestObject testObject) { + return ((long) Math.round(testObject.value)) % 3 == 1; + } + }); + + DownsamplingPreprocessorFactory downsamplingPreproc = new DownsamplingPreprocessorFactory<>( + new DownsampleValueChooser.Fixed(downsampling), + 314, + c -> (long) c.weight, + TestObject::setWeight); + SetPreprocessorFactory preproc = filter.then(downsamplingPreproc); + + DiversityCharacteristic diversityCh = + new DiversityCharacteristic<>("diversity", t -> t.weight, preproc); + + SetPreprocessorFactory downsamplingPreproc2 = new SelectTop.Factory<>(t -> t.weight, 0.8); + SetPreprocessorFactory preproc2 = downsamplingPreproc2.then(new SelectTop.Factory<>(t -> t.weight, 0.8)); + DiversityCharacteristic diversityCh2 = new DiversityCharacteristic<>("d50", t -> t.weight, preproc2); + + PostanalysisRunner runner = new PostanalysisRunner<>(); + runner.addCharacteristics(diversityCh, diversityCh2); + PostanalysisResult result = runner.run(datasets); + + // two preprocessors + assertEquals(2, result.preprocSummary.size()); + + double[] wts = result.preprocSummary.get(result.data.get(diversityCh.name).preproc) + .result.values().stream() + .map(SetPreprocessorStat::cumulative) + .mapToDouble(t -> t.sumWeightAfter) + .filter(t -> t != 0) // filter dropped + .distinct() + .toArray(); + + + // assert that all diversity metrics have same sum wt + assertEquals(1, wts.length); + assertEquals(downsampling, wts[0], 0e-5); + + double[] div2wts = result.preprocSummary.get(result.data.get(diversityCh2.name).preproc) + .result.values().stream() + .map(SetPreprocessorStat::cumulative) + .mapToDouble(t -> t.sumWeightAfter) + .filter(t -> t != 0) // filter dropped + .distinct() + .toArray(); + + + // assert that all d50 metrics have different sum wt + assertTrue(div2wts.length > nDatasets / 2); + } +} \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java index c542f3274..a5c75a475 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java @@ -4,11 +4,11 @@ import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.IteratorOutputPortAdapter; import com.milaboratory.mixcr.util.OutputPortWithProgress; +import org.apache.commons.math3.random.RandomDataGenerator; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; -import java.util.UUID; +import java.util.*; +import java.util.function.ToDoubleFunction; +import java.util.function.ToIntFunction; import java.util.stream.Stream; /** @@ -61,4 +61,45 @@ public T take() { } }); } + + public static ToIntFunction DEFAULT_SIZE_GEN = r -> r.nextInt(1, 5000); + public static ToDoubleFunction DEFAULT_VALUE_GEN = r -> r.nextUniform(0, 10); + public static ToDoubleFunction DEFAULT_WT_GEN = r -> r.nextUniform(0, 1.0); + + public static TestDataset generateDataset(RandomDataGenerator rng, int size) { + return generateDataset(rng, size, DEFAULT_VALUE_GEN, DEFAULT_WT_GEN); + } + + public static TestDataset generateDataset(RandomDataGenerator rng, int size, + ToDoubleFunction values, + ToDoubleFunction weights) { + TestObject[] r = new TestObject[size]; + for (int i = 0; i < size; i++) { + r[i] = new TestObject( + values.applyAsDouble(rng), + weights.applyAsDouble(rng)); + } + return new TestDataset<>(Arrays.asList(r)); + } + + public static TestDataset[] generateDatasets(int nDatasets, RandomDataGenerator rng) { + return generateDatasets(nDatasets, rng, DEFAULT_SIZE_GEN, DEFAULT_VALUE_GEN, DEFAULT_WT_GEN); + } + + public static TestDataset[] generateDatasets(int nDatasets, RandomDataGenerator rng, + ToIntFunction sizes, + ToDoubleFunction values, + ToDoubleFunction weights) { + int[] nElements = new int[nDatasets]; + for (int i = 0; i < nDatasets; i++) { + nElements[i] = sizes.applyAsInt(rng); + } + @SuppressWarnings("unchecked") + TestDataset[] datasets = new TestDataset[nDatasets]; + for (int i = 0; i < datasets.length; i++) { + datasets[i] = generateDataset(rng, nElements[i], values, weights); + } + return datasets; + } + } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java index ee303d6af..5198f7835 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java @@ -1,11 +1,6 @@ package com.milaboratory.mixcr.postanalysis; -import org.apache.commons.math3.random.RandomDataGenerator; - -import java.util.Arrays; import java.util.Objects; -import java.util.function.ToDoubleFunction; -import java.util.function.ToIntFunction; /** * @@ -19,6 +14,14 @@ public TestObject(double value, double weight) { this.weight = weight; } + public TestObject setValue(double newValue) { + return new TestObject(newValue, weight); + } + + public TestObject setWeight(double newWeight) { + return new TestObject(value, newWeight); + } + @Override public String toString() { return value + ": " + weight; @@ -36,34 +39,4 @@ public boolean equals(Object o) { public int hashCode() { return Objects.hash(value, weight); } - - public static TestDataset[] generateDatasets(int nDatasets, RandomDataGenerator rng) { - return generateDatasets(nDatasets, rng, - r -> r.nextInt(1, 1000), - r -> r.nextUniform(0, 10), - r -> r.nextUniform(0, 10)); - } - - public static TestDataset[] generateDatasets(int nDatasets, RandomDataGenerator rng, - ToIntFunction sizes, - ToDoubleFunction values, - ToDoubleFunction weights) { - int[] nElements = new int[nDatasets]; - for (int i = 0; i < nDatasets; i++) { - nElements[i] = sizes.applyAsInt(rng); - } - @SuppressWarnings("unchecked") - TestDataset[] datasets = new TestDataset[nDatasets]; - for (int i = 0; i < datasets.length; i++) { - TestObject[] ds = new TestObject[nElements[i]]; - for (int j = 0; j < nElements[i]; j++) { - TestObject w = new TestObject( - values.applyAsDouble(rng), - weights.applyAsDouble(rng)); - ds[j] = w; - } - datasets[i] = new TestDataset<>(Arrays.asList(ds)); - } - return datasets; - } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java index 38b29304f..4e4fbebda 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java @@ -59,7 +59,7 @@ public void testWeightedDescriptiveStat() { RandomDataGenerator rng = new RandomDataGenerator(new Well44497a()); int nDatasets = 1000; - TestDataset[] datasets = TestObject.generateDatasets(nDatasets, rng); + TestDataset[] datasets = TestDataset.generateDatasets(nDatasets, rng); PostanalysisRunner runner = new PostanalysisRunner<>(); runner.addCharacteristics(sum, mean, std); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index 582b467ae..152e48d9f 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -9,7 +9,6 @@ import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResultCell; import com.milaboratory.mixcr.postanalysis.ui.GroupSummary; -import com.milaboratory.util.RandomUtil; import org.apache.commons.math3.random.RandomDataGenerator; import org.apache.commons.math3.random.Well512a; import org.junit.Assert; @@ -30,7 +29,7 @@ public void test1() { RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); int nDatasets = 100; - TestDataset[] datasets = TestObject.generateDatasets(nDatasets, rng, + TestDataset[] datasets = TestDataset.generateDatasets(nDatasets, rng, r -> r.nextInt(1000, 10000), r -> r.nextUniform(0, 1), r -> r.nextInt(10, 20)); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index ed920d405..36f641249 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -112,7 +112,7 @@ public void test3() { } long dsValue = dsChooser.compute(Arrays.stream(initial).mapToLong(d -> d.count).toArray()); - DatasetSupport[] downsampled = Arrays.stream(SetPreprocessorFactory.processDatasets(proc, initial)) + DatasetSupport[] downsampled = Arrays.stream(SetPreprocessor.processDatasets(proc, initial)) .map(DatasetSupport::new) .toArray(DatasetSupport[]::new); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index 8ba26fc41..b22b83b4f 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -42,7 +42,7 @@ public void test1() { "" ); - Dataset>[] downsampled = SetPreprocessorFactory.processDatasets(new OverlapPreprocessorAdapter<>(proc), datasets); + Dataset>[] downsampled = SetPreprocessor.processDatasets(new OverlapPreprocessorAdapter<>(proc), datasets); for (int i = 0; i < datasets.length; i++) { DatasetSupport in = datasets[i]; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java index 6a88cd220..dfe8ad4ad 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.postanalysis.preproc; +import cc.redberry.pipe.CUtils; import cc.redberry.pipe.InputPort; import com.milaboratory.mixcr.postanalysis.*; import gnu.trove.list.array.TLongArrayList; @@ -11,7 +12,6 @@ import java.util.ArrayList; import java.util.Arrays; -import java.util.Collections; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.Stream; @@ -39,7 +39,7 @@ public void test1() { RandomDataGenerator rng = new RandomDataGenerator(new Well512a(System.currentTimeMillis())); TestDataset ds = rndDataset(rng, 10000); - TestDataset r = new TestDataset<>(SetPreprocessorFactory.processDatasets(preproc.newInstance(), ds)[0]); + TestDataset r = new TestDataset<>(SetPreprocessor.processDatasets(preproc.newInstance(), ds)[0]); List expected = new ArrayList<>(); for (TestObject c : ds) { @@ -50,6 +50,58 @@ public void test1() { Assert.assertEquals(expected, r.data); } + @Test + @SuppressWarnings("unchecked") + public void testSetupDuplication1() { + long p1 = 17; + long p2 = 13; + long p3 = 11; + long p4 = 7; + + SetPreprocessor preproc = new PreprocessorChain.Factory<>( + new TestPreprocFactory(p1), + new TestPreprocFactory(p2), + new TestPreprocFactory(p3), + new TestPreprocFactory(p4) + ).newInstance(); + + RandomDataGenerator rng = new RandomDataGenerator(new Well512a(System.currentTimeMillis())); + TestDataset ds = rndDataset(rng, 10000); + + while (true) { + SetPreprocessorSetup setup = preproc.nextSetupStep(); + if (setup == null) + break; + setup.initialize(1); + InputPort consumer = setup.consumer(0); + for (TestObject t : CUtils.it(ds.mkElementsPort())) { + consumer.put(t); + } + consumer.put(null); + } + // excessive setup call + SetPreprocessorSetup nullSetup = preproc.nextSetupStep(); + Assert.assertNull(nullSetup); + + MappingFunction m = preproc.getMapper(0); + List r = new ArrayList<>(); + for (TestObject t : CUtils.it(ds.mkElementsPort())) { + TestObject t1 = m.apply(t); + if (t1 != null) + r.add(t1); + } + + TestDataset result = new TestDataset<>(r); + + List expected = new ArrayList<>(); + for (TestObject c : ds) { + if (Stream.of(p1, p2, p3, p4).allMatch(mod -> ((long) c.weight) % mod != 0)) + expected.add(c); + } + + Assert.assertEquals(expected, result.data); + } + public static final class TestPreprocFactory implements SetPreprocessorFactory { final long modulus; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java index 7c09f9f7d..942b4b2ab 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java @@ -25,10 +25,13 @@ public void test1() { RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); int nIterations = 10; for (int i = 0; i < nIterations; i++) { - TestDataset dataset = rndDataset(rng, 10000); - double total = 0; + TestDataset dataset = TestDataset.generateDataset(rng, + 10000, + r -> r.nextInt(10, 1000), + r -> r.nextUniform(1, 50)); + double sumWeight = 0; for (TestObject d : dataset) { - total += d.weight; + sumWeight += d.weight; } double topFraction = 0.5 + (1.0 * i / nIterations / 10); @@ -38,41 +41,43 @@ public void test1() { list.sort(Comparator.comparing(t -> -t.weight)); double expectedSumCum = 0; double expectedSumFixed = 0; - boolean sumDone = false; int counter = 0; + double roundErr = 0.0; for (TestObject o : list) { - if (!sumDone && expectedSumCum < topFraction * total) + if (expectedSumCum < topFraction * sumWeight) { expectedSumCum += o.weight; - else - sumDone = true; + } if (counter < nTop) { expectedSumFixed += o.weight; ++counter; } + roundErr += Math.abs(SelectTop.round(o.weight) - o.weight); - if (expectedSumCum > topFraction * total && counter > nTop) + if (expectedSumCum > topFraction * sumWeight && counter > nTop) break; + } + Assert.assertTrue(roundErr / expectedSumCum < 3e-2); SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1, ""); - Dataset topCumulative = SetPreprocessorFactory.processDatasets(cumulativeTopProc, dataset)[0]; + Dataset topCumulative = SetPreprocessor.processDatasets(cumulativeTopProc, dataset)[0]; - double actualCum = 0; + double actualSumCum = 0; for (TestObject o : CUtils.it(topCumulative.mkElementsPort())) { - actualCum += o.weight; + actualSumCum += o.weight; } - Assert.assertEquals(expectedSumCum, actualCum, 1e-5); + Assert.assertEquals(expectedSumCum, actualSumCum, roundErr); SelectTop fixedTopProc = new SelectTop<>(o -> o.weight, Double.NaN, nTop, ""); - Dataset topFixed = SetPreprocessorFactory.processDatasets(fixedTopProc, dataset)[0]; + Dataset topFixed = SetPreprocessor.processDatasets(fixedTopProc, dataset)[0]; double actualFixed = 0; int actualNTop = 0; for (TestObject o : CUtils.it(topFixed.mkElementsPort())) { actualFixed += o.weight; ++actualNTop; } - Assert.assertEquals(expectedSumFixed, actualFixed, 1e-5); + Assert.assertEquals(expectedSumFixed, actualFixed, roundErr); Assert.assertEquals(nTop, actualNTop); } } @@ -130,7 +135,7 @@ private void assertFraction(double topFraction, TestDataset dataset, list.sort(Comparator.comparing(t -> -t.weight)); SelectTop cumulativeTopProc = new SelectTop<>(o -> o.weight, topFraction, -1, ""); - Dataset topCumulative = SetPreprocessorFactory.processDatasets(cumulativeTopProc, dataset)[0]; + Dataset topCumulative = SetPreprocessor.processDatasets(cumulativeTopProc, dataset)[0]; double actualCum = 0; for (TestObject o : CUtils.it(topCumulative.mkElementsPort())) { @@ -139,16 +144,6 @@ private void assertFraction(double topFraction, TestDataset dataset, Assert.assertEquals(expectedSum, actualCum, 1e-5); } - public static TestDataset rndDataset(RandomDataGenerator rng, int size) { - TestObject[] r = new TestObject[size]; - for (int i = 0; i < size; i++) { - r[i] = new TestObject( - rng.nextUniform(0, 1), - Math.round(rng.nextUniform(1, 100))); - } - return new TestDataset<>(Arrays.asList(r)); - } - @Test public void testJson() throws JsonProcessingException { SelectTop.Factory top = new SelectTop.Factory<>(WeightFunctions.Count, 0.8); From dd2e03abce3a90f154cc2969d68009e1ebccc17a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 12 May 2022 01:53:16 +0400 Subject: [PATCH 192/282] New code for tags, WIP. --- build.gradle.kts | 5 +- .../mixcr/assembler/CloneAssembler.java | 6 +- .../mixcr/assembler/CloneAssemblerRunner.java | 5 +- .../assembler/fullseq/FullSeqAssembler.java | 2 + .../mixcr/basictypes/ClnAReader.java | 14 +- .../mixcr/basictypes/ClnAWriter.java | 8 +- .../mixcr/basictypes/ClnsReader.java | 5 +- .../mixcr/basictypes/ClnsWriter.java | 8 +- .../mixcr/basictypes/CloneSet.java | 16 +- .../basictypes/VDJCAlignmentsReader.java | 8 + .../basictypes/VDJCAlignmentsWriter.java | 18 +- .../basictypes/VDJCAlignmentsWriterI.java | 42 +- .../milaboratory/mixcr/basictypes/tag/IO.java | 44 +- .../tag/SequenceAndQualityTagValue.java | 35 + .../basictypes/tag/SequenceTagValue.java | 48 + .../mixcr/basictypes/tag/TagCounter.java | 7 +- .../mixcr/basictypes/tag/TagInfo.java | 77 ++ .../mixcr/basictypes/tag/TagTuple.java | 8 +- .../mixcr/basictypes/tag/TagType.java | 7 + .../mixcr/basictypes/tag/TagValue.java | 12 + .../mixcr/basictypes/tag/TagValueType.java | 18 + .../mixcr/basictypes/tag/TagsInfo.java | 33 + .../milaboratory/mixcr/cli/AlignerReport.java | 15 + .../milaboratory/mixcr/cli/CommandAlign.java | 237 +++-- .../mixcr/cli/CommandAlignmentsDiff.java | 8 +- .../mixcr/cli/CommandAssemble.java | 23 +- .../mixcr/cli/CommandAssembleContigs.java | 7 +- .../cli/CommandExportAlignmentsForClones.java | 3 +- .../milaboratory/mixcr/cli/CommandExtend.java | 5 +- .../mixcr/cli/CommandFilterAlignments.java | 13 +- .../mixcr/cli/CommandGroupCells.java | 633 +++++++------ .../mixcr/cli/CommandMergeAlignments.java | 15 +- .../milaboratory/mixcr/cli/CommandSlice.java | 4 +- .../mixcr/cli/CommandSortAlignments.java | 5 +- .../java/com/milaboratory/mixcr/cli/Main.java | 2 +- .../mixcr/export/FieldExtractors.java | 149 ++-- .../PartialAlignmentsAssembler.java | 4 +- .../mixcr/tags/CloneTagTupleFilter.java | 253 +++--- .../mixcr/tags/DropletCloneGraph.java | 830 +++++++++--------- .../tags/DropletCloneGraphParameters.java | 95 +- .../mixcr/tags/DropletCloneGraphReport.java | 686 +++++++-------- .../com/milaboratory/mixcr/util/RunMiXCR.java | 13 +- .../assembler/CloneAssemblerRunnerTest.java | 4 +- .../mixcr/basictypes/ClnAReaderTest.java | 2 + .../milaboratory/mixcr/basictypes/IOTest.java | 2 +- .../mixcr/basictypes/tag/TagInfoTest.java | 12 + .../mixcr/cli/CommandAlignTest.java | 80 -- .../mixcr/tags/CloneTagTupleFilterTest.java | 27 +- .../mixcr/tags/DropletCloneGraphTest.java | 64 +- .../milaboratory/mixcr/util/RunMiXCRTest.java | 4 +- .../mixcr/vdjaligners/VDJCAlignerSTest.java | 10 +- 51 files changed, 1989 insertions(+), 1642 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java create mode 100644 src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java delete mode 100644 src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java diff --git a/build.gradle.kts b/build.gradle.kts index 194adff5c..fa0e5d90f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -80,9 +80,10 @@ repositories { } } -val miplotsVersion = "0.1-19-master" val milibVersion = "1.15.0-29-master" val repseqioVersion = "1.3.5-25-master" +val mitoolVersion = "1.3.5-25-master" +val miplotsVersion = "0.1-19-master" val jacksonVersion = "2.13.2.2" dependencies { @@ -92,6 +93,8 @@ dependencies { } api("com.milaboratory:miplots:$miplotsVersion") + api("com.milaboratory:mitool:$miplotsVersion") + // implementation("com.milaboratory:milm2-jvm:0.2.0-test-2") { isChanging = true } implementation("com.milaboratory:milm2-jvm:1.1.0") diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index d8ef7cca9..3eef2d718 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -42,6 +42,7 @@ import com.milaboratory.core.tree.NeighborhoodIterator; import com.milaboratory.core.tree.SequenceTreeMap; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.Factory; @@ -54,7 +55,6 @@ import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; import gnu.trove.map.hash.TObjectFloatHashMap; -import gnu.trove.procedure.TObjectProcedure; import io.repseq.core.*; import java.util.*; @@ -374,8 +374,8 @@ else if (assertAllMatch) } } - public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters) { - return new CloneSet(Arrays.asList(realClones), usedGenes.values(), alignerParameters, parameters, new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); + public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters, TagsInfo tagsInfo) { + return new CloneSet(Arrays.asList(realClones), usedGenes.values(), alignerParameters, parameters, tagsInfo, new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); } public OutputPortCloseable getAssembledReadsPort() { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index d112210be..fbd5c98d0 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -35,6 +35,7 @@ import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.CanReportProgressAndStage; @@ -137,7 +138,7 @@ public void run() { // return alignmentReader.getQueueSize(); // } - public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters) { - return assembler.getCloneSet(alignerParameters); + public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters, TagsInfo tagsInfo) { + return assembler.getCloneSet(alignerParameters, tagsInfo); } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index b139032b5..9fed6880c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -39,6 +39,8 @@ import com.milaboratory.core.sequence.quality.QualityTrimmer; import com.milaboratory.mixcr.assembler.CloneFactory; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import gnu.trove.impl.Constants; import gnu.trove.iterator.TIntIntIterator; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index d287a0222..e461947ea 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -34,6 +34,7 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.blocks.*; @@ -83,6 +84,7 @@ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implement final PipelineConfiguration configuration; final VDJCAlignerParameters alignerParameters; final CloneAssemblerParameters assemblerParameters; + final TagsInfo tagsInfo; final VDJCSProperties.CloneOrdering ordering; final List genes; @@ -164,6 +166,7 @@ public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, LambdaSemaphor this.configuration = pi.readObject(PipelineConfiguration.class); this.alignerParameters = pi.readObject(VDJCAlignerParameters.class); this.assemblerParameters = pi.readObject(CloneAssemblerParameters.class); + this.tagsInfo = pi.readObject(TagsInfo.class); this.ordering = pi.readObject(VDJCSProperties.CloneOrdering.class); this.genes = IOUtil.stdVDJCPrimitivIStateInit(pi, this.alignerParameters, libraryRegistry); } @@ -192,6 +195,13 @@ public CloneAssemblerParameters getAssemblerParameters() { return assemblerParameters; } + /** + * Tags info + */ + public TagsInfo getTagsInfo() { + return tagsInfo; + } + /** * Clone ordering */ @@ -253,7 +263,7 @@ public CloneSet readCloneSet() throws IOException { clones.add(reader.take()); } - return new CloneSet(clones, genes, alignerParameters, assemblerParameters, ordering); + return new CloneSet(clones, genes, alignerParameters, assemblerParameters, tagsInfo, ordering); } /** @@ -311,7 +321,7 @@ public final class CloneAlignmentsPort CloneAlignmentsPort() { this.clones = input.beginRandomAccessPrimitivIBlocks(Clone.class, firstClonePosition); - this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, genes, alignerParameters, assemblerParameters, ordering); + this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, genes, alignerParameters, assemblerParameters, tagsInfo, ordering); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index e19a81445..39dcfd28b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -35,6 +35,7 @@ import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.cli.PipelineConfigurationWriter; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.util.MiXCRDebug; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.primitivio.PrimitivIOStateBuilder; @@ -74,8 +75,8 @@ public final class ClnAWriter implements PipelineConfigurationWriter, AutoCloseable, CanReportProgressAndStage { - static final String MAGIC_V5 = "MiXCR.CLNA.V05"; - static final String MAGIC = MAGIC_V5; + static final String MAGIC_V6 = "MiXCR.CLNA.V06"; + static final String MAGIC = MAGIC_V6; static final int MAGIC_LENGTH = MAGIC.length(); //14 /** @@ -174,8 +175,9 @@ public void writeClones(CloneSet cloneSet) { o.writeObject(cloneSet.alignmentParameters); featureToAlignProvider = cloneSet.alignmentParameters; - // Writing assembler parameters and cloneset ordering + // Writing assembler parameters, tags info and cloneset ordering o.writeObject(cloneSet.assemblerParameters); + o.writeObject(cloneSet.tagsInfo); o.writeObject(cloneSet.ordering); // During deserialization, the same procedure (in the same order) will be applied to diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index 74b691b7b..c0084b4df 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -33,6 +33,7 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.blocks.PrimitivIHybrid; @@ -59,6 +60,7 @@ public class ClnsReader extends PipelineConfigurationReaderMiXCR implements Clon private final PipelineConfiguration pipelineConfiguration; private final VDJCAlignerParameters alignerParameters; private final CloneAssemblerParameters assemblerParameters; + private final TagsInfo tagsInfo; private final VDJCSProperties.CloneOrdering ordering; private final String versionInfo; private final List genes; @@ -113,6 +115,7 @@ private ClnsReader(PrimitivIHybrid input, VDJCLibraryRegistry libraryRegistry) { pipelineConfiguration = i.readObject(PipelineConfiguration.class); alignerParameters = i.readObject(VDJCAlignerParameters.class); assemblerParameters = i.readObject(CloneAssemblerParameters.class); + tagsInfo = i.readObject(TagsInfo.class); ordering = i.readObject(VDJCSProperties.CloneOrdering.class); numberOfClones = i.readInt(); @@ -131,7 +134,7 @@ public CloneSet getCloneSet() { List clones = new ArrayList<>(); for (Clone clone : CUtils.it(readClones())) clones.add(clone); - CloneSet cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters, ordering); + CloneSet cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters, tagsInfo, ordering); cloneSet.versionInfo = versionInfo; return cloneSet; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index 8bd5831be..b0c4b366d 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -34,6 +34,7 @@ import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.cli.PipelineConfigurationWriter; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivO; @@ -50,8 +51,8 @@ * */ public final class ClnsWriter implements PipelineConfigurationWriter, AutoCloseable { - static final String MAGIC_V10 = "MiXCR.CLNS.V10"; - static final String MAGIC = MAGIC_V10; + static final String MAGIC_V11 = "MiXCR.CLNS.V11"; + static final String MAGIC = MAGIC_V11; static final int MAGIC_LENGTH = 14; static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII); @@ -75,6 +76,7 @@ public void writeHeaderFromCloneSet( writeHeader(configuration, cloneSet.getAlignmentParameters(), cloneSet.getAssemblerParameters(), + cloneSet.getTagsInfo(), cloneSet.getOrdering(), cloneSet.getUsedGenes(), cloneSet, @@ -85,6 +87,7 @@ public void writeHeader( PipelineConfiguration configuration, VDJCAlignerParameters alignmentParameters, CloneAssemblerParameters assemblerParameters, + TagsInfo tagsInfo, VDJCSProperties.CloneOrdering ordering, List genes, HasFeatureToAlign featureToAlign, @@ -103,6 +106,7 @@ public void writeHeader( o.writeObject(configuration); o.writeObject(alignmentParameters); o.writeObject(assemblerParameters); + o.writeObject(tagsInfo); o.writeObject(ordering); o.writeInt(numberOfClones); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index 1130b345e..ea7811f71 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -33,6 +33,7 @@ import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -48,6 +49,7 @@ public final class CloneSet implements Iterable, HasFeatureToAlign { String versionInfo; final CloneAssemblerParameters assemblerParameters; final VDJCAlignerParameters alignmentParameters; + final TagsInfo tagsInfo; final VDJCSProperties.CloneOrdering ordering; final List usedGenes; final List clones; @@ -57,6 +59,7 @@ public final class CloneSet implements Iterable, HasFeatureToAlign { public CloneSet(List clones, Collection usedGenes, VDJCAlignerParameters alignmentParameters, CloneAssemblerParameters assemblerParameters, + TagsInfo tagsInfo, VDJCSProperties.CloneOrdering ordering) { ArrayList list = new ArrayList<>(clones); list.sort(ordering.comparator()); @@ -71,11 +74,13 @@ public CloneSet(List clones, Collection usedGenes, this.totalTagCounts = tagCounterBuilder.createAndDestroy(); this.alignmentParameters = alignmentParameters; this.assemblerParameters = assemblerParameters; + this.tagsInfo = tagsInfo; this.ordering = ordering; this.usedGenes = Collections.unmodifiableList(new ArrayList<>(usedGenes)); this.totalCount = totalCount; } + /** To be used in tests only */ public CloneSet(List clones) { this.clones = Collections.unmodifiableList(new ArrayList<>(clones)); long totalCount = 0; @@ -99,6 +104,7 @@ public CloneSet(List clones) { this.totalTagCounts = tagCounterBuilder.createAndDestroy(); this.assemblerParameters = null; this.alignmentParameters = null; + this.tagsInfo = null; this.ordering = new VDJCSProperties.CloneOrdering(); this.usedGenes = Collections.unmodifiableList(new ArrayList<>(genes.values())); this.totalCount = totalCount; @@ -128,6 +134,10 @@ public VDJCAlignerParameters getAlignmentParameters() { return alignmentParameters; } + public TagsInfo getTagsInfo() { + return tagsInfo; + } + public VDJCSProperties.CloneOrdering getOrdering() { return ordering; } @@ -166,7 +176,8 @@ public static CloneSet reorder(CloneSet in, VDJCSProperties.CloneOrdering newOrd newClones.sort(newOrdering.comparator()); for (Clone nc : newClones) nc.parent = null; - return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters, newOrdering); + return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters, + in.tagsInfo, newOrdering); } /** @@ -181,6 +192,7 @@ public static CloneSet transform(CloneSet in, Filter filter) { newClones.add(c); } } - return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters, in.ordering); + return new CloneSet(newClones, in.usedGenes, in.alignmentParameters, in.assemblerParameters, + in.tagsInfo, in.ordering); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index 4c584d7a0..3b51816f4 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -31,6 +31,7 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.cli.PipelineConfiguration; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.blocks.PrimitivIBlocks; @@ -66,6 +67,7 @@ public final class VDJCAlignmentsReader extends PipelineConfigurationReaderMiXCR VDJCAlignerParameters parameters; PipelineConfiguration pipelineConfiguration; List usedGenes; + TagsInfo tagsInfo; String versionInfo; String magic; @@ -154,6 +156,7 @@ public void init() { parameters = i.readObject(VDJCAlignerParameters.class); pipelineConfiguration = i.readObject(PipelineConfiguration.class); + tagsInfo = i.readObject(TagsInfo.class); this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, parameters, vdjcRegistry); } @@ -183,6 +186,11 @@ public synchronized PipelineConfiguration getPipelineConfiguration() { return pipelineConfiguration; } + public TagsInfo getTagsInfo() { + init(); + return tagsInfo; + } + /** * Returns information about version of MiXCR which produced this file. * diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java index c9d9e248e..6d9c2d054 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java @@ -31,6 +31,7 @@ import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.cli.PipelineConfiguration; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.util.MiXCRDebug; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; @@ -52,8 +53,8 @@ public final class VDJCAlignmentsWriter implements VDJCAlignmentsWriterI, HasPosition { public static final int DEFAULT_ENCODER_THREADS = 3; public static final int DEFAULT_ALIGNMENTS_IN_BLOCK = 1 << 10; // 805-1024 bytes per alignment - static final String MAGIC_V15 = "MiXCR.VDJC.V15"; - static final String MAGIC = MAGIC_V15; + static final String MAGIC_V16 = "MiXCR.VDJC.V16"; + static final String MAGIC = MAGIC_V16; static final int MAGIC_LENGTH = 14; static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII); @@ -118,12 +119,12 @@ public void setNumberOfProcessedReads(long numberOfProcessedReads) { this.numberOfProcessedReads = numberOfProcessedReads; } - public void header(VDJCAlignmentsReader reader, PipelineConfiguration pipelineConfiguration) { - header(reader.getParameters(), reader.getUsedGenes(), pipelineConfiguration); + public void header(VDJCAlignmentsReader reader, PipelineConfiguration pipelineConfiguration, TagsInfo tagsInfo) { + header(reader.getParameters(), reader.getUsedGenes(), pipelineConfiguration, tagsInfo); } - public void header(VDJCAligner aligner, PipelineConfiguration pipelineConfiguration) { - header(aligner.getParameters(), aligner.getUsedGenes(), pipelineConfiguration); + public void header(VDJCAligner aligner, PipelineConfiguration pipelineConfiguration, TagsInfo tagsInfo) { + header(aligner.getParameters(), aligner.getUsedGenes(), pipelineConfiguration, tagsInfo); } /** History to write in the header */ @@ -138,7 +139,7 @@ else if (!configuration.equals(this.pipelineConfiguration)) @Override public void header(VDJCAlignerParameters parameters, List genes, - PipelineConfiguration ppConfiguration) { + PipelineConfiguration ppConfiguration, TagsInfo tags) { if (parameters == null || genes == null) throw new IllegalArgumentException(); @@ -164,6 +165,9 @@ public void header(VDJCAlignerParameters parameters, List genes, this.pipelineConfiguration = ppConfiguration; o.writeObject(pipelineConfiguration); + // Information about tags + o.writeObject(tags); + IOUtil.stdVDJCPrimitivOStateInit(o, genes, parameters); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java index 08991c51e..b322334db 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java @@ -31,10 +31,10 @@ import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.cli.PipelineConfigurationWriter; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.VDJCGene; -import java.util.ArrayList; import java.util.List; /** @@ -44,7 +44,7 @@ public interface VDJCAlignmentsWriterI extends PipelineConfigurationWriter, AutoCloseable { void setNumberOfProcessedReads(long numberOfProcessedReads); - void header(VDJCAlignerParameters parameters, List genes, PipelineConfiguration pipelineConfiguration); + void header(VDJCAlignerParameters parameters, List genes, PipelineConfiguration pipelineConfiguration, TagsInfo tagsInfo); void write(VDJCAlignments alignment); @@ -62,7 +62,7 @@ public void setNumberOfProcessedReads(long numberOfProcessedReads) { } @Override - public void header(VDJCAlignerParameters parameters, List genes, PipelineConfiguration pipelineConfiguration) { + public void header(VDJCAlignerParameters parameters, List genes, PipelineConfiguration pipelineConfiguration, TagsInfo tagsInfo) { } @Override @@ -73,40 +73,4 @@ public void write(VDJCAlignments alignment) { public void close() { } } - - final class ArrayWriter implements VDJCAlignmentsWriterI { - public long numberOfProcessedReads; - public VDJCAlignerParameters parameters; - public List genes; - public PipelineConfiguration pipelineConfiguration; - public final ArrayList data; - - public ArrayWriter(int capacity) { - data = new ArrayList<>(capacity); - } - - public ArrayWriter() { - this(10); - } - - @Override - public void setNumberOfProcessedReads(long numberOfProcessedReads) { - this.numberOfProcessedReads = numberOfProcessedReads; - } - - @Override - public void header(VDJCAlignerParameters parameters, List genes, PipelineConfiguration pipelineConfiguration) { - this.parameters = parameters; - this.genes = genes; - this.pipelineConfiguration = pipelineConfiguration; - } - - @Override - public synchronized void write(VDJCAlignments alignment) { - data.add(alignment); - } - - @Override - public void close() {} - } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java index 9b994abc8..e7e0e7ca5 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java @@ -1,5 +1,7 @@ package com.milaboratory.mixcr.basictypes.tag; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.Serializer; @@ -8,10 +10,49 @@ import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TObjectDoubleHashMap; +import java.util.Objects; + public final class IO { private IO() { } + public static class TagValueSerializer implements Serializer { + @Override + public void write(PrimitivO output, TagValue obj) { + if (obj instanceof SequenceTagValue) { + output.writeByte(0); + output.writeObject(((SequenceTagValue) obj).sequence); + } else if (obj instanceof SequenceAndQualityTagValue) { + output.writeByte(1); + output.writeObject(((SequenceAndQualityTagValue) obj).data); + } else + throw new IllegalArgumentException("Unsupported type."); + } + + @Override + public TagValue read(PrimitivI input) { + byte t = input.readByte(); + switch (t) { + case 0: + return new SequenceTagValue(input.readObject(NucleotideSequence.class)); + case 1: + return new SequenceAndQualityTagValue(input.readObject(NSequenceWithQuality.class)); + default: + throw new IllegalArgumentException("Malformed data."); + } + } + + @Override + public boolean isReference() { + return true; + } + + @Override + public boolean handlesReference() { + return false; + } + } + public static class TagCounterSerializer implements Serializer { @Override public void write(PrimitivO output, TagCounter object) { @@ -31,7 +72,8 @@ public TagCounter read(PrimitivI input) { return TagCounter.EMPTY; TObjectDoubleHashMap r = new TObjectDoubleHashMap<>(len, Constants.DEFAULT_LOAD_FACTOR, 0.0); for (int i = 0; i < len; ++i) { - ByteString[] tags = input.readObject(String[].class); + TagValue[] tags = input.readObject(TagValue[].class); + Objects.requireNonNull(tags); double count = input.readDouble(); r.put(new TagTuple(tags), count); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java new file mode 100644 index 000000000..8f2319e2c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java @@ -0,0 +1,35 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.milaboratory.core.sequence.NSequenceWithQuality; +import org.jetbrains.annotations.NotNull; + +import java.util.Objects; + +public final class SequenceAndQualityTagValue implements TagValue { + public final NSequenceWithQuality data; + + public SequenceAndQualityTagValue(NSequenceWithQuality data) { + Objects.requireNonNull(data); + this.data = data; + } + + @Override + public boolean isKey() { + return false; + } + + @Override + public TagValue extractKey() { + return new SequenceTagValue(data.getSequence()); + } + + @Override + public int compareTo(@NotNull TagValue o) { + return data.compareTo(((SequenceAndQualityTagValue) o).data); + } + + @Override + public String toString() { + return data.toString(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java new file mode 100644 index 000000000..2f1abe829 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java @@ -0,0 +1,48 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.milaboratory.core.sequence.NucleotideSequence; +import org.jetbrains.annotations.NotNull; + +import java.util.Objects; + +public final class SequenceTagValue implements TagValue { + public final NucleotideSequence sequence; + + public SequenceTagValue(NucleotideSequence sequence) { + Objects.requireNonNull(sequence); + this.sequence = sequence; + } + + @Override + public boolean isKey() { + return true; + } + + @Override + public TagValue extractKey() { + return this; + } + + @Override + public int compareTo(@NotNull TagValue o) { + return sequence.compareTo(((SequenceTagValue) o).sequence); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + SequenceTagValue that = (SequenceTagValue) o; + return sequence.equals(that.sequence); + } + + @Override + public int hashCode() { + return Objects.hash(sequence); + } + + @Override + public String toString() { + return sequence.toString(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java index 6a4a43726..b4c6be6fc 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java @@ -1,6 +1,5 @@ package com.milaboratory.mixcr.basictypes.tag; -import com.milaboratory.mixcr.basictypes.IO; import com.milaboratory.primitivio.annotations.Serializable; import gnu.trove.TDoubleCollection; import gnu.trove.iterator.TDoubleIterator; @@ -146,7 +145,7 @@ public TagCounter filter(Predicate predicate) { } public TagCounter[] splitBy(int index) { - Map map = new HashMap<>(); + Map map = new HashMap<>(); TObjectDoubleIterator it = iterator(); while (it.hasNext()) { it.advance(); @@ -182,8 +181,8 @@ public TagCounter toFractions() { return new TagCounter(result); } - public Set tags(int index) { - Set set = new HashSet<>(); + public Set tags(int index) { + Set set = new HashSet<>(); TObjectDoubleIterator it = iterator(); while (it.hasNext()) { it.advance(); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java new file mode 100644 index 000000000..8e35f6a2f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java @@ -0,0 +1,77 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.primitivio.annotations.Serializable; +import org.jetbrains.annotations.NotNull; + +import java.util.Objects; + +@Serializable(asJson = true) +public final class TagInfo implements Comparable { + @JsonProperty("type") + private final TagType type; + @JsonProperty("valueType") + private final TagValueType valueType; + @JsonProperty("name") + private final String name; + @JsonProperty("index") + private final int index; + + @JsonCreator + public TagInfo(@JsonProperty("type") TagType type, + @JsonProperty("valueType") TagValueType valueType, + @JsonProperty("name") String name, + @JsonProperty("index") int index) { + Objects.requireNonNull(type); + Objects.requireNonNull(valueType); + Objects.requireNonNull(name); + this.type = type; + this.valueType = valueType; + this.name = name; + this.index = index; + } + + public TagType getType() { + return type; + } + + public TagValueType getValueType() { + return valueType; + } + + public String getName() { + return name; + } + + public int getIndex() { + return index; + } + + public TagInfo withIndex(int idx) { + return new TagInfo(type, valueType, name, idx); + } + + @Override + public int compareTo(@NotNull TagInfo o) { + int c; + if ((c = Integer.compare(type.ordinal(), o.type.ordinal())) != 0) + return c; + if ((c = name.compareTo(o.name)) != 0) + return c; + return Integer.compare(index, o.index); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagInfo tagInfo = (TagInfo) o; + return index == tagInfo.index && type == tagInfo.type && valueType == tagInfo.valueType && name.equals(tagInfo.name); + } + + @Override + public int hashCode() { + return Objects.hash(type, valueType, name, index); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index af48e1756..7af77934c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -12,16 +12,16 @@ * Tag may be a sample name, cell marker or unique molecular identifier. */ public final class TagTuple implements Comparable { - public final ByteString[] tags; + public final TagValue[] tags; private final int hash; @SuppressWarnings("UnstableApiUsage") - public TagTuple(ByteString... tags) { + public TagTuple(TagValue... tags) { if (tags.length == 0) throw new IllegalArgumentException(); this.tags = tags; Hasher hasher = Hashing.murmur3_32_fixed().newHasher(); - for (ByteString tag : tags) + for (TagValue tag : tags) hasher.putInt(tag.hashCode()); this.hash = hasher.hash().hashCode(); } @@ -52,7 +52,7 @@ public int hashCode() { @Override public String toString() { StringBuilder sb = new StringBuilder(); - for (ByteString tag : tags) { + for (TagValue tag : tags) { if (sb.length() != 0) sb.append('+'); sb.append(tag.toString()); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java new file mode 100644 index 000000000..84cdf295f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java @@ -0,0 +1,7 @@ +package com.milaboratory.mixcr.basictypes.tag; + +public enum TagType { + SampleTag, + CellTag, + MoleculeTag +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java new file mode 100644 index 000000000..53a565e0a --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java @@ -0,0 +1,12 @@ +package com.milaboratory.mixcr.basictypes.tag; + +public interface TagValue extends Comparable { + /** + * Returns true for tag values that can be used as a grouping key, + * use {@link #extractKey()} to extract a key value from the tag value. + */ + boolean isKey(); + + /** Extracts TagValue that can be used as a key, basically by ripping off all auxiliary information. */ + TagValue extractKey(); +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java new file mode 100644 index 000000000..9a8d68f85 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java @@ -0,0 +1,18 @@ +package com.milaboratory.mixcr.basictypes.tag; + +public enum TagValueType { + Enum(null), + ByteString(null), + Sequence(null), + SequenceAndQuality(TagValueType.Sequence); + + private final TagValueType keyType; + + TagValueType(TagValueType keyType) { + this.keyType = keyType; + } + + public TagValueType getKeyType() { + return keyType == null ? this : keyType; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java new file mode 100644 index 000000000..4fdec4ed5 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -0,0 +1,33 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.primitivio.annotations.Serializable; + +import java.util.Arrays; +import java.util.Objects; + +@Serializable(asJson = true) +public final class TagsInfo { + @JsonProperty("tags") + public final TagInfo[] tags; + + @JsonCreator + public TagsInfo(@JsonProperty("tags") TagInfo... tags) { + Objects.requireNonNull(tags); + this.tags = tags; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagsInfo tagsInfo = (TagsInfo) o; + return Arrays.equals(tags, tagsInfo.tags); + } + + @Override + public int hashCode() { + return Arrays.hashCode(tags); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 5c9891934..5140bc6b0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -32,6 +32,7 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.core.io.sequence.SequenceRead; import com.milaboratory.core.sequence.quality.ReadTrimmerReport; +import com.milaboratory.mitool.report.ParseReport; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerEventListener; import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentFailCause; @@ -63,6 +64,8 @@ public final class AlignerReport extends AbstractCommandReport implements VDJCAl private final AtomicLong realignedWithForcedNonFloatingLeftBoundInRightRead = new AtomicLong(0); private ReadTrimmerReport trimmingReport; + private ParseReport tagReport; + public AlignerReport() { } @@ -84,6 +87,15 @@ public void setTrimmingReport(ReadTrimmerReport trimmingReport) { this.trimmingReport = trimmingReport; } + // @JsonProperty("trimmingReport") + public ParseReport getTagReport() { + return tagReport; + } + + public void setTagReport(ParseReport tagReport) { + this.tagReport = tagReport; + } + @JsonProperty("totalReadsProcessed") public long getTotal() { long total = 0; @@ -344,5 +356,8 @@ public void writeReport(ReportHelper helper) { helper.writeField("Average R2 Nucleotides Trimmed Right", 1.0 * trimmingReport.getR2RightTrimmedNucleotides() / total); } } + + if (tagReport != null) + helper.println(tagReport.humanReadable()); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index c7f598b9e..244149e38 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -47,10 +47,7 @@ import com.milaboratory.core.PairedEndReadsLayout; import com.milaboratory.core.Target; import com.milaboratory.core.io.CompressionType; -import com.milaboratory.core.io.sequence.SequenceRead; -import com.milaboratory.core.io.sequence.SequenceReaderCloseable; -import com.milaboratory.core.io.sequence.SequenceWriter; -import com.milaboratory.core.io.sequence.SingleRead; +import com.milaboratory.core.io.sequence.*; import com.milaboratory.core.io.sequence.fasta.FastaReader; import com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper; import com.milaboratory.core.io.sequence.fastq.PairedFastqReader; @@ -58,24 +55,21 @@ import com.milaboratory.core.io.sequence.fastq.SingleFastqReader; import com.milaboratory.core.io.sequence.fastq.SingleFastqWriter; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.core.sequence.ShortSequenceSet; import com.milaboratory.core.sequence.quality.QualityTrimmerParameters; import com.milaboratory.core.sequence.quality.ReadTrimmerProcessor; import com.milaboratory.core.sequence.quality.ReadTrimmerReport; +import com.milaboratory.mitool.pattern.search.*; +import com.milaboratory.mitool.report.ParseReport; import com.milaboratory.mixcr.basictypes.SequenceHistory; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; -import com.milaboratory.mixcr.tags.WhitelistReader; +import com.milaboratory.mixcr.basictypes.tag.*; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.mixcr.vdjaligners.*; import com.milaboratory.util.*; import io.repseq.core.*; -import picocli.CommandLine; import picocli.CommandLine.Command; -import picocli.CommandLine.ExecutionException; import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; @@ -90,6 +84,8 @@ import static cc.redberry.pipe.CUtils.chunked; import static cc.redberry.pipe.CUtils.unchunked; import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.DEFAULT_ALIGNMENTS_IN_BLOCK; +import static com.milaboratory.mixcr.basictypes.tag.TagType.*; +import static com.milaboratory.mixcr.basictypes.tag.TagValueType.SequenceAndQuality; import static com.milaboratory.mixcr.cli.CommandAlign.ALIGN_COMMAND_NAME; @Command(name = ALIGN_COMMAND_NAME, @@ -225,14 +221,23 @@ public void setSaveOriginalReads(boolean b) { names = {"--buffers"}, hidden = true) public boolean reportBuffers = false; - // @Option(description = "Names for groups that contain barcodes, for MiNNN FASTQ input file.", - // names = {"--tag"}) - // public List tags = new ArrayList<>(); + // @Option(description = "Specify this option for 10x datasets to extract cell and UMI barcode information from " + + // "the first read", + // names = {"--10x"}) + // public boolean tenX = false; - @Option(description = "Specify this option for 10x datasets to extract cell and UMI barcode information from " + - "the first read", - names = {"--10x"}) - public boolean tenX = false; + @Option(description = "Tag pattern to extract from the read.", + names = {"--tag-pattern"}) + public String tagPattern; + + @Option(description = "If paired-end input is used, determines whether to try all combinations of mate-pairs or only match " + + "reads to the corresponding pattern sections (i.e. first file to first section, etc...)", + names = {"--tag-parse-unstranded"}) + public boolean tagUnstranded = false; + + @Option(description = "Maximal bit budget, higher values allows more substitutions in small letters.", + names = {"--tag-max-budget"}) + public double tagMaxBudget = 10.0; private VDJCAlignerParameters vdjcAlignerParameters = null; @@ -429,6 +434,29 @@ public int hashCode() { } } + public TagSearchPlan getTagPattern() { + if (tagPattern == null) + return null; + + ReadSearchSettings searchSettings = new ReadSearchSettings(new SearchSettings(tagMaxBudget, 0.1, + new MatcherSettings(3, 7)), + isInputPaired() + ? tagUnstranded + ? ReadSearchMode.PairedUnknown + : ReadSearchMode.PairedDirect + : ReadSearchMode.Single); + ReadSearchPlan readSearchPlan = ReadSearchPlan.Companion.create(tagPattern, searchSettings); + ParseInfo parseInfo = ParseInfo.fromSet(readSearchPlan.getAllTags()); + List tagShortcuts = parseInfo.getTags().stream() + .map(t -> readSearchPlan.tagShortcut(t.getName())) + .collect(Collectors.toList()); + List readShortcuts = parseInfo.getReadTags().stream() + .map(readSearchPlan::tagShortcut) + .collect(Collectors.toList()); + + return new TagSearchPlan(readSearchPlan, tagShortcuts, readShortcuts, parseInfo.getTags()); + } + @Override public void validate() { super.validate(); @@ -449,20 +477,6 @@ public void validate() { /** Alignment report */ public final AlignerReport report = new AlignerReport(); - static TagTuple parseTags(CommandLine commandLine, List tags, SequenceRead r) { - String description = r.getRead(0).getDescription(); - String descTrimmed = description.replaceAll("[|~]*$", "").replaceAll("\\{[^}]*}", ""); - Map matchedGroups = Arrays.stream(descTrimmed.split("\\|")) - .map(str -> str.split("~")).filter(tokens -> tokens.length >= 3) - .collect(Collectors.toMap(tokens -> tokens[tokens.length - 3], tokens -> tokens[tokens.length - 2])); - return new TagTuple(tags.stream().map(tag -> { - String tagSeq = matchedGroups.get(tag); - if (tagSeq == null) - throw new ExecutionException(commandLine, "Group " + tag + " not found in FASTQ description!"); - return tagSeq; - }).toArray(String[]::new)); - } - private QualityTrimmerParameters getQualityTrimmerParameters() { return new QualityTrimmerParameters(trimmingQualityThreshold, trimmingWindowSize); @@ -542,12 +556,14 @@ else if (featureSequence.containsWildcards()) report.setOutputFiles(getOutput()); report.setCommandLine(getCommandLineArguments()); + // Tags + TagSearchPlan tagSearchPlan = getTagPattern(); + if (tagSearchPlan != null) + report.setTagReport(tagSearchPlan.report); + // Attaching report to aligner aligner.setEventsListener(report); - if (tenX && !isInputPaired()) - throwValidationException("Option \"--10x\" requires paired-end input data"); - try (SequenceReaderCloseable reader = createReader(); VDJCAlignmentsWriter writer = getOutput().equals(".") @@ -562,7 +578,10 @@ else if (featureSequence.containsWildcards()) : new SingleFastqWriter(failedReadsR1)); ) { if (writer != null) - writer.header(aligner, getFullPipelineConfiguration()); + writer.header(aligner, getFullPipelineConfiguration(), + tagSearchPlan != null + ? new TagsInfo(tagSearchPlan.tagInfos.toArray(new TagInfo[0])) + : null); OutputPort sReads = reader; CanReportProgress progress = (CanReportProgress) reader; @@ -586,44 +605,36 @@ else if (featureSequence.containsWildcards()) Merger> mainInputReads = CUtils.buffered((OutputPort) chunked(sReads, 64), Math.max(16, threads)); OutputPort> mainInputReadsPreprocessed = mainInputReads; - // TODO do this after barcode extraction + + ReadTrimmerProcessor readTrimmerProcessor; if (trimmingQualityThreshold > 0) { ReadTrimmerReport rep = new ReadTrimmerReport(); - mainInputReadsPreprocessed = CUtils.wrap( - mainInputReadsPreprocessed, - CUtils.chunked(new ReadTrimmerProcessor(getQualityTrimmerParameters(), rep))); + readTrimmerProcessor = new ReadTrimmerProcessor(getQualityTrimmerParameters(), rep); report.setTrimmingReport(rep); - } + } else + readTrimmerProcessor = null; // Creating processor from aligner Processor> processor = aligner; - if (tenX) { - final ShortSequenceSet whitelist = WhitelistReader.Whitelist10X2016(); + if (tagSearchPlan != null) { final Processor> oldProcessor = processor; processor = input -> { - SingleRead r1 = input.getRead(0); - NucleotideSequence seq = r1.getData().getSequence(); - if (seq.size() < 26) { - report.onFailedAlignment(input, VDJCAlignmentFailCause.NoBarcode); - return new VDJCAlignmentResult(input); - } + TaggedSequence parsed = tagSearchPlan.parse(input); - if (!whitelist.contains(seq.getRange(0, 16))) { - report.onFailedAlignment(input, VDJCAlignmentFailCause.BarcodeNotInWhitelist); + if (parsed == null) { + report.onFailedAlignment(input, VDJCAlignmentFailCause.NoBarcode); return new VDJCAlignmentResult(input); } - String seqString = seq.toString(); - TagTuple tt = new TagTuple(seqString.substring(0, 16), seqString.substring(16, 26)); - - SequenceRead trimmed = input.mapReadsWithIndex((index, val) -> index == 0 - ? val.mapSequence(s -> s.getRange(26, s.size())) - : val); + SequenceRead read = parsed.read; + if (readTrimmerProcessor != null) + read = readTrimmerProcessor.process(read); - VDJCAlignmentResult alignmentResult = oldProcessor.process(trimmed); - return alignmentResult.withTagTuple(tt); + VDJCAlignmentResult alignmentResult = oldProcessor.process(read); + return alignmentResult.withTagTuple(parsed.tags); }; - } + } else if (readTrimmerProcessor != null) + mainInputReadsPreprocessed = CUtils.wrap(mainInputReadsPreprocessed, CUtils.chunked(readTrimmerProcessor)); ParallelProcessor alignedChunks = new ParallelProcessor(mainInputReadsPreprocessed, chunked(processor), Math.max(16, threads), threads); if (reportBuffers) { @@ -701,4 +712,112 @@ public String getStatus() { if (jsonReport != null) Util.writeJsonReport(jsonReport, report); } + + static final class TaggedSequence { + final TagTuple tags; + final SequenceRead read; + + public TaggedSequence(TagTuple tags, SequenceRead read) { + this.tags = tags; + this.read = read; + } + } + + static final class TagSearchPlan { + final ReadSearchPlan plan; + final List tagShortcuts; + final List readShortcuts; + final List tagInfos; + + final ParseReport report; + + public TagSearchPlan(ReadSearchPlan plan, + List tagShortcuts, List readShortcuts, + List tagInfos) { + this.plan = plan; + this.tagShortcuts = tagShortcuts; + this.readShortcuts = readShortcuts; + this.tagInfos = tagInfos; + this.report = new ParseReport(plan); + } + + public TaggedSequence parse(SequenceRead read) { + ReadSearchResult result = plan.search(read); + report.consume(result); + ReadSearchHit hit = result.getHit(); + if (hit == null) + return null; + + TagValue[] tags = tagShortcuts.stream() + .map(s -> new SequenceAndQualityTagValue(result.getTagValue(s).getValue())) + .toArray(TagValue[]::new); + + SingleRead[] reads = new SingleRead[readShortcuts.size()]; + for (int i = 0; i < reads.length; i++) { + reads[i] = new SingleReadImpl( + read.getId(), + result.getTagValue(readShortcuts.get(i)).getValue(), + read.numberOfReads() <= i + ? read.getRead(0).getDescription() + : read.getRead(i).getDescription()); + } + + return new TaggedSequence(new TagTuple(tags), SequenceReadUtil.construct(reads)); + } + } + + public static final class ParseInfo { + private final List tags; + private final List readTags; + + public ParseInfo(List tags, List readTags) { + Objects.requireNonNull(tags); + Objects.requireNonNull(readTags); + this.tags = tags; + this.readTags = readTags; + } + + public List getTags() { + return tags; + } + + public List getReadTags() { + return readTags; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + ParseInfo parseInfo = (ParseInfo) o; + return tags.equals(parseInfo.tags) && readTags.equals(parseInfo.readTags); + } + + @Override + public int hashCode() { + return Objects.hash(tags, readTags); + } + + public static ParseInfo fromSet(Set names) { + List tags = new ArrayList<>(); + List readTags = new ArrayList<>(); + for (String name : names) { + if (name.startsWith("S")) + tags.add(new TagInfo(SampleTag, SequenceAndQuality, name, 0)); + else if (name.startsWith("CELL")) + tags.add(new TagInfo(CellTag, SequenceAndQuality, name, 0)); + else if (name.startsWith("UMI") || name.startsWith("MI")) + tags.add(new TagInfo(MoleculeTag, SequenceAndQuality, name, 0)); + else if (name.startsWith("R")) + readTags.add(name); + else + throw new IllegalArgumentException("Can't recognize tag type for name: " + name); + } + Collections.sort(tags); + for (int i = 0; i < tags.size(); i++) + tags.set(i, tags.get(i).withIndex(i)); + Collections.sort(readTags); + return new ParseInfo(tags, readTags); + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java index 777942707..4a837a0da 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java @@ -112,10 +112,10 @@ public void run0() throws Exception { long same = 0, onlyIn1 = 0, onlyIn2 = 0, diffFeature = 0, justDiff = 0; long[] diffHits = new long[GeneType.NUMBER_OF_TYPES]; - only1.header(reader1.getParameters(), reader1.getUsedGenes(), null); - diff1.header(reader1.getParameters(), reader1.getUsedGenes(), null); - only2.header(reader2.getParameters(), reader2.getUsedGenes(), null); - diff2.header(reader2.getParameters(), reader2.getUsedGenes(), null); + only1.header(reader1.getParameters(), reader1.getUsedGenes(), null, reader1.getTagsInfo()); + diff1.header(reader1.getParameters(), reader1.getUsedGenes(), null, reader1.getTagsInfo()); + only2.header(reader2.getParameters(), reader2.getUsedGenes(), null, reader2.getTagsInfo()); + diff2.header(reader2.getParameters(), reader2.getUsedGenes(), null, reader2.getTagsInfo()); VDJCAlignmentsDifferenceReader diffReader = new VDJCAlignmentsDifferenceReader(reader1, reader2, getFeature(), hitsCompareLevel); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 8b2f67f06..e231b496a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -41,6 +41,7 @@ import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.ArraysUtils; import com.milaboratory.util.JsonOverrider; @@ -105,7 +106,7 @@ public class CommandAssemble extends ACommandWithSmartOverwriteWithSingleInputMi "This file then can be used to build wider contigs for clonal sequence and extract original " + "reads for each clone (if -OsaveOriginalReads=true was use on 'align' stage).", names = {"-a", "--write-alignments"}) - public boolean clna = false; + public boolean isClnaOutput = false; @Option(description = "Enable tag-based read to clone assignment", names = {"--attach-reads-by-tags"}) @@ -119,12 +120,13 @@ public class CommandAssemble extends ACommandWithSmartOverwriteWithSingleInputMi @Override public ActionConfiguration getConfiguration() { ensureParametersInitialized(); - return new AssembleConfiguration(getCloneAssemblerParameters(), clna, ordering); + return new AssembleConfiguration(getCloneAssemblerParameters(), isClnaOutput, ordering); } // Extracting V/D/J/C gene list from input vdjca file private List genes = null; private VDJCAlignerParameters alignerParameters = null; + private TagsInfo tagsInfo = null; private CloneAssemblerParameters assemblerParameters = null; private VDJCSProperties.CloneOrdering ordering = null; @@ -137,6 +139,7 @@ private void ensureParametersInitialized() { genes = reader.getUsedGenes(); // Saving aligner parameters to correct assembler parameters alignerParameters = reader.getParameters(); + tagsInfo = reader.getTagsInfo(); } catch (IOException e) { throw new RuntimeException(e); } @@ -192,6 +195,11 @@ public VDJCAlignerParameters getAlignerParameters() { return alignerParameters; } + public TagsInfo getTagsInfo() { + ensureParametersInitialized(); + return tagsInfo; + } + public VDJCSProperties.CloneOrdering getOrdering() { ensureParametersInitialized(); return ordering; @@ -208,8 +216,8 @@ public void run1() throws Exception { long beginTimestamp = System.currentTimeMillis(); // Checking consistency between actionParameters.doWriteClnA() value and file extension - if ((getOutput().toLowerCase().endsWith(".clna") && !clna) || - (getOutput().toLowerCase().endsWith(".clns") && clna)) + if ((getOutput().toLowerCase().endsWith(".clna") && !isClnaOutput) || + (getOutput().toLowerCase().endsWith(".clns") && isClnaOutput)) warn("WARNING: Unexpected file extension, use .clns extension for clones-only (normal) output and\n" + ".clna if -a / --write-alignments options specified."); @@ -220,10 +228,11 @@ public void run1() throws Exception { CloneAssemblerParameters assemblerParameters = getCloneAssemblerParameters(); List genes = getGenes(); VDJCAlignerParameters alignerParameters = getAlignerParameters(); + TagsInfo tagsInfo = getTagsInfo(); // Performing assembly try (CloneAssembler assembler = new CloneAssembler(assemblerParameters, - clna, + isClnaOutput, genes, alignerParameters.getFeaturesToAlignMap())) { // Creating event listener to collect run statistics report.setStartMillis(beginTimestamp); @@ -250,14 +259,14 @@ public void run1() throws Exception { assemblerRunner.run(); // Getting results - final CloneSet cloneSet = CloneSet.reorder(assemblerRunner.getCloneSet(alignerParameters), getOrdering()); + final CloneSet cloneSet = CloneSet.reorder(assemblerRunner.getCloneSet(alignerParameters, tagsInfo), getOrdering()); // Passing final cloneset to assemble last pieces of statistics for report report.onClonesetFinished(cloneSet); // Writing results PipelineConfiguration pipelineConfiguration = getFullPipelineConfiguration(); - if (clna) { + if (isClnaOutput) { try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, highCompression)) { // writer will supply current stage and completion percent to the progress reporter diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index e5fa7ad30..be0de7307 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -43,6 +43,8 @@ import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerParameters; import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerReport; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PipeDataInputReader; @@ -126,6 +128,7 @@ public void run1() throws Exception { List genes; VDJCAlignerParameters alignerParameters; CloneAssemblerParameters cloneAssemblerParameters; + TagsInfo tagsInfo; VDJCSProperties.CloneOrdering ordering; try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(out))); // TODO ???? @@ -138,6 +141,7 @@ public void run1() throws Exception { alignerParameters = reader.getAlignerParameters(); cloneAssemblerParameters = reader.getAssemblerParameters(); + tagsInfo = reader.getTagsInfo(); genes = reader.getGenes(); IOUtil.registerGeneReferences(tmpOut, genes, alignerParameters); @@ -265,7 +269,8 @@ public void run1() throws Exception { clones[i++] = clone.setId(cloneId++); } - CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters, cloneAssemblerParameters, ordering); + CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters, cloneAssemblerParameters, + tagsInfo, ordering); try (ClnsWriter writer = new ClnsWriter(out)) { writer.writeCloneSet(getFullPipelineConfiguration(), cloneSet); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java index 34e84dab6..4a1a391c4 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java @@ -60,7 +60,8 @@ public int[] getCloneIds() { public void run1() throws Exception { try (ClnAReader clna = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(getOutput())) { - writer.header(clna.getAlignerParameters(), clna.getGenes(), getFullPipelineConfiguration()); + writer.header(clna.getAlignerParameters(), clna.getGenes(), + getFullPipelineConfiguration(), clna.getTagsInfo()); long count = 0; if (getCloneIds().length == 0) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index e24308359..ad7410b05 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -155,7 +155,7 @@ void processClns() throws IOException { clones.sort(Comparator.comparing(Clone::getId)); CloneSet newCloneSet = new CloneSet(clones, cloneSet.getUsedGenes(), cloneSet.getAlignmentParameters(), - cloneSet.getAssemblerParameters(), cloneSet.getOrdering()); + cloneSet.getAssemblerParameters(), cloneSet.getTagsInfo(), cloneSet.getOrdering()); try (ClnsWriter writer = new ClnsWriter(out)) { writer.writeCloneSet(getFullPipelineConfiguration(), newCloneSet); @@ -168,7 +168,8 @@ void processVDJCA() throws IOException { final VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { SmartProgressReporter.startProgressReport("Extending alignments", reader); - writer.header(reader.getParameters(), reader.getUsedGenes(), getFullPipelineConfiguration()); + writer.header(reader.getParameters(), reader.getUsedGenes(), + getFullPipelineConfiguration(), reader.getTagsInfo()); ProcessWrapper process = new ProcessWrapper<>(reader, reader.getParameters().getVAlignerParameters().getParameters().getScoring(), diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java index 890e54a77..46579d8fc 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java @@ -33,11 +33,17 @@ import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.util.CountLimitingOutputPort; import cc.redberry.primitives.Filter; -import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; +import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.set.hash.TLongHashSet; @@ -145,7 +151,8 @@ public void run1() throws Exception { sReads = new CountLimitingOutputPort<>(sReads, limit); progress = SmartProgressReporter.extractProgress((CountLimitingOutputPort) sReads); } - writer.header(reader.getParameters(), reader.getUsedGenes(), getFullPipelineConfiguration()); + writer.header(reader.getParameters(), reader.getUsedGenes(), + getFullPipelineConfiguration(), reader.getTagsInfo()); SmartProgressReporter.startProgressReport("Filtering", progress); int total = 0, passed = 0; final AlignmentsFilter filter = getFilter(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index cc043ee00..8a3329801 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -1,334 +1,303 @@ package com.milaboratory.mixcr.cli; -import cc.redberry.pipe.OutputPortCloseable; -import com.fasterxml.jackson.annotation.JsonAutoDetect; -import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonProperty; -import com.fasterxml.jackson.annotation.JsonTypeInfo; -import com.milaboratory.cli.ActionConfiguration; -import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; -import com.milaboratory.mixcr.tags.CloneGroup; -import com.milaboratory.mixcr.tags.DropletCloneGraph; -import com.milaboratory.mixcr.tags.DropletCloneGraphParameters; -import com.milaboratory.mixcr.tags.DropletCloneGraphReport; -import com.milaboratory.util.JsonOverrider; -import com.milaboratory.util.ProgressAndStage; -import com.milaboratory.util.SmartProgressReporter; -import gnu.trove.impl.Constants; -import gnu.trove.map.hash.TIntObjectHashMap; -import gnu.trove.map.hash.TObjectIntHashMap; -import io.repseq.core.VDJCLibraryRegistry; -import picocli.CommandLine.Command; -import picocli.CommandLine.Option; - -import java.io.FileNotFoundException; -import java.io.PrintStream; -import java.util.*; -import java.util.concurrent.atomic.AtomicInteger; -import java.util.function.Consumer; - -import static com.milaboratory.mixcr.basictypes.IOUtil.*; - -/** - * - */ -@Command(name = CommandGroupCells.GROUP_CLONE_COMMAND_NAME, - sortOptions = true, - separator = " ", - description = "Group clones for single cell data (e.g. alpha-beta / heavy-light chain pairing).") -public class CommandGroupCells extends ACommandWithSmartOverwriteWithSingleInputMiXCR { - public static final String GROUP_CLONE_COMMAND_NAME = "groupCells"; - @Option(description = "Cell barcode group name", - names = {"-t", "--tag"}) - public int tagIndex; - - @Option(description = CommonDescriptions.REPORT, - names = {"-r", "--report"}) - public String reportFile; - - @Option(description = CommonDescriptions.JSON_REPORT, - names = {"-j", "--json-report"}) - public String jsonReportFile; - - @Option(description = "Generate separate file with group mapping for cell barcodes", - names = {"--tag-mapping"}) - public String tagMappingFile; - - @Option(description = "Minimal fraction of reads in clone that were not assigned to any group and will be separated into 'unassigned' clone (default is 0).", - names = {"--minimal-ungrouped-fraction"}) - public double minimalUngroupedFraction = 0; - - @Option(names = {"-O"}, description = "Overrides default aligner parameter values") - public Map overrides = new HashMap<>(); - - @Override - public GroupingPipelineConfiguration getConfiguration() { - return new GroupingPipelineConfiguration(getParameters(), minimalUngroupedFraction); - } - - private DropletCloneGraphReport report; - private DropletCloneGraphParameters parameters; - - DropletCloneGraphParameters getParameters() { - if (parameters != null) - return parameters; - - parameters = DropletCloneGraphParameters.getDefault(); - if (!overrides.isEmpty()) { - // Perform parameters overriding - parameters = JsonOverrider.override(parameters, DropletCloneGraphParameters.class, overrides); - if (parameters == null) - throwValidationException("Failed to override some parameter: " + overrides); - } - return parameters; - } - - @Override - public void run1() throws Exception { - String in = this.in; - - report = new DropletCloneGraphReport(); - - switch (Objects.requireNonNull(fileInfoExtractorInstance.getFileInfo(in)).fileType) { - case MAGIC_CLNS: - runClns(); - break; - case MAGIC_CLNA: - runClna(); - break; - default: - throwExecutionException("Illegal input format"); - } - - // Writing report to stout - System.out.println("============= Report =============="); - Util.writeReportToStdout(report); - - if (reportFile != null) - Util.writeReport(reportFile, report); - - if (jsonReportFile != null) - Util.writeJsonReport(jsonReportFile, report); - } - - private static final class CloneIdWithTag { - public final String tag; - public final int cloneId; - - public CloneIdWithTag(String tag, int cloneId) { - this.tag = tag; - this.cloneId = cloneId; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - CloneIdWithTag that = (CloneIdWithTag) o; - return cloneId == that.cloneId && - Objects.equals(tag, that.tag); - } - - @Override - public int hashCode() { - return Objects.hash(tag, cloneId); - } - - @Override - public String toString() { - return cloneId + " " + tag; - } - } - - private void runClns() throws Exception { - CloneSet cloneSet = CloneSetIO.read(in); - CloneSet resultCloneSet = doClustering(cloneSet, null); - try (ClnsWriter writer = new ClnsWriter(out)) { - writer.writeCloneSet(getFullPipelineConfiguration(), resultCloneSet); - } - } - - private void runClna() throws Exception { - try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), 3); - ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { - - CloneSet cloneSet = reader.readCloneSet(); - - TObjectIntHashMap idMapping = new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); - CloneSet resultCloneSet = doClustering(cloneSet, idMapping); - - SmartProgressReporter.startProgressReport(writer); - - writer.writeClones(resultCloneSet); - - OutputPortCloseable alignments = reader.readAllAlignments(); - writer.collateAlignments(() -> { - VDJCAlignments als = alignments.take(); - if (als == null) - return null; - TagTuple tt = als.getTagCounter().singleOrNull(); - if (tt == null) - return als.updateCloneIndex(-1); - int newCloneIndex = idMapping.get(new CloneIdWithTag(tt.tags[tagIndex], als.getCloneIndex())); - if (newCloneIndex == -1) - return als.updateCloneIndex(-1); - - return als.updateCloneIndex(newCloneIndex); - }, reader.numberOfAlignments()); - - writer.writeAlignmentsAndIndex(); - } - } - - private CloneSet doClustering(CloneSet cloneSet, TObjectIntHashMap idMapping) { - report.before(cloneSet); - - ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); - SmartProgressReporter.startProgressReport(progressAndStage); - List groups = DropletCloneGraph.calculateGroups(DropletCloneGraph.calculateTuples(cloneSet, tagIndex), parameters, report, progressAndStage); - - if (tagMappingFile != null) - try (PrintStream os = new PrintStream(tagMappingFile)) { - os.println("GroupId\tTag\tTotalReads\tTotalUMIs\tNumberOfClones"); - for (CloneGroup group : groups) - for (String tag : group.groupTags) { - os.print(group.groupId); - os.print('\t'); - os.print(tag); - os.print('\t'); - os.print(group.reads); - os.print('\t'); - os.print(group.umis); - os.print('\t'); - os.print(group.groupClones.size()); - os.println(); - } - } catch (FileNotFoundException e) { - throw new RuntimeException(e); - } - - TIntObjectHashMap> groupsByClones = new TIntObjectHashMap<>(); - for (CloneGroup group : groups) { - group.groupClones.forEach(i -> { - ArrayList list = new ArrayList<>(); - List val = groupsByClones.putIfAbsent(i, list); - if (val != null) val.add(group); - else list.add(group); - return true; - }); - } - - List resultingClones = new ArrayList<>(); - - final AtomicInteger cloneId = new AtomicInteger(); - Consumer addClone = clone -> { - if (clone.getGroup() < 0) - report.onUngroupedClone(clone); - else - report.onGroupedClone(clone); - - int oldCloneId = clone.getId(); - int newCloneId = cloneId.getAndIncrement(); - - if (idMapping != null) - for (TagTuple key : clone.getTagCounter().keys()) { - int put = idMapping.put(new CloneIdWithTag(key.tags[tagIndex], oldCloneId), newCloneId); - assert put == -1 || put == newCloneId; - } - - resultingClones.add(clone.setId(newCloneId)); - }; - - for (Clone clone : cloneSet) { - List cloneGroups = groupsByClones.get(clone.getId()); - if (cloneGroups == null) { - addClone.accept(clone.setGroup(-1 - clone.getId())); - continue; - } - - report.onCloneBeforeSplit(clone); - - List splitCounters = new ArrayList<>(); - double sumTotal = 0; - for (CloneGroup cloneGroup : cloneGroups) { - TagCounter filtered = clone.getTagCounter().filter(p -> cloneGroup.groupTags.contains(p.tags[tagIndex])); - sumTotal += filtered.sum(); - splitCounters.add(filtered); - } - - boolean includeUngrouped = (1 - sumTotal / clone.getTagCounter().sum()) > minimalUngroupedFraction; - TagCounter ungroupedCounter = null; - if (includeUngrouped) { - ungroupedCounter = clone.getTagCounter().filter(p -> cloneGroups.stream().noneMatch(g -> g.groupTags.contains(p.tags[tagIndex]))); - sumTotal += ungroupedCounter.sum(); - assert Math.abs(sumTotal - clone.getTagCounter().sum()) < 0.1; - } - - // TODO if cloneGroups.size() == 1, ungroupedCounter can be added to the splitCounters[0] - - for (int i = 0; i < splitCounters.size(); ++i) { - TagCounter tc = splitCounters.get(i); - addClone.accept(clone - .setTagCounts(tc) - .setGroup(cloneGroups.get(i).groupId) // same index - .setCount(clone.getCount() * tc.sum() / sumTotal)); - } - - if (includeUngrouped && ungroupedCounter.size() != 0) - addClone.accept(clone - .setTagCounts(ungroupedCounter) - .setGroup(-1 - clone.getId()) - .setCount(clone.getCount() * ungroupedCounter.sum() / sumTotal)); - } - - return new CloneSet(resultingClones, - cloneSet.getUsedGenes(), - cloneSet.getAlignmentParameters(), - cloneSet.getAssemblerParameters(), - cloneSet.getOrdering()); - } - - @JsonAutoDetect( - fieldVisibility = JsonAutoDetect.Visibility.ANY, - isGetterVisibility = JsonAutoDetect.Visibility.NONE, - getterVisibility = JsonAutoDetect.Visibility.NONE) - @JsonTypeInfo( - use = JsonTypeInfo.Id.CLASS, - include = JsonTypeInfo.As.PROPERTY, - property = "type") - private static final class GroupingPipelineConfiguration - implements ActionConfiguration { - @JsonProperty("parameters") - final DropletCloneGraphParameters parameters; - @JsonProperty("minimalUngroupedFraction") - final double minimalUngroupedFraction; - - @JsonCreator - public GroupingPipelineConfiguration(@JsonProperty("parameters") DropletCloneGraphParameters parameters, - @JsonProperty("minimalUngroupedFraction") double minimalUngroupedFraction) { - this.parameters = parameters; - this.minimalUngroupedFraction = minimalUngroupedFraction; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - GroupingPipelineConfiguration that = (GroupingPipelineConfiguration) o; - return Double.compare(that.minimalUngroupedFraction, minimalUngroupedFraction) == 0 && - Objects.equals(parameters, that.parameters); - } - - @Override - public int hashCode() { - return Objects.hash(parameters, minimalUngroupedFraction); - } - - @Override - public String actionName() { - return GROUP_CLONE_COMMAND_NAME; - } - } -} +// /** +// * +// */ +// @Command(name = CommandGroupCells.GROUP_CLONE_COMMAND_NAME, +// sortOptions = true, +// separator = " ", +// description = "Group clones for single cell data (e.g. alpha-beta / heavy-light chain pairing).") +// public class CommandGroupCells extends ACommandWithSmartOverwriteWithSingleInputMiXCR { +// public static final String GROUP_CLONE_COMMAND_NAME = "groupCells"; +// @Option(description = "Cell barcode group name", +// names = {"-t", "--tag"}) +// public int tagIndex; +// +// @Option(description = CommonDescriptions.REPORT, +// names = {"-r", "--report"}) +// public String reportFile; +// +// @Option(description = CommonDescriptions.JSON_REPORT, +// names = {"-j", "--json-report"}) +// public String jsonReportFile; +// +// @Option(description = "Generate separate file with group mapping for cell barcodes", +// names = {"--tag-mapping"}) +// public String tagMappingFile; +// +// @Option(description = "Minimal fraction of reads in clone that were not assigned to any group and will be separated into 'unassigned' clone (default is 0).", +// names = {"--minimal-ungrouped-fraction"}) +// public double minimalUngroupedFraction = 0; +// +// @Option(names = {"-O"}, description = "Overrides default aligner parameter values") +// public Map overrides = new HashMap<>(); +// +// @Override +// public GroupingPipelineConfiguration getConfiguration() { +// return new GroupingPipelineConfiguration(getParameters(), minimalUngroupedFraction); +// } +// +// private DropletCloneGraphReport report; +// private DropletCloneGraphParameters parameters; +// +// DropletCloneGraphParameters getParameters() { +// if (parameters != null) +// return parameters; +// +// parameters = DropletCloneGraphParameters.getDefault(); +// if (!overrides.isEmpty()) { +// // Perform parameters overriding +// parameters = JsonOverrider.override(parameters, DropletCloneGraphParameters.class, overrides); +// if (parameters == null) +// throwValidationException("Failed to override some parameter: " + overrides); +// } +// return parameters; +// } +// +// @Override +// public void run1() throws Exception { +// String in = this.in; +// +// report = new DropletCloneGraphReport(); +// +// switch (Objects.requireNonNull(fileInfoExtractorInstance.getFileInfo(in)).fileType) { +// case MAGIC_CLNS: +// runClns(); +// break; +// case MAGIC_CLNA: +// runClna(); +// break; +// default: +// throwExecutionException("Illegal input format"); +// } +// +// // Writing report to stout +// System.out.println("============= Report =============="); +// Util.writeReportToStdout(report); +// +// if (reportFile != null) +// Util.writeReport(reportFile, report); +// +// if (jsonReportFile != null) +// Util.writeJsonReport(jsonReportFile, report); +// } +// +// private static final class CloneIdWithTag { +// public final String tag; +// public final int cloneId; +// +// public CloneIdWithTag(String tag, int cloneId) { +// this.tag = tag; +// this.cloneId = cloneId; +// } +// +// @Override +// public boolean equals(Object o) { +// if (this == o) return true; +// if (o == null || getClass() != o.getClass()) return false; +// CloneIdWithTag that = (CloneIdWithTag) o; +// return cloneId == that.cloneId && +// Objects.equals(tag, that.tag); +// } +// +// @Override +// public int hashCode() { +// return Objects.hash(tag, cloneId); +// } +// +// @Override +// public String toString() { +// return cloneId + " " + tag; +// } +// } +// +// private void runClns() throws Exception { +// CloneSet cloneSet = CloneSetIO.read(in); +// CloneSet resultCloneSet = doClustering(cloneSet, null); +// try (ClnsWriter writer = new ClnsWriter(out)) { +// writer.writeCloneSet(getFullPipelineConfiguration(), resultCloneSet); +// } +// } +// +// private void runClna() throws Exception { +// try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), 3); +// ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { +// +// CloneSet cloneSet = reader.readCloneSet(); +// +// TObjectIntHashMap idMapping = new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); +// CloneSet resultCloneSet = doClustering(cloneSet, idMapping); +// +// SmartProgressReporter.startProgressReport(writer); +// +// writer.writeClones(resultCloneSet); +// +// OutputPortCloseable alignments = reader.readAllAlignments(); +// writer.collateAlignments(() -> { +// VDJCAlignments als = alignments.take(); +// if (als == null) +// return null; +// TagTuple tt = als.getTagCounter().singleOrNull(); +// if (tt == null) +// return als.updateCloneIndex(-1); +// int newCloneIndex = idMapping.get(new CloneIdWithTag(tt.tags[tagIndex], als.getCloneIndex())); +// if (newCloneIndex == -1) +// return als.updateCloneIndex(-1); +// +// return als.updateCloneIndex(newCloneIndex); +// }, reader.numberOfAlignments()); +// +// writer.writeAlignmentsAndIndex(); +// } +// } +// +// private CloneSet doClustering(CloneSet cloneSet, TObjectIntHashMap idMapping) { +// report.before(cloneSet); +// +// ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); +// SmartProgressReporter.startProgressReport(progressAndStage); +// List groups = DropletCloneGraph.calculateGroups(DropletCloneGraph.calculateTuples(cloneSet, tagIndex), parameters, report, progressAndStage); +// +// if (tagMappingFile != null) +// try (PrintStream os = new PrintStream(tagMappingFile)) { +// os.println("GroupId\tTag\tTotalReads\tTotalUMIs\tNumberOfClones"); +// for (CloneGroup group : groups) +// for (String tag : group.groupTags) { +// os.print(group.groupId); +// os.print('\t'); +// os.print(tag); +// os.print('\t'); +// os.print(group.reads); +// os.print('\t'); +// os.print(group.umis); +// os.print('\t'); +// os.print(group.groupClones.size()); +// os.println(); +// } +// } catch (FileNotFoundException e) { +// throw new RuntimeException(e); +// } +// +// TIntObjectHashMap> groupsByClones = new TIntObjectHashMap<>(); +// for (CloneGroup group : groups) { +// group.groupClones.forEach(i -> { +// ArrayList list = new ArrayList<>(); +// List val = groupsByClones.putIfAbsent(i, list); +// if (val != null) val.add(group); +// else list.add(group); +// return true; +// }); +// } +// +// List resultingClones = new ArrayList<>(); +// +// final AtomicInteger cloneId = new AtomicInteger(); +// Consumer addClone = clone -> { +// if (clone.getGroup() < 0) +// report.onUngroupedClone(clone); +// else +// report.onGroupedClone(clone); +// +// int oldCloneId = clone.getId(); +// int newCloneId = cloneId.getAndIncrement(); +// +// if (idMapping != null) +// for (TagTuple key : clone.getTagCounter().keys()) { +// int put = idMapping.put(new CloneIdWithTag(key.tags[tagIndex], oldCloneId), newCloneId); +// assert put == -1 || put == newCloneId; +// } +// +// resultingClones.add(clone.setId(newCloneId)); +// }; +// +// for (Clone clone : cloneSet) { +// List cloneGroups = groupsByClones.get(clone.getId()); +// if (cloneGroups == null) { +// addClone.accept(clone.setGroup(-1 - clone.getId())); +// continue; +// } +// +// report.onCloneBeforeSplit(clone); +// +// List splitCounters = new ArrayList<>(); +// double sumTotal = 0; +// for (CloneGroup cloneGroup : cloneGroups) { +// TagCounter filtered = clone.getTagCounter().filter(p -> cloneGroup.groupTags.contains(p.tags[tagIndex])); +// sumTotal += filtered.sum(); +// splitCounters.add(filtered); +// } +// +// boolean includeUngrouped = (1 - sumTotal / clone.getTagCounter().sum()) > minimalUngroupedFraction; +// TagCounter ungroupedCounter = null; +// if (includeUngrouped) { +// ungroupedCounter = clone.getTagCounter().filter(p -> cloneGroups.stream().noneMatch(g -> g.groupTags.contains(p.tags[tagIndex]))); +// sumTotal += ungroupedCounter.sum(); +// assert Math.abs(sumTotal - clone.getTagCounter().sum()) < 0.1; +// } +// +// // TODO if cloneGroups.size() == 1, ungroupedCounter can be added to the splitCounters[0] +// +// for (int i = 0; i < splitCounters.size(); ++i) { +// TagCounter tc = splitCounters.get(i); +// addClone.accept(clone +// .setTagCounts(tc) +// .setGroup(cloneGroups.get(i).groupId) // same index +// .setCount(clone.getCount() * tc.sum() / sumTotal)); +// } +// +// if (includeUngrouped && ungroupedCounter.size() != 0) +// addClone.accept(clone +// .setTagCounts(ungroupedCounter) +// .setGroup(-1 - clone.getId()) +// .setCount(clone.getCount() * ungroupedCounter.sum() / sumTotal)); +// } +// +// return new CloneSet(resultingClones, +// cloneSet.getUsedGenes(), +// cloneSet.getAlignmentParameters(), +// cloneSet.getAssemblerParameters(), +// cloneSet.getOrdering()); +// } +// +// @JsonAutoDetect( +// fieldVisibility = JsonAutoDetect.Visibility.ANY, +// isGetterVisibility = JsonAutoDetect.Visibility.NONE, +// getterVisibility = JsonAutoDetect.Visibility.NONE) +// @JsonTypeInfo( +// use = JsonTypeInfo.Id.CLASS, +// include = JsonTypeInfo.As.PROPERTY, +// property = "type") +// private static final class GroupingPipelineConfiguration +// implements ActionConfiguration { +// @JsonProperty("parameters") +// final DropletCloneGraphParameters parameters; +// @JsonProperty("minimalUngroupedFraction") +// final double minimalUngroupedFraction; +// +// @JsonCreator +// public GroupingPipelineConfiguration(@JsonProperty("parameters") DropletCloneGraphParameters parameters, +// @JsonProperty("minimalUngroupedFraction") double minimalUngroupedFraction) { +// this.parameters = parameters; +// this.minimalUngroupedFraction = minimalUngroupedFraction; +// } +// +// @Override +// public boolean equals(Object o) { +// if (this == o) return true; +// if (o == null || getClass() != o.getClass()) return false; +// GroupingPipelineConfiguration that = (GroupingPipelineConfiguration) o; +// return Double.compare(that.minimalUngroupedFraction, minimalUngroupedFraction) == 0 && +// Objects.equals(parameters, that.parameters); +// } +// +// @Override +// public int hashCode() { +// return Objects.hash(parameters, minimalUngroupedFraction); +// } +// +// @Override +// public String actionName() { +// return GROUP_CLONE_COMMAND_NAME; +// } +// } +// } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java index 62d2f46e2..9aa50539f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java @@ -31,10 +31,16 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; -import com.fasterxml.jackson.annotation.*; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.cli.PipelineConfiguration; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.PipelineConfigurationReaderMiXCR; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.SmartProgressReporter; @@ -92,7 +98,8 @@ public void run1() throws Exception { VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(getOutput())) { reader.initNextReader(); SmartProgressReporter.startProgressReport("Merging", reader); - writer.header(reader.currentInnerReader.getParameters(), reader.currentInnerReader.getUsedGenes(), getFullPipelineConfiguration()); + writer.header(reader.currentInnerReader.getParameters(), reader.currentInnerReader.getUsedGenes(), + getFullPipelineConfiguration(), reader.currentInnerReader.getTagsInfo()); for (VDJCAlignments record : CUtils.it(reader)) writer.write(record); writer.setNumberOfProcessedReads(reader.readIdOffset.get()); @@ -136,7 +143,7 @@ public int hashCode() { // Not thread-safe ! private static final class MultiReader implements - OutputPort, CanReportProgress, AutoCloseable { + OutputPort, CanReportProgress, AutoCloseable { final VDJCLibraryRegistry registry = VDJCLibraryRegistry.getDefault(); final List files; final AtomicInteger fileId = new AtomicInteger(0); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java index f95216ad9..4cc9b39b5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java @@ -94,7 +94,7 @@ void sliceVDJCA() throws Exception { try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { - writer.header(reader, getFullPipelineConfiguration()); + writer.header(reader, getFullPipelineConfiguration(), reader.getTagsInfo()); for (VDJCAlignments alignments : CUtils.it(reader)) { if (set.removeAll(alignments.getReadIds())) writer.write(alignments); @@ -138,7 +138,7 @@ void sliceClnA() throws Exception { } CloneSet newCloneSet = new CloneSet(clones, cloneSet.getUsedGenes(), cloneSet.getAlignmentParameters(), - cloneSet.getAssemblerParameters(), cloneSet.getOrdering()); + cloneSet.getAssemblerParameters(), cloneSet.getTagsInfo(), cloneSet.getOrdering()); OutputPort allAlignmentsPortRaw = new FlatteningOutputPort<>(CUtils.asOutputPort(allAlignmentsList)); AtomicLong idGen = new AtomicLong(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java index d0d75a9e3..4122a3e04 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java @@ -45,8 +45,8 @@ import com.milaboratory.primitivio.PipeWriter; import com.milaboratory.util.ObjectSerializer; import com.milaboratory.util.SmartProgressReporter; -import com.milaboratory.util.sorting.Sorter; import com.milaboratory.util.TempFileManager; +import com.milaboratory.util.sorting.Sorter; import io.repseq.core.VDJCGene; import picocli.CommandLine.Command; @@ -80,7 +80,8 @@ public void run1() throws Exception { new VDJCAlignmentsSerializer(reader), TempFileManager.getTempFile()); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { - writer.header(reader.getParameters(), reader.getUsedGenes(), getFullPipelineConfiguration()); + writer.header(reader.getParameters(), reader.getUsedGenes(), + getFullPipelineConfiguration(), reader.getTagsInfo()); final long nReads = reader.getNumberOfReads(); final CountingOutputPort counter = new CountingOutputPort<>(sorted); diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index a98e3d193..eb48440ba 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -227,7 +227,7 @@ public static CommandLine mkCmd() { .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) - .addSubcommand("groupCells", CommandGroupCells.class) + // .addSubcommand("groupCells", CommandGroupCells.class) .addSubcommand("assembleContigs", CommandAssembleContigs.class) .addSubcommand("assemblePartial", CommandAssemblePartialAlignments.class) diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 207f57c1f..7b137f8c9 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -41,11 +41,11 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.TranslationParameters; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; -import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.VDJCObject; import com.milaboratory.util.GlobalObjectMappers; -import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.iterator.TObjectFloatIterator; import gnu.trove.map.hash.TObjectFloatHashMap; import io.repseq.core.GeneFeature; @@ -54,8 +54,9 @@ import io.repseq.core.SequencePartitioning; import java.text.DecimalFormat; -import java.util.*; -import java.util.stream.Collectors; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; public final class FieldExtractors { static final String NULL = ""; @@ -686,75 +687,75 @@ protected String extract(Clone object) { } }); - descriptorsList.add(new WP_O("-tag", "Tag value", 1) { - @Override - protected Integer getParameters(String[] string) { - return Integer.parseInt(string[0]); - } - - @Override - protected String getHeader(OutputMode outputMode, Integer index) { - switch (outputMode) { - case HumanFriendly: return "Tag" + index; - case ScriptingFriendly: return "tag" + index; - } - throw new RuntimeException(); - } - - @Override - protected String extractValue(VDJCObject object, Integer index) { - TagCounter tc = object.getTagCounter(); - Set set = tc.tags(index); - if (set.size() == 0) - return NULL; - if (set.size() > 1) - throw new IllegalArgumentException("object has multiple tag tuples: " + tc); - return set.iterator().next(); - } - - @Override - public String metaVars() { - return "index"; - } - }); - - descriptorsList.add(new WP_O("-uniqueTagCount", "Unique tag count", 1) { - @Override - protected int[] getParameters(String[] string) { - return Arrays.stream(string[0].split("\\+")).mapToInt(Integer::parseInt).toArray(); - } - - @Override - protected String getHeader(OutputMode outputMode, int[] index) { - String str = Arrays.stream(index).mapToObj(Integer::toString).collect(Collectors.joining("+")); - switch (outputMode) { - case HumanFriendly: return "Unique Tag Count " + str; - case ScriptingFriendly: return "uniqueTagCount" + str; - } - throw new RuntimeException(); - } - - @Override - protected String extractValue(VDJCObject object, int[] indices) { - TagCounter tc = object.getTagCounter(); - Set set = new HashSet<>(); - TObjectDoubleIterator it = tc.iterator(); - while (it.hasNext()) { - it.advance(); - StringBuilder sb = new StringBuilder(); - TagTuple t = it.key(); - for (int i : indices) - sb.append(t.tags[i]).append("+"); - set.add(sb.toString()); - } - return "" + set.size(); - } + // descriptorsList.add(new WP_O("-tag", "Tag value", 1) { + // @Override + // protected String getParameters(String[] string) { + // return string[0]; + // } + // + // @Override + // protected String getHeader(OutputMode outputMode, String name) { + // switch (outputMode) { + // case HumanFriendly: return "Tag" + name; + // case ScriptingFriendly: return "tag" + name; + // } + // throw new RuntimeException(); + // } + // + // @Override + // protected String extractValue(VDJCObject object, String name) { + // TagCounter tc = object.getTagCounter(); + // Set set = tc.tags(name); + // if (set.size() == 0) + // return NULL; + // if (set.size() > 1) + // throw new IllegalArgumentException("object has multiple tag tuples: " + tc); + // return set.iterator().next(); + // } + // + // @Override + // public String metaVars() { + // return "index"; + // } + // }); - @Override - public String metaVars() { - return "Tags"; - } - }); + // descriptorsList.add(new WP_O("-uniqueTagCount", "Unique tag count", 1) { + // @Override + // protected int[] getParameters(String[] string) { + // return Arrays.stream(string[0].split("\\+")).mapToInt(Integer::parseInt).toArray(); + // } + // + // @Override + // protected String getHeader(OutputMode outputMode, int[] index) { + // String str = Arrays.stream(index).mapToObj(Integer::toString).collect(Collectors.joining("+")); + // switch (outputMode) { + // case HumanFriendly: return "Unique Tag Count " + str; + // case ScriptingFriendly: return "uniqueTagCount" + str; + // } + // throw new RuntimeException(); + // } + // + // @Override + // protected String extractValue(VDJCObject object, int[] indices) { + // TagCounter tc = object.getTagCounter(); + // Set set = new HashSet<>(); + // TObjectDoubleIterator it = tc.iterator(); + // while (it.hasNext()) { + // it.advance(); + // StringBuilder sb = new StringBuilder(); + // TagTuple t = it.key(); + // for (int i : indices) + // sb.append(t.tags[i]).append("+"); + // set.add(sb.toString()); + // } + // return "" + set.size(); + // } + // + // @Override + // public String metaVars() { + // return "Tags"; + // } + // }); descriptorsList.add(new PL_C("-cellGroup", "Cell group", "Cell group", "cellGroup") { @Override diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 102329178..d2d580b1b 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -39,8 +39,8 @@ import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.cli.Report; -import com.milaboratory.util.ReportHelper; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.util.ReportHelper; import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TLongObjectHashMap; import gnu.trove.set.hash.TLongHashSet; @@ -117,7 +117,7 @@ public boolean maxRightMatchesLimitReached() { public void buildLeftPartsIndex(VDJCAlignmentsReader reader) { geneTypesToShiftIndels = reader.getParameters().getGeneTypesWithLinearScoring(); - writer.header(reader.getParameters(), reader.getUsedGenes(), null); + writer.header(reader.getParameters(), reader.getUsedGenes(), null, reader.getTagsInfo()); for (VDJCAlignments alignment : CUtils.it(reader)) { if (alignment.getFeature(GeneFeature.CDR3) != null) continue; diff --git a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java index 7263311a9..4cb77a60c 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java +++ b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java @@ -2,7 +2,6 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.mixcr.tags.DropletCloneGraph.CloneTagTupleList; import java.util.List; import java.util.Objects; @@ -10,129 +9,129 @@ import static java.lang.Double.isNaN; -/** - * - */ -public final class CloneTagTupleFilter { - @JsonProperty("minReadFractionInTag") - public final double minReadFractionInTag; - @JsonProperty("maxCloneRankInTag") - public final int maxCloneRankInTag; - @JsonProperty("minTagReads") - public final double minTagReads; - @JsonProperty("minTagUMIs") - public final double minTagUMIs; - @JsonProperty("tagReadsQuantile") - public final double tagReadsQuantile; - @JsonProperty("tagReadsQuantileCoefficient") - public final double tagReadsQuantileCoefficient; - @JsonProperty("tagUMIsQuantile") - public final double tagUMIsQuantile; - @JsonProperty("tagUMIsQuantileCoefficient") - public final double tagUMIsQuantileCoefficient; - - @JsonCreator - public CloneTagTupleFilter(@JsonProperty("minReadFractionInTag") double minReadFractionInTag, - @JsonProperty("maxCloneRankInTag") int maxCloneRankInTag, - @JsonProperty("minTagReads") double minTagReads, - @JsonProperty("minTagUMIs") double minTagUMIs, - @JsonProperty("tagReadsQuantile") double tagReadsQuantile, - @JsonProperty("tagReadsQuantileCoefficient") double tagReadsQuantileCoefficient, - @JsonProperty("tagUMIsQuantile") double tagUMIsQuantile, - @JsonProperty("tagUMIsQuantileCoefficient") double tagUMIsQuantileCoefficient) { - if (!isNaN(tagReadsQuantile) && isNaN(tagReadsQuantileCoefficient)) - throw new IllegalArgumentException("Please specify tagReadsQuantileCoefficient."); - if (!isNaN(tagUMIsQuantile) && isNaN(tagUMIsQuantileCoefficient)) - throw new IllegalArgumentException("Please specify tagUMIsQuantileCoefficient."); - this.minReadFractionInTag = minReadFractionInTag; - this.maxCloneRankInTag = maxCloneRankInTag; - this.minTagReads = minTagReads; - this.minTagUMIs = minTagUMIs; - this.tagReadsQuantile = tagReadsQuantile; - this.tagReadsQuantileCoefficient = tagReadsQuantileCoefficient; - this.tagUMIsQuantile = tagUMIsQuantile; - this.tagUMIsQuantileCoefficient = tagUMIsQuantileCoefficient; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - CloneTagTupleFilter that = (CloneTagTupleFilter) o; - return minReadFractionInTag == that.minReadFractionInTag && - maxCloneRankInTag == that.maxCloneRankInTag && - Double.compare(that.minTagReads, minTagReads) == 0 && - Double.compare(that.minTagUMIs, minTagUMIs) == 0 && - Double.compare(that.tagReadsQuantile, tagReadsQuantile) == 0 && - Double.compare(that.tagUMIsQuantile, tagUMIsQuantile) == 0; - } - - @Override - public int hashCode() { - return Objects.hash(minReadFractionInTag, maxCloneRankInTag, minTagReads, minTagUMIs, tagReadsQuantile, tagUMIsQuantile); - } - - public List filter(CloneTagTupleList tuples, DropletCloneGraphReport report) { - - double minTagReads = 0.0, minTagUMIs = 0.0; - if (!isNaN(tagReadsQuantile)) { - minTagReads = tuples.readsTopQuantile(tagReadsQuantile); - minTagReads = minTagReads * tagReadsQuantileCoefficient; - } - if (!isNaN(tagUMIsQuantile)) { - minTagUMIs = tuples.umisTopQuantile(tagUMIsQuantile); - minTagUMIs = minTagUMIs * tagUMIsQuantileCoefficient; - } - - if (!isNaN(this.minTagReads)) - minTagReads = Math.max(minTagReads, this.minTagReads); - if (!isNaN(this.minTagUMIs)) - minTagUMIs = Math.max(minTagUMIs, this.minTagUMIs); - - report.effectiveMinReadsInTag = minTagReads; - report.effectiveMinUMIsInTag = minTagUMIs; - - double minTagReadsFinal = minTagReads; - double minTagUMIsFinal = minTagUMIs; - - List result = tuples.tuples.stream().filter(tup -> { - - if (tup.readFractionInTag < this.minReadFractionInTag) - return false; - - if (tup.rank > this.maxCloneRankInTag) - return false; - - if (tup.getReadsInTag() < minTagReadsFinal) - return false; - - if (tup.getUMIsInTag() < minTagUMIsFinal) - return false; - - return true; - }).collect(Collectors.toList()); - - - int tuplesBefore = tuples.tuples.size(); - int tagsBefore = tuples.umisPerDroplet.size(); - long umisBefore = tuples.tuples.stream().mapToLong(s -> s.umiCount).sum(); - double readsBefore = tuples.tuples.stream().mapToDouble(s -> s.readCount).sum(); - - int tuplesAfter = result.size(); - int tagsAfter = (int) result.stream().map(s -> s.tag).distinct().count(); - long umisAfter = result.stream().mapToLong(s -> s.umiCount).sum(); - double readsAfter = result.stream().mapToDouble(s -> s.readCount).sum(); - - report.tagTuplesTotal.set(tuplesBefore); - report.tagsTotal.set(tagsBefore); - report.umisTotal.set(umisBefore); - report.readsTotal.set(readsBefore); - - report.tagTuplesFiltered.set(tuplesAfter); - report.tagsFiltered.set(tagsAfter); - report.umisFiltered.set(umisAfter); - report.readsFiltered.set(readsAfter); - - return result; - } -} +// /** +// * +// */ +// public final class CloneTagTupleFilter { +// @JsonProperty("minReadFractionInTag") +// public final double minReadFractionInTag; +// @JsonProperty("maxCloneRankInTag") +// public final int maxCloneRankInTag; +// @JsonProperty("minTagReads") +// public final double minTagReads; +// @JsonProperty("minTagUMIs") +// public final double minTagUMIs; +// @JsonProperty("tagReadsQuantile") +// public final double tagReadsQuantile; +// @JsonProperty("tagReadsQuantileCoefficient") +// public final double tagReadsQuantileCoefficient; +// @JsonProperty("tagUMIsQuantile") +// public final double tagUMIsQuantile; +// @JsonProperty("tagUMIsQuantileCoefficient") +// public final double tagUMIsQuantileCoefficient; +// +// @JsonCreator +// public CloneTagTupleFilter(@JsonProperty("minReadFractionInTag") double minReadFractionInTag, +// @JsonProperty("maxCloneRankInTag") int maxCloneRankInTag, +// @JsonProperty("minTagReads") double minTagReads, +// @JsonProperty("minTagUMIs") double minTagUMIs, +// @JsonProperty("tagReadsQuantile") double tagReadsQuantile, +// @JsonProperty("tagReadsQuantileCoefficient") double tagReadsQuantileCoefficient, +// @JsonProperty("tagUMIsQuantile") double tagUMIsQuantile, +// @JsonProperty("tagUMIsQuantileCoefficient") double tagUMIsQuantileCoefficient) { +// if (!isNaN(tagReadsQuantile) && isNaN(tagReadsQuantileCoefficient)) +// throw new IllegalArgumentException("Please specify tagReadsQuantileCoefficient."); +// if (!isNaN(tagUMIsQuantile) && isNaN(tagUMIsQuantileCoefficient)) +// throw new IllegalArgumentException("Please specify tagUMIsQuantileCoefficient."); +// this.minReadFractionInTag = minReadFractionInTag; +// this.maxCloneRankInTag = maxCloneRankInTag; +// this.minTagReads = minTagReads; +// this.minTagUMIs = minTagUMIs; +// this.tagReadsQuantile = tagReadsQuantile; +// this.tagReadsQuantileCoefficient = tagReadsQuantileCoefficient; +// this.tagUMIsQuantile = tagUMIsQuantile; +// this.tagUMIsQuantileCoefficient = tagUMIsQuantileCoefficient; +// } +// +// @Override +// public boolean equals(Object o) { +// if (this == o) return true; +// if (o == null || getClass() != o.getClass()) return false; +// CloneTagTupleFilter that = (CloneTagTupleFilter) o; +// return minReadFractionInTag == that.minReadFractionInTag && +// maxCloneRankInTag == that.maxCloneRankInTag && +// Double.compare(that.minTagReads, minTagReads) == 0 && +// Double.compare(that.minTagUMIs, minTagUMIs) == 0 && +// Double.compare(that.tagReadsQuantile, tagReadsQuantile) == 0 && +// Double.compare(that.tagUMIsQuantile, tagUMIsQuantile) == 0; +// } +// +// @Override +// public int hashCode() { +// return Objects.hash(minReadFractionInTag, maxCloneRankInTag, minTagReads, minTagUMIs, tagReadsQuantile, tagUMIsQuantile); +// } +// +// public List filter(CloneTagTupleList tuples, DropletCloneGraphReport report) { +// +// double minTagReads = 0.0, minTagUMIs = 0.0; +// if (!isNaN(tagReadsQuantile)) { +// minTagReads = tuples.readsTopQuantile(tagReadsQuantile); +// minTagReads = minTagReads * tagReadsQuantileCoefficient; +// } +// if (!isNaN(tagUMIsQuantile)) { +// minTagUMIs = tuples.umisTopQuantile(tagUMIsQuantile); +// minTagUMIs = minTagUMIs * tagUMIsQuantileCoefficient; +// } +// +// if (!isNaN(this.minTagReads)) +// minTagReads = Math.max(minTagReads, this.minTagReads); +// if (!isNaN(this.minTagUMIs)) +// minTagUMIs = Math.max(minTagUMIs, this.minTagUMIs); +// +// report.effectiveMinReadsInTag = minTagReads; +// report.effectiveMinUMIsInTag = minTagUMIs; +// +// double minTagReadsFinal = minTagReads; +// double minTagUMIsFinal = minTagUMIs; +// +// List result = tuples.tuples.stream().filter(tup -> { +// +// if (tup.readFractionInTag < this.minReadFractionInTag) +// return false; +// +// if (tup.rank > this.maxCloneRankInTag) +// return false; +// +// if (tup.getReadsInTag() < minTagReadsFinal) +// return false; +// +// if (tup.getUMIsInTag() < minTagUMIsFinal) +// return false; +// +// return true; +// }).collect(Collectors.toList()); +// +// +// int tuplesBefore = tuples.tuples.size(); +// int tagsBefore = tuples.umisPerDroplet.size(); +// long umisBefore = tuples.tuples.stream().mapToLong(s -> s.umiCount).sum(); +// double readsBefore = tuples.tuples.stream().mapToDouble(s -> s.readCount).sum(); +// +// int tuplesAfter = result.size(); +// int tagsAfter = (int) result.stream().map(s -> s.tag).distinct().count(); +// long umisAfter = result.stream().mapToLong(s -> s.umiCount).sum(); +// double readsAfter = result.stream().mapToDouble(s -> s.readCount).sum(); +// +// report.tagTuplesTotal.set(tuplesBefore); +// report.tagsTotal.set(tagsBefore); +// report.umisTotal.set(umisBefore); +// report.readsTotal.set(readsBefore); +// +// report.tagTuplesFiltered.set(tuplesAfter); +// report.tagsFiltered.set(tagsAfter); +// report.umisFiltered.set(umisAfter); +// report.readsFiltered.set(readsAfter); +// +// return result; +// } +// } diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java index 80b9bd040..1fd90eacc 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java @@ -47,418 +47,418 @@ import java.util.concurrent.atomic.AtomicReference; import java.util.stream.Collectors; -public final class DropletCloneGraph { - - private static TIntIntHashMap newTIntIntHashMap() { - return new TIntIntHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1, -1); - } - - private static TObjectIntHashMap newTObjectIntHashMap() { - return new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); - } - - private static TObjectDoubleHashMap newTObjectDoubleHashMap() { - return new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); - } - - public static List calculateGroups(CloneTagTupleList tuplesList, - DropletCloneGraphParameters parameters, - DropletCloneGraphReport report, - ProgressAndStage progressAndStage) { - List tuples = parameters.filter.filter(tuplesList, report); - Map> byTags = new HashMap<>(); - TIntObjectHashMap> byCloneId = new TIntObjectHashMap<>(); - List tmpList = new ArrayList<>(); - for (CloneTagTuple tup : tuples) { - byTags.computeIfAbsent(tup.tag, __ -> new ArrayList<>()).add(tup); - List list = byCloneId.putIfAbsent(tup.clone.getId(), tmpList); - if (list == null) { - tmpList.add(tup); - tmpList = new ArrayList<>(); - } else - list.add(tup); - } - - ArrayList groups = new ArrayList<>(); - - long initialTagCount = byTags.size(); - long counter = 0; - - int groupId = 0; - // loop over connected components - while (!byTags.isEmpty()) { - Map> byTagsInComponent = new HashMap<>(); - TIntObjectHashMap> byCloneIdInComponent = new TIntObjectHashMap<>(); - - // Calculating connected component starting from: - // tag = byTags.keySet().iterator().next() - { - Set currentTags = new HashSet<>(); - TIntHashSet currentClones = new TIntHashSet(); - currentTags.add(byTags.keySet().iterator().next()); - while (!currentTags.isEmpty()) { - for (String currentTag : currentTags) { - List inDroplet = byTags.remove(currentTag); - if (inDroplet == null) - continue; - - for (CloneTagTuple tup : inDroplet) { - List list = byCloneIdInComponent.putIfAbsent(tup.clone.getId(), tmpList); - if (list == null) { - currentClones.add(tup.clone.getId()); - tmpList.add(tup); - tmpList = new ArrayList<>(); - } else - list.add(tup); - } - } - currentTags.clear(); - - TIntIterator cIt = currentClones.iterator(); - while (cIt.hasNext()) - for (CloneTagTuple tup : byCloneId.remove(cIt.next())) { - byTagsInComponent.computeIfAbsent(tup.tag, __ -> { - currentTags.add(tup.tag); - return new ArrayList<>(); - }).add(tup); - } - currentClones.clear(); - } - } - - report.onConnectedComponent(byTagsInComponent, byCloneIdInComponent); - - // form adjacency matrix of connected tags - AdjacencyMatrix tagMatrix = new AdjacencyMatrix(byTagsInComponent.size()); - // tagId <-> tag - TIntObjectHashMap indexToTag = new TIntObjectHashMap<>(); - TObjectIntHashMap tagToIndex = newTObjectIntHashMap(); - int idx = 0; - for (String tag : byTagsInComponent.keySet()) { - indexToTag.put(idx, tag); - tagToIndex.put(tag, idx); - ++idx; - } - - for (int i = 0; i < indexToTag.size(); ++i) { - tagMatrix.setConnected(i, i); - for (CloneTagTuple tup : byTagsInComponent.get(indexToTag.get(i))) - for (CloneTagTuple end : byCloneIdInComponent.get(tup.clone.getId())) - tagMatrix.setConnected(i, tagToIndex.get(end.tag)); - } - - List tagCliques = null; - List tagCliqueInfos = null; - // searching all cliques in tags - while (!tagToIndex.isEmpty()) { - if (tagCliques == null) { - tagCliques = tagMatrix.calculateMaximalCliques(); - tagCliqueInfos = new ArrayList<>(); - for (BitArrayInt clique : tagCliques) { - int[] bits = clique.getBits(); - if (bits.length == 1 && !tagMatrix.isConnected(bits[0], bits[0])) - continue; - - TIntIntHashMap nTagsByClones = newTIntIntHashMap(); - - double readCount = 0; - for (int tagIndex : bits) - for (CloneTagTuple tup : byTagsInComponent.get(indexToTag.get(tagIndex))) { - nTagsByClones.adjustOrPutValue(tup.clone.getId(), 1, 1); - readCount += tup.readCount; - } - - - TIntIntIterator it = nTagsByClones.iterator(); - double score = 0; - while (it.hasNext()) { - it.advance(); - int count = it.value(); - - score += Math.pow(count - 1, parameters.tagCliqueScorePower); - } - - tagCliqueInfos.add(new CliqueInfo(clique, score, readCount)); - } - } - - Optional topTagCliqueO = tagCliqueInfos.stream().max(CliqueInfo::compareTo); - if (!topTagCliqueO.isPresent()) - break; - - CliqueInfo topTagClique = topTagCliqueO.get(); - - Set tags = new HashSet<>(); - int[] topTagCliqueBits = topTagClique.clique.getBits(); - for (int i : topTagCliqueBits) - tags.add(indexToTag.get(i)); - - TIntIntHashMap indexToCloneId = newTIntIntHashMap(); - // !!! used as cloneId -> count in the loop below - TIntIntHashMap cloneIdToIndex = newTIntIntHashMap(); - - { - for (String tag : tags) - for (CloneTagTuple tup : byTagsInComponent.get(tag)) - cloneIdToIndex.adjustOrPutValue(tup.clone.getId(), 1, 1); - - idx = 0; - TIntIntIterator it = cloneIdToIndex.iterator(); - while (it.hasNext()) { - it.advance(); - assert it.value() > 0; - // if tags.size == 1 => single tag in clique, so just writing - // index (presence of clones is enough, i.e. do not require clones to link any tags) - if (tags.size() > 1 && it.value() == 1) - it.remove(); - else { - indexToCloneId.put(idx, it.key()); - it.setValue(idx); - ++idx; - } - } - } - - AdjacencyMatrix clonesMatrix = new AdjacencyMatrix(cloneIdToIndex.size()); - - for (String tag : tags) { - List tuplesForTag = byTagsInComponent.get(tag); - for (int i1 = 0; i1 < tuplesForTag.size(); i1++) - for (int i2 = i1 + 1; i2 < tuplesForTag.size(); i2++) { - int index1 = cloneIdToIndex.get(tuplesForTag.get(i1).clone.getId()); - int index2 = cloneIdToIndex.get(tuplesForTag.get(i2).clone.getId()); - if (index1 >= 0 && index2 >= 0) - clonesMatrix.setConnected(index1, index2); - } - } - - List cloneCliques = clonesMatrix.calculateMaximalCliques(); - List cloneCliqueInfos = new ArrayList<>(); - - for (BitArrayInt clique : cloneCliques) { - TObjectIntHashMap nClonesByTags = newTObjectIntHashMap(); - - double readCount = 0; - for (int cloneIndex : clique.getBits()) - for (CloneTagTuple tup : byCloneIdInComponent.get(indexToCloneId.get(cloneIndex))) - if (tags.contains(tup.tag)) { - nClonesByTags.adjustOrPutValue(tup.tag, 1, 1); - readCount += tup.readCount; - } - - TObjectIntIterator it = nClonesByTags.iterator(); - double score = 0; - while (it.hasNext()) { - it.advance(); - int count = it.value(); - - score += Math.pow(count - 1, parameters.cloneCliqueScorePower); - } - - cloneCliqueInfos.add(new CliqueInfo(clique, score, readCount)); - } - - CliqueInfo topCloneClique = cloneCliqueInfos.stream().max(CliqueInfo::compareTo).get(); - - // dropping tags - - Set groupTags = new HashSet<>(); - TIntHashSet groupClones = new TIntHashSet(); - - for (int cloneIdx : topCloneClique.clique.getBits()) { - for (CloneTagTuple tup : byCloneIdInComponent.get(indexToCloneId.get(cloneIdx))) { - if (tags.contains(tup.tag)) { - String tag = tup.tag; - - int index = tagToIndex.remove(tag); - ++counter; - if (progressAndStage != null) - progressAndStage.setProgress(1.0 * counter / initialTagCount); - - if (index >= 0) { - indexToTag.remove(index); - tagMatrix.clear(index); - } - - groupClones.add(tup.clone.getId()); - groupTags.add(tag); - } - } - } - - double readTotal = 0.0; - long umiTotal = 0; - - for (String tag : groupTags) - for (CloneTagTuple ctt : byTagsInComponent.get(tag)) { - readTotal += ctt.readCount; - umiTotal += ctt.umiCount; - } - - CloneGroup group = new CloneGroup(groupId, readTotal, umiTotal, groupTags, groupClones); - report.onGroup(topTagClique, topCloneClique, group); - groups.add(group); - - tagCliques = null; - - ++groupId; - } - } - - // Clustering - TIntObjectHashMap>> byClones = new TIntObjectHashMap<>(); - groups.sort(Comparator - .comparingInt(c -> c.groupClones.size()) - .thenComparingInt(c -> c.groupTags.size()) - .reversed()); - - ArrayList> groupsAfterClustering = new ArrayList<>(); - ArrayList> tmpList2 = new ArrayList<>(); - for (CloneGroup minor : groups) { - // Major candidates - Set> majorCandidates = Collections.newSetFromMap(new IdentityHashMap<>()); - int[] minorCloneIds = minor.groupClones.toArray(); - for (int cId : minorCloneIds) { - List> grps = byClones.get(cId); - if (grps == null) - break; // This guarantees that no candidates will be found (such clone was never seen before) - for (AtomicReference preCandidate : grps) - if (preCandidate.get().groupClones.containsAll(minor.groupClones) - && 1.0 * minor.groupTags.size() / preCandidate.get().groupTags.size() <= parameters.maxTagCountRatio) - majorCandidates.add(preCandidate); - } - if (majorCandidates.size() != 1) { - AtomicReference minorRef = new AtomicReference<>(minor); - groupsAfterClustering.add(minorRef); - for (int cId : minorCloneIds) { - List> cloneGroups = byClones.putIfAbsent(cId, tmpList2); - if (cloneGroups != null) - cloneGroups.add(minorRef); - else { - tmpList2.add(minorRef); - tmpList2 = new ArrayList<>(); - } - } - } else { // Clustering - AtomicReference majorRef = majorCandidates.iterator().next(); - report.onClustered(majorRef.get(), minor); - majorRef.set(majorRef.get().mergeFrom(minor)); - } - } - - if (progressAndStage != null) - progressAndStage.setFinished(true); - - return groupsAfterClustering.stream().map(AtomicReference::get).collect(Collectors.toList()); - } - - public static CloneTagTupleList calculateTuples(CloneSet cloneset, int tagIndex) { - TObjectDoubleHashMap readsPerDroplet = newTObjectDoubleHashMap(); - - // Approximation: same UMIs in different clonotypes will be counted several times - TObjectLongHashMap umisPerDroplet = new TObjectLongHashMap<>(); - - for (Clone clone : cloneset) { - TObjectDoubleIterator it = clone.getTagCounter().iterator(); - while (it.hasNext()) { - it.advance(); - umisPerDroplet.adjustOrPutValue(it.key().tags[tagIndex], 1, 1); - readsPerDroplet.adjustOrPutValue(it.key().tags[tagIndex], it.value(), it.value()); - } - } - - List links = new ArrayList<>(); - for (Clone clone : cloneset) { - Map mlink = new HashMap<>(); - TObjectDoubleIterator it = clone.getTagCounter().iterator(); - while (it.hasNext()) { - it.advance(); - CloneTagTuple link = mlink.computeIfAbsent(it.key().tags[tagIndex], tag -> new CloneTagTuple(clone, tag)); - link.umiCount++; - link.readCount += it.value(); - } - // ArrayList alinks = new ArrayList<>(mlink.size()); - for (CloneTagTuple link : mlink.values()) { - link.readFractionInTag = link.readCount / readsPerDroplet.get(link.tag); - link.umiFractionInTag = 1.0 * link.umiCount / umisPerDroplet.get(link.tag); - links.add(link); - } - } - links.sort(Comparator. - comparingLong(l -> l.umiCount) - .thenComparingDouble(l -> l.readCount) - .reversed()); - TObjectIntHashMap rankCounter = new TObjectIntHashMap<>(); - for (CloneTagTuple link : links) - link.rank = rankCounter.adjustOrPutValue(link.tag, 1, 1); - - return new CloneTagTupleList(readsPerDroplet, umisPerDroplet, links); - } - - public static final class CloneTagTupleList { - final TObjectDoubleHashMap readsPerDroplet; - final TObjectLongHashMap umisPerDroplet; - final List tuples; - - public CloneTagTupleList(TObjectDoubleHashMap readsPerDroplet, - TObjectLongHashMap umisPerDroplet, - List tuples) { - this.readsPerDroplet = readsPerDroplet; - this.umisPerDroplet = umisPerDroplet; - this.tuples = tuples; - } - - public double readsTopQuantile(double quantile) { - if (quantile > 1.0 || quantile < 0) - throw new IllegalArgumentException(); - - double[] values = readsPerDroplet.values(); - if (values.length == 0) - return 0; - - Arrays.sort(values); - int index = (int) Math.floor(quantile * values.length); - if (index >= values.length) - index = values.length - 1; - - return values[index]; - } - - public double umisTopQuantile(double quantile) { - if (quantile > 1.0 || quantile < 0) - throw new IllegalArgumentException(); - - long[] values = umisPerDroplet.values(); - if (values.length == 0) - return 0; - - Arrays.sort(values); - int index = (int) Math.floor(quantile * values.length); - if (index >= values.length) - index = values.length - 1; - - return values[index]; - } - } - - static final class CliqueInfo implements Comparable { - final BitArrayInt clique; - final double score; - final double readCount; - - public CliqueInfo(BitArrayInt clique, double score, double readCount) { - this.clique = clique; - this.score = score; - this.readCount = readCount; - } - - @Override - public int compareTo(DropletCloneGraph.CliqueInfo o) { - int c = Double.compare(score, o.score); - if (c != 0) - return c; - return Double.compare(readCount, o.readCount); - } - } - -} +// public final class DropletCloneGraph { +// +// private static TIntIntHashMap newTIntIntHashMap() { +// return new TIntIntHashMap(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1, -1); +// } +// +// private static TObjectIntHashMap newTObjectIntHashMap() { +// return new TObjectIntHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); +// } +// +// private static TObjectDoubleHashMap newTObjectDoubleHashMap() { +// return new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, -1); +// } +// +// public static List calculateGroups(CloneTagTupleList tuplesList, +// DropletCloneGraphParameters parameters, +// DropletCloneGraphReport report, +// ProgressAndStage progressAndStage) { +// List tuples = parameters.filter.filter(tuplesList, report); +// Map> byTags = new HashMap<>(); +// TIntObjectHashMap> byCloneId = new TIntObjectHashMap<>(); +// List tmpList = new ArrayList<>(); +// for (CloneTagTuple tup : tuples) { +// byTags.computeIfAbsent(tup.tag, __ -> new ArrayList<>()).add(tup); +// List list = byCloneId.putIfAbsent(tup.clone.getId(), tmpList); +// if (list == null) { +// tmpList.add(tup); +// tmpList = new ArrayList<>(); +// } else +// list.add(tup); +// } +// +// ArrayList groups = new ArrayList<>(); +// +// long initialTagCount = byTags.size(); +// long counter = 0; +// +// int groupId = 0; +// // loop over connected components +// while (!byTags.isEmpty()) { +// Map> byTagsInComponent = new HashMap<>(); +// TIntObjectHashMap> byCloneIdInComponent = new TIntObjectHashMap<>(); +// +// // Calculating connected component starting from: +// // tag = byTags.keySet().iterator().next() +// { +// Set currentTags = new HashSet<>(); +// TIntHashSet currentClones = new TIntHashSet(); +// currentTags.add(byTags.keySet().iterator().next()); +// while (!currentTags.isEmpty()) { +// for (String currentTag : currentTags) { +// List inDroplet = byTags.remove(currentTag); +// if (inDroplet == null) +// continue; +// +// for (CloneTagTuple tup : inDroplet) { +// List list = byCloneIdInComponent.putIfAbsent(tup.clone.getId(), tmpList); +// if (list == null) { +// currentClones.add(tup.clone.getId()); +// tmpList.add(tup); +// tmpList = new ArrayList<>(); +// } else +// list.add(tup); +// } +// } +// currentTags.clear(); +// +// TIntIterator cIt = currentClones.iterator(); +// while (cIt.hasNext()) +// for (CloneTagTuple tup : byCloneId.remove(cIt.next())) { +// byTagsInComponent.computeIfAbsent(tup.tag, __ -> { +// currentTags.add(tup.tag); +// return new ArrayList<>(); +// }).add(tup); +// } +// currentClones.clear(); +// } +// } +// +// report.onConnectedComponent(byTagsInComponent, byCloneIdInComponent); +// +// // form adjacency matrix of connected tags +// AdjacencyMatrix tagMatrix = new AdjacencyMatrix(byTagsInComponent.size()); +// // tagId <-> tag +// TIntObjectHashMap indexToTag = new TIntObjectHashMap<>(); +// TObjectIntHashMap tagToIndex = newTObjectIntHashMap(); +// int idx = 0; +// for (String tag : byTagsInComponent.keySet()) { +// indexToTag.put(idx, tag); +// tagToIndex.put(tag, idx); +// ++idx; +// } +// +// for (int i = 0; i < indexToTag.size(); ++i) { +// tagMatrix.setConnected(i, i); +// for (CloneTagTuple tup : byTagsInComponent.get(indexToTag.get(i))) +// for (CloneTagTuple end : byCloneIdInComponent.get(tup.clone.getId())) +// tagMatrix.setConnected(i, tagToIndex.get(end.tag)); +// } +// +// List tagCliques = null; +// List tagCliqueInfos = null; +// // searching all cliques in tags +// while (!tagToIndex.isEmpty()) { +// if (tagCliques == null) { +// tagCliques = tagMatrix.calculateMaximalCliques(); +// tagCliqueInfos = new ArrayList<>(); +// for (BitArrayInt clique : tagCliques) { +// int[] bits = clique.getBits(); +// if (bits.length == 1 && !tagMatrix.isConnected(bits[0], bits[0])) +// continue; +// +// TIntIntHashMap nTagsByClones = newTIntIntHashMap(); +// +// double readCount = 0; +// for (int tagIndex : bits) +// for (CloneTagTuple tup : byTagsInComponent.get(indexToTag.get(tagIndex))) { +// nTagsByClones.adjustOrPutValue(tup.clone.getId(), 1, 1); +// readCount += tup.readCount; +// } +// +// +// TIntIntIterator it = nTagsByClones.iterator(); +// double score = 0; +// while (it.hasNext()) { +// it.advance(); +// int count = it.value(); +// +// score += Math.pow(count - 1, parameters.tagCliqueScorePower); +// } +// +// tagCliqueInfos.add(new CliqueInfo(clique, score, readCount)); +// } +// } +// +// Optional topTagCliqueO = tagCliqueInfos.stream().max(CliqueInfo::compareTo); +// if (!topTagCliqueO.isPresent()) +// break; +// +// CliqueInfo topTagClique = topTagCliqueO.get(); +// +// Set tags = new HashSet<>(); +// int[] topTagCliqueBits = topTagClique.clique.getBits(); +// for (int i : topTagCliqueBits) +// tags.add(indexToTag.get(i)); +// +// TIntIntHashMap indexToCloneId = newTIntIntHashMap(); +// // !!! used as cloneId -> count in the loop below +// TIntIntHashMap cloneIdToIndex = newTIntIntHashMap(); +// +// { +// for (String tag : tags) +// for (CloneTagTuple tup : byTagsInComponent.get(tag)) +// cloneIdToIndex.adjustOrPutValue(tup.clone.getId(), 1, 1); +// +// idx = 0; +// TIntIntIterator it = cloneIdToIndex.iterator(); +// while (it.hasNext()) { +// it.advance(); +// assert it.value() > 0; +// // if tags.size == 1 => single tag in clique, so just writing +// // index (presence of clones is enough, i.e. do not require clones to link any tags) +// if (tags.size() > 1 && it.value() == 1) +// it.remove(); +// else { +// indexToCloneId.put(idx, it.key()); +// it.setValue(idx); +// ++idx; +// } +// } +// } +// +// AdjacencyMatrix clonesMatrix = new AdjacencyMatrix(cloneIdToIndex.size()); +// +// for (String tag : tags) { +// List tuplesForTag = byTagsInComponent.get(tag); +// for (int i1 = 0; i1 < tuplesForTag.size(); i1++) +// for (int i2 = i1 + 1; i2 < tuplesForTag.size(); i2++) { +// int index1 = cloneIdToIndex.get(tuplesForTag.get(i1).clone.getId()); +// int index2 = cloneIdToIndex.get(tuplesForTag.get(i2).clone.getId()); +// if (index1 >= 0 && index2 >= 0) +// clonesMatrix.setConnected(index1, index2); +// } +// } +// +// List cloneCliques = clonesMatrix.calculateMaximalCliques(); +// List cloneCliqueInfos = new ArrayList<>(); +// +// for (BitArrayInt clique : cloneCliques) { +// TObjectIntHashMap nClonesByTags = newTObjectIntHashMap(); +// +// double readCount = 0; +// for (int cloneIndex : clique.getBits()) +// for (CloneTagTuple tup : byCloneIdInComponent.get(indexToCloneId.get(cloneIndex))) +// if (tags.contains(tup.tag)) { +// nClonesByTags.adjustOrPutValue(tup.tag, 1, 1); +// readCount += tup.readCount; +// } +// +// TObjectIntIterator it = nClonesByTags.iterator(); +// double score = 0; +// while (it.hasNext()) { +// it.advance(); +// int count = it.value(); +// +// score += Math.pow(count - 1, parameters.cloneCliqueScorePower); +// } +// +// cloneCliqueInfos.add(new CliqueInfo(clique, score, readCount)); +// } +// +// CliqueInfo topCloneClique = cloneCliqueInfos.stream().max(CliqueInfo::compareTo).get(); +// +// // dropping tags +// +// Set groupTags = new HashSet<>(); +// TIntHashSet groupClones = new TIntHashSet(); +// +// for (int cloneIdx : topCloneClique.clique.getBits()) { +// for (CloneTagTuple tup : byCloneIdInComponent.get(indexToCloneId.get(cloneIdx))) { +// if (tags.contains(tup.tag)) { +// String tag = tup.tag; +// +// int index = tagToIndex.remove(tag); +// ++counter; +// if (progressAndStage != null) +// progressAndStage.setProgress(1.0 * counter / initialTagCount); +// +// if (index >= 0) { +// indexToTag.remove(index); +// tagMatrix.clear(index); +// } +// +// groupClones.add(tup.clone.getId()); +// groupTags.add(tag); +// } +// } +// } +// +// double readTotal = 0.0; +// long umiTotal = 0; +// +// for (String tag : groupTags) +// for (CloneTagTuple ctt : byTagsInComponent.get(tag)) { +// readTotal += ctt.readCount; +// umiTotal += ctt.umiCount; +// } +// +// CloneGroup group = new CloneGroup(groupId, readTotal, umiTotal, groupTags, groupClones); +// report.onGroup(topTagClique, topCloneClique, group); +// groups.add(group); +// +// tagCliques = null; +// +// ++groupId; +// } +// } +// +// // Clustering +// TIntObjectHashMap>> byClones = new TIntObjectHashMap<>(); +// groups.sort(Comparator +// .comparingInt(c -> c.groupClones.size()) +// .thenComparingInt(c -> c.groupTags.size()) +// .reversed()); +// +// ArrayList> groupsAfterClustering = new ArrayList<>(); +// ArrayList> tmpList2 = new ArrayList<>(); +// for (CloneGroup minor : groups) { +// // Major candidates +// Set> majorCandidates = Collections.newSetFromMap(new IdentityHashMap<>()); +// int[] minorCloneIds = minor.groupClones.toArray(); +// for (int cId : minorCloneIds) { +// List> grps = byClones.get(cId); +// if (grps == null) +// break; // This guarantees that no candidates will be found (such clone was never seen before) +// for (AtomicReference preCandidate : grps) +// if (preCandidate.get().groupClones.containsAll(minor.groupClones) +// && 1.0 * minor.groupTags.size() / preCandidate.get().groupTags.size() <= parameters.maxTagCountRatio) +// majorCandidates.add(preCandidate); +// } +// if (majorCandidates.size() != 1) { +// AtomicReference minorRef = new AtomicReference<>(minor); +// groupsAfterClustering.add(minorRef); +// for (int cId : minorCloneIds) { +// List> cloneGroups = byClones.putIfAbsent(cId, tmpList2); +// if (cloneGroups != null) +// cloneGroups.add(minorRef); +// else { +// tmpList2.add(minorRef); +// tmpList2 = new ArrayList<>(); +// } +// } +// } else { // Clustering +// AtomicReference majorRef = majorCandidates.iterator().next(); +// report.onClustered(majorRef.get(), minor); +// majorRef.set(majorRef.get().mergeFrom(minor)); +// } +// } +// +// if (progressAndStage != null) +// progressAndStage.setFinished(true); +// +// return groupsAfterClustering.stream().map(AtomicReference::get).collect(Collectors.toList()); +// } +// +// public static CloneTagTupleList calculateTuples(CloneSet cloneset, int tagIndex) { +// TObjectDoubleHashMap readsPerDroplet = newTObjectDoubleHashMap(); +// +// // Approximation: same UMIs in different clonotypes will be counted several times +// TObjectLongHashMap umisPerDroplet = new TObjectLongHashMap<>(); +// +// for (Clone clone : cloneset) { +// TObjectDoubleIterator it = clone.getTagCounter().iterator(); +// while (it.hasNext()) { +// it.advance(); +// umisPerDroplet.adjustOrPutValue(it.key().tags[tagIndex], 1, 1); +// readsPerDroplet.adjustOrPutValue(it.key().tags[tagIndex], it.value(), it.value()); +// } +// } +// +// List links = new ArrayList<>(); +// for (Clone clone : cloneset) { +// Map mlink = new HashMap<>(); +// TObjectDoubleIterator it = clone.getTagCounter().iterator(); +// while (it.hasNext()) { +// it.advance(); +// CloneTagTuple link = mlink.computeIfAbsent(it.key().tags[tagIndex], tag -> new CloneTagTuple(clone, tag)); +// link.umiCount++; +// link.readCount += it.value(); +// } +// // ArrayList alinks = new ArrayList<>(mlink.size()); +// for (CloneTagTuple link : mlink.values()) { +// link.readFractionInTag = link.readCount / readsPerDroplet.get(link.tag); +// link.umiFractionInTag = 1.0 * link.umiCount / umisPerDroplet.get(link.tag); +// links.add(link); +// } +// } +// links.sort(Comparator. +// comparingLong(l -> l.umiCount) +// .thenComparingDouble(l -> l.readCount) +// .reversed()); +// TObjectIntHashMap rankCounter = new TObjectIntHashMap<>(); +// for (CloneTagTuple link : links) +// link.rank = rankCounter.adjustOrPutValue(link.tag, 1, 1); +// +// return new CloneTagTupleList(readsPerDroplet, umisPerDroplet, links); +// } +// +// public static final class CloneTagTupleList { +// final TObjectDoubleHashMap readsPerDroplet; +// final TObjectLongHashMap umisPerDroplet; +// final List tuples; +// +// public CloneTagTupleList(TObjectDoubleHashMap readsPerDroplet, +// TObjectLongHashMap umisPerDroplet, +// List tuples) { +// this.readsPerDroplet = readsPerDroplet; +// this.umisPerDroplet = umisPerDroplet; +// this.tuples = tuples; +// } +// +// public double readsTopQuantile(double quantile) { +// if (quantile > 1.0 || quantile < 0) +// throw new IllegalArgumentException(); +// +// double[] values = readsPerDroplet.values(); +// if (values.length == 0) +// return 0; +// +// Arrays.sort(values); +// int index = (int) Math.floor(quantile * values.length); +// if (index >= values.length) +// index = values.length - 1; +// +// return values[index]; +// } +// +// public double umisTopQuantile(double quantile) { +// if (quantile > 1.0 || quantile < 0) +// throw new IllegalArgumentException(); +// +// long[] values = umisPerDroplet.values(); +// if (values.length == 0) +// return 0; +// +// Arrays.sort(values); +// int index = (int) Math.floor(quantile * values.length); +// if (index >= values.length) +// index = values.length - 1; +// +// return values[index]; +// } +// } +// +// static final class CliqueInfo implements Comparable { +// final BitArrayInt clique; +// final double score; +// final double readCount; +// +// public CliqueInfo(BitArrayInt clique, double score, double readCount) { +// this.clique = clique; +// this.score = score; +// this.readCount = readCount; +// } +// +// @Override +// public int compareTo(DropletCloneGraph.CliqueInfo o) { +// int c = Double.compare(score, o.score); +// if (c != 0) +// return c; +// return Double.compare(readCount, o.readCount); +// } +// } +// +// } diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java index 868e876c9..480fc495a 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java @@ -29,54 +29,47 @@ */ package com.milaboratory.mixcr.tags; -import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonProperty; -import com.milaboratory.util.GlobalObjectMappers; - -import java.io.IOException; -import java.util.Objects; - -public class DropletCloneGraphParameters { - @JsonProperty("tagCliqueScorePower") - public final double tagCliqueScorePower; - @JsonProperty("cloneCliqueScorePower") - public final double cloneCliqueScorePower; - @JsonProperty("filter") - public final CloneTagTupleFilter filter; - @JsonProperty("maxTagCountRatio") - public final double maxTagCountRatio; - - @JsonCreator - public DropletCloneGraphParameters(@JsonProperty("tagCliqueScorePower") double tagCliqueScorePower, - @JsonProperty("cloneCliqueScorePower") double cloneCliqueScorePower, - @JsonProperty("filter") CloneTagTupleFilter filter, - @JsonProperty("maxTagCountRatio") double maxTagCountRatio) { - this.tagCliqueScorePower = tagCliqueScorePower; - this.cloneCliqueScorePower = cloneCliqueScorePower; - this.filter = filter; - this.maxTagCountRatio = maxTagCountRatio; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - DropletCloneGraphParameters that = (DropletCloneGraphParameters) o; - return Double.compare(that.tagCliqueScorePower, tagCliqueScorePower) == 0 && - Double.compare(that.cloneCliqueScorePower, cloneCliqueScorePower) == 0 && - Objects.equals(filter, that.filter); - } - - @Override - public int hashCode() { - return Objects.hash(tagCliqueScorePower, cloneCliqueScorePower, filter); - } - - public static DropletCloneGraphParameters getDefault() { - try { - return GlobalObjectMappers.ONE_LINE.readValue(CloneTagTupleFilter.class.getClassLoader().getResourceAsStream("parameters/droplet_clone_graph_parameters.json"), DropletCloneGraphParameters.class); - } catch (IOException e) { - throw new RuntimeException(e); - } - } -} +// public class DropletCloneGraphParameters { +// @JsonProperty("tagCliqueScorePower") +// public final double tagCliqueScorePower; +// @JsonProperty("cloneCliqueScorePower") +// public final double cloneCliqueScorePower; +// @JsonProperty("filter") +// public final CloneTagTupleFilter filter; +// @JsonProperty("maxTagCountRatio") +// public final double maxTagCountRatio; +// +// @JsonCreator +// public DropletCloneGraphParameters(@JsonProperty("tagCliqueScorePower") double tagCliqueScorePower, +// @JsonProperty("cloneCliqueScorePower") double cloneCliqueScorePower, +// @JsonProperty("filter") CloneTagTupleFilter filter, +// @JsonProperty("maxTagCountRatio") double maxTagCountRatio) { +// this.tagCliqueScorePower = tagCliqueScorePower; +// this.cloneCliqueScorePower = cloneCliqueScorePower; +// this.filter = filter; +// this.maxTagCountRatio = maxTagCountRatio; +// } +// +// @Override +// public boolean equals(Object o) { +// if (this == o) return true; +// if (o == null || getClass() != o.getClass()) return false; +// DropletCloneGraphParameters that = (DropletCloneGraphParameters) o; +// return Double.compare(that.tagCliqueScorePower, tagCliqueScorePower) == 0 && +// Double.compare(that.cloneCliqueScorePower, cloneCliqueScorePower) == 0 && +// Objects.equals(filter, that.filter); +// } +// +// @Override +// public int hashCode() { +// return Objects.hash(tagCliqueScorePower, cloneCliqueScorePower, filter); +// } +// +// public static DropletCloneGraphParameters getDefault() { +// try { +// return GlobalObjectMappers.ONE_LINE.readValue(CloneTagTupleFilter.class.getClassLoader().getResourceAsStream("parameters/droplet_clone_graph_parameters.json"), DropletCloneGraphParameters.class); +// } catch (IOException e) { +// throw new RuntimeException(e); +// } +// } +// } diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java index 301bdde32..2971fb23c 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java @@ -42,346 +42,346 @@ import java.util.concurrent.atomic.AtomicInteger; import java.util.concurrent.atomic.AtomicLong; -public class DropletCloneGraphReport implements Report { - final AtomicInteger - clonesBefore = new AtomicInteger(), - connectedComponents = new AtomicInteger(), - maxClonesInConnectedComponents = new AtomicInteger(), - maxTagsInConnectedComponents = new AtomicInteger(), - numberOfGroups = new AtomicInteger(), - maxTagsClique = new AtomicInteger(), - maxTagsCliqueDelta = new AtomicInteger(), - sumTagsCliqueDelta = new AtomicInteger(), - maxClonesPerGroup = new AtomicInteger(), - sumClonesPerGroup = new AtomicInteger(), - maxTagsPerGroup = new AtomicInteger(), - sumTagsPerGroup = new AtomicInteger(), - ungroupedClones = new AtomicInteger(), - groupedClonesBefore = new AtomicInteger(), - groupedClonesAfter = new AtomicInteger(); - - final AtomicLong - maxUMIsInConnectedComponents = new AtomicLong(), - sumUMIs = new AtomicLong(); - - final AtomicDouble - readsBefore = new AtomicDouble(), - readsInUngroupedClones = new AtomicDouble(), - readsInGroupedClones = new AtomicDouble(), - maxReadsInConnectedComponents = new AtomicDouble(), - sumReads = new AtomicDouble(); - - public void onConnectedComponent(Map> byTagsInComponent, - TIntObjectHashMap> byCloneIdInComponent) { - connectedComponents.incrementAndGet(); - - maxClonesInConnectedComponents.accumulateAndGet(byCloneIdInComponent.size(), Integer::max); - maxTagsInConnectedComponents.accumulateAndGet(byTagsInComponent.size(), Integer::max); - - double reads = 0; - long umis = 0; - for (List list : byTagsInComponent.values()) - for (CloneTagTuple tt : list) { - reads += tt.readCount; - umis += tt.umiCount; - } - - double val; - do { - val = maxReadsInConnectedComponents.get(); - } while (!maxReadsInConnectedComponents.compareAndSet(val, Double.max(val, reads))); - - maxUMIsInConnectedComponents.accumulateAndGet(umis, Long::max); - - sumReads.addAndGet(reads); - sumUMIs.addAndGet(umis); - } - - public void before(CloneSet cs) { - clonesBefore.set(cs.size()); - readsBefore.set(cs.getTotalCount()); - } - - public void onUngroupedClone(Clone c) { - ungroupedClones.incrementAndGet(); - readsInUngroupedClones.addAndGet(c.getCount()); - } - - public void onCloneBeforeSplit(Clone c) { - groupedClonesBefore.incrementAndGet(); - } - - public void onGroupedClone(Clone c) { - readsInGroupedClones.addAndGet(c.getCount()); - groupedClonesAfter.incrementAndGet(); - } - - public void onGroup(DropletCloneGraph.CliqueInfo topTagClique, DropletCloneGraph.CliqueInfo topCloneClique, - CloneGroup group) { - numberOfGroups.incrementAndGet(); - maxTagsClique.accumulateAndGet(topTagClique.clique.bitCount(), Integer::max); - - int tagsCliqueDelta = topTagClique.clique.bitCount() - group.groupTags.size(); - maxTagsCliqueDelta.accumulateAndGet(tagsCliqueDelta, Integer::max); - sumTagsCliqueDelta.addAndGet(tagsCliqueDelta); - - maxClonesPerGroup.accumulateAndGet(group.groupClones.size(), Integer::max); - sumClonesPerGroup.addAndGet(group.groupClones.size()); - - maxTagsPerGroup.accumulateAndGet(group.groupTags.size(), Integer::max); - sumTagsPerGroup.addAndGet(group.groupTags.size()); - } - - public void onClustered(CloneGroup major, CloneGroup minor) { - groupsClustered.incrementAndGet(); - readsClustered.addAndGet(minor.reads); - unisClustered.addAndGet(minor.umis); - tagsClustered.addAndGet(minor.groupTags.size()); - } - - double - effectiveMinReadsInTag = Double.NaN, - effectiveMinUMIsInTag = Double.NaN; - - final AtomicInteger - tagTuplesTotal = new AtomicInteger(), - tagTuplesFiltered = new AtomicInteger(), - tagsTotal = new AtomicInteger(), - tagsFiltered = new AtomicInteger(), - tagsClustered = new AtomicInteger(), - groupsClustered = new AtomicInteger(); - - final AtomicDouble - readsTotal = new AtomicDouble(), - readsFiltered = new AtomicDouble(), - readsClustered = new AtomicDouble(); - - final AtomicLong - umisTotal = new AtomicLong(), - umisFiltered = new AtomicLong(), - unisClustered = new AtomicLong(); - - @JsonProperty("clonesBefore") - public int getClonesBefore() { - return clonesBefore.get(); - } - - @JsonProperty("connectedComponents") - public int getConnectedComponents() { - return connectedComponents.get(); - } - - @JsonProperty("maxClonesInConnectedComponents") - public int getMaxClonesInConnectedComponents() { - return maxClonesInConnectedComponents.get(); - } - - @JsonProperty("maxTagsInConnectedComponents") - public int getMaxTagsInConnectedComponents() { - return maxTagsInConnectedComponents.get(); - } - - @JsonProperty("numberOfGroups") - public int getNumberOfGroups() { - return numberOfGroups.get(); - } - - @JsonProperty("maxTagsClique") - public int getMaxTagsClique() { - return maxTagsClique.get(); - } - - @JsonProperty("maxTagsCliqueDelta") - public int getMaxTagsCliqueDelta() { - return maxTagsCliqueDelta.get(); - } - - @JsonProperty("sumTagsCliqueDelta") - public int getSumTagsCliqueDelta() { - return sumTagsCliqueDelta.get(); - } - - @JsonProperty("maxClonesPerGroup") - public int getMaxClonesPerGroup() { - return maxClonesPerGroup.get(); - } - - @JsonProperty("sumClonesPerGroup") - public int getSumClonesPerGroup() { - return sumClonesPerGroup.get(); - } - - @JsonProperty("maxTagsPerGroup") - public int getMaxTagsPerGroup() { - return maxTagsPerGroup.get(); - } - - @JsonProperty("sumTagsPerGroup") - public int getSumTagsPerGroup() { - return sumTagsPerGroup.get(); - } - - @JsonProperty("ungroupedClones") - public int getUngroupedClones() { - return ungroupedClones.get(); - } - - @JsonProperty("groupedClonesBefore") - public int getGroupedClonesBefore() { - return groupedClonesBefore.get(); - } - - @JsonProperty("groupedClonesAfter") - public int getGroupedClonesAfter() { - return groupedClonesAfter.get(); - } - - @JsonProperty("maxUMIsInConnectedComponents") - public long getMaxUMIsInConnectedComponents() { - return maxUMIsInConnectedComponents.get(); - } - - @JsonProperty("sumUMIs") - public long getSumUMIs() { - return sumUMIs.get(); - } - - @JsonProperty("readsBefore") - public double getReadsBefore() { - return readsBefore.get(); - } - - @JsonProperty("readsInUngroupedClones") - public double getReadsInUngroupedClones() { - return readsInUngroupedClones.get(); - } - - @JsonProperty("readsInGroupedClones") - public double getReadsInGroupedClones() { - return readsInGroupedClones.get(); - } - - @JsonProperty("maxReadsInConnectedComponents") - public double getMaxReadsInConnectedComponents() { - return maxReadsInConnectedComponents.get(); - } - - @JsonProperty("sumReads") - public double getSumReads() { - return sumReads.get(); - } - - @JsonProperty("effectiveMinReadsInTag") - public double getEffectiveMinReadsInTag() { - return effectiveMinReadsInTag; - } - - @JsonProperty("effectiveMinUMIsInTag") - public double getEffectiveMinUMIsInTag() { - return effectiveMinUMIsInTag; - } - - @JsonProperty("tagTuplesTotal") - public int getTagTuplesTotal() { - return tagTuplesTotal.get(); - } - - @JsonProperty("tagTuplesFiltered") - public int getTagTuplesFiltered() { - return tagTuplesFiltered.get(); - } - - @JsonProperty("tagsTotal") - public int getTagsTotal() { - return tagsTotal.get(); - } - - @JsonProperty("tagsFiltered") - public int getTagsFiltered() { - return tagsFiltered.get(); - } - - @JsonProperty("readsTotal") - public double getReadsTotal() { - return readsTotal.get(); - } - - @JsonProperty("readsFiltered") - public double getReadsFiltered() { - return readsFiltered.get(); - } - - @JsonProperty("umisTotal") - public long getUmisTotal() { - return umisTotal.get(); - } - - @JsonProperty("umisFiltered") - public long getUmisFiltered() { - return umisFiltered.get(); - } - - @JsonProperty("tagsClustered") - public int getTagsClustered() { - return tagsClustered.get(); - } - - @JsonProperty("groupsClustered") - public int getGroupsClustered() { - return groupsClustered.get(); - } - - @JsonProperty("readsClustered") - public double getReadsClustered() { - return readsClustered.get(); - } - - @JsonProperty("unisClustered") - public long getUnisClustered() { - return unisClustered.get(); - } - - @Override - public void writeReport(ReportHelper helper) { - int finalClones = ungroupedClones.get() + groupedClonesAfter.get(); - - helper - .writePercentAndAbsoluteField("Clones after grouping", finalClones, clonesBefore.get()) - .writePercentAndAbsoluteField("Ungrouped clones", ungroupedClones.get(), finalClones) - .writePercentAndAbsoluteField("Clones split", groupedClonesAfter.get(), groupedClonesBefore.get()) - .writePercentAndAbsoluteField("Reads in ungrouped clones", (long) readsInUngroupedClones.get(), readsBefore.get()); - - helper - .writePercentAndAbsoluteField("Clone Tag associations after filtering", tagTuplesFiltered.get(), tagTuplesTotal.get()) - .writePercentAndAbsoluteField("Tags after filtering", tagsFiltered.get(), tagsTotal.get()) - .writePercentAndAbsoluteField("Reads after filtering", readsFiltered.get(), readsTotal.get()) - .writePercentAndAbsoluteField("UMIs after filtering", umisFiltered.get(), umisTotal.get()); - - helper - .writeField("Connected components (CC)", connectedComponents.get()) - .writePercentAndAbsoluteField("Clones in max CC", maxClonesInConnectedComponents.get(), sumClonesPerGroup.get()) - .writePercentAndAbsoluteField("Reads in max CC", maxReadsInConnectedComponents.get(), sumReads.get()) - .writePercentAndAbsoluteField("UMIs in max CC", maxUMIsInConnectedComponents.get(), sumUMIs.get()); - - helper - .writeField("Groups", numberOfGroups.get() - groupsClustered.get()) - .writeField("Groups before clustering", numberOfGroups.get()) - .writeField("Max clones per group", maxClonesPerGroup.get()) - .writeField("Mean clones per group", ReportHelper.PERCENT_FORMAT.format(1.0 * sumClonesPerGroup.get() / numberOfGroups.get())) - .writeField("Max tags per group", maxTagsPerGroup.get()) - .writeField("Mean tags per group", ReportHelper.PERCENT_FORMAT.format(1.0 * sumTagsPerGroup.get() / numberOfGroups.get())) - .writeField("Max tags clique", maxTagsClique.get()) - .writeField("Max tags clique delta", maxTagsCliqueDelta.get()) - .writeField("Mean tags clique delta", ReportHelper.PERCENT_FORMAT.format(1.0 * sumTagsCliqueDelta.get() / numberOfGroups.get())); - - helper - .writePercentAndAbsoluteField("Groups clustered", groupsClustered.get(), numberOfGroups.get()) - .writePercentAndAbsoluteField("Tags clustered", tagsClustered.get(), tagsTotal.get()) - .writePercentAndAbsoluteField("Reads clustered", readsClustered.get(), readsTotal.get()) - .writePercentAndAbsoluteField("UMIs clustered", unisClustered.get(), umisTotal.get()); - - helper - .writeField("Effective reads in tags threshold", effectiveMinReadsInTag) - .writeField("Effective UMIs in tags threshold", effectiveMinUMIsInTag); - } -} +// public class DropletCloneGraphReport implements Report { +// final AtomicInteger +// clonesBefore = new AtomicInteger(), +// connectedComponents = new AtomicInteger(), +// maxClonesInConnectedComponents = new AtomicInteger(), +// maxTagsInConnectedComponents = new AtomicInteger(), +// numberOfGroups = new AtomicInteger(), +// maxTagsClique = new AtomicInteger(), +// maxTagsCliqueDelta = new AtomicInteger(), +// sumTagsCliqueDelta = new AtomicInteger(), +// maxClonesPerGroup = new AtomicInteger(), +// sumClonesPerGroup = new AtomicInteger(), +// maxTagsPerGroup = new AtomicInteger(), +// sumTagsPerGroup = new AtomicInteger(), +// ungroupedClones = new AtomicInteger(), +// groupedClonesBefore = new AtomicInteger(), +// groupedClonesAfter = new AtomicInteger(); +// +// final AtomicLong +// maxUMIsInConnectedComponents = new AtomicLong(), +// sumUMIs = new AtomicLong(); +// +// final AtomicDouble +// readsBefore = new AtomicDouble(), +// readsInUngroupedClones = new AtomicDouble(), +// readsInGroupedClones = new AtomicDouble(), +// maxReadsInConnectedComponents = new AtomicDouble(), +// sumReads = new AtomicDouble(); +// +// public void onConnectedComponent(Map> byTagsInComponent, +// TIntObjectHashMap> byCloneIdInComponent) { +// connectedComponents.incrementAndGet(); +// +// maxClonesInConnectedComponents.accumulateAndGet(byCloneIdInComponent.size(), Integer::max); +// maxTagsInConnectedComponents.accumulateAndGet(byTagsInComponent.size(), Integer::max); +// +// double reads = 0; +// long umis = 0; +// for (List list : byTagsInComponent.values()) +// for (CloneTagTuple tt : list) { +// reads += tt.readCount; +// umis += tt.umiCount; +// } +// +// double val; +// do { +// val = maxReadsInConnectedComponents.get(); +// } while (!maxReadsInConnectedComponents.compareAndSet(val, Double.max(val, reads))); +// +// maxUMIsInConnectedComponents.accumulateAndGet(umis, Long::max); +// +// sumReads.addAndGet(reads); +// sumUMIs.addAndGet(umis); +// } +// +// public void before(CloneSet cs) { +// clonesBefore.set(cs.size()); +// readsBefore.set(cs.getTotalCount()); +// } +// +// public void onUngroupedClone(Clone c) { +// ungroupedClones.incrementAndGet(); +// readsInUngroupedClones.addAndGet(c.getCount()); +// } +// +// public void onCloneBeforeSplit(Clone c) { +// groupedClonesBefore.incrementAndGet(); +// } +// +// public void onGroupedClone(Clone c) { +// readsInGroupedClones.addAndGet(c.getCount()); +// groupedClonesAfter.incrementAndGet(); +// } +// +// public void onGroup(DropletCloneGraph.CliqueInfo topTagClique, DropletCloneGraph.CliqueInfo topCloneClique, +// CloneGroup group) { +// numberOfGroups.incrementAndGet(); +// maxTagsClique.accumulateAndGet(topTagClique.clique.bitCount(), Integer::max); +// +// int tagsCliqueDelta = topTagClique.clique.bitCount() - group.groupTags.size(); +// maxTagsCliqueDelta.accumulateAndGet(tagsCliqueDelta, Integer::max); +// sumTagsCliqueDelta.addAndGet(tagsCliqueDelta); +// +// maxClonesPerGroup.accumulateAndGet(group.groupClones.size(), Integer::max); +// sumClonesPerGroup.addAndGet(group.groupClones.size()); +// +// maxTagsPerGroup.accumulateAndGet(group.groupTags.size(), Integer::max); +// sumTagsPerGroup.addAndGet(group.groupTags.size()); +// } +// +// public void onClustered(CloneGroup major, CloneGroup minor) { +// groupsClustered.incrementAndGet(); +// readsClustered.addAndGet(minor.reads); +// unisClustered.addAndGet(minor.umis); +// tagsClustered.addAndGet(minor.groupTags.size()); +// } +// +// double +// effectiveMinReadsInTag = Double.NaN, +// effectiveMinUMIsInTag = Double.NaN; +// +// final AtomicInteger +// tagTuplesTotal = new AtomicInteger(), +// tagTuplesFiltered = new AtomicInteger(), +// tagsTotal = new AtomicInteger(), +// tagsFiltered = new AtomicInteger(), +// tagsClustered = new AtomicInteger(), +// groupsClustered = new AtomicInteger(); +// +// final AtomicDouble +// readsTotal = new AtomicDouble(), +// readsFiltered = new AtomicDouble(), +// readsClustered = new AtomicDouble(); +// +// final AtomicLong +// umisTotal = new AtomicLong(), +// umisFiltered = new AtomicLong(), +// unisClustered = new AtomicLong(); +// +// @JsonProperty("clonesBefore") +// public int getClonesBefore() { +// return clonesBefore.get(); +// } +// +// @JsonProperty("connectedComponents") +// public int getConnectedComponents() { +// return connectedComponents.get(); +// } +// +// @JsonProperty("maxClonesInConnectedComponents") +// public int getMaxClonesInConnectedComponents() { +// return maxClonesInConnectedComponents.get(); +// } +// +// @JsonProperty("maxTagsInConnectedComponents") +// public int getMaxTagsInConnectedComponents() { +// return maxTagsInConnectedComponents.get(); +// } +// +// @JsonProperty("numberOfGroups") +// public int getNumberOfGroups() { +// return numberOfGroups.get(); +// } +// +// @JsonProperty("maxTagsClique") +// public int getMaxTagsClique() { +// return maxTagsClique.get(); +// } +// +// @JsonProperty("maxTagsCliqueDelta") +// public int getMaxTagsCliqueDelta() { +// return maxTagsCliqueDelta.get(); +// } +// +// @JsonProperty("sumTagsCliqueDelta") +// public int getSumTagsCliqueDelta() { +// return sumTagsCliqueDelta.get(); +// } +// +// @JsonProperty("maxClonesPerGroup") +// public int getMaxClonesPerGroup() { +// return maxClonesPerGroup.get(); +// } +// +// @JsonProperty("sumClonesPerGroup") +// public int getSumClonesPerGroup() { +// return sumClonesPerGroup.get(); +// } +// +// @JsonProperty("maxTagsPerGroup") +// public int getMaxTagsPerGroup() { +// return maxTagsPerGroup.get(); +// } +// +// @JsonProperty("sumTagsPerGroup") +// public int getSumTagsPerGroup() { +// return sumTagsPerGroup.get(); +// } +// +// @JsonProperty("ungroupedClones") +// public int getUngroupedClones() { +// return ungroupedClones.get(); +// } +// +// @JsonProperty("groupedClonesBefore") +// public int getGroupedClonesBefore() { +// return groupedClonesBefore.get(); +// } +// +// @JsonProperty("groupedClonesAfter") +// public int getGroupedClonesAfter() { +// return groupedClonesAfter.get(); +// } +// +// @JsonProperty("maxUMIsInConnectedComponents") +// public long getMaxUMIsInConnectedComponents() { +// return maxUMIsInConnectedComponents.get(); +// } +// +// @JsonProperty("sumUMIs") +// public long getSumUMIs() { +// return sumUMIs.get(); +// } +// +// @JsonProperty("readsBefore") +// public double getReadsBefore() { +// return readsBefore.get(); +// } +// +// @JsonProperty("readsInUngroupedClones") +// public double getReadsInUngroupedClones() { +// return readsInUngroupedClones.get(); +// } +// +// @JsonProperty("readsInGroupedClones") +// public double getReadsInGroupedClones() { +// return readsInGroupedClones.get(); +// } +// +// @JsonProperty("maxReadsInConnectedComponents") +// public double getMaxReadsInConnectedComponents() { +// return maxReadsInConnectedComponents.get(); +// } +// +// @JsonProperty("sumReads") +// public double getSumReads() { +// return sumReads.get(); +// } +// +// @JsonProperty("effectiveMinReadsInTag") +// public double getEffectiveMinReadsInTag() { +// return effectiveMinReadsInTag; +// } +// +// @JsonProperty("effectiveMinUMIsInTag") +// public double getEffectiveMinUMIsInTag() { +// return effectiveMinUMIsInTag; +// } +// +// @JsonProperty("tagTuplesTotal") +// public int getTagTuplesTotal() { +// return tagTuplesTotal.get(); +// } +// +// @JsonProperty("tagTuplesFiltered") +// public int getTagTuplesFiltered() { +// return tagTuplesFiltered.get(); +// } +// +// @JsonProperty("tagsTotal") +// public int getTagsTotal() { +// return tagsTotal.get(); +// } +// +// @JsonProperty("tagsFiltered") +// public int getTagsFiltered() { +// return tagsFiltered.get(); +// } +// +// @JsonProperty("readsTotal") +// public double getReadsTotal() { +// return readsTotal.get(); +// } +// +// @JsonProperty("readsFiltered") +// public double getReadsFiltered() { +// return readsFiltered.get(); +// } +// +// @JsonProperty("umisTotal") +// public long getUmisTotal() { +// return umisTotal.get(); +// } +// +// @JsonProperty("umisFiltered") +// public long getUmisFiltered() { +// return umisFiltered.get(); +// } +// +// @JsonProperty("tagsClustered") +// public int getTagsClustered() { +// return tagsClustered.get(); +// } +// +// @JsonProperty("groupsClustered") +// public int getGroupsClustered() { +// return groupsClustered.get(); +// } +// +// @JsonProperty("readsClustered") +// public double getReadsClustered() { +// return readsClustered.get(); +// } +// +// @JsonProperty("unisClustered") +// public long getUnisClustered() { +// return unisClustered.get(); +// } +// +// @Override +// public void writeReport(ReportHelper helper) { +// int finalClones = ungroupedClones.get() + groupedClonesAfter.get(); +// +// helper +// .writePercentAndAbsoluteField("Clones after grouping", finalClones, clonesBefore.get()) +// .writePercentAndAbsoluteField("Ungrouped clones", ungroupedClones.get(), finalClones) +// .writePercentAndAbsoluteField("Clones split", groupedClonesAfter.get(), groupedClonesBefore.get()) +// .writePercentAndAbsoluteField("Reads in ungrouped clones", (long) readsInUngroupedClones.get(), readsBefore.get()); +// +// helper +// .writePercentAndAbsoluteField("Clone Tag associations after filtering", tagTuplesFiltered.get(), tagTuplesTotal.get()) +// .writePercentAndAbsoluteField("Tags after filtering", tagsFiltered.get(), tagsTotal.get()) +// .writePercentAndAbsoluteField("Reads after filtering", readsFiltered.get(), readsTotal.get()) +// .writePercentAndAbsoluteField("UMIs after filtering", umisFiltered.get(), umisTotal.get()); +// +// helper +// .writeField("Connected components (CC)", connectedComponents.get()) +// .writePercentAndAbsoluteField("Clones in max CC", maxClonesInConnectedComponents.get(), sumClonesPerGroup.get()) +// .writePercentAndAbsoluteField("Reads in max CC", maxReadsInConnectedComponents.get(), sumReads.get()) +// .writePercentAndAbsoluteField("UMIs in max CC", maxUMIsInConnectedComponents.get(), sumUMIs.get()); +// +// helper +// .writeField("Groups", numberOfGroups.get() - groupsClustered.get()) +// .writeField("Groups before clustering", numberOfGroups.get()) +// .writeField("Max clones per group", maxClonesPerGroup.get()) +// .writeField("Mean clones per group", ReportHelper.PERCENT_FORMAT.format(1.0 * sumClonesPerGroup.get() / numberOfGroups.get())) +// .writeField("Max tags per group", maxTagsPerGroup.get()) +// .writeField("Mean tags per group", ReportHelper.PERCENT_FORMAT.format(1.0 * sumTagsPerGroup.get() / numberOfGroups.get())) +// .writeField("Max tags clique", maxTagsClique.get()) +// .writeField("Max tags clique delta", maxTagsCliqueDelta.get()) +// .writeField("Mean tags clique delta", ReportHelper.PERCENT_FORMAT.format(1.0 * sumTagsCliqueDelta.get() / numberOfGroups.get())); +// +// helper +// .writePercentAndAbsoluteField("Groups clustered", groupsClustered.get(), numberOfGroups.get()) +// .writePercentAndAbsoluteField("Tags clustered", tagsClustered.get(), tagsTotal.get()) +// .writePercentAndAbsoluteField("Reads clustered", readsClustered.get(), readsTotal.get()) +// .writePercentAndAbsoluteField("UMIs clustered", unisClustered.get(), umisTotal.get()); +// +// helper +// .writeField("Effective reads in tags threshold", effectiveMinReadsInTag) +// .writeField("Effective UMIs in tags threshold", effectiveMinUMIsInTag); +// } +// } diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 25bc39035..183d9bac5 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -48,6 +48,7 @@ import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler; import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerParameters; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.cli.AlignerReport; import com.milaboratory.mixcr.cli.CloneAssemblerReport; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; @@ -109,7 +110,7 @@ public long getTotalNumberOfReads() { assemblerRunner.run(); - CloneSet cloneSet = assemblerRunner.getCloneSet(align.parameters.alignerParameters); + CloneSet cloneSet = assemblerRunner.getCloneSet(align.parameters.alignerParameters, align.tagsInfo); return new AssembleResult(align, cloneSet, report, assembler); } finally { if (close) @@ -187,7 +188,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl } CloneSet cloneSet = new CloneSet(Arrays.asList(clones), align.usedGenes, align.parameters.alignerParameters, - align.parameters.cloneAssemblerParameters, VDJCSProperties.CO_BY_COUNT); + align.parameters.cloneAssemblerParameters, align.tagsInfo, VDJCSProperties.CO_BY_COUNT); return new FullSeqAssembleResult(assemble, cloneSet); } @@ -234,7 +235,7 @@ public long getIndex(VDJCAlignmentResult r) { als.add(t.alignment); } } - return new AlignResult(parameters, reader.getNumberOfReads(), report, als, genes, aligner); + return new AlignResult(parameters, reader.getNumberOfReads(), report, als, genes, null, aligner); } } @@ -268,15 +269,17 @@ public static final class AlignResult { public final AlignerReport report; public final List alignments; public final List usedGenes; + public final TagsInfo tagsInfo; public final VDJCAligner aligner; public AlignResult(RunMiXCRAnalysis parameters, long totalNumberOfReads, AlignerReport report, - List alignments, List usedGenes, VDJCAligner aligner) { + List alignments, List usedGenes, TagsInfo tagsInfo, VDJCAligner aligner) { this.parameters = parameters; this.totalNumberOfReads = totalNumberOfReads; this.report = report; this.alignments = alignments; this.usedGenes = usedGenes; + this.tagsInfo = tagsInfo; this.aligner = aligner; } @@ -286,7 +289,7 @@ public VDJCAlignmentsReader resultReader() throws IOException { if (alignmentsFile == null) { alignmentsFile = TempFileManager.getTempFile(); try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(alignmentsFile)) { - writer.header(aligner, null); + writer.header(aligner, null, tagsInfo); for (VDJCAlignments alignment : alignments) writer.write(alignment); writer.setNumberOfProcessedReads(totalNumberOfReads); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index 77656d724..e6785a1fe 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -92,7 +92,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException //write alignments to byte array File vdjcaFile = TempFileManager.getTempFile(); try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(vdjcaFile)) { - writer.header(aligner, null); + writer.header(aligner, null, null); for (Object read : CUtils.it(reader)) { VDJCAlignmentResult result = (VDJCAlignmentResult) aligner.process((SequenceRead) read); if (result.alignment != null) @@ -125,7 +125,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException SmartProgressReporter.startProgressReport(assemblerRunner); assemblerRunner.run(); - CloneSet cloneSet = assemblerRunner.getCloneSet(null); + CloneSet cloneSet = assemblerRunner.getCloneSet(null, null); File tmpClnsFile = TempFileManager.getTempFile(); diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java index 45958b333..caf947e06 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java @@ -96,6 +96,7 @@ public void testGeneric(Function, List> modifyClones, modifyClones.apply(newClones), align.usedGenes, align.parameters.alignerParameters, CloneAssemblerParametersPresets.getByName("default"), + null, new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); writer.writeClones(newCloneSet); OutputPort als = modifyAlignments.apply(merged); @@ -139,6 +140,7 @@ public void test2Empty() throws Exception { writer.writeClones(new CloneSet(Collections.EMPTY_LIST, align.usedGenes, align.parameters.alignerParameters, CloneAssemblerParametersPresets.getByName("default"), + null, new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount()))); writer.collateAlignments(CUtils.asOutputPort(align.alignments), align.alignments.size()); writer.writeAlignmentsAndIndex(); diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java index 7a2f853e9..10e37077e 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java @@ -78,7 +78,7 @@ public void testSerialization1() throws Exception { try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(tmpFile)) { - writer.header(aligner, null); + writer.header(aligner, null, null); header = writer.getPosition(); diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java new file mode 100644 index 000000000..71a8a565f --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java @@ -0,0 +1,12 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.milaboratory.test.TestUtil; +import org.junit.Test; + +public class TagInfoTest { + @Test + public void test1() { + TestUtil.assertJson(new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2)); + TestUtil.assertJson(new TagsInfo(new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2))); + } +} \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java deleted file mode 100644 index ab1244314..000000000 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandAlignTest.java +++ /dev/null @@ -1,80 +0,0 @@ -/* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail, - * Popov Aleksandr (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. - */ -package com.milaboratory.mixcr.cli; - -import com.milaboratory.core.io.sequence.SequenceRead; -import com.milaboratory.core.io.sequence.SingleReadImpl; -import com.milaboratory.core.sequence.NSequenceWithQuality; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; -import org.junit.*; -import picocli.CommandLine; - -import java.util.*; - -import static com.milaboratory.mixcr.cli.CommandAlign.parseTags; -import static org.junit.Assert.*; - -public class CommandAlignTest { - @Test - public void parseTagsTest() { - List testData = Arrays.asList( - new ParseTagsTestData( - Arrays.asList("G1", "G2"), - "M01:24:0000-A5Y06:1:11011 1:N:0:1~G1~GGTC~?/EA{49~53}|G2~CCAAA~AF100{53~58}", - new String[] { "GGTC", "CCAAA" }), - new ParseTagsTestData( - Collections.singletonList("UMI"), - "UMI~GGAWNVGA~E?EGGE?/{57~65}", - new String[] { "GGAWNVGA" }), - new ParseTagsTestData( - Arrays.asList("A", "B"), - "A~TTAG~????|B~C~D", - new String[] { "TTAG", "C" }) - ); - - for (ParseTagsTestData currentTestData : testData) { - TagTuple tagTuple = parseTags(new CommandLine(CommandAlign.class), - currentTestData.tags, currentTestData.read); - assertArrayEquals(currentTestData.expectedTags, tagTuple.tags); - } - } - - private static class ParseTagsTestData { - final List tags; - final SequenceRead read; - final String[] expectedTags; - - ParseTagsTestData(List tags, String description, String[] expectedTags) { - this.tags = tags; - this.read = new SingleReadImpl(0, NSequenceWithQuality.EMPTY, description); - this.expectedTags = expectedTags; - } - } -} diff --git a/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java index a63035097..7baecc9d0 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java @@ -1,16 +1,15 @@ package com.milaboratory.mixcr.tags; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.milaboratory.util.GlobalObjectMappers; -import org.junit.Test; - -/** - * - */ -public class CloneTagTupleFilterTest { - - @Test - public void name() throws JsonProcessingException { - System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(new CloneTagTupleFilter(0, 0, 0, 0, 0, 0, 0.0 / 0.0, 0))); - } -} +// import com.fasterxml.jackson.core.JsonProcessingException; +// import com.milaboratory.util.GlobalObjectMappers; +// import org.junit.Test; +// +// /** +// * +// */ +// public class CloneTagTupleFilterTest { +// @Test +// public void name() throws JsonProcessingException { +// System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(new CloneTagTupleFilter(0, 0, 0, 0, 0, 0, 0.0 / 0.0, 0))); +// } +// } diff --git a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java index 06998f661..a305391b6 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java @@ -14,35 +14,35 @@ /** * */ -public class DropletCloneGraphTest { - @Test - @Ignore - public void test1() throws Exception { - try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/b_analysis.clna"), VDJCLibraryRegistry.getDefault(), 3)) { - CloneSet clns = reader.readCloneSet(); - System.out.println("# clones " + clns.size()); - DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); - DropletCloneGraphReport report = new DropletCloneGraphReport(); - ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); - SmartProgressReporter.startProgressReport(progressAndStage); - DropletCloneGraph.calculateGroups(links, DropletCloneGraphParameters.getDefault(), report, progressAndStage); - report.writeReport(ReportHelper.STDOUT); - } - } - - @Test - @Ignore - public void test2() throws Exception { - try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/t_analysis.clna"), VDJCLibraryRegistry.getDefault(), 3)) { - CloneSet clns = reader.readCloneSet(); - System.out.println("# clones " + clns.size()); - DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); - DropletCloneGraphReport report = new DropletCloneGraphReport(); - ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); - SmartProgressReporter.startProgressReport(progressAndStage); - DropletCloneGraphParameters parameters = DropletCloneGraphParameters.getDefault(); - DropletCloneGraph.calculateGroups(links, parameters, report, progressAndStage); - report.writeReport(ReportHelper.STDOUT); - } - } -} +// public class DropletCloneGraphTest { +// @Test +// @Ignore +// public void test1() throws Exception { +// try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/b_analysis.clna"), VDJCLibraryRegistry.getDefault(), 3)) { +// CloneSet clns = reader.readCloneSet(); +// System.out.println("# clones " + clns.size()); +// DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); +// DropletCloneGraphReport report = new DropletCloneGraphReport(); +// ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); +// SmartProgressReporter.startProgressReport(progressAndStage); +// DropletCloneGraph.calculateGroups(links, DropletCloneGraphParameters.getDefault(), report, progressAndStage); +// report.writeReport(ReportHelper.STDOUT); +// } +// } +// +// @Test +// @Ignore +// public void test2() throws Exception { +// try (ClnAReader reader = new ClnAReader(Paths.get("./tmp/t_analysis.clna"), VDJCLibraryRegistry.getDefault(), 3)) { +// CloneSet clns = reader.readCloneSet(); +// System.out.println("# clones " + clns.size()); +// DropletCloneGraph.CloneTagTupleList links = DropletCloneGraph.calculateTuples(clns, 0); +// DropletCloneGraphReport report = new DropletCloneGraphReport(); +// ProgressAndStage progressAndStage = new ProgressAndStage("Grouping"); +// SmartProgressReporter.startProgressReport(progressAndStage); +// DropletCloneGraphParameters parameters = DropletCloneGraphParameters.getDefault(); +// DropletCloneGraph.calculateGroups(links, parameters, report, progressAndStage); +// report.writeReport(ReportHelper.STDOUT); +// } +// } +// } diff --git a/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java b/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java index 1f5f31849..95e9937bc 100644 --- a/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java @@ -129,7 +129,7 @@ public void test2() throws Exception { File tempFile = TempFileManager.getTempFile(); try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(tempFile)) { - writer.header(align.aligner, null); + writer.header(align.aligner, null, null); for (VDJCAlignments alignment : align.alignments) writer.write(alignment); } @@ -166,7 +166,7 @@ public void test3() throws Exception { File tempFile = TempFileManager.getTempFile(); try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(tempFile)) { - writer.header(align.aligner, null); + writer.header(align.aligner, null, null); for (VDJCAlignments alignment : align.alignments) writer.write(alignment); } diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java index bef54f1e5..8594a8187 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java @@ -72,7 +72,7 @@ public void testSerialization1() throws Exception { if (parameters.containsRequiredFeature(gene)) aligner.addGene(gene); try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(tmpFile)) { - writer.header(aligner, null); + writer.header(aligner, null, null); header = writer.getPosition(); for (SingleRead read : CUtils.it(reader)) { VDJCAlignmentResult result = aligner.process(read); @@ -97,10 +97,10 @@ public void testSerialization1() throws Exception { @Test @Ignore public void test2() throws Exception { -// @ -// GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCC -// + -// CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + // @ + // GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCC + // + + // CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default"); From cfb95845da97223105a978200d68e819d54f4637 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 12 May 2022 02:01:34 +0400 Subject: [PATCH 193/282] fix: for threads in analyze passed to assemble --- .../milaboratory/mixcr/cli/CommandAssemble.java | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index e231b496a..dc8ba00b4 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -60,7 +60,6 @@ import static com.milaboratory.mixcr.cli.CommandAssemble.ASSEMBLE_COMMAND_NAME; @Command(name = ASSEMBLE_COMMAND_NAME, - sortOptions = true, separator = " ", description = "Assemble clones.") public class CommandAssemble extends ACommandWithSmartOverwriteWithSingleInputMiXCR { @@ -70,15 +69,11 @@ public class CommandAssemble extends ACommandWithSmartOverwriteWithSingleInputMi names = {"-p", "--preset"}) public String assemblerParametersName = "default"; - // public int threads = Runtime.getRuntime().availableProcessors(); - // - // @Option(description = "Processing threads", - // names = {"-t", "--threads"}) - // public void setThreads(int threads) { - // if (threads <= 0) - // throwValidationException("-t / --threads must be positive"); - // this.threads = threads; - // } + @Option(description = "Processing threads", + names = {"-t", "--threads"}) + public void setThreads(int threads) { + System.out.println("-t / --threads is deprecated for \"mixcr assemble ...\" and ignored for this call..."); + } @Option(description = "Use higher compression for output file.", names = {"--high-compression"}) From 2c573fb65ea579b58d92585de9c75aa3b9d592bd Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 12 May 2022 02:16:00 +0400 Subject: [PATCH 194/282] chore: full stack trace for exceptions in tests --- build.gradle.kts | 2 ++ 1 file changed, 2 insertions(+) diff --git a/build.gradle.kts b/build.gradle.kts index fa0e5d90f..24313e965 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -1,6 +1,7 @@ import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar import com.palantir.gradle.gitversion.VersionDetails import groovy.lang.Closure +import org.gradle.api.tasks.testing.logging.TestExceptionFormat.FULL import java.net.InetAddress gradle.startParameter.excludedTaskNames += listOf( @@ -182,6 +183,7 @@ tasks.test { testLogging { showStandardStreams = true + exceptionFormat = FULL } miCiStage?.let { From e88be90a7365cdd281a322f7985d53c2a6a2f903 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 13 May 2022 16:35:13 +0200 Subject: [PATCH 195/282] Small bug fix for `filter` in exportPlots --- .../mixcr/cli/postanalysis/CommandPaExportPlots.java | 2 +- .../mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java index c39a42047..5899999a4 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java @@ -44,7 +44,7 @@ public void validate() { super.validate(); if (!out.endsWith(".pdf")) throwValidationException("Output file must ends with .pdf extension"); - if (filterByMetadata != null && metadata == null) + if (filterByMetadata != null && metadata() == null) throwValidationException("Filter is specified by metadata is not."); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java index 63d2d5529..87a5f8a74 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -44,7 +44,6 @@ DataFrame filterOverlap(DataFrame df) { void run(PaResultByGroup result) { CharacteristicGroup ch = result.schema.getGroup(CommandPaOverlap.Overlap); PostanalysisResult paResult = result.result.forGroup(ch); - Map preprocSummary = paResult.preprocSummary; DataFrame metadata = metadata(); DataFrame df = Overlap.INSTANCE.dataFrame( From fdd48fc45c88f3a79aeb6ebc0289b8562bd226f3 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 15 May 2022 18:02:56 +0400 Subject: [PATCH 196/282] feat: report migrated to milib --- build.gradle.kts | 2 +- .../fullseq/FullSeqAssemblerReport.java | 2 +- .../mixcr/cli/ChainUsageStats.java | 1 + .../milaboratory/mixcr/cli/CommandAlign.java | 6 +-- .../mixcr/cli/CommandAssemble.java | 7 +-- .../mixcr/cli/CommandAssembleContigs.java | 7 +-- .../cli/CommandAssemblePartialAlignments.java | 7 +-- .../milaboratory/mixcr/cli/CommandExtend.java | 7 +-- .../mixcr/cli/CommandGroupCells.java | 7 +-- .../milaboratory/mixcr/cli/CommandReport.java | 1 + .../com/milaboratory/mixcr/cli/Report.java | 44 --------------- .../milaboratory/mixcr/cli/ReportWrapper.java | 1 + .../java/com/milaboratory/mixcr/cli/Util.java | 53 ------------------- .../PartialAlignmentsAssembler.java | 2 +- .../mixcr/tags/DropletCloneGraphReport.java | 2 +- .../mixcr/util/VDJCObjectExtender.java | 2 +- .../com/milaboratory/mixcr/cli/UtilTest.java | 11 ++-- 17 files changed, 34 insertions(+), 128 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/Report.java diff --git a/build.gradle.kts b/build.gradle.kts index d32bde2da..d73ddb57f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -79,7 +79,7 @@ repositories { } val miplotsVersion = "0.1-19-master" -val milibVersion = "1.15.0-29-master" +val milibVersion = "1.15.0-32-master" val repseqioVersion = "1.3.5-25-master" val jacksonVersion = "2.13.2.2" diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java index 0b9b4fea8..0e0954a60 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java @@ -35,7 +35,7 @@ import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler.VariantBranch; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.VDJCObject; -import com.milaboratory.mixcr.cli.Report; +import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; import io.repseq.core.GeneFeature; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java index 82e39db2f..358387b94 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java @@ -35,6 +35,7 @@ import com.fasterxml.jackson.databind.SerializerProvider; import com.fasterxml.jackson.databind.annotation.JsonSerialize; import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; import io.repseq.core.Chains; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 34511d4f5..4f7adfd3a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -649,12 +649,12 @@ public String getStatus() { // Writing report to stout System.out.println("============= Report =============="); - Util.writeReportToStdout(report); + ReportUtil.writeReportToStdout(report); if (reportFile != null) - Util.writeReport(reportFile, report); + ReportUtil.appendReport(reportFile, report); if (jsonReport != null) - Util.writeJsonReport(jsonReport, report); + ReportUtil.appendJsonReport(jsonReport, report); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index c382eb468..aa5955536 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -42,6 +42,7 @@ import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.ArraysUtils; import com.milaboratory.util.JsonOverrider; +import com.milaboratory.util.ReportUtil; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.*; @@ -372,13 +373,13 @@ public void run1() throws Exception { // Writing report to stout System.out.println("============= Report =============="); - Util.writeReportToStdout(report); + ReportUtil.writeReportToStdout(report); if (reportFile != null) - Util.writeReport(reportFile, report); + ReportUtil.appendReport(reportFile, report); if (jsonReport != null) - Util.writeJsonReport(jsonReport, report); + ReportUtil.appendJsonReport(jsonReport, report); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index 1c7fced65..a30a504c8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -50,6 +50,7 @@ import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.util.JsonOverrider; +import com.milaboratory.util.ReportUtil; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; @@ -272,13 +273,13 @@ public void run1() throws Exception { // Writing report to stout System.out.println("============= Report =============="); - Util.writeReportToStdout(report); + ReportUtil.writeReportToStdout(report); if (reportFile != null) - Util.writeReport(reportFile, reportWrapper); + ReportUtil.appendReport(reportFile, reportWrapper); if (jsonReport != null) - Util.writeJsonReport(jsonReport, reportWrapper); + ReportUtil.appendJsonReport(jsonReport, reportWrapper); } @JsonAutoDetect( diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 65b3cd823..0c65df7cb 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -36,6 +36,7 @@ import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssembler; import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssemblerParameters; import com.milaboratory.util.JsonOverrider; +import com.milaboratory.util.ReportUtil; import com.milaboratory.util.SmartProgressReporter; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -131,7 +132,7 @@ public void run1() throws Exception { // Writing report to stout System.out.println("============= Report =============="); - Util.writeReportToStdout(report); + ReportUtil.writeReportToStdout(report); if (assembler.leftPartsLimitReached()) { warn("WARNING: too many partial alignments detected, consider skipping assemblePartial (enriched library?). /leftPartsLimitReached/"); @@ -144,10 +145,10 @@ public void run1() throws Exception { } if (reportFile != null) - Util.writeReport(reportFile, report); + ReportUtil.appendReport(reportFile, report); if (jsonReport != null) - Util.writeJsonReport(jsonReport, report); + ReportUtil.appendJsonReport(jsonReport, report); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 02ec57d8c..7c5293e39 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -43,6 +43,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.util.VDJCObjectExtender; +import com.milaboratory.util.ReportUtil; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.Chains; import io.repseq.core.GeneType; @@ -215,13 +216,13 @@ public void finish() throws JsonProcessingException { // Writing report to stout System.out.println("============= Report =============="); - Util.writeReportToStdout(report); + ReportUtil.writeReportToStdout(report); if (reportFile != null) - Util.writeReport(reportFile, report); + ReportUtil.appendReport(reportFile, report); if (jsonReport != null) - Util.writeJsonReport(jsonReport, report); + ReportUtil.appendJsonReport(jsonReport, report); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 44193b324..8b176eab8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -13,6 +13,7 @@ import com.milaboratory.mixcr.tags.DropletCloneGraphReport; import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.ProgressAndStage; +import com.milaboratory.util.ReportUtil; import com.milaboratory.util.SmartProgressReporter; import gnu.trove.impl.Constants; import gnu.trove.map.hash.TIntObjectHashMap; @@ -102,13 +103,13 @@ public void run1() throws Exception { // Writing report to stout System.out.println("============= Report =============="); - Util.writeReportToStdout(report); + ReportUtil.writeReportToStdout(report); if (reportFile != null) - Util.writeReport(reportFile, report); + ReportUtil.appendReport(reportFile, report); if (jsonReportFile != null) - Util.writeJsonReport(jsonReportFile, report); + ReportUtil.appendJsonReport(jsonReportFile, report); } private static final class CloneIdWithTag { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java index bf4e227c2..2337a5935 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java @@ -30,6 +30,7 @@ package com.milaboratory.mixcr.cli; import com.fasterxml.jackson.annotation.JsonProperty; +import com.milaboratory.util.Report; public interface CommandReport extends Report { /** diff --git a/src/main/java/com/milaboratory/mixcr/cli/Report.java b/src/main/java/com/milaboratory/mixcr/cli/Report.java deleted file mode 100644 index d6a8b8958..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/Report.java +++ /dev/null @@ -1,44 +0,0 @@ -/* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. - */ -package com.milaboratory.mixcr.cli; - -import com.fasterxml.jackson.annotation.JsonAutoDetect; -import com.milaboratory.util.ReportHelper; - -@JsonAutoDetect( - getterVisibility = JsonAutoDetect.Visibility.NONE, - isGetterVisibility = JsonAutoDetect.Visibility.NONE, - fieldVisibility = JsonAutoDetect.Visibility.NONE, - setterVisibility = JsonAutoDetect.Visibility.NONE, - creatorVisibility = JsonAutoDetect.Visibility.NONE -) -public interface Report { - void writeReport(ReportHelper helper); -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java index 681327d3c..a8d41ecc6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java @@ -30,6 +30,7 @@ package com.milaboratory.mixcr.cli; import com.fasterxml.jackson.annotation.JsonUnwrapped; +import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; public final class ReportWrapper extends AbstractCommandReport { diff --git a/src/main/java/com/milaboratory/mixcr/cli/Util.java b/src/main/java/com/milaboratory/mixcr/cli/Util.java index 25b9c8cce..009c996f3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Util.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Util.java @@ -29,23 +29,10 @@ */ package com.milaboratory.mixcr.cli; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.milaboratory.util.GlobalObjectMappers; -import com.milaboratory.util.ReportHelper; import gnu.trove.map.hash.TIntObjectHashMap; -import java.io.ByteArrayOutputStream; -import java.io.File; -import java.io.IOException; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; -import java.nio.channels.FileLock; -import java.nio.charset.StandardCharsets; import java.nio.file.Path; import java.nio.file.Paths; -import java.nio.file.StandardOpenOption; -import java.text.DecimalFormat; -import java.text.DecimalFormatSymbols; import java.util.ArrayList; import java.util.List; @@ -53,46 +40,6 @@ public final class Util { private Util() { } - public static void writeReportToStdout(Report report) { - report.writeReport(new ReportHelper(System.out, true)); - } - - static void appendAtomically(String fileName, byte[] content) { - appendAtomically(new File(fileName), content); - } - - static void appendAtomically(File file, byte[] content) { - try (FileChannel channel = FileChannel.open(file.toPath(), StandardOpenOption.WRITE, StandardOpenOption.CREATE); - FileLock lock = lockIfPossible(channel)) { - channel.position(channel.size()); - channel.write(ByteBuffer.wrap(content)); - } catch (IOException ioe) { - throw new RuntimeException(ioe); - } - } - - static FileLock lockIfPossible(FileChannel channel) { - try { - return channel.lock(); - } catch (Exception e) { - return null; - } - } - - public static void writeReport(String reportFileName, Report report) { - ByteArrayOutputStream bos = new ByteArrayOutputStream(); - ReportHelper helper = new ReportHelper(bos, false); - report.writeReport(helper); - helper.end(); - appendAtomically(reportFileName, bos.toByteArray()); - } - - public static void writeJsonReport(String reportFileName, Report report) throws JsonProcessingException { - String content = GlobalObjectMappers.toOneLine(report) + "\n"; - appendAtomically(reportFileName, content.getBytes(StandardCharsets.UTF_8)); - } - - public static String printTwoColumns(List left, List right, int leftWidth, int rightWidth, int sep) { return printTwoColumns(left, right, leftWidth, rightWidth, sep, ""); } diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 63bc32999..0ad0a4c14 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -36,7 +36,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.cli.Report; +import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import gnu.trove.iterator.TObjectDoubleIterator; diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java index 301bdde32..2791d2f2c 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java @@ -33,7 +33,7 @@ import com.google.common.util.concurrent.AtomicDouble; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; -import com.milaboratory.mixcr.cli.Report; +import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; import gnu.trove.map.hash.TIntObjectHashMap; diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java index d2c0357f4..45c1bad6c 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java @@ -41,7 +41,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.SequenceQuality; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.cli.Report; +import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; import io.repseq.core.*; diff --git a/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java b/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java index 53106b723..a2ed928ca 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java @@ -29,27 +29,22 @@ */ package com.milaboratory.mixcr.cli; -import com.milaboratory.core.io.util.IOTestUtil; -import com.milaboratory.test.TestUtil; +import com.milaboratory.util.ReportUtil; import com.milaboratory.util.TempFileManager; import org.junit.Assert; import org.junit.Ignore; import org.junit.Test; import java.io.File; -import java.nio.charset.StandardCharsets; import java.nio.file.Files; import java.util.ArrayList; -import java.util.HashSet; -import java.util.List; -import java.util.Set; public class UtilTest { @Test public void testAtomicAppend1() throws Exception { File file = TempFileManager.getTempFile(); - Util.appendAtomically(file, "ATTAG".getBytes()); - Util.appendAtomically(file, "GACAG".getBytes()); + ReportUtil.appendAtomically(file, "ATTAG".getBytes()); + ReportUtil.appendAtomically(file, "GACAG".getBytes()); byte[] bytes = Files.readAllBytes(file.toPath()); Assert.assertEquals("ATTAGGACAG", new String(bytes)); } From 8607cf8930432348b7be093bc4e61d13ff37f43e Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 18 May 2022 01:31:28 +0200 Subject: [PATCH 197/282] Convert numeric column to categorial when needed. --- .../mixcr/cli/postanalysis/CommandPa.java | 2 +- .../CommandPaExportPlotsBasicStatistics.java | 8 ++ .../postanalysis/plots/BasicStatistics.kt | 128 ++++++++++++------ 3 files changed, 95 insertions(+), 43 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index b78f46547..62577d77f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -60,7 +60,7 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { names = {"-g", "--group"}) public List isolationGroups; - @Option(description = "Tabular results output path.", + @Option(description = "Tabular results output path (path/table.tsv).", names = {"--tables"}) public String tablesOut; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index 39e744354..107fc7238 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -8,6 +8,7 @@ import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.plots.BasicStatRow; import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics; +import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics.PlotType; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; @@ -19,6 +20,8 @@ public abstract class CommandPaExportPlotsBasicStatistics extends CommandPaExportPlots { abstract String group(); + @Option(description = "Plot type", names = {"--plot-type"}) + public String plotType; @Option(description = "Primary group", names = {"-p", "--primary-group"}) public String primaryGroup; @Option(description = "Secondary group", names = {"-s", "--secondary-group"}) @@ -63,7 +66,12 @@ void run(PaResultByGroup result) { else if (refGroup != null) rg = RefGroup.Companion.of(refGroup); + PlotType plotType = this.plotType == null + ? PlotType.Auto + : PlotType.Companion.parse(this.plotType); + BasicStatistics.PlotParameters par = new BasicStatistics.PlotParameters( + plotType, primaryGroup, secondaryGroup, facetBy, diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt index fb6f7c4e9..45cb3b75c 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt @@ -14,11 +14,9 @@ import com.milaboratory.miplots.stat.xdiscrete.statCompareMeans import com.milaboratory.miplots.toPDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat -import jetbrains.letsPlot.facet.facetWrap -import jetbrains.letsPlot.geom.geomBoxplot +import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics.PlotType.* +import jetbrains.letsPlot.intern.Plot import jetbrains.letsPlot.label.ggtitle -import jetbrains.letsPlot.label.xlab -import jetbrains.letsPlot.letsPlot import org.jetbrains.kotlinx.dataframe.DataFrame import org.jetbrains.kotlinx.dataframe.annotations.DataSchema import org.jetbrains.kotlinx.dataframe.api.* @@ -95,6 +93,7 @@ object BasicStatistics { ) = dataFrame(paResult, metricsFilter, readMetadata(metadataPath)) data class PlotParameters( + val plotType: PlotType = Auto, val primaryGroup: String? = null, val secondaryGroup: String? = null, val facetBy: String? = null, @@ -112,12 +111,36 @@ object BasicStatistics { val correlationMethod: CorrelationMethod = CorrelationMethod.Pearson, ) + enum class PlotType { + Auto, + BoxPlot, + LinePlot, + Scatter; + + companion object { + fun parse(str: String) = + values().find { it.name.equals(str, ignoreCase = true) } + ?: throw IllegalArgumentException("invalid plot type: $str") + } + } + + private fun isCategorial(t: PlotType) = when (t) { + Scatter, LinePlot -> false + else -> true + } + + private fun guessPlotType(par: PlotParameters, meta: Metadata?) = + if (par.primaryGroup == null || meta == null || meta.isCategorial(par.primaryGroup)) + BoxPlot + else + Scatter + fun plots( df: DataFrame, - pp: PlotParameters, + par: PlotParameters, ) = df.groupBy { metric }.groups.toList() .filter { !it.isEmpty() } - .map { mdf -> plot(mdf, pp) + ggtitle(mdf.first()[BasicStatRow::metric.name]!!.toString()) } + .map { mdf -> plot(mdf, par) + ggtitle(mdf.first()[BasicStatRow::metric.name]!!.toString()) } fun plotsAndSummary( df: DataFrame, @@ -148,47 +171,44 @@ object BasicStatistics { listOf(summary) + plots } + private fun toCategorical(df: DataFrame, vararg cols: String) = run { + var r = df + for (col in cols) + r = r.replace { col() }.with { it.convertToString() } + r + } + fun plot( df: DataFrame, par: PlotParameters, - ) = - if (par.primaryGroup == null) { - val data = df.add(List(df.rowsCount()) { "" }.toColumn("__x__")).toMap() - var plt = letsPlot(data) { - x = "__x__" - y = BasicStatRow::value.name - } - plt += geomBoxplot() - if (par.facetBy != null) - plt += facetWrap(par.facetBy) - - plt += xlab("") - plt - } else if (df.isNumeric(par.primaryGroup)) { - val plt = GGScatter( - df, - x = par.primaryGroup, - y = BasicStatRow::value.name, - facetBy = par.facetBy, - facetNRow = 1, - ) { - shape = par.secondaryGroup - color = par.secondaryGroup - linetype = par.secondaryGroup - } + ): Plot = run { + val type = if (par.plotType == Auto) guessPlotType(par, df) else par.plotType - plt += statCor(method = par.correlationMethod) + val dfRefined = ( + if (isCategorial(type)) { + if (par.primaryGroup == null) + df.add(List(df.rowsCount()) { "" }.toColumn("__x__")) + else if (df.isNumeric(par.primaryGroup) || (par.secondaryGroup != null && df.isNumeric(par.secondaryGroup))) { + toCategorical(df, *listOfNotNull(par.primaryGroup, par.secondaryGroup).toTypedArray()) + } else + df + } else { + df + } + ) - plt.plot - } else { - val plt = GGBoxPlot( - df, - x = par.primaryGroup, - y = BasicStatRow::value.name, - facetBy = par.facetBy, - facetNRow = 1, - ) { - fill = par.secondaryGroup ?: par.primaryGroup + if (isCategorial(type)) { + val plt = when (type) { + BoxPlot -> GGBoxPlot( + dfRefined, + x = par.primaryGroup ?: "__x__", + y = BasicStatRow::value.name, + facetBy = par.facetBy, + facetNRow = 1, + ) { + fill = par.secondaryGroup ?: par.primaryGroup + } + else -> throw RuntimeException("$type") } if (par.showPairwisePValue) @@ -221,5 +241,29 @@ object BasicStatistics { ) plt.plot + + } else { + + par.primaryGroup!! + val plt = when (type) { + Scatter -> GGScatter( + dfRefined, + x = par.primaryGroup, + y = BasicStatRow::value.name, + facetBy = par.facetBy, + facetNRow = 1, + ) { + shape = par.secondaryGroup + color = par.secondaryGroup + linetype = par.secondaryGroup + } + LinePlot -> TODO() + else -> throw RuntimeException("$type") + } + + plt += statCor(method = par.correlationMethod) + + plt.plot } + } } From 40f8effeb8ab475b0c126b6028ab5097eeedf0ec Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 18 May 2022 23:57:03 +0300 Subject: [PATCH 198/282] wip --- .../java/com/milaboratory/mixcr/basictypes/tag/TagValue.java | 1 + src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java index 53a565e0a..ecd192b5a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.basictypes.tag; +// @Serializable(custom = {@CustomSerializer(id = 1, type = )}) public interface TagValue extends Comparable { /** * Returns true for tag values that can be used as a grouping key, diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 5140bc6b0..71fde1686 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -358,6 +358,6 @@ public void writeReport(ReportHelper helper) { } if (tagReport != null) - helper.println(tagReport.humanReadable()); + tagReport.writeReport(helper); } } From e7b923541b7d66819293a832fbfc6ea2232dd98b Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 19 May 2022 16:00:41 +0200 Subject: [PATCH 199/282] Fix bug in preprocessor statistics. --- .../DownsamplingPreprocessor.java | 3 +- .../preproc/FilterPreprocessor.java | 1 + .../mixcr/postanalysis/preproc/SelectTop.java | 1 + .../preproc/PreprocessorChainTest.java | 39 ++++++++++++++++--- 4 files changed, 38 insertions(+), 6 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index 58554a911..cc0af95d4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -65,6 +65,8 @@ public SetPreprocessorSetup nextSetupStep() { @Override public MappingFunction getMapper(int iDataset) { + stats.clear(iDataset); + if (downsampling == -1) downsampling = downsampleValueChooser.compute(setup.counts); @@ -78,7 +80,6 @@ public MappingFunction getMapper(int iDataset) { long[] countsDownsampled = downsample_mvhg(counts, downsampling, rnd); AtomicInteger idx = new AtomicInteger(0); - stats.clear(iDataset); return t -> { stats.before(iDataset, t); int i = idx.getAndIncrement(); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index bd88b6e44..e84b73400 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -33,6 +33,7 @@ public SetPreprocessorSetup nextSetupStep() { @Override public MappingFunction getMapper(int iDataset) { + stats.clear(iDataset); return t -> { stats.before(iDataset, t); if (!predicates.stream().allMatch(p -> p.test(t))) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java index 90f8d895c..0dc9d227a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java @@ -57,6 +57,7 @@ public SetPreprocessorSetup nextSetupStep() { @Override public MappingFunction getMapper(int iDataset) { + stats.clear(iDataset); TLongLongHashMap hist = computeHists.downsampledHist(iDataset); if (hist.isEmpty()) { stats.drop(iDataset); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java index dfe8ad4ad..264ce0395 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java @@ -102,6 +102,35 @@ public void testSetupDuplication1() { Assert.assertEquals(expected, result.data); } + @Test + @SuppressWarnings("unchecked") + public void testStat1() { + long p1 = 17; + long p2 = 13; + long p3 = 11; + long p4 = 7; + + SetPreprocessor preproc = new PreprocessorChain.Factory<>( + new TestPreprocFactory(p1), + new TestPreprocFactory(p2), + new TestPreprocFactory(p3), + new TestPreprocFactory(p4) + ).newInstance(); + + RandomDataGenerator rng = new RandomDataGenerator(new Well512a(System.currentTimeMillis())); + TestDataset ds = rndDataset(rng, 10000); + SetPreprocessor.processDatasets(preproc, ds); + + for (List stat : preproc.getStat().valueCollection()) { + Assert.assertEquals(4, stat.size()); + for (int i = 0; i < stat.size() - 1; i++) { + Assert.assertEquals(stat.get(i).nElementsAfter, stat.get(i + 1).nElementsBefore); + Assert.assertEquals(stat.get(i).sumWeightAfter, stat.get(i + 1).sumWeightBefore, 1e-10); + } + } + } + + public static final class TestPreprocFactory implements SetPreprocessorFactory { final long modulus; @@ -116,16 +145,18 @@ public SetPreprocessor newInstance() { @Override public String id() { - return ""; + return "" + modulus; } } public static final class TestPreproc implements SetPreprocessor { final TLongArrayList l = new TLongArrayList(); final long modulus; + private final SetPreprocessorStat.Builder stats; public TestPreproc(long modulus) { this.modulus = modulus; + this.stats = new SetPreprocessorStat.Builder<>("" + modulus, t -> t.weight); } boolean initialized = false; @@ -151,11 +182,9 @@ public InputPort consumer(int i) { return null; } - - private final SetPreprocessorStat.Builder stats = new SetPreprocessorStat.Builder<>("", t -> t.weight); - @Override public MappingFunction getMapper(int iDataset) { + stats.clear(iDataset); AtomicInteger idx = new AtomicInteger(0); return element -> { stats.before(iDataset, element); @@ -173,7 +202,7 @@ public TIntObjectHashMap> getStat() { @Override public String id() { - return ""; + return "" + modulus; } } From 766fbc53765d9ea63fcab992df1c9db7be0c7ca9 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 14:25:48 +0300 Subject: [PATCH 200/282] chore: repseqio upgrade --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index d73ddb57f..de315e843 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -80,7 +80,7 @@ repositories { val miplotsVersion = "0.1-19-master" val milibVersion = "1.15.0-32-master" -val repseqioVersion = "1.3.5-25-master" +val repseqioVersion = "1.3.5-26-master" val jacksonVersion = "2.13.2.2" dependencies { From 87ffd49543fff51f93f5132ba8d715c376d8d419 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 14:37:01 +0300 Subject: [PATCH 201/282] fix --- .../mixcr/partialassembler/PartialAlignmentsAssembler.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index cd5995db2..6710d3206 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -35,7 +35,7 @@ import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.basictypes.*;= +import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.util.Report; From 8550e4741ce292d72d3aa05896b28c6391accb84 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 14:50:23 +0300 Subject: [PATCH 202/282] feat: relativeMinScore -> 0.97 --- .../parameters/vdjcaligner_parameters.json | 1026 ++++++++--------- 1 file changed, 513 insertions(+), 513 deletions(-) diff --git a/src/main/resources/parameters/vdjcaligner_parameters.json b/src/main/resources/parameters/vdjcaligner_parameters.json index 79fcd57cc..c66afde9a 100644 --- a/src/main/resources/parameters/vdjcaligner_parameters.json +++ b/src/main/resources/parameters/vdjcaligner_parameters.json @@ -1,518 +1,518 @@ { - "default": { - "fixSeed" : true, - "libraryStructure": "Unknown", - "vParameters": { - "geneFeatureToAlign": "VRegionWithP", - "minSumScore" : 50, - "relativeMinScore" : 0.87, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": true, - "floatingRightBound": true, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.7, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 10, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 40.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - } - }, - "dParameters": { - "geneFeatureToAlign": "DRegionWithP", - "absoluteMinScore": 25.0, - "relativeMinScore": 0.85, - "maxHits": 3, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - }, - "jParameters": { - "geneFeatureToAlign": "JRegionWithP", - "minSumScore" : 40, - "relativeMinScore" : 0.87, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": true, - "floatingRightBound": false, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.75, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 10, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 40.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - } - }, - "cParameters": { - "geneFeatureToAlign": "CExon1", - "minSumScore" : 40, - "relativeMinScore" : 0.87, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": false, - "floatingRightBound": false, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.75, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 10, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 40.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - } - }, - "vjAlignmentOrder": "VThenJ", - "includeDScore": false, - "includeCScore": false, - "mergerParameters": { - "qualityMergingAlgorithm" : "MaxSubtraction", - "minimalOverlap": 17, - "minimalIdentity": 0.9, - "identityType": "Unweighted" - }, - "minSumScore": 120.0, - "maxHits": 5, - "relativeMinVFR3CDR3Score": 0.7, - "allowPartialAlignments": false, - "allowNoCDR3PartAlignments": false, - "allowChimeras": false, - "alignmentBoundaryTolerance": 5, - "minChimeraDetectionScore": 120, - "vjOverlapWindow": 3, - "readsLayout": "Opposite", - "saveOriginalReads": false, - "smartForceEdgeAlignments": true + "default": { + "fixSeed": true, + "libraryStructure": "Unknown", + "vParameters": { + "geneFeatureToAlign": "VRegionWithP", + "minSumScore": 50, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": true, + "floatingRightBound": true, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.7, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 40.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + } }, - "kaligner2": { - "fixSeed" : true, - "libraryStructure": "Unknown", - "vParameters": { - "geneFeatureToAlign": "VRegionWithP", - "minSumScore" : 150, - "relativeMinScore" : 0.8, - "parameters":{ - "type" : "kaligner2", - "mapperNValue" : 8, - "mapperKValue" : 1, - "floatingLeftBound" : true, - "floatingRightBound" : true, - "mapperAbsoluteMinClusterScore" : 102, - "mapperExtraClusterScore" : -38, - "mapperMatchScore" : 95, - "mapperMismatchScore" : -14, - "mapperOffsetShiftScore" : -82, - "mapperSlotCount" : 6, - "mapperMaxClusters" : 4, - "mapperMaxClusterIndels" : 4, - "mapperKMersPerPosition" : 4, - "mapperAbsoluteMinScore" : 100, - "mapperRelativeMinScore" : 0.8, - "mapperMinSeedsDistance" : 5, - "mapperMaxSeedsDistance" : 5, - "alignmentStopPenalty" : 0, - "absoluteMinScore" : 150, - "relativeMinScore" : 0.8, - "maxHits" : 3, - "scoring" : { - "type" : "affine", - "subsMatrix" : "simple(match = 10, mismatch = -19)", - "gapOpenPenalty" : -40, - "gapExtensionPenalty" : -11 - } - } - }, - "dParameters": { - "geneFeatureToAlign": "DRegionWithP", - "absoluteMinScore": 25.0, - "relativeMinScore": 0.85, - "maxHits": 3, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - }, - "jParameters": { - "geneFeatureToAlign": "JRegionWithP", - "minSumScore" : 150, - "relativeMinScore" : 0.8, - "parameters": { - "type" : "kaligner2", - "mapperNValue" : 8, - "mapperKValue" : 1, - "floatingLeftBound" : true, - "floatingRightBound" : false, - "mapperAbsoluteMinClusterScore" : 102, - "mapperExtraClusterScore" : -38, - "mapperMatchScore" : 95, - "mapperMismatchScore" : -14, - "mapperOffsetShiftScore" : -82, - "mapperSlotCount" : 6, - "mapperMaxClusters" : 4, - "mapperMaxClusterIndels" : 4, - "mapperKMersPerPosition" : 4, - "mapperAbsoluteMinScore" : 100, - "mapperRelativeMinScore" : 0.8, - "mapperMinSeedsDistance" : 5, - "mapperMaxSeedsDistance" : 5, - "alignmentStopPenalty" : 0, - "absoluteMinScore" : 150, - "relativeMinScore" : 0.8, - "maxHits" : 3, - "scoring" : { - "type" : "affine", - "subsMatrix" : "simple(match = 10, mismatch = -19)", - "gapOpenPenalty" : -40, - "gapExtensionPenalty" : -11 - } - } - }, - "cParameters": { - "geneFeatureToAlign": "CExon1", - "minSumScore" : 40, - "relativeMinScore" : 0.8, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": false, - "floatingRightBound": false, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.75, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 10, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 40.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - } - }, - "vjAlignmentOrder": "VThenJ", - "includeDScore": false, - "includeCScore": false, - "mergerParameters": { - "qualityMergingAlgorithm" : "MaxSubtraction", - "minimalOverlap": 17, - "minimalIdentity": 0.9, - "identityType": "Unweighted" - }, - "minSumScore": 120.0, - "maxHits": 5, - "relativeMinVFR3CDR3Score": 0.7, - "allowPartialAlignments": false, - "allowNoCDR3PartAlignments": false, - "allowChimeras": false, - "alignmentBoundaryTolerance": 5, - "minChimeraDetectionScore": 120, - "vjOverlapWindow": 3, - "readsLayout": "Opposite", - "saveOriginalReads": false, - "smartForceEdgeAlignments": true + "dParameters": { + "geneFeatureToAlign": "DRegionWithP", + "absoluteMinScore": 25.0, + "relativeMinScore": 0.85, + "maxHits": 3, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } }, - "rna-seq": { - "fixSeed" : true, - "libraryStructure": "Unknown", - "vParameters": { - "geneFeatureToAlign": "VTranscriptWithP", - "minSumScore" : 80, - "relativeMinScore" : 0.87, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": false, - "floatingRightBound": true, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.7, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 10, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 55.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -11)", - "gapPenalty": -21 - } - } - }, - "dParameters": { - "geneFeatureToAlign": "DRegionWithP", - "absoluteMinScore": 25.0, - "relativeMinScore": 0.85, - "maxHits": 3, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -11)", - "gapPenalty": -21 - } - }, - "jParameters": { - "geneFeatureToAlign": "JRegionWithP", - "minSumScore" : 60, - "relativeMinScore" : 0.87, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": true, - "floatingRightBound": false, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.75, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 8, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 50.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -11)", - "gapPenalty": -21 - } - } - }, - "cParameters": { - "geneFeatureToAlign": "CExon1", - "minSumScore" : 40, - "relativeMinScore" : 0.87, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": false, - "floatingRightBound": false, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.75, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 10, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 40.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -11)", - "gapPenalty": -21 - } - } - }, - "vjAlignmentOrder": "VThenJ", - "includeDScore": true, - "includeCScore": true, - "mergerParameters": { - "qualityMergingAlgorithm" : "MaxSubtraction", - "minimalOverlap": 17, - "minimalIdentity": 0.9, - "identityType": "Unweighted" - }, - "minSumScore": 200.0, - "maxHits": 5, - "relativeMinVFR3CDR3Score": 0.7, - "allowPartialAlignments": false, - "allowNoCDR3PartAlignments": false, - "allowChimeras": false, - "alignmentBoundaryTolerance": 5, - "minChimeraDetectionScore": 120, - "vjOverlapWindow": 3, - "readsLayout": "Opposite", - "saveOriginalReads": false, - "smartForceEdgeAlignments": true + "jParameters": { + "geneFeatureToAlign": "JRegionWithP", + "minSumScore": 40, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": true, + "floatingRightBound": false, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.75, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 40.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + } }, - "dna.multiplex.rstrand.v1": { - "fixSeed": true, - "libraryStructure": "R1V", - "vParameters": { - "geneFeatureToAlign": "VRegionWithP", - "minSumScore": 200, - "relativeMinScore": 0.9, - "parameters": { - "type": "kaligner2", - "mapperNValue": 10, - "mapperKValue": 1, - "floatingLeftBound": false, - "floatingRightBound": true, - "mapperAbsoluteMinClusterScore": 102, - "mapperExtraClusterScore": -38, - "mapperMatchScore": 95, - "mapperMismatchScore": -14, - "mapperOffsetShiftScore": -82, - "mapperSlotCount": 6, - "mapperMaxClusters": 4, - "mapperMaxClusterIndels": 4, - "mapperKMersPerPosition": 4, - "mapperAbsoluteMinScore": 100, - "mapperRelativeMinScore": 0.8, - "mapperMinSeedsDistance": 5, - "mapperMaxSeedsDistance": 15, - "alignmentStopPenalty": 0, - "absoluteMinScore": 150, - "relativeMinScore": 0.8, - "maxHits": 4, - "scoring": { - "type": "affine", - "subsMatrix": "simple(match = 10, mismatch = -19)", - "gapOpenPenalty": -40, - "gapExtensionPenalty": -11 - } - } - }, - "dParameters": { - "geneFeatureToAlign": "DRegionWithP", - "absoluteMinScore": 25.0, - "relativeMinScore": 0.85, - "maxHits": 3, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - }, - "jParameters": { - "geneFeatureToAlign": "JRegionWithP", - "minSumScore": 140, - "relativeMinScore": 0.8, - "parameters": { - "type": "kaligner2", - "mapperNValue": 7, - "mapperKValue": 1, - "floatingLeftBound": true, - "floatingRightBound": false, - "mapperAbsoluteMinClusterScore": 102, - "mapperExtraClusterScore": -38, - "mapperMatchScore": 95, - "mapperMismatchScore": -14, - "mapperOffsetShiftScore": -82, - "mapperSlotCount": 6, - "mapperMaxClusters": 4, - "mapperMaxClusterIndels": 4, - "mapperKMersPerPosition": 4, - "mapperAbsoluteMinScore": 100, - "mapperRelativeMinScore": 0.8, - "mapperMinSeedsDistance": 5, - "mapperMaxSeedsDistance": 5, - "alignmentStopPenalty": 0, - "absoluteMinScore": 140, - "relativeMinScore": 0.8, - "maxHits": 3, - "scoring": { - "type": "affine", - "subsMatrix": "simple(match = 10, mismatch = -19)", - "gapOpenPenalty": -40, - "gapExtensionPenalty": -11 - } - } - }, - "cParameters": { - "geneFeatureToAlign": "CExon1", - "minSumScore": 40, - "relativeMinScore": 0.8, - "parameters": { - "type": "kaligner", - "mapperKValue": 5, - "floatingLeftBound": false, - "floatingRightBound": false, - "mapperAbsoluteMinScore": 1.5, - "mapperRelativeMinScore": 0.75, - "mapperMatchScore": 1.0, - "mapperMismatchPenalty": -0.1, - "mapperOffsetShiftPenalty": -0.3, - "mapperMinSeedsDistance": 4, - "mapperMaxSeedsDistance": 10, - "minAlignmentLength": 15, - "maxAdjacentIndels": 2, - "alignmentStopPenalty": -1000, - "absoluteMinScore": 40.0, - "relativeMinScore": 0.87, - "maxHits": 7, - "scoring": { - "type": "linear", - "subsMatrix": "simple(match = 5, mismatch = -9)", - "gapPenalty": -12 - } - } - }, - "vjAlignmentOrder": "VThenJ", - "includeDScore": false, - "includeCScore": false, - "mergerParameters": { - "qualityMergingAlgorithm": "MaxSubtraction", - "minimalOverlap": 17, - "minimalIdentity": 0.9, - "identityType": "Unweighted" - }, - "minSumScore": 300, - "maxHits": 5, - "relativeMinVFR3CDR3Score": 0.7, - "allowPartialAlignments": false, - "allowNoCDR3PartAlignments": false, - "allowChimeras": false, - "alignmentBoundaryTolerance": 5, - "minChimeraDetectionScore": 120, - "vjOverlapWindow": 3, - "readsLayout": "ReverseOnly", - "saveOriginalReads": false, - "smartForceEdgeAlignments": true - } + "cParameters": { + "geneFeatureToAlign": "CExon1", + "minSumScore": 40, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": false, + "floatingRightBound": false, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.75, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 40.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + } + }, + "vjAlignmentOrder": "VThenJ", + "includeDScore": false, + "includeCScore": false, + "mergerParameters": { + "qualityMergingAlgorithm": "MaxSubtraction", + "minimalOverlap": 17, + "minimalIdentity": 0.9, + "identityType": "Unweighted" + }, + "minSumScore": 120.0, + "maxHits": 5, + "relativeMinVFR3CDR3Score": 0.7, + "allowPartialAlignments": false, + "allowNoCDR3PartAlignments": false, + "allowChimeras": false, + "alignmentBoundaryTolerance": 5, + "minChimeraDetectionScore": 120, + "vjOverlapWindow": 3, + "readsLayout": "Opposite", + "saveOriginalReads": false, + "smartForceEdgeAlignments": true + }, + "kaligner2": { + "fixSeed": true, + "libraryStructure": "Unknown", + "vParameters": { + "geneFeatureToAlign": "VRegionWithP", + "minSumScore": 150, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner2", + "mapperNValue": 8, + "mapperKValue": 1, + "floatingLeftBound": true, + "floatingRightBound": true, + "mapperAbsoluteMinClusterScore": 102, + "mapperExtraClusterScore": -38, + "mapperMatchScore": 95, + "mapperMismatchScore": -14, + "mapperOffsetShiftScore": -82, + "mapperSlotCount": 6, + "mapperMaxClusters": 4, + "mapperMaxClusterIndels": 4, + "mapperKMersPerPosition": 4, + "mapperAbsoluteMinScore": 100, + "mapperRelativeMinScore": 0.8, + "mapperMinSeedsDistance": 5, + "mapperMaxSeedsDistance": 5, + "alignmentStopPenalty": 0, + "absoluteMinScore": 150, + "relativeMinScore": 0.8, + "maxHits": 3, + "scoring": { + "type": "affine", + "subsMatrix": "simple(match = 10, mismatch = -19)", + "gapOpenPenalty": -40, + "gapExtensionPenalty": -11 + } + } + }, + "dParameters": { + "geneFeatureToAlign": "DRegionWithP", + "absoluteMinScore": 25.0, + "relativeMinScore": 0.85, + "maxHits": 3, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + }, + "jParameters": { + "geneFeatureToAlign": "JRegionWithP", + "minSumScore": 150, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner2", + "mapperNValue": 8, + "mapperKValue": 1, + "floatingLeftBound": true, + "floatingRightBound": false, + "mapperAbsoluteMinClusterScore": 102, + "mapperExtraClusterScore": -38, + "mapperMatchScore": 95, + "mapperMismatchScore": -14, + "mapperOffsetShiftScore": -82, + "mapperSlotCount": 6, + "mapperMaxClusters": 4, + "mapperMaxClusterIndels": 4, + "mapperKMersPerPosition": 4, + "mapperAbsoluteMinScore": 100, + "mapperRelativeMinScore": 0.8, + "mapperMinSeedsDistance": 5, + "mapperMaxSeedsDistance": 5, + "alignmentStopPenalty": 0, + "absoluteMinScore": 150, + "relativeMinScore": 0.8, + "maxHits": 3, + "scoring": { + "type": "affine", + "subsMatrix": "simple(match = 10, mismatch = -19)", + "gapOpenPenalty": -40, + "gapExtensionPenalty": -11 + } + } + }, + "cParameters": { + "geneFeatureToAlign": "CExon1", + "minSumScore": 40, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": false, + "floatingRightBound": false, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.75, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 40.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + } + }, + "vjAlignmentOrder": "VThenJ", + "includeDScore": false, + "includeCScore": false, + "mergerParameters": { + "qualityMergingAlgorithm": "MaxSubtraction", + "minimalOverlap": 17, + "minimalIdentity": 0.9, + "identityType": "Unweighted" + }, + "minSumScore": 120.0, + "maxHits": 5, + "relativeMinVFR3CDR3Score": 0.7, + "allowPartialAlignments": false, + "allowNoCDR3PartAlignments": false, + "allowChimeras": false, + "alignmentBoundaryTolerance": 5, + "minChimeraDetectionScore": 120, + "vjOverlapWindow": 3, + "readsLayout": "Opposite", + "saveOriginalReads": false, + "smartForceEdgeAlignments": true + }, + "rna-seq": { + "fixSeed": true, + "libraryStructure": "Unknown", + "vParameters": { + "geneFeatureToAlign": "VTranscriptWithP", + "minSumScore": 80, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": false, + "floatingRightBound": true, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.7, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 55.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -11)", + "gapPenalty": -21 + } + } + }, + "dParameters": { + "geneFeatureToAlign": "DRegionWithP", + "absoluteMinScore": 25.0, + "relativeMinScore": 0.85, + "maxHits": 3, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -11)", + "gapPenalty": -21 + } + }, + "jParameters": { + "geneFeatureToAlign": "JRegionWithP", + "minSumScore": 60, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": true, + "floatingRightBound": false, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.75, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 8, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 50.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -11)", + "gapPenalty": -21 + } + } + }, + "cParameters": { + "geneFeatureToAlign": "CExon1", + "minSumScore": 40, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": false, + "floatingRightBound": false, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.75, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 40.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -11)", + "gapPenalty": -21 + } + } + }, + "vjAlignmentOrder": "VThenJ", + "includeDScore": true, + "includeCScore": true, + "mergerParameters": { + "qualityMergingAlgorithm": "MaxSubtraction", + "minimalOverlap": 17, + "minimalIdentity": 0.9, + "identityType": "Unweighted" + }, + "minSumScore": 200.0, + "maxHits": 5, + "relativeMinVFR3CDR3Score": 0.7, + "allowPartialAlignments": false, + "allowNoCDR3PartAlignments": false, + "allowChimeras": false, + "alignmentBoundaryTolerance": 5, + "minChimeraDetectionScore": 120, + "vjOverlapWindow": 3, + "readsLayout": "Opposite", + "saveOriginalReads": false, + "smartForceEdgeAlignments": true + }, + "dna.multiplex.rstrand.v1": { + "fixSeed": true, + "libraryStructure": "R1V", + "vParameters": { + "geneFeatureToAlign": "VRegionWithP", + "minSumScore": 200, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner2", + "mapperNValue": 10, + "mapperKValue": 1, + "floatingLeftBound": false, + "floatingRightBound": true, + "mapperAbsoluteMinClusterScore": 102, + "mapperExtraClusterScore": -38, + "mapperMatchScore": 95, + "mapperMismatchScore": -14, + "mapperOffsetShiftScore": -82, + "mapperSlotCount": 6, + "mapperMaxClusters": 4, + "mapperMaxClusterIndels": 4, + "mapperKMersPerPosition": 4, + "mapperAbsoluteMinScore": 100, + "mapperRelativeMinScore": 0.8, + "mapperMinSeedsDistance": 5, + "mapperMaxSeedsDistance": 15, + "alignmentStopPenalty": 0, + "absoluteMinScore": 150, + "relativeMinScore": 0.8, + "maxHits": 4, + "scoring": { + "type": "affine", + "subsMatrix": "simple(match = 10, mismatch = -19)", + "gapOpenPenalty": -40, + "gapExtensionPenalty": -11 + } + } + }, + "dParameters": { + "geneFeatureToAlign": "DRegionWithP", + "absoluteMinScore": 25.0, + "relativeMinScore": 0.85, + "maxHits": 3, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + }, + "jParameters": { + "geneFeatureToAlign": "JRegionWithP", + "minSumScore": 140, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner2", + "mapperNValue": 7, + "mapperKValue": 1, + "floatingLeftBound": true, + "floatingRightBound": false, + "mapperAbsoluteMinClusterScore": 102, + "mapperExtraClusterScore": -38, + "mapperMatchScore": 95, + "mapperMismatchScore": -14, + "mapperOffsetShiftScore": -82, + "mapperSlotCount": 6, + "mapperMaxClusters": 4, + "mapperMaxClusterIndels": 4, + "mapperKMersPerPosition": 4, + "mapperAbsoluteMinScore": 100, + "mapperRelativeMinScore": 0.8, + "mapperMinSeedsDistance": 5, + "mapperMaxSeedsDistance": 5, + "alignmentStopPenalty": 0, + "absoluteMinScore": 140, + "relativeMinScore": 0.8, + "maxHits": 3, + "scoring": { + "type": "affine", + "subsMatrix": "simple(match = 10, mismatch = -19)", + "gapOpenPenalty": -40, + "gapExtensionPenalty": -11 + } + } + }, + "cParameters": { + "geneFeatureToAlign": "CExon1", + "minSumScore": 40, + "relativeMinScore": 0.97, + "parameters": { + "type": "kaligner", + "mapperKValue": 5, + "floatingLeftBound": false, + "floatingRightBound": false, + "mapperAbsoluteMinScore": 1.5, + "mapperRelativeMinScore": 0.75, + "mapperMatchScore": 1.0, + "mapperMismatchPenalty": -0.1, + "mapperOffsetShiftPenalty": -0.3, + "mapperMinSeedsDistance": 4, + "mapperMaxSeedsDistance": 10, + "minAlignmentLength": 15, + "maxAdjacentIndels": 2, + "alignmentStopPenalty": -1000, + "absoluteMinScore": 40.0, + "relativeMinScore": 0.87, + "maxHits": 7, + "scoring": { + "type": "linear", + "subsMatrix": "simple(match = 5, mismatch = -9)", + "gapPenalty": -12 + } + } + }, + "vjAlignmentOrder": "VThenJ", + "includeDScore": false, + "includeCScore": false, + "mergerParameters": { + "qualityMergingAlgorithm": "MaxSubtraction", + "minimalOverlap": 17, + "minimalIdentity": 0.9, + "identityType": "Unweighted" + }, + "minSumScore": 300, + "maxHits": 5, + "relativeMinVFR3CDR3Score": 0.7, + "allowPartialAlignments": false, + "allowNoCDR3PartAlignments": false, + "allowChimeras": false, + "alignmentBoundaryTolerance": 5, + "minChimeraDetectionScore": 120, + "vjOverlapWindow": 3, + "readsLayout": "ReverseOnly", + "saveOriginalReads": false, + "smartForceEdgeAlignments": true + } } \ No newline at end of file From bc8d0ae9c41e82cd8bbf3b4d769e8c00c7449571 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 14:52:10 +0300 Subject: [PATCH 203/282] feat: gap open penalty made more strict -> -62 --- src/main/resources/parameters/vdjcaligner_parameters.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/parameters/vdjcaligner_parameters.json b/src/main/resources/parameters/vdjcaligner_parameters.json index c66afde9a..1e748a6b6 100644 --- a/src/main/resources/parameters/vdjcaligner_parameters.json +++ b/src/main/resources/parameters/vdjcaligner_parameters.json @@ -155,7 +155,7 @@ "scoring": { "type": "affine", "subsMatrix": "simple(match = 10, mismatch = -19)", - "gapOpenPenalty": -40, + "gapOpenPenalty": -62, "gapExtensionPenalty": -11 } } @@ -201,7 +201,7 @@ "scoring": { "type": "affine", "subsMatrix": "simple(match = 10, mismatch = -19)", - "gapOpenPenalty": -40, + "gapOpenPenalty": -62, "gapExtensionPenalty": -11 } } From 607b8885b097c2fffa7b2337d8d5d33179c0c71e Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 20:56:22 +0300 Subject: [PATCH 204/282] wip --- .../basictypes/VDJCAlignmentsReader.java | 30 +- .../milaboratory/mixcr/basictypes/tag/IO.java | 48 ++-- .../tag/SequenceAndQualityTagValue.java | 2 + .../basictypes/tag/SequenceTagValue.java | 2 + .../mixcr/basictypes/tag/TagValue.java | 8 +- .../milaboratory/mixcr/cli/CommandAlign.java | 33 ++- .../mixcr/cli/CommandCorrectTags.java | 265 ++++++++++++++++++ .../mixcr/cli/CommandVersionInfo.java | 2 +- .../java/com/milaboratory/mixcr/cli/Main.java | 7 +- 9 files changed, 348 insertions(+), 49 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index 3b51816f4..42d250e74 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -34,6 +34,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.PrimitivIState; import com.milaboratory.primitivio.blocks.PrimitivIBlocks; import com.milaboratory.primitivio.blocks.PrimitivIBlocksStats; import com.milaboratory.primitivio.blocks.PrimitivIHybrid; @@ -69,6 +70,8 @@ public final class VDJCAlignmentsReader extends PipelineConfigurationReaderMiXCR List usedGenes; TagsInfo tagsInfo; + PrimitivIState iState; + String versionInfo; String magic; long counter = 0; @@ -128,11 +131,7 @@ public VDJCAlignmentsReader(Path path, VDJCLibraryRegistry vdjcRegistry, int con } } - // public void init() { - // init(null); - // } - - public void init() { + public void ensureInitialized() { if (reader != null) return; @@ -159,6 +158,7 @@ public void init() { tagsInfo = i.readObject(TagsInfo.class); this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, parameters, vdjcRegistry); + this.iState = i.getState(); } this.reader = input.beginPrimitivIBlocks(VDJCAlignments.class, readAheadBlocks); @@ -171,23 +171,23 @@ public PrimitivIBlocksStats getStats() { } public synchronized VDJCAlignerParameters getParameters() { - init(); + ensureInitialized(); return parameters; } public synchronized List getUsedGenes() { - init(); + ensureInitialized(); return usedGenes; } @Override public synchronized PipelineConfiguration getPipelineConfiguration() { - init(); + ensureInitialized(); return pipelineConfiguration; } public TagsInfo getTagsInfo() { - init(); + ensureInitialized(); return tagsInfo; } @@ -197,7 +197,7 @@ public TagsInfo getTagsInfo() { * @return information about version of MiXCR which produced this file */ public String getVersionInfo() { - init(); + ensureInitialized(); return versionInfo; } @@ -207,10 +207,16 @@ public String getVersionInfo() { * @return magic bytes of this file */ public String getMagic() { - init(); + ensureInitialized(); return magic; } + /** Return primitivI state that can be used to read or write alignments returned by the reader */ + public PrimitivIState getIState() { + ensureInitialized(); + return iState; + } + public long getNumberOfReads() { return numberOfReads; } @@ -252,7 +258,7 @@ public synchronized VDJCAlignments take() { if (closed) return null; - init(); + ensureInitialized(); VDJCAlignments al = reader.take(); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java index e7e0e7ca5..cc1c9788c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java @@ -5,7 +5,6 @@ import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.Serializer; -import com.milaboratory.util.ByteString; import gnu.trove.impl.Constants; import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TObjectDoubleHashMap; @@ -16,30 +15,37 @@ public final class IO { private IO() { } - public static class TagValueSerializer implements Serializer { + public static class SequenceAndQualityTagValueSerializer implements Serializer { @Override - public void write(PrimitivO output, TagValue obj) { - if (obj instanceof SequenceTagValue) { - output.writeByte(0); - output.writeObject(((SequenceTagValue) obj).sequence); - } else if (obj instanceof SequenceAndQualityTagValue) { - output.writeByte(1); - output.writeObject(((SequenceAndQualityTagValue) obj).data); - } else - throw new IllegalArgumentException("Unsupported type."); + public void write(PrimitivO output, SequenceAndQualityTagValue obj) { + output.writeObject(obj.data); } @Override - public TagValue read(PrimitivI input) { - byte t = input.readByte(); - switch (t) { - case 0: - return new SequenceTagValue(input.readObject(NucleotideSequence.class)); - case 1: - return new SequenceAndQualityTagValue(input.readObject(NSequenceWithQuality.class)); - default: - throw new IllegalArgumentException("Malformed data."); - } + public SequenceAndQualityTagValue read(PrimitivI input) { + return new SequenceAndQualityTagValue(input.readObject(NSequenceWithQuality.class)); + } + + @Override + public boolean isReference() { + return true; + } + + @Override + public boolean handlesReference() { + return false; + } + } + + public static class SequenceTagValueSerializer implements Serializer { + @Override + public void write(PrimitivO output, SequenceTagValue obj) { + output.writeObject(obj.sequence); + } + + @Override + public SequenceTagValue read(PrimitivI input) { + return new SequenceTagValue(input.readObject(NucleotideSequence.class)); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java index 8f2319e2c..e9420af00 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java @@ -1,10 +1,12 @@ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.primitivio.annotations.Serializable; import org.jetbrains.annotations.NotNull; import java.util.Objects; +@Serializable(by = IO.SequenceAndQualityTagValueSerializer.class) public final class SequenceAndQualityTagValue implements TagValue { public final NSequenceWithQuality data; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java index 2f1abe829..d67e4f8c6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java @@ -1,10 +1,12 @@ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.primitivio.annotations.Serializable; import org.jetbrains.annotations.NotNull; import java.util.Objects; +@Serializable(by = IO.SequenceTagValueSerializer.class) public final class SequenceTagValue implements TagValue { public final NucleotideSequence sequence; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java index ecd192b5a..2c2a8018b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java @@ -1,6 +1,12 @@ package com.milaboratory.mixcr.basictypes.tag; -// @Serializable(custom = {@CustomSerializer(id = 1, type = )}) +import com.milaboratory.primitivio.annotations.CustomSerializer; +import com.milaboratory.primitivio.annotations.Serializable; + +@Serializable(custom = { + @CustomSerializer(id = 1, type = SequenceAndQualityTagValue.class), + @CustomSerializer(id = 2, type = SequenceTagValue.class) +}) public interface TagValue extends Comparable { /** * Returns true for tag values that can be used as a grouping key, diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 4e827f184..d67cc8573 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -364,7 +364,8 @@ public ActionConfiguration getConfiguration() { !noMerge, getLibrary().getLibraryId(), limit, - getQualityTrimmerParameters()); + getQualityTrimmerParameters(), + tagPattern); } /** Set of parameters that completely (uniquely) determine align action */ @@ -375,7 +376,8 @@ public ActionConfiguration getConfiguration() { @JsonTypeInfo( use = JsonTypeInfo.Id.CLASS, include = JsonTypeInfo.As.PROPERTY, - property = "type") + property = "type" + ) public static class AlignConfiguration implements ActionConfiguration { /** * Aligner parameters @@ -397,18 +399,22 @@ public static class AlignConfiguration implements ActionConfiguration 2) + throwValidationException("Tag pattern contains too many read groups, only R1 or R1+R2 combinations are supported.", false); + return new TagSearchPlan(readSearchPlan, tagShortcuts, readShortcuts, parseInfo.getTags()); } @@ -508,9 +516,12 @@ public void run1() throws Exception { warn(l); } + // Tags + TagSearchPlan tagSearchPlan = getTagPattern(); + // Creating aligner VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters, - isInputPaired(), !noMerge); + tagSearchPlan.readShortcuts.size() == 2, !noMerge); int numberOfExcludedNFGenes = 0; int numberOfExcludedFGenes = 0; @@ -556,8 +567,6 @@ else if (featureSequence.containsWildcards()) report.setOutputFiles(getOutput()); report.setCommandLine(getCommandLineArguments()); - // Tags - TagSearchPlan tagSearchPlan = getTagPattern(); if (tagSearchPlan != null) report.setTagReport(tagSearchPlan.report); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java new file mode 100644 index 000000000..c57e493e5 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java @@ -0,0 +1,265 @@ +package com.milaboratory.mixcr.cli; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.Processor; +import cc.redberry.pipe.blocks.FilteringPort; +import cc.redberry.pipe.util.CountingOutputPort; +import com.google.common.hash.Hasher; +import com.google.common.hash.Hashing; +import com.milaboratory.cli.ActionConfiguration; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.mitool.refinement.CorrectionNode; +import com.milaboratory.mitool.refinement.CorrectionReport; +import com.milaboratory.mitool.refinement.TagCorrector; +import com.milaboratory.mitool.refinement.TagCorrectorParameters; +import com.milaboratory.mixcr.basictypes.IOUtil; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; +import com.milaboratory.mixcr.basictypes.tag.*; +import com.milaboratory.primitivio.PrimitivIOStateBuilder; +import com.milaboratory.util.ReportHelper; +import com.milaboratory.util.SmartProgressReporter; +import com.milaboratory.util.TempFileManager; +import com.milaboratory.util.sorting.HashSorter; +import gnu.trove.list.array.TIntArrayList; +import org.apache.commons.io.FileUtils; +import picocli.CommandLine; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.Comparator; +import java.util.List; +import java.util.Objects; +import java.util.function.ToIntFunction; + +import static com.milaboratory.mixcr.cli.CommandCorrectTags.CORRECT_TAGS_COMMAND_NAME; +import static picocli.CommandLine.Option; + +@CommandLine.Command(name = CORRECT_TAGS_COMMAND_NAME, + sortOptions = false, + separator = " ", + description = "Builds alignments with V,D,J and C genes for input sequencing reads.") +public class CommandCorrectTags extends ACommandWithSmartOverwriteWithSingleInputMiXCR { + static final String CORRECT_TAGS_COMMAND_NAME = "correctTags"; + + @Option(description = "This parameter determines how thorough the procedure should eliminate variants looking like errors. " + + "Smaller value leave less erroneous variants at the cost of accidentally correcting true variants. " + + "This value approximates the fraction of erroneous variants the algorithm will miss (type II errors).", + names = {"-p", "--power"}) + public double power = 1E-3; + + @Option(description = "Expected background non-sequencing-related substitution rate", + names = {"-s", "--substitution-rate"}) + public double backgroundSubstitutionRate = 1E-3; + + @Option(description = "Expected background non-sequencing-related indel rate", + names = {"-i", "--indel-rate"}) + public double backgroundIndelRate = 1E-5; + + @Option(description = "Minimal quality score for the tag. " + + "Tags having positions with lower quality score will be discarded, if not corrected.", + names = {"-q", "--min-quality"}) + public int minQuality = 12; + + @Option(description = "Maximal number of substitutions to search for.", + names = {"--max-substitutions"}) + public int maxSubstitutions = 2; + + @Option(description = "Maximal number of indels to search for.", + names = {"--max-indels"}) + public int maxIndels = 1; + + @Option(description = "Use system temp folder for temporary files.", + names = {"--use-system-temp"}) + public boolean useSystemTemp = false; + + @Option(description = "Memory budget", + names = {"--memory-budget"}) + public long memoryBudget = 1L << 32; // 4 GB + + @Option(description = CommonDescriptions.REPORT, + names = {"-r", "--report"}) + public String reportFile; + + private Path tempFolder() { + try { + File tempFolder; + if (useSystemTemp) + tempFolder = Paths.get(System.getProperty("java.io.tmpdir")) + .resolve(Paths.get(out).getFileName().getFileName() + "." + + Long.toString(System.nanoTime(), 36)) + .toFile(); + else + tempFolder = new File(out + ".tmp"); + if (tempFolder.exists()) + FileUtils.deleteDirectory(tempFolder); + Files.createDirectory(tempFolder.toPath()); + TempFileManager.register(tempFolder); + return tempFolder.toPath(); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + TagCorrectorParameters getParameters() { + return new TagCorrectorParameters( + power, backgroundSubstitutionRate, backgroundIndelRate, + minQuality, maxSubstitutions, maxIndels + ); + } + + @Override + public ActionConfiguration getConfiguration() { + return new CorrectTagsConfiguration(getParameters()); + } + + @Override + public void run1() throws Exception { + CorrectionNode correctioResult; + CorrectionReport report; + int[] targetTagIndices; + try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in)) { + TagCorrector corrector = new TagCorrector(getParameters(), + tempFolder(), "", + memoryBudget, + 4, 4); + SmartProgressReporter.startProgressReport(corrector); + TagsInfo tagsInfo = reader.getTagsInfo(); + + List tagNames = new ArrayList<>(); + TIntArrayList indicesBuilder = new TIntArrayList(); + for (int i = 0; i < tagsInfo.tags.length; i++) { + TagInfo tag = tagsInfo.tags[i]; + assert i == tag.getIndex(); // just in case + if (tag.getValueType() == TagValueType.SequenceAndQuality) + indicesBuilder.add(i); + tagNames.add(tag.getName()); + } + targetTagIndices = indicesBuilder.toArray(); + + System.out.println("Correction will be applied to the following tags: " + String.join(", ", tagNames)); + + // Extractor of tag information from the alignments for the tag corrector + Processor mapper = input -> { + if (input.getTagCounter().size() != 1) + throwExecutionException("This procedure don't support aggregated tags. " + + "Please run tag correction for *.vdjca files produced by 'align'."); + TagTuple tagTuple = input.getTagCounter().keys().iterator().next(); + NSequenceWithQuality[] tags = new NSequenceWithQuality[targetTagIndices.length]; + for (int i = 0; i < targetTagIndices.length; i++) + tags[i] = ((SequenceAndQualityTagValue) tagTuple.tags[targetTagIndices[i]]).data; + return tags; + }; + OutputPort cInput = CUtils.wrap(reader, mapper); + correctioResult = corrector.correct(cInput, tagNames, reader); + report = corrector.getReport(); + } + + ToIntFunction hashFunction = al -> { + TagValue[] tags = al.getTagCounter().keys().iterator().next().tags; + //noinspection UnstableApiUsage + Hasher hasher = Hashing.murmur3_32_fixed().newHasher(); + for (int i : targetTagIndices) + //noinspection UnstableApiUsage + hasher.putInt(((SequenceAndQualityTagValue) tags[i]).data.getSequence().hashCode()); + //noinspection UnstableApiUsage + return hasher.hash().hashCode(); + }; + + Comparator comparator = (al1, al2) -> { + TagValue[] tags1 = al1.getTagCounter().keys().iterator().next().tags; + TagValue[] tags2 = al2.getTagCounter().keys().iterator().next().tags; + int c; + for (int i : targetTagIndices) + if ((c = ((SequenceAndQualityTagValue) tags1[i]).data.getSequence().compareTo( + ((SequenceAndQualityTagValue) tags2[i]).data.getSequence())) != 0) + return c; + return 0; + }; + + try ( + VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in); + VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out) + ) { + PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); + IOUtil.registerGeneReferences(stateBuilder, reader.getUsedGenes(), reader.getParameters()); + + HashSorter hashSorter = new HashSorter<>( + VDJCAlignments.class, + hashFunction, comparator, + 4, tempFolder().resolve("hashsorter"), + 4, 4, + stateBuilder.getOState(), stateBuilder.getIState(), + memoryBudget, 10000 + ); + + SmartProgressReporter.startProgressReport("Applying correction & sorting alignments", reader); + + Processor mapper = al -> { + TagTuple tt = al.getTagCounter().keys().iterator().next(); + TagValue[] newTags = tt.tags.clone(); + CorrectionNode cn = correctioResult; + for (int i : targetTagIndices) { + NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); + cn = cn.getNextLevel().get(current); + if (cn == null) { + report.setFilteredRecords(report.getFilteredRecords() + 1); + return al.setTagCounter(null); // will be filtered right before hash sorter + } + newTags[i] = new SequenceAndQualityTagValue(cn.getCorrectValue()); + } + return al.setTagCounter(new TagCounter(new TagTuple(newTags))); + }; + + // Creating output port with corrected and filtered tags + OutputPort hsInput = new FilteringPort<>( + CUtils.wrap(reader, mapper), al -> al.getTagCounter() != null); + + // Running hash sorter + CountingOutputPort sorted = new CountingOutputPort<>(hashSorter.port(hsInput)); + + SmartProgressReporter.startProgressReport("Writing result", + SmartProgressReporter.extractProgress(sorted, reader.getNumberOfReads())); + + // Initializing and writing results to the output file + writer.header(reader, getFullPipelineConfiguration(), reader.getTagsInfo()); + for (VDJCAlignments al : CUtils.it(sorted)) + writer.write(al); + } + + report.writeReport(ReportHelper.STDOUT); + } + + public static final class CorrectTagsConfiguration implements ActionConfiguration { + final TagCorrectorParameters params; + + public CorrectTagsConfiguration(TagCorrectorParameters params) { + this.params = params; + } + + @Override + public String actionName() { + return CORRECT_TAGS_COMMAND_NAME; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + CorrectTagsConfiguration that = (CorrectTagsConfiguration) o; + return params.equals(that.params); + } + + @Override + public int hashCode() { + return Objects.hash(params); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java index ecffe53fa..6be1ead74 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java @@ -49,7 +49,7 @@ public void run0() throws Exception { String i = inputFile.toLowerCase(); if (i.endsWith(".vdjca.gz") || i.endsWith(".vdjca")) { try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(inputFile)) { - reader.init(); + reader.ensureInitialized(); System.out.println("MagicBytes = " + reader.getMagic()); System.out.println(reader.getVersionInfo()); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index eb48440ba..e326d370c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -30,10 +30,10 @@ package com.milaboratory.mixcr.cli; import com.milaboratory.cli.ValidationException; -import com.milaboratory.mixcr.cli.postanalysis.*; import com.milaboratory.milm.LM; import com.milaboratory.milm.LicenseError; import com.milaboratory.milm.LicenseErrorType; +import com.milaboratory.mixcr.cli.postanalysis.*; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.VersionInfo; import io.repseq.core.VDJCLibraryRegistry; @@ -53,6 +53,8 @@ import java.util.function.Consumer; import java.util.prefs.Preferences; +import static com.milaboratory.mixcr.cli.CommandCorrectTags.CORRECT_TAGS_COMMAND_NAME; + public final class Main { private static boolean initialized = false; @@ -224,12 +226,13 @@ public static CommandLine mkCmd() { .addSubcommand("exportTables", CommandPaExportTables.class) .addSubcommand("exportPreprocTables", CommandPaExportTablesPreprocSummary.class) - .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) // .addSubcommand("groupCells", CommandGroupCells.class) .addSubcommand("assembleContigs", CommandAssembleContigs.class) + .addSubcommand(CORRECT_TAGS_COMMAND_NAME, CommandCorrectTags.class) + .addSubcommand("assemblePartial", CommandAssemblePartialAlignments.class) .addSubcommand("extend", CommandExtend.class) From 26850b3b86318c0ef74335e21dc18dbb57da0dfe Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 23:17:20 +0300 Subject: [PATCH 205/282] feat: migration to encapsulated global object mappers --- build.gradle.kts | 8 +++++--- .../assembler/CloneAssemblerParametersPresets.java | 2 +- .../assembler/fullseq/FullSeqAssemblerParameters.java | 2 +- .../mixcr/basictypes/VDJCSProperties.java | 2 +- .../java/com/milaboratory/mixcr/cli/CommandAlign.java | 2 +- .../milaboratory/mixcr/cli/CommandPipelineInfo.java | 2 +- src/main/java/com/milaboratory/mixcr/cli/Main.java | 5 +++++ .../mixcr/cli/postanalysis/CommandPaListMetrics.java | 2 +- .../milaboratory/mixcr/cli/postanalysis/PaResult.java | 8 ++++---- .../PartialAlignmentsAssemblerParameters.java | 4 ++-- .../mixcr/vdjaligners/VDJCParametersPresets.java | 2 +- .../mixcr/assembler/CloneAssemblerParametersTest.java | 8 ++++---- .../assembler/CloneClusteringParametersTest.java | 4 ++-- .../mixcr/assembler/CloneFactoryParametersTest.java | 11 ++++------- .../mixcr/assembler/ClusteringFilterTest.java | 4 ++-- .../assembler/VJCClonalAlignerParametersTest.java | 4 ++-- .../com/milaboratory/mixcr/cli/AlignerReportTest.java | 2 +- .../milaboratory/mixcr/cli/ChainUsageStatsTest.java | 2 +- .../mixcr/cli/postanalysis/IsolationGroupTest.java | 4 ++-- .../milaboratory/mixcr/util/MiXCRVersionInfoTest.java | 4 ++-- .../mixcr/vdjaligners/DAlignerParametersTest.java | 4 ++-- .../vdjaligners/KGeneAlignmentParametersTest.java | 4 ++-- .../mixcr/vdjaligners/VDJCAlignerParametersTest.java | 4 ++-- 23 files changed, 49 insertions(+), 45 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index e96001daa..5d8b3f25c 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -81,11 +81,11 @@ repositories { } } -val milibVersion = "1.15.0-32-master" +val milibVersion = "1.15.0-38-master" val repseqioVersion = "1.3.5-26-master" val mitoolVersion = "1.3.5-25-master" val miplotsVersion = "0.1-19-master" -val jacksonVersion = "2.13.2.2" +val jacksonBomVersion = "2.13.3" dependencies { api("com.milaboratory:milib:$milibVersion") @@ -99,7 +99,9 @@ dependencies { // implementation("com.milaboratory:milm2-jvm:0.2.0-test-2") { isChanging = true } implementation("com.milaboratory:milm2-jvm:1.1.0") - implementation("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion") + implementation(platform("com.fasterxml.jackson:jackson-bom:$jacksonBomVersion")) + implementation("com.fasterxml.jackson.module:jackson-module-kotlin") + implementation("commons-io:commons-io:2.11.0") implementation("org.lz4:lz4-java:1.8.0") implementation("net.sf.trove4j:trove4j:3.0.3") diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java index 9bd46c5fc..bf0fe32c9 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java @@ -54,7 +54,7 @@ private static void ensureInitialized() { TypeReference> typeRef = new TypeReference>() { }; - map = GlobalObjectMappers.ONE_LINE.readValue(is, typeRef); + map = GlobalObjectMappers.getOneLine().readValue(is, typeRef); } catch (IOException ioe) { throw new RuntimeException(ioe); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java index dfd11c843..e2f50f840 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java @@ -281,7 +281,7 @@ private static void ensureInitialized() { TypeReference> typeRef = new TypeReference>() { }; - map = GlobalObjectMappers.ONE_LINE.readValue(is, typeRef); + map = GlobalObjectMappers.getOneLine().readValue(is, typeRef); } catch (IOException ioe) { throw new RuntimeException(ioe); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java index 4e94bd716..1ec73415b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java @@ -117,7 +117,7 @@ public int hashCode() { @Override public String toString() { try { - return GlobalObjectMappers.PRETTY.writeValueAsString(this); + return GlobalObjectMappers.getPretty().writeValueAsString(this); } catch (JsonProcessingException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index d67cc8573..f2fa9a51d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -248,7 +248,7 @@ public VDJCAlignerParameters getAlignerParameters() { VDJCAlignerParameters alignerParameters; if (alignerParametersName.endsWith(".json")) { try { - alignerParameters = GlobalObjectMappers.ONE_LINE.readValue(new File(alignerParametersName), VDJCAlignerParameters.class); + alignerParameters = GlobalObjectMappers.getOneLine().readValue(new File(alignerParametersName), VDJCAlignerParameters.class); } catch (IOException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java index 5bdb07f57..05ac58900 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java @@ -64,7 +64,7 @@ public void run0() throws Exception { } public static void analysisPipelineInfoJson(String file) throws JsonProcessingException { - System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(PipelineConfigurationReaderMiXCR + System.out.println(GlobalObjectMappers.getPretty().writeValueAsString(PipelineConfigurationReaderMiXCR .sFromFile(file))); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index e326d370c..5e09907e9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -34,10 +34,12 @@ import com.milaboratory.milm.LicenseError; import com.milaboratory.milm.LicenseErrorType; import com.milaboratory.mixcr.cli.postanalysis.*; +import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.VersionInfo; import io.repseq.core.VDJCLibraryRegistry; import io.repseq.seqbase.SequenceResolvers; +import kotlin.Unit; import picocli.CommandLine; import picocli.CommandLine.Model.CommandSpec; import picocli.CommandLine.ParameterException; @@ -53,6 +55,7 @@ import java.util.function.Consumer; import java.util.prefs.Preferences; +import static com.fasterxml.jackson.module.kotlin.ExtensionsKt.kotlinModule; import static com.milaboratory.mixcr.cli.CommandCorrectTags.CORRECT_TAGS_COMMAND_NAME; public final class Main { @@ -131,6 +134,8 @@ public static void main(String... args) { System.exit(2); }); + GlobalObjectMappers.addModifier(om -> om.registerModule(kotlinModule(builder -> Unit.INSTANCE))); + handleParseResult(parseArgs(args).getParseResult(), args); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java index 604215448..2001c3620 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java @@ -23,7 +23,7 @@ public class CommandPaListMetrics extends ACommandMiXCR { public void run0() { PaResult paResult; try { - paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + paResult = GlobalObjectMappers.getPretty().readValue(new File(in), PaResult.class); } catch (IOException e) { throwValidationException("Corrupted PA file."); throw new RuntimeException(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java index c0685032e..ee29b5a03 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java @@ -39,14 +39,14 @@ public PaResult(@JsonProperty("metadata") Map> metadata, public static void writeJson(Path path, PaResult paResult) { if (path.getFileName().toString().endsWith(".json")) { try { - GlobalObjectMappers.PRETTY.writeValue(path.toFile(), paResult); + GlobalObjectMappers.getPretty().writeValue(path.toFile(), paResult); } catch (IOException e) { throw new RuntimeException(e); } } else if (path.getFileName().toString().endsWith(".json.gz")) { try (FileOutputStream fs = new FileOutputStream(path.toFile()); GZIPOutputStream zs = new GZIPOutputStream(new BufferedOutputStream(fs))) { - GlobalObjectMappers.ONE_LINE.writeValue(zs, paResult); + GlobalObjectMappers.getOneLine().writeValue(zs, paResult); } catch (IOException e) { throw new RuntimeException(e); } @@ -57,14 +57,14 @@ public static void writeJson(Path path, PaResult paResult) { public static PaResult readJson(Path path) { if (path.getFileName().toString().endsWith(".json")) { try { - return GlobalObjectMappers.PRETTY.readValue(path.toFile(), PaResult.class); + return GlobalObjectMappers.getPretty().readValue(path.toFile(), PaResult.class); } catch (IOException e) { throw new RuntimeException(e); } } else if (path.getFileName().toString().endsWith(".json.gz")) try (FileInputStream fs = new FileInputStream(path.toFile()); GZIPInputStream zs = new GZIPInputStream(new BufferedInputStream(fs))) { - return GlobalObjectMappers.ONE_LINE.readValue(zs, PaResult.class); + return GlobalObjectMappers.getOneLine().readValue(zs, PaResult.class); } catch (IOException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java index e45d59f8d..2aa37c8e4 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java @@ -156,7 +156,7 @@ public int hashCode() { @Override public String toString() { try { - return GlobalObjectMappers.PRETTY.writeValueAsString(this); + return GlobalObjectMappers.getPretty().writeValueAsString(this); } catch (JsonProcessingException e) { throw new RuntimeException(); } @@ -164,7 +164,7 @@ public String toString() { public static PartialAlignmentsAssemblerParameters getDefault() { try { - return GlobalObjectMappers.ONE_LINE.readValue( + return GlobalObjectMappers.getOneLine().readValue( PartialAlignmentsAssemblerParameters.class.getClassLoader().getResourceAsStream("parameters/partial_assembler_parameters.json") , PartialAlignmentsAssemblerParameters.class); } catch (IOException e) { diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java index 686ed4126..b0ee36c0f 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java @@ -52,7 +52,7 @@ private static void ensureInitialized() { try { InputStream is = VDJCAlignerParameters.class.getClassLoader().getResourceAsStream("parameters/vdjcaligner_parameters.json"); TypeReference> typeRef = new TypeReference>() {}; - map = GlobalObjectMappers.ONE_LINE.readValue(is, typeRef); + map = GlobalObjectMappers.getOneLine().readValue(is, typeRef); } catch (IOException ioe) { throw new RuntimeException(ioe); } diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java index 40d569a65..076813965 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java @@ -56,9 +56,9 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge new CloneClusteringParameters(2, 1,-1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2", (byte) 15); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(params); + String str = GlobalObjectMappers.getPretty().writeValueAsString(params); //System.out.println(str); - CloneAssemblerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneAssemblerParameters.class); + CloneAssemblerParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneAssemblerParameters.class); assertEquals(params, deser); CloneAssemblerParameters clone = deser.clone(); assertEquals(params, clone); @@ -84,9 +84,9 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge new CloneClusteringParameters(2, 1, -1,TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(params); + String str = GlobalObjectMappers.getPretty().writeValueAsString(params); //System.out.println(str); - CloneAssemblerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneAssemblerParameters.class); + CloneAssemblerParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneAssemblerParameters.class); assertEquals(params, deser); CloneAssemblerParameters clone = deser.clone(); assertEquals(params, clone); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java index eba2323cc..2a1648f42 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java @@ -39,8 +39,8 @@ public class CloneClusteringParametersTest { @Test public void test1() throws Exception { CloneClusteringParameters paramentrs = new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - CloneClusteringParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneClusteringParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + CloneClusteringParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneClusteringParameters.class); assertEquals(paramentrs, deser); CloneClusteringParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java index 166dcf04c..e97641354 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java @@ -30,11 +30,8 @@ package com.milaboratory.mixcr.assembler; import com.milaboratory.core.alignment.AffineGapAlignmentScoring; -import com.milaboratory.core.alignment.BandedAlignerParameters; import com.milaboratory.core.alignment.LinearGapAlignmentScoring; -import com.milaboratory.mixcr.vdjaligners.DAlignerParameters; import com.milaboratory.util.GlobalObjectMappers; -import io.repseq.core.GeneFeature; import org.junit.Test; import static org.junit.Assert.assertEquals; @@ -52,9 +49,9 @@ public void test1() throws Exception { LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 9), new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) ); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); //System.out.println(str); - CloneFactoryParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneFactoryParameters.class); + CloneFactoryParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneFactoryParameters.class); assertEquals(paramentrs, deser); CloneFactoryParameters clone = deser.clone(); assertEquals(paramentrs, clone); @@ -71,9 +68,9 @@ public void test2() throws Exception { LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5), null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) ); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); //System.out.println(str); - CloneFactoryParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneFactoryParameters.class); + CloneFactoryParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneFactoryParameters.class); assertEquals(paramentrs, deser); CloneFactoryParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java index 1e25f3111..b9dbc2261 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java @@ -38,8 +38,8 @@ public class ClusteringFilterTest { @Test public void test1() throws Exception { ClusteringFilter paramentrs = new RelativeConcentrationFilter(1E-6); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - ClusteringFilter deser = GlobalObjectMappers.PRETTY.readValue(str, ClusteringFilter.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + ClusteringFilter deser = GlobalObjectMappers.getPretty().readValue(str, ClusteringFilter.class); assertEquals(paramentrs, deser); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java index 8f415662d..4218fb940 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java @@ -41,8 +41,8 @@ public class VJCClonalAlignerParametersTest { public void test1() throws Exception { VJCClonalAlignerParameters paramentrs = new VJCClonalAlignerParameters(0.3f, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - VJCClonalAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, VJCClonalAlignerParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + VJCClonalAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, VJCClonalAlignerParameters.class); assertEquals(paramentrs, deser); assertEquals(paramentrs, deser.clone()); } diff --git a/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java b/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java index 5fd7d5677..65d71879f 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java @@ -39,6 +39,6 @@ public class AlignerReportTest { @Test public void test1() throws Exception { AlignerReport rep = new AlignerReport(); - assertNotNull(GlobalObjectMappers.PRETTY.writeValueAsString(rep)); + assertNotNull(GlobalObjectMappers.getPretty().writeValueAsString(rep)); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java b/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java index 46f7eea72..3c13474c1 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java @@ -42,6 +42,6 @@ public void serializationTest() throws JsonProcessingException { stats.total.incrementAndGet(); stats.chimeras.incrementAndGet(); stats.getCounter(Chains.TRB).incrementAndGet(); - System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(stats)); + System.out.println(GlobalObjectMappers.getPretty().writeValueAsString(stats)); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java index fe7635df4..8b51c5160 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java @@ -13,8 +13,8 @@ public class IsolationGroupTest { @Test public void test1() throws JsonProcessingException { IsolationGroup expected = new IsolationGroup(Chains.TRA_NAMED, new HashMap<>()); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(expected); - IsolationGroup actual = GlobalObjectMappers.PRETTY.readValue(str, IsolationGroup.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(expected); + IsolationGroup actual = GlobalObjectMappers.getPretty().readValue(str, IsolationGroup.class); Assert.assertEquals(expected, actual); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java index 613fa83d7..4f62af8bc 100644 --- a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java @@ -49,8 +49,8 @@ public void testSerialize1() throws IOException { Assert.assertTrue(versionString.contains("RepSeq.IO")); Assert.assertTrue(versionString.contains("MiLib")); Assert.assertTrue(versionString.contains("MiXCR")); - String pretty = GlobalObjectMappers.PRETTY.writeValueAsString(version); - MiXCRVersionInfo v = GlobalObjectMappers.PRETTY.readValue(pretty, MiXCRVersionInfo.class); + String pretty = GlobalObjectMappers.getPretty().writeValueAsString(version); + MiXCRVersionInfo v = GlobalObjectMappers.getPretty().readValue(pretty, MiXCRVersionInfo.class); assertEquals(version, v); } } diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java index 00305e4c6..7a76d5b17 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java @@ -42,8 +42,8 @@ public class DAlignerParametersTest { public void test1() throws Exception { DAlignerParameters paramentrs = new DAlignerParameters(GeneFeature.DRegion, 0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - DAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, DAlignerParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + DAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, DAlignerParameters.class); assertEquals(paramentrs, deser); DAlignerParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java index 7ec95f9df..a45919759 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java @@ -44,9 +44,9 @@ public void test1() throws Exception { new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring())); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); System.out.println(str); - KGeneAlignmentParameters deser = GlobalObjectMappers.PRETTY.readValue(str, KGeneAlignmentParameters.class); + KGeneAlignmentParameters deser = GlobalObjectMappers.getPretty().readValue(str, KGeneAlignmentParameters.class); assertEquals(paramentrs, deser); KGeneAlignmentParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java index 519f2ec4d..888aafa57 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java @@ -65,8 +65,8 @@ public void test1() throws Exception { 120.0f, 5, 0.7f, false, false, false, PairedEndReadsLayout.Opposite, new MergerParameters( QualityMergingAlgorithm.SumSubtraction, null, 12, null, 0.12, Unweighted), false, 5, 120, 10, true, true); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - VDJCAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, VDJCAlignerParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + VDJCAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, VDJCAlignerParameters.class); assertEquals(paramentrs, deser); VDJCAlignerParameters clone = deser.clone(); assertEquals(paramentrs, clone); From aca9108d8f84190b0c851e356955db3d5b6aca22 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 23:17:39 +0300 Subject: [PATCH 206/282] WIP --- .../mixcr/cli/CommandCorrectTags.java | 24 +++++++++++-------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java index c57e493e5..fb2350c6c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java @@ -5,6 +5,8 @@ import cc.redberry.pipe.Processor; import cc.redberry.pipe.blocks.FilteringPort; import cc.redberry.pipe.util.CountingOutputPort; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; import com.google.common.hash.Hasher; import com.google.common.hash.Hashing; import com.milaboratory.cli.ActionConfiguration; @@ -126,11 +128,6 @@ public void run1() throws Exception { CorrectionReport report; int[] targetTagIndices; try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in)) { - TagCorrector corrector = new TagCorrector(getParameters(), - tempFolder(), "", - memoryBudget, - 4, 4); - SmartProgressReporter.startProgressReport(corrector); TagsInfo tagsInfo = reader.getTagsInfo(); List tagNames = new ArrayList<>(); @@ -146,6 +143,12 @@ public void run1() throws Exception { System.out.println("Correction will be applied to the following tags: " + String.join(", ", tagNames)); + TagCorrector corrector = new TagCorrector(getParameters(), + tempFolder(), "", + memoryBudget, + 4, 4); + SmartProgressReporter.startProgressReport(corrector); + // Extractor of tag information from the alignments for the tag corrector Processor mapper = input -> { if (input.getTagCounter().size() != 1) @@ -238,10 +241,11 @@ public void run1() throws Exception { } public static final class CorrectTagsConfiguration implements ActionConfiguration { - final TagCorrectorParameters params; + final TagCorrectorParameters parameters; - public CorrectTagsConfiguration(TagCorrectorParameters params) { - this.params = params; + @JsonCreator + public CorrectTagsConfiguration(@JsonProperty("parameters") TagCorrectorParameters parameters) { + this.parameters = parameters; } @Override @@ -254,12 +258,12 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; CorrectTagsConfiguration that = (CorrectTagsConfiguration) o; - return params.equals(that.params); + return parameters.equals(that.parameters); } @Override public int hashCode() { - return Objects.hash(params); + return Objects.hash(parameters); } } } From cfa7fa541dd60f07c96447e0b6d1747a2b55b3bd Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 21 May 2022 23:17:20 +0300 Subject: [PATCH 207/282] feat: migration to encapsulated global object mappers in milib --- build.gradle.kts | 11 +++++++---- .../assembler/CloneAssemblerParametersPresets.java | 2 +- .../assembler/fullseq/FullSeqAssemblerParameters.java | 2 +- .../mixcr/basictypes/VDJCSProperties.java | 2 +- .../java/com/milaboratory/mixcr/cli/CommandAlign.java | 2 +- .../milaboratory/mixcr/cli/CommandPipelineInfo.java | 2 +- src/main/java/com/milaboratory/mixcr/cli/Main.java | 6 ++++++ .../mixcr/cli/postanalysis/CommandPaListMetrics.java | 2 +- .../milaboratory/mixcr/cli/postanalysis/PaResult.java | 8 ++++---- .../PartialAlignmentsAssemblerParameters.java | 4 ++-- .../mixcr/tags/DropletCloneGraphParameters.java | 5 ++++- .../mixcr/vdjaligners/VDJCParametersPresets.java | 2 +- .../mixcr/assembler/CloneAssemblerParametersTest.java | 8 ++++---- .../assembler/CloneClusteringParametersTest.java | 4 ++-- .../mixcr/assembler/CloneFactoryParametersTest.java | 11 ++++------- .../mixcr/assembler/ClusteringFilterTest.java | 4 ++-- .../assembler/VJCClonalAlignerParametersTest.java | 4 ++-- .../com/milaboratory/mixcr/cli/AlignerReportTest.java | 2 +- .../milaboratory/mixcr/cli/ChainUsageStatsTest.java | 2 +- .../mixcr/cli/postanalysis/IsolationGroupTest.java | 4 ++-- .../mixcr/tags/CloneTagTupleFilterTest.java | 2 +- .../milaboratory/mixcr/util/MiXCRVersionInfoTest.java | 4 ++-- .../mixcr/vdjaligners/DAlignerParametersTest.java | 4 ++-- .../vdjaligners/KGeneAlignmentParametersTest.java | 4 ++-- .../mixcr/vdjaligners/VDJCAlignerParametersTest.java | 4 ++-- 25 files changed, 57 insertions(+), 48 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index de315e843..d2119957b 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -78,10 +78,11 @@ repositories { } } -val miplotsVersion = "0.1-19-master" -val milibVersion = "1.15.0-32-master" +val milibVersion = "1.15.0-38-master" val repseqioVersion = "1.3.5-26-master" -val jacksonVersion = "2.13.2.2" +val mitoolVersion = "1.3.5-25-master" +val miplotsVersion = "0.1-19-master" +val jacksonBomVersion = "2.13.3" dependencies { api("com.milaboratory:milib:$milibVersion") @@ -93,7 +94,9 @@ dependencies { // implementation("com.milaboratory:milm2-jvm:0.2.0-test-2") { isChanging = true } implementation("com.milaboratory:milm2-jvm:1.1.0") - implementation("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion") + implementation(platform("com.fasterxml.jackson:jackson-bom:$jacksonBomVersion")) + implementation("com.fasterxml.jackson.module:jackson-module-kotlin") + implementation("commons-io:commons-io:2.11.0") implementation("org.lz4:lz4-java:1.8.0") implementation("net.sf.trove4j:trove4j:3.0.3") diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java index 9bd46c5fc..bf0fe32c9 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java @@ -54,7 +54,7 @@ private static void ensureInitialized() { TypeReference> typeRef = new TypeReference>() { }; - map = GlobalObjectMappers.ONE_LINE.readValue(is, typeRef); + map = GlobalObjectMappers.getOneLine().readValue(is, typeRef); } catch (IOException ioe) { throw new RuntimeException(ioe); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java index dfd11c843..e2f50f840 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java @@ -281,7 +281,7 @@ private static void ensureInitialized() { TypeReference> typeRef = new TypeReference>() { }; - map = GlobalObjectMappers.ONE_LINE.readValue(is, typeRef); + map = GlobalObjectMappers.getOneLine().readValue(is, typeRef); } catch (IOException ioe) { throw new RuntimeException(ioe); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java index 4e94bd716..1ec73415b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java @@ -117,7 +117,7 @@ public int hashCode() { @Override public String toString() { try { - return GlobalObjectMappers.PRETTY.writeValueAsString(this); + return GlobalObjectMappers.getPretty().writeValueAsString(this); } catch (JsonProcessingException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 4f7adfd3a..9398589e8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -232,7 +232,7 @@ public VDJCAlignerParameters getAlignerParameters() { VDJCAlignerParameters alignerParameters; if (alignerParametersName.endsWith(".json")) { try { - alignerParameters = GlobalObjectMappers.ONE_LINE.readValue(new File(alignerParametersName), VDJCAlignerParameters.class); + alignerParameters = GlobalObjectMappers.getOneLine().readValue(new File(alignerParametersName), VDJCAlignerParameters.class); } catch (IOException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java index 5bdb07f57..05ac58900 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java @@ -64,7 +64,7 @@ public void run0() throws Exception { } public static void analysisPipelineInfoJson(String file) throws JsonProcessingException { - System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(PipelineConfigurationReaderMiXCR + System.out.println(GlobalObjectMappers.getPretty().writeValueAsString(PipelineConfigurationReaderMiXCR .sFromFile(file))); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 2330308d3..d9caaaf59 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -34,10 +34,12 @@ import com.milaboratory.milm.LM; import com.milaboratory.milm.LicenseError; import com.milaboratory.milm.LicenseErrorType; +import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.VersionInfo; import io.repseq.core.VDJCLibraryRegistry; import io.repseq.seqbase.SequenceResolvers; +import kotlin.Unit; import picocli.CommandLine; import picocli.CommandLine.Model.CommandSpec; import picocli.CommandLine.ParameterException; @@ -53,6 +55,8 @@ import java.util.function.Consumer; import java.util.prefs.Preferences; +import static com.fasterxml.jackson.module.kotlin.ExtensionsKt.kotlinModule; + public final class Main { private static boolean initialized = false; @@ -129,6 +133,8 @@ public static void main(String... args) { System.exit(2); }); + GlobalObjectMappers.addModifier(om -> om.registerModule(kotlinModule(builder -> Unit.INSTANCE))); + handleParseResult(parseArgs(args).getParseResult(), args); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java index 604215448..2001c3620 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java @@ -23,7 +23,7 @@ public class CommandPaListMetrics extends ACommandMiXCR { public void run0() { PaResult paResult; try { - paResult = GlobalObjectMappers.PRETTY.readValue(new File(in), PaResult.class); + paResult = GlobalObjectMappers.getPretty().readValue(new File(in), PaResult.class); } catch (IOException e) { throwValidationException("Corrupted PA file."); throw new RuntimeException(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java index c0685032e..ee29b5a03 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java @@ -39,14 +39,14 @@ public PaResult(@JsonProperty("metadata") Map> metadata, public static void writeJson(Path path, PaResult paResult) { if (path.getFileName().toString().endsWith(".json")) { try { - GlobalObjectMappers.PRETTY.writeValue(path.toFile(), paResult); + GlobalObjectMappers.getPretty().writeValue(path.toFile(), paResult); } catch (IOException e) { throw new RuntimeException(e); } } else if (path.getFileName().toString().endsWith(".json.gz")) { try (FileOutputStream fs = new FileOutputStream(path.toFile()); GZIPOutputStream zs = new GZIPOutputStream(new BufferedOutputStream(fs))) { - GlobalObjectMappers.ONE_LINE.writeValue(zs, paResult); + GlobalObjectMappers.getOneLine().writeValue(zs, paResult); } catch (IOException e) { throw new RuntimeException(e); } @@ -57,14 +57,14 @@ public static void writeJson(Path path, PaResult paResult) { public static PaResult readJson(Path path) { if (path.getFileName().toString().endsWith(".json")) { try { - return GlobalObjectMappers.PRETTY.readValue(path.toFile(), PaResult.class); + return GlobalObjectMappers.getPretty().readValue(path.toFile(), PaResult.class); } catch (IOException e) { throw new RuntimeException(e); } } else if (path.getFileName().toString().endsWith(".json.gz")) try (FileInputStream fs = new FileInputStream(path.toFile()); GZIPInputStream zs = new GZIPInputStream(new BufferedInputStream(fs))) { - return GlobalObjectMappers.ONE_LINE.readValue(zs, PaResult.class); + return GlobalObjectMappers.getOneLine().readValue(zs, PaResult.class); } catch (IOException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java index e45d59f8d..2aa37c8e4 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java @@ -156,7 +156,7 @@ public int hashCode() { @Override public String toString() { try { - return GlobalObjectMappers.PRETTY.writeValueAsString(this); + return GlobalObjectMappers.getPretty().writeValueAsString(this); } catch (JsonProcessingException e) { throw new RuntimeException(); } @@ -164,7 +164,7 @@ public String toString() { public static PartialAlignmentsAssemblerParameters getDefault() { try { - return GlobalObjectMappers.ONE_LINE.readValue( + return GlobalObjectMappers.getOneLine().readValue( PartialAlignmentsAssemblerParameters.class.getClassLoader().getResourceAsStream("parameters/partial_assembler_parameters.json") , PartialAlignmentsAssemblerParameters.class); } catch (IOException e) { diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java index 868e876c9..81ecc2766 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java @@ -74,7 +74,10 @@ public int hashCode() { public static DropletCloneGraphParameters getDefault() { try { - return GlobalObjectMappers.ONE_LINE.readValue(CloneTagTupleFilter.class.getClassLoader().getResourceAsStream("parameters/droplet_clone_graph_parameters.json"), DropletCloneGraphParameters.class); + return GlobalObjectMappers.getOneLine() + .readValue(CloneTagTupleFilter.class.getClassLoader() + .getResourceAsStream("parameters/droplet_clone_graph_parameters.json"), + DropletCloneGraphParameters.class); } catch (IOException e) { throw new RuntimeException(e); } diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java index 686ed4126..b0ee36c0f 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java @@ -52,7 +52,7 @@ private static void ensureInitialized() { try { InputStream is = VDJCAlignerParameters.class.getClassLoader().getResourceAsStream("parameters/vdjcaligner_parameters.json"); TypeReference> typeRef = new TypeReference>() {}; - map = GlobalObjectMappers.ONE_LINE.readValue(is, typeRef); + map = GlobalObjectMappers.getOneLine().readValue(is, typeRef); } catch (IOException ioe) { throw new RuntimeException(ioe); } diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java index 40d569a65..076813965 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java @@ -56,9 +56,9 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge new CloneClusteringParameters(2, 1,-1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2", (byte) 15); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(params); + String str = GlobalObjectMappers.getPretty().writeValueAsString(params); //System.out.println(str); - CloneAssemblerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneAssemblerParameters.class); + CloneAssemblerParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneAssemblerParameters.class); assertEquals(params, deser); CloneAssemblerParameters clone = deser.clone(); assertEquals(params, clone); @@ -84,9 +84,9 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge new CloneClusteringParameters(2, 1, -1,TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(params); + String str = GlobalObjectMappers.getPretty().writeValueAsString(params); //System.out.println(str); - CloneAssemblerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneAssemblerParameters.class); + CloneAssemblerParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneAssemblerParameters.class); assertEquals(params, deser); CloneAssemblerParameters clone = deser.clone(); assertEquals(params, clone); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java index eba2323cc..2a1648f42 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java @@ -39,8 +39,8 @@ public class CloneClusteringParametersTest { @Test public void test1() throws Exception { CloneClusteringParameters paramentrs = new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - CloneClusteringParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneClusteringParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + CloneClusteringParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneClusteringParameters.class); assertEquals(paramentrs, deser); CloneClusteringParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java index 166dcf04c..e97641354 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java @@ -30,11 +30,8 @@ package com.milaboratory.mixcr.assembler; import com.milaboratory.core.alignment.AffineGapAlignmentScoring; -import com.milaboratory.core.alignment.BandedAlignerParameters; import com.milaboratory.core.alignment.LinearGapAlignmentScoring; -import com.milaboratory.mixcr.vdjaligners.DAlignerParameters; import com.milaboratory.util.GlobalObjectMappers; -import io.repseq.core.GeneFeature; import org.junit.Test; import static org.junit.Assert.assertEquals; @@ -52,9 +49,9 @@ public void test1() throws Exception { LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 9), new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) ); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); //System.out.println(str); - CloneFactoryParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneFactoryParameters.class); + CloneFactoryParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneFactoryParameters.class); assertEquals(paramentrs, deser); CloneFactoryParameters clone = deser.clone(); assertEquals(paramentrs, clone); @@ -71,9 +68,9 @@ public void test2() throws Exception { LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5), null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) ); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); //System.out.println(str); - CloneFactoryParameters deser = GlobalObjectMappers.PRETTY.readValue(str, CloneFactoryParameters.class); + CloneFactoryParameters deser = GlobalObjectMappers.getPretty().readValue(str, CloneFactoryParameters.class); assertEquals(paramentrs, deser); CloneFactoryParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java index 1e25f3111..b9dbc2261 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java @@ -38,8 +38,8 @@ public class ClusteringFilterTest { @Test public void test1() throws Exception { ClusteringFilter paramentrs = new RelativeConcentrationFilter(1E-6); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - ClusteringFilter deser = GlobalObjectMappers.PRETTY.readValue(str, ClusteringFilter.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + ClusteringFilter deser = GlobalObjectMappers.getPretty().readValue(str, ClusteringFilter.class); assertEquals(paramentrs, deser); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java index 8f415662d..4218fb940 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java @@ -41,8 +41,8 @@ public class VJCClonalAlignerParametersTest { public void test1() throws Exception { VJCClonalAlignerParameters paramentrs = new VJCClonalAlignerParameters(0.3f, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - VJCClonalAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, VJCClonalAlignerParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + VJCClonalAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, VJCClonalAlignerParameters.class); assertEquals(paramentrs, deser); assertEquals(paramentrs, deser.clone()); } diff --git a/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java b/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java index 5fd7d5677..65d71879f 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java @@ -39,6 +39,6 @@ public class AlignerReportTest { @Test public void test1() throws Exception { AlignerReport rep = new AlignerReport(); - assertNotNull(GlobalObjectMappers.PRETTY.writeValueAsString(rep)); + assertNotNull(GlobalObjectMappers.getPretty().writeValueAsString(rep)); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java b/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java index 46f7eea72..3c13474c1 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java @@ -42,6 +42,6 @@ public void serializationTest() throws JsonProcessingException { stats.total.incrementAndGet(); stats.chimeras.incrementAndGet(); stats.getCounter(Chains.TRB).incrementAndGet(); - System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(stats)); + System.out.println(GlobalObjectMappers.getPretty().writeValueAsString(stats)); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java index fe7635df4..8b51c5160 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java @@ -13,8 +13,8 @@ public class IsolationGroupTest { @Test public void test1() throws JsonProcessingException { IsolationGroup expected = new IsolationGroup(Chains.TRA_NAMED, new HashMap<>()); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(expected); - IsolationGroup actual = GlobalObjectMappers.PRETTY.readValue(str, IsolationGroup.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(expected); + IsolationGroup actual = GlobalObjectMappers.getPretty().readValue(str, IsolationGroup.class); Assert.assertEquals(expected, actual); } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java index a63035097..5d842c187 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java @@ -11,6 +11,6 @@ public class CloneTagTupleFilterTest { @Test public void name() throws JsonProcessingException { - System.out.println(GlobalObjectMappers.PRETTY.writeValueAsString(new CloneTagTupleFilter(0, 0, 0, 0, 0, 0, 0.0 / 0.0, 0))); + System.out.println(GlobalObjectMappers.getPretty().writeValueAsString(new CloneTagTupleFilter(0, 0, 0, 0, 0, 0, 0.0 / 0.0, 0))); } } diff --git a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java index 613fa83d7..4f62af8bc 100644 --- a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java @@ -49,8 +49,8 @@ public void testSerialize1() throws IOException { Assert.assertTrue(versionString.contains("RepSeq.IO")); Assert.assertTrue(versionString.contains("MiLib")); Assert.assertTrue(versionString.contains("MiXCR")); - String pretty = GlobalObjectMappers.PRETTY.writeValueAsString(version); - MiXCRVersionInfo v = GlobalObjectMappers.PRETTY.readValue(pretty, MiXCRVersionInfo.class); + String pretty = GlobalObjectMappers.getPretty().writeValueAsString(version); + MiXCRVersionInfo v = GlobalObjectMappers.getPretty().readValue(pretty, MiXCRVersionInfo.class); assertEquals(version, v); } } diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java index 00305e4c6..7a76d5b17 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java @@ -42,8 +42,8 @@ public class DAlignerParametersTest { public void test1() throws Exception { DAlignerParameters paramentrs = new DAlignerParameters(GeneFeature.DRegion, 0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - DAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, DAlignerParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + DAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, DAlignerParameters.class); assertEquals(paramentrs, deser); DAlignerParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java index 7ec95f9df..a45919759 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java @@ -44,9 +44,9 @@ public void test1() throws Exception { new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring())); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); System.out.println(str); - KGeneAlignmentParameters deser = GlobalObjectMappers.PRETTY.readValue(str, KGeneAlignmentParameters.class); + KGeneAlignmentParameters deser = GlobalObjectMappers.getPretty().readValue(str, KGeneAlignmentParameters.class); assertEquals(paramentrs, deser); KGeneAlignmentParameters clone = deser.clone(); assertEquals(paramentrs, clone); diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java index 519f2ec4d..888aafa57 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java @@ -65,8 +65,8 @@ public void test1() throws Exception { 120.0f, 5, 0.7f, false, false, false, PairedEndReadsLayout.Opposite, new MergerParameters( QualityMergingAlgorithm.SumSubtraction, null, 12, null, 0.12, Unweighted), false, 5, 120, 10, true, true); - String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs); - VDJCAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, VDJCAlignerParameters.class); + String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); + VDJCAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, VDJCAlignerParameters.class); assertEquals(paramentrs, deser); VDJCAlignerParameters clone = deser.clone(); assertEquals(paramentrs, clone); From 35fa5ce8042eaab5258342a1f98db8b0ec7ed7d1 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 22 May 2022 01:09:47 +0300 Subject: [PATCH 208/282] tag data exporting --- .../mixcr/basictypes/ClnAReader.java | 3 +- .../mixcr/basictypes/ClnsReader.java | 7 +- .../mixcr/basictypes/CloneSet.java | 3 +- .../basictypes/VDJCAlignmentsReader.java | 2 + .../mixcr/basictypes/VDJCFileHeaderData.java | 7 ++ .../milaboratory/mixcr/cli/CommandExport.java | 83 +++++++++------- .../cli/CommandExportAlignmentsPretty.java | 3 +- .../com/milaboratory/mixcr/export/Field.java | 4 +- .../mixcr/export/FieldExtractors.java | 96 +++++++++++++++---- .../mixcr/export/FieldParameterless.java | 4 +- .../mixcr/export/FieldWithParameters.java | 4 +- 11 files changed, 157 insertions(+), 59 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index e461947ea..9c81a8fd8 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -59,7 +59,7 @@ /** * Reader of CLNA file format. */ -public final class ClnAReader extends PipelineConfigurationReaderMiXCR implements CloneReader, AutoCloseable { +public final class ClnAReader extends PipelineConfigurationReaderMiXCR implements CloneReader, VDJCFileHeaderData, AutoCloseable { final PrimitivIHybrid input; // Index data @@ -198,6 +198,7 @@ public CloneAssemblerParameters getAssemblerParameters() { /** * Tags info */ + @Override public TagsInfo getTagsInfo() { return tagsInfo; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index c0084b4df..d7f571628 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -53,7 +53,7 @@ /** * */ -public class ClnsReader extends PipelineConfigurationReaderMiXCR implements CloneReader, AutoCloseable { +public class ClnsReader extends PipelineConfigurationReaderMiXCR implements CloneReader, VDJCFileHeaderData, AutoCloseable { private final PrimitivIHybrid input; private final VDJCLibraryRegistry libraryRegistry; @@ -144,6 +144,11 @@ public PipelineConfiguration getPipelineConfiguration() { return pipelineConfiguration; } + @Override + public TagsInfo getTagsInfo() { + return tagsInfo; + } + public VDJCAlignerParameters getAlignerParameters() { return alignerParameters; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index ea7811f71..fa87bcd0c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -45,7 +45,7 @@ /** * Created by poslavsky on 10/07/14. */ -public final class CloneSet implements Iterable, HasFeatureToAlign { +public final class CloneSet implements Iterable, VDJCFileHeaderData, HasFeatureToAlign { String versionInfo; final CloneAssemblerParameters assemblerParameters; final VDJCAlignerParameters alignmentParameters; @@ -134,6 +134,7 @@ public VDJCAlignerParameters getAlignmentParameters() { return alignmentParameters; } + @Override public TagsInfo getTagsInfo() { return tagsInfo; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index 42d250e74..fed9d921d 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -55,6 +55,7 @@ public final class VDJCAlignmentsReader extends PipelineConfigurationReaderMiXCR implements OutputPortCloseable, + VDJCFileHeaderData, CanReportProgress { public static final int DEFAULT_CONCURRENCY = 4; public static final int DEFAULT_READ_AHEAD_BLOCKS = 5; @@ -186,6 +187,7 @@ public synchronized PipelineConfiguration getPipelineConfiguration() { return pipelineConfiguration; } + @Override public TagsInfo getTagsInfo() { ensureInitialized(); return tagsInfo; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java new file mode 100644 index 000000000..1e8702602 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java @@ -0,0 +1,7 @@ +package com.milaboratory.mixcr.basictypes; + +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; + +public interface VDJCFileHeaderData { + TagsInfo getTagsInfo(); +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index f295a1194..a8bc135ff 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -162,16 +162,10 @@ public void run0() throws Exception { if (fields.isEmpty()) fields.addAll(presets.get(clazz).get(DEFAULT_PRESET)); - OutputMode oMode = humanReadable ? OutputMode.HumanFriendly : OutputMode.ScriptingFriendly; - List> extractors = fields - .stream() - .flatMap(f -> extractor(f, clazz, oMode).stream()) - .collect(Collectors.toList()); - - run1(extractors); + run1(fields, humanReadable ? OutputMode.HumanFriendly : OutputMode.ScriptingFriendly); } - abstract void run1(List> extractors) throws Exception; + abstract void run1(List fields, OutputMode oMode) throws Exception; @Command(name = "exportAlignments", separator = " ", @@ -183,9 +177,14 @@ public CommandExportAlignments() { } @Override - void run1(List> exporters) throws Exception { - try (OutputPortCloseable reader = openAlignmentsPort(in); + void run1(List fields, OutputMode oMode) throws Exception { + try (AlignmentsAndHeader readerAndHeader = openAlignmentsPort(in); InfoWriter writer = new InfoWriter<>(out)) { + OutputPortCloseable reader = readerAndHeader.port; + List> exporters = fields + .stream() + .flatMap(f -> extractor(f, VDJCAlignments.class, readerAndHeader.header, oMode).stream()) + .collect(Collectors.toList()); if (reader instanceof CanReportProgress) SmartProgressReporter.startProgressReport("Exporting alignments", (CanReportProgress) reader, System.err); writer.attachInfoProviders(exporters); @@ -238,10 +237,14 @@ public Filter mkFilter() { } @Override - void run1(List> exporters) throws Exception { + void run1(List fields, OutputMode oMode) throws Exception { try (InfoWriter writer = new InfoWriter<>(out)) { CloneSet initialSet = CloneSetIO.read(in, VDJCLibraryRegistry.getDefault()); CloneSet set = CloneSet.transform(initialSet, mkFilter()); + List> exporters = fields + .stream() + .flatMap(f -> extractor(f, Clone.class, initialSet, oMode).stream()) + .collect(Collectors.toList()); writer.attachInfoProviders(exporters); writer.ensureHeader(); @@ -362,19 +365,19 @@ void run() { } @SuppressWarnings("unchecked") - List> extractor(FieldData fd, Class clazz, OutputMode m) { + List> extractor(FieldData fd, Class clazz, VDJCFileHeaderData header, OutputMode m) { for (Field f : FieldExtractors.getFields()) { if (fd.field.equalsIgnoreCase(f.getCommand()) && f.canExtractFrom(clazz)) { if (f.nArguments() == 0) { if (!(fd.args.length == 0 || ( fd.args.length == 1 && (fd.args[0].equalsIgnoreCase("true") || fd.args[0].equalsIgnoreCase("false"))))) throw new RuntimeException(); - return Collections.singletonList(f.create(m, new String[0])); + return Collections.singletonList(f.create(m, header, new String[0])); } else { int i = 0; ArrayList> extractors = new ArrayList<>(); while (i < fd.args.length) { - extractors.add(f.create(m, Arrays.copyOfRange(fd.args, i, i + f.nArguments()))); + extractors.add(f.create(m, header, Arrays.copyOfRange(fd.args, i, i + f.nArguments()))); i += f.nArguments(); } return extractors; @@ -560,32 +563,48 @@ public static CommandSpec mkClonesSpec() { public interface OPAWithReport extends OutputPortCloseable, CanReportProgress { } - public static OutputPortCloseable openAlignmentsPort(String in) { + public static class AlignmentsAndHeader implements AutoCloseable { + public final OutputPortCloseable port; + public final VDJCFileHeaderData header; + + public AlignmentsAndHeader(OutputPortCloseable port, VDJCFileHeaderData header) { + this.port = port; + this.header = header; + } + + @Override + public void close() { + port.close(); + } + } + + public static AlignmentsAndHeader openAlignmentsPort(String in) { try { switch (fileInfoExtractorInstance.getFileInfo(in).fileType) { case MAGIC_VDJC: VDJCAlignmentsReader vdjcaReader = null; vdjcaReader = new VDJCAlignmentsReader(in, VDJCLibraryRegistry.getDefault()); - return vdjcaReader; + return new AlignmentsAndHeader(vdjcaReader, vdjcaReader); case MAGIC_CLNA: ClnAReader clnaReader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); OutputPortCloseable source = clnaReader.readAllAlignments(); - return new OutputPortCloseable() { - @Override - public void close() { - try { - source.close(); - clnaReader.close(); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - - @Override - public VDJCAlignments take() { - return source.take(); - } - }; + return new AlignmentsAndHeader( + new OutputPortCloseable() { + @Override + public void close() { + try { + source.close(); + clnaReader.close(); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + @Override + public VDJCAlignments take() { + return source.take(); + } + }, clnaReader); case MAGIC_CLNS: throw new RuntimeException("Can't export alignments from *.clns file: " + in); default: diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java index 971162a15..a78dd447a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java @@ -200,10 +200,11 @@ public Filter mkFilter() { public void run0() throws Exception { Filter filter = mkFilter(); long total = 0, filtered = 0; - try (OutputPortCloseable reader = CommandExport.openAlignmentsPort(in); + try (CommandExport.AlignmentsAndHeader readerAndHeader = CommandExport.openAlignmentsPort(in); PrintStream output = out == null ? System.out : new PrintStream(new BufferedOutputStream(new FileOutputStream(out), 32768)) ) { + OutputPortCloseable reader = readerAndHeader.port; long countBefore = limitBefore == null ? Long.MAX_VALUE : limitBefore; long countAfter = limitAfter == null ? Long.MAX_VALUE : limitAfter; long skipAfter = this.skipAfter == null ? 0 : this.skipAfter; diff --git a/src/main/java/com/milaboratory/mixcr/export/Field.java b/src/main/java/com/milaboratory/mixcr/export/Field.java index aa84c8f34..33552fe52 100644 --- a/src/main/java/com/milaboratory/mixcr/export/Field.java +++ b/src/main/java/com/milaboratory/mixcr/export/Field.java @@ -29,6 +29,8 @@ */ package com.milaboratory.mixcr.export; +import com.milaboratory.mixcr.basictypes.VDJCFileHeaderData; + public interface Field { boolean canExtractFrom(Class type); @@ -40,5 +42,5 @@ public interface Field { String metaVars(); - FieldExtractor create(OutputMode outputMode, String[] args); + FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args); } diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 7b137f8c9..7c60c2e44 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -41,10 +41,11 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.TranslationParameters; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.VDJCObject; +import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagInfo; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.util.GlobalObjectMappers; import gnu.trove.iterator.TObjectFloatIterator; import gnu.trove.map.hash.TObjectFloatHashMap; @@ -57,6 +58,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import java.util.Set; public final class FieldExtractors { static final String NULL = ""; @@ -448,9 +450,9 @@ protected String extract(VDJCAlignments object) { } @Override - public FieldExtractor create(OutputMode outputMode, String[] args) { + public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { System.out.println("WARNING: -readId is deprecated. Use -readIds"); - return super.create(outputMode, args); + return super.create(outputMode, headerData, args); } }); @@ -510,9 +512,9 @@ protected String extract(VDJCAlignments object) { } @Override - public FieldExtractor create(OutputMode outputMode, String[] args) { + public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { System.out.println("WARNING: -descrR1 is deprecated. Use -descrsR1"); - return super.create(outputMode, args); + return super.create(outputMode, headerData, args); } }); @@ -532,9 +534,9 @@ protected String extract(VDJCAlignments object) { } @Override - public FieldExtractor create(OutputMode outputMode, String[] args) { + public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { System.out.println("WARNING: -descrR2 is deprecated. Use -descrsR2"); - return super.create(outputMode, args); + return super.create(outputMode, headerData, args); } }); @@ -687,6 +689,56 @@ protected String extract(Clone object) { } }); + descriptorsList.add(new AbstractField(VDJCObject.class, "-tag", + "Tag value (i.e. CELL barcode or UMI sequence)") { + @Override + public int nArguments() { + return 1; + } + + @Override + public String metaVars() { + return "tag_name"; + } + + private String getHeader(OutputMode outputMode, String name) { + switch (outputMode) { + case HumanFriendly: + return "Tag Value " + name; + case ScriptingFriendly: + return "tagValue" + name; + } + throw new RuntimeException(); + } + + @Override + public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { + String tagName = args[0]; + TagsInfo tagsInfo = headerData.getTagsInfo(); + int idx = -1; + for (TagInfo ti : tagsInfo.tags) + if (ti.getName().equals(tagName)) { + idx = ti.getIndex(); + break; + } + if (idx == -1) + throw new IllegalArgumentException("No tag with name " + tagName); + int finalIdx = idx; + return new AbstractFieldExtractor(getHeader(outputMode, tagName), this) { + @Override + public String extractValue(VDJCObject object) { + TagCounter tc = object.getTagCounter(); + Set keys = tc.keys(); + if (keys.size() == 0) + return NULL; + if (keys.size() > 1) + throw new IllegalArgumentException("object has multiple tag tuples: " + tc); + return keys.iterator().next().tags[finalIdx].extractKey().toString(); + } + }; + } + }); + // descriptorsList.add(new WP_O("-tag", "Tag value", 1) { // @Override // protected String getParameters(String[] string) { @@ -696,8 +748,10 @@ protected String extract(Clone object) { // @Override // protected String getHeader(OutputMode outputMode, String name) { // switch (outputMode) { - // case HumanFriendly: return "Tag" + name; - // case ScriptingFriendly: return "tag" + name; + // case HumanFriendly: + // return "Tag" + name; + // case ScriptingFriendly: + // return "tag" + name; // } // throw new RuntimeException(); // } @@ -729,8 +783,10 @@ protected String extract(Clone object) { // protected String getHeader(OutputMode outputMode, int[] index) { // String str = Arrays.stream(index).mapToObj(Integer::toString).collect(Collectors.joining("+")); // switch (outputMode) { - // case HumanFriendly: return "Unique Tag Count " + str; - // case ScriptingFriendly: return "uniqueTagCount" + str; + // case HumanFriendly: + // return "Unique Tag Count " + str; + // case ScriptingFriendly: + // return "uniqueTagCount" + str; // } // throw new RuntimeException(); // } @@ -777,12 +833,12 @@ public static boolean hasField(String name) { return false; } - public static FieldExtractor parse(OutputMode outputMode, Class clazz, String[] args) { - for (Field field : getFields()) - if (field.canExtractFrom(clazz) && args[0].equalsIgnoreCase(field.getCommand())) - return field.create(outputMode, Arrays.copyOfRange(args, 1, args.length)); - throw new IllegalArgumentException("Not a valid options: " + Arrays.toString(args)); - } + // public static FieldExtractor parse(OutputMode outputMode, Class clazz, String[] args) { + // for (Field field : getFields()) + // if (field.canExtractFrom(clazz) && args[0].equalsIgnoreCase(field.getCommand())) + // return field.create(outputMode, , Arrays.copyOfRange(args, 1, args.length)); + // throw new IllegalArgumentException("Not a valid options: " + Arrays.toString(args)); + // } public static ArrayList[] getDescription(Class clazz) { ArrayList[] description = new ArrayList[]{new ArrayList(), new ArrayList()}; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java b/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java index a6a93d3a0..f031a9c3b 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java @@ -29,6 +29,8 @@ */ package com.milaboratory.mixcr.export; +import com.milaboratory.mixcr.basictypes.VDJCFileHeaderData; + public abstract class FieldParameterless extends AbstractField { final String hHeader, sHeader; @@ -59,7 +61,7 @@ public String getHeader(OutputMode outputMode) { } @Override - public FieldExtractor create(OutputMode outputMode, String[] args) { + public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { return new AbstractFieldExtractor(getHeader(outputMode), this) { @Override public String extractValue(T object) { diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java b/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java index 2d5c7af1a..ee6620cf4 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java @@ -29,6 +29,8 @@ */ package com.milaboratory.mixcr.export; +import com.milaboratory.mixcr.basictypes.VDJCFileHeaderData; + public abstract class FieldWithParameters extends AbstractField { final int nArguments; @@ -49,7 +51,7 @@ public int nArguments() { protected abstract String extractValue(T object, P parameters); @Override - public FieldExtractor create(OutputMode outputMode, String[] args) { + public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { final P params = getParameters(args); String header = getHeader(outputMode, params); return new AbstractFieldExtractor(header, this) { From a9d1f8c6fb34d5c41ff471c15daae52e0679e22a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 22 May 2022 14:56:03 +0300 Subject: [PATCH 209/282] feat: concatenation of input files for multilane fastqs --- build.gradle.kts | 2 +- .../milaboratory/mixcr/cli/CommandAlign.java | 57 +++++++++++++------ 2 files changed, 41 insertions(+), 18 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 5d8b3f25c..3d3aff3c3 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -82,7 +82,7 @@ repositories { } val milibVersion = "1.15.0-38-master" -val repseqioVersion = "1.3.5-26-master" +val repseqioVersion = "1.3.5-27-master" val mitoolVersion = "1.3.5-25-master" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index f2fa9a51d..04db9099f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -58,6 +58,7 @@ import com.milaboratory.core.sequence.quality.QualityTrimmerParameters; import com.milaboratory.core.sequence.quality.ReadTrimmerProcessor; import com.milaboratory.core.sequence.quality.ReadTrimmerReport; +import com.milaboratory.mitool.helpers.FSKt; import com.milaboratory.mitool.pattern.search.*; import com.milaboratory.mitool.report.ParseReport; import com.milaboratory.mixcr.basictypes.SequenceHistory; @@ -76,8 +77,10 @@ import java.io.File; import java.io.FileInputStream; import java.io.IOException; +import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; +import java.util.function.Function; import java.util.regex.Pattern; import java.util.stream.Collectors; @@ -95,10 +98,11 @@ public class CommandAlign extends ACommandWithSmartOverwriteMiXCR { static final String ALIGN_COMMAND_NAME = "align"; @Parameters(arity = "2..3", - descriptionKey = "file", paramLabel = "files", hideParamSyntax = true, - description = "file_R1.(fastq[.gz]|fasta) [file_R2.fastq[.gz]] alignments.vdjca") + description = "file_R1.(fastq[.gz]|fasta) [file_R2.fastq[.gz]] alignments.vdjca\n" + + "Use \"{{n}}\" if you want to concatenate files from multiple lanes, like:\n" + + "my_file_L{{n}}_R1.fastq.gz my_file_L{{n}}_R2.fastq.gz") private List inOut = new ArrayList<>(); @Override @@ -113,7 +117,7 @@ protected List getOutputFiles() { @Option(description = CommonDescriptions.SPECIES, names = {"--read-buffer"}) - public int readBufferSize = 1 << 20; + public int readBufferSize = 1 << 22; @Option(description = CommonDescriptions.SPECIES, names = {"-s", "--species"}, @@ -326,14 +330,31 @@ public boolean isInputPaired() { } public SequenceReaderCloseable createReader() throws IOException { - if (isInputPaired()) - return new PairedFastqReader(new FileInputStream(getInputFiles().get(0)), new FileInputStream(getInputFiles().get(1)), - SingleFastqReader.DEFAULT_QUALITY_FORMAT, - CompressionType.detectCompressionType(getInputFiles().get(0)), - true, - readBufferSize, - true, true); - else { + // Common single fastq reader constructor + Function readerFactory = r -> { + try { + return new SingleFastqReader( + new FileInputStream(r.toFile()), + SingleFastqReader.DEFAULT_QUALITY_FORMAT, + CompressionType.detectCompressionType(getInputFiles().get(0)), + false, readBufferSize, + true, true); + } catch (IOException e) { + throw new RuntimeException(e); + } + }; + + if (isInputPaired()) { + List readers = getInputFiles().stream() + .map(rf -> FSKt.expandPathNPattern(Paths.get(rf))) + .map(rs -> new ConcatenatingSingleReader( + rs.stream() + .map(readerFactory) + .collect(Collectors.toList()) + )) + .collect(Collectors.toList()); + return new PairedFastqReader(readers.get(0), readers.get(1)); + } else { String in = getInputFiles().get(0); String[] s = in.split("\\."); if (s[s.length - 1].equals("fasta") || s[s.length - 1].equals("fa")) @@ -342,12 +363,9 @@ public SequenceReaderCloseable createReader() throws IOE true ); else - return new SingleFastqReader(new FileInputStream(in), - SingleFastqReader.DEFAULT_QUALITY_FORMAT, - CompressionType.detectCompressionType(in), - true, - readBufferSize, - true, true); + return new ConcatenatingSingleReader(FSKt.expandPathNPattern(Paths.get(in)).stream() + .map(readerFactory) + .collect(Collectors.toList())); } } @@ -465,6 +483,11 @@ public TagSearchPlan getTagPattern() { return new TagSearchPlan(readSearchPlan, tagShortcuts, readShortcuts, parseInfo.getTags()); } + @Override + protected boolean inputsMustExist() { + return false; + } + @Override public void validate() { super.validate(); From 098c1fdec72e243c6961728693b986bde91a3279 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 22 May 2022 21:00:26 +0300 Subject: [PATCH 210/282] feat: hierarchal sorting of tags, sorted meta field vdjca file --- .../mixcr/basictypes/tag/TagsInfo.java | 15 +- .../milaboratory/mixcr/cli/CommandAlign.java | 2 +- ...gs.java => CommandCorrectAndSortTags.java} | 217 +++++++++++------- .../java/com/milaboratory/mixcr/cli/Main.java | 4 +- .../mixcr/basictypes/tag/TagInfoTest.java | 2 +- 5 files changed, 151 insertions(+), 89 deletions(-) rename src/main/java/com/milaboratory/mixcr/cli/{CommandCorrectTags.java => CommandCorrectAndSortTags.java} (50%) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index 4fdec4ed5..8b41ef7dc 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -9,25 +9,34 @@ @Serializable(asJson = true) public final class TagsInfo { + @JsonProperty("sorted") + public final boolean sorted; @JsonProperty("tags") public final TagInfo[] tags; @JsonCreator - public TagsInfo(@JsonProperty("tags") TagInfo... tags) { + public TagsInfo(@JsonProperty("sorted") boolean sorted, @JsonProperty("tags") TagInfo... tags) { Objects.requireNonNull(tags); + this.sorted = sorted; this.tags = tags; } + public TagsInfo setSorted(boolean sorted){ + return new TagsInfo(sorted, tags); + } + @Override public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; TagsInfo tagsInfo = (TagsInfo) o; - return Arrays.equals(tags, tagsInfo.tags); + return sorted == tagsInfo.sorted && Arrays.equals(tags, tagsInfo.tags); } @Override public int hashCode() { - return Arrays.hashCode(tags); + int result = Objects.hash(sorted); + result = 31 * result + Arrays.hashCode(tags); + return result; } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 04db9099f..02f6b680d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -612,7 +612,7 @@ else if (featureSequence.containsWildcards()) if (writer != null) writer.header(aligner, getFullPipelineConfiguration(), tagSearchPlan != null - ? new TagsInfo(tagSearchPlan.tagInfos.toArray(new TagInfo[0])) + ? new TagsInfo(false, tagSearchPlan.tagInfos.toArray(new TagInfo[0])) : null); OutputPort sReads = reader; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java similarity index 50% rename from src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java rename to src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index fb2350c6c..d45f3a8fe 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -7,8 +7,6 @@ import cc.redberry.pipe.util.CountingOutputPort; import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import com.google.common.hash.Hasher; -import com.google.common.hash.Hashing; import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; @@ -39,17 +37,22 @@ import java.util.Comparator; import java.util.List; import java.util.Objects; +import java.util.function.IntFunction; import java.util.function.ToIntFunction; -import static com.milaboratory.mixcr.cli.CommandCorrectTags.CORRECT_TAGS_COMMAND_NAME; +import static com.milaboratory.mixcr.cli.CommandCorrectAndSortTags.CORRECT_AND_SORT_TAGS_COMMAND_NAME; import static picocli.CommandLine.Option; -@CommandLine.Command(name = CORRECT_TAGS_COMMAND_NAME, +@CommandLine.Command(name = CORRECT_AND_SORT_TAGS_COMMAND_NAME, sortOptions = false, separator = " ", - description = "Builds alignments with V,D,J and C genes for input sequencing reads.") -public class CommandCorrectTags extends ACommandWithSmartOverwriteWithSingleInputMiXCR { - static final String CORRECT_TAGS_COMMAND_NAME = "correctTags"; + description = "Applies error correction algorithm for tag sequences and sorts resulting file by tags.") +public class CommandCorrectAndSortTags extends ACommandWithSmartOverwriteWithSingleInputMiXCR { + static final String CORRECT_AND_SORT_TAGS_COMMAND_NAME = "correctAndSortTags"; + + @Option(description = "Don't correct barcodes, only sort alignments by tags.", + names = {"--dont-correct"}) + public boolean noCorrect = false; @Option(description = "This parameter determines how thorough the procedure should eliminate variants looking like errors. " + "Smaller value leave less erroneous variants at the cost of accidentally correcting true variants. " + @@ -124,13 +127,14 @@ public ActionConfiguration getConfiguration() { @Override public void run1() throws Exception { - CorrectionNode correctioResult; - CorrectionReport report; - int[] targetTagIndices; + final CorrectionNode correctionResult; + final CorrectionReport report; + final int[] targetTagIndices; + final List tagNames; try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in)) { TagsInfo tagsInfo = reader.getTagsInfo(); - List tagNames = new ArrayList<>(); + tagNames = new ArrayList<>(); TIntArrayList indicesBuilder = new TIntArrayList(); for (int i = 0; i < tagsInfo.tags.length; i++) { TagInfo tag = tagsInfo.tags[i]; @@ -143,49 +147,55 @@ public void run1() throws Exception { System.out.println("Correction will be applied to the following tags: " + String.join(", ", tagNames)); - TagCorrector corrector = new TagCorrector(getParameters(), - tempFolder(), "", - memoryBudget, - 4, 4); - SmartProgressReporter.startProgressReport(corrector); - - // Extractor of tag information from the alignments for the tag corrector - Processor mapper = input -> { - if (input.getTagCounter().size() != 1) - throwExecutionException("This procedure don't support aggregated tags. " + - "Please run tag correction for *.vdjca files produced by 'align'."); - TagTuple tagTuple = input.getTagCounter().keys().iterator().next(); - NSequenceWithQuality[] tags = new NSequenceWithQuality[targetTagIndices.length]; - for (int i = 0; i < targetTagIndices.length; i++) - tags[i] = ((SequenceAndQualityTagValue) tagTuple.tags[targetTagIndices[i]]).data; - return tags; - }; - OutputPort cInput = CUtils.wrap(reader, mapper); - correctioResult = corrector.correct(cInput, tagNames, reader); - report = corrector.getReport(); + if (!noCorrect) { + TagCorrector corrector = new TagCorrector(getParameters(), + tempFolder(), "", + memoryBudget, + 4, 4); + SmartProgressReporter.startProgressReport(corrector); + + // Extractor of tag information from the alignments for the tag corrector + Processor mapper = input -> { + if (input.getTagCounter().size() != 1) + throwExecutionException("This procedure don't support aggregated tags. " + + "Please run tag correction for *.vdjca files produced by 'align'."); + TagTuple tagTuple = input.getTagCounter().keys().iterator().next(); + NSequenceWithQuality[] tags = new NSequenceWithQuality[targetTagIndices.length]; + for (int i = 0; i < targetTagIndices.length; i++) + tags[i] = ((SequenceAndQualityTagValue) tagTuple.tags[targetTagIndices[i]]).data; + return tags; + }; + OutputPort cInput = CUtils.wrap(reader, mapper); + correctionResult = corrector.correct(cInput, tagNames, reader); + report = corrector.getReport(); + } else { + correctionResult = null; + report = null; + } } - ToIntFunction hashFunction = al -> { - TagValue[] tags = al.getTagCounter().keys().iterator().next().tags; - //noinspection UnstableApiUsage - Hasher hasher = Hashing.murmur3_32_fixed().newHasher(); - for (int i : targetTagIndices) - //noinspection UnstableApiUsage - hasher.putInt(((SequenceAndQualityTagValue) tags[i]).data.getSequence().hashCode()); - //noinspection UnstableApiUsage - return hasher.hash().hashCode(); - }; - - Comparator comparator = (al1, al2) -> { - TagValue[] tags1 = al1.getTagCounter().keys().iterator().next().tags; - TagValue[] tags2 = al2.getTagCounter().keys().iterator().next().tags; - int c; - for (int i : targetTagIndices) - if ((c = ((SequenceAndQualityTagValue) tags1[i]).data.getSequence().compareTo( - ((SequenceAndQualityTagValue) tags2[i]).data.getSequence())) != 0) - return c; - return 0; - }; + // ToIntFunction hashFunction = al -> { + // TagValue[] tags = al.getTagCounter().keys().iterator().next().tags; + // //noinspection UnstableApiUsage + // Hasher hasher = Hashing.murmur3_32_fixed().newHasher(); + // for (int i : targetTagIndices) + // //noinspection UnstableApiUsage + // hasher.putInt(((SequenceAndQualityTagValue) tags[i]).data.getSequence().hashCode()); + // //noinspection UnstableApiUsage + // return hasher.hash().hashCode(); + // }; + // + // Comparator comparator = (al1, al2) -> { + // TagValue[] tags1 = al1.getTagCounter().keys().iterator().next().tags; + // TagValue[] tags2 = al2.getTagCounter().keys().iterator().next().tags; + // int c; + // for (int i : targetTagIndices) + // if ((c = ((SequenceAndQualityTagValue) tags1[i]).data.getSequence().compareTo( + // ((SequenceAndQualityTagValue) tags2[i]).data.getSequence())) != 0) + // return c; + // return 0; + // }; + try ( VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in); @@ -194,50 +204,69 @@ public void run1() throws Exception { PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); IOUtil.registerGeneReferences(stateBuilder, reader.getUsedGenes(), reader.getParameters()); - HashSorter hashSorter = new HashSorter<>( - VDJCAlignments.class, - hashFunction, comparator, - 4, tempFolder().resolve("hashsorter"), - 4, 4, - stateBuilder.getOState(), stateBuilder.getIState(), - memoryBudget, 10000 - ); - - SmartProgressReporter.startProgressReport("Applying correction & sorting alignments", reader); - - Processor mapper = al -> { - TagTuple tt = al.getTagCounter().keys().iterator().next(); - TagValue[] newTags = tt.tags.clone(); - CorrectionNode cn = correctioResult; - for (int i : targetTagIndices) { - NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); - cn = cn.getNextLevel().get(current); - if (cn == null) { - report.setFilteredRecords(report.getFilteredRecords() + 1); - return al.setTagCounter(null); // will be filtered right before hash sorter - } - newTags[i] = new SequenceAndQualityTagValue(cn.getCorrectValue()); - } - return al.setTagCounter(new TagCounter(new TagTuple(newTags))); + IntFunction> hashSorterFactory = tagIdx -> { + SortingStep sortingStep = new SortingStep(tagIdx); + return new HashSorter<>( + VDJCAlignments.class, + sortingStep.getHashFunction(), sortingStep.getComparator(), + 4, tempFolder().resolve("hashsorter." + tagIdx + "."), + 4, 4, + stateBuilder.getOState(), stateBuilder.getIState(), + memoryBudget, 10000 + ); }; + HashSorter initialHashSorter = hashSorterFactory.apply(targetTagIndices[targetTagIndices.length - 1]); + + SmartProgressReporter.startProgressReport(!noCorrect + ? "Applying correction & sorting alignments by " + tagNames.get(targetTagIndices.length - 1) + : "Sorting alignments by " + tagNames.get(targetTagIndices.length - 1), + reader); + + Processor mapper = !noCorrect + ? + al -> { + TagTuple tt = al.getTagCounter().keys().iterator().next(); + TagValue[] newTags = tt.tags.clone(); + CorrectionNode cn = correctionResult; + for (int i : targetTagIndices) { + NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); + cn = cn.getNextLevel().get(current); + if (cn == null) { + report.setFilteredRecords(report.getFilteredRecords() + 1); + return al.setTagCounter(null); // will be filtered right before hash sorter + } + newTags[i] = new SequenceAndQualityTagValue(cn.getCorrectValue()); + } + return al.setTagCounter(new TagCounter(new TagTuple(newTags))); + } + : al -> al; + // Creating output port with corrected and filtered tags OutputPort hsInput = new FilteringPort<>( CUtils.wrap(reader, mapper), al -> al.getTagCounter() != null); - // Running hash sorter - CountingOutputPort sorted = new CountingOutputPort<>(hashSorter.port(hsInput)); + // Running initial hash sorter + CountingOutputPort sorted = new CountingOutputPort<>(initialHashSorter.port(hsInput)); + + // Sorting by other tags + for (int tagIdxIdx = targetTagIndices.length - 2; tagIdxIdx >= 0; tagIdxIdx--) { + SmartProgressReporter.startProgressReport("Sorting alignments by " + tagNames.get(tagIdxIdx), + SmartProgressReporter.extractProgress(sorted, reader.getNumberOfReads())); + sorted = new CountingOutputPort<>(hashSorterFactory.apply(targetTagIndices[tagIdxIdx]).port(sorted)); + } SmartProgressReporter.startProgressReport("Writing result", SmartProgressReporter.extractProgress(sorted, reader.getNumberOfReads())); // Initializing and writing results to the output file - writer.header(reader, getFullPipelineConfiguration(), reader.getTagsInfo()); + writer.header(reader, getFullPipelineConfiguration(), reader.getTagsInfo().setSorted(true)); for (VDJCAlignments al : CUtils.it(sorted)) writer.write(al); } - report.writeReport(ReportHelper.STDOUT); + if (report != null) + report.writeReport(ReportHelper.STDOUT); } public static final class CorrectTagsConfiguration implements ActionConfiguration { @@ -250,7 +279,7 @@ public CorrectTagsConfiguration(@JsonProperty("parameters") TagCorrectorParamete @Override public String actionName() { - return CORRECT_TAGS_COMMAND_NAME; + return CORRECT_AND_SORT_TAGS_COMMAND_NAME; } @Override @@ -266,4 +295,28 @@ public int hashCode() { return Objects.hash(parameters); } } + + private static final class SortingStep { + final int tagIdx; + + public SortingStep(int tagIdx) { + this.tagIdx = tagIdx; + } + + public ToIntFunction getHashFunction() { + return al -> { + TagValue[] tags = al.getTagCounter().keys().iterator().next().tags; + return ((SequenceAndQualityTagValue) tags[tagIdx]).data.getSequence().hashCode(); + }; + } + + public Comparator getComparator() { + return (al1, al2) -> { + TagValue[] tags1 = al1.getTagCounter().keys().iterator().next().tags; + TagValue[] tags2 = al2.getTagCounter().keys().iterator().next().tags; + return ((SequenceAndQualityTagValue) tags1[tagIdx]).data.getSequence().compareTo( + ((SequenceAndQualityTagValue) tags2[tagIdx]).data.getSequence()); + }; + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 5e09907e9..47f2f6ef5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -56,7 +56,7 @@ import java.util.prefs.Preferences; import static com.fasterxml.jackson.module.kotlin.ExtensionsKt.kotlinModule; -import static com.milaboratory.mixcr.cli.CommandCorrectTags.CORRECT_TAGS_COMMAND_NAME; +import static com.milaboratory.mixcr.cli.CommandCorrectAndSortTags.CORRECT_AND_SORT_TAGS_COMMAND_NAME; public final class Main { @@ -236,7 +236,7 @@ public static CommandLine mkCmd() { // .addSubcommand("groupCells", CommandGroupCells.class) .addSubcommand("assembleContigs", CommandAssembleContigs.class) - .addSubcommand(CORRECT_TAGS_COMMAND_NAME, CommandCorrectTags.class) + .addSubcommand(CORRECT_AND_SORT_TAGS_COMMAND_NAME, CommandCorrectAndSortTags.class) .addSubcommand("assemblePartial", CommandAssemblePartialAlignments.class) .addSubcommand("extend", CommandExtend.class) diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java index 71a8a565f..064eab892 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java @@ -7,6 +7,6 @@ public class TagInfoTest { @Test public void test1() { TestUtil.assertJson(new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2)); - TestUtil.assertJson(new TagsInfo(new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2))); + TestUtil.assertJson(new TagsInfo(false, new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2))); } } \ No newline at end of file From 33402c10f5d8285216915e17c6f819f245e1ce37 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 23 May 2022 00:59:16 +0300 Subject: [PATCH 211/282] feat: assemblePartial now executed separately for each tag group --- .../basictypes/VDJCAlignmentsWriter.java | 14 +- .../mixcr/basictypes/tag/TagCounter.java | 7 + .../mixcr/basictypes/tag/TagTuple.java | 16 +- .../cli/CommandAssemblePartialAlignments.java | 56 +++++-- .../mixcr/cli/CommandCorrectAndSortTags.java | 9 +- .../PartialAlignmentsAssembler.java | 153 ++++++++++-------- .../mixcr/partialassembler/TargetMerger.java | 25 +-- .../mixcr/vdjaligners/VDJCAlignerPVFirst.java | 80 ++++----- .../PartialAlignmentsAssemblerTest.java | 27 ++-- 9 files changed, 217 insertions(+), 170 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java index 6d9c2d054..fe4444e58 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java @@ -127,19 +127,9 @@ public void header(VDJCAligner aligner, PipelineConfiguration pipelineConfigurat header(aligner.getParameters(), aligner.getUsedGenes(), pipelineConfiguration, tagsInfo); } - /** History to write in the header */ - private PipelineConfiguration pipelineConfiguration = null; - - public synchronized void setPipelineConfiguration(PipelineConfiguration configuration) { - if (pipelineConfiguration == null) - pipelineConfiguration = configuration; - else if (!configuration.equals(this.pipelineConfiguration)) - throw new IllegalStateException(); - } - @Override public void header(VDJCAlignerParameters parameters, List genes, - PipelineConfiguration ppConfiguration, TagsInfo tags) { + PipelineConfiguration pipelineConfiguration, TagsInfo tags) { if (parameters == null || genes == null) throw new IllegalArgumentException(); @@ -161,8 +151,6 @@ public void header(VDJCAlignerParameters parameters, List genes, o.writeObject(parameters); // Writing history - if (ppConfiguration != null) - this.pipelineConfiguration = ppConfiguration; o.writeObject(pipelineConfiguration); // Information about tags diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java index b4c6be6fc..6eab5a7bf 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java @@ -43,6 +43,13 @@ public TagTuple singleOrNull() { return it.key(); } + public TagTuple singleOrError() { + TagTuple result = singleOrNull(); + if (result == null) + throw new IllegalStateException("Aggregated tag information, single tag tuple expected."); + return result; + } + public Set keys() { return tags.keySet(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index 7af77934c..da9da75cf 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -2,7 +2,6 @@ import com.google.common.hash.Hasher; import com.google.common.hash.Hashing; -import com.milaboratory.util.ByteString; import java.util.Arrays; @@ -26,6 +25,21 @@ public TagTuple(TagValue... tags) { this.hash = hasher.hash().hashCode(); } + public TagTuple toKeys() { + boolean hasNonKey = false; + for (TagValue tag : tags) + if (!tag.isKey()) { + hasNonKey = true; + break; + } + if (!hasNonKey) + return this; + TagValue[] newTags = tags.clone(); + for (int i = 0; i < newTags.length; i++) + newTags[i] = newTags[i].extractKey(); + return new TagTuple(newTags); + } + @Override public int compareTo(TagTuple o) { int l = Math.min(tags.length, o.tags.length); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 0c65df7cb..4f29d4059 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -29,15 +29,25 @@ */ package com.milaboratory.mixcr.cli; -import com.fasterxml.jackson.annotation.*; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.annotation.JsonTypeInfo; import com.milaboratory.cli.ActionConfiguration; +import com.milaboratory.mitool.helpers.GroupOP; +import com.milaboratory.mitool.helpers.PipeKt; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssembler; import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssemblerParameters; import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.ReportUtil; import com.milaboratory.util.SmartProgressReporter; +import kotlin.jvm.functions.Function1; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -108,10 +118,18 @@ public void run1() throws Exception { long beginTimestamp = System.currentTimeMillis(); PartialAlignmentsAssemblerParameters assemblerParameters = getPartialAlignmentsAssemblerParameters(); - VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out); - writer.setPipelineConfiguration(getFullPipelineConfiguration()); - try (PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(assemblerParameters, - writer, !dropPartial, overlappedOnly)) { + + // Two readers will be used to feed two-pass assemble partial algorithm + try (VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(in); + VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(in); + VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { + + writer.header(reader1.getParameters(), reader1.getUsedGenes(), getFullPipelineConfiguration(), reader1.getTagsInfo()); + + PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(assemblerParameters, reader1.getParameters(), + reader1.getUsedGenes(), !dropPartial, overlappedOnly, + writer::write); + this.report = assembler; ReportWrapper report = new ReportWrapper(ASSEMBLE_PARTIAL_COMMAND_NAME, assembler); report.setStartMillis(beginTimestamp); @@ -119,13 +137,24 @@ public void run1() throws Exception { report.setOutputFiles(out); report.setCommandLine(getCommandLineArguments()); - try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in)) { - SmartProgressReporter.startProgressReport("Building index", reader); - assembler.buildLeftPartsIndex(reader); - } - try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in)) { - SmartProgressReporter.startProgressReport("Searching for overlaps", reader); - assembler.searchOverlaps(reader); + if (reader1.getTagsInfo() != null && reader1.getTagsInfo().tags.length > 0) { + SmartProgressReporter.startProgressReport("Running assemble partial", reader1); + + Function1 key = al -> al.getTagCounter().singleOrError().toKeys(); + OutputPort> groups1 = PipeKt.group(reader1, key); + OutputPort> groups2 = PipeKt.group(reader2, key); + + for (GroupOP grp1 : CUtils.it(groups1)) { + assembler.buildLeftPartsIndex(grp1); + GroupOP grp2 = groups2.take(); + assert grp2.getKey().equals(grp1.getKey()) : grp1.getKey() + " != " + grp2.getKey(); + assembler.searchOverlaps(grp2); + } + } else { + SmartProgressReporter.startProgressReport("Building index", reader1); + assembler.buildLeftPartsIndex(reader1); + SmartProgressReporter.startProgressReport("Searching for overlaps", reader2); + assembler.searchOverlaps(reader2); } report.setFinishMillis(System.currentTimeMillis()); @@ -149,6 +178,9 @@ public void run1() throws Exception { if (jsonReport != null) ReportUtil.appendJsonReport(jsonReport, report); + + // TODO ???? + // output.setNumberOfProcessedReads(input.getNumberOfReads() - overlapped.get()); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index d45f3a8fe..dab2c3964 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -226,8 +226,7 @@ public void run1() throws Exception { Processor mapper = !noCorrect ? al -> { - TagTuple tt = al.getTagCounter().keys().iterator().next(); - TagValue[] newTags = tt.tags.clone(); + TagValue[] newTags = al.getTagCounter().singleOrError().tags.clone(); CorrectionNode cn = correctionResult; for (int i : targetTagIndices) { NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); @@ -305,15 +304,15 @@ public SortingStep(int tagIdx) { public ToIntFunction getHashFunction() { return al -> { - TagValue[] tags = al.getTagCounter().keys().iterator().next().tags; + TagValue[] tags = al.getTagCounter().singleOrError().tags; return ((SequenceAndQualityTagValue) tags[tagIdx]).data.getSequence().hashCode(); }; } public Comparator getComparator() { return (al1, al2) -> { - TagValue[] tags1 = al1.getTagCounter().keys().iterator().next().tags; - TagValue[] tags2 = al2.getTagCounter().keys().iterator().next().tags; + TagValue[] tags1 = al1.getTagCounter().singleOrError().tags; + TagValue[] tags2 = al2.getTagCounter().singleOrError().tags; return ((SequenceAndQualityTagValue) tags1[tagIdx]).data.getSequence().compareTo( ((SequenceAndQualityTagValue) tags2[tagIdx]).data.getSequence()); }; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 6710d3206..f968accfc 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -30,44 +30,51 @@ package com.milaboratory.mixcr.partialassembler; import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.InputPort; +import cc.redberry.pipe.OutputPort; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.core.Range; import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.SequenceHistory; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence; import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; -import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; -import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TLongObjectHashMap; import gnu.trove.set.hash.TLongHashSet; import io.repseq.core.*; -import java.io.IOException; import java.util.ArrayList; import java.util.List; -import java.util.Objects; import java.util.Set; import java.util.concurrent.atomic.AtomicLong; -public class PartialAlignmentsAssembler implements AutoCloseable, Report { +public class PartialAlignmentsAssembler implements Report { final TLongObjectHashMap> kToIndexLeft = new TLongObjectHashMap<>(); final TLongHashSet alreadyMergedIds = new TLongHashSet(); final TLongHashSet notInLeftIndexIds = new TLongHashSet(); - final VDJCAlignmentsWriter writer; + final InputPort output; final int kValue; final int kOffset; final int minimalAssembleOverlap; final int minimalNOverlap; final boolean writePartial, overlappedOnly; + final VDJCAlignerParameters alignerParameters; final TargetMerger targetMerger; + final List usedGenes; + final Set geneTypesToShiftIndels; final long maxLeftParts; final int maxLeftMatches; - public final AtomicLong leftParts = new AtomicLong(), + public final AtomicLong + independentRuns = new AtomicLong(), + leftParts = new AtomicLong(), rightParts = new AtomicLong(), noKMer = new AtomicLong(), wildcardsInKMer = new AtomicLong(), @@ -82,25 +89,26 @@ public class PartialAlignmentsAssembler implements AutoCloseable, Report { complexOverlapped = new AtomicLong(), containsCDR3 = new AtomicLong(); - public PartialAlignmentsAssembler(PartialAlignmentsAssemblerParameters params, VDJCAlignmentsWriter writer, - boolean writePartial, boolean overlappedOnly) { + public PartialAlignmentsAssembler(PartialAlignmentsAssemblerParameters params, + VDJCAlignerParameters alignerParameters, + List usedGenes, + boolean writePartial, boolean overlappedOnly, + InputPort output) { this.kValue = params.getKValue(); if (kValue >= 32) throw new IllegalArgumentException("kValue should be less than 32"); this.kOffset = params.getKOffset(); this.minimalAssembleOverlap = params.getMinimalAssembleOverlap(); this.minimalNOverlap = params.getMinimalNOverlap(); - this.targetMerger = new TargetMerger(params.getMergerParameters(), params.getMinimalAlignmentMergeIdentity()); + this.alignerParameters = alignerParameters; + this.targetMerger = new TargetMerger(params.getMergerParameters(), alignerParameters, params.getMinimalAlignmentMergeIdentity()); + this.usedGenes = usedGenes; + this.geneTypesToShiftIndels = alignerParameters.getGeneTypesWithLinearScoring(); this.maxLeftParts = params.getMaxLeftParts(); this.maxLeftMatches = params.getMaxLeftMatches(); this.writePartial = writePartial; this.overlappedOnly = overlappedOnly; - this.writer = writer; - } - - public PartialAlignmentsAssembler(PartialAlignmentsAssemblerParameters params, String output, - boolean writePartial, boolean overlappedOnly) throws IOException { - this(params, new VDJCAlignmentsWriter(output), writePartial, overlappedOnly); + this.output = output; } public boolean leftPartsLimitReached() { @@ -113,12 +121,16 @@ public boolean maxRightMatchesLimitReached() { return maxRightMatchesLimitReached; } - private Set geneTypesToShiftIndels; - public void buildLeftPartsIndex(VDJCAlignmentsReader reader) { - geneTypesToShiftIndels = reader.getParameters().getGeneTypesWithLinearScoring(); - writer.header(reader.getParameters(), reader.getUsedGenes(), null, reader.getTagsInfo()); - for (VDJCAlignments alignment : CUtils.it(reader)) { + public void buildLeftPartsIndex(OutputPort input) { + // Resetting internal state if this object was reused + kToIndexLeft.clear(); + alreadyMergedIds.clear(); + notInLeftIndexIds.clear(); + + independentRuns.incrementAndGet(); + + for (VDJCAlignments alignment : CUtils.it(input)) { if (alignment.getFeature(GeneFeature.CDR3) != null) continue; if (!addLeftToIndex(alignment)) @@ -128,21 +140,19 @@ public void buildLeftPartsIndex(VDJCAlignmentsReader reader) { } } - public void searchOverlaps(VDJCAlignmentsReader reader) { - final VDJCAlignerParameters alignerParameters = reader.getParameters(); + public void searchOverlaps(OutputPort input) { PartialAlignmentsAssemblerAligner aligner = new PartialAlignmentsAssemblerAligner(alignerParameters); - targetMerger.setAlignerParameters(alignerParameters); - for (VDJCGene gene : reader.getUsedGenes()) + for (VDJCGene gene : usedGenes) aligner.addGene(gene); - for (final VDJCAlignments alignment : CUtils.it(reader)) { + for (final VDJCAlignments alignment : CUtils.it(input)) { total.incrementAndGet(); if (alignment.getFeature(GeneFeature.CDR3) != null) { containsCDR3.incrementAndGet(); if (!overlappedOnly) { totalWritten.incrementAndGet(); - writer.write(alignment); + output.put(alignment); } continue; } @@ -154,17 +164,14 @@ public void searchOverlaps(VDJCAlignmentsReader reader) { // Common procedure to cancel processing of current input alignment if it fails to pass some good // overlap filtering criterion - final Runnable cancelCurrentResult = new Runnable() { - @Override - public void run() { - if (searchResult != null) - searchResult.cancel(); - if (writePartial && !overlappedOnly && - notInLeftIndexIds.contains(alignment.getAlignmentsIndex())) { - totalWritten.incrementAndGet(); - partialAsIs.incrementAndGet(); - writer.write(alignment); - } + final Runnable cancelCurrentResult = () -> { + if (searchResult != null) + searchResult.cancel(); + if (writePartial && !overlappedOnly && + notInLeftIndexIds.contains(alignment.getAlignmentsIndex())) { + totalWritten.incrementAndGet(); + partialAsIs.incrementAndGet(); + output.put(alignment); } }; @@ -247,7 +254,8 @@ public void run() { overlapped.incrementAndGet(); totalWritten.incrementAndGet(); - writer.write(mAlignment.shiftIndelsAtHomopolymers(geneTypesToShiftIndels)); + + output.put(mAlignment.shiftIndelsAtHomopolymers(geneTypesToShiftIndels)); // Saving alignment that where merge to prevent it's use as left part alreadyMergedIds.add(alignment.getAlignmentsIndex()); @@ -260,13 +268,10 @@ public void run() { if (alreadyMergedIds.add(kMerInfo.alignments.getAlignmentsIndex())) { totalWritten.incrementAndGet(); partialAsIs.incrementAndGet(); - writer.write(kMerInfo.getAlignments()); + output.put(kMerInfo.getAlignments()); } - - writer.setNumberOfProcessedReads(reader.getNumberOfReads() - overlapped.get()); } - static class OverlapSearchResult { final List originKMerList; final KMerInfo KMerInfo; @@ -306,7 +311,8 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, else stop -= kOffset; - TagTuple tagTuple = extractTagTuple(rightAl); + TagCounter rightTagCounter = rightAl.getTagCounter(); + // black list of left parts failed due to inconsistent overlapped alignments (failed AMerge) TLongHashSet blackList = new TLongHashSet(); SEARCH_LEFT_PARTS: @@ -317,7 +323,7 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, List maxOverlapList = null; boolean isMaxOverOverlapped = false; for (int rFrom = 0; rFrom < stop && rFrom + kValue < rightSeqQ.size(); rFrom++) { - long kMer = kMer(tagTuple, rightSeqQ.getSequence(), rFrom, kValue); + long kMer = kMer(rightSeqQ.getSequence(), rFrom, kValue); List match = kToIndexLeft.get(kMer); if (match == null) continue; @@ -330,8 +336,8 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, boolean isOverOverlapped = false; final VDJCAlignments leftAl = match.get(i).getAlignments(); - if (!Objects.equals(extractTagTuple(leftAl), tagTuple)) - continue; + // if (!Objects.equals(extractTagTuple(leftAl), tagTuple)) + // continue; if (blackList.contains(leftAl.getAlignmentsIndex())) continue; @@ -392,6 +398,8 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, final KMerInfo left = maxOverlapList.remove(maxOverlapIndexInList); VDJCAlignments leftAl = left.alignments; + TagCounter leftTagCounter = leftAl.getTagCounter(); + //final long readId = rightAl.getReadId(); ArrayList leftTargets = extractAlignedTargets(leftAl); @@ -478,8 +486,12 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, result.add(central); result.addAll(rightDescriptors); + TagCounterBuilder tcBuilder = new TagCounterBuilder(); + tcBuilder.add(leftTagCounter); + tcBuilder.add(rightTagCounter); + // Ordering and filtering final targets - return new OverlapSearchResult(maxOverlapList, left, AlignedTarget.orderTargets(result), central.getAlignments().getTagCounter()); + return new OverlapSearchResult(maxOverlapList, left, AlignedTarget.orderTargets(result), tcBuilder.createAndDestroy()); } } @@ -487,6 +499,11 @@ private static String mergeTypePrefix(boolean usingAlignment) { return usingAlignment ? "A" : "S"; } + @JsonProperty("independentRuns") + public long getIndependentRuns() { + return independentRuns.get(); + } + @JsonProperty("totalProcessed") public long getTotalProcessed() { return total.get(); @@ -560,6 +577,8 @@ public long getPartialAlignmentsAsIs() { @Override public void writeReport(ReportHelper helper) { long total = this.total.get(); + if (independentRuns.get() != 1) + helper.writeField("Independent runs", total); helper.writeField("Total alignments analysed", total); helper.writePercentAndAbsoluteField("Number of output alignments", totalWritten, total); helper.writePercentAndAbsoluteField("Alignments already with CDR3 (no overlapping is performed)", containsCDR3, total); @@ -628,16 +647,16 @@ private static int getAlignmentLength(VDJCAlignments alignment, GeneType gt, int return al.getSequence2Range().length(); } - private static TagTuple extractTagTuple(VDJCAlignments alignments) { - TagCounter tagCounter = alignments.getTagCounter(); - if (tagCounter.size() > 1) - throw new IllegalArgumentException(); - if (tagCounter.size() == 0) - return null; - final TObjectDoubleIterator it = tagCounter.iterator(); - it.advance(); - return it.key(); - } + // private static TagTuple extractTagTuple(VDJCAlignments alignments) { + // TagCounter tagCounter = alignments.getTagCounter(); + // if (tagCounter.size() > 1) + // throw new IllegalArgumentException(); + // if (tagCounter.size() == 0) + // return null; + // final TObjectDoubleIterator it = tagCounter.iterator(); + // it.advance(); + // return it.key(); + // } private boolean addLeftToIndex(VDJCAlignments alignment) { int leftTargetId = getLeftPartitionedSequence(alignment); @@ -651,9 +670,10 @@ private boolean addLeftToIndex(VDJCAlignments alignment) { noKMer.incrementAndGet(); return false; } - TagTuple tagTuple = extractTagTuple(alignment); + + // TagTuple tagTuple = extractTagTuple(alignment); for (int kFrom = kFromFirst; kFrom < seq.size() - kValue; ++kFrom) { - long kmer = kMer(tagTuple, seq.getSequence(), kFrom, kValue); + long kmer = kMer(seq.getSequence(), kFrom, kValue); if (kmer == -1) { wildcardsInKMer.incrementAndGet(); continue; @@ -671,8 +691,8 @@ private boolean addLeftToIndex(VDJCAlignments alignment) { return true; } - private static long kMer(TagTuple tagTuple, NucleotideSequence seq, int from, int length) { - long kmer = tagTuple == null ? 0 : tagTuple.hashCode(); + private static long kMer(NucleotideSequence seq, int from, int length) { + long kmer = 0; // tagTuple == null ? 0 : tagTuple.hashCode(); for (int j = from; j < from + length; ++j) { byte c = seq.codeAt(j); if (NucleotideSequence.ALPHABET.isWildcard(c)) @@ -704,11 +724,6 @@ public static ArrayList extractAlignedTargets(VDJCAlignments alig targets.add(new AlignedTarget(alignments, i)); return targets; } - - @Override - public void close() throws IOException { - writer.close(); - } } // vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv jjjjjjjjjjjjjjjjjjjjjcccccccccccccccccccccccc diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java index 1b6924694..954d715bd 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java @@ -44,9 +44,9 @@ import com.milaboratory.core.sequence.SequencesUtils; import com.milaboratory.mixcr.basictypes.SequenceHistory; import com.milaboratory.mixcr.basictypes.SequenceHistory.OverlapType; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import com.milaboratory.mixcr.vdjaligners.KGeneAlignmentParameters; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.GeneFeature; @@ -57,19 +57,16 @@ import java.util.*; public class TargetMerger { - final MismatchOnlyPairedReadMerger merger; - final IdentityType identityType; - private volatile VDJCAlignerParameters alignerParameters; - final float minimalAlignmentMergeIdentity; + private final MismatchOnlyPairedReadMerger merger; + private final IdentityType identityType; + private final VDJCAlignerParameters alignerParameters; + private final float minimalAlignmentMergeIdentity; - public TargetMerger(MergerParameters mergerParameters, float minimalAlignmentMergeIdentity) { + public TargetMerger(MergerParameters mergerParameters, VDJCAlignerParameters alignerParameters, float minimalAlignmentMergeIdentity) { this.merger = new MismatchOnlyPairedReadMerger(mergerParameters); this.identityType = mergerParameters.getIdentityType(); - this.minimalAlignmentMergeIdentity = minimalAlignmentMergeIdentity; - } - - public void setAlignerParameters(VDJCAlignerParameters alignerParameters) { this.alignerParameters = alignerParameters; + this.minimalAlignmentMergeIdentity = minimalAlignmentMergeIdentity; } @SuppressWarnings("unchecked") @@ -366,14 +363,6 @@ public final static class TargetMergingResult { private final int matched, mismatched; private final int offset; -// public TargetMergingResult(AlignedTarget result, int score, boolean usingAlignments, int matched, int mismatched) { -// this.result = result; -// this.score = score; -// this.usingAlignments = usingAlignments; -// this.matched = matched; -// this.mismatched = mismatched; -// } - private TargetMergingResult() { this(false, null, null, 0, 0, 0, 0); } diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java index 340243645..185e99eb0 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java @@ -45,7 +45,10 @@ import com.milaboratory.core.merger.MergerParameters; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.HasGene; +import com.milaboratory.mixcr.basictypes.SequenceHistory; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.partialassembler.AlignedTarget; import com.milaboratory.mixcr.partialassembler.TargetMerger; @@ -68,8 +71,7 @@ public final class VDJCAlignerPVFirst extends VDJCAlignerAbstract { public VDJCAlignerPVFirst(VDJCAlignerParameters parameters) { super(parameters); MergerParameters mp = parameters.getMergerParameters().overrideReadsLayout(PairedEndReadsLayout.CollinearDirect); - alignmentsMerger = new TargetMerger(mp, (float) parameters.getMergerParameters().getMinimalIdentity()); - alignmentsMerger.setAlignerParameters(parameters); + alignmentsMerger = new TargetMerger(mp, parameters, (float) parameters.getMergerParameters().getMinimalIdentity()); } public void setSAligner(VDJCAlignerS sAligner) { @@ -614,9 +616,9 @@ List> performJAlignment( if (vHit == null) return jAligner.align(targetSequence, 0, targetSequence.size(), filterForJ).getHits(); -// parameters.getAllowPartialAlignments() -// ? jAligner.align(targetSequence).getHits() -// : Collections.EMPTY_LIST; + // parameters.getAllowPartialAlignments() + // ? jAligner.align(targetSequence).getHits() + // : Collections.EMPTY_LIST; //TODO remove @@ -777,8 +779,8 @@ void performCDAlignment() { continue; int from = jAlignment == null ? 0 : jAlignment.getSequence2Range().getTo(); List> temp = cAligner.align(target.targets[i].getSequence(), from, - target.targets[i].size(), - getFilter(GeneType.Constant, vHits, jHits)) + target.targets[i].size(), + getFilter(GeneType.Constant, vHits, jHits)) .getHits(); results[i] = temp.toArray(new AlignmentHit[temp.size()]); } @@ -790,8 +792,8 @@ void performCDAlignment() { // Searching for C gene in second read List> temp = cAligner.align(target.targets[1].getSequence(), - 0, target.targets[1].size(), - getFilter(GeneType.Constant, vHits)) + 0, target.targets[1].size(), + getFilter(GeneType.Constant, vHits)) .getHits(); results[1] = temp.toArray(new AlignmentHit[temp.size()]); @@ -960,35 +962,35 @@ private static VDJCHit[] convert(PairedHit[] preHits, return hits; } -// /** -// * Calculates alignment score only for FR3 and CDR3 part of V gene. -// */ -// float calculateVEndScore(AlignmentHit hit) { -// final VDJCGene gene = hit.getRecordPayload(); -// final int boundary = gene.getPartitioning().getRelativePosition( -// parameters.getFeatureToAlign(GeneType.Variable), -// ReferencePoint.FR3Begin); -// final Alignment alignment = hit.getAlignment(); -// -// if (alignment.getSequence1Range().getUpper() <= boundary) -// return 0.0f; -// -// if (alignment.getSequence1Range().getLower() >= boundary) -// return alignment.getScore(); -// -// final Range range = new Range(boundary, alignment.getSequence1Range().getUpper()); -// Mutations vEndMutations = alignment.getAbsoluteMutations() -// .extractMutationsForRange(range); -// -// return AlignmentUtils.calculateScore( -// alignment.getSequence1().getRange(range), -// vEndMutations, -// parameters.getVAlignerParameters().getParameters().getScoring()); -// -//// return AlignmentUtils.calculateScore( -//// parameters.getVAlignerParameters().getParameters().getScoring(), -//// range.length(), vEndMutations); -// } + // /** + // * Calculates alignment score only for FR3 and CDR3 part of V gene. + // */ + // float calculateVEndScore(AlignmentHit hit) { + // final VDJCGene gene = hit.getRecordPayload(); + // final int boundary = gene.getPartitioning().getRelativePosition( + // parameters.getFeatureToAlign(GeneType.Variable), + // ReferencePoint.FR3Begin); + // final Alignment alignment = hit.getAlignment(); + // + // if (alignment.getSequence1Range().getUpper() <= boundary) + // return 0.0f; + // + // if (alignment.getSequence1Range().getLower() >= boundary) + // return alignment.getScore(); + // + // final Range range = new Range(boundary, alignment.getSequence1Range().getUpper()); + // Mutations vEndMutations = alignment.getAbsoluteMutations() + // .extractMutationsForRange(range); + // + // return AlignmentUtils.calculateScore( + // alignment.getSequence1().getRange(range), + // vEndMutations, + // parameters.getVAlignerParameters().getParameters().getScoring()); + // + //// return AlignmentUtils.calculateScore( + //// parameters.getVAlignerParameters().getParameters().getScoring(), + //// range.length(), vEndMutations); + // } static final Comparator V_END_SCORE_COMPARATOR = new Comparator() { @Override diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java index ab1890447..4411fd2b6 100644 --- a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java @@ -130,8 +130,8 @@ public void test2() throws Exception { final TestResult testResult = processData(data, input); for (VDJCAlignments al : testResult.assembled) { MiXCRTestUtils.printAlignment(al); -// System.out.println(input.VJJunction); -// System.out.println(al.getFeature(GeneFeature.VJJunction).getSequence()); + // System.out.println(input.VJJunction); + // System.out.println(al.getFeature(GeneFeature.VJJunction).getSequence()); Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString())); } } @@ -154,9 +154,9 @@ public void test2a() throws Exception { final TestResult testResult = processData(data, input); for (VDJCAlignments al : testResult.assembled) { MiXCRTestUtils.printAlignment(al); -// System.out.println(input.VJJunction); -// System.out.println(al.getFeature(GeneFeature.VJJunction).getSequence()); -// Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString())); + // System.out.println(input.VJJunction); + // System.out.println(al.getFeature(GeneFeature.VJJunction).getSequence()); + // Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString())); } } @@ -164,7 +164,7 @@ public void test2a() throws Exception { public void test3() throws Exception { for (int i = 0; i < 100; i++) { RandomUtil.reseedThreadLocal(i); -// System.out.println(i); + // System.out.println(i); final InputTestData input = createTestData(i); final NucleotideSequence reference = input.reference; final EnumMap refPositions = input.refPositions; @@ -175,10 +175,10 @@ public void test3() throws Exception { final TestResult testResult = processData(data, input); for (VDJCAlignments al : testResult.assembled) { -// printAlignment(al); + // printAlignment(al); if (al.numberOfTargets() == 1) { -// System.out.println(input.VJJunction); -// System.out.println(al.getFeature(GeneFeature.VJJunction).getSequence()); + // System.out.println(input.VJJunction); + // System.out.println(al.getFeature(GeneFeature.VJJunction).getSequence()); Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString())); } } @@ -241,18 +241,19 @@ public static TestResult processData(PairedRead[] data, InputTestData input) thr break; } } -// Assert.assertTrue(yes); + // Assert.assertTrue(yes); } -// if (al.getFeature(GeneFeature.VJJunction) != null) -// Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString())); + // if (al.getFeature(GeneFeature.VJJunction) != null) + // Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString())); } File overlappedAlignments = TempFileManager.getTempFile(); try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(overlappedAlignments)) { final PartialAlignmentsAssemblerParameters pParameters = PartialAlignmentsAssemblerParameters.getDefault(); pParameters.setMergerParameters(pParameters.getMergerParameters().overrideMinimalIdentity(0.0)); - PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(pParameters, writer, true, false); + PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(pParameters, inputAlignments.parameters.alignerParameters, + inputAlignments.usedGenes, true, false, writer::write); try (final VDJCAlignmentsReader reader = inputAlignments.resultReader()) { assembler.buildLeftPartsIndex(reader); From f27472fe908d948e63f91ac1ff573db7097f1c14 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 23 May 2022 19:03:19 +0300 Subject: [PATCH 212/282] feat: named tag pattern --- .../milaboratory/mixcr/cli/CommandAlign.java | 33 ++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 02f6b680d..82c97cb81 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -59,6 +59,7 @@ import com.milaboratory.core.sequence.quality.ReadTrimmerProcessor; import com.milaboratory.core.sequence.quality.ReadTrimmerReport; import com.milaboratory.mitool.helpers.FSKt; +import com.milaboratory.mitool.pattern.PatternCollection; import com.milaboratory.mitool.pattern.search.*; import com.milaboratory.mitool.report.ParseReport; import com.milaboratory.mixcr.basictypes.SequenceHistory; @@ -77,6 +78,7 @@ import java.io.File; import java.io.FileInputStream; import java.io.IOException; +import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; @@ -234,6 +236,14 @@ public void setSaveOriginalReads(boolean b) { names = {"--tag-pattern"}) public String tagPattern; + @Option(description = "Tag pattern name from the built-in list.", + names = {"--tag-pattern-name"}) + public String tagPatternName; + + @Option(description = "Read tag pattern from a file.", + names = {"--tag-pattern-file"}) + public String tagPatternFile; + @Option(description = "If paired-end input is used, determines whether to try all combinations of mate-pairs or only match " + "reads to the corresponding pattern sections (i.e. first file to first section, etc...)", names = {"--tag-parse-unstranded"}) @@ -455,9 +465,30 @@ public int hashCode() { } public TagSearchPlan getTagPattern() { - if (tagPattern == null) + if (tagPattern == null && tagPatternName == null && tagPatternFile == null) return null; + if ((tagPattern != null ? 1 : 0) + (tagPatternName != null ? 1 : 0) + (tagPatternFile != null ? 1 : 0) != 1) + throwValidationException("--tag-pattern, --tag-pattern-name and --tag-pattern-file can't be used together"); + + String tagPattern; + if (this.tagPattern != null) + tagPattern = this.tagPattern; + else if (this.tagPatternName != null) + tagPattern = PatternCollection.INSTANCE.getPatternByName(this.tagPatternName); + else if (this.tagPatternFile != null) + try { + tagPattern = new String(Files.readAllBytes(Paths.get(this.tagPatternFile))); + } catch (IOException e) { + throwValidationException(e.getMessage()); + throw new AssertionError(); + } + else + throw new AssertionError(); + + System.out.println("Tags will be extracted using the following pattern:"); + System.out.println(tagPattern); + ReadSearchSettings searchSettings = new ReadSearchSettings(new SearchSettings(tagMaxBudget, 0.1, new MatcherSettings(3, 7)), isInputPaired() From 93b695e50dcbbcfef63cc4ade9463b1a7ad3b591 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 23 May 2022 21:21:01 +0300 Subject: [PATCH 213/282] chore: fix of CI build with mitool & downgrade to JDK 8 --- .github/workflows/build.yaml | 2 +- build.gradle.kts | 19 ++++++++++--------- .../mixcr/assembler/CloneAssemblerRunner.java | 2 +- .../mixcr/cli/CommandSortClones.java | 5 +++-- 4 files changed, 15 insertions(+), 13 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 94ebcc1b1..36e5bd72c 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -29,7 +29,7 @@ jobs: uses: milaboratory/github-ci/.github/workflows/java-gradle-app.yaml@v2 with: # Environment - java-version: '11' + java-version: '8' app-name: MiXCR app-name-slug: 'mixcr' diff --git a/build.gradle.kts b/build.gradle.kts index 3d3aff3c3..2039410cf 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -23,7 +23,7 @@ plugins { `maven-publish` kotlin("jvm") version "1.6.21" id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-rc-8" - id("com.palantir.git-version") version "0.15.0" + id("com.palantir.git-version") version "0.13.0" // don't upgrade, latest version that runs on Java 8 id("com.github.johnrengelman.shadow") version "7.1.2" } // Make IDE aware of the generated code: @@ -81,20 +81,21 @@ repositories { } } -val milibVersion = "1.15.0-38-master" -val repseqioVersion = "1.3.5-27-master" -val mitoolVersion = "1.3.5-25-master" +val milibVersion = "1.15.0-42-master" +val repseqioVersion = "1.3.5-28-master" +val mitoolVersion = "0.9.1-7-main" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" dependencies { - api("com.milaboratory:milib:$milibVersion") - api("io.repseq:repseqio:$repseqioVersion") { + implementation("com.milaboratory:milib:$milibVersion") + implementation("io.repseq:repseqio:$repseqioVersion") { exclude("com.milaboratory", "milib") } - api("com.milaboratory:miplots:$miplotsVersion") - - api("com.milaboratory:mitool:$miplotsVersion") + implementation("com.milaboratory:mitool:$mitoolVersion"){ + exclude("com.milaboratory", "milib") + } + implementation("com.milaboratory:miplots:$miplotsVersion") // implementation("com.milaboratory:milm2-jvm:0.2.0-test-2") { isChanging = true } implementation("com.milaboratory:milm2-jvm:1.1.0") diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index fbd5c98d0..60cc80bf5 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -72,7 +72,7 @@ public boolean isFinished() { } public void run() { - //run initial assembler + // run initial assembler try (OutputPortCloseable alignmentsPort = alignmentsProvider.create()) { if (alignmentsPort instanceof VDJCAlignmentsReaderWrapper.OP) alignmentReader = ((VDJCAlignmentsReaderWrapper.OP) alignmentsPort).reader; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java index 936ffebc3..773b00c99 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java @@ -13,6 +13,7 @@ import java.io.File; import java.nio.file.Path; +import java.nio.file.Paths; import java.util.Objects; import static com.milaboratory.mixcr.basictypes.IOUtil.MAGIC_CLNA; @@ -36,7 +37,7 @@ public ActionConfiguration getConfiguration() { public void run1() throws Exception { switch (Objects.requireNonNull(IOUtil.fileInfoExtractorInstance.getFileInfo(new File(in))).fileType) { case MAGIC_CLNS: - try (ClnsReader reader = new ClnsReader(Path.of(in), VDJCLibraryRegistry.getDefault()); + try (ClnsReader reader = new ClnsReader(Paths.get(in), VDJCLibraryRegistry.getDefault()); ClnsWriter writer = new ClnsWriter(out)) { GeneFeature[] assemblingFeatures = reader.getAssemblerParameters().getAssemblingFeatures(); @@ -57,7 +58,7 @@ public void run1() throws Exception { return; case MAGIC_CLNA: - try (ClnAReader reader = new ClnAReader(Path.of(in), VDJCLibraryRegistry.getDefault(), Runtime.getRuntime().availableProcessors()); + try (ClnAReader reader = new ClnAReader(Paths.get(in), VDJCLibraryRegistry.getDefault(), Runtime.getRuntime().availableProcessors()); ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { SmartProgressReporter.startProgressReport(writer); From 4bd657c5d8fb946aef637a6759b637f67e7be15e Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 23 May 2022 21:28:44 +0300 Subject: [PATCH 214/282] chore: CI fixes & downgrade to JDK 8 --- .github/workflows/build.yaml | 2 +- build.gradle.kts | 13 ++++++------- .../mixcr/assembler/CloneAssemblerRunner.java | 2 +- .../milaboratory/mixcr/cli/CommandSortClones.java | 5 +++-- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 94ebcc1b1..36e5bd72c 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -29,7 +29,7 @@ jobs: uses: milaboratory/github-ci/.github/workflows/java-gradle-app.yaml@v2 with: # Environment - java-version: '11' + java-version: '8' app-name: MiXCR app-name-slug: 'mixcr' diff --git a/build.gradle.kts b/build.gradle.kts index d2119957b..af92b4532 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -22,7 +22,7 @@ plugins { `maven-publish` kotlin("jvm") version "1.6.21" id("org.jetbrains.kotlin.plugin.dataframe") version "0.8.0-rc-8" - id("com.palantir.git-version") version "0.15.0" + id("com.palantir.git-version") version "0.13.0" // don't upgrade, latest version that runs on Java 8 id("com.github.johnrengelman.shadow") version "7.1.2" } // Make IDE aware of the generated code: @@ -78,18 +78,17 @@ repositories { } } -val milibVersion = "1.15.0-38-master" -val repseqioVersion = "1.3.5-26-master" -val mitoolVersion = "1.3.5-25-master" +val milibVersion = "1.15.0-42-master" +val repseqioVersion = "1.3.5-28-master" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" dependencies { - api("com.milaboratory:milib:$milibVersion") - api("io.repseq:repseqio:$repseqioVersion") { + implementation("com.milaboratory:milib:$milibVersion") + implementation("io.repseq:repseqio:$repseqioVersion") { exclude("com.milaboratory", "milib") } - api("com.milaboratory:miplots:$miplotsVersion") + implementation("com.milaboratory:miplots:$miplotsVersion") // implementation("com.milaboratory:milm2-jvm:0.2.0-test-2") { isChanging = true } implementation("com.milaboratory:milm2-jvm:1.1.0") diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index 7f32f9c62..c1ebb7b1f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -72,7 +72,7 @@ public boolean isFinished() { } public void run() { - //run initial assembler + // run initial assembler try (OutputPortCloseable alignmentsPort = alignmentsProvider.create()) { if (alignmentsPort instanceof VDJCAlignmentsReaderWrapper.OP) alignmentReader = ((VDJCAlignmentsReaderWrapper.OP) alignmentsPort).reader; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java index 936ffebc3..773b00c99 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java @@ -13,6 +13,7 @@ import java.io.File; import java.nio.file.Path; +import java.nio.file.Paths; import java.util.Objects; import static com.milaboratory.mixcr.basictypes.IOUtil.MAGIC_CLNA; @@ -36,7 +37,7 @@ public ActionConfiguration getConfiguration() { public void run1() throws Exception { switch (Objects.requireNonNull(IOUtil.fileInfoExtractorInstance.getFileInfo(new File(in))).fileType) { case MAGIC_CLNS: - try (ClnsReader reader = new ClnsReader(Path.of(in), VDJCLibraryRegistry.getDefault()); + try (ClnsReader reader = new ClnsReader(Paths.get(in), VDJCLibraryRegistry.getDefault()); ClnsWriter writer = new ClnsWriter(out)) { GeneFeature[] assemblingFeatures = reader.getAssemblerParameters().getAssemblingFeatures(); @@ -57,7 +58,7 @@ public void run1() throws Exception { return; case MAGIC_CLNA: - try (ClnAReader reader = new ClnAReader(Path.of(in), VDJCLibraryRegistry.getDefault(), Runtime.getRuntime().availableProcessors()); + try (ClnAReader reader = new ClnAReader(Paths.get(in), VDJCLibraryRegistry.getDefault(), Runtime.getRuntime().availableProcessors()); ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { SmartProgressReporter.startProgressReport(writer); From a26559c2880b6ce9762a301981d37c3906ec042e Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 23 May 2022 21:58:08 +0300 Subject: [PATCH 215/282] fix: initialisation of headers in assemble partial test --- src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java | 3 ++- .../mixcr/partialassembler/PartialAlignmentsAssemblerTest.java | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 82c97cb81..16af43ede 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -575,7 +575,8 @@ public void run1() throws Exception { // Creating aligner VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters, - tagSearchPlan.readShortcuts.size() == 2, !noMerge); + tagSearchPlan != null ? tagSearchPlan.readShortcuts.size() == 2 : isInputPaired(), + !noMerge); int numberOfExcludedNFGenes = 0; int numberOfExcludedFGenes = 0; diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java index 4411fd2b6..61647d621 100644 --- a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java @@ -256,6 +256,7 @@ public static TestResult processData(PairedRead[] data, InputTestData input) thr inputAlignments.usedGenes, true, false, writer::write); try (final VDJCAlignmentsReader reader = inputAlignments.resultReader()) { + writer.header(reader.getParameters(), reader.getUsedGenes(), null, reader.getTagsInfo()); assembler.buildLeftPartsIndex(reader); } try (final VDJCAlignmentsReader reader = inputAlignments.resultReader()) { From 8fd38617294ba1e1d6ee9c1c43dcd8ac04b4ca46 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 23 May 2022 23:06:27 +0300 Subject: [PATCH 216/282] fix: test fix --- .../java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java b/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java index e2d1ed700..8654b8415 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java @@ -79,7 +79,7 @@ public void importWL(String inputFile, String resourceName) throws IOException { Assert.assertEquals(expectedWhitelist, whitelist); } - // @Ignore + @Ignore @Test public void test1() throws IOException { importWL("/Volumes/Data/Projects/MiLaboratory/data/10x/3M-february-2018.txt", "10x-3M-february-2018.bin"); From e4bdce009d7298b9fe1cf1b28931826823cd688e Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 24 May 2022 02:09:44 +0300 Subject: [PATCH 217/282] fix: correct number of readsProcessed in the output of assemble partial --- .../com/milaboratory/mixcr/assembler/AlignmentsProvider.java | 2 +- src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java | 1 - .../mixcr/cli/CommandAssemblePartialAlignments.java | 3 +-- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java index ce445e3b7..ea15a4abd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java @@ -58,7 +58,7 @@ public static AlignmentsProvider createProvider(File file, final VDJCLibraryRegi }); } - public static AlignmentsProvider createProvider(String file, final VDJCLibraryRegistry geneResolver) { + public static AlignmentsProvider createProvider(String file, VDJCLibraryRegistry geneResolver) { return new VDJCAlignmentsReaderWrapper(() -> { try { return new VDJCAlignmentsReader(file, geneResolver); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 2c868fb51..12cf3e548 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -438,7 +438,6 @@ public boolean equals(Object o) { @Override public int hashCode() { - return Objects.hash(assemblerParameters, clna); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 4f29d4059..d00c39e59 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -179,8 +179,7 @@ public void run1() throws Exception { if (jsonReport != null) ReportUtil.appendJsonReport(jsonReport, report); - // TODO ???? - // output.setNumberOfProcessedReads(input.getNumberOfReads() - overlapped.get()); + writer.setNumberOfProcessedReads(reader1.getNumberOfReads() - assembler.overlapped.get()); } } From e9f9015cdd7bcd0f18f0414ee9fa2334dd2fadd3 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 24 May 2022 02:26:12 +0200 Subject: [PATCH 218/282] Pa fixes (#46) - Added JSON postanalysis parameters - Added ability to choose overlap type - Improved automatic downsampling value chooser - Add ability to preserve outliers in downsampling --- .../mixcr/basictypes/ClnAReader.java | 14 +- .../mixcr/basictypes/ClnsReader.java | 12 +- .../mixcr/basictypes/CloneReader.java | 8 + .../mixcr/basictypes/CloneSetOverlap.java | 137 ++++++++---- .../mixcr/cli/CommandAssembleContigs.java | 4 +- .../cli/CommandExportAlignmentsForClones.java | 2 +- .../mixcr/cli/postanalysis/CommandPa.java | 67 +----- .../CommandPaExportPlotsBasicStatistics.java | 5 +- .../CommandPaExportPlotsGeneUsage.java | 7 +- .../CommandPaExportPlotsOverlap.java | 5 +- .../CommandPaExportPlotsVJUsage.java | 3 +- .../cli/postanalysis/CommandPaIndividual.java | 127 +++-------- .../postanalysis/CommandPaListMetrics.java | 5 +- .../cli/postanalysis/CommandPaOverlap.java | 150 +++++++------ .../postanalysis/SetPreprocessorStat.java | 7 +- .../diversity/DiversityAggregator.java | 12 +- .../diversity/DiversityMeasure.java | 13 +- ...ClonesDownsamplingPreprocessorFactory.java | 7 +- .../downsampling/DownsampleValueChooser.java | 4 +- .../DownsamplingPreprocessor.java | 16 +- .../DownsamplingPreprocessorFactory.java | 13 +- .../overlap/OverlapCharacteristic.java | 2 +- .../preproc/PreprocessorChain.java | 3 +- .../ui/PostanalysisParameters.java | 122 +++++++++++ .../ui/PostanalysisParametersIndividual.java | 199 ++++++++++++++++++ .../ui/PostanalysisParametersOverlap.java | 65 ++++++ .../ui/PostanalysisParametersPreset.java | 56 +++++ .../com/milaboratory/mixcr/util/RunMiXCR.java | 2 +- .../parameters/postanalysis_individual.json | 111 ++++++++++ .../parameters/postanalysis_overlap.json | 42 ++++ .../cli/postanalysis/CommandPaExportTest.java | 34 +++ .../postanalysis/PostanalysisRunnerTest.java | 1 + .../DiversityCharacteristicTest.java | 2 +- .../DownsampleValueChooserTest.java | 8 +- .../DownsamplingPreprocessorTest.java | 1 + .../OverlapDownsamplingPreprocessorTest.java | 1 + .../PostanalysisParametersIndividualTest.java | 23 ++ .../ui/PostanalysisParametersOverlapTest.java | 13 ++ .../ui/PostanalysisSchemaIntegrationTest.java | 9 +- 39 files changed, 988 insertions(+), 324 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java create mode 100644 src/main/resources/parameters/postanalysis_individual.json create mode 100644 src/main/resources/parameters/postanalysis_overlap.json create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index d287a0222..a770215d6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -85,7 +85,7 @@ public final class ClnAReader extends PipelineConfigurationReaderMiXCR implement final CloneAssemblerParameters assemblerParameters; final VDJCSProperties.CloneOrdering ordering; - final List genes; + final List usedGenes; final int numberOfClones; @@ -165,7 +165,7 @@ public ClnAReader(Path path, VDJCLibraryRegistry libraryRegistry, LambdaSemaphor this.alignerParameters = pi.readObject(VDJCAlignerParameters.class); this.assemblerParameters = pi.readObject(CloneAssemblerParameters.class); this.ordering = pi.readObject(VDJCSProperties.CloneOrdering.class); - this.genes = IOUtil.stdVDJCPrimitivIStateInit(pi, this.alignerParameters, libraryRegistry); + this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(pi, this.alignerParameters, libraryRegistry); } } @@ -181,6 +181,7 @@ public PipelineConfiguration getPipelineConfiguration() { /** * Aligner parameters */ + @Override public VDJCAlignerParameters getAlignerParameters() { return alignerParameters; } @@ -212,8 +213,9 @@ public int numberOfClones() { return numberOfClones; } - public List getGenes() { - return genes; + @Override + public List getUsedGenes() { + return usedGenes; } /** @@ -253,7 +255,7 @@ public CloneSet readCloneSet() throws IOException { clones.add(reader.take()); } - return new CloneSet(clones, genes, alignerParameters, assemblerParameters, ordering); + return new CloneSet(clones, usedGenes, alignerParameters, assemblerParameters, ordering); } /** @@ -311,7 +313,7 @@ public final class CloneAlignmentsPort CloneAlignmentsPort() { this.clones = input.beginRandomAccessPrimitivIBlocks(Clone.class, firstClonePosition); - this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, genes, alignerParameters, assemblerParameters, ordering); + this.fakeCloneSet = new CloneSet(Collections.EMPTY_LIST, usedGenes, alignerParameters, assemblerParameters, ordering); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index 74b691b7b..6e23d4fca 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -61,7 +61,7 @@ public class ClnsReader extends PipelineConfigurationReaderMiXCR implements Clon private final CloneAssemblerParameters assemblerParameters; private final VDJCSProperties.CloneOrdering ordering; private final String versionInfo; - private final List genes; + private final List usedGenes; private final int numberOfClones; private final long clonesPosition; @@ -116,7 +116,7 @@ private ClnsReader(PrimitivIHybrid input, VDJCLibraryRegistry libraryRegistry) { ordering = i.readObject(VDJCSProperties.CloneOrdering.class); numberOfClones = i.readInt(); - genes = IOUtil.stdVDJCPrimitivIStateInit(i, alignerParameters, libraryRegistry); + usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, alignerParameters, libraryRegistry); } this.clonesPosition = input.getPosition(); @@ -131,7 +131,7 @@ public CloneSet getCloneSet() { List clones = new ArrayList<>(); for (Clone clone : CUtils.it(readClones())) clones.add(clone); - CloneSet cloneSet = new CloneSet(clones, genes, alignerParameters, assemblerParameters, ordering); + CloneSet cloneSet = new CloneSet(clones, usedGenes, alignerParameters, assemblerParameters, ordering); cloneSet.versionInfo = versionInfo; return cloneSet; } @@ -141,6 +141,7 @@ public PipelineConfiguration getPipelineConfiguration() { return pipelineConfiguration; } + @Override public VDJCAlignerParameters getAlignerParameters() { return alignerParameters; } @@ -159,6 +160,11 @@ public int numberOfClones() { return numberOfClones; } + @Override + public List getUsedGenes() { + return usedGenes; + } + @Override public void close() throws IOException { input.close(); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java index 22af042ec..26a1b7d6c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -30,6 +30,10 @@ package com.milaboratory.mixcr.basictypes; import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import io.repseq.core.VDJCGene; + +import java.util.List; public interface CloneReader extends AutoCloseable { /** @@ -42,4 +46,8 @@ public interface CloneReader extends AutoCloseable { OutputPortCloseable readClones(); int numberOfClones(); + + List getUsedGenes(); + + VDJCAlignerParameters getAlignerParameters(); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java index 7bc75bff5..154506600 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java @@ -31,7 +31,10 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.util.OutputPortWithProgress; +import com.milaboratory.primitivio.PrimitivIOStateBuilder; +import com.milaboratory.util.TempFileManager; import com.milaboratory.util.sorting.MergeStrategy; +import com.milaboratory.util.sorting.UnorderedMerger; import java.util.List; import java.util.concurrent.atomic.AtomicBoolean; @@ -45,55 +48,115 @@ private CloneSetOverlap() { public static OutputPortWithProgress>> overlap( List> by, List readers) { - VDJCSProperties.CloneOrdering ordering = readers.get(0).ordering(); - for (int i = 1; i < readers.size(); i++) - if (!ordering.equals(readers.get(i).ordering())) - throw new RuntimeException("All clonesets must be sorted the same way."); - MergeStrategy strategy = MergeStrategy.calculateStrategy(ordering.getProperties(), by); - if (!strategy.usesStreamOrdering()) - throw new RuntimeException("Clone sorting is incompatible with overlap criteria."); List> individualPorts = readers .stream() .map(r -> OutputPortWithProgress.wrap(r.numberOfClones(), r.readClones())) .collect(Collectors.toList()); - OutputPortCloseable>> joinedPort = strategy.join(individualPorts); - AtomicLong index = new AtomicLong(0); - AtomicBoolean isFinished = new AtomicBoolean(false); - long totalClones = readers.stream().mapToLong(CloneReader::numberOfClones).sum(); - return new OutputPortWithProgress>>() { - @Override - public long index() { - return index.get(); + VDJCSProperties.CloneOrdering ordering = readers.get(0).ordering(); + boolean needSort = false; + for (int i = 1; i < readers.size(); i++) + if (!ordering.equals(readers.get(i).ordering())) { + needSort = true; + break; } - @Override - public void close() { - joinedPort.close(); - } + if (!needSort && !MergeStrategy.calculateStrategy(ordering.getProperties(), by).usesStreamOrdering()) + needSort = true; - @Override - public List> take() { - List> t = joinedPort.take(); - if (t == null) { - isFinished.set(true); - return null; + if (needSort) { + // HDD-offloading collator of alignments + // Collate solely by cloneId (no sorting by mapping type, etc.); + // less fields to sort by -> faster the procedure + long memoryBudget = + Runtime.getRuntime().maxMemory() > 10_000_000_000L /* -Xmx10g */ + ? Runtime.getRuntime().maxMemory() / 4L /* 1 Gb */ + : 1 << 28 /* 256 Mb */; + PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); + IOUtil.registerGeneReferences(stateBuilder, readers.get(0).getUsedGenes(), readers.get(0).getAlignerParameters()); + UnorderedMerger merger = new UnorderedMerger<>( + Clone.class, + readers.stream() + .map(CloneReader::readClones) + .collect(Collectors.toList()), + by, + 5, + TempFileManager.getTempDir().toPath(), + 4, 6, + memoryBudget, 1 << 18 /* 256 Kb */, stateBuilder); + merger.loadData(); + AtomicLong index = new AtomicLong(0); + return new OutputPortWithProgress>>() { + @Override + public long index() { + return index.get(); } - index.incrementAndGet(); - return t; - } - @Override - public double getProgress() { - return 1.0 * individualPorts.stream().mapToLong(OutputPortWithProgress::index).sum() / totalClones; - } + @Override + public void close() { + merger.close(); + } - @Override - public boolean isFinished() { - return isFinished.get(); - } - }; + @Override + public List> take() { + List> t = merger.take(); + if (t == null) { + return null; + } + index.incrementAndGet(); + return t; + } + + @Override + public double getProgress() { + return merger.getProgress(); + } + + @Override + public boolean isFinished() { + return merger.isFinished(); + } + }; + } else { + MergeStrategy strategy = MergeStrategy.calculateStrategy(ordering.getProperties(), by); + OutputPortCloseable>> joinedPort = strategy.join(individualPorts); + AtomicLong index = new AtomicLong(0); + AtomicBoolean isFinished = new AtomicBoolean(false); + long totalClones = readers.stream().mapToLong(CloneReader::numberOfClones).sum(); + return new OutputPortWithProgress>>() { + @Override + public long index() { + return index.get(); + } + + @Override + public void close() { + joinedPort.close(); + } + + @Override + public List> take() { + List> t = joinedPort.take(); + if (t == null) { + isFinished.set(true); + return null; + } + index.incrementAndGet(); + return t; + } + + @Override + public double getProgress() { + return 1.0 * individualPorts.stream().mapToLong(OutputPortWithProgress::index).sum() / totalClones; + } + + @Override + public boolean isFinished() { + return isFinished.get(); + } + }; + } } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index a30a504c8..02e918ae5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -132,11 +132,11 @@ public void run1() throws Exception { ordering = reader.ordering(); final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), - reader.getAssemblingFeatures(), reader.getGenes(), reader.getAlignerParameters().getFeaturesToAlignMap()); + reader.getAssemblingFeatures(), reader.getUsedGenes(), reader.getAlignerParameters().getFeaturesToAlignMap()); alignerParameters = reader.getAlignerParameters(); cloneAssemblerParameters = reader.getAssemblerParameters(); - genes = reader.getGenes(); + genes = reader.getUsedGenes(); IOUtil.registerGeneReferences(tmpOut, genes, alignerParameters); ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java index 34e84dab6..c3806428a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java @@ -60,7 +60,7 @@ public int[] getCloneIds() { public void run1() throws Exception { try (ClnAReader clna = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(getOutput())) { - writer.header(clna.getAlignerParameters(), clna.getGenes(), getFullPipelineConfiguration()); + writer.header(clna.getAlignerParameters(), clna.getUsedGenes(), getFullPipelineConfiguration()); long count = 0; if (getCloneIds().length == 0) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 62577d77f..93df69da9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -1,17 +1,8 @@ package com.milaboratory.mixcr.cli.postanalysis; -import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.WeightFunctions; -import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; -import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; -import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; -import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; import com.milaboratory.util.StringUtil; import io.repseq.core.Chains; -import io.repseq.core.GeneFeature; import picocli.CommandLine; import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; @@ -39,10 +30,14 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { names = {"--only-productive"}) public boolean onlyProductive = false; + @Option(description = "Drop outliers.", + names = {"--drop-outliers"}) + public boolean dropOutliers = false; + @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", - names = {"--downsampling"}, + names = {"--default-downsampling"}, required = true) - public String downsampling; + public String defaultDownsampling; @Option(description = "Filter specific chains", names = {"-c", "--chains"}) @@ -51,10 +46,6 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { @Option(description = "Metadata file (csv/tsv). Must have \"sample\" column.", names = {"-m", "--meta", "--metadata"}) public String metadata; -// -// @Option(description = "Metadata column for chains.", -// names = {"--chains-column"}) -// public String chainsColumn; @Option(description = "Metadata categories used to isolate samples into separate groups", names = {"-g", "--group"}) @@ -68,6 +59,9 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { names = {"--preproc-tables"}) public String preprocOut; + @Option(names = {"-O"}, description = "Overrides default postanalysis settings") + public Map overrides = new HashMap<>(); + @Override protected List getInputFiles() { return inOut.subList(0, inOut.size() - 1) @@ -131,49 +125,6 @@ static String getSampleId(String file) { return Paths.get(file).getFileName().toString(); } - private static int downsamplingValue(String downsampling) { - return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); - } - - private static SetPreprocessorFactory parseDownsampling(String downsampling) { - if (downsampling.equalsIgnoreCase("no-downsampling")) { - return new NoPreprocessing.Factory<>(); - } else if (downsampling.startsWith("umi-count")) { - if (downsampling.endsWith("auto")) - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314); - else { - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), 314); - } - } else { - int value = downsamplingValue(downsampling); - if (downsampling.startsWith("cumulative-top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); - } else if (downsampling.startsWith("top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, value); - } else { - throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); - } - } - } - - protected SetPreprocessorFactory downsampling() { - return downsampling(this.downsampling); - } - - protected SetPreprocessorFactory downsampling(String downsamplingStr) { - SetPreprocessorFactory downsampling = - parseDownsampling(downsamplingStr); - - if (onlyProductive) { - List> filters = new ArrayList<>(); - filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); - filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); - downsampling = downsampling.filterFirst(filters); - } - - return downsampling; - } - private Map> _metadata = null; protected Map> metadata() { diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index 107fc7238..7ac34e849 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -10,6 +10,7 @@ import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics; import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics.PlotType; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; import picocli.CommandLine.Option; @@ -100,7 +101,7 @@ else if (refGroup != null) public static class ExportBiophysics extends CommandPaExportPlotsBasicStatistics { @Override String group() { - return CommandPaIndividual.Biophysics; + return PostanalysisParametersIndividual.Biophysics; } } @@ -111,7 +112,7 @@ String group() { public static class ExportDiversity extends CommandPaExportPlotsBasicStatistics { @Override String group() { - return CommandPaIndividual.Diversity; + return PostanalysisParametersIndividual.Diversity; } } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java index ae134eda8..d679b4388 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java @@ -8,6 +8,7 @@ import com.milaboratory.mixcr.postanalysis.plots.GeneUsageRow; import com.milaboratory.mixcr.postanalysis.plots.HeatmapParameters; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; import picocli.CommandLine.Option; @@ -66,7 +67,7 @@ void run(PaResultByGroup result) { public static class ExportVUsage extends CommandPaExportPlotsGeneUsage { @Override String group() { - return CommandPaIndividual.VUsage; + return PostanalysisParametersIndividual.VUsage; } } @@ -77,7 +78,7 @@ String group() { public static class ExportJUsage extends CommandPaExportPlotsGeneUsage { @Override String group() { - return CommandPaIndividual.JUsage; + return PostanalysisParametersIndividual.JUsage; } } @@ -88,7 +89,7 @@ String group() { public static class ExportIsotypeUsage extends CommandPaExportPlotsGeneUsage { @Override String group() { - return CommandPaIndividual.IsotypeUsage; + return PostanalysisParametersIndividual.IsotypeUsage; } } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java index 87a5f8a74..072182390 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -3,16 +3,15 @@ import com.milaboratory.miplots.Position; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; import com.milaboratory.mixcr.postanalysis.plots.*; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersOverlap; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; import picocli.CommandLine.Option; import java.util.ArrayList; import java.util.List; -import java.util.Map; import java.util.stream.Collectors; @CommandLine.Command(name = "overlap", @@ -42,7 +41,7 @@ DataFrame filterOverlap(DataFrame df) { @Override void run(PaResultByGroup result) { - CharacteristicGroup ch = result.schema.getGroup(CommandPaOverlap.Overlap); + CharacteristicGroup ch = result.schema.getGroup(PostanalysisParametersOverlap.Overlap); PostanalysisResult paResult = result.result.forGroup(ch); DataFrame metadata = metadata(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java index d172817c1..9b1c87cd8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java @@ -5,6 +5,7 @@ import com.milaboratory.mixcr.postanalysis.plots.VJUsage; import com.milaboratory.mixcr.postanalysis.plots.VJUsageRow; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; import picocli.CommandLine; @@ -25,7 +26,7 @@ public class CommandPaExportPlotsVJUsage extends CommandPaExportPlotsHeatmap { @Override void run(PaResultByGroup result) { - CharacteristicGroup ch = result.schema.getGroup(CommandPaIndividual.VJUsage); + CharacteristicGroup ch = result.schema.getGroup(PostanalysisParametersIndividual.VJUsage); DataFrame metadata = metadata(); DataFrame df = VJUsage.INSTANCE.dataFrame( diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index edce0b9ee..08c50a569 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -3,126 +3,51 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.WeightFunctions; -import com.milaboratory.mixcr.postanalysis.additive.AAProperties; -import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; -import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; -import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; -import com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure; import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; -import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; -import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; -import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; import com.milaboratory.mixcr.postanalysis.ui.*; +import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.SmartProgressReporter; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine.Command; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; import java.util.List; +import java.util.Map; import java.util.stream.Collectors; -import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; - -@SuppressWarnings("ArraysAsListWithZeroOrOneArgument") @Command(name = "individual", sortOptions = false, separator = " ", description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") public class CommandPaIndividual extends CommandPa { - static final String - Biophysics = "biophysics", - Diversity = "diversity", - VUsage = "vUsage", - JUsage = "JUsage", - VJUsage = "VJUsage", - IsotypeUsage = "IsotypeUsage", - CDR3Spectratype = "CDR3Spectratype", - VSpectratype = "VSpectratype", - VSpectratypeMean = "VSpectratypeMean"; - public CommandPaIndividual() {} + private PostanalysisParametersIndividual _parameters; + + private PostanalysisParametersIndividual getParameters() { + if (_parameters != null) + return _parameters; + _parameters = PostanalysisParametersPreset.getByNameIndividual("default"); + _parameters.defaultDownsampling = defaultDownsampling; + _parameters.defaultDropOutliers = dropOutliers; + _parameters.defaultOnlyProductive = onlyProductive; + if (!overrides.isEmpty()) { + for (Map.Entry o : overrides.entrySet()) + _parameters = JsonOverrider.override(_parameters, PostanalysisParametersIndividual.class, overrides); + if (_parameters == null) + throwValidationException("Failed to override some parameter: " + overrides); + } + return _parameters; + } + @Override @SuppressWarnings({"unchecked", "rawtypes"}) PaResultByGroup run(IsolationGroup group, List samples) { - List> groups = new ArrayList<>(); - - SetPreprocessorFactory downsampling = downsampling() - .filterFirst(new ElementPredicate.IncludeChains(group.chains.chains)); - - groups.add(new CharacteristicGroup<>(Biophysics, - Arrays.asList( - weightedLengthOf(downsampling, GeneFeature.CDR3, false).setName("CDR3 length, nt"), - weightedLengthOf(downsampling, GeneFeature.CDR3, true).setName("CDR3 length, aa"), - weightedLengthOf(downsampling, GeneFeature.VJJunction, false).setName("NDN length, nt"), - weightedAddedNucleotides(downsampling).setName("Added N, nt"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Strength"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Hydrophobicity"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Surface"), - weightedBiophysics(downsampling, AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), - weightedBiophysics(downsampling, AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") - ), - Arrays.asList(new GroupSummary<>()) - )); - - groups.add(new CharacteristicGroup<>(Diversity, - Arrays.asList(new DiversityCharacteristic<>("Diversity", new WeightFunctions.Count(), - downsampling, - new DiversityMeasure[]{ - DiversityMeasure.Observed, - DiversityMeasure.Clonality, - DiversityMeasure.ShannonWeiner, - DiversityMeasure.InverseSimpson, - DiversityMeasure.Chao1, - DiversityMeasure.Gini - }), - new DiversityCharacteristic<>("d50", new WeightFunctions.Count(), - downsampling.then(new SelectTop.Factory<>(WeightFunctions.Default(), 0.5)), - new DiversityMeasure[]{ - DiversityMeasure.Observed.overrideName("d50") - })), - Arrays.asList(new GroupSummary<>()) - )); - - groups.add(new CharacteristicGroup<>(VUsage, - Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Variable)), - Arrays.asList(new GroupSummary<>()) - )); - groups.add(new CharacteristicGroup<>(JUsage, - Arrays.asList(AdditiveCharacteristics.segmentUsage(downsampling, GeneType.Joining)), - Arrays.asList(new GroupSummary<>()) - )); - groups.add(new CharacteristicGroup<>(VJUsage, - Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(downsampling)), - Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) - )); - - groups.add(new CharacteristicGroup<>(IsotypeUsage, - Arrays.asList(AdditiveCharacteristics.isotypeUsage(downsampling)), - Arrays.asList(new GroupSummary<>()) - )); - - groups.add(new CharacteristicGroup<>(CDR3Spectratype, - Arrays.asList(new SpectratypeCharacteristic("CDR3 spectratype", - downsampling, 10, - new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), - Collections.singletonList(new GroupSummary<>()))); - - groups.add(new CharacteristicGroup<>(VSpectratype, - Arrays.asList(AdditiveCharacteristics.VSpectratype(downsampling)), - Collections.singletonList(new GroupSummary<>()))); - - groups.add(new CharacteristicGroup<>(VSpectratypeMean, - Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(downsampling)), - Collections.singletonList(new GroupSummary<>()))); - - PostanalysisSchema schema = new PostanalysisSchema<>(groups); + List> groups = getParameters().getGroups(); + PostanalysisSchema schema = new PostanalysisSchema<>(groups) + .transform(ch -> ch.override(ch.name, + ch.preprocessor + .filterFirst(new ElementPredicate.IncludeChains(group.chains.chains))) + ); PostanalysisRunner runner = new PostanalysisRunner<>(); runner.addCharacteristics(schema.getAllCharacterisitcs()); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java index 2001c3620..460deed0b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java @@ -3,6 +3,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.ACommandMiXCR; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import com.milaboratory.util.GlobalObjectMappers; import picocli.CommandLine.Command; import picocli.CommandLine.Parameters; @@ -31,8 +32,8 @@ public void run0() { PaResultByGroup result = paResult.results.get(0); CharacteristicGroup - biophys = result.schema.getGroup(CommandPaIndividual.Biophysics), - diversity = result.schema.getGroup(CommandPaIndividual.Diversity); + biophys = result.schema.getGroup(PostanalysisParametersIndividual.Biophysics), + diversity = result.schema.getGroup(PostanalysisParametersIndividual.Diversity); for (int i = 0; i < 2; i++) { System.out.println(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index 84c3a5e74..0d97a759d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -2,17 +2,26 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.postanalysis.*; -import com.milaboratory.mixcr.postanalysis.overlap.*; +import com.milaboratory.mixcr.postanalysis.PostanalysisResult; +import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapDataset; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapUtil; import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.FilterPreprocessor; import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; -import com.milaboratory.mixcr.postanalysis.ui.OverlapSummary; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersOverlap; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersPreset; import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.util.JsonOverrider; import com.milaboratory.util.LambdaSemaphore; import com.milaboratory.util.SmartProgressReporter; -import io.repseq.core.Chains; import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -20,44 +29,77 @@ import java.io.IOException; import java.nio.file.Path; import java.nio.file.Paths; -import java.util.*; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; import java.util.stream.Collectors; -import static java.util.stream.Collectors.*; +import static java.util.stream.Collectors.toList; @Command(name = "overlap", sortOptions = false, separator = " ", description = "Overlap analysis") public class CommandPaOverlap extends CommandPa { - public static String Overlap = "overlap"; - - @Option(description = "Override downsampling for F2 umi|d[number]|f[number]", - names = {"--f2-downsampling"}) - public String f2downsampling; + @Option(description = "Overlap criteria. Default CDR|AA|V|J", + names = {"--criteria"}) + public String overlapCriteria = "CDR3|AA|V|J"; public CommandPaOverlap() {} + private PostanalysisParametersOverlap _parameters; + + private PostanalysisParametersOverlap getParameters() { + if (_parameters != null) + return _parameters; + _parameters = PostanalysisParametersPreset.getByNameOverlap("default"); + _parameters.defaultDownsampling = defaultDownsampling; + _parameters.defaultDropOutliers = dropOutliers; + _parameters.defaultOnlyProductive = onlyProductive; + if (!overrides.isEmpty()) { + for (Map.Entry o : overrides.entrySet()) + _parameters = JsonOverrider.override(_parameters, PostanalysisParametersOverlap.class, overrides); + if (_parameters == null) + throwValidationException("Failed to override some parameter: " + overrides); + } + return _parameters; + } + + private List> parseCriteria() { + String[] parts = overlapCriteria.toLowerCase().split("\\|"); + if (parts.length < 2) + throwValidationException("Illegal criteria input: " + overlapCriteria); + GeneFeature feature = GeneFeature.parse(parts[0]); + if (!parts[1].equals("aa") && !parts[1].equals("nt")) + throwValidationException("Illegal criteria input: " + overlapCriteria); + boolean isAA = parts[1].equals("aa"); + List geneTypes = new ArrayList<>(); + if (parts.length > 2) + if (!parts[2].equals("v")) + throwValidationException("Illegal criteria input: " + overlapCriteria); + else + geneTypes.add(GeneType.Variable); + if (parts.length > 3) + if (!parts[3].equals("j")) + throwValidationException("Illegal criteria input: " + overlapCriteria); + else + geneTypes.add(GeneType.Joining); + + if (isAA) + return VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{feature}, geneTypes.toArray(new GeneType[0])); + else + return VDJCSProperties.orderingByNucleotide(new GeneFeature[]{feature}, geneTypes.toArray(new GeneType[0])); + } + @Override @SuppressWarnings("unchecked") PaResultByGroup run(IsolationGroup group, List samples) { - SetPreprocessorFactory downsampling = downsampling(); - - Map> downsamplingByType = new HashMap<>(); - downsamplingByType.put(OverlapType.D, downsampling); - downsamplingByType.put(OverlapType.F2, f2downsampling == null - ? downsampling - : downsampling(f2downsampling)); - downsamplingByType.put(OverlapType.R_Intersection, downsampling); - - List> ordering = VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{GeneFeature.CDR3}); - OverlapPostanalysisSettings overlapPA = new OverlapPostanalysisSettings( - ordering, - new WeightFunctions.Count(), - downsamplingByType - ); - - PostanalysisSchema> schema = overlapPA.getSchema(samples.size(), group.chains.chains); + List>> groups = getParameters().getGroups(samples.size()); + PostanalysisSchema> schema = new PostanalysisSchema<>(groups) + .transform(ch -> ch.override(ch.name, + ch.preprocessor + .before(new OverlapPreprocessorAdapter.Factory<>(new FilterPreprocessor.Factory<>(WeightFunctions.Count, new ElementPredicate.IncludeChains(group.chains.chains))))) + ); // Limits concurrency across all readers LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(32); @@ -76,7 +118,7 @@ PaResultByGroup run(IsolationGroup group, List samples) { OverlapDataset overlapDataset = OverlapUtil.overlap( samples.stream().map(CommandPa::getSampleId).collect(toList()), - ordering, + parseCriteria(), readers); PostanalysisRunner> runner = new PostanalysisRunner<>(); @@ -131,48 +173,16 @@ public void close() throws Exception { public int numberOfClones() { return inner.numberOfClones(); } - }; - } - @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") - static final class OverlapPostanalysisSettings { - final List> ordering; - final WeightFunction weight; - final Map> preprocessors; - final Map, List> groupped; - - OverlapPostanalysisSettings(List> ordering, - WeightFunction weight, - Map> preprocessors) { - this.ordering = ordering; - this.weight = weight; - this.preprocessors = preprocessors; - this.groupped = preprocessors.entrySet().stream().collect(groupingBy(Map.Entry::getValue, mapping(Map.Entry::getKey, toList()))); - } - - private SetPreprocessorFactory> getPreprocessor(OverlapType type, Chains chain) { - return new OverlapPreprocessorAdapter.Factory<>(preprocessors.get(type).filterFirst(new ElementPredicate.IncludeChains(chain))); - } - - //fixme only productive?? - public List> getCharacteristics(int i, int j, Chains chain) { - return groupped.entrySet().stream().map(e -> new OverlapCharacteristic<>("overlap_" + i + "_" + j + " / " + e.getValue().stream().map(t -> t.name).collect(Collectors.joining(" / ")), weight, - new OverlapPreprocessorAdapter.Factory<>(e.getKey().filterFirst(new ElementPredicate.IncludeChains(chain))), - e.getValue().toArray(new OverlapType[0]), - i, j)).collect(toList()); - } + @Override + public List getUsedGenes() { + return inner.getUsedGenes(); + } - public PostanalysisSchema> getSchema(int nSamples, Chains chain) { - List> overlaps = new ArrayList<>(); - for (int i = 0; i < nSamples; ++i) - for (int j = i; j < nSamples; ++j) // j=i to include diagonal elements - overlaps.addAll(getCharacteristics(i, j, chain)); - - return new PostanalysisSchema<>(Collections.singletonList( - new CharacteristicGroup<>(Overlap, - overlaps, - Arrays.asList(new OverlapSummary<>()) - ))); - } + @Override + public VDJCAlignerParameters getAlignerParameters() { + return inner.getAlignerParameters(); + } + }; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java index db56196cd..93d58b09e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java @@ -163,7 +163,7 @@ public void drop(int iDataset) { } public void clear(int iDataset) { - map.remove(iDataset); + map.put(iDataset, new BuilderForSample<>(preprocId, wtFunc)); } public void before(int iDataset, T t) { @@ -174,6 +174,11 @@ public void after(int iDataset, T t) { builder(iDataset).after(t); } + public void asis(int iDataset, T t) { + before(iDataset, t); + after(iDataset, t); + } + public SetPreprocessorStat getStat(int iDataset) { BuilderForSample b = map.get(iDataset); if (b == null) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java index 0f639f7d3..b343a8e3b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -68,11 +68,11 @@ private List> computeChao1() { /** Clonality, Gini and Shannon-Weiner */ private List> computeClonality() { if (!(measures.containsKey(ShannonWeiner) - || measures.containsKey(Clonality) + || measures.containsKey(NormalizedShannonWeinerIndex) || measures.containsKey(InverseSimpson) || measures.containsKey(Gini))) return Collections.emptyList(); - double shannonWeiner = 0; + double shannonWeinerIndex = 0; double gini = 0; TLongIntIterator it = freqTable.iterator(); @@ -84,14 +84,14 @@ private List> computeClonality() { double cloneFreq = cloneCount / countSum; gini += -nClones * cloneFreq * cloneFreq; - shannonWeiner += -nClones * cloneFreq * Math.log(cloneFreq); + shannonWeinerIndex += -nClones * cloneFreq * Math.log(cloneFreq); } List> result = new ArrayList<>(); if (measures.containsKey(ShannonWeiner)) - result.add(new MetricValue<>(measures.get(ShannonWeiner), shannonWeiner)); - if (measures.containsKey(Clonality)) - result.add(new MetricValue<>(measures.get(Clonality), 1 - shannonWeiner / Math.log(diversity))); + result.add(new MetricValue<>(measures.get(ShannonWeiner), Math.exp(shannonWeinerIndex))); + if (measures.containsKey(NormalizedShannonWeinerIndex)) + result.add(new MetricValue<>(measures.get(NormalizedShannonWeinerIndex), shannonWeinerIndex / Math.log(diversity))); if (measures.containsKey(InverseSimpson)) result.add(new MetricValue<>(measures.get(InverseSimpson), -1 / gini)); if (measures.containsKey(Gini)) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java index b39463d16..b9c3c5fd1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java @@ -49,8 +49,8 @@ public static DiversityMeasure[] basic() { Chao1, Chao1Std, ShannonWeiner, - Clonality, - Gini, + NormalizedShannonWeinerIndex, + GiniIndex, InverseSimpson, EfronThisted, EfronThistedStd, @@ -61,19 +61,20 @@ public static DiversityMeasure[] basic() { public static final DiversityMeasure Chao1 = Measure.Chao1.toDiversityMeasure(); public static final DiversityMeasure Chao1Std = Measure.Chao1Std.toDiversityMeasure(); public static final DiversityMeasure ShannonWeiner = Measure.ShannonWeiner.toDiversityMeasure(); - public static final DiversityMeasure Clonality = Measure.Clonality.toDiversityMeasure(); - public static final DiversityMeasure Gini = Measure.Gini.toDiversityMeasure(); + public static final DiversityMeasure NormalizedShannonWeinerIndex = Measure.NormalizedShannonWeinerIndex.toDiversityMeasure(); + public static final DiversityMeasure GiniIndex = Measure.Gini.toDiversityMeasure(); public static final DiversityMeasure InverseSimpson = Measure.InverseSimpson.toDiversityMeasure(); public static final DiversityMeasure EfronThisted = Measure.EfronThisted.toDiversityMeasure(); public static final DiversityMeasure EfronThistedStd = Measure.EfronThistedStd.toDiversityMeasure(); - enum Measure { + public enum Measure { Observed, Chao1, Chao1Std, ShannonWeiner, - Clonality, + NormalizedShannonWeinerIndex, Gini, + GiniDiversity, InverseSimpson, EfronThisted, EfronThistedStd; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java index f0100f550..db0f74c95 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java @@ -18,9 +18,10 @@ public class ClonesDownsamplingPreprocessorFactory extends DownsamplingPreprocessorFactory { @JsonCreator public ClonesDownsamplingPreprocessorFactory(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, - @JsonProperty("seed") long seed) { - super(downsampleValueChooser, seed, c -> Math.round(c.getCount()), - Clone::setCount); + @JsonProperty("seed") long seed, + @JsonProperty("dropOutliers") boolean dropOutliers) { + super(downsampleValueChooser, seed, dropOutliers, + c -> Math.round(c.getCount()), Clone::setCount); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java index 73fd16dcc..401b4033c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java @@ -111,7 +111,9 @@ public long compute(long... totalCounts) { long q = (long) (new Percentile(quantile).evaluate(Arrays.stream(totalCounts).mapToDouble(l -> l).toArray()) * scale); long min = Arrays.stream(totalCounts).min().orElse(0); long d = Math.max(q, min); - return Math.max(d, threshold); + long max = Math.max(d, threshold); + long r = Arrays.stream(totalCounts).filter(l -> l > max).min().orElse(0); + return Math.max(r, max); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index cc0af95d4..61721a1fa 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -2,7 +2,6 @@ import cc.redberry.pipe.InputPort; -import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.postanalysis.MappingFunction; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import com.milaboratory.mixcr.postanalysis.SetPreprocessorSetup; @@ -25,9 +24,8 @@ public class DownsamplingPreprocessor implements SetPreprocessor { public final ToLongFunction getCount; public final BiFunction setCount; - @JsonProperty("downsampleValueChooser") public final DownsampleValueChooser downsampleValueChooser; - @JsonProperty("seed") + public final boolean dropOutliers; public final long seed; final String id; private final SetPreprocessorStat.Builder stats; @@ -35,11 +33,13 @@ public class DownsamplingPreprocessor implements SetPreprocessor { public DownsamplingPreprocessor(ToLongFunction getCount, BiFunction setCount, DownsampleValueChooser downsampleValueChooser, + boolean dropOutliers, long seed, String id) { this.getCount = getCount; this.setCount = setCount; this.downsampleValueChooser = downsampleValueChooser; + this.dropOutliers = dropOutliers; this.seed = seed; this.id = id; this.stats = new SetPreprocessorStat.Builder<>(id, getCount::applyAsLong); @@ -71,8 +71,14 @@ public MappingFunction getMapper(int iDataset) { downsampling = downsampleValueChooser.compute(setup.counts); if (downsampling > setup.counts[iDataset]) { - stats.drop(iDataset); - return t -> null; + if (dropOutliers) { + stats.drop(iDataset); + return t -> null; + } else + return t -> { + stats.asis(iDataset, t); + return t; + }; } long[] counts = setup.countLists[iDataset].toArray(); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java index c72d92678..07213ade3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java @@ -16,15 +16,19 @@ public class DownsamplingPreprocessorFactory implements SetPreprocessorFactor public final DownsampleValueChooser downsampleValueChooser; @JsonProperty("seed") public final long seed; + @JsonProperty("dropOutliers") + public final boolean dropOutliers; public final ToLongFunction getCount; public final BiFunction setCount; public DownsamplingPreprocessorFactory(DownsampleValueChooser downsampleValueChooser, long seed, + boolean dropOutliers, ToLongFunction getCount, BiFunction setCount) { this.downsampleValueChooser = downsampleValueChooser; this.seed = seed; + this.dropOutliers = dropOutliers; this.getCount = getCount; this.setCount = setCount; } @@ -36,9 +40,10 @@ public String id() { @Override public SetPreprocessor newInstance() { - return new DownsamplingPreprocessor<>( + return new DownsamplingPreprocessor( getCount, - setCount, downsampleValueChooser, seed, id()); + setCount, downsampleValueChooser, + dropOutliers, seed, id()); } @Override @@ -46,11 +51,11 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; DownsamplingPreprocessorFactory that = (DownsamplingPreprocessorFactory) o; - return seed == that.seed && Objects.equals(downsampleValueChooser, that.downsampleValueChooser) && Objects.equals(getCount, that.getCount) && Objects.equals(setCount, that.setCount); + return seed == that.seed && Objects.equals(downsampleValueChooser, that.downsampleValueChooser) && Objects.equals(dropOutliers, that.dropOutliers) && Objects.equals(getCount, that.getCount) && Objects.equals(setCount, that.setCount); } @Override public int hashCode() { - return Objects.hash(downsampleValueChooser, seed, getCount, setCount); + return Objects.hash(downsampleValueChooser, seed, dropOutliers, getCount, setCount); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java index f100ede42..c68a2c762 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java @@ -28,7 +28,7 @@ public OverlapCharacteristic(@JsonProperty("name") String name, @JsonProperty("overlapTypes") OverlapType[] overlapTypes, @JsonProperty("i1") int i1, @JsonProperty("i2") int i2) { - super(name, preprocessor, __ -> 1L); + super(name, preprocessor, new WeightFunctions.NoWeight<>()); this.overlapTypes = overlapTypes; this.i1 = i1; this.i2 = i2; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index b8b34a0e9..2165d535c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -113,8 +113,7 @@ public InputPort consumer(int i) { @Override public MappingFunction getMapper(int iDataset) { Function> mapper = mapperRef.get(); - if (mapper == null) - return MappingFunction.identity(); + assert (mapper != null); return mapper.apply(iDataset); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java new file mode 100644 index 000000000..b741cd221 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java @@ -0,0 +1,122 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; +import com.milaboratory.primitivio.annotations.Serializable; +import io.repseq.core.GeneFeature; + +import java.util.*; +import java.util.function.BiFunction; +import java.util.stream.Collectors; + +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) +@JsonIgnoreProperties(ignoreUnknown = false) +@Serializable(asJson = true) +public abstract class PostanalysisParameters { + public String defaultDownsampling; + public boolean defaultOnlyProductive; + public boolean defaultDropOutliers; + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) + public static class PreprocessorParameters { + public String downsampling; + public Boolean onlyProductive; + public Boolean dropOutliers; + + public SetPreprocessorFactory preproc(PostanalysisParameters base) { + SetPreprocessorFactory p = parseDownsampling(base); + + boolean onlyProductive = this.onlyProductive == null ? base.defaultOnlyProductive : this.onlyProductive; + if (onlyProductive) { + List> filters = new ArrayList<>(); + filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); + filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); + p = p.filterFirst(filters); + } + return p; + } + + public SetPreprocessorFactory> overlapPreproc(PostanalysisParameters base) { + return new OverlapPreprocessorAdapter.Factory<>(preproc(base)); + } + + SetPreprocessorFactory parseDownsampling(PostanalysisParameters base) { + String downsampling = this.downsampling == null ? base.defaultDownsampling : this.downsampling; + boolean dropOutliers = this.dropOutliers == null ? base.defaultDropOutliers : this.dropOutliers; + if (downsampling.equalsIgnoreCase("no-downsampling")) { + return new NoPreprocessing.Factory<>(); + } else if (downsampling.startsWith("umi-count")) { + if (downsampling.endsWith("auto")) + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314, dropOutliers); + else { + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), 314, dropOutliers); + } + } else { + int value = downsamplingValue(downsampling); + if (downsampling.startsWith("cumulative-top")) { + return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); + } else if (downsampling.startsWith("top")) { + return new SelectTop.Factory<>(WeightFunctions.Count, value); + } else { + throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); + } + } + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + PreprocessorParameters that = (PreprocessorParameters) o; + return Objects.equals(downsampling, that.downsampling) && Objects.equals(onlyProductive, that.onlyProductive) && Objects.equals(dropOutliers, that.dropOutliers); + } + + @Override + public int hashCode() { + return Objects.hash(downsampling, onlyProductive, dropOutliers); + } + } + + private static int downsamplingValue(String downsampling) { + return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); + } + + static List> groupByPreproc(PostanalysisParameters base, + Map> preprocs, + BiFunction, List, List>> factory) { + + Map, List> byPreproc = preprocs.entrySet().stream() + .collect(Collectors.toMap(Map.Entry::getValue, + e -> Collections.singletonList(e.getKey()), + (a, b) -> { + List l = new ArrayList<>(); + l.addAll(a); + l.addAll(b); + return l; + })); + + List> chars = new ArrayList<>(); + for (Map.Entry, List> e : byPreproc.entrySet()) { + chars.addAll(factory.apply(e.getKey(), e.getValue())); + } + + return chars; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java new file mode 100644 index 000000000..0b74242a9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java @@ -0,0 +1,199 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.additive.AAProperties; +import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; +import com.milaboratory.mixcr.postanalysis.diversity.DiversityMeasure; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeCharacteristic; +import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; + +import java.util.*; +import java.util.stream.Collectors; + +import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; + +@SuppressWarnings("ArraysAsListWithZeroOrOneArgument") +public class PostanalysisParametersIndividual extends PostanalysisParameters { + public static final String + Biophysics = "biophysics", + Diversity = "diversity", + VUsage = "vUsage", + JUsage = "JUsage", + VJUsage = "VJUsage", + IsotypeUsage = "IsotypeUsage", + CDR3Spectratype = "CDR3Spectratype", + VSpectratype = "VSpectratype", + VSpectratypeMean = "VSpectratypeMean"; + + public BiophysicsParameters biophysics = new BiophysicsParameters(); + public DiversityParameters diversity = new DiversityParameters(); + public PreprocessorParameters vUsage = new PreprocessorParameters(); + public PreprocessorParameters jUsage = new PreprocessorParameters(); + public PreprocessorParameters vjUsage = new PreprocessorParameters(); + public PreprocessorParameters isotypeUsage = new PreprocessorParameters(); + public PreprocessorParameters cdr3Spectratype = new PreprocessorParameters(); + public PreprocessorParameters vSpectratype = new PreprocessorParameters(); + public PreprocessorParameters vSpectratypeMean = new PreprocessorParameters(); + + public List> getGroups() { + return Arrays.asList( + biophysics.getGroup(this), + diversity.getGroup(this), + new CharacteristicGroup<>(VUsage, + Arrays.asList(AdditiveCharacteristics.segmentUsage(vUsage.preproc(this), GeneType.Variable)), + Arrays.asList(new GroupSummary<>()) + ), + + new CharacteristicGroup<>(JUsage, + Arrays.asList(AdditiveCharacteristics.segmentUsage(jUsage.preproc(this), GeneType.Joining)), + Arrays.asList(new GroupSummary<>()) + ), + + new CharacteristicGroup<>(VJUsage, + Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(vjUsage.preproc(this))), + Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) + ), + + new CharacteristicGroup<>(IsotypeUsage, + Arrays.asList(AdditiveCharacteristics.isotypeUsage(isotypeUsage.preproc(this))), + Arrays.asList(new GroupSummary<>()) + ), + + new CharacteristicGroup<>(CDR3Spectratype, + Arrays.asList(new SpectratypeCharacteristic("CDR3 spectratype", + cdr3Spectratype.preproc(this), 10, + new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), + Collections.singletonList(new GroupSummary<>())), + + new CharacteristicGroup<>(VSpectratype, + Arrays.asList(AdditiveCharacteristics.VSpectratype(vSpectratype.preproc(this))), + Collections.singletonList(new GroupSummary<>())), + + new CharacteristicGroup<>(VSpectratypeMean, + Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(vSpectratypeMean.preproc(this))), + Collections.singletonList(new GroupSummary<>())) + ); + } + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) + public static class BiophysicsParameters { + public PreprocessorParameters cdr3lenAA = new PreprocessorParameters(); + public PreprocessorParameters cdr3lenNT = new PreprocessorParameters(); + public PreprocessorParameters ndnLenNT = new PreprocessorParameters(); + public PreprocessorParameters addedNNT = new PreprocessorParameters(); + public PreprocessorParameters Strength = new PreprocessorParameters(); + public PreprocessorParameters Hydrophobicity = new PreprocessorParameters(); + public PreprocessorParameters Surface = new PreprocessorParameters(); + public PreprocessorParameters Volume = new PreprocessorParameters(); + public PreprocessorParameters Charge = new PreprocessorParameters(); + + public CharacteristicGroup getGroup(PostanalysisParameters base) { + return new CharacteristicGroup<>(Biophysics, + Arrays.asList( + weightedLengthOf(cdr3lenNT.preproc(base), GeneFeature.CDR3, false).setName("CDR3 length, nt"), + weightedLengthOf(cdr3lenAA.preproc(base), GeneFeature.CDR3, true).setName("CDR3 length, aa"), + weightedLengthOf(ndnLenNT.preproc(base), GeneFeature.VJJunction, false).setName("NDN length, nt"), + weightedAddedNucleotides(addedNNT.preproc(base)).setName("Added N, nt"), + weightedBiophysics(Strength.preproc(base), AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Strength"), + weightedBiophysics(Hydrophobicity.preproc(base), AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Hydrophobicity"), + weightedBiophysics(Surface.preproc(base), AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Surface"), + weightedBiophysics(Volume.preproc(base), AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), + weightedBiophysics(Charge.preproc(base), AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") + ), + Collections.singletonList(new GroupSummary<>())); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + BiophysicsParameters that = (BiophysicsParameters) o; + return Objects.equals(cdr3lenAA, that.cdr3lenAA) && Objects.equals(cdr3lenNT, that.cdr3lenNT) && Objects.equals(ndnLenNT, that.ndnLenNT) && Objects.equals(addedNNT, that.addedNNT) && Objects.equals(Strength, that.Strength) && Objects.equals(Hydrophobicity, that.Hydrophobicity) && Objects.equals(Surface, that.Surface) && Objects.equals(Volume, that.Volume) && Objects.equals(Charge, that.Charge); + } + + @Override + public int hashCode() { + return Objects.hash(cdr3lenAA, cdr3lenNT, ndnLenNT, addedNNT, Strength, Hydrophobicity, Surface, Volume, Charge); + } + } + + @JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.ANY, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE) + public static class DiversityParameters { + public PreprocessorParameters observed = new PreprocessorParameters(); + public PreprocessorParameters shannonWeiner = new PreprocessorParameters(); + public PreprocessorParameters chao1 = new PreprocessorParameters(); + public PreprocessorParameters clonality = new PreprocessorParameters(); + public PreprocessorParameters inverseSimpson = new PreprocessorParameters(); + public PreprocessorParameters gini = new PreprocessorParameters(); + public PreprocessorParameters d50 = new PreprocessorParameters(); + + public CharacteristicGroup getGroup(PostanalysisParameters base) { + List> chars = new ArrayList<>(groupByPreproc( + base, + new HashMap>() {{ + put(DiversityMeasure.Observed, observed.preproc(base)); + put(DiversityMeasure.ShannonWeiner, shannonWeiner.preproc(base)); + put(DiversityMeasure.Chao1, chao1.preproc(base)); + put(DiversityMeasure.NormalizedShannonWeinerIndex, clonality.preproc(base)); + put(DiversityMeasure.InverseSimpson, inverseSimpson.preproc(base)); + put(DiversityMeasure.GiniIndex, gini.preproc(base)); + }}, + (p, l) -> Collections.singletonList(new DiversityCharacteristic<>("Diversity " + + l.stream().map(m -> m.name).collect(Collectors.joining("/")), + new WeightFunctions.Count(), p, l.toArray(new DiversityMeasure[0]))))); + + chars.add(new DiversityCharacteristic<>("d50", new WeightFunctions.Count(), + d50.preproc(base).then(new SelectTop.Factory<>(WeightFunctions.Count, 0.5)), + new DiversityMeasure[]{ + DiversityMeasure.Observed.overrideName("d50") + })); + + //noinspection unchecked,rawtypes + return new CharacteristicGroup(Diversity, + chars, + Arrays.asList(new GroupSummary<>()) + ); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + DiversityParameters that = (DiversityParameters) o; + return Objects.equals(observed, that.observed) && Objects.equals(shannonWeiner, that.shannonWeiner) && Objects.equals(chao1, that.chao1) && Objects.equals(clonality, that.clonality) && Objects.equals(inverseSimpson, that.inverseSimpson) && Objects.equals(gini, that.gini) && Objects.equals(d50, that.d50); + } + + @Override + public int hashCode() { + return Objects.hash(observed, shannonWeiner, chao1, clonality, inverseSimpson, gini, d50); + } + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + PostanalysisParametersIndividual that = (PostanalysisParametersIndividual) o; + return Objects.equals(biophysics, that.biophysics) && Objects.equals(diversity, that.diversity) && Objects.equals(vUsage, that.vUsage) && Objects.equals(jUsage, that.jUsage) && Objects.equals(vjUsage, that.vjUsage) && Objects.equals(isotypeUsage, that.isotypeUsage); + } + + @Override + public int hashCode() { + return Objects.hash(biophysics, diversity, vUsage, jUsage, vjUsage, isotypeUsage); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java new file mode 100644 index 000000000..e829cd6c3 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java @@ -0,0 +1,65 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.Characteristic; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapCharacteristic; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapType; + +import java.util.*; +import java.util.stream.Collectors; + +@SuppressWarnings("ArraysAsListWithZeroOrOneArgument") +public class PostanalysisParametersOverlap extends PostanalysisParameters> { + public static final String Overlap = "Overlap"; + + public PreprocessorParameters d = new PreprocessorParameters(); + public PreprocessorParameters sharedClonotypes = new PreprocessorParameters(); + public PreprocessorParameters f1 = new PreprocessorParameters(); + public PreprocessorParameters f2 = new PreprocessorParameters(); + public PreprocessorParameters jaccard = new PreprocessorParameters(); + public PreprocessorParameters rIntersection = new PreprocessorParameters(); + public PreprocessorParameters rAll = new PreprocessorParameters(); + + public List>> getGroups(int nSamples) { + PostanalysisParametersOverlap base = this; + List>> chars = groupByPreproc(this, new HashMap>>() {{ + put(OverlapType.D, d.overlapPreproc(base)); + put(OverlapType.SharedClonotypes, sharedClonotypes.overlapPreproc(base)); + put(OverlapType.F1, f1.overlapPreproc(base)); + put(OverlapType.F2, f2.overlapPreproc(base)); + put(OverlapType.Jaccard, jaccard.overlapPreproc(base)); + put(OverlapType.R_Intersection, rIntersection.overlapPreproc(base)); + put(OverlapType.R_All, rAll.overlapPreproc(base)); + }}, + (p, l) -> { + List> overlaps = new ArrayList<>(); + for (int i = 0; i < nSamples; ++i) + for (int j = i; j < nSamples; ++j) // j=i to include diagonal elements + overlaps.add(new OverlapCharacteristic<>( + "overlap_" + i + "_" + j + " / " + l.stream().map(t -> t.name).collect(Collectors.joining(" / ")), + new WeightFunctions.Count(), + p, + l.toArray(new OverlapType[0]), + i, j)); + return overlaps; + }); + //noinspection unchecked,rawtypes + return Collections.singletonList(new CharacteristicGroup(Overlap, chars, Arrays.asList(new OverlapSummary<>()))); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + PostanalysisParametersOverlap that = (PostanalysisParametersOverlap) o; + return Objects.equals(d, that.d) && Objects.equals(sharedClonotypes, that.sharedClonotypes) && Objects.equals(f1, that.f1) && Objects.equals(f2, that.f2) && Objects.equals(jaccard, that.jaccard) && Objects.equals(rIntersection, that.rIntersection) && Objects.equals(rAll, that.rAll); + } + + @Override + public int hashCode() { + return Objects.hash(d, sharedClonotypes, f1, f2, jaccard, rIntersection, rAll); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java new file mode 100644 index 000000000..49344bb53 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java @@ -0,0 +1,56 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; +import com.milaboratory.util.GlobalObjectMappers; + +import java.io.IOException; +import java.io.InputStream; +import java.util.HashMap; +import java.util.Map; + +public class PostanalysisParametersPreset { + private static volatile Map knownParametersIndividual; + private static volatile Map knownParametersOverlap; + + private static void ensureInitialized() { + if (knownParametersIndividual == null) + synchronized (PostanalysisParametersPreset.class) { + if (knownParametersIndividual == null) { + Map map; + try { + InputStream is = CloneAssemblerParameters.class.getClassLoader().getResourceAsStream("parameters/postanalysis_individual.json"); + TypeReference> typeRef + = new TypeReference>() { + }; + map = GlobalObjectMappers.getOneLine().readValue(is, typeRef); + } catch (IOException ioe) { + throw new RuntimeException(ioe); + } + knownParametersIndividual = map; + + Map map2; + try { + InputStream is = CloneAssemblerParameters.class.getClassLoader().getResourceAsStream("parameters/postanalysis_overlap.json"); + TypeReference> typeRef + = new TypeReference>() { + }; + map2 = GlobalObjectMappers.getOneLine().readValue(is, typeRef); + } catch (IOException ioe) { + throw new RuntimeException(ioe); + } + knownParametersOverlap = map2; + } + } + } + + public static PostanalysisParametersIndividual getByNameIndividual(String name) { + ensureInitialized(); + return knownParametersIndividual.get(name); + } + + public static PostanalysisParametersOverlap getByNameOverlap(String name) { + ensureInitialized(); + return knownParametersOverlap.get(name); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 87616923e..bd87b94a5 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -146,7 +146,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl IOUtil.registerGeneReferences(tmpOut, align.usedGenes, align.parameters.alignerParameters); final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), - reader.getAssemblingFeatures(), reader.getGenes(), reader.getAlignerParameters().getFeaturesToAlignMap()); + reader.getAssemblingFeatures(), reader.getUsedGenes(), reader.getAlignerParameters().getFeaturesToAlignMap()); ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments(); SmartProgressReporter.startProgressReport("Assembling", cloneAlignmentsPort); diff --git a/src/main/resources/parameters/postanalysis_individual.json b/src/main/resources/parameters/postanalysis_individual.json new file mode 100644 index 000000000..b18ee72e3 --- /dev/null +++ b/src/main/resources/parameters/postanalysis_individual.json @@ -0,0 +1,111 @@ +{ + "default": { + "defaultDownsampling": null, + "defaultOnlyProductive": true, + "defaultDropOutliers": false, + "biophysics": { + "cdr3lenAA": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "cdr3lenNT": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "ndnLenNT": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "addedNNT": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "Strength": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "Hydrophobicity": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "Surface": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "Volume": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "Charge": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + } + }, + "diversity": { + "observed": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "shannonWeiner": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "chao1": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "clonality": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "inverseSimpson": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "gini": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "d50": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + } + }, + "vUsage": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "jUsage": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "vjUsage": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "isotypeUsage": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + } + } +} diff --git a/src/main/resources/parameters/postanalysis_overlap.json b/src/main/resources/parameters/postanalysis_overlap.json new file mode 100644 index 000000000..75dfb2298 --- /dev/null +++ b/src/main/resources/parameters/postanalysis_overlap.json @@ -0,0 +1,42 @@ +{ + "default": { + "defaultDownsampling": null, + "defaultOnlyProductive": false, + "defaultDropOutliers": false, + "d": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "sharedClonotypes": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "f1": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "f2": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "jaccard": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "rIntersection": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "rAll": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + } + } +} \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java index 1e032d79b..946cff6c5 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java @@ -61,4 +61,38 @@ public void test4() { "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json", "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/tables/preproc/overlap.tsv"); } + + @Ignore + @Test + public void test5() { + Main.main("postanalysis", + "individual", + "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", + "--only-productive", "-f", "--default-downsampling", "umi-count-auto", + "-Odiversity.observed.downsampling=top-100", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_a.clns", 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"/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m3_young_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m4_young_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_spl_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m5_young_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_spl_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m6_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4naiv_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD4naiv_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_spl_Cd8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4m_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_dp_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m7_ct_65w_th_dp_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m8_ct_65w_th_DP_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD4naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_spl_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD4mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8mem_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_CD8naive_b.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_a.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m9_ct_65w_th_DP_b.clns", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/individualPa.json.gz"); + } + + @Ignore + @Test + public void test6() { + Main.main("exportPlots", "diversity", + "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", + "--primary-group", "Tissue", + "--secondary-group", "MouseIDNum", + "--plot-type", "boxplot", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/individualPa.json.gz", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/i/diversity.pdf"); + } + + @Ignore + @Test + public void test7() { + Main.main("exportPlots", "overlap", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json.gz", + "/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/o/overlap.pdf"); + } + +// mixcr exportPlots overlap --filter "CellPopulation=CD4naive" --color-key x_CellPopulation --metadata metadata.tsv pa/overlapPa.json.gz pa/o/overlap.pdf } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java index e13780bfe..0e2225ef8 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java @@ -41,6 +41,7 @@ public boolean test(TestObject testObject) { DownsamplingPreprocessorFactory downsamplingPreproc = new DownsamplingPreprocessorFactory<>( new DownsampleValueChooser.Fixed(downsampling), 314, + true, c -> (long) c.weight, TestObject::setWeight); SetPreprocessorFactory preproc = filter.then(downsamplingPreproc); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index 152e48d9f..05b15b4cf 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -48,7 +48,7 @@ public void test1() { if (cell.key == DiversityMeasure.InverseSimpson) Assert.assertEquals(SimpsonIndex(ds.data), cell.value, 1e-6); if (cell.key == DiversityMeasure.ShannonWeiner) - Assert.assertEquals(ShannonEntropy(ds.data), cell.value, 1e-6); + Assert.assertEquals(Math.exp(ShannonEntropy(ds.data)), cell.value, 1e-6); } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java index c5165b465..e982eb32b 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java @@ -10,7 +10,13 @@ public class DownsampleValueChooserTest { @Test public void testAuto1() { DownsampleValueChooser.Auto auto = new DownsampleValueChooser.Auto(); - Assert.assertEquals(501, auto.compute(501, 200_000, 300_000, 400_000)); + Assert.assertEquals(200_000, auto.compute(501, 200_000, 300_000, 400_000)); Assert.assertTrue(501 < auto.compute(501, 200_000, 300_000, 400_000, 500_000)); } + + @Test + public void testAuto2() { + DownsampleValueChooser.Auto auto = new DownsampleValueChooser.Auto(); + Assert.assertEquals(10001, auto.compute(501, 1000, 10001, 10002, 10002, 10002, 10001, 10001, 200_000, 300_000, 400_000)); + } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index 36f641249..694350bdc 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -101,6 +101,7 @@ public void test3() { t -> Math.round(t.weight), (t, w) -> new TestObject(t.value, 1d * w), dsChooser, + true, rng.nextLong(0, Long.MAX_VALUE / 2), "" ); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index b22b83b4f..009db9d3f 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -38,6 +38,7 @@ public void test1() { t -> Math.round(t.weight), (t, newW) -> new TestObject(t.value, newW), chooser, + true, System.currentTimeMillis(), "" ); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java new file mode 100644 index 000000000..d22a52992 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java @@ -0,0 +1,23 @@ +package com.milaboratory.mixcr.postanalysis.ui; + + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.milaboratory.util.GlobalObjectMappers; +import org.junit.Assert; +import org.junit.Test; + +import java.io.IOException; + +public class PostanalysisParametersIndividualTest { + @Test + public void test1() throws JsonProcessingException { + PostanalysisParametersIndividual par = new PostanalysisParametersIndividual(); + String str = GlobalObjectMappers.getPretty().writeValueAsString(par); + Assert.assertEquals(par, GlobalObjectMappers.getPretty().readValue(str, PostanalysisParametersIndividual.class)); + } + + @Test + public void test2() throws IOException { + PostanalysisParametersPreset.getByNameIndividual("default"); + } +} \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java new file mode 100644 index 000000000..4a7f82858 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java @@ -0,0 +1,13 @@ +package com.milaboratory.mixcr.postanalysis.ui; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.milaboratory.util.GlobalObjectMappers; +import org.junit.Test; + +public class PostanalysisParametersOverlapTest { + @Test + public void test1() throws JsonProcessingException { + PostanalysisParametersOverlap par = new PostanalysisParametersOverlap(); + System.out.println(GlobalObjectMappers.getPretty().writeValueAsString(par)); + } +} \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index 2659616c7..b0c6bd353 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -36,7 +36,10 @@ import java.io.IOException; import java.nio.file.Paths; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; import java.util.stream.Collectors; import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedBiophysics; @@ -79,7 +82,7 @@ public void test1() throws IOException { )); groups.add(new CharacteristicGroup<>( "diversity", - Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314))), + Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314, true))), Arrays.asList(new GroupSummary<>()) )); @@ -183,7 +186,7 @@ public void testOverlap1() throws JsonProcessingException { ClonesDownsamplingPreprocessorFactory downsamplePreprocessor = new ClonesDownsamplingPreprocessorFactory( new DownsampleValueChooser.Minimal(), - 332142); + 332142, true); List> overlaps = new ArrayList<>(); for (int i = 0; i < readers.size(); ++i) { From f02cffe4128fef62084b41d2d56f8e6fabd10fd1 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 24 May 2022 23:26:28 +0200 Subject: [PATCH 219/282] feat(PA): Better VJ-usage tabular output --- build.gradle.kts | 2 +- .../CommandPaExportPlotsVJUsage.java | 9 +-- .../postanalysis/additive/KeyFunctions.java | 14 ++-- .../CharacteristicGroupOutputExtractor.java | 5 +- .../ui/CharacteristicGroupResult.java | 3 +- .../mixcr/postanalysis/ui/GroupMelt.java | 2 +- .../mixcr/postanalysis/ui/GroupSummary.java | 61 ++++++++++++++--- .../mixcr/postanalysis/ui/OutputTable.java | 66 +++++-------------- .../postanalysis/ui/OutputTableBuilder.java | 8 ++- .../postanalysis/ui/OutputTableCell.java | 6 +- .../postanalysis/ui/OutputTableExtractor.java | 21 ++++++ .../ui/PostanalysisParameters.java | 1 + .../ui/PostanalysisParametersIndividual.java | 18 ++--- .../mixcr/postanalysis/plots/VJUsage.kt | 2 +- .../additive/AdditiveCharacteristicsTest.java | 6 +- .../DiversityCharacteristicTest.java | 2 +- .../overlap/OverlapCharacteristicTest.java | 10 +-- .../ui/PostanalysisSchemaIntegrationTest.java | 20 +++--- 18 files changed, 148 insertions(+), 108 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index af92b4532..4ce5988d4 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -79,7 +79,7 @@ repositories { } val milibVersion = "1.15.0-42-master" -val repseqioVersion = "1.3.5-28-master" +val repseqioVersion = "1.3.5-29-master" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java index 9b1c87cd8..9664bde3b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java @@ -8,16 +8,17 @@ import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; -import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.util.Collections; import java.util.List; -@CommandLine.Command(name = "vjUsage", +@Command(name = "vjUsage", sortOptions = false, separator = " ", - description = "Export V-J usage heatmap") + description = "Export V-J usage heatmap", + hidden = true) public class CommandPaExportPlotsVJUsage extends CommandPaExportPlotsHeatmap { @Option(description = "Plot dendrogram for hierarchical clusterization of V genes.", names = {"--no-v-dendro"}) public boolean noVDendro; @@ -46,7 +47,7 @@ void run(PaResultByGroup result) { null, hLabelsSize, vLabelsSize, - false, + true, width, height )); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java index 931f0e839..6fa5e9122 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java @@ -135,22 +135,22 @@ public FamiltyUsage(GeneType geneType) { public static final class VJGenes implements JsonSupport { public Gene vGene; - public Gene jJene; + public Gene jGene; public VJGenes() {} - public VJGenes(Gene vGene, Gene jJene) { + public VJGenes(Gene vGene, Gene jGene) { this.vGene = vGene; - this.jJene = jJene; + this.jGene = jGene; } public VJGenes map(Function mapper) { - return new VJGenes<>(mapper.apply(vGene), mapper.apply(jJene)); + return new VJGenes<>(mapper.apply(vGene), mapper.apply(jGene)); } @Override public String toString() { - return vGene + "+" + jJene; + return vGene + "+" + jGene; } @Override @@ -159,12 +159,12 @@ public boolean equals(Object o) { if (o == null || getClass() != o.getClass()) return false; VJGenes vjGenes = (VJGenes) o; return Objects.equals(vGene, vjGenes.vGene) && - Objects.equals(jJene, vjGenes.jJene); + Objects.equals(jGene, vjGenes.jGene); } @Override public int hashCode() { - return Objects.hash(vGene, jJene); + return Objects.hash(vGene, jGene); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java index c50e4980f..6842b020e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java @@ -11,9 +11,10 @@ */ @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") @JsonSubTypes({ - @JsonSubTypes.Type(value = GroupSummary.class, name = "summary"), + @JsonSubTypes.Type(value = GroupSummary.Simple.class, name = "summary"), + @JsonSubTypes.Type(value = GroupSummary.VJUsage.class, name = "vjUsage"), + @JsonSubTypes.Type(value = GroupMelt.VJUsageMelt.class, name = "vjUsageMelt"), @JsonSubTypes.Type(value = OverlapSummary.class, name = "overlapSummary"), - @JsonSubTypes.Type(value = GroupMelt.VJUsageMelt.class, name = "vjUsage") }) @JsonAutoDetect( fieldVisibility = JsonAutoDetect.Visibility.NONE, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java index 989966d54..b60f529d5 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java @@ -27,7 +27,8 @@ public final class CharacteristicGroupResult { public final List> cells; public CharacteristicGroupResult(CharacteristicGroup group, - Set datasetIds, Set keys, + Set datasetIds, + Set keys, List> cells) { this.group = group; this.datasetIds = datasetIds; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java index 728094c2b..91f2c48b3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java @@ -51,7 +51,7 @@ public static final class VJUsageMelt extends GroupMelt cell.datasetId, - () -> key -> new Coordinates(key.key.vGene, key.key.jJene)); + () -> key -> new Coordinates(key.key.vGene, key.key.jGene)); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java index 4dbd59ba3..772b548c9 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java @@ -1,28 +1,69 @@ package com.milaboratory.mixcr.postanalysis.ui; +import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; + import java.util.Collections; +import java.util.HashMap; +import java.util.LinkedHashMap; import java.util.Map; +import java.util.function.Function; /** * */ -public class GroupSummary implements CharacteristicGroupOutputExtractor { +public abstract class GroupSummary implements CharacteristicGroupOutputExtractor { public static final String key = "summary"; + public final Function, Map> columnsFunction; + + public GroupSummary(Function, Map> columnsFunction) { + this.columnsFunction = columnsFunction; + } + @Override public Map getTables(CharacteristicGroupResult result) { - return Collections.singletonMap(key, OutputTableExtractor.summary().getTable(result)); + return Collections.singletonMap(key, columnsFunction == null + ? OutputTableExtractor.summary().getTable(result) + : OutputTableExtractor.summary(columnsFunction).getTable(result)); } - @Override - public boolean equals(Object o1) { - if (this == o1) return true; - if (o1 == null || getClass() != o1.getClass()) return false; - return true; + public static final class Simple extends GroupSummary { + public Simple() {super(null);} + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Simple simple = (Simple) o; + return true; + } + + @Override + public int hashCode() { + return 12349911; + } } - @Override - public int hashCode() { - return 17; + public static final class VJUsage extends GroupSummary> { + public VJUsage() { + super(r -> new LinkedHashMap() {{ + put("VGene", r.key.vGene); + put("JGene", r.key.jGene); + put("Value", r.value); + }}); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + VJUsage vjUsage = (VJUsage) o; + return true; + } + + @Override + public int hashCode() { + return 123499113; + } } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java index 9264d891b..80e7fc55c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java @@ -1,17 +1,14 @@ package com.milaboratory.mixcr.postanalysis.ui; -import com.milaboratory.mixcr.postanalysis.clustering.HierarchicalClustering; -import com.milaboratory.mixcr.postanalysis.clustering.HierarchyNode; - import java.io.BufferedWriter; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.StandardOpenOption; import java.util.Arrays; -import java.util.Collections; import java.util.List; import java.util.Map; +import java.util.Objects; import java.util.stream.Collectors; import java.util.stream.IntStream; @@ -46,76 +43,45 @@ public int colIdx(Object colId) { return colId2idx.get(colId); } - private volatile List columnsHierarchy, rowsHierarchy; - - public synchronized List columnsHierarchy() { - if (columnsHierarchy == null) - columnsHierarchy = Collections.unmodifiableList(HierarchicalClustering.clusterize(columns(0.0, 0.0), 0.0, HierarchicalClustering::EuclideanDistance)); - return columnsHierarchy; - } - - public synchronized List rowsHierarchy() { - if (rowsHierarchy == null) - rowsHierarchy = Collections.unmodifiableList(HierarchicalClustering.clusterize(rows(0.0, 0.0), 0.0, HierarchicalClustering::EuclideanDistance)); - return rowsHierarchy; - } - public OutputTable reorder(List rowIds, List colIds) { return new OutputTable(name, rowIds, colIds, cells); } - public double[][] columns(double naValue, double nan) { + public double[][] drows(double naValue, double nan) { int nRows = rowIds.size(), nCols = colIds.size(); - double[][] r = new double[nCols][nRows]; - if (naValue != 0.0) + double[][] r = new double[nRows][nCols]; + if (naValue != 0) for (double[] doubles : r) Arrays.fill(doubles, naValue); for (OutputTableCell cell : cells) - r[colIdx(cell.iCol)][rowIdx(cell.iRow)] = Double.isNaN(cell.value) ? nan : cell.value; + r[rowIdx(cell.iRow)][colIdx(cell.iCol)] = cell.value == null ? nan : (double) cell.value; return r; } - public Double[][] columns() { + public Object[][] rows(Object naValue, Object nan) { int nRows = rowIds.size(), nCols = colIds.size(); - Double[][] r = new Double[nCols][nRows]; - for (OutputTableCell cell : cells) - r[colIdx(cell.iCol)][rowIdx(cell.iRow)] = cell.value; - - return r; - } - - public double[][] rows(double naValue, double nan) { - int nRows = rowIds.size(), nCols = colIds.size(); - double[][] r = new double[nRows][nCols]; - if (naValue != 0.0) - for (double[] doubles : r) + Object[][] r = new Object[nRows][nCols]; + if (naValue != null) + for (Object[] doubles : r) Arrays.fill(doubles, naValue); for (OutputTableCell cell : cells) - r[rowIdx(cell.iRow)][colIdx(cell.iCol)] = Double.isNaN(cell.value) ? nan : cell.value; + r[rowIdx(cell.iRow)][colIdx(cell.iCol)] = cell.value == null ? nan : cell.value; return r; } - public Double[][] rows() { + public Object[][] rows() { int nRows = rowIds.size(), nCols = colIds.size(); - Double[][] r = new Double[nRows][nCols]; + Object[][] r = new Object[nRows][nCols]; for (OutputTableCell cell : cells) r[rowIdx(cell.iRow)][colIdx(cell.iCol)] = cell.value; return r; } - public double minValue() { - return cells.stream().mapToDouble(c -> c.value).filter(v -> !Double.isNaN(v)).min().orElse(Double.NaN); - } - - public double maxValue() { - return cells.stream().mapToDouble(c -> c.value).filter(v -> !Double.isNaN(v)).max().orElse(Double.NaN); - } - @Override public String toString() { return cells.toString(); @@ -138,7 +104,7 @@ public void writeTSV(Path dir, String prefix) { } public void writeCSV(Path dir, String prefix, String sep, String ext) { - Double[][] rows2d = rows(); + Object[][] rows2d = rows(); Path outName = dir.resolve(prefix + name + ext); try (BufferedWriter writer = Files.newBufferedWriter(outName, StandardOpenOption.CREATE)) { writer.write(""); @@ -150,10 +116,10 @@ public void writeCSV(Path dir, String prefix, String sep, String ext) { for (int iRow = 0; iRow < rowIds.size(); ++iRow) { writer.write("\n"); writer.write(rowIds.get(iRow).toString()); - Double[] row = rows2d[iRow]; - for (Double val : row) { + Object[] row = rows2d[iRow]; + for (Object val : row) { writer.write(sep); - writer.write(Double.toString(val == null ? Double.NaN : val)); + writer.write(Objects.toString(val)); } } } catch (IOException e) { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java index 3faaa6630..f49bf47a1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java @@ -21,12 +21,16 @@ void add(Coordinates coords, CharacteristicGroupResultCell original) { add(coords.iRow, coords.iCol, original); } - synchronized void add(Object iRow, Object iCol, CharacteristicGroupResultCell original) { - cells.add(new OutputTableCell(iRow, iCol, original.value)); + synchronized void add(Object iRow, Object iCol, Object value) { + cells.add(new OutputTableCell(iRow, iCol, value)); rows.add(iRow); cols.add(iCol); } + synchronized void add(Object iRow, Object iCol, CharacteristicGroupResultCell original) { + add(iRow, iCol, original.value); + } + OutputTable build() { return new OutputTable(name, new ArrayList<>(rows), new ArrayList<>(cols), cells); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java index 65944656c..094ac6567 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java @@ -8,9 +8,9 @@ public final class OutputTableCell { /** row & col keys */ public final Object iRow, iCol; - public final double value; + public final Object value; - public OutputTableCell(Object iRow, Object iCol, double value) { + public OutputTableCell(Object iRow, Object iCol, Object value) { this.iRow = iRow; this.iCol = iCol; this.value = value; @@ -26,7 +26,7 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; OutputTableCell that = (OutputTableCell) o; - return Double.compare(that.value, value) == 0 && Objects.equals(iRow, that.iRow) && Objects.equals(iCol, that.iCol); + return Objects.equals(iRow, that.iRow) && Objects.equals(iCol, that.iCol) && Objects.equals(value, that.value); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java index 099445392..11f5294c7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java @@ -2,6 +2,8 @@ import java.util.ArrayList; import java.util.List; +import java.util.Map; +import java.util.function.Function; /** * @@ -20,4 +22,23 @@ static OutputTableExtractor summary() { new ArrayList<>(result.keys), cells); }; } + + static OutputTableExtractor summary(Function, Map> columnsFunction) { + return result -> { + List cells = new ArrayList<>(); + List columns = null; + for (CharacteristicGroupResultCell cell : result.cells) { + Map split = columnsFunction.apply(cell); + if (columns == null) + columns = new ArrayList<>(split.keySet()); + for (Map.Entry e : split.entrySet()) { + cells.add(new OutputTableCell(cell.datasetId, e.getKey(), e.getValue())); + } + } + + return new OutputTable(result.group.name, + new ArrayList<>(result.datasetIds), + columns, cells); + }; + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java index b741cd221..8b83b0810 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java @@ -39,6 +39,7 @@ public static class PreprocessorParameters { public String downsampling; public Boolean onlyProductive; public Boolean dropOutliers; + public Long seed; public SetPreprocessorFactory preproc(PostanalysisParameters base) { SetPreprocessorFactory p = parseDownsampling(base); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java index 0b74242a9..4d01df57f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java @@ -50,37 +50,37 @@ public List> getGroups() { diversity.getGroup(this), new CharacteristicGroup<>(VUsage, Arrays.asList(AdditiveCharacteristics.segmentUsage(vUsage.preproc(this), GeneType.Variable)), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) ), new CharacteristicGroup<>(JUsage, Arrays.asList(AdditiveCharacteristics.segmentUsage(jUsage.preproc(this), GeneType.Joining)), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) ), new CharacteristicGroup<>(VJUsage, Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(vjUsage.preproc(this))), - Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) + Arrays.asList(new GroupSummary.VJUsage<>()) ), new CharacteristicGroup<>(IsotypeUsage, Arrays.asList(AdditiveCharacteristics.isotypeUsage(isotypeUsage.preproc(this))), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) ), new CharacteristicGroup<>(CDR3Spectratype, Arrays.asList(new SpectratypeCharacteristic("CDR3 spectratype", cdr3Spectratype.preproc(this), 10, new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), - Collections.singletonList(new GroupSummary<>())), + Collections.singletonList(new GroupSummary.Simple<>())), new CharacteristicGroup<>(VSpectratype, Arrays.asList(AdditiveCharacteristics.VSpectratype(vSpectratype.preproc(this))), - Collections.singletonList(new GroupSummary<>())), + Collections.singletonList(new GroupSummary.Simple<>())), new CharacteristicGroup<>(VSpectratypeMean, Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(vSpectratypeMean.preproc(this))), - Collections.singletonList(new GroupSummary<>())) + Collections.singletonList(new GroupSummary.Simple<>())) ); } @@ -112,7 +112,7 @@ public CharacteristicGroup getGroup(PostanalysisParameters base) { weightedBiophysics(Volume.preproc(base), AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), weightedBiophysics(Charge.preproc(base), AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") ), - Collections.singletonList(new GroupSummary<>())); + Collections.singletonList(new GroupSummary.Simple<>())); } @Override @@ -166,7 +166,7 @@ public CharacteristicGroup getGroup(PostanalysisParameters base) { //noinspection unchecked,rawtypes return new CharacteristicGroup(Diversity, chars, - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) ); } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt index 6b43c0545..dca3f6a1d 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt @@ -35,7 +35,7 @@ object VJUsage { for ((sampleId, keys) in charData.data) { for (metric in keys.data) { val key = metric.key as? KeyFunctions.VJGenes ?: throw RuntimeException() - data += VJUsageRow(sampleId, key.vGene, key.jJene, metric.value) + data += VJUsageRow(sampleId, key.vGene, key.jGene, metric.value) } } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java index 4e4fbebda..74039d502 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java @@ -67,14 +67,14 @@ public void testWeightedDescriptiveStat() { CharacteristicGroup group = new CharacteristicGroup<>("stat", Arrays.asList(mean, std), - Arrays.asList(new GroupSummary<>())); + Arrays.asList(new GroupSummary.Simple<>())); CharacteristicGroupResult table = result.getTable(group); OutputTable summary = table.getOutputs().get(GroupSummary.key); - Double[][] rows = summary.rows(); + Object[][] rows = summary.rows(); for (int i = 0; i < nDatasets; i++) { - Double[] metrics = rows[i]; + Double[] metrics = Arrays.stream(rows[i]).map(d -> (Double) d).toArray(Double[]::new); double[] vals = datasets[i].stream().mapToDouble(o -> o.value).toArray(); double[] weights = datasets[i].stream().mapToDouble(o -> o.weight).toArray(); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index 05b15b4cf..6e339cc4a 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -40,7 +40,7 @@ public void test1() { CharacteristicGroup group = new CharacteristicGroup<>("diversity", Arrays.asList(diversity), - Arrays.asList(new GroupSummary<>())); + Arrays.asList(new GroupSummary.Simple<>())); CharacteristicGroupResult table = result.getTable(group); for (CharacteristicGroupResultCell cell : table.cells) { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java index a0e5f11a1..672420db2 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -220,19 +220,19 @@ public boolean isFinished() { System.out.println(Arrays.stream(expectedSharedElements).map(Arrays::toString).collect(Collectors.joining("\n"))); assert2dEquals(expectedSharedElements, outputs.get(OverlapType.SharedClonotypes) .reorder(datasetIds, datasetIds) - .rows(0, 0)); + .drows(0, 0)); assert2dEquals(expectedD, outputs.get(OverlapType.D) .reorder(datasetIds, datasetIds) - .rows(0, 0)); + .drows(0, 0)); assert2dEquals(expectedF1, outputs.get(OverlapType.F1) .reorder(datasetIds, datasetIds) - .rows(0, 0)); + .drows(0, 0)); assert2dEquals(expectedF2, outputs.get(OverlapType.F2) .reorder(datasetIds, datasetIds) - .rows(0, 0)); + .drows(0, 0)); assert2dEquals(expectedR, outputs.get(OverlapType.R_Intersection) .reorder(datasetIds, datasetIds) - .rows(0, 0)); + .drows(0, 0)); } interface OverlapScanFunction { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index b0c6bd353..909fb6062 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -78,35 +78,35 @@ public void test1() throws IOException { weightedBiophysics(AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5), weightedBiophysics(AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5) ), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) )); groups.add(new CharacteristicGroup<>( "diversity", Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314, true))), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) )); groups.add(new CharacteristicGroup<>( "vUsage", Arrays.asList(AdditiveCharacteristics.segmentUsage(GeneType.Variable)), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) )); groups.add(new CharacteristicGroup<>( "jUsage", Arrays.asList(AdditiveCharacteristics.segmentUsage(GeneType.Joining)), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) )); groups.add(new CharacteristicGroup<>( "vjUsage", Arrays.asList(AdditiveCharacteristics.vjSegmentUsage()), - Arrays.asList(new GroupSummary<>(), new GroupMelt.VJUsageMelt<>()) + Arrays.asList(new GroupSummary.VJUsage<>()) )); groups.add(new CharacteristicGroup<>( "isotypeUsage", Arrays.asList(AdditiveCharacteristics.isotypeUsage()), - Arrays.asList(new GroupSummary<>()) + Arrays.asList(new GroupSummary.Simple<>()) )); groups.add(new CharacteristicGroup<>( @@ -114,12 +114,12 @@ public void test1() throws IOException { Arrays.asList(new SpectratypeCharacteristic("cdr3Spectratype", NoPreprocessing.factory(), 10, new SpectratypeKeyFunction<>(new KeyFunctions.NTFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), - Collections.singletonList(new GroupSummary<>()))); + Collections.singletonList(new GroupSummary.Simple<>()))); groups.add(new CharacteristicGroup<>( "VSpectratype", Arrays.asList(AdditiveCharacteristics.VSpectratype()), - Collections.singletonList(new GroupSummary<>()))); + Collections.singletonList(new GroupSummary.Simple<>()))); PostanalysisSchema individualPA = new PostanalysisSchema<>(groups); @@ -145,6 +145,10 @@ public void test1() throws IOException { .values().stream().allMatch(l -> l.size() <= 11)); System.out.println(result.getTable(individualPA.getGroup("VSpectratype"))); + + + Object[][] vjUsages = result.getTable(individualPA.getGroup("vjUsage")).getOutputs().get(GroupSummary.key).rows(); + System.out.println(Arrays.deepToString(vjUsages)); } @Test From 68c04bdda765d27014a652f260f6eaf7d17e3d16 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 25 May 2022 00:32:50 +0200 Subject: [PATCH 220/282] Added downsample command. --- .../mixcr/basictypes/ClnAReader.java | 1 + .../mixcr/basictypes/ClnsReader.java | 6 + .../mixcr/basictypes/CloneReader.java | 3 + .../java/com/milaboratory/mixcr/cli/Main.java | 1 + .../cli/postanalysis/CommandDownsample.java | 112 ++++++++++++++++++ .../cli/postanalysis/CommandPaOverlap.java | 6 + .../mixcr/postanalysis/SetPreprocessor.java | 24 ++-- .../downsampling/DownsamplingUtil.java | 41 +++++++ .../postanalysis/ui/ClonotypeDataset.java | 60 +++++++++- .../ui/PostanalysisParameters.java | 59 +++------ .../ui/PostanalysisParametersIndividual.java | 7 +- .../ui/PostanalysisParametersOverlap.java | 5 +- .../parameters/postanalysis_individual.json | 1 + .../parameters/postanalysis_overlap.json | 1 + 14 files changed, 262 insertions(+), 65 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index a770215d6..1ad49281a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -189,6 +189,7 @@ public VDJCAlignerParameters getAlignerParameters() { /** * Clone assembler parameters */ + @Override public CloneAssemblerParameters getAssemblerParameters() { return assemblerParameters; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index 6e23d4fca..c5a262e7b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -42,6 +42,7 @@ import java.io.IOException; import java.nio.file.Path; +import java.nio.file.Paths; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -66,6 +67,10 @@ public class ClnsReader extends PipelineConfigurationReaderMiXCR implements Clon private final long clonesPosition; + public ClnsReader(String file, VDJCLibraryRegistry libraryRegistry) throws IOException { + this(Paths.get(file), libraryRegistry, 3); + } + public ClnsReader(Path file, VDJCLibraryRegistry libraryRegistry) throws IOException { this(file, libraryRegistry, 3); } @@ -146,6 +151,7 @@ public VDJCAlignerParameters getAlignerParameters() { return alignerParameters; } + @Override public CloneAssemblerParameters getAssemblerParameters() { return assemblerParameters; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java index 26a1b7d6c..f62d11ba0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -30,6 +30,7 @@ package com.milaboratory.mixcr.basictypes; import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.VDJCGene; @@ -50,4 +51,6 @@ public interface CloneReader extends AutoCloseable { List getUsedGenes(); VDJCAlignerParameters getAlignerParameters(); + + CloneAssemblerParameters getAssemblerParameters(); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index d9caaaf59..708ad3ab2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -226,6 +226,7 @@ public static CommandLine mkCmd() { .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) .addSubcommand("postanalysis", CommandPa.CommandPostanalysisMain.class) + .addSubcommand("downsample", CommandDownsample.class) .addSubcommand("exportPlots", CommandPaExportPlots.CommandExportPlotsMain.class) .addSubcommand("exportTables", CommandPaExportTables.class) .addSubcommand("exportPreprocTables", CommandPaExportTablesPreprocSummary.class) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java new file mode 100644 index 000000000..bae0450b1 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java @@ -0,0 +1,112 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import cc.redberry.pipe.CUtils; +import com.milaboratory.mixcr.basictypes.ClnsWriter; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.ui.ClonotypeDataset; +import io.repseq.core.Chains; +import io.repseq.core.VDJCLibraryRegistry; +import picocli.CommandLine.Command; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; + +@Command(name = "downsample", + separator = " ", + description = "Downsample clonesets.") +public class CommandDownsample extends ACommandWithOutputMiXCR { + @Parameters(description = "cloneset.{clns|clna}...") + public List in; + + @Option(description = "Filter specific chains", + names = {"-c", "--chains"}, + required = true) + public String chains = "ALL"; + + @Option(description = "Use only productive CDR3s.", + names = {"--only-productive"}) + public boolean onlyProductive = false; + + @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", + names = {"--downsampling"}, + required = true) + public String downsampling; + + @Option(description = "Random seed.", + names = {"--random-seed"}) + public long seed = 111; + + @Option(description = "Suffix to add to output clns file.", + names = {"--suffix"}) + public String suffix = "downsampled"; + + @Option(description = "Output path prefix.", + names = {"--out"}) + public String out; + + private Path output(String input) { + String outName = Paths.get(input).getFileName().toString() + .replace(".clna", "") + .replace(".clns", "") + + "." + chains + "." + suffix + ".clns"; + return out == null + ? Paths.get(outName).toAbsolutePath() + : Paths.get(out).resolve(outName).toAbsolutePath(); + } + + private void ensureOutputPathExists() { + if (out != null) { + try { + Files.createDirectories(Paths.get(out).toAbsolutePath()); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + } + + @Override + public void run0() throws Exception { + List datasets = in.stream() + .map(file -> + new ClonotypeDataset(file, file, VDJCLibraryRegistry.getDefault()) + ).collect(Collectors.toList()); + + SetPreprocessorFactory preproc = DownsamplingUtil + .parseDownsampling(this.downsampling, false, seed) + .filterFirst(new ElementPredicate.IncludeChains(Chains.getByName(chains))); + if (onlyProductive) + preproc = DownsamplingUtil.filterOnlyProductive(preproc); + + Dataset[] result = SetPreprocessor.processDatasets(preproc.newInstance(), datasets); + + ensureOutputPathExists(); + for (int i = 0; i < result.length; i++) { + String input = in.get(i); + try (ClnsWriter clnsWriter = new ClnsWriter(output(input).toFile())) { + List downsampled = new ArrayList<>(); + for (Clone c : CUtils.it(result[i].mkElementsPort())) + downsampled.add(c); + + ClonotypeDataset r = datasets.get(i); + clnsWriter.writeHeader(null, + r.getAlignerParameters(), r.getAssemblerParameters(), + r.ordering(), r.getUsedGenes(), r.getAlignerParameters(), downsampled.size()); + + CUtils.drain(CUtils.asOutputPort(downsampled), clnsWriter.cloneWriter()); + } + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index 0d97a759d..92e9ba515 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.cli.postanalysis; import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; @@ -183,6 +184,11 @@ public List getUsedGenes() { public VDJCAlignerParameters getAlignerParameters() { return inner.getAlignerParameters(); } + + @Override + public CloneAssemblerParameters getAssemblerParameters() { + return inner.getAssemblerParameters(); + } }; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index 0a3cd07ba..62522b28f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -6,6 +6,7 @@ import com.milaboratory.mixcr.util.OutputPortWithProgress; import gnu.trove.map.hash.TIntObjectHashMap; +import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; import java.util.stream.IntStream; @@ -26,24 +27,29 @@ public interface SetPreprocessor { /** Id from {@link SetPreprocessorFactory#id()} */ String id(); - @SuppressWarnings("unchecked") + @SafeVarargs static Dataset[] processDatasets(SetPreprocessor proc, Dataset... initial) { + return processDatasets(proc, Arrays.asList(initial)); + } + + @SuppressWarnings("unchecked") + static Dataset[] processDatasets(SetPreprocessor proc, List> initial) { while (true) { SetPreprocessorSetup setup = proc.nextSetupStep(); if (setup == null) { - Dataset[] result = new Dataset[initial.length]; - for (int i = 0; i < initial.length; i++) { + Dataset[] result = new Dataset[initial.size()]; + for (int i = 0; i < initial.size(); i++) { int datasetIdx = i; MappingFunction mapper = proc.getMapper(datasetIdx); result[i] = new Dataset() { @Override public String id() { - return initial[datasetIdx].id(); + return initial.get(datasetIdx).id(); } @Override public OutputPortWithProgress mkElementsPort() { - OutputPortWithProgress inner = initial[datasetIdx].mkElementsPort(); + OutputPortWithProgress inner = initial.get(datasetIdx).mkElementsPort(); return new OutputPortWithProgress() { @Override public double getProgress() { @@ -84,14 +90,14 @@ public T take() { } return result; } - setup.initialize(initial.length); + setup.initialize(initial.size()); - List> consumers = IntStream.range(0, initial.length) + List> consumers = IntStream.range(0, initial.size()) .mapToObj(setup::consumer) .collect(Collectors.toList()); - for (int i = 0; i < initial.length; i++) { - try (OutputPortCloseable port = initial[i].mkElementsPort()) { + for (int i = 0; i < initial.size(); i++) { + try (OutputPortCloseable port = initial.get(i).mkElementsPort()) { for (T t : CUtils.it(port)) { consumers.get(i).put(t); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index 40723661b..dac1a1dff 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -31,9 +31,18 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; +import io.repseq.core.GeneFeature; import org.apache.commons.math3.random.RandomGenerator; +import java.util.ArrayList; +import java.util.List; import java.util.function.ToLongFunction; import java.util.stream.LongStream; @@ -63,4 +72,36 @@ public static long[] downsample_counts(long[] counts, long downSampleSize, Rando RandomMvhgCounts.random_multivariate_hypergeometric_count(rnd, total, counts, downSampleSize, result); return result; } + + public static SetPreprocessorFactory parseDownsampling(String downsampling, boolean dropOutliers, long seed) { + if (downsampling.equalsIgnoreCase("no-downsampling")) { + return new NoPreprocessing.Factory<>(); + } else if (downsampling.startsWith("umi-count")) { + if (downsampling.endsWith("auto")) + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), seed, dropOutliers); + else { + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), seed, dropOutliers); + } + } else { + int value = downsamplingValue(downsampling); + if (downsampling.startsWith("cumulative-top")) { + return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); + } else if (downsampling.startsWith("top")) { + return new SelectTop.Factory<>(WeightFunctions.Count, value); + } else { + throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); + } + } + } + + public static SetPreprocessorFactory filterOnlyProductive(SetPreprocessorFactory p) { + List> filters = new ArrayList<>(); + filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); + filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); + return p.filterFirst(filters); + } + + private static int downsamplingValue(String downsampling) { + return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java index 51db885f7..95aaf7581 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java @@ -1,21 +1,27 @@ package com.milaboratory.mixcr.postanalysis.ui; +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneReader; import com.milaboratory.mixcr.basictypes.CloneSetIO; +import com.milaboratory.mixcr.basictypes.VDJCSProperties; import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.util.OutputPortWithProgress; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.LambdaSemaphore; +import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; import java.io.IOException; import java.nio.file.Path; import java.nio.file.Paths; +import java.util.List; /** * */ -public class ClonotypeDataset implements Dataset { +public class ClonotypeDataset implements Dataset, CloneReader { final String id; final Path path; final VDJCLibraryRegistry registry; @@ -45,13 +51,55 @@ public String id() { return id; } + private volatile CloneReader reader; + @Override public OutputPortWithProgress mkElementsPort() { - try { - CloneReader reader = CloneSetIO.mkReader(path, registry, concurrencyLimiter); - return OutputPortWithProgress.wrap(reader.numberOfClones(), reader.readClones()); - } catch (IOException e) { - throw new RuntimeException(e); + if (reader == null) { + synchronized (this) { + if (reader == null) + try { + reader = CloneSetIO.mkReader(path, registry, concurrencyLimiter); + } catch (IOException e) { + throw new RuntimeException(e); + } + } } + return OutputPortWithProgress.wrap(reader.numberOfClones(), reader.readClones()); + } + + @Override + public VDJCSProperties.CloneOrdering ordering() { + return reader.ordering(); + } + + @Override + public OutputPortCloseable readClones() { + return mkElementsPort(); + } + + @Override + public int numberOfClones() { + return reader.numberOfClones(); + } + + @Override + public List getUsedGenes() { + return reader.getUsedGenes(); + } + + @Override + public VDJCAlignerParameters getAlignerParameters() { + return reader.getAlignerParameters(); + } + + @Override + public void close() throws Exception { + reader.close(); + } + + @Override + public CloneAssemblerParameters getAssemblerParameters() { + return reader.getAssemblerParameters(); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java index 8b83b0810..c69ae8c02 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java @@ -5,16 +5,10 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.Characteristic; import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.WeightFunctions; -import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; -import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; -import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; -import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; import com.milaboratory.primitivio.annotations.Serializable; -import io.repseq.core.GeneFeature; import java.util.*; import java.util.function.BiFunction; @@ -26,10 +20,11 @@ getterVisibility = JsonAutoDetect.Visibility.NONE) @JsonIgnoreProperties(ignoreUnknown = false) @Serializable(asJson = true) -public abstract class PostanalysisParameters { +public abstract class PostanalysisParameters { public String defaultDownsampling; public boolean defaultOnlyProductive; public boolean defaultDropOutliers; + public long randomSeed; @JsonAutoDetect( fieldVisibility = JsonAutoDetect.Visibility.ANY, @@ -39,46 +34,27 @@ public static class PreprocessorParameters { public String downsampling; public Boolean onlyProductive; public Boolean dropOutliers; - public Long seed; + public Long randomSeed; - public SetPreprocessorFactory preproc(PostanalysisParameters base) { + public SetPreprocessorFactory preproc(PostanalysisParameters base) { SetPreprocessorFactory p = parseDownsampling(base); boolean onlyProductive = this.onlyProductive == null ? base.defaultOnlyProductive : this.onlyProductive; - if (onlyProductive) { - List> filters = new ArrayList<>(); - filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); - filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); - p = p.filterFirst(filters); - } + if (onlyProductive) + p = DownsamplingUtil.filterOnlyProductive(p); return p; } - public SetPreprocessorFactory> overlapPreproc(PostanalysisParameters base) { + public SetPreprocessorFactory> overlapPreproc(PostanalysisParameters base) { return new OverlapPreprocessorAdapter.Factory<>(preproc(base)); } - SetPreprocessorFactory parseDownsampling(PostanalysisParameters base) { - String downsampling = this.downsampling == null ? base.defaultDownsampling : this.downsampling; - boolean dropOutliers = this.dropOutliers == null ? base.defaultDropOutliers : this.dropOutliers; - if (downsampling.equalsIgnoreCase("no-downsampling")) { - return new NoPreprocessing.Factory<>(); - } else if (downsampling.startsWith("umi-count")) { - if (downsampling.endsWith("auto")) - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314, dropOutliers); - else { - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), 314, dropOutliers); - } - } else { - int value = downsamplingValue(downsampling); - if (downsampling.startsWith("cumulative-top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); - } else if (downsampling.startsWith("top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, value); - } else { - throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); - } - } + SetPreprocessorFactory parseDownsampling(PostanalysisParameters base) { + return DownsamplingUtil.parseDownsampling( + this.downsampling == null ? base.defaultDownsampling : this.downsampling, + this.dropOutliers == null ? base.defaultDropOutliers : this.dropOutliers, + this.randomSeed == null ? base.randomSeed : this.randomSeed + ); } @Override @@ -95,12 +71,7 @@ public int hashCode() { } } - private static int downsamplingValue(String downsampling) { - return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); - } - - static List> groupByPreproc(PostanalysisParameters base, - Map> preprocs, + static List> groupByPreproc(Map> preprocs, BiFunction, List, List>> factory) { Map, List> byPreproc = preprocs.entrySet().stream() diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java index 4d01df57f..2954a442f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java @@ -22,7 +22,7 @@ import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.*; @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") -public class PostanalysisParametersIndividual extends PostanalysisParameters { +public class PostanalysisParametersIndividual extends PostanalysisParameters { public static final String Biophysics = "biophysics", Diversity = "diversity", @@ -99,7 +99,7 @@ public static class BiophysicsParameters { public PreprocessorParameters Volume = new PreprocessorParameters(); public PreprocessorParameters Charge = new PreprocessorParameters(); - public CharacteristicGroup getGroup(PostanalysisParameters base) { + public CharacteristicGroup getGroup(PostanalysisParameters base) { return new CharacteristicGroup<>(Biophysics, Arrays.asList( weightedLengthOf(cdr3lenNT.preproc(base), GeneFeature.CDR3, false).setName("CDR3 length, nt"), @@ -142,9 +142,8 @@ public static class DiversityParameters { public PreprocessorParameters gini = new PreprocessorParameters(); public PreprocessorParameters d50 = new PreprocessorParameters(); - public CharacteristicGroup getGroup(PostanalysisParameters base) { + public CharacteristicGroup getGroup(PostanalysisParameters base) { List> chars = new ArrayList<>(groupByPreproc( - base, new HashMap>() {{ put(DiversityMeasure.Observed, observed.preproc(base)); put(DiversityMeasure.ShannonWeiner, shannonWeiner.preproc(base)); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java index e829cd6c3..8ecccc442 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java @@ -12,7 +12,7 @@ import java.util.stream.Collectors; @SuppressWarnings("ArraysAsListWithZeroOrOneArgument") -public class PostanalysisParametersOverlap extends PostanalysisParameters> { +public class PostanalysisParametersOverlap extends PostanalysisParameters { public static final String Overlap = "Overlap"; public PreprocessorParameters d = new PreprocessorParameters(); @@ -25,7 +25,8 @@ public class PostanalysisParametersOverlap extends PostanalysisParameters>> getGroups(int nSamples) { PostanalysisParametersOverlap base = this; - List>> chars = groupByPreproc(this, new HashMap>>() {{ + List>> chars = groupByPreproc( + new HashMap>>() {{ put(OverlapType.D, d.overlapPreproc(base)); put(OverlapType.SharedClonotypes, sharedClonotypes.overlapPreproc(base)); put(OverlapType.F1, f1.overlapPreproc(base)); diff --git a/src/main/resources/parameters/postanalysis_individual.json b/src/main/resources/parameters/postanalysis_individual.json index b18ee72e3..2b95ee37d 100644 --- a/src/main/resources/parameters/postanalysis_individual.json +++ b/src/main/resources/parameters/postanalysis_individual.json @@ -3,6 +3,7 @@ "defaultDownsampling": null, "defaultOnlyProductive": true, "defaultDropOutliers": false, + "randomSeed": 111, "biophysics": { "cdr3lenAA": { "downsampling": null, diff --git a/src/main/resources/parameters/postanalysis_overlap.json b/src/main/resources/parameters/postanalysis_overlap.json index 75dfb2298..37be8c767 100644 --- a/src/main/resources/parameters/postanalysis_overlap.json +++ b/src/main/resources/parameters/postanalysis_overlap.json @@ -3,6 +3,7 @@ "defaultDownsampling": null, "defaultOnlyProductive": false, "defaultDropOutliers": false, + "randomSeed": 111, "d": { "downsampling": null, "onlyProductive": null, From 1be9f4be595bd316ec1429409e5befd5673fe184 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 25 May 2022 02:12:26 +0300 Subject: [PATCH 221/282] chore: repseqio upgrade; library inside upgraded to v2.0 --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 4ce5988d4..33a606ab5 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -79,7 +79,7 @@ repositories { } val milibVersion = "1.15.0-42-master" -val repseqioVersion = "1.3.5-29-master" +val repseqioVersion = "1.3.5-30-master" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" From 4633435fedc06cdb6af4631b027f89385eab15ed Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 25 May 2022 02:58:05 +0300 Subject: [PATCH 222/282] fix: expected values in regression tests (itest8 and itest9) adjusted because of a new reference library --- itests/case8.sh | 6 +++--- itests/case9.sh | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/itests/case8.sh b/itests/case8.sh index 3f767f33d..d258d2830 100755 --- a/itests/case8.sh +++ b/itests/case8.sh @@ -23,9 +23,9 @@ mixcr analyze amplicon \ --impute-germline-on-export --json-report case8 \ CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case8 -assert "cat case8.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197642" -assert "cat case8.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161771" +assert "cat case8.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "198684" +assert "cat case8.assemble.jsonl | head -n 1 | jq -r .readsInClones" "162731" assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "227" assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "978" assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" -assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22384" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22477" diff --git a/itests/case9.sh b/itests/case9.sh index b650f934a..7365c1825 100755 --- a/itests/case9.sh +++ b/itests/case9.sh @@ -24,9 +24,9 @@ mixcr analyze amplicon \ --impute-germline-on-export --json-report case9 \ CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case9 -assert "cat case9.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "197642" -assert "cat case9.assemble.jsonl | head -n 1 | jq -r .readsInClones" "161771" +assert "cat case9.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "198684" +assert "cat case9.assemble.jsonl | head -n 1 | jq -r .readsInClones" "162731" assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "227" assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "978" assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" -assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22384" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22477" From 018bc7a1bacfb3337968adee229584a2a02fc4ba Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 25 May 2022 16:14:08 +0200 Subject: [PATCH 223/282] feat(PA): Polish CLI docs. --- .../java/com/milaboratory/mixcr/cli/Main.java | 3 +- .../mixcr/cli/postanalysis/CommandPa.java | 36 +++++++--- .../cli/postanalysis/CommandPaExport.java | 51 +++++++++++---- .../postanalysis/CommandPaExportPlots.java | 28 +++----- .../CommandPaExportPlotsBasicStatistics.java | 65 +++++++++++++------ .../CommandPaExportPlotsGeneUsage.java | 14 ++-- .../CommandPaExportPlotsHeatmap.java | 1 + .../CommandPaExportPlotsOverlap.java | 12 ++-- .../CommandPaExportPlotsVJUsage.java | 8 ++- .../postanalysis/CommandPaExportTables.java | 3 +- .../cli/postanalysis/CommandPaIndividual.java | 2 +- .../downsampling/DownsamplingUtil.java | 2 + .../postanalysis/plots/BasicStatistics.kt | 8 +-- .../mixcr/postanalysis/plots/Metadata.kt | 2 +- 14 files changed, 153 insertions(+), 82 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 708ad3ab2..fdbba922d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -30,10 +30,10 @@ package com.milaboratory.mixcr.cli; import com.milaboratory.cli.ValidationException; -import com.milaboratory.mixcr.cli.postanalysis.*; import com.milaboratory.milm.LM; import com.milaboratory.milm.LicenseError; import com.milaboratory.milm.LicenseErrorType; +import com.milaboratory.mixcr.cli.postanalysis.*; import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.VersionInfo; @@ -225,6 +225,7 @@ public static CommandLine mkCmd() { .setCommandName(command) .addSubcommand("help", CommandLine.HelpCommand.class) .addSubcommand("analyze", CommandAnalyze.CommandAnalyzeMain.class) + .addSubcommand("postanalysis", CommandPa.CommandPostanalysisMain.class) .addSubcommand("downsample", CommandDownsample.class) .addSubcommand("exportPlots", CommandPaExportPlots.CommandExportPlotsMain.class) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 93df69da9..4cf13a9cd 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; import com.milaboratory.util.StringUtil; import io.repseq.core.Chains; import picocli.CommandLine; @@ -26,29 +27,29 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { @Parameters(description = "cloneset.{clns|clna}... result.json.gz|result.json") public List inOut; - @Option(description = "Use only productive CDR3s.", + @Option(description = "Filter out-of-frame sequences and clonotypes with stop-codons", names = {"--only-productive"}) public boolean onlyProductive = false; - @Option(description = "Drop outliers.", + @Option(description = "Drop samples which have less abundance than the computed downsampling threshold.", names = {"--drop-outliers"}) public boolean dropOutliers = false; - @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", + @Option(description = "Default downsampling. Possible values: umi-count-[1000|auto|min]|cumulative-top-[percent]|top-[number]|no-downsampling", names = {"--default-downsampling"}, required = true) public String defaultDownsampling; - @Option(description = "Filter specific chains", - names = {"-c", "--chains"}) + @Option(description = "Filter specified chains", + names = {"--chains"}) public String chains = "ALL"; @Option(description = "Metadata file (csv/tsv). Must have \"sample\" column.", - names = {"-m", "--meta", "--metadata"}) + names = {"--metadata"}) public String metadata; @Option(description = "Metadata categories used to isolate samples into separate groups", - names = {"-g", "--group"}) + names = {"--group"}) public List isolationGroups; @Option(description = "Tabular results output path (path/table.tsv).", @@ -88,10 +89,27 @@ protected List getOutputFiles() { @Override public void validate() { super.validate(); - if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) - throwValidationException("Metadata should be .csv or .tsv"); if (!out().endsWith(".json") && !out().endsWith(".json.gz")) throwValidationException("Output file name should ends with .json.gz or .json"); + try { + DownsamplingUtil.parseDownsampling(defaultDownsampling, dropOutliers, 0); + } catch (Throwable t) { + throwValidationException("Illegal downsampling string: " + defaultDownsampling); + } + if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) + throwValidationException("Metadata should be .csv or .tsv"); + if (metadata != null) { + if (!metadata().containsKey("sample")) + throwValidationException("Metadata must contain 'sample' column"); + List samples = getInputFiles(); + Map mapping = StringUtil.matchLists( + samples, + metadata().get("sample").stream() + .map(Object::toString).collect(toList()) + ); + if (mapping.size() < samples.size() || mapping.values().stream().anyMatch(Objects::isNull)) + throwValidationException("Metadata samples does not match input file names."); + } } private String outBase() { diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java index 69c29646c..efc6706ce 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java @@ -1,32 +1,34 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.postanalysis.plots.MetadataKt; +import com.milaboratory.util.StringUtil; import io.repseq.core.Chains; import io.repseq.core.Chains.NamedChains; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import org.jetbrains.kotlinx.dataframe.api.DataFrameIterableKt; import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; import java.nio.file.Paths; -import java.util.Collections; -import java.util.List; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; +import static java.util.stream.Collectors.toList; + /** * */ public abstract class CommandPaExport extends ACommandWithOutputMiXCR { - @Parameters(description = "Input file with PA results", index = "0", defaultValue = "pa.json.gz") + @Parameters(description = "Input file with postanalysis results.", index = "0", defaultValue = "pa.json.gz") public String in; - @Option(description = "Metadata file (csv/tsv).", - names = {"-m", "--meta", "--metadata"}) + @Option(description = "Metadata file (csv/tsv). Must have 'sample' column.", + names = {"--metadata"}) public String metadata; @Option(description = "Export for specific chains only", names = {"--chains"}) public List chains; - /** - * Cached PA result - */ + /** Cached PA result */ private PaResult paResult = null; public CommandPaExport() {} @@ -41,14 +43,39 @@ protected List getInputFiles() { return Collections.singletonList(in); } + private DataFrame metadataDf; + + /** Get metadata from file */ + protected DataFrame metadata() { + if (metadataDf != null) + return metadataDf; + if (metadata != null) + return metadataDf = MetadataKt.readMetadata(metadata); + if (getPaResult().metadata != null) + return metadataDf = DataFrameIterableKt.toDataFrame(getPaResult().metadata); + return null; + } + @Override - public void validateInfo(String inputFile) { - super.validateInfo(inputFile); + public void validate() { + super.validate(); if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) throwValidationException("Metadata should be .csv or .tsv"); + if (metadata != null) { + if (!metadata().containsColumn("sample")) + throwValidationException("Metadata must contain 'sample' column"); + List samples = getInputFiles(); + @SuppressWarnings("unchecked") + Map mapping = StringUtil.matchLists( + samples, + ((List) metadata().get("sample").toList()) + .stream().map(Object::toString).collect(toList()) + ); + if (mapping.size() < samples.size() || mapping.values().stream().anyMatch(Objects::isNull)) + throwValidationException("Metadata samples does not match input file names."); + } } - /** * Get full PA result */ diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java index 5899999a4..07df531a0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java @@ -5,7 +5,6 @@ import com.milaboratory.mixcr.postanalysis.plots.MetadataKt; import jetbrains.letsPlot.intern.Plot; import org.jetbrains.kotlinx.dataframe.DataFrame; -import org.jetbrains.kotlinx.dataframe.api.DataFrameIterableKt; import picocli.CommandLine; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -22,13 +21,18 @@ separator = " ", description = "Export postanalysis plots.") public abstract class CommandPaExportPlots extends CommandPaExport { - @Option(description = "Plot width", names = {"--width"}) + @Option(description = "Plot width", + names = {"--width"}) public int width = 0; - @Option(description = "Plot height", names = {"--height"}) + + @Option(description = "Plot height", + names = {"--height"}) public int height = 0; + @Option(description = "Filter by metadata. Possible filters column=value, column>=value etc.", names = {"--filter"}) public List filterByMetadata; + @Parameters(description = "Output PDF file name", index = "1", defaultValue = "plot.pdf") public String out; @@ -48,19 +52,6 @@ public void validate() { throwValidationException("Filter is specified by metadata is not."); } - private DataFrame metadataDf; - - /** Get metadata from file */ - protected DataFrame metadata() { - if (metadataDf != null) - return metadataDf; - if (metadata != null) - return metadataDf = MetadataKt.readMetadata(metadata); - if (getPaResult().metadata != null) - return metadataDf = DataFrameIterableKt.toDataFrame(getPaResult().metadata); - return null; - } - String plotDestStr(IsolationGroup group) { return out.substring(0, out.length() - 4) + group.extension() + ".pdf"; } @@ -92,10 +83,9 @@ void writePlots(IsolationGroup group, Plot plot) { ExportKt.writePDF(plotDestPath(group), plot); } - - @CommandLine.Command(name = "exportPlots", + @Command(name = "exportPlots", separator = " ", - description = "Export postanalysis results.", + description = "Export postanalysis plots.", subcommands = { CommandLine.HelpCommand.class }) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index 7ac34e849..eecd5ae85 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -12,42 +12,67 @@ import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import org.jetbrains.kotlinx.dataframe.DataFrame; -import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.util.List; import java.util.Objects; public abstract class CommandPaExportPlotsBasicStatistics extends CommandPaExportPlots { - abstract String group(); - - @Option(description = "Plot type", names = {"--plot-type"}) + @Option(description = "Plot type. Possible values: auto, boxplot, barplot, dotplot, lineplot, scatter.", + names = {"--plot-type"}) public String plotType; - @Option(description = "Primary group", names = {"-p", "--primary-group"}) + + @Option(description = "Primary group", + names = {"-p", "--primary-group"}) public String primaryGroup; - @Option(description = "Secondary group", names = {"-s", "--secondary-group"}) + + @Option(description = "Secondary group", + names = {"-s", "--secondary-group"}) public String secondaryGroup; - @Option(description = "Facet by", names = {"--facet-by"}) + + @Option(description = "Facet by", + names = {"--facet-by"}) public String facetBy; - @Option(description = "Select specific metrics to export.", names = {"--metric"}) + + @Option(description = "Select specific metrics to export.", + names = {"--metric"}) public List metrics; - @Option(description = "Hide overall p-value.", names = {"--hide-overall-p-value"}) + + @Option(description = "Hide overall p-value", + names = {"--hide-overall-p-value"}) public boolean hideOverallPValue; - @Option(description = "Hide pairwise p-values.", names = {"--hide-pairwise-p-value"}) + + @Option(description = "Hide pairwise p-values", + names = {"--hide-pairwise-p-value"}) public boolean hidePairwisePValue; - @Option(description = "Reference group. Can be \"all\" or some specific value.", names = {"--ref-group"}) + + @Option(description = "Reference group. Can be \"all\" or some specific value.", + names = {"--ref-group"}) public String refGroup; - @Option(description = "Hide non-significant observations.", names = {"--hide-ns"}) + + @Option(description = "Hide non-significant observations", + names = {"--hide-ns"}) public boolean hideNS; - @Option(description = "Do paired analysis.", names = {"--paired"}) + + @Option(description = "Do paired analysis", + names = {"--paired"}) public boolean paired; - @Option(description = "Test method. Default is Wilcoxon. Available methods: Wilcoxon, ANOVA, TTest, KruskalWallis, KolmogorovSmirnov", names = {"--method"}) + + @Option(description = "Test method. Default is Wilcoxon. Available methods: Wilcoxon, ANOVA, TTest, KruskalWallis, KolmogorovSmirnov", + names = {"--method"}) public String method = "Wilcoxon"; - @Option(description = "Test method for multiple groups comparison. Default is KruskalWallis. Available methods: ANOVA, KruskalWallis, KolmogorovSmirnov", names = {"--method-multiple-groups"}) + + @Option(description = "Test method for multiple groups comparison. Default is KruskalWallis. Available methods: ANOVA, KruskalWallis, KolmogorovSmirnov", + names = {"--method-multiple-groups"}) public String methodForMultipleGroups = "KruskalWallis"; - @Option(description = "Test method for multiple groups comparison. Default is KruskalWallis. Available methods: none, BenjaminiHochberg, BenjaminiYekutieli, Bonferroni, Hochberg, Holm, Hommel", names = {"--p-adjust-method"}) + + @Option(description = "Method used to adjust p-values. Default is Holm. Available methods: none, BenjaminiHochberg, BenjaminiYekutieli, Bonferroni, Hochberg, Holm, Hommel", + names = {"--p-adjust-method"}) public String pAdjustMethod = "Holm"; + abstract String group(); + @Override void run(PaResultByGroup result) { CharacteristicGroup ch = result.schema.getGroup(group()); @@ -94,10 +119,10 @@ else if (refGroup != null) writePlotsAndSummary(result.group, plots); } - @CommandLine.Command(name = "biophysics", + @Command(name = "biophysics", sortOptions = false, separator = " ", - description = "Export biophysical characteristics") + description = "Export biophysics metrics") public static class ExportBiophysics extends CommandPaExportPlotsBasicStatistics { @Override String group() { @@ -105,10 +130,10 @@ String group() { } } - @CommandLine.Command(name = "diversity", + @Command(name = "diversity", sortOptions = false, separator = " ", - description = "Export diversity characteristics") + description = "Export diversity metrics") public static class ExportDiversity extends CommandPaExportPlotsBasicStatistics { @Override String group() { diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java index d679b4388..a10d63637 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java @@ -10,7 +10,7 @@ import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import org.jetbrains.kotlinx.dataframe.DataFrame; -import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.util.ArrayList; @@ -20,12 +20,14 @@ public abstract class CommandPaExportPlotsGeneUsage extends CommandPaExportPlotsHeatmapWithGroupBy { abstract String group(); - @Option(description = "Do not plot dendrogram for hierarchical clusterization of samples.", + @Option(description = "Don't add samples dendrogram.", names = {"--no-samples-dendro"}) public boolean noSamplesDendro; - @Option(description = "Do not plot dendrogram for hierarchical clusterization of genes.", + + @Option(description = "Don't add genes dendrogram.", names = {"--no-genes-dendro"}) public boolean noGenesDendro; + @Option(description = "Add color key layer.", names = {"--color-key"}) public List colorKey = new ArrayList<>(); @@ -60,7 +62,7 @@ void run(PaResultByGroup result) { writePlotsAndSummary(result.group, plot); } - @CommandLine.Command(name = "vUsage", + @Command(name = "vUsage", sortOptions = false, separator = " ", description = "Export V gene usage heatmap") @@ -71,7 +73,7 @@ String group() { } } - @CommandLine.Command(name = "jUsage", + @Command(name = "jUsage", sortOptions = false, separator = " ", description = "Export J gene usage heatmap") @@ -82,7 +84,7 @@ String group() { } } - @CommandLine.Command(name = "isotypeUsage", + @Command(name = "isotypeUsage", sortOptions = false, separator = " ", description = "Export isotype usage heatmap") diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java index 535115d63..c82f3efc2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java @@ -6,6 +6,7 @@ public abstract class CommandPaExportPlotsHeatmap extends CommandPaExportPlots { @Option(description = "Width of horizontal labels. One unit corresponds to the width of one tile.", names = {"--h-labels-size"}) public double hLabelsSize = -1.0; + @Option(description = "Height of vertical labels. One unit corresponds to the height of one tile.", names = {"--v-labels-size"}) public double vLabelsSize = -1.0; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java index 072182390..d699287af 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -7,24 +7,26 @@ import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersOverlap; import org.jetbrains.kotlinx.dataframe.DataFrame; -import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.util.ArrayList; import java.util.List; import java.util.stream.Collectors; -@CommandLine.Command(name = "overlap", +@Command(name = "overlap", sortOptions = false, separator = " ", - description = "Export overlap heatmap") + description = "Export overlap heatmaps") public class CommandPaExportPlotsOverlap extends CommandPaExportPlotsHeatmapWithGroupBy { - @Option(description = "Plot dendrogram for hierarchical clusterization of V genes.", + @Option(description = "Don't add dendrograms", names = {"--no-dendro"}) public boolean noDendro; - @Option(description = "Add color key layer.", + + @Option(description = "Add color key layer; prefix 'x_' (add to the bottom) or 'y_' (add to the left) should be used.", names = {"--color-key"}) public List colorKey = new ArrayList<>(); + @Option(description = "Select specific metrics to export.", names = {"--metric"}) public List metrics; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java index 9664bde3b..ca338fcb8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java @@ -20,9 +20,11 @@ description = "Export V-J usage heatmap", hidden = true) public class CommandPaExportPlotsVJUsage extends CommandPaExportPlotsHeatmap { - @Option(description = "Plot dendrogram for hierarchical clusterization of V genes.", names = {"--no-v-dendro"}) + @Option(description = "Don't add V genes dendrogram", + names = {"--no-v-dendro"}) public boolean noVDendro; - @Option(description = "Plot dendrogram for hierarchical clusterization of genes.", names = {"--no-j-dendro"}) + @Option(description = "Don't add J genes dendrogram", + names = {"--no-j-dendro"}) public boolean noJDendro; @Override @@ -47,7 +49,7 @@ void run(PaResultByGroup result) { null, hLabelsSize, vLabelsSize, - true, + false, width, height )); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java index ae1ce481e..f07920329 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java @@ -5,8 +5,9 @@ import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroupResult; import com.milaboratory.mixcr.postanalysis.ui.OutputTable; import picocli.CommandLine; +import picocli.CommandLine.Command; -@CommandLine.Command(name = "exportTables", +@Command(name = "exportTables", sortOptions = false, separator = " ", description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype, Overlap") diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index 08c50a569..8f7945340 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -17,7 +17,7 @@ @Command(name = "individual", sortOptions = false, separator = " ", - description = "Biophysics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype") + description = "Run postanalysis for biophysics, diversity, V/J/VJ-usage, CDR3/V-Spectratype metrics") public class CommandPaIndividual extends CommandPa { public CommandPaIndividual() {} diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index dac1a1dff..827e62e3c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -79,6 +79,8 @@ public static SetPreprocessorFactory parseDownsampling(String downsamplin } else if (downsampling.startsWith("umi-count")) { if (downsampling.endsWith("auto")) return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), seed, dropOutliers); + else if (downsampling.endsWith("min")) + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Minimal(), seed, dropOutliers); else { return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), seed, dropOutliers); } diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt index 45cb3b75c..b8e5150f5 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt @@ -124,13 +124,13 @@ object BasicStatistics { } } - private fun isCategorial(t: PlotType) = when (t) { + private fun isCategorical(t: PlotType) = when (t) { Scatter, LinePlot -> false else -> true } private fun guessPlotType(par: PlotParameters, meta: Metadata?) = - if (par.primaryGroup == null || meta == null || meta.isCategorial(par.primaryGroup)) + if (par.primaryGroup == null || meta == null || meta.isCategorical(par.primaryGroup)) BoxPlot else Scatter @@ -185,7 +185,7 @@ object BasicStatistics { val type = if (par.plotType == Auto) guessPlotType(par, df) else par.plotType val dfRefined = ( - if (isCategorial(type)) { + if (isCategorical(type)) { if (par.primaryGroup == null) df.add(List(df.rowsCount()) { "" }.toColumn("__x__")) else if (df.isNumeric(par.primaryGroup) || (par.secondaryGroup != null && df.isNumeric(par.secondaryGroup))) { @@ -197,7 +197,7 @@ object BasicStatistics { } ) - if (isCategorial(type)) { + if (isCategorical(type)) { val plt = when (type) { BoxPlot -> GGBoxPlot( dfRefined, diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt index ea6618505..6400cb1c2 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt @@ -9,7 +9,7 @@ import org.jetbrains.kotlinx.dataframe.io.read import org.jetbrains.kotlinx.dataframe.io.readTSV fun AnyFrame.isNumeric(col: String) = this[col].all { it == null || it is Number } -fun AnyFrame.isCategorial(col: String) = !isNumeric(col) +fun AnyFrame.isCategorical(col: String) = !isNumeric(col) typealias Metadata = AnyFrame From 48abb139db4ba549e002058f0781db9b9403688d Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 25 May 2022 19:47:05 +0300 Subject: [PATCH 224/282] chore: milib upgrade --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 33a606ab5..32de59ea2 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -78,7 +78,7 @@ repositories { } } -val milibVersion = "1.15.0-42-master" +val milibVersion = "1.15.0-44-master" val repseqioVersion = "1.3.5-30-master" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" From bf675e446377404648a9175e7c74d1cb2a335838 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 26 May 2022 00:16:48 +0300 Subject: [PATCH 225/282] fixes after merge --- .../java/com/milaboratory/mixcr/basictypes/CloneReader.java | 3 +++ .../mixcr/cli/postanalysis/CommandDownsample.java | 2 +- .../mixcr/cli/postanalysis/CommandPaOverlap.java | 6 ++++++ .../mixcr/postanalysis/ui/ClonotypeDataset.java | 6 ++++++ 4 files changed, 16 insertions(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java index f62d11ba0..a726aefd6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -31,6 +31,7 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.VDJCGene; @@ -48,6 +49,8 @@ public interface CloneReader extends AutoCloseable { int numberOfClones(); + TagsInfo getTagsInfo(); + List getUsedGenes(); VDJCAlignerParameters getAlignerParameters(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java index bae0450b1..ab4ae6b60 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java @@ -103,7 +103,7 @@ public void run0() throws Exception { ClonotypeDataset r = datasets.get(i); clnsWriter.writeHeader(null, r.getAlignerParameters(), r.getAssemblerParameters(), - r.ordering(), r.getUsedGenes(), r.getAlignerParameters(), downsampled.size()); + r.getTagsInfo(), r.ordering(), r.getUsedGenes(), r.getAlignerParameters(), downsampled.size()); CUtils.drain(CUtils.asOutputPort(downsampled), clnsWriter.cloneWriter()); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index 92e9ba515..2139f6f0b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -3,6 +3,7 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; import com.milaboratory.mixcr.postanalysis.WeightFunctions; @@ -180,6 +181,11 @@ public List getUsedGenes() { return inner.getUsedGenes(); } + @Override + public TagsInfo getTagsInfo() { + return inner.getTagsInfo(); + } + @Override public VDJCAlignerParameters getAlignerParameters() { return inner.getAlignerParameters(); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java index 95aaf7581..9ad8a1586 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java @@ -6,6 +6,7 @@ import com.milaboratory.mixcr.basictypes.CloneReader; import com.milaboratory.mixcr.basictypes.CloneSetIO; import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; @@ -88,6 +89,11 @@ public List getUsedGenes() { return reader.getUsedGenes(); } + @Override + public TagsInfo getTagsInfo() { + return reader.getTagsInfo(); + } + @Override public VDJCAlignerParameters getAlignerParameters() { return reader.getAlignerParameters(); From 3b0bf4b1acc7f6b8ade6f8388b708368c0f009b6 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 26 May 2022 06:56:15 +0300 Subject: [PATCH 226/282] refactor: VDJCGeneScoreAccumulator factored out --- build.gradle.kts | 2 +- .../mixcr/assembler/CloneAccumulator.java | 87 ++-------------- .../mixcr/assembler/CloneAssembler.java | 34 ++----- .../mixcr/assembler/CloneFactory.java | 4 +- .../assembler/CloneFactoryParameters.java | 11 ++- .../assembler/VDJCGeneScoreAccumulator.java | 99 +++++++++++++++++++ .../mixcr/basictypes/HasRelativeMinScore.java | 7 ++ 7 files changed, 134 insertions(+), 110 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneScoreAccumulator.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java diff --git a/build.gradle.kts b/build.gradle.kts index d3cd82a45..5076d01a2 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -83,7 +83,7 @@ repositories { val milibVersion = "1.15.0-44-master" val repseqioVersion = "1.3.5-30-master" -val mitoolVersion = "0.9.1-7-main" +val mitoolVersion = "0.9.1-10-main" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index a2fdcca69..22d700ec5 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -37,18 +37,13 @@ import com.milaboratory.core.sequence.quality.QualityAggregationType; import com.milaboratory.core.sequence.quality.QualityAggregator; import com.milaboratory.mixcr.basictypes.ClonalSequence; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCHit; -import gnu.trove.iterator.TObjectFloatIterator; -import gnu.trove.map.hash.TObjectFloatHashMap; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; -import java.util.EnumMap; - public final class CloneAccumulator { - final EnumMap> geneScores = new EnumMap<>(GeneType.class); + final VDJCGeneScoreAccumulator geneScoreAccumulator = new VDJCGeneScoreAccumulator(); private ClonalSequence sequence; private final QualityAggregator aggregator; private long coreCount = 0, mappedCount = 0, initialCoreCount = -1; @@ -77,7 +72,6 @@ public void rebuildClonalSequence() { pointer += s.size(); } sequence = new ClonalSequence(updated); - return; } public void onBeforeMapping() { @@ -85,34 +79,13 @@ public void onBeforeMapping() { } public float getBestScore(GeneType geneType) { - TObjectFloatHashMap scores = geneScores.get(geneType); - if (scores == null) - return 0; - float maxScore = 0; - TObjectFloatIterator iterator = scores.iterator(); - while (iterator.hasNext()) { - iterator.advance(); - if (maxScore < iterator.value()) - maxScore = iterator.value(); - } - return maxScore; + VDJCGeneScoreAccumulator.GeneAndScore bestGene = geneScoreAccumulator.getBestGene(geneType); + return bestGene == null ? 0 : bestGene.score; } public VDJCGeneId getBestGene(GeneType geneType) { - TObjectFloatHashMap scores = geneScores.get(geneType); - if (scores == null) - return null; - float maxScore = 0; - VDJCGeneId maxAllele = null; - TObjectFloatIterator iterator = scores.iterator(); - while (iterator.hasNext()) { - iterator.advance(); - if (maxAllele == null || maxScore < iterator.value()) { - maxAllele = iterator.key(); - maxScore = iterator.value(); - } - } - return maxAllele; + VDJCGeneScoreAccumulator.GeneAndScore bestGene = geneScoreAccumulator.getBestGene(geneType); + return bestGene == null ? null : bestGene.geneId; } public Range[] getNRegions() { @@ -145,37 +118,6 @@ public long getMappedCount() { return mappedCount; } - public void calculateScores(CloneFactoryParameters parameters) { - for (GeneType geneType : GeneType.VJC_REFERENCE) { - VJCClonalAlignerParameters vjcParameters = parameters.getVJCParameters(geneType); - if (vjcParameters == null) - continue; - - TObjectFloatHashMap accumulatorGeneIds = geneScores.get(geneType); - if (accumulatorGeneIds == null) - continue; - - TObjectFloatIterator iterator = accumulatorGeneIds.iterator(); - float maxScore = 0; - while (iterator.hasNext()) { - iterator.advance(); - float value = iterator.value(); - if (value > maxScore) - maxScore = value; - } - - maxScore = maxScore * vjcParameters.getRelativeMinScore(); - iterator = accumulatorGeneIds.iterator(); - while (iterator.hasNext()) { - iterator.advance(); - if (maxScore > iterator.value()) - iterator.remove(); - else - iterator.setValue(Math.round(iterator.value() * 10f / coreCount) / 10f); - } - } - } - public void mergeCounts(CloneAccumulator acc) { coreCount += acc.coreCount; mappedCount += acc.mappedCount; @@ -190,22 +132,7 @@ public synchronized void accumulate(ClonalSequence data, VDJCAlignments alignmen // Accumulate information about V-D-J alignments only for strictly clustered reads // (only for core clonotypes members) - float score; - - // Accumulate information about all genes - for (GeneType geneType : GeneType.VJC_REFERENCE) { - TObjectFloatHashMap geneScores = this.geneScores.get(geneType); - VDJCHit[] hits = alignment.getHits(geneType); - if (hits.length == 0) - continue; - if (geneScores == null) - this.geneScores.put(geneType, geneScores = new TObjectFloatHashMap<>()); - for (VDJCHit hit : hits) { - // Calculating sum of natural logarithms of scores - score = hit.getScore(); - geneScores.adjustOrPutValue(hit.getGene().getId(), score, score); - } - } + geneScoreAccumulator.accumulate(alignment); aggregator.aggregate(data.getConcatenated().getQuality()); } else // Mapped sequence accumulation diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index 3eef2d718..736f57b27 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -50,7 +50,6 @@ import com.milaboratory.util.RandomUtil; import gnu.trove.iterator.TIntIntIterator; import gnu.trove.iterator.TIntIterator; -import gnu.trove.iterator.TObjectFloatIterator; import gnu.trove.list.array.TIntArrayList; import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; @@ -656,7 +655,7 @@ synchronized CloneAccumulator accumulate(ClonalSequence sequence, VDJCAlignments public List build() { CloneAccumulator[] accs = accumulators.values().toArray(new CloneAccumulator[0]); for (CloneAccumulator acc : accs) - acc.calculateScores(parameters.cloneFactoryParameters); + acc.geneScoreAccumulator.aggregateInformation(parameters.cloneFactoryParameters); // Stores list of clonotypes clustered into specific clonotype final TIntObjectHashMap reversePreClustered = new TIntObjectHashMap<>(); @@ -813,11 +812,11 @@ VJCSignature extractSignature(VDJCAlignments alignments) { ); } - VJCSignature extractSignature(CloneAccumulator alignments) { + VJCSignature extractSignature(CloneAccumulator cloneAccumulator) { return new VJCSignature( - parameters.getSeparateByV() ? getGeneId(alignments, GeneType.Variable) : DO_NOT_CHECK, - parameters.getSeparateByJ() ? getGeneId(alignments, GeneType.Joining) : DO_NOT_CHECK, - parameters.getSeparateByC() ? getGeneId(alignments, GeneType.Constant) : DO_NOT_CHECK + parameters.getSeparateByV() ? cloneAccumulator.getBestGene(GeneType.Variable) : DO_NOT_CHECK, + parameters.getSeparateByJ() ? cloneAccumulator.getBestGene(GeneType.Joining) : DO_NOT_CHECK, + parameters.getSeparateByC() ? cloneAccumulator.getBestGene(GeneType.Constant) : DO_NOT_CHECK ); } @@ -842,7 +841,7 @@ boolean matchHits(CloneAccumulator acc) { TObjectFloatHashMap minor; if (vGene != DO_NOT_CHECK) { - minor = acc.geneScores.get(GeneType.Variable); + minor = acc.geneScoreAccumulator.geneScores.get(GeneType.Variable); if (vGene == null && (minor != null && !minor.isEmpty())) return false; if (vGene != null && minor != null && !minor.containsKey(vGene)) @@ -850,7 +849,7 @@ boolean matchHits(CloneAccumulator acc) { } if (jGene != DO_NOT_CHECK) { - minor = acc.geneScores.get(GeneType.Joining); + minor = acc.geneScoreAccumulator.geneScores.get(GeneType.Joining); if (jGene == null && (minor != null && !minor.isEmpty())) return false; if (jGene != null && minor != null && !minor.containsKey(jGene)) @@ -858,7 +857,7 @@ boolean matchHits(CloneAccumulator acc) { } if (cGene != DO_NOT_CHECK) { - minor = acc.geneScores.get(GeneType.Constant); + minor = acc.geneScoreAccumulator.geneScores.get(GeneType.Constant); if (cGene == null && (minor != null && !minor.isEmpty())) return false; if (cGene != null && minor != null && !minor.containsKey(cGene)) @@ -895,23 +894,6 @@ static VDJCGeneId getGeneId(VDJCAlignments alignments, GeneType type) { return hit == null ? null : hit.getGene().getId(); } - static VDJCGeneId getGeneId(CloneAccumulator acc, GeneType type) { - TObjectFloatHashMap aScores = acc.geneScores.get(type); - if (aScores == null || aScores.isEmpty()) - return null; - VDJCGeneId id = null; - float maxScore = Float.MIN_VALUE; - TObjectFloatIterator it = aScores.iterator(); - while (it.hasNext()) { - it.advance(); - if (maxScore < it.value()) { - maxScore = it.value(); - id = it.key(); - } - } - return id; - } - static final Comparator CLONE_ACCUMULATOR_COMPARATOR = new Comparator() { @Override public int compare(CloneAccumulator o1, CloneAccumulator o2) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index db3255196..3797a0d19 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -34,8 +34,8 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.vdjaligners.SingleDAligner; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; import gnu.trove.iterator.TObjectFloatIterator; @@ -254,7 +254,7 @@ public Clone create(int id, double count, } public Clone create(int id, CloneAccumulator accumulator) { - return create(id, accumulator.getCount(), accumulator.geneScores, accumulator.tagBuilder.createAndDestroy(), accumulator.getSequence().sequences, null); + return create(id, accumulator.getCount(), accumulator.geneScoreAccumulator.geneScores, accumulator.tagBuilder.createAndDestroy(), accumulator.getSequence().sequences, null); } private static boolean containsD(GeneFeature feature) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java index f7f6299f1..a3b369e6e 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java @@ -36,6 +36,7 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.databind.annotation.JsonSerialize; import com.milaboratory.mixcr.basictypes.ClonalUpdatableParameters; +import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.GeneType; @@ -44,7 +45,7 @@ @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE) -public final class CloneFactoryParameters implements java.io.Serializable { +public final class CloneFactoryParameters implements HasRelativeMinScore, java.io.Serializable { EnumMap vdcParameters = new EnumMap<>(GeneType.class); @JsonSerialize(as = DClonalAlignerParameters.class) DClonalAlignerParameters dParameters; @@ -145,6 +146,14 @@ public CloneFactoryParameters setDParameters(DClonalAlignerParameters dParameter return this; } + @Override + public float getRelativeMinScore(GeneType gt) { + if (gt == GeneType.Diversity) + return getDParameters().getRelativeMinScore(); + VJCClonalAlignerParameters geneSpecificParameters = getVJCParameters(gt); + return geneSpecificParameters == null ? Float.NaN : geneSpecificParameters.getRelativeMinScore(); + } + @Override protected CloneFactoryParameters clone() { EnumMap vjc = new EnumMap<>(GeneType.class); diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneScoreAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneScoreAccumulator.java new file mode 100644 index 000000000..b9ce9a566 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneScoreAccumulator.java @@ -0,0 +1,99 @@ +package com.milaboratory.mixcr.assembler; + +import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import gnu.trove.iterator.TObjectFloatIterator; +import gnu.trove.map.hash.TObjectFloatHashMap; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGeneId; + +import java.util.EnumMap; + +public final class VDJCGeneScoreAccumulator { + int observations = 0; + final EnumMap> geneScores = new EnumMap<>(GeneType.class); + + public synchronized void accumulate(VDJCAlignments alignment) { + if (observations == -1) + throw new IllegalStateException("Already aggregated"); + + // Accumulate information about all genes + for (GeneType geneType : GeneType.VJC_REFERENCE) { + TObjectFloatHashMap geneScores = this.geneScores.get(geneType); + VDJCHit[] hits = alignment.getHits(geneType); + if (hits.length == 0) + continue; + if (geneScores == null) + this.geneScores.put(geneType, geneScores = new TObjectFloatHashMap<>()); + for (VDJCHit hit : hits) { + // Calculating sum of natural logarithms of scores + geneScores.adjustOrPutValue(hit.getGene().getId(), hit.getScore(), hit.getScore()); + } + } + } + + public GeneAndScore getBestGene(GeneType geneType) { + TObjectFloatHashMap scores = geneScores.get(geneType); + if (scores == null) + return null; + float maxScore = 0; + VDJCGeneId maxAllele = null; + TObjectFloatIterator iterator = scores.iterator(); + while (iterator.hasNext()) { + iterator.advance(); + if (maxAllele == null || maxScore < iterator.value()) { + maxAllele = iterator.key(); + maxScore = iterator.value(); + } + } + return new GeneAndScore(maxAllele, maxScore); + } + + public void aggregateInformation(HasRelativeMinScore hasRelativeMinScore) { + if (observations == -1) + throw new IllegalStateException("Already aggregated"); + + for (GeneType geneType : GeneType.VJC_REFERENCE) { + float relativeMinScore = hasRelativeMinScore.getRelativeMinScore(geneType); + if (Float.isNaN(relativeMinScore)) + continue; + + TObjectFloatHashMap accumulatorGeneIds = geneScores.get(geneType); + if (accumulatorGeneIds == null) + continue; + + TObjectFloatIterator iterator = accumulatorGeneIds.iterator(); + float maxScore = 0; + while (iterator.hasNext()) { + iterator.advance(); + float value = iterator.value(); + if (value > maxScore) + maxScore = value; + } + + maxScore = maxScore * relativeMinScore; + iterator = accumulatorGeneIds.iterator(); + while (iterator.hasNext()) { + iterator.advance(); + if (maxScore > iterator.value()) + iterator.remove(); + else + iterator.setValue(Math.round(iterator.value() * 10f / observations) / 10f); + } + } + + // To prevent double aggregation + observations = -1; + } + + public static final class GeneAndScore { + public final VDJCGeneId geneId; + public final float score; + + public GeneAndScore(VDJCGeneId geneId, float score) { + this.geneId = geneId; + this.score = score; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java b/src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java new file mode 100644 index 000000000..b73091ff1 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java @@ -0,0 +1,7 @@ +package com.milaboratory.mixcr.basictypes; + +import io.repseq.core.GeneType; + +public interface HasRelativeMinScore { + float getRelativeMinScore(GeneType gt); +} From 59106993099128666de08d9759416b177fb6f9cc Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 27 May 2022 01:22:01 +0200 Subject: [PATCH 227/282] feat(exportClonesOverlap): cloneset overlap table CLI --- .../milaboratory/mixcr/cli/CommandExport.java | 17 +- .../mixcr/cli/CommandExportOverlap.java | 387 ++++++++++++++++++ .../java/com/milaboratory/mixcr/cli/Main.java | 3 +- .../cli/postanalysis/CommandPaOverlap.java | 124 +----- .../postanalysis/overlap/OverlapDataset.java | 4 + .../postanalysis/overlap/OverlapGroup.java | 2 +- .../postanalysis/overlap/OverlapUtil.java | 173 +++++++- 7 files changed, 577 insertions(+), 133 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 1c647ccfd..1021e7ae3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -361,7 +361,7 @@ void run() { } @SuppressWarnings("unchecked") - List> extractor(FieldData fd, Class clazz, OutputMode m) { + public static List> extractor(FieldData fd, Class clazz, OutputMode m) { for (Field f : FieldExtractors.getFields()) { if (fd.field.equalsIgnoreCase(f.getCommand()) && f.canExtractFrom(clazz)) { if (f.nArguments() == 0) { @@ -380,11 +380,10 @@ List> extractor(FieldData fd, Class clazz, OutputMode m } } } - throwValidationException("illegal field: " + fd.field); - return null; + throw new IllegalArgumentException("illegal field: " + fd.field); } - private static final class FieldData { + public static final class FieldData { final String field; final String[] args; @@ -527,8 +526,13 @@ public static List parseSpec(ParseResult parseResult) { public static CommandSpec mkCommandSpec(CommandExport export) { CommandSpec spec = CommandSpec.forAnnotatedObject(export); export.spec = spec; // inject spec manually - for (Field field : FieldExtractors.getFields()) { - if (!field.canExtractFrom(export.clazz)) + addOptionsToSpec(spec, export.clazz); + return spec; + } + + public static void addOptionsToSpec(CommandSpec spec, Class clazz) { + for (Field field : FieldExtractors.getFields()) { + if (!field.canExtractFrom(clazz)) continue; spec.addOption(OptionSpec .builder(field.getCommand()) @@ -539,7 +543,6 @@ public static CommandSpec mkCommandSpec(CommandExport .descriptionKey(field.getCommand() + " " + field.metaVars()) .build()); } - return spec; } /** diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java new file mode 100644 index 000000000..3c3933066 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java @@ -0,0 +1,387 @@ +package com.milaboratory.mixcr.cli; + +import cc.redberry.pipe.CUtils; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneReader; +import com.milaboratory.mixcr.basictypes.CloneSetIO; +import com.milaboratory.mixcr.export.FieldExtractor; +import com.milaboratory.mixcr.export.OutputMode; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapDataset; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapUtil; +import com.milaboratory.mixcr.util.OutputPortWithProgress; +import com.milaboratory.util.CanReportProgress; +import com.milaboratory.util.SmartProgressReporter; +import io.repseq.core.Chains; +import io.repseq.core.Chains.NamedChains; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; +import picocli.CommandLine.Command; +import picocli.CommandLine.Model.CommandSpec; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.io.FileWriter; +import java.io.IOException; +import java.io.PrintWriter; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.function.Predicate; +import java.util.stream.Collectors; + +@Command(separator = " ", + description = "Build cloneset overlap and export into tab delimited file." +) +public class CommandExportOverlap extends ACommandWithOutputMiXCR { + @Parameters(description = "cloneset.{clns|clna}...") + public List inOut; + + @Option(description = "Chains to export", + names = "--chains") + public List chains = null; + + @Option(description = "Filter out-of-frame sequences and clonotypes with stop-codons", + names = {"--only-productive"}) + public boolean onlyProductive = false; + + @Option(description = "Overlap criteria. Default CDR3|AA|V|J", + names = {"--criteria"}) + public String overlapCriteria = "CDR3|AA|V|J"; + + /** auto-generated opts (exporters) injected manually */ + private CommandSpec spec; + + @Override + public List getInputFiles() { + return inOut.subList(0, inOut.size() - 1); + } + + public Path getOut(NamedChains chains) { + Path out = Paths.get(inOut.get(inOut.size() - 1)).toAbsolutePath(); + if (chains == Chains.ALL_NAMED) + return out; + String fName = out.getFileName().toString(); + if (fName.endsWith(".tsv")) + fName = fName.replace("tsv", "") + chains.name + ".tsv"; + else + fName = fName + "_" + chains.name; + return out.getParent().resolve(fName); + } + + @Override + public void run0() throws Exception { + List samples = getInputFiles(); + boolean needRecalculateCount = this.chains != null || onlyProductive; + + List chains = this.chains == null + ? Collections.singletonList(Chains.ALL_NAMED) + : this.chains.stream().map(Chains::getNamedChains).collect(Collectors.toList()); + Map counts = null; + if (needRecalculateCount) { + counts = new HashMap<>(); + AtomicInteger sampleIndex = new AtomicInteger(0); + SmartProgressReporter.startProgressReport("Calculating samples counts", new CanReportProgress() { + @Override + public double getProgress() { + return 1.0 * sampleIndex.get() / samples.size(); + } + + @Override + public boolean isFinished() { + return sampleIndex.get() == samples.size(); + } + }); + for (int i = 0; i < samples.size(); i++) { + try (CloneReader reader = CloneSetIO.mkReader(Paths.get(samples.get(i)), VDJCLibraryRegistry.getDefault())) { + for (Clone cl : CUtils.it(reader.readClones())) { + if (!isProductive(cl)) + continue; + for (NamedChains ch : chains) { + if (!hasChains(cl, ch)) + continue; + counts.computeIfAbsent(ch, __ -> new double[samples.size()])[i] += cl.getCount(); + } + } + } + sampleIndex.set(i + 1); + } + } + +// try (OutputPortWithProgress> port = overlap.mkElementsPort()) { +// SmartProgressReporter.startProgressReport("Computing total counts", port); +// for (OverlapGroup row : CUtils.it(port)) { +// filterProductive(row, true); +// for (NamedChains ch : chains) { +// double[] c = counts.computeIfAbsent(ch.chains, __ -> new double[getInputFiles().size()]); +// OverlapGroup projected = forChains(row, ch.chains); +// for (int i = 0; i < projected.size(); i++) { +// c[i] += projected.getBySample(i).stream().mapToDouble(Clone::getCount).sum(); +// } +// } +// } +// } + OverlapUtil.OverlapCriteria criteria = OverlapUtil.parseCriteria(this.overlapCriteria); + List extractors = new ArrayList<>(); + + extractors.add(new ExtractorUnique( + new FieldExtractor() { + @Override + public String getHeader() { + return (criteria.isAA ? "aaSeq" : "nSeq") + GeneFeature.encode(criteria.feature); + } + + @Override + public String extractValue(Clone object) { + return criteria.isAA + ? object.getAAFeature(criteria.feature).toString() + : object.getNFeature(criteria.feature).toString(); + } + } + )); + if (criteria.withV) + extractors.add(new ExtractorUnique( + new FieldExtractor() { + @Override + public String getHeader() { + return "vGene"; + } + + @Override + public String extractValue(Clone object) { + return object.getBestHit(GeneType.Variable).getGene().getName(); + } + } + )); + if (criteria.withJ) + extractors.add(new ExtractorUnique( + new FieldExtractor() { + @Override + public String getHeader() { + return "jGene"; + } + + @Override + public String extractValue(Clone object) { + return object.getBestHit(GeneType.Joining).getGene().getName(); + } + } + )); + + extractors.add(new NumberOfSamples()); + extractors.add(new TotalCount()); + extractors.add(new TotalFraction()); + + List> fieldExtractors = CommandExport + .parseSpec(spec.commandLine().getParseResult()) + .stream() + .flatMap(f -> CommandExport.extractor(f, Clone.class, OutputMode.ScriptingFriendly).stream()) + .collect(Collectors.toList()); + + for (FieldExtractor fe : fieldExtractors) + extractors.add(new ExtractorPerSample(fe)); + + Map writers = new HashMap<>(); + for (NamedChains chain : chains) { + InfoWriter writer = new InfoWriter(getOut(chain), samples, extractors); + writer.writeHeader(); + writers.put(chain, writer); + } + OverlapDataset overlap = OverlapUtil.overlap(samples, criteria.ordering()); + try (OutputPortWithProgress> port = overlap.mkElementsPort()) { + SmartProgressReporter.startProgressReport("Calculating overlap", port); + for (OverlapGroup row : CUtils.it(port)) { + row = filterProductive(row, true); + if (row == null) + continue; + + for (NamedChains ch : chains) { + OverlapGroup forChain = forChains(row, ch); + if (forChain == null) + continue; + + if (needRecalculateCount) { + double[] cs = counts.get(ch); + for (int i = 0; i < forChain.size(); i++) + for (Clone cl : forChain.getBySample(i)) + cl.overrideFraction(cl.getCount() / cs[i]); + } + + writers.get(ch).writeRow(forChain); + } + } + } + writers.forEach((___, w) -> w.close()); + } + + private static OverlapGroup filter(OverlapGroup row, Predicate criteria, boolean inPlace) { + if (inPlace) { + boolean empty = true; + for (List l : row) { + l.removeIf(c -> !criteria.test(c)); + if (!l.isEmpty()) + empty = false; + } + if (empty) + return null; + else + return row; + } else { + boolean empty = true; + List> r = new ArrayList<>(); + for (List l : row) { + List f = l.stream().filter(criteria).collect(Collectors.toList()); + r.add(f); + if (!f.isEmpty()) + empty = false; + } + if (empty) + return null; + else + return new OverlapGroup<>(r); + } + } + + private static boolean isProductive(Clone c) { + return !c.isOutOfFrame(GeneFeature.CDR3) && !c.containsStops(GeneFeature.CDR3); + } + + private static boolean hasChains(Clone c, NamedChains chains) { + return chains == Chains.ALL_NAMED || Arrays.stream(GeneType.VJC_REFERENCE).anyMatch(gt -> { + Chains clChains = c.getAllChains(gt); + if (clChains == null) + return false; + return clChains.intersects(chains.chains); + }); + } + + private static OverlapGroup forChains(OverlapGroup row, NamedChains chains) { + return chains == Chains.ALL_NAMED ? row : filter(row, c -> hasChains(c, chains), false); + } + + private OverlapGroup filterProductive(OverlapGroup row, boolean inPlace) { + return onlyProductive ? filter(row, CommandExportOverlap::isProductive, inPlace) : row; + } + + private static final class InfoWriter implements AutoCloseable { + final PrintWriter writer; + final List samples; + final List extractors; + + public InfoWriter(Path out, List samples, + List extractors) { + try { + this.writer = new PrintWriter(new FileWriter(out.toFile())); + } catch (IOException e) { + throw new RuntimeException(e); + } + this.samples = samples; + this.extractors = extractors; + } + + void writeHeader() { + writer.println(extractors.stream().flatMap(e -> e.header(samples).stream()).collect(Collectors.joining("\t"))); + } + + void writeRow(OverlapGroup row) { + writer.println(extractors.stream().flatMap(e -> e.values(row).stream()).collect(Collectors.joining("\t"))); + } + + @Override + public void close() { + writer.close(); + } + } + + private interface OverlapFieldExtractor { + List header(List samples); + + List values(OverlapGroup row); + } + + private static final class TotalCount implements OverlapFieldExtractor { + @Override + public List header(List samples) { + return samples.stream().map(s -> s + "_countAggregated").collect(Collectors.toList()); + } + + @Override + public List values(OverlapGroup row) { + return row.stream().map(l -> Double.toString(l.stream().mapToDouble(Clone::getCount).sum())) + .collect(Collectors.toList()); + } + } + + private static final class TotalFraction implements OverlapFieldExtractor { + @Override + public List header(List samples) { + return samples.stream().map(s -> s + "_fractionAggregated").collect(Collectors.toList()); + } + + @Override + public List values(OverlapGroup row) { + return row.stream().map(l -> Double.toString(l.stream().mapToDouble(Clone::getFraction).sum())) + .collect(Collectors.toList()); + } + } + + private static final class NumberOfSamples implements OverlapFieldExtractor { + @Override + public List header(List samples) { + return Collections.singletonList("nSamples"); + } + + @Override + public List values(OverlapGroup row) { + return Collections.singletonList("" + row.stream().filter(l -> l.size() > 0).count()); + } + } + + private static final class ExtractorUnique implements OverlapFieldExtractor { + final FieldExtractor extractor; + + public ExtractorUnique(FieldExtractor extractor) { + this.extractor = extractor; + } + + @Override + public List header(List samples) { + return Collections.singletonList(extractor.getHeader()); + } + + @Override + public List values(OverlapGroup row) { + return Collections.singletonList(extractor.extractValue(row.stream().filter(l -> l.size() > 0).findAny().get().get(0))); + } + } + + private static final class ExtractorPerSample implements OverlapFieldExtractor { + final FieldExtractor extractor; + + public ExtractorPerSample(FieldExtractor extractor) { + this.extractor = extractor; + } + + @Override + public List header(List samples) { + return samples.stream().map(s -> s + "_" + extractor.getHeader()).collect(Collectors.toList()); + } + + @Override + public List values(OverlapGroup row) { + return row.stream().map(s -> + s.stream().map(extractor::extractValue).collect(Collectors.joining(",")) + ).collect(Collectors.toList()); + } + } + + public static CommandSpec mkSpec() { + CommandExportOverlap export = new CommandExportOverlap(); + CommandSpec spec = CommandSpec.forAnnotatedObject(export); + export.spec = spec; // inject spec manually + CommandExport.addOptionsToSpec(spec, Clone.class); + return spec; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index fdbba922d..0f324137e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -232,7 +232,6 @@ public static CommandLine mkCmd() { .addSubcommand("exportTables", CommandPaExportTables.class) .addSubcommand("exportPreprocTables", CommandPaExportTablesPreprocSummary.class) - .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) .addSubcommand("groupCells", CommandGroupCells.class) @@ -246,6 +245,8 @@ public static CommandLine mkCmd() { .addSubcommand("exportClones", CommandExport.mkClonesSpec()) .addSubcommand("exportClonesPretty", CommandExportClonesPretty.class) + .addSubcommand("exportClonesOverlap", CommandExportOverlap.mkSpec()) + .addSubcommand("exportAirr", CommandExportAirr.class) .addSubcommand("exportReadsForClones", CommandExportReadsForClones.class) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index 92e9ba515..e9d604d6c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -1,8 +1,6 @@ package com.milaboratory.mixcr.cli.postanalysis; -import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; import com.milaboratory.mixcr.postanalysis.WeightFunctions; @@ -16,26 +14,13 @@ import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersOverlap; import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersPreset; import com.milaboratory.mixcr.postanalysis.ui.PostanalysisSchema; -import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.JsonOverrider; -import com.milaboratory.util.LambdaSemaphore; import com.milaboratory.util.SmartProgressReporter; -import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; -import io.repseq.core.VDJCGene; -import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine.Command; import picocli.CommandLine.Option; -import java.io.IOException; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.ArrayList; import java.util.List; import java.util.Map; -import java.util.stream.Collectors; - -import static java.util.stream.Collectors.toList; @Command(name = "overlap", sortOptions = false, @@ -66,32 +51,6 @@ private PostanalysisParametersOverlap getParameters() { return _parameters; } - private List> parseCriteria() { - String[] parts = overlapCriteria.toLowerCase().split("\\|"); - if (parts.length < 2) - throwValidationException("Illegal criteria input: " + overlapCriteria); - GeneFeature feature = GeneFeature.parse(parts[0]); - if (!parts[1].equals("aa") && !parts[1].equals("nt")) - throwValidationException("Illegal criteria input: " + overlapCriteria); - boolean isAA = parts[1].equals("aa"); - List geneTypes = new ArrayList<>(); - if (parts.length > 2) - if (!parts[2].equals("v")) - throwValidationException("Illegal criteria input: " + overlapCriteria); - else - geneTypes.add(GeneType.Variable); - if (parts.length > 3) - if (!parts[3].equals("j")) - throwValidationException("Illegal criteria input: " + overlapCriteria); - else - geneTypes.add(GeneType.Joining); - - if (isAA) - return VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{feature}, geneTypes.toArray(new GeneType[0])); - else - return VDJCSProperties.orderingByNucleotide(new GeneFeature[]{feature}, geneTypes.toArray(new GeneType[0])); - } - @Override @SuppressWarnings("unchecked") PaResultByGroup run(IsolationGroup group, List samples) { @@ -102,25 +61,10 @@ PaResultByGroup run(IsolationGroup group, List samples) { .before(new OverlapPreprocessorAdapter.Factory<>(new FilterPreprocessor.Factory<>(WeightFunctions.Count, new ElementPredicate.IncludeChains(group.chains.chains))))) ); - // Limits concurrency across all readers - LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(32); - List readers = samples - .stream() - .map(s -> { - try { - return mkCheckedReader( - Paths.get(s).toAbsolutePath(), - concurrencyLimiter); - } catch (IOException e) { - throw new RuntimeException(e); - } - }) - .collect(Collectors.toList()); - OverlapDataset overlapDataset = OverlapUtil.overlap( - samples.stream().map(CommandPa::getSampleId).collect(toList()), - parseCriteria(), - readers); + samples, + OverlapUtil.parseCriteria(overlapCriteria).ordering() + ); PostanalysisRunner> runner = new PostanalysisRunner<>(); runner.addCharacteristics(schema.getAllCharacterisitcs()); @@ -131,64 +75,4 @@ PaResultByGroup run(IsolationGroup group, List samples) { return new PaResultByGroup(group, schema, result); } - - public static CloneReader mkCheckedReader(Path path, - LambdaSemaphore concurrencyLimiter) throws IOException { - ClnsReader inner = new ClnsReader( - path, - VDJCLibraryRegistry.getDefault(), - concurrencyLimiter); - return new CloneReader() { - @Override - public VDJCSProperties.CloneOrdering ordering() { - return inner.ordering(); - } - - @Override - public OutputPortCloseable readClones() { - OutputPortCloseable in = inner.readClones(); - return new OutputPortCloseable() { - @Override - public void close() { - in.close(); - } - - @Override - public Clone take() { - Clone t = in.take(); - if (t == null) - return null; - if (t.getFeature(GeneFeature.CDR3) == null) - return take(); - return t; - } - }; - } - - @Override - public void close() throws Exception { - inner.close(); - } - - @Override - public int numberOfClones() { - return inner.numberOfClones(); - } - - @Override - public List getUsedGenes() { - return inner.getUsedGenes(); - } - - @Override - public VDJCAlignerParameters getAlignerParameters() { - return inner.getAlignerParameters(); - } - - @Override - public CloneAssemblerParameters getAssemblerParameters() { - return inner.getAssemblerParameters(); - } - }; - } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java index 9a5a544d0..b31285a4e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java @@ -14,6 +14,10 @@ public OverlapDataset(List datasetIds) { this.datasetIds = datasetIds; } + public int nSamples() { + return datasetIds.size(); + } + @Override public String id() { return "overlap"; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java index 244ada9b6..f63d410d7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java @@ -38,7 +38,7 @@ public final class OverlapGroup implements Iterable> { /** * Elements in group separated by sample */ - final List> elements; + public final List> elements; public OverlapGroup(List> elements) { this.elements = elements; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java index 2fc4552c0..11bb86a01 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java @@ -29,14 +29,27 @@ */ package com.milaboratory.mixcr.postanalysis.overlap; +import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.util.SimpleProcessorWrapper; -import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.CloneReader; -import com.milaboratory.mixcr.basictypes.CloneSetOverlap; -import com.milaboratory.mixcr.basictypes.VDJCSProperties; +import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; +import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.util.OutputPortWithProgress; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.util.LambdaSemaphore; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGene; +import io.repseq.core.VDJCLibraryRegistry; +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; import java.util.List; +import java.util.Objects; +import java.util.stream.Collectors; + +import static java.util.stream.Collectors.toList; public final class OverlapUtil { private OverlapUtil() { @@ -80,4 +93,156 @@ public boolean isFinished() { } }; } + + public static OverlapDataset overlap( + List samples, + List> by + ) { + // Limits concurrency across all readers + LambdaSemaphore concurrencyLimiter = new LambdaSemaphore(32); + List readers = samples + .stream() + .map(s -> { + try { + return mkCheckedReader( + Paths.get(s).toAbsolutePath(), + concurrencyLimiter); + } catch (IOException e) { + throw new RuntimeException(e); + } + }) + .collect(Collectors.toList()); + + return OverlapUtil.overlap( + samples.stream().map(OverlapUtil::getSampleId).collect(toList()), + by, + readers); + } + + /** Get sample id from file name */ + static String getSampleId(String file) { + return Paths.get(file).getFileName().toString(); + } + + public static CloneReader mkCheckedReader(Path path, + LambdaSemaphore concurrencyLimiter) throws IOException { + ClnsReader inner = new ClnsReader( + path, + VDJCLibraryRegistry.getDefault(), + concurrencyLimiter); + return new CloneReader() { + @Override + public VDJCSProperties.CloneOrdering ordering() { + return inner.ordering(); + } + + @Override + public OutputPortCloseable readClones() { + OutputPortCloseable in = inner.readClones(); + return new OutputPortCloseable() { + @Override + public void close() { + in.close(); + } + + @Override + public Clone take() { + Clone t = in.take(); + if (t == null) + return null; + if (t.getFeature(GeneFeature.CDR3) == null) + return take(); + return t; + } + }; + } + + @Override + public void close() throws Exception { + inner.close(); + } + + @Override + public int numberOfClones() { + return inner.numberOfClones(); + } + + @Override + public List getUsedGenes() { + return inner.getUsedGenes(); + } + + @Override + public VDJCAlignerParameters getAlignerParameters() { + return inner.getAlignerParameters(); + } + + @Override + public CloneAssemblerParameters getAssemblerParameters() { + return inner.getAssemblerParameters(); + } + }; + } + + public static final class OverlapCriteria { + public final GeneFeature feature; + public final boolean isAA; + public final boolean withV; + public final boolean withJ; + + public OverlapCriteria(GeneFeature feature, boolean isAA, boolean withV, boolean withJ) { + this.feature = feature; + this.isAA = isAA; + this.withV = withV; + this.withJ = withJ; + } + + public List> ordering() { + List geneTypes = new ArrayList<>(); + if (withV) + geneTypes.add(GeneType.Variable); + if (withJ) + geneTypes.add(GeneType.Joining); + if (isAA) + return VDJCSProperties.orderingByAminoAcid(new GeneFeature[]{feature}, geneTypes.toArray(new GeneType[0])); + else + return VDJCSProperties.orderingByNucleotide(new GeneFeature[]{feature}, geneTypes.toArray(new GeneType[0])); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OverlapCriteria that = (OverlapCriteria) o; + return isAA == that.isAA && withV == that.withV && withJ == that.withJ && Objects.equals(feature, that.feature); + } + + @Override + public int hashCode() { + return Objects.hash(feature, isAA, withV, withJ); + } + } + + public static OverlapCriteria parseCriteria(String overlapCriteria) { + String[] parts = overlapCriteria.toLowerCase().split("\\|"); + if (parts.length < 2) + throw new IllegalArgumentException("Illegal criteria input: " + overlapCriteria); + GeneFeature feature = GeneFeature.parse(parts[0]); + if (!parts[1].equals("aa") && !parts[1].equals("nt")) + throw new IllegalArgumentException("Illegal criteria input: " + overlapCriteria); + boolean isAA = parts[1].equals("aa"); + boolean withV = false, withJ = false; + if (parts.length > 2) + if (!parts[2].equals("v")) + throw new IllegalArgumentException("Illegal criteria input: " + overlapCriteria); + else + withV = true; + if (parts.length > 3) + if (!parts[3].equals("j")) + throw new IllegalArgumentException("Illegal criteria input: " + overlapCriteria); + else + withJ = true; + + return new OverlapCriteria(feature, isAA, withV, withJ); + } } From b2db6bd6df0cd56677e1887674c4b5e5bfb4d954 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 27 May 2022 12:16:25 +0200 Subject: [PATCH 228/282] feat(OverlapBrowser): move common part from cli to separate class --- .../mixcr/cli/CommandExportOverlap.java | 80 ++------- .../postanalysis/util/OverlapBrowser.java | 168 ++++++++++++++++++ .../postanalysis/plots/OverlapScatter.kt | 9 + 3 files changed, 189 insertions(+), 68 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java create mode 100644 src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java index 3c3933066..287f0267d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java @@ -2,21 +2,18 @@ import cc.redberry.pipe.CUtils; import com.milaboratory.mixcr.basictypes.Clone; -import com.milaboratory.mixcr.basictypes.CloneReader; -import com.milaboratory.mixcr.basictypes.CloneSetIO; import com.milaboratory.mixcr.export.FieldExtractor; import com.milaboratory.mixcr.export.OutputMode; import com.milaboratory.mixcr.postanalysis.overlap.OverlapDataset; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; import com.milaboratory.mixcr.postanalysis.overlap.OverlapUtil; +import com.milaboratory.mixcr.postanalysis.util.OverlapBrowser; import com.milaboratory.mixcr.util.OutputPortWithProgress; -import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.Chains; import io.repseq.core.Chains.NamedChains; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; -import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine.Command; import picocli.CommandLine.Model.CommandSpec; import picocli.CommandLine.Option; @@ -28,7 +25,6 @@ import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; -import java.util.concurrent.atomic.AtomicInteger; import java.util.function.Predicate; import java.util.stream.Collectors; @@ -75,54 +71,10 @@ public Path getOut(NamedChains chains) { public void run0() throws Exception { List samples = getInputFiles(); boolean needRecalculateCount = this.chains != null || onlyProductive; - List chains = this.chains == null ? Collections.singletonList(Chains.ALL_NAMED) : this.chains.stream().map(Chains::getNamedChains).collect(Collectors.toList()); - Map counts = null; - if (needRecalculateCount) { - counts = new HashMap<>(); - AtomicInteger sampleIndex = new AtomicInteger(0); - SmartProgressReporter.startProgressReport("Calculating samples counts", new CanReportProgress() { - @Override - public double getProgress() { - return 1.0 * sampleIndex.get() / samples.size(); - } - - @Override - public boolean isFinished() { - return sampleIndex.get() == samples.size(); - } - }); - for (int i = 0; i < samples.size(); i++) { - try (CloneReader reader = CloneSetIO.mkReader(Paths.get(samples.get(i)), VDJCLibraryRegistry.getDefault())) { - for (Clone cl : CUtils.it(reader.readClones())) { - if (!isProductive(cl)) - continue; - for (NamedChains ch : chains) { - if (!hasChains(cl, ch)) - continue; - counts.computeIfAbsent(ch, __ -> new double[samples.size()])[i] += cl.getCount(); - } - } - } - sampleIndex.set(i + 1); - } - } -// try (OutputPortWithProgress> port = overlap.mkElementsPort()) { -// SmartProgressReporter.startProgressReport("Computing total counts", port); -// for (OverlapGroup row : CUtils.it(port)) { -// filterProductive(row, true); -// for (NamedChains ch : chains) { -// double[] c = counts.computeIfAbsent(ch.chains, __ -> new double[getInputFiles().size()]); -// OverlapGroup projected = forChains(row, ch.chains); -// for (int i = 0; i < projected.size(); i++) { -// c[i] += projected.getBySample(i).stream().mapToDouble(Clone::getCount).sum(); -// } -// } -// } -// } OverlapUtil.OverlapCriteria criteria = OverlapUtil.parseCriteria(this.overlapCriteria); List extractors = new ArrayList<>(); @@ -189,27 +141,18 @@ public String extractValue(Clone object) { writer.writeHeader(); writers.put(chain, writer); } + + OverlapBrowser overlapBrowser = new OverlapBrowser(chains, onlyProductive); + SmartProgressReporter.startProgressReport(overlapBrowser); + Map counts = null; + if (needRecalculateCount) + counts = overlapBrowser.computeCounts(samples); + OverlapDataset overlap = OverlapUtil.overlap(samples, criteria.ordering()); try (OutputPortWithProgress> port = overlap.mkElementsPort()) { - SmartProgressReporter.startProgressReport("Calculating overlap", port); - for (OverlapGroup row : CUtils.it(port)) { - row = filterProductive(row, true); - if (row == null) - continue; - - for (NamedChains ch : chains) { - OverlapGroup forChain = forChains(row, ch); - if (forChain == null) - continue; - - if (needRecalculateCount) { - double[] cs = counts.get(ch); - for (int i = 0; i < forChain.size(); i++) - for (Clone cl : forChain.getBySample(i)) - cl.overrideFraction(cl.getCount() / cs[i]); - } - - writers.get(ch).writeRow(forChain); + for (Map> row : CUtils.it(overlapBrowser.overlap(counts, port))) { + for (Map.Entry> e : row.entrySet()) { + writers.get(e.getKey()).writeRow(e.getValue()); } } } @@ -375,6 +318,7 @@ public List values(OverlapGroup row) { s.stream().map(extractor::extractValue).collect(Collectors.joining(",")) ).collect(Collectors.toList()); } + } public static CommandSpec mkSpec() { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java new file mode 100644 index 000000000..7a2a5339e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java @@ -0,0 +1,168 @@ +package com.milaboratory.mixcr.postanalysis.util; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneReader; +import com.milaboratory.mixcr.basictypes.CloneSetIO; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.util.OutputPortWithProgress; +import com.milaboratory.util.CanReportProgress; +import com.milaboratory.util.CanReportProgressAndStage; +import com.milaboratory.util.ProgressAndStage; +import io.repseq.core.Chains; +import io.repseq.core.Chains.NamedChains; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCLibraryRegistry; + +import java.nio.file.Paths; +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.function.Predicate; +import java.util.stream.Collectors; + +public class OverlapBrowser implements CanReportProgressAndStage { + final List chains; + final boolean onlyProductive; + + public OverlapBrowser(List chains, boolean onlyProductive) { + this.chains = chains; + this.onlyProductive = onlyProductive; + } + + private final ProgressAndStage pas = new ProgressAndStage(""); + + @Override + public double getProgress() { + return pas.getProgress(); + } + + @Override + public boolean isFinished() { + return pas.isFinished(); + } + + @Override + public String getStage() { + return pas.getStage(); + } + + + public Map computeCounts(List samples) { + Map counts = new HashMap<>(); + AtomicInteger sampleIndex = new AtomicInteger(0); + pas.setStage("Calculating dataset counts"); + pas.delegate(new CanReportProgress() { + @Override + public double getProgress() { + return 1.0 * sampleIndex.get() / samples.size(); + } + + @Override + public boolean isFinished() { + return sampleIndex.get() == samples.size(); + } + }); + for (int i = 0; i < samples.size(); i++) { + try (CloneReader reader = CloneSetIO.mkReader(Paths.get(samples.get(i)), VDJCLibraryRegistry.getDefault())) { + for (Clone cl : CUtils.it(reader.readClones())) { + if (!isProductive(cl)) + continue; + for (NamedChains ch : chains) { + if (!hasChains(cl, ch)) + continue; + counts.computeIfAbsent(ch, __ -> new double[samples.size()])[i] += cl.getCount(); + } + } + } catch (Exception e) { + throw new RuntimeException(e); + } + sampleIndex.set(i + 1); + } + return counts; + } + + public OutputPort>> + overlap(Map counts, + OutputPortWithProgress> port) { + pas.setStage("Calculating overlap"); + pas.delegate(port); + return () -> { + while (true) { + OverlapGroup row = port.take(); + if (row == null) + return null; + + Map> map = new HashMap<>(); + for (NamedChains ch : chains) { + OverlapGroup forChain = forChains(row, ch); + if (forChain == null) + continue; + + if (counts != null) { + double[] cs = counts.get(ch); + for (int i = 0; i < forChain.size(); i++) + for (Clone cl : forChain.getBySample(i)) + cl.overrideFraction(cl.getCount() / cs[i]); + } + + map.put(ch, forChain); + } + + if (map.size() > 0) + return map; + } + }; + } + + + private static OverlapGroup filter(OverlapGroup row, Predicate criteria, boolean inPlace) { + if (inPlace) { + boolean empty = true; + for (List l : row) { + l.removeIf(c -> !criteria.test(c)); + if (!l.isEmpty()) + empty = false; + } + if (empty) + return null; + else + return row; + } else { + boolean empty = true; + List> r = new ArrayList<>(); + for (List l : row) { + List f = l.stream().filter(criteria).collect(Collectors.toList()); + r.add(f); + if (!f.isEmpty()) + empty = false; + } + if (empty) + return null; + else + return new OverlapGroup<>(r); + } + } + + private static boolean isProductive(Clone c) { + return !c.isOutOfFrame(GeneFeature.CDR3) && !c.containsStops(GeneFeature.CDR3); + } + + private static boolean hasChains(Clone c, NamedChains chains) { + return chains == Chains.ALL_NAMED || Arrays.stream(GeneType.VJC_REFERENCE).anyMatch(gt -> { + Chains clChains = c.getAllChains(gt); + if (clChains == null) + return false; + return clChains.intersects(chains.chains); + }); + } + + private static OverlapGroup forChains(OverlapGroup row, NamedChains chains) { + return chains == Chains.ALL_NAMED ? row : filter(row, c -> hasChains(c, chains), false); + } + + private OverlapGroup filterProductive(OverlapGroup row, boolean inPlace) { + return onlyProductive ? filter(row, OverlapBrowser::isProductive, inPlace) : row; + } +} diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt new file mode 100644 index 000000000..08ccef500 --- /dev/null +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt @@ -0,0 +1,9 @@ +package com.milaboratory.mixcr.postanalysis.plots + +data class OverlapScatterRow( + val count1: Double, + val count2: Double, +) + +object OverlapScatter { +} \ No newline at end of file From b3cd9e9e6caf4fa68ecb8faa6d43f655514deb8a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Fri, 27 May 2022 21:31:58 +0300 Subject: [PATCH 229/282] WIP, full code for PreCloneAssembler, not tested, no reports --- .../mixcr/assembler/CloneAccumulator.java | 49 +++- .../mixcr/assembler/CloneAssembler.java | 84 +----- .../mixcr/assembler/CloneFactory.java | 17 +- .../mixcr/assembler/GeneAndScore.java | 39 +++ ...umulator.java => VDJCGeneAccumulator.java} | 69 +++-- .../mixcr/assembler/VJCSignature.java | 70 +++++ .../assembler/fullseq/FullSeqAssembler.java | 31 ++- .../mixcr/basictypes/VDJCHit.java | 5 + .../mixcr/basictypes/tag/TagCounter.java | 46 +++- .../mixcr/basictypes/tag/TagTuple.java | 55 +++- .../cli/CommandAssemblePartialAlignments.java | 2 +- .../mixcr/cli/CommandCorrectAndSortTags.java | 16 +- .../mixcr/export/FieldExtractors.java | 2 +- .../com/milaboratory/mixcr/tags/PreClone.java | 32 +++ .../mixcr/tags/PreCloneAssembler.java | 254 ++++++++++++++++++ .../tags/PreCloneAssemblerParameters.java | 21 ++ .../mixcr/tags/PreCloneAssemblerReport.java | 5 + 17 files changed, 639 insertions(+), 158 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java rename src/main/java/com/milaboratory/mixcr/assembler/{VDJCGeneScoreAccumulator.java => VDJCGeneAccumulator.java} (56%) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/PreClone.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerParameters.java create mode 100644 src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index 22d700ec5..2ee573be1 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -37,13 +37,18 @@ import com.milaboratory.core.sequence.quality.QualityAggregationType; import com.milaboratory.core.sequence.quality.QualityAggregator; import com.milaboratory.mixcr.basictypes.ClonalSequence; +import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; +import java.util.List; +import java.util.Map; + public final class CloneAccumulator { - final VDJCGeneScoreAccumulator geneScoreAccumulator = new VDJCGeneScoreAccumulator(); + VDJCGeneAccumulator geneAccumulator = new VDJCGeneAccumulator(); + Map> genes; private ClonalSequence sequence; private final QualityAggregator aggregator; private long coreCount = 0, mappedCount = 0, initialCoreCount = -1; @@ -79,15 +84,39 @@ public void onBeforeMapping() { } public float getBestScore(GeneType geneType) { - VDJCGeneScoreAccumulator.GeneAndScore bestGene = geneScoreAccumulator.getBestGene(geneType); - return bestGene == null ? 0 : bestGene.score; + if (genes == null) + throw new IllegalStateException("Gene information not aggregated"); + List genes = this.genes.get(geneType); + return genes == null || genes.isEmpty() ? Float.NaN : genes.get(0).score; } public VDJCGeneId getBestGene(GeneType geneType) { - VDJCGeneScoreAccumulator.GeneAndScore bestGene = geneScoreAccumulator.getBestGene(geneType); - return bestGene == null ? null : bestGene.geneId; + if (genes == null) + throw new IllegalStateException("Gene information not aggregated"); + List genes = this.genes.get(geneType); + return genes == null || genes.isEmpty() ? null : genes.get(0).geneId; + } + + public boolean hasInfoFor(GeneType geneType) { + if (genes == null) + throw new IllegalStateException("Gene information not aggregated"); + List genes = this.genes.get(geneType); + return genes != null && !genes.isEmpty(); + } + + public boolean hasInfoFor(GeneType geneType, VDJCGeneId gene) { + if (genes == null) + throw new IllegalStateException("Gene information not aggregated"); + List genes = this.genes.get(geneType); + if (genes == null) + return false; + for (GeneAndScore gs : genes) + if (gs.geneId.equals(gene)) + return true; + return false; } + public Range[] getNRegions() { return nRegions; } @@ -124,7 +153,15 @@ public void mergeCounts(CloneAccumulator acc) { tagBuilder.add(acc.tagBuilder); } + public void aggregateGeneInfo(HasRelativeMinScore geneParameters) { + genes = geneAccumulator.aggregateInformation(geneParameters); + geneAccumulator = null; + } + public synchronized void accumulate(ClonalSequence data, VDJCAlignments alignment, boolean mapped) { + if (geneAccumulator == null) + throw new IllegalStateException("Gene information already aggregated"); + if (!mapped) { // Core sequence accumulation coreCount += alignment.getNumberOfReads(); @@ -132,7 +169,7 @@ public synchronized void accumulate(ClonalSequence data, VDJCAlignments alignmen // Accumulate information about V-D-J alignments only for strictly clustered reads // (only for core clonotypes members) - geneScoreAccumulator.accumulate(alignment); + geneAccumulator.accumulate(alignment); aggregator.aggregate(data.getConcatenated().getQuality()); } else // Mapped sequence accumulation diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index 736f57b27..6a7e8b5c1 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -53,7 +53,6 @@ import gnu.trove.list.array.TIntArrayList; import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; -import gnu.trove.map.hash.TObjectFloatHashMap; import io.repseq.core.*; import java.util.*; @@ -655,7 +654,7 @@ synchronized CloneAccumulator accumulate(ClonalSequence sequence, VDJCAlignments public List build() { CloneAccumulator[] accs = accumulators.values().toArray(new CloneAccumulator[0]); for (CloneAccumulator acc : accs) - acc.geneScoreAccumulator.aggregateInformation(parameters.cloneFactoryParameters); + acc.aggregateGeneInfo(parameters.cloneFactoryParameters); // Stores list of clonotypes clustered into specific clonotype final TIntObjectHashMap reversePreClustered = new TIntObjectHashMap<>(); @@ -806,89 +805,20 @@ private Range[] extractNRegions(ClonalSequence clonalSequence, VDJCAlignments al VJCSignature extractSignature(VDJCAlignments alignments) { return new VJCSignature( - parameters.getSeparateByV() ? getGeneId(alignments, GeneType.Variable) : DO_NOT_CHECK, - parameters.getSeparateByJ() ? getGeneId(alignments, GeneType.Joining) : DO_NOT_CHECK, - parameters.getSeparateByC() ? getGeneId(alignments, GeneType.Constant) : DO_NOT_CHECK + parameters.getSeparateByV() ? getGeneId(alignments, GeneType.Variable) : VJCSignature.DO_NOT_CHECK, + parameters.getSeparateByJ() ? getGeneId(alignments, GeneType.Joining) : VJCSignature.DO_NOT_CHECK, + parameters.getSeparateByC() ? getGeneId(alignments, GeneType.Constant) : VJCSignature.DO_NOT_CHECK ); } VJCSignature extractSignature(CloneAccumulator cloneAccumulator) { return new VJCSignature( - parameters.getSeparateByV() ? cloneAccumulator.getBestGene(GeneType.Variable) : DO_NOT_CHECK, - parameters.getSeparateByJ() ? cloneAccumulator.getBestGene(GeneType.Joining) : DO_NOT_CHECK, - parameters.getSeparateByC() ? cloneAccumulator.getBestGene(GeneType.Constant) : DO_NOT_CHECK + parameters.getSeparateByV() ? cloneAccumulator.getBestGene(GeneType.Variable) : VJCSignature.DO_NOT_CHECK, + parameters.getSeparateByJ() ? cloneAccumulator.getBestGene(GeneType.Joining) : VJCSignature.DO_NOT_CHECK, + parameters.getSeparateByC() ? cloneAccumulator.getBestGene(GeneType.Constant) : VJCSignature.DO_NOT_CHECK ); } - /** - * Special marker GeneID used to make matchHits procedure to ignore V, J or C genes during matchHits procedure - */ - private static final VDJCGeneId DO_NOT_CHECK = new VDJCGeneId(new VDJCLibraryId("NO_LIBRARY", 0), "DO_NOT_CHECK"); - - static final class VJCSignature { - final VDJCGeneId vGene, jGene, cGene; - - /** - * null for absent hits, DO_NOT_CHECK to ignore corresponding gene - */ - VJCSignature(VDJCGeneId vGene, VDJCGeneId jGene, VDJCGeneId cGene) { - this.vGene = vGene; - this.jGene = jGene; - this.cGene = cGene; - } - - boolean matchHits(CloneAccumulator acc) { - TObjectFloatHashMap minor; - - if (vGene != DO_NOT_CHECK) { - minor = acc.geneScoreAccumulator.geneScores.get(GeneType.Variable); - if (vGene == null && (minor != null && !minor.isEmpty())) - return false; - if (vGene != null && minor != null && !minor.containsKey(vGene)) - return false; - } - - if (jGene != DO_NOT_CHECK) { - minor = acc.geneScoreAccumulator.geneScores.get(GeneType.Joining); - if (jGene == null && (minor != null && !minor.isEmpty())) - return false; - if (jGene != null && minor != null && !minor.containsKey(jGene)) - return false; - } - - if (cGene != DO_NOT_CHECK) { - minor = acc.geneScoreAccumulator.geneScores.get(GeneType.Constant); - if (cGene == null && (minor != null && !minor.isEmpty())) - return false; - if (cGene != null && minor != null && !minor.containsKey(cGene)) - return false; - } - - return true; - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - - VJCSignature that = (VJCSignature) o; - - if (vGene != null ? !vGene.equals(that.vGene) : that.vGene != null) return false; - if (jGene != null ? !jGene.equals(that.jGene) : that.jGene != null) return false; - return !(cGene != null ? !cGene.equals(that.cGene) : that.cGene != null); - - } - - @Override - public int hashCode() { - int result = vGene != null ? vGene.hashCode() : 0; - result = 31 * result + (jGene != null ? jGene.hashCode() : 0); - result = 31 * result + (cGene != null ? cGene.hashCode() : 0); - return result; - } - } - static VDJCGeneId getGeneId(VDJCAlignments alignments, GeneType type) { VDJCHit hit = alignments.getBestHit(type); return hit == null ? null : hit.getGene().getId(); diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index 3797a0d19..e56d642b4 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -38,8 +38,6 @@ import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.vdjaligners.SingleDAligner; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; -import gnu.trove.iterator.TObjectFloatIterator; -import gnu.trove.map.hash.TObjectFloatHashMap; import io.repseq.core.*; import java.util.*; @@ -83,7 +81,7 @@ public CloneFactory(CloneFactoryParameters parameters, GeneFeature[] assemblingF } public Clone create(int id, double count, - EnumMap> geneScores, + Map> geneScores, TagCounter tagCounter, NSequenceWithQuality[] targets, Integer group) { @@ -95,7 +93,7 @@ public Clone create(int id, double count, GeneFeature featureToAlign = featuresToAlign.get(geneType); - TObjectFloatHashMap gtGeneScores = geneScores.get(geneType); + List gtGeneScores = geneScores.get(geneType); if (gtGeneScores == null) continue; @@ -118,10 +116,8 @@ public Clone create(int id, double count, VDJCHit[] result = new VDJCHit[gtGeneScores.size()]; int pointer = 0; - TObjectFloatIterator iterator = gtGeneScores.iterator(); - while (iterator.hasNext()) { - iterator.advance(); - VDJCGene gene = usedGenes.get(iterator.key()); + for (GeneAndScore gs : gtGeneScores) { + VDJCGene gene = usedGenes.get(gs.geneId); Alignment[] alignments = new Alignment[assemblingFeatures.length]; for (int i = 0; i < assemblingFeatures.length; ++i) { if (intersectingFeatures[i] == null) @@ -206,8 +202,9 @@ public Clone create(int id, double count, } } } - result[pointer++] = new VDJCHit(gene, alignments, featureToAlign, iterator.value()); + result[pointer++] = new VDJCHit(gene, alignments, featureToAlign, gs.score); } + // might actually not be needed Arrays.sort(result, 0, pointer); hits.put(geneType, pointer < result.length ? Arrays.copyOf(result, pointer) : result); } @@ -254,7 +251,7 @@ public Clone create(int id, double count, } public Clone create(int id, CloneAccumulator accumulator) { - return create(id, accumulator.getCount(), accumulator.geneScoreAccumulator.geneScores, accumulator.tagBuilder.createAndDestroy(), accumulator.getSequence().sequences, null); + return create(id, accumulator.getCount(), accumulator.genes, accumulator.tagBuilder.createAndDestroy(), accumulator.getSequence().sequences, null); } private static boolean containsD(GeneFeature feature) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java b/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java new file mode 100644 index 000000000..ddbad7439 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java @@ -0,0 +1,39 @@ +package com.milaboratory.mixcr.assembler; + +import io.repseq.core.VDJCGeneId; + +import java.util.Objects; + +public final class GeneAndScore implements Comparable { + public final VDJCGeneId geneId; + public final float score; + + public GeneAndScore(VDJCGeneId geneId, float score) { + Objects.requireNonNull(geneId); + this.geneId = geneId; + this.score = score; + } + + @Override + public int compareTo(GeneAndScore o) { + int c; + + if ((c = Float.compare(o.score, score)) != 0) // from high to low score (reversed order) + return c; + + return geneId.compareTo(o.geneId); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + GeneAndScore that = (GeneAndScore) o; + return Float.compare(that.score, score) == 0 && geneId.equals(that.geneId); + } + + @Override + public int hashCode() { + return Objects.hash(geneId, score); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneScoreAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java similarity index 56% rename from src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneScoreAccumulator.java rename to src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java index b9ce9a566..1e4b18063 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneScoreAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java @@ -8,22 +8,20 @@ import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; -import java.util.EnumMap; +import java.util.*; -public final class VDJCGeneScoreAccumulator { - int observations = 0; - final EnumMap> geneScores = new EnumMap<>(GeneType.class); +public final class VDJCGeneAccumulator { + private final int[] observations = new int[GeneType.values().length]; + private final EnumMap> geneScores = new EnumMap<>(GeneType.class); public synchronized void accumulate(VDJCAlignments alignment) { - if (observations == -1) - throw new IllegalStateException("Already aggregated"); - // Accumulate information about all genes for (GeneType geneType : GeneType.VJC_REFERENCE) { TObjectFloatHashMap geneScores = this.geneScores.get(geneType); VDJCHit[] hits = alignment.getHits(geneType); if (hits.length == 0) continue; + observations[geneType.ordinal()]++; if (geneScores == null) this.geneScores.put(geneType, geneScores = new TObjectFloatHashMap<>()); for (VDJCHit hit : hits) { @@ -33,6 +31,33 @@ public synchronized void accumulate(VDJCAlignments alignment) { } } + public synchronized void accumulate(EnumMap genesAndScores) { + // Accumulate information about all genes + for (GeneType geneType : GeneType.VJC_REFERENCE) { + TObjectFloatHashMap geneScores = this.geneScores.get(geneType); + GeneAndScore[] data = genesAndScores.get(geneType); + if (data == null || data.length == 0) + continue; + observations[geneType.ordinal()]++; + if (geneScores == null) + this.geneScores.put(geneType, geneScores = new TObjectFloatHashMap<>()); + for (GeneAndScore gs : data) { + // Calculating sum of natural logarithms of scores + geneScores.adjustOrPutValue(gs.geneId, gs.score, gs.score); + } + } + } + + public boolean hasInfoFor(GeneType geneType) { + TObjectFloatHashMap scores = geneScores.get(geneType); + return scores != null && !scores.isEmpty(); + } + + public boolean contains(GeneType geneType, VDJCGeneId gene) { + TObjectFloatHashMap scores = geneScores.get(geneType); + return scores != null && scores.contains(gene); + } + public GeneAndScore getBestGene(GeneType geneType) { TObjectFloatHashMap scores = geneScores.get(geneType); if (scores == null) @@ -50,10 +75,8 @@ public GeneAndScore getBestGene(GeneType geneType) { return new GeneAndScore(maxAllele, maxScore); } - public void aggregateInformation(HasRelativeMinScore hasRelativeMinScore) { - if (observations == -1) - throw new IllegalStateException("Already aggregated"); - + public Map> aggregateInformation(HasRelativeMinScore hasRelativeMinScore) { + EnumMap> result = new EnumMap<>(GeneType.class); for (GeneType geneType : GeneType.VJC_REFERENCE) { float relativeMinScore = hasRelativeMinScore.getRelativeMinScore(geneType); if (Float.isNaN(relativeMinScore)) @@ -73,27 +96,19 @@ public void aggregateInformation(HasRelativeMinScore hasRelativeMinScore) { } maxScore = maxScore * relativeMinScore; + + List geneList = new ArrayList<>(); iterator = accumulatorGeneIds.iterator(); while (iterator.hasNext()) { iterator.advance(); - if (maxScore > iterator.value()) - iterator.remove(); - else - iterator.setValue(Math.round(iterator.value() * 10f / observations) / 10f); + if (iterator.value() > maxScore) + geneList.add(new GeneAndScore(iterator.key(), + Math.round(iterator.value() * 10f / observations[geneType.ordinal()]) / 10f)); } + Collections.sort(geneList); + result.put(geneType, geneList); } - // To prevent double aggregation - observations = -1; - } - - public static final class GeneAndScore { - public final VDJCGeneId geneId; - public final float score; - - public GeneAndScore(VDJCGeneId geneId, float score) { - this.geneId = geneId; - this.score = score; - } + return result; } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java b/src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java new file mode 100644 index 000000000..b1a56b91f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java @@ -0,0 +1,70 @@ +package com.milaboratory.mixcr.assembler; + +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGeneId; +import io.repseq.core.VDJCLibraryId; + +import java.util.Objects; + +public final class VJCSignature { + /** + * Special marker GeneID used to make matchHits procedure to ignore V, J or C genes during matchHits procedure + */ + public static final VDJCGeneId DO_NOT_CHECK = new VDJCGeneId(new VDJCLibraryId("NO_LIBRARY", 0), "DO_NOT_CHECK"); + private final VDJCGeneId vGene, jGene, cGene; + + /** + * null for absent hits, DO_NOT_CHECK to ignore corresponding gene + */ + VJCSignature(VDJCGeneId vGene, VDJCGeneId jGene, VDJCGeneId cGene) { + this.vGene = vGene; + this.jGene = jGene; + this.cGene = cGene; + } + + boolean matchHits(CloneAccumulator acc) { + if (vGene != DO_NOT_CHECK) { + if (vGene == null && acc.hasInfoFor(GeneType.Variable)) + return false; + if (vGene != null && acc.hasInfoFor(GeneType.Variable, vGene)) + return false; + } + + if (jGene != DO_NOT_CHECK) { + if (jGene == null && acc.hasInfoFor(GeneType.Joining)) + return false; + if (jGene != null && acc.hasInfoFor(GeneType.Joining, jGene)) + return false; + } + + if (cGene != DO_NOT_CHECK) { + if (cGene == null && acc.hasInfoFor(GeneType.Constant)) + return false; + if (cGene != null && acc.hasInfoFor(GeneType.Constant, cGene)) + return false; + } + + return true; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + + VJCSignature that = (VJCSignature) o; + + if (!Objects.equals(vGene, that.vGene)) return false; + if (!Objects.equals(jGene, that.jGene)) return false; + return Objects.equals(cGene, that.cGene); + + } + + @Override + public int hashCode() { + int result = vGene != null ? vGene.hashCode() : 0; + result = 31 * result + (jGene != null ? jGene.hashCode() : 0); + result = 31 * result + (cGene != null ? cGene.hashCode() : 0); + return result; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 9fed6880c..77bc77e52 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -38,7 +38,11 @@ import com.milaboratory.core.sequence.*; import com.milaboratory.core.sequence.quality.QualityTrimmer; import com.milaboratory.mixcr.assembler.CloneFactory; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.assembler.GeneAndScore; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence; import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; @@ -48,7 +52,6 @@ import gnu.trove.list.array.TIntArrayList; import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; -import gnu.trove.map.hash.TObjectFloatHashMap; import gnu.trove.map.hash.TObjectIntHashMap; import gnu.trove.set.hash.TIntHashSet; import io.repseq.core.*; @@ -245,15 +248,15 @@ public FullSeqAssemblerReport getReport() { return report; } - private EnumMap> originalGeneScores = null; + private EnumMap> originalGeneScores = null; - private EnumMap> getOriginalGeneScores() { + private EnumMap> getOriginalGeneScores() { if (originalGeneScores == null) { originalGeneScores = new EnumMap<>(GeneType.class); for (GeneType gt : GeneType.VDJC_REFERENCE) { - TObjectFloatHashMap scores = new TObjectFloatHashMap<>(); + List scores = new ArrayList<>(); for (VDJCHit hit : clone.getHits(gt)) - scores.put(hit.getGene().getId(), hit.getScore()); + scores.add(new GeneAndScore(hit.getGene().getId(), hit.getScore())); originalGeneScores.put(gt, scores); } } @@ -1426,7 +1429,7 @@ public RawVariantsData calculateRawData(Supplier> ali int groupCounter = 0; for (VDJCAlignments al : CUtils.it(alignments.get())) { if (taggedAnalysis()) { - TagTuple tagTuple = al.getTagCounter().singleOrNull(); + TagTuple tagTuple = al.getTagCounter().asKeyOrNull(); int grp = tagTupleToGroup.get(tagTuple); if (grp == -1) { grp = groupCounter++; @@ -1725,13 +1728,13 @@ PointSequence[] toPointSequences(VDJCAlignments alignments) { assemblingFeaturePointSeq = Stream.empty(); return Stream.concat( - assemblingFeaturePointSeq, - IntStream.range(0, alignments.numberOfTargets()) - .mapToObj(i -> toPointSequences(alignments, i)) - .flatMap(Collection::stream) - .collect(Collectors.groupingBy(s -> s.point)) - .values().stream() - .map(l -> l.stream().max(Comparator.comparingInt(a -> a.quality)).get())) + assemblingFeaturePointSeq, + IntStream.range(0, alignments.numberOfTargets()) + .mapToObj(i -> toPointSequences(alignments, i)) + .flatMap(Collection::stream) + .collect(Collectors.groupingBy(s -> s.point)) + .values().stream() + .map(l -> l.stream().max(Comparator.comparingInt(a -> a.quality)).get())) .toArray(PointSequence[]::new); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java index f927017e4..f05fb3dba 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java @@ -32,6 +32,7 @@ import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.alignment.AlignmentHelper; import com.milaboratory.core.sequence.NucleotideSequence; +import com.milaboratory.mixcr.assembler.GeneAndScore; import com.milaboratory.primitivio.annotations.Serializable; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -113,6 +114,10 @@ public VDJCGene getGene() { return gene; } + public GeneAndScore getGeneAndScore() { + return new GeneAndScore(getGene().getId(), getScore()); + } + public GeneFeature getAlignedFeature() { return alignedFeature; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java index 6eab5a7bf..d590073a1 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java @@ -6,11 +6,9 @@ import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.map.hash.TObjectDoubleHashMap; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Map; -import java.util.Set; +import java.util.*; import java.util.function.Predicate; +import java.util.stream.Collectors; /** * @@ -34,22 +32,50 @@ public TagCounter(TagTuple tags) { this(tags, 1.0); } - public TagTuple singleOrNull() { + public TagTuple asKeyPrefixOrNull(int level) { + TagTuple fullKey = asKeyOrNull(); + if (fullKey != null) + return fullKey.keyPrefix(level); + Set keySet = tags.keySet().stream() + .map(t -> t.keyPrefix(level)) + .collect(Collectors.toSet()); + if (keySet.size() != 1) + return null; + return keySet.iterator().next(); + } + + public TagTuple asKeyOrNull() { if (size() > 1 || size() == 0) return null; TObjectDoubleIterator it = iterator(); it.advance(); - return it.key(); + return it.key().key(); + } + + public TagTuple asKeyPrefixOrError(int level) { + TagTuple result = asKeyPrefixOrNull(level); + if (result == null) + throw new IllegalStateException("Aggregated tag information, single tag tuple expected."); + return result; } - public TagTuple singleOrError() { - TagTuple result = singleOrNull(); + public TagTuple asKeyOrError() { + TagTuple result = asKeyOrNull(); if (result == null) throw new IllegalStateException("Aggregated tag information, single tag tuple expected."); return result; } + public Set keySuffixes(int depth) { + TagTuple fullKey = asKeyOrNull(); + if (fullKey != null) + return Collections.singleton(fullKey.keySuffix(depth)); + return tags.keySet().stream() + .map(t -> t.keySuffix(depth)) + .collect(Collectors.toSet()); + } + public Set keys() { return tags.keySet(); } @@ -160,7 +186,7 @@ public TagCounter[] splitBy(int index) { TagTuple t = it.key(); double count = it.value(); - TagCounterBuilder tb = map.computeIfAbsent(t.tags[index], __ -> new TagCounterBuilder()); + TagCounterBuilder tb = map.computeIfAbsent(t.get(index), __ -> new TagCounterBuilder()); tb.add(t, count); } return map.values().stream().map(TagCounterBuilder::createAndDestroy).toArray(TagCounter[]::new); @@ -193,7 +219,7 @@ public Set tags(int index) { TObjectDoubleIterator it = iterator(); while (it.hasNext()) { it.advance(); - set.add(it.key().tags[index]); + set.add(it.key().get(index)); } return set; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index da9da75cf..297c84121 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -11,13 +11,13 @@ * Tag may be a sample name, cell marker or unique molecular identifier. */ public final class TagTuple implements Comparable { - public final TagValue[] tags; + public static final TagTuple EMPTY = new TagTuple(); + + final TagValue[] tags; private final int hash; @SuppressWarnings("UnstableApiUsage") public TagTuple(TagValue... tags) { - if (tags.length == 0) - throw new IllegalArgumentException(); this.tags = tags; Hasher hasher = Hashing.murmur3_32_fixed().newHasher(); for (TagValue tag : tags) @@ -25,7 +25,11 @@ public TagTuple(TagValue... tags) { this.hash = hasher.hash().hashCode(); } - public TagTuple toKeys() { + /** + * Strips all non-key information (i.e. quality scores) from tags inside the tuple, + * and returns tag tuple intended to be used as a grouping key. + */ + public TagTuple key() { boolean hasNonKey = false; for (TagValue tag : tags) if (!tag.isKey()) { @@ -40,6 +44,49 @@ public TagTuple toKeys() { return new TagTuple(newTags); } + /** + * Strips all non-key information (i.e. quality scores) from tags inside the tuple, + * and returns tag tuple prefix of a specified depth, intended to be used as a grouping key. + */ + public TagTuple keyPrefix(int depth) { + if (depth == tags.length) + return key(); + if (depth == 0) + return EMPTY; + TagValue[] newTags = Arrays.copyOf(tags, depth); + for (int i = 0; i < newTags.length; i++) + newTags[i] = newTags[i].extractKey(); + return new TagTuple(newTags); + } + + /** + * Strips all non-key information from tags inside the tuple, + * and returns tag tuple suffix, by discarding a specified number of tuple elements from the left. + */ + public TagTuple keySuffix(int depth) { + if (depth == 0) + return key(); + if (depth == tags.length) + return EMPTY; + TagValue[] newTags = Arrays.copyOfRange(tags, depth + 1, tags.length); + for (int i = 0; i < newTags.length; i++) + newTags[i] = newTags[i].extractKey(); + return new TagTuple(newTags); + } + + public TagValue get(int idx) { + return tags[idx]; + } + + public int size() { + return tags.length; + } + + /** Returns clone of internal array */ + public TagValue[] asArray() { + return tags.clone(); + } + @Override public int compareTo(TagTuple o) { int l = Math.min(tags.length, o.tags.length); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index d00c39e59..33f36e027 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -140,7 +140,7 @@ public void run1() throws Exception { if (reader1.getTagsInfo() != null && reader1.getTagsInfo().tags.length > 0) { SmartProgressReporter.startProgressReport("Running assemble partial", reader1); - Function1 key = al -> al.getTagCounter().singleOrError().toKeys(); + Function1 key = al -> al.getTagCounter().asKeyOrError().key(); OutputPort> groups1 = PipeKt.group(reader1, key); OutputPort> groups2 = PipeKt.group(reader2, key); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index dab2c3964..955ee2e38 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -162,7 +162,7 @@ public void run1() throws Exception { TagTuple tagTuple = input.getTagCounter().keys().iterator().next(); NSequenceWithQuality[] tags = new NSequenceWithQuality[targetTagIndices.length]; for (int i = 0; i < targetTagIndices.length; i++) - tags[i] = ((SequenceAndQualityTagValue) tagTuple.tags[targetTagIndices[i]]).data; + tags[i] = ((SequenceAndQualityTagValue) tagTuple.get(targetTagIndices[i])).data; return tags; }; OutputPort cInput = CUtils.wrap(reader, mapper); @@ -226,7 +226,7 @@ public void run1() throws Exception { Processor mapper = !noCorrect ? al -> { - TagValue[] newTags = al.getTagCounter().singleOrError().tags.clone(); + TagValue[] newTags = al.getTagCounter().asKeyOrError().asArray(); CorrectionNode cn = correctionResult; for (int i : targetTagIndices) { NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); @@ -304,17 +304,17 @@ public SortingStep(int tagIdx) { public ToIntFunction getHashFunction() { return al -> { - TagValue[] tags = al.getTagCounter().singleOrError().tags; - return ((SequenceAndQualityTagValue) tags[tagIdx]).data.getSequence().hashCode(); + TagTuple tagTuple = al.getTagCounter().asKeyOrError(); + return ((SequenceAndQualityTagValue) tagTuple.get(tagIdx)).data.getSequence().hashCode(); }; } public Comparator getComparator() { return (al1, al2) -> { - TagValue[] tags1 = al1.getTagCounter().singleOrError().tags; - TagValue[] tags2 = al2.getTagCounter().singleOrError().tags; - return ((SequenceAndQualityTagValue) tags1[tagIdx]).data.getSequence().compareTo( - ((SequenceAndQualityTagValue) tags2[tagIdx]).data.getSequence()); + TagTuple tagTuple1 = al1.getTagCounter().asKeyOrError(); + TagTuple tagTuple2 = al2.getTagCounter().asKeyOrError(); + return ((SequenceAndQualityTagValue) tagTuple1.get(tagIdx)).data.getSequence().compareTo( + ((SequenceAndQualityTagValue) tagTuple2.get(tagIdx)).data.getSequence()); }; } } diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 7c60c2e44..19384e939 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -733,7 +733,7 @@ public String extractValue(VDJCObject object) { return NULL; if (keys.size() > 1) throw new IllegalArgumentException("object has multiple tag tuples: " + tc); - return keys.iterator().next().tags[finalIdx].extractKey().toString(); + return keys.iterator().next().get(finalIdx).extractKey().toString(); } }; } diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java new file mode 100644 index 000000000..d65979c9e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java @@ -0,0 +1,32 @@ +package com.milaboratory.mixcr.tags; + +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.mixcr.assembler.GeneAndScore; +import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.util.BitArray; +import io.repseq.core.GeneType; + +import java.util.List; +import java.util.Map; + +public final class PreClone { + /** Tag counter aggregating information about alignments with clonal sequence */ + public final TagCounter coreTagCounter; + /** Tag counter aggregating information across all alignments assigned to this pre-clone */ + public final TagCounter fullTagCounter; + /** Assembled clonal sequence */ + public final NSequenceWithQuality[] clonalSequence; + /** Aggregated V, J, C gene scoring and content information */ + public final Map> geneScores; + /** Ids of alignments assigned to this pre-clone */ + public final BitArray alignments; + + public PreClone(TagCounter coreTagCounter, TagCounter fullTagCounter, NSequenceWithQuality[] clonalSequence, + Map> geneScores, BitArray alignments) { + this.coreTagCounter = coreTagCounter; + this.fullTagCounter = fullTagCounter; + this.clonalSequence = clonalSequence; + this.geneScores = geneScores; + this.alignments = alignments; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java new file mode 100644 index 000000000..dcf6b7d2f --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java @@ -0,0 +1,254 @@ +package com.milaboratory.mixcr.tags; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.mitool.consensus.ConsensusResult; +import com.milaboratory.mitool.consensus.GConsensusAssembler; +import com.milaboratory.mitool.helpers.GroupOP; +import com.milaboratory.mitool.helpers.PipeKt; +import com.milaboratory.mixcr.assembler.GeneAndScore; +import com.milaboratory.mixcr.assembler.VDJCGeneAccumulator; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.util.BitArray; +import gnu.trove.map.hash.TObjectIntHashMap; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGeneId; +import kotlin.jvm.functions.Function1; + +import java.util.*; +import java.util.concurrent.atomic.AtomicInteger; + +public final class PreCloneAssembler { + final AtomicInteger idGenerator = new AtomicInteger(); + final PreCloneAssemblerParameters parameters; + final OutputPort> alignmentsReader1, alignmentsReader2; + + public PreCloneAssembler(PreCloneAssemblerParameters parameters, + OutputPort alignmentsReader1, + OutputPort alignmentsReader2) { + this.parameters = parameters; + Function1 gFunction = + vdjcAlignments -> vdjcAlignments.getTagCounter().asKeyPrefixOrError(parameters.groupingLevel); + this.alignmentsReader1 = PipeKt.group(alignmentsReader1, gFunction); + this.alignmentsReader2 = PipeKt.group(alignmentsReader2, gFunction); + } + + public List getForNextGroup() { + GroupOP grp1 = alignmentsReader1.take(); + List assemblerInput = new ArrayList<>(); + // Alignment infos for alignments containing all assembling features + // (i.e. for the rows from assemblerInput) + List alignmentInfos = new ArrayList<>(); + + // Pre-allocated data row + NSequenceWithQuality[] row = new NSequenceWithQuality[parameters.assemblingFeatures.length]; + + // Index inside the group + int localIdx = -1; + + // Step #1 + // First Pass over the data; Building input dataset for the consensus assembler and collecting + // required information about alignments for the step #3 + + outer: + for (VDJCAlignments al : CUtils.it(grp1)) { + localIdx++; + for (int i = 0; i < parameters.assemblingFeatures.length; i++) + if ((row[i] = al.getFeature(parameters.assemblingFeatures[i])) == null) + continue outer; + + assemblerInput.add(row); + EnumMap geneAndScores = new EnumMap<>(GeneType.class); + for (GeneType gt : GeneType.VJC_REFERENCE) { + VDJCHit[] hits = al.getHits(gt); + GeneAndScore[] gss = new GeneAndScore[hits.length]; + for (int i = 0; i < hits.length; i++) + gss[i] = hits[i].getGeneAndScore(); + geneAndScores.put(gt, gss); + } + alignmentInfos.add(new AlignmentInfo(localIdx, + al.getTagCounter().keySuffixes(parameters.groupingLevel), geneAndScores)); + + // Allocating array for the next data row + row = new NSequenceWithQuality[parameters.assemblingFeatures.length]; + } + + // Step #2 + // Building consensuses from the records collected on the step #1, and creating indices for + // clonotype assignment of alignments left after the previous step + + GConsensusAssembler gAssembler = new GConsensusAssembler(parameters.assemblerParameters, assemblerInput); + List consensuses = gAssembler.calculateConsensuses(); + int numberOfClones = consensuses.size(); + + // Accumulates V, J and C gene information for each consensus + // noinspection unchecked + Map>[] geneInfos = new Map[numberOfClones]; + // Saves local record indices, assigned to each of the consensuses + BitArray[] contents = new BitArray[numberOfClones]; + // I.e. UMIs for sole cell-barcode assembly use-case + Set[] tagSuffixess = new Set[numberOfClones]; + + // Union of all contents + // BitArray allAssignedToClonotypes = new BitArray((int) grp1.getCount()); + + // Tag suffixes unambiguously linked to a clonotype (store cloneId+1; -1 for ambiguous cases; 0 - not found) + TObjectIntHashMap tagSuffixToCloneId = new TObjectIntHashMap<>(); + // V, J and C genes unambiguously linked to a clonotype (store cloneId+1; -1 for ambiguous cases; 0 - not found) + TObjectIntHashMap vjcGenesToCloneId = new TObjectIntHashMap<>(); + + // Special map to simplify collection of additional information from already assigned alignment + // -1 = not assigned to any consensus / clonotype + // 0 = no assembling feature (target for empirical assignment) + // >0 = assigned to a specific consensus / clonotype (store cloneId+1) + int[] alignmentIndexToClonotypeIndex = new int[(int) grp1.getCount()]; + + for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { + ConsensusResult c = consensuses.get(cIdx); + VDJCGeneAccumulator acc = new VDJCGeneAccumulator(); + BitArray content = new BitArray((int) grp1.getCount()); + Set tagSuffixes = new HashSet<>(); + + int rIdx = -1; + while ((rIdx = c.recordsUsed.nextBit(rIdx + 1)) != -1) { + AlignmentInfo ai = alignmentInfos.get(rIdx); + acc.accumulate(ai.genesAndScores); + content.set(ai.localIdx); + tagSuffixes.addAll(ai.tagSuffixes); + alignmentIndexToClonotypeIndex[ai.localIdx] = cIdx + 1; + } + + // allAssignedToClonotypes.or(content); + + geneInfos[cIdx] = acc.aggregateInformation(parameters.relativeMinScores); + contents[cIdx] = content; + tagSuffixess[cIdx] = tagSuffixes; + + for (TagTuple ts : tagSuffixes) + if (tagSuffixToCloneId.get(ts) > 0) + tagSuffixToCloneId.put(ts, -1); // ambiguity detected + else + tagSuffixToCloneId.put(ts, cIdx + 1); + + for (GeneType gt : GeneType.VJC_REFERENCE) { + List gss = geneInfos[cIdx].get(gt); + if (gss == null) + continue; + for (GeneAndScore gs : gss) + if (vjcGenesToCloneId.get(gs.geneId) > 0) + vjcGenesToCloneId.put(gs.geneId, -1); + else + vjcGenesToCloneId.put(gs.geneId, cIdx + 1); + } + } + + // Information from the alignments with assembling features, but not assigned to any contigs interpreted as + // ambiguous + for (AlignmentInfo ai : alignmentInfos) { + if (alignmentIndexToClonotypeIndex[ai.localIdx] > 0) + continue; + + alignmentIndexToClonotypeIndex[ai.localIdx] = -1; + + for (TagTuple ts : ai.tagSuffixes) + tagSuffixToCloneId.put(ts, -1); + + for (GeneType gt : GeneType.VJC_REFERENCE) { + GeneAndScore[] gss = ai.genesAndScores.get(gt); + if (gss == null) + continue; + for (GeneAndScore gs : gss) + vjcGenesToCloneId.put(gs.geneId, -1); + } + } + + // Step #3 + // Assigning leftover alignments + + TagCounterBuilder[] coreTagCounterBuilders = new TagCounterBuilder[numberOfClones]; + TagCounterBuilder[] fullTagCounterBuilders = new TagCounterBuilder[numberOfClones]; + for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { + coreTagCounterBuilders[cIdx] = new TagCounterBuilder(); + fullTagCounterBuilders[cIdx] = new TagCounterBuilder(); + } + + GroupOP grp2 = alignmentsReader2.take(); + assert grp1.getKey().equals(grp2.getKey()); + + localIdx = -1; + for (VDJCAlignments al : CUtils.it(grp1)) { + localIdx++; + + int cIdx = alignmentIndexToClonotypeIndex[localIdx]; + + // Running empirical assignment for the alignments not yet assigned + if (cIdx == 0) { + // V, J and C gene based assignment + for (GeneType gt : GeneType.VJC_REFERENCE) + for (VDJCHit hit : al.getHits(gt)) { + int c = vjcGenesToCloneId.get(hit.getGene().getId()); + if (c <= 0) + continue; + if (cIdx == 0) + cIdx = c; + else if (cIdx != c) + cIdx = -1; + } + + // TagSuffix based assignment + for (TagTuple ts : al.getTagCounter().keySuffixes(parameters.groupingLevel)) { + int c = tagSuffixToCloneId.get(ts); + if (c <= 0) + continue; + if (cIdx == 0) + cIdx = c; + else if (cIdx != c) + cIdx = -1; + } + + if (cIdx > 0) + // Adding alignment to the clone + contents[cIdx - 1].set(localIdx); + } else if (cIdx > 0) + // Using second iteration over the alignments to assemble TagCounters from the alignments assigned to + // clonotypes based on their contig assignment + coreTagCounterBuilders[cIdx - 1].add(al.getTagCounter()); + + if (cIdx > 0) + fullTagCounterBuilders[cIdx].add(al.getTagCounter()); + } + + List result = new ArrayList<>(); + for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { + ConsensusResult.SingleConsensus[] cs = consensuses.get(cIdx).consensuses; + NSequenceWithQuality[] clonalSequence = new NSequenceWithQuality[cs.length]; + for (int i = 0; i < cs.length; i++) + clonalSequence[i] = cs[i].consensus; + result.add(new PreClone( + coreTagCounterBuilders[cIdx].createAndDestroy(), + fullTagCounterBuilders[cIdx].createAndDestroy(), + clonalSequence, + geneInfos[cIdx], + contents[cIdx] + )); + } + + return result; + } + + private static final class AlignmentInfo { + final int localIdx; + final Set tagSuffixes; + final EnumMap genesAndScores; + + public AlignmentInfo(int localIdx, Set tagSuffixes, EnumMap genesAndScores) { + this.localIdx = localIdx; + this.tagSuffixes = tagSuffixes; + this.genesAndScores = genesAndScores; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerParameters.java new file mode 100644 index 000000000..16ac5aa57 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerParameters.java @@ -0,0 +1,21 @@ +package com.milaboratory.mixcr.tags; + +import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; +import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; +import io.repseq.core.GeneFeature; + +public final class PreCloneAssemblerParameters { + final GConsensusAssemblerParameters assemblerParameters; + final HasRelativeMinScore relativeMinScores; + final GeneFeature[] assemblingFeatures; + final int groupingLevel; + + public PreCloneAssemblerParameters(GConsensusAssemblerParameters assemblerParameters, + HasRelativeMinScore relativeMinScores, + GeneFeature[] assemblingFeatures, int groupingLevel) { + this.assemblerParameters = assemblerParameters; + this.relativeMinScores = relativeMinScores; + this.assemblingFeatures = assemblingFeatures; + this.groupingLevel = groupingLevel; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java new file mode 100644 index 000000000..82e114308 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java @@ -0,0 +1,5 @@ +package com.milaboratory.mixcr.tags; + +public final class PreCloneAssemblerReport { + // final AtomicLong +} From d555469a8be14a4462a314285c63609a95b413cf Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Fri, 27 May 2022 22:56:57 +0300 Subject: [PATCH 230/282] chore: milib & mitool upgrade --- build.gradle.kts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 5076d01a2..a54926e04 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -81,9 +81,9 @@ repositories { } } -val milibVersion = "1.15.0-44-master" +val milibVersion = "1.15.0-45-master" val repseqioVersion = "1.3.5-30-master" -val mitoolVersion = "0.9.1-10-main" +val mitoolVersion = "0.9.1-11-main" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" From ce4192a7d44da5eeb09f983f2113d6a83c57aaa3 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 28 May 2022 02:44:43 +0300 Subject: [PATCH 231/282] WIP --- .../mixcr/basictypes/tag/TagsInfo.java | 35 +++++++--- .../milaboratory/mixcr/cli/CommandAlign.java | 2 +- .../cli/CommandAssemblePartialAlignments.java | 1 + .../mixcr/cli/CommandAssemblePreClones.java | 67 +++++++++++++++++++ .../mixcr/cli/CommandCorrectAndSortTags.java | 2 +- .../java/com/milaboratory/mixcr/cli/Main.java | 2 + .../com/milaboratory/mixcr/tags/PreClone.java | 5 +- .../mixcr/tags/PreCloneAssembler.java | 31 +++++++-- .../mixcr/tags/PreCloneAssemblerReport.java | 34 +++++++++- .../vdjaligners/VDJCAlignerParameters.java | 9 ++- .../mixcr/basictypes/tag/TagInfoTest.java | 2 +- 11 files changed, 171 insertions(+), 19 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index 8b41ef7dc..27211ec50 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -9,20 +9,39 @@ @Serializable(asJson = true) public final class TagsInfo { - @JsonProperty("sorted") - public final boolean sorted; + @JsonProperty("sortingLevel") + public final int sortingLevel; @JsonProperty("tags") public final TagInfo[] tags; @JsonCreator - public TagsInfo(@JsonProperty("sorted") boolean sorted, @JsonProperty("tags") TagInfo... tags) { + public TagsInfo(@JsonProperty("sortingLevel") int sortingLevel, @JsonProperty("tags") TagInfo... tags) { Objects.requireNonNull(tags); - this.sorted = sorted; + this.sortingLevel = sortingLevel; this.tags = tags; } - public TagsInfo setSorted(boolean sorted){ - return new TagsInfo(sorted, tags); + public int getDepthFor(TagType groupingLevel) { + for (int i = 0; i < tags.length; i++) + if (tags[i].getType().ordinal() > groupingLevel.ordinal()) + return i; + return tags.length; + } + + public TagInfo get(int idx) { + return tags[idx]; + } + + public int size() { + return tags.length; + } + + public int getSortingLevel() { + return sortingLevel; + } + + public TagsInfo setSorted(int sortedLevel) { + return new TagsInfo(sortedLevel, tags); } @Override @@ -30,12 +49,12 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; TagsInfo tagsInfo = (TagsInfo) o; - return sorted == tagsInfo.sorted && Arrays.equals(tags, tagsInfo.tags); + return sortingLevel == tagsInfo.sortingLevel && Arrays.equals(tags, tagsInfo.tags); } @Override public int hashCode() { - int result = Objects.hash(sorted); + int result = Objects.hash(sortingLevel); result = 31 * result + Arrays.hashCode(tags); return result; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 16af43ede..d822e35a7 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -644,7 +644,7 @@ else if (featureSequence.containsWildcards()) if (writer != null) writer.header(aligner, getFullPipelineConfiguration(), tagSearchPlan != null - ? new TagsInfo(false, tagSearchPlan.tagInfos.toArray(new TagInfo[0])) + ? new TagsInfo(0, tagSearchPlan.tagInfos.toArray(new TagInfo[0])) : null); OutputPort sReads = reader; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 33f36e027..f9175a171 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -124,6 +124,7 @@ public void run1() throws Exception { VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(in); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { + // FIXME sorting level !!!!! writer.header(reader1.getParameters(), reader1.getUsedGenes(), getFullPipelineConfiguration(), reader1.getTagsInfo()); PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(assemblerParameters, reader1.getParameters(), diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java new file mode 100644 index 000000000..0ca68cbe0 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java @@ -0,0 +1,67 @@ +package com.milaboratory.mixcr.cli; + +import com.milaboratory.core.alignment.LinearGapAlignmentScoring; +import com.milaboratory.mitool.consensus.AAssemblerParameters; +import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.tag.TagType; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; +import com.milaboratory.mixcr.tags.PreClone; +import com.milaboratory.mixcr.tags.PreCloneAssembler; +import com.milaboratory.mixcr.tags.PreCloneAssemblerParameters; +import com.milaboratory.util.ReportHelper; +import io.repseq.core.GeneFeature; + +import java.util.List; + +import static picocli.CommandLine.Command; +import static picocli.CommandLine.Parameters; + +@Command(name = "assemblePreClones", + separator = " ", + hidden = true) +public class CommandAssemblePreClones extends ACommandMiXCR { + @Parameters(description = "input_file") + public String inputFile; + + private static final AAssemblerParameters aAssemblerParams = AAssemblerParameters.builder() + .bandWidth(4) + .scoring(LinearGapAlignmentScoring.getNucleotideBLASTScoring()) + .minAlignmentScore(40) + .maxAlignmentPenalty(90) + .trimMinimalSumQuality(20) + .trimReferenceRegion(false) + .maxQuality((byte) 45) + .build(); + private static final GConsensusAssemblerParameters gAssemblerParams = GConsensusAssemblerParameters.builder() + .aAssemblerParameters(aAssemblerParams) + .maxIterations(4) + .minAltSeedQualityScore((byte) 11) + .minimalRecordShare(0.001) + .minimalRecordCount(2) + .build(); + + @Override + public void run0() throws Exception { + + try ( + VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(inputFile); + VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(inputFile) + ) { + TagsInfo tagsInfo = reader1.getTagsInfo(); + int depth = tagsInfo.getDepthFor(TagType.CellTag); + if (tagsInfo.getSortingLevel() < depth) + throwValidationException("Input file has insufficient sorting level"); + + PreCloneAssemblerParameters params = new PreCloneAssemblerParameters( + gAssemblerParams, reader1.getParameters(), + new GeneFeature[]{GeneFeature.CDR3}, + depth); + PreCloneAssembler assembler = new PreCloneAssembler(params, reader1, reader2); + List clones; + while ((clones = assembler.getForNextGroup()) != null) { + } + assembler.getReport().writeReport(ReportHelper.STDOUT); + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index 955ee2e38..0fd63af96 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -259,7 +259,7 @@ public void run1() throws Exception { SmartProgressReporter.extractProgress(sorted, reader.getNumberOfReads())); // Initializing and writing results to the output file - writer.header(reader, getFullPipelineConfiguration(), reader.getTagsInfo().setSorted(true)); + writer.header(reader, getFullPipelineConfiguration(), reader.getTagsInfo().setSorted(reader.getTagsInfo().tags.length)); for (VDJCAlignments al : CUtils.it(sorted)) writer.write(al); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 3efb9db36..19e2172e1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -264,6 +264,8 @@ public static CommandLine mkCmd() { .addSubcommand("alignmentsDiff", CommandAlignmentsDiff.class) .addSubcommand("clonesDiff", CommandClonesDiff.class) + .addSubcommand("assemblePreClones", CommandAssemblePreClones.class) + .addSubcommand("alignmentsStat", CommandAlignmentsStats.class) .addSubcommand("listLibraries", CommandListLibraries.class) .addSubcommand("versionInfo", CommandVersionInfo.class) diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java index d65979c9e..1a21bbaad 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java @@ -10,6 +10,8 @@ import java.util.Map; public final class PreClone { + /** Pre-clonotype id */ + public long id; /** Tag counter aggregating information about alignments with clonal sequence */ public final TagCounter coreTagCounter; /** Tag counter aggregating information across all alignments assigned to this pre-clone */ @@ -21,8 +23,9 @@ public final class PreClone { /** Ids of alignments assigned to this pre-clone */ public final BitArray alignments; - public PreClone(TagCounter coreTagCounter, TagCounter fullTagCounter, NSequenceWithQuality[] clonalSequence, + public PreClone(long id, TagCounter coreTagCounter, TagCounter fullTagCounter, NSequenceWithQuality[] clonalSequence, Map> geneScores, BitArray alignments) { + this.id = id; this.coreTagCounter = coreTagCounter; this.fullTagCounter = fullTagCounter; this.clonalSequence = clonalSequence; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java index dcf6b7d2f..1b95e8c4d 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java @@ -23,9 +23,10 @@ import java.util.concurrent.atomic.AtomicInteger; public final class PreCloneAssembler { - final AtomicInteger idGenerator = new AtomicInteger(); - final PreCloneAssemblerParameters parameters; - final OutputPort> alignmentsReader1, alignmentsReader2; + private final PreCloneAssemblerReport report = new PreCloneAssemblerReport(); + private final AtomicInteger idGenerator = new AtomicInteger(); + private final PreCloneAssemblerParameters parameters; + private final OutputPort> alignmentsReader1, alignmentsReader2; public PreCloneAssembler(PreCloneAssemblerParameters parameters, OutputPort alignmentsReader1, @@ -37,8 +38,18 @@ public PreCloneAssembler(PreCloneAssemblerParameters parameters, this.alignmentsReader2 = PipeKt.group(alignmentsReader2, gFunction); } + public PreCloneAssemblerReport getReport() { + return report; + } + public List getForNextGroup() { GroupOP grp1 = alignmentsReader1.take(); + + if (grp1 == null) + return null; + + report.inputGroups.incrementAndGet(); + List assemblerInput = new ArrayList<>(); // Alignment infos for alignments containing all assembling features // (i.e. for the rows from assemblerInput) @@ -77,6 +88,8 @@ public List getForNextGroup() { row = new NSequenceWithQuality[parameters.assemblingFeatures.length]; } + report.inputAlignments.addAndGet(localIdx); + // Step #2 // Building consensuses from the records collected on the step #1, and creating indices for // clonotype assignment of alignments left after the previous step @@ -84,6 +97,8 @@ public List getForNextGroup() { GConsensusAssembler gAssembler = new GConsensusAssembler(parameters.assemblerParameters, assemblerInput); List consensuses = gAssembler.calculateConsensuses(); int numberOfClones = consensuses.size(); + report.clonotypes.addAndGet(numberOfClones); + report.clonotypesPerGroup.get(numberOfClones).incrementAndGet(); // Accumulates V, J and C gene information for each consensus // noinspection unchecked @@ -120,6 +135,7 @@ public List getForNextGroup() { content.set(ai.localIdx); tagSuffixes.addAll(ai.tagSuffixes); alignmentIndexToClonotypeIndex[ai.localIdx] = cIdx + 1; + report.coreAlignments.incrementAndGet(); } // allAssignedToClonotypes.or(content); @@ -154,6 +170,8 @@ public List getForNextGroup() { alignmentIndexToClonotypeIndex[ai.localIdx] = -1; + report.discardedCoreAlignments.incrementAndGet(); + for (TagTuple ts : ai.tagSuffixes) tagSuffixToCloneId.put(ts, -1); @@ -210,9 +228,11 @@ else if (cIdx != c) cIdx = -1; } - if (cIdx > 0) + if (cIdx > 0) { // Adding alignment to the clone contents[cIdx - 1].set(localIdx); + report.empiricallyAssignedAlignments.incrementAndGet(); + } } else if (cIdx > 0) // Using second iteration over the alignments to assemble TagCounters from the alignments assigned to // clonotypes based on their contig assignment @@ -220,6 +240,8 @@ else if (cIdx != c) if (cIdx > 0) fullTagCounterBuilders[cIdx].add(al.getTagCounter()); + else + report.unassignedAlignments.incrementAndGet(); } List result = new ArrayList<>(); @@ -229,6 +251,7 @@ else if (cIdx != c) for (int i = 0; i < cs.length; i++) clonalSequence[i] = cs[i].consensus; result.add(new PreClone( + idGenerator.incrementAndGet(), coreTagCounterBuilders[cIdx].createAndDestroy(), fullTagCounterBuilders[cIdx].createAndDestroy(), clonalSequence, diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java index 82e114308..9024a5167 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java @@ -1,5 +1,35 @@ package com.milaboratory.mixcr.tags; -public final class PreCloneAssemblerReport { - // final AtomicLong +import com.milaboratory.mitool.pattern.search.FormatSettings; +import com.milaboratory.mitool.pattern.search.ReportKt; +import com.milaboratory.mitool.report.ConcurrentAtomicLongMap; +import com.milaboratory.util.Report; +import com.milaboratory.util.ReportHelper; + +import java.util.concurrent.atomic.AtomicLong; + +public final class PreCloneAssemblerReport implements Report { + final AtomicLong inputGroups = new AtomicLong(); + final AtomicLong inputAlignments = new AtomicLong(); + final AtomicLong clonotypes = new AtomicLong(); + final ConcurrentAtomicLongMap clonotypesPerGroup = new ConcurrentAtomicLongMap<>(); + final AtomicLong coreAlignments = new AtomicLong(); + final AtomicLong discardedCoreAlignments = new AtomicLong(); + final AtomicLong empiricallyAssignedAlignments = new AtomicLong(); + final AtomicLong unassignedAlignments = new AtomicLong(); + + @Override + public void writeReport(ReportHelper helper) { + helper.writeField("Number of input groups", inputGroups.get()); + helper.writeField("Number of input alignments", inputAlignments.get()); + helper.writeField("Number of output clonotypes", inputAlignments.get()); + helper.println("Number of clonotypes per group"); + helper.print(ReportKt.format(clonotypesPerGroup.getImmutable(), " ", + new StringBuilder(), new FormatSettings(0), 0).toString()); + helper.writePercentAndAbsoluteField("Number of core alignments", coreAlignments.get(), inputAlignments.get()); + helper.writePercentAndAbsoluteField("Discarded core alignments", discardedCoreAlignments.get(), coreAlignments.get()); + helper.writePercentAndAbsoluteField("Empirically assigned alignments", empiricallyAssignedAlignments.get(), inputAlignments.get()); + helper.writePercentAndAbsoluteField("Unassigned alignments", unassignedAlignments.get(), inputAlignments.get()); + + } } diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java index 822f8362a..836ac0e17 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java @@ -35,6 +35,7 @@ import com.milaboratory.core.merger.MergerParameters; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.HasFeatureToAlign; +import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; import com.milaboratory.primitivio.annotations.Serializable; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -46,7 +47,7 @@ getterVisibility = JsonAutoDetect.Visibility.NONE) @Serializable(asJson = true) @JsonIgnoreProperties(ignoreUnknown = true) -public final class VDJCAlignerParameters implements HasFeatureToAlign, java.io.Serializable { +public final class VDJCAlignerParameters implements HasRelativeMinScore, HasFeatureToAlign, java.io.Serializable { @JsonIgnore private final EnumMap alignmentParameters; private VJAlignmentOrder vjAlignmentOrder; @@ -376,6 +377,12 @@ public Set getGeneTypesWithLinearScoring() { return Collections.unmodifiableSet(gtRequiringIndelShifts); } + @Override + public float getRelativeMinScore(GeneType gt) { + GeneAlignmentParameters ap = getGeneAlignerParameters(gt); + return ap == null ? Float.NaN : ap.getRelativeMinScore(); + } + @Override public String toString() { return "VDJCAlignerParameters{" + diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java index 064eab892..85b06d10b 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java @@ -7,6 +7,6 @@ public class TagInfoTest { @Test public void test1() { TestUtil.assertJson(new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2)); - TestUtil.assertJson(new TagsInfo(false, new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2))); + TestUtil.assertJson(new TagsInfo(12, new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2))); } } \ No newline at end of file From 6bbbec4d852d01783ca66d6575daea4c20f732b2 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 28 May 2022 21:27:22 +0300 Subject: [PATCH 232/282] bu commit, in the middle of TagCount, etc.. abstraction refactoring, first code that compiles, refactoring not yet finished. --- .../mixcr/assembler/CloneAccumulator.java | 6 +- .../assembler/CloneClusteringStrategy.java | 6 +- .../mixcr/assembler/CloneFactory.java | 6 +- .../assembler/fullseq/FullSeqAssembler.java | 16 +- .../milaboratory/mixcr/basictypes/Clone.java | 26 +- .../mixcr/basictypes/CloneSet.java | 20 +- .../com/milaboratory/mixcr/basictypes/IO.java | 18 +- .../mixcr/basictypes/VDJCAlignments.java | 40 +-- .../mixcr/basictypes/VDJCObject.java | 16 +- .../milaboratory/mixcr/basictypes/tag/IO.java | 27 +- .../mixcr/basictypes/tag/TagCount.java | 308 ++++++++++++++++++ .../basictypes/tag/TagCountAggregator.java | 114 +++++++ .../mixcr/basictypes/tag/TagCounter.java | 226 ------------- .../basictypes/tag/TagCounterBuilder.java | 92 ------ .../mixcr/basictypes/tag/TagTuple.java | 14 +- .../milaboratory/mixcr/cli/CommandAlign.java | 4 +- .../mixcr/cli/CommandAssemble.java | 6 +- .../mixcr/cli/CommandAssembleContigs.java | 5 +- .../cli/CommandAssemblePartialAlignments.java | 2 +- .../mixcr/cli/CommandCorrectAndSortTags.java | 16 +- .../milaboratory/mixcr/cli/CommandExport.java | 8 +- .../mixcr/export/FieldExtractors.java | 8 +- .../PartialAlignmentsAssembler.java | 22 +- .../PartialAlignmentsAssemblerAligner.java | 4 +- .../mixcr/partialassembler/TargetMerger.java | 4 +- .../com/milaboratory/mixcr/tags/PreClone.java | 12 +- .../mixcr/tags/PreCloneAssembler.java | 24 +- .../mixcr/util/VDJCObjectExtender.java | 4 +- .../mixcr/vdjaligners/VDJCAlignerPVFirst.java | 4 +- .../mixcr/vdjaligners/VDJCAlignerS.java | 8 +- 30 files changed, 591 insertions(+), 475 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java delete mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java delete mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounterBuilder.java diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index 2ee573be1..f1f0bde82 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -39,7 +39,7 @@ import com.milaboratory.mixcr.basictypes.ClonalSequence; import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; @@ -54,7 +54,7 @@ public final class CloneAccumulator { private long coreCount = 0, mappedCount = 0, initialCoreCount = -1; private volatile int cloneIndex = -1; final Range[] nRegions; - final TagCounterBuilder tagBuilder = new TagCounterBuilder(); + final TagCountAggregator tagBuilder = new TagCountAggregator(); public CloneAccumulator(ClonalSequence sequence, Range[] nRegions, QualityAggregationType qualityAggregationType) { this.sequence = sequence; @@ -165,7 +165,7 @@ public synchronized void accumulate(ClonalSequence data, VDJCAlignments alignmen if (!mapped) { // Core sequence accumulation coreCount += alignment.getNumberOfReads(); - tagBuilder.add(alignment.getTagCounter()); + tagBuilder.add(alignment.getTagCount()); // Accumulate information about V-D-J alignments only for strictly clustered reads // (only for core clonotypes members) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java index 4e8d3230d..c8d003800 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java @@ -36,7 +36,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.tree.NeighborhoodIterator; import com.milaboratory.core.tree.TreeSearchParameters; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; public class CloneClusteringStrategy implements ClusteringStrategy { final CloneClusteringParameters parameters; @@ -57,8 +57,8 @@ public boolean canAddToCluster(Cluster cluster, return false; double minimalTagSetOverlap = parameters.getMinimalTagSetOverlap(); if (minimalTagSetOverlap > 0) { - TagCounterBuilder headTags = cluster.getHead().tagBuilder; - TagCounterBuilder minorTags = minorObject.tagBuilder; + TagCountAggregator headTags = cluster.getHead().tagBuilder; + TagCountAggregator minorTags = minorObject.tagBuilder; if (headTags.intersectionFractionOf(minorTags) >= minimalTagSetOverlap) return true; } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index e56d642b4..c48ec8bc3 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -35,7 +35,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.vdjaligners.SingleDAligner; import com.milaboratory.mixcr.vdjaligners.VDJCAligner; import io.repseq.core.*; @@ -82,7 +82,7 @@ public CloneFactory(CloneFactoryParameters parameters, GeneFeature[] assemblingF public Clone create(int id, double count, Map> geneScores, - TagCounter tagCounter, + TagCount tagCount, NSequenceWithQuality[] targets, Integer group) { EnumMap hits = new EnumMap<>(GeneType.class); @@ -247,7 +247,7 @@ public Clone create(int id, double count, else hits.put(GeneType.Diversity, new VDJCHit[0]); - return new Clone(targets, hits, tagCounter, count, id, group); + return new Clone(targets, hits, tagCount, count, id, group); } public Clone create(int id, CloneAccumulator accumulator) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 77bc77e52..8aba67a5c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -43,7 +43,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import gnu.trove.impl.Constants; @@ -149,7 +149,7 @@ public FullSeqAssembler(CloneFactory cloneFactory, this.parameters = parameters; this.clone = clone; - if (clone.getTagCounter() == null || clone.getTagCounter().isEmpty()) { + if (clone.getTagCount() == null || clone.getTagCount().isNoTag()) { this.tagTupleToGroup = null; this.groupToTagTuple = null; } else { @@ -944,7 +944,7 @@ else if (floatingRightBound) NSequenceWithQuality assemblingFeatureSeq = targets.sequences[targets.assemblingFeatureTargetId] .getRange(targets.assemblingFeatureOffset, targets.assemblingFeatureOffset + targets.assemblingFeatureLength); - Clone clone = cloneFactory.create(0, targets.count, getOriginalGeneScores(), this.clone.getTagCounter(), + Clone clone = cloneFactory.create(0, targets.count, getOriginalGeneScores(), this.clone.getTagCount(), new NSequenceWithQuality[]{assemblingFeatureSeq}, this.clone.getGroup()); vHitAlignments[targets.assemblingFeatureTargetId] = @@ -980,16 +980,16 @@ else if (floatingRightBound) } else tmp[0] = substituteAlignments(tmp[0], jHitAlignments); - TagCounter tagCounter = this.clone.getTagCounter(); - if (tagCounter != null && targets.groups != null) { + TagCount tagCount = this.clone.getTagCount(); + if (tagCount != null && targets.groups != null) { Set tagTuples = new HashSet<>(); TIntIterator it = targets.groups.iterator(); while (it.hasNext()) tagTuples.add(groupToTagTuple.get(it.next())); - tagCounter = tagCounter.filter(tagTuples::contains); + tagCount = tagCount.filter(tagTuples::contains); } - return new Clone(targets.sequences, hits, tagCounter, targets.count, 0, clone.getGroup()); + return new Clone(targets.sequences, hits, tagCount, targets.count, 0, clone.getGroup()); } static int indexOfGene(VDJCHit[] hits, VDJCGeneId gene) { @@ -1429,7 +1429,7 @@ public RawVariantsData calculateRawData(Supplier> ali int groupCounter = 0; for (VDJCAlignments al : CUtils.it(alignments.get())) { if (taggedAnalysis()) { - TagTuple tagTuple = al.getTagCounter().asKeyOrNull(); + TagTuple tagTuple = al.getTagCount().asKeyOrNull(); int grp = tagTupleToGroup.get(tagTuple); if (grp == -1) { grp = groupCounter++; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index ac79fe1d4..51de4ea03 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -30,8 +30,8 @@ package com.milaboratory.mixcr.basictypes; import com.milaboratory.core.sequence.NSequenceWithQuality; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.primitivio.annotations.Serializable; import gnu.trove.iterator.TObjectDoubleIterator; @@ -47,19 +47,19 @@ public final class Clone extends VDJCObject { CloneSet parent = null; final Integer group; - public Clone(NSequenceWithQuality[] targets, EnumMap hits, TagCounter tagCounter, double count, int id, Integer group) { - super(hits, tagCounter, targets); + public Clone(NSequenceWithQuality[] targets, EnumMap hits, TagCount tagCount, double count, int id, Integer group) { + super(hits, tagCount, targets); this.count = count; this.id = id; this.group = group; } public Clone setCount(double count) { - return new Clone(targets, hits, tagCounter, count, id, group); + return new Clone(targets, hits, tagCount, count, id, group); } public Clone setGroup(Integer group) { - return new Clone(targets, hits, tagCounter, count, id, group); + return new Clone(targets, hits, tagCount, count, id, group); } public Integer getGroup() { @@ -67,14 +67,14 @@ public Integer getGroup() { } public Clone setId(int id) { - Clone r = new Clone(targets, hits, tagCounter, count, id, group); + Clone r = new Clone(targets, hits, tagCount, count, id, group); r.setParentCloneSet(parent); return r; } /** Returns new instance with parent clone set set to null */ public Clone resetParentCloneSet() { - return new Clone(targets, hits, tagCounter, count, id, group); + return new Clone(targets, hits, tagCount, count, id, group); } public void setParentCloneSet(CloneSet set) { @@ -87,7 +87,7 @@ public CloneSet getParentCloneSet() { return parent; } - public Clone setTagCounts(TagCounter tc) { + public Clone setTagCount(TagCount tc) { Objects.requireNonNull(tc); Clone c = new Clone(targets, hits, tc, count, id, group); c.setParentCloneSet(getParentCloneSet()); @@ -109,13 +109,13 @@ public double getFraction() { return getFraction(parent.getTotalCount()); } - public TagCounter getTagFractions() { + public TagCount getTagFractions() { if (parent == null) return null; - TagCounter totalFractions = parent.getTotalTagCounts(); + TagCount totalFractions = parent.getTotalTagCounts(); - TagCounterBuilder result = new TagCounterBuilder(); - TObjectDoubleIterator it = tagCounter.iterator(); + TagCountAggregator result = new TagCountAggregator(); + TObjectDoubleIterator it = tagCount.iterator(); while (it.hasNext()) { it.advance(); TagTuple tt = it.key(); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index fa87bcd0c..58f086628 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -31,8 +31,8 @@ import cc.redberry.primitives.Filter; import com.milaboratory.mixcr.assembler.CloneAssemblerParameters; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.GeneFeature; @@ -54,7 +54,7 @@ public final class CloneSet implements Iterable, VDJCFileHeaderData, HasF final List usedGenes; final List clones; final double totalCount; - final TagCounter totalTagCounts; + final TagCount totalTagCounts; public CloneSet(List clones, Collection usedGenes, VDJCAlignerParameters alignmentParameters, @@ -65,13 +65,13 @@ public CloneSet(List clones, Collection usedGenes, list.sort(ordering.comparator()); this.clones = Collections.unmodifiableList(list); long totalCount = 0; - TagCounterBuilder tagCounterBuilder = new TagCounterBuilder(); + TagCountAggregator tagCountAggregator = new TagCountAggregator(); for (Clone clone : clones) { totalCount += clone.count; clone.setParentCloneSet(this); - tagCounterBuilder.add(clone.tagCounter); + tagCountAggregator.add(clone.tagCount); } - this.totalTagCounts = tagCounterBuilder.createAndDestroy(); + this.totalTagCounts = tagCountAggregator.createAndDestroy(); this.alignmentParameters = alignmentParameters; this.assemblerParameters = assemblerParameters; this.tagsInfo = tagsInfo; @@ -86,10 +86,10 @@ public CloneSet(List clones) { long totalCount = 0; HashMap genes = new HashMap<>(); EnumMap alignedFeatures = new EnumMap<>(GeneType.class); - TagCounterBuilder tagCounterBuilder = new TagCounterBuilder(); + TagCountAggregator tagCountAggregator = new TagCountAggregator(); for (Clone clone : clones) { totalCount += clone.count; - tagCounterBuilder.add(clone.tagCounter); + tagCountAggregator.add(clone.tagCount); clone.setParentCloneSet(this); for (GeneType geneType : GeneType.values()) for (VDJCHit hit : clone.getHits(geneType)) { @@ -101,7 +101,7 @@ public CloneSet(List clones) { throw new IllegalArgumentException("Different aligned feature for clones."); } } - this.totalTagCounts = tagCounterBuilder.createAndDestroy(); + this.totalTagCounts = tagCountAggregator.createAndDestroy(); this.assemblerParameters = null; this.alignmentParameters = null; this.tagsInfo = null; @@ -156,7 +156,7 @@ public double getTotalCount() { return totalCount; } - public TagCounter getTotalTagCounts() { + public TagCount getTotalTagCounts() { return totalTagCounts; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index 7bc51f49a..f111e0e80 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -34,14 +34,10 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.Serializer; -import gnu.trove.impl.Constants; -import gnu.trove.iterator.TObjectDoubleIterator; -import gnu.trove.map.hash.TObjectDoubleHashMap; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; @@ -90,7 +86,7 @@ public void write(PrimitivO output, VDJCAlignments object) { output.writeObject(object.targets); output.writeObject(object.originalReads); output.writeObject(object.history); - output.writeObject(object.tagCounter); + output.writeObject(object.tagCount); output.writeByte(object.hits.size()); for (Map.Entry entry : object.hits.entrySet()) { output.writeObject(entry.getKey()); @@ -106,7 +102,7 @@ public VDJCAlignments read(PrimitivI input) { NSequenceWithQuality[] targets = input.readObject(NSequenceWithQuality[].class); SequenceRead[] originalReads = input.readObject(SequenceRead[].class); SequenceHistory[] history = input.readObject(SequenceHistory[].class); - TagCounter tagCounter = input.readObject(TagCounter.class); + TagCount tagCount = input.readObject(TagCount.class); int size = input.readByte(); EnumMap hits = new EnumMap<>(GeneType.class); for (int i = 0; i < size; i++) { @@ -119,7 +115,7 @@ public VDJCAlignments read(PrimitivI input) { int cloneIndex = -1; if (!ReadToCloneMapping.isDropped(mappingType)) cloneIndex = input.readVarInt(); - return new VDJCAlignments(hits, tagCounter, targets, history, originalReads, mappingType, cloneIndex); + return new VDJCAlignments(hits, tagCount, targets, history, originalReads, mappingType, cloneIndex); } @Override @@ -137,7 +133,7 @@ public static class CloneSerializer implements Serializer { @Override public void write(PrimitivO output, Clone object) { output.writeObject(object.targets); - output.writeObject(object.tagCounter); + output.writeObject(object.tagCount); output.writeByte(object.hits.size()); for (Map.Entry entry : object.hits.entrySet()) { output.writeObject(entry.getKey()); @@ -151,7 +147,7 @@ public void write(PrimitivO output, Clone object) { @Override public Clone read(PrimitivI input) { NSequenceWithQuality[] targets = input.readObject(NSequenceWithQuality[].class); - TagCounter tagCounter = input.readObject(TagCounter.class); + TagCount tagCount = input.readObject(TagCount.class); int size = input.readByte(); EnumMap hits = new EnumMap<>(GeneType.class); for (int i = 0; i < size; i++) { @@ -161,7 +157,7 @@ public Clone read(PrimitivI input) { double count = input.readDouble(); int id = input.readInt(); Integer group = input.readObject(Integer.class); - return new Clone(targets, hits, tagCounter, count, id, group); + return new Clone(targets, hits, tagCount, count, id, group); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 6c90563d4..bcf14c5dd 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -36,7 +36,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.primitivio.annotations.Serializable; import com.milaboratory.util.ArraysUtils; import gnu.trove.map.hash.TLongObjectHashMap; @@ -55,12 +55,12 @@ public final class VDJCAlignments extends VDJCObject { public VDJCAlignments(long alignmentsIndex, EnumMap hits, - TagCounter tagCounter, + TagCount tagCount, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads, byte mappingType, int cloneIndex) { - super(hits, tagCounter, targets); + super(hits, tagCount, targets); if (!ReadToCloneMapping.isCorrect(mappingType) || (ReadToCloneMapping.isDropped(mappingType) && cloneIndex != -1)) @@ -75,37 +75,37 @@ public VDJCAlignments(long alignmentsIndex, public VDJCAlignments(long alignmentsIndex, EnumMap hits, - TagCounter tagCounter, + TagCount tagCount, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads) { - this(alignmentsIndex, hits, tagCounter, targets, history, originalReads, + this(alignmentsIndex, hits, tagCount, targets, history, originalReads, ReadToCloneMapping.DROPPED_MASK, -1); } public VDJCAlignments(EnumMap hits, - TagCounter tagCounter, + TagCount tagCount, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads, byte mappingType, int cloneIndex) { - this(-1, hits, tagCounter, targets, history, originalReads, mappingType, cloneIndex); + this(-1, hits, tagCount, targets, history, originalReads, mappingType, cloneIndex); } public VDJCAlignments(EnumMap hits, - TagCounter tagCounter, + TagCount tagCount, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads) { - this(-1, hits, tagCounter, targets, history, originalReads); + this(-1, hits, tagCount, targets, history, originalReads); } public VDJCAlignments(VDJCHit[] vHits, VDJCHit[] dHits, VDJCHit[] jHits, VDJCHit[] cHits, - TagCounter tagCounter, + TagCount tagCount, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads) { - this(-1, createHits(vHits, dHits, jHits, cHits), tagCounter, targets, history, originalReads); + this(-1, createHits(vHits, dHits, jHits, cHits), tagCount, targets, history, originalReads); } public VDJCAlignments shiftIndelsAtHomopolymers(Set gts) { @@ -118,7 +118,7 @@ public VDJCAlignments mapHits(Function mapper) { EnumMap result = new EnumMap<>(GeneType.class); for (Map.Entry e : hits.entrySet()) result.put(e.getKey(), Arrays.stream(e.getValue()).map(mapper).toArray(VDJCHit[]::new)); - return new VDJCAlignments(alignmentsIndex, result, tagCounter, targets, history, originalReads, mappingType, cloneIndex); + return new VDJCAlignments(alignmentsIndex, result, tagCount, targets, history, originalReads, mappingType, cloneIndex); } public boolean isClustered() { @@ -149,33 +149,33 @@ public int getCloneIndex() { return cloneIndex; } - public VDJCAlignments setTagCounter(TagCounter tc) { + public VDJCAlignments setTagCounter(TagCount tc) { return new VDJCAlignments(alignmentsIndex, hits, tc, targets, history, originalReads, mappingType, cloneIndex); } public VDJCAlignments setMapping(ReadToCloneMapping mapping) { - return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads, + return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads, mapping.getMappingTypeByte(), mapping.getCloneIndex()); } public VDJCAlignments updateCloneIndex(int newCloneIndex) { - return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads, + return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads, mappingType, newCloneIndex); } public VDJCAlignments updateCloneIndexAndMappingType(int newCloneIndex, byte newMappingType) { - return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads, + return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads, newMappingType, newCloneIndex); } public VDJCAlignments updateAlignments(Function, Alignment> processor) { EnumMap newHits = this.hits.clone(); newHits.replaceAll((k, v) -> Arrays.stream(v).map(h -> h.mapAlignments(processor)).toArray(VDJCHit[]::new)); - return new VDJCAlignments(alignmentsIndex, newHits, tagCounter, targets, history, originalReads, mappingType, cloneIndex); + return new VDJCAlignments(alignmentsIndex, newHits, tagCount, targets, history, originalReads, mappingType, cloneIndex); } public VDJCAlignments shiftReadId(long newAlignmentIndex, long shift) { - return new VDJCAlignments(newAlignmentIndex, hits, tagCounter, targets, shift(history, shift), shift(originalReads, shift)); + return new VDJCAlignments(newAlignmentIndex, hits, tagCount, targets, shift(history, shift), shift(originalReads, shift)); } public static SequenceRead[] mergeOriginalReads(VDJCAlignments... array) { @@ -256,7 +256,7 @@ public int getNumberOfReads() { } public VDJCAlignments setHistory(SequenceHistory[] history, SequenceRead[] originalReads) { - return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads); + return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads); } public VDJCAlignments removeBestHitAlignment(GeneType geneType, int targetId) { @@ -269,7 +269,7 @@ public VDJCAlignments removeBestHitAlignment(GeneType geneType, int targetId) { gHits[0] = new VDJCHit(gHits[0].getGene(), als, gHits[0].getAlignedFeature()); Arrays.sort(gHits); hits.put(geneType, gHits); - return new VDJCAlignments(alignmentsIndex, hits, tagCounter, targets, history, originalReads); + return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads); } public boolean hasNoHitsInTarget(int i) { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index d895d8f15..f31c309ee 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -32,7 +32,7 @@ import com.milaboratory.core.Range; import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.sequence.*; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.util.Cache; import io.repseq.core.*; import io.repseq.gen.VDJCGenes; @@ -48,21 +48,21 @@ public abstract class VDJCObject { protected final EnumMap hits; protected volatile EnumMap allChains; protected VDJCPartitionedSequence[] partitionedTargets; - protected final TagCounter tagCounter; + protected final TagCount tagCount; protected final Cache cache = new Cache(); - public VDJCObject(EnumMap hits, TagCounter tagCounter, NSequenceWithQuality... targets) { + public VDJCObject(EnumMap hits, TagCount tagCount, NSequenceWithQuality... targets) { this.targets = targets; this.hits = hits; - this.tagCounter = tagCounter; + this.tagCount = tagCount; // Sorting hits for (VDJCHit[] h : hits.values()) Arrays.sort(h); } - public TagCounter getTagCounter() { - return tagCounter; + public TagCount getTagCount() { + return tagCount; } protected static EnumMap createHits(VDJCHit[] vHits, VDJCHit[] dHits, @@ -848,7 +848,7 @@ public boolean equals(Object o) { return false; } - if (!tagCounter.equals(that.tagCounter)) return false; + if (!tagCount.equals(that.tagCount)) return false; if (!Arrays.equals(targets, that.targets)) return false; return true; @@ -858,7 +858,7 @@ public boolean equals(Object o) { public int hashCode() { int result = Arrays.hashCode(targets); result = 31 * result + hits.hashCode(); - result = 29 * result + tagCounter.hashCode(); + result = 29 * result + tagCount.hashCode(); return result; } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java index cc1c9788c..7b395c6a0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java @@ -59,11 +59,11 @@ public boolean handlesReference() { } } - public static class TagCounterSerializer implements Serializer { + public static class TagCounterSerializer implements Serializer { @Override - public void write(PrimitivO output, TagCounter object) { - output.writeInt(object.tags.size()); - TObjectDoubleIterator it = object.tags.iterator(); + public void write(PrimitivO output, TagCount object) { + output.writeInt(object.size()); + TObjectDoubleIterator it = object.iterator(); while (it.hasNext()) { it.advance(); output.writeObject(it.key().tags); @@ -72,18 +72,25 @@ public void write(PrimitivO output, TagCounter object) { } @Override - public TagCounter read(PrimitivI input) { + public TagCount read(PrimitivI input) { int len = input.readInt(); if (len == 0) - return TagCounter.EMPTY; - TObjectDoubleHashMap r = new TObjectDoubleHashMap<>(len, Constants.DEFAULT_LOAD_FACTOR, 0.0); - for (int i = 0; i < len; ++i) { + throw new IllegalArgumentException(); + else if (len == 1) { TagValue[] tags = input.readObject(TagValue[].class); Objects.requireNonNull(tags); double count = input.readDouble(); - r.put(new TagTuple(tags), count); + return new TagCount(tags.length == 0 ? TagTuple.NO_TAGS : new TagTuple(tags), count); + } else { + TObjectDoubleHashMap r = new TObjectDoubleHashMap<>(len, Constants.DEFAULT_LOAD_FACTOR, 0.0); + for (int i = 0; i < len; ++i) { + TagValue[] tags = input.readObject(TagValue[].class); + Objects.requireNonNull(tags); + double count = input.readDouble(); + r.put(new TagTuple(tags), count); + } + return new TagCount(r); } - return new TagCounter(r); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java new file mode 100644 index 000000000..34c5d5124 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java @@ -0,0 +1,308 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.milaboratory.primitivio.annotations.Serializable; +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.map.hash.TObjectDoubleHashMap; + +import java.util.*; +import java.util.function.Predicate; +import java.util.stream.Collectors; + +@Serializable(by = IO.TagCounterSerializer.class) +public final class TagCount { + public static final TagCount NO_TAGS_1 = new TagCount(TagTuple.NO_TAGS); + + final TagTuple singletonTuple; + final double singletonCount; + final TObjectDoubleHashMap tagMap; + + public TagCount(TagTuple singletonTuple) { + this.singletonTuple = singletonTuple; + this.singletonCount = 1.0; + this.tagMap = null; + } + + public TagCount(TagTuple singletonTuple, double singletonCount) { + if (!singletonTuple.isKey() && singletonCount != 1.0) + throw new IllegalArgumentException("Non-key tuples can be associated only with 1.0 count."); + this.singletonTuple = singletonTuple; + this.singletonCount = singletonCount; + this.tagMap = null; + } + + TagCount(TObjectDoubleHashMap tagMap) { + if (tagMap.isEmpty()) + throw new IllegalStateException(); + + TagTuple sTuple = null; + double sCount = Double.NaN; + if (tagMap.size() == 1) { + TObjectDoubleIterator it = tagMap.iterator(); + it.advance(); + sTuple = it.key(); + sCount = it.value(); + } + + if (sTuple != null) { + if (!sTuple.isKey() && sCount != 1.0) + throw new IllegalArgumentException("Non-key tuples can be associated only with 1.0 count."); + this.singletonTuple = sTuple; + this.singletonCount = sCount; + this.tagMap = null; + } else { + this.singletonTuple = null; + this.singletonCount = Double.NaN; + this.tagMap = tagMap; + } + } + + /** + * If this is a singleton non-key counter, converts it to a singleton key counter; + * returns this for all other cases. + */ + public TagCount ensureIsKey() { + if (singletonTuple != null && !singletonTuple.isKey()) { + assert singletonCount == 1.0; + return new TagCount(singletonTuple.key()); + } else + return this; + } + + public TagTuple asKeyPrefixOrNull(int depth) { + TagTuple fullKey = asKeyOrNull(); + if (fullKey != null) + return fullKey.keyPrefix(depth); + Set keySet = tagMap.keySet().stream() + .map(t -> t.keyPrefix(depth)) + .collect(Collectors.toSet()); + if (keySet.size() != 1) + return null; + return keySet.iterator().next(); + } + + public TagTuple asKeyOrNull() { + return singletonTuple != null + ? singletonTuple.key() + : null; + } + + public TagTuple asKeyPrefixOrError(int depth) { + TagTuple result = asKeyPrefixOrNull(depth); + if (result == null) + throw new IllegalStateException("Aggregated tag information, single tag tuple expected."); + return result; + } + + public TagTuple asKeyOrError() { + TagTuple result = asKeyOrNull(); + if (result == null) + throw new IllegalStateException("Aggregated tag information, single tag tuple expected."); + return result; + } + + public Set keySuffixes(int depth) { + TagTuple fullKey = asKeyOrNull(); + if (fullKey != null) + return Collections.singleton(fullKey.keySuffix(depth)); + return tagMap.keySet().stream() + .map(t -> t.keySuffix(depth)) + .collect(Collectors.toSet()); + } + + public Set tuples() { + if (singletonTuple != null) + return Collections.singleton(singletonTuple); + else + return tagMap.keySet(); + } + + public boolean isSingleton() { + return singletonTuple != null; + } + + public TagTuple getSingletonTuple() { + return singletonTuple; + } + + public double getSingletonCount() { + return singletonCount; + } + + public boolean isNoTag() { + return TagTuple.NO_TAGS.equals(getSingletonTuple()); + } + + public int size() { + return isSingleton() + ? 1 + : tagMap.size(); + } + + public double get(TagTuple tt) { + if (isSingleton()) { + if (tt.equals(singletonTuple)) + return singletonCount; + return 0.0; + } else + return tagMap.get(tt); + } + + public TObjectDoubleIterator iterator() { + if (singletonTuple != null) + // Singleton iterator + return new TObjectDoubleIterator() { + int position = -1; + + @Override + public TagTuple key() { + return position == 0 + ? singletonTuple + : null; + } + + @Override + public double value() { + return position == 0 + ? singletonCount + : Double.NaN; + } + + @Override + public double setValue(double val) { + throw new UnsupportedOperationException(); + } + + @Override + public void advance() { + ++position; + } + + @Override + public boolean hasNext() { + return position == -1; + } + + @Override + public void remove() { + throw new UnsupportedOperationException(); + } + }; + + TObjectDoubleIterator it = tagMap.iterator(); + return new TObjectDoubleIterator() { + @Override + public TagTuple key() { + return it.key(); + } + + @Override + public double value() { + return it.value(); + } + + @Override + public double setValue(double val) { + throw new UnsupportedOperationException(); + } + + @Override + public void advance() { + it.advance(); + } + + @Override + public boolean hasNext() { + return it.hasNext(); + } + + @Override + public void remove() { + throw new UnsupportedOperationException(); + } + }; + } + + @Override + public String toString() { + if (isSingleton()) + return singletonTuple + ": " + singletonCount; + else + return tagMap.toString(); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagCount that = (TagCount) o; + return Double.compare(that.singletonCount, singletonCount) == 0 && Objects.equals(singletonTuple, that.singletonTuple) && Objects.equals(tagMap, that.tagMap); + } + + @Override + public int hashCode() { + return Objects.hash(singletonTuple, singletonCount, tagMap); + } + + public TagCount filter(Predicate predicate) { + TObjectDoubleIterator it = iterator(); + TagCountAggregator tb = new TagCountAggregator(); + while (it.hasNext()) { + it.advance(); + + TagTuple t = it.key(); + double count = it.value(); + if (!predicate.test(t)) + continue; + tb.add(t, count); + } + return tb.createAndDestroy(); + } + + public TagCount[] splitBy(int index) { + Map map = new HashMap<>(); + TObjectDoubleIterator it = iterator(); + while (it.hasNext()) { + it.advance(); + + TagTuple t = it.key(); + double count = it.value(); + + TagCountAggregator tb = map.computeIfAbsent(t.get(index), __ -> new TagCountAggregator()); + tb.add(t, count); + } + return map.values().stream().map(TagCountAggregator::createAndDestroy).toArray(TagCount[]::new); + } + + public double sum() { + TObjectDoubleIterator it = iterator(); + double sum = 0; + while (it.hasNext()) { + it.advance(); + sum += it.value(); + } + return sum; + } + + // public TagCounter toFractions() { + // double sum = sum(); + // if (sum == 0) + // return this; + // TObjectDoubleHashMap result = new TObjectDoubleHashMap<>(); + // TObjectDoubleIterator it = iterator(); + // while (it.hasNext()) { + // it.advance(); + // result.put(it.key(), it.value() / sum); + // } + // return new TagCounter(result); + // } + + public Set tags(int index) { + Set set = new HashSet<>(); + TObjectDoubleIterator it = iterator(); + while (it.hasNext()) { + it.advance(); + set.add(it.key().get(index)); + } + return set; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java new file mode 100644 index 000000000..8fba6b5dc --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java @@ -0,0 +1,114 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import gnu.trove.iterator.TObjectDoubleIterator; +import gnu.trove.map.hash.TObjectDoubleHashMap; + +/** + * + */ +public final class TagCountAggregator { + private TagTuple singletonTuple = null; + private double singletonCount = Double.NaN; + private TObjectDoubleHashMap tagMap = null; + private boolean destroyed = false; + + public TagCountAggregator() { + } + + public TagCountAggregator add(TagTuple tc, double count) { + if (destroyed) + throw new IllegalStateException("destroyed"); + + if (!tc.isKey() && count != 1.0) + throw new IllegalArgumentException("count != 1.0 for non-key tuple."); + + if (tagMap == null) { + if (singletonTuple == null) { + singletonTuple = tc; + singletonCount = count; + return this; + } else if (singletonTuple.equals(tc)) { + singletonCount += count; + return this; + } else { + tagMap = new TObjectDoubleHashMap<>(); + tagMap.put(singletonTuple, singletonCount); + tagMap.put(tc, count); + return this; + } + } else { + tagMap.adjustOrPutValue(tc, count, count); + return this; + } + } + + private void add(TObjectDoubleIterator it) { + while (it.hasNext()) { + it.advance(); + add(it.key(), it.value()); + } + } + + public TagCountAggregator add(TagCount tc) { + add(tc.iterator()); + return this; + } + + public TagCountAggregator add(TagCountAggregator tc) { + if (tc.tagMap == null) { + if (tc.singletonTuple == null) + return this; + add(tc.singletonTuple, tc.singletonCount); + } else + add(tc.tagMap.iterator()); + return this; + } + + public TagCountAggregator add(TObjectDoubleHashMap tc) { + if (tc.size() == 0) + return this; + + add(tc.iterator()); + + return this; + } + + public double intersectionFractionOf(TagCountAggregator minor) { + if (tagMap == null || minor.tagMap == null) + throw new IllegalStateException("tag aware clusterization for non-tagged clones."); + + TagCount thisTagCount = createTagCounter(); + TObjectDoubleIterator it = minor.createTagCounter().iterator(); + double minorTotal = 0, totalIntersection = 0; + while (it.hasNext()) { + it.advance(); + TagTuple key = it.key(); + double v = it.value(); + minorTotal += v; + if (thisTagCount.get(key) > 0) + totalIntersection += v; + } + return totalIntersection / minorTotal; + } + + private TagCount createTagCounter() { + if (singletonTuple == null && tagMap == null) + return TagCount.NO_TAGS_1; + + if (singletonTuple != null) + return new TagCount(singletonTuple, singletonCount); + + return new TagCount(tagMap); + } + + public TagCount createAndDestroy() { + if (destroyed) + throw new IllegalStateException("destroyed"); + destroyed = true; + return createTagCounter(); + } + + public static TagCount merge(TagCount a, TagCount b) { + return new TagCountAggregator().add(a).add(b).createAndDestroy(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java deleted file mode 100644 index d590073a1..000000000 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounter.java +++ /dev/null @@ -1,226 +0,0 @@ -package com.milaboratory.mixcr.basictypes.tag; - -import com.milaboratory.primitivio.annotations.Serializable; -import gnu.trove.TDoubleCollection; -import gnu.trove.iterator.TDoubleIterator; -import gnu.trove.iterator.TObjectDoubleIterator; -import gnu.trove.map.hash.TObjectDoubleHashMap; - -import java.util.*; -import java.util.function.Predicate; -import java.util.stream.Collectors; - -/** - * - */ -@Serializable(by = IO.TagCounterSerializer.class) -public final class TagCounter { - public static final TagCounter EMPTY = new TagCounter(new TObjectDoubleHashMap<>()); - - final TObjectDoubleHashMap tags; - - TagCounter(TObjectDoubleHashMap tags) { - this.tags = tags; - } - - public TagCounter(TagTuple tags, double count) { - this.tags = new TObjectDoubleHashMap<>(); - this.tags.put(tags, count); - } - - public TagCounter(TagTuple tags) { - this(tags, 1.0); - } - - public TagTuple asKeyPrefixOrNull(int level) { - TagTuple fullKey = asKeyOrNull(); - if (fullKey != null) - return fullKey.keyPrefix(level); - Set keySet = tags.keySet().stream() - .map(t -> t.keyPrefix(level)) - .collect(Collectors.toSet()); - if (keySet.size() != 1) - return null; - return keySet.iterator().next(); - } - - public TagTuple asKeyOrNull() { - if (size() > 1 || size() == 0) - return null; - - TObjectDoubleIterator it = iterator(); - it.advance(); - return it.key().key(); - } - - public TagTuple asKeyPrefixOrError(int level) { - TagTuple result = asKeyPrefixOrNull(level); - if (result == null) - throw new IllegalStateException("Aggregated tag information, single tag tuple expected."); - return result; - } - - public TagTuple asKeyOrError() { - TagTuple result = asKeyOrNull(); - if (result == null) - throw new IllegalStateException("Aggregated tag information, single tag tuple expected."); - return result; - } - - public Set keySuffixes(int depth) { - TagTuple fullKey = asKeyOrNull(); - if (fullKey != null) - return Collections.singleton(fullKey.keySuffix(depth)); - return tags.keySet().stream() - .map(t -> t.keySuffix(depth)) - .collect(Collectors.toSet()); - } - - public Set keys() { - return tags.keySet(); - } - - public double getOrDefault(TagTuple tt, double d) { - if (!tags.containsKey(tt)) - return d; - else - return tags.get(tt); - } - - public TagCounter multiply(double factor) { - TagCounterBuilder tb = new TagCounterBuilder(); - TObjectDoubleIterator iterator = iterator(); - while (iterator.hasNext()) { - iterator.advance(); - tb.add(iterator.key(), iterator.value() * factor); - } - return tb.createAndDestroy(); - } - - public int size() { - return tags.size(); - } - - public double get(TagTuple tt) { - return getOrDefault(tt, Double.NaN); - } - - public TObjectDoubleIterator iterator() { - TObjectDoubleIterator it = tags.iterator(); - return new TObjectDoubleIterator() { - @Override - public TagTuple key() { - return it.key(); - } - - @Override - public double value() { - return it.value(); - } - - @Override - public double setValue(double val) { - throw new UnsupportedOperationException(); - } - - @Override - public void advance() { - it.advance(); - } - - @Override - public boolean hasNext() { - return it.hasNext(); - } - - @Override - public void remove() { - throw new UnsupportedOperationException(); - } - }; - } - - public boolean isEmpty() { - return this.equals(EMPTY); - } - - @Override - public String toString() { - return tags.toString(); - } - - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - TagCounter that = (TagCounter) o; - return tags.equals(that.tags); - } - - @Override - public int hashCode() { - return tags.hashCode(); - } - - public TagCounter filter(Predicate predicate) { - TObjectDoubleIterator it = iterator(); - TagCounterBuilder tb = new TagCounterBuilder(); - while (it.hasNext()) { - it.advance(); - - TagTuple t = it.key(); - double count = it.value(); - if (!predicate.test(t)) - continue; - tb.add(t, count); - } - return tb.createAndDestroy(); - } - - public TagCounter[] splitBy(int index) { - Map map = new HashMap<>(); - TObjectDoubleIterator it = iterator(); - while (it.hasNext()) { - it.advance(); - - TagTuple t = it.key(); - double count = it.value(); - - TagCounterBuilder tb = map.computeIfAbsent(t.get(index), __ -> new TagCounterBuilder()); - tb.add(t, count); - } - return map.values().stream().map(TagCounterBuilder::createAndDestroy).toArray(TagCounter[]::new); - } - - public double sum() { - TDoubleCollection c = tags.valueCollection(); - TDoubleIterator it = c.iterator(); - double sum = 0; - while (it.hasNext()) - sum += it.next(); - return sum; - } - - public TagCounter toFractions() { - double sum = sum(); - if (sum == 0) - return this; - TObjectDoubleHashMap result = new TObjectDoubleHashMap<>(); - TObjectDoubleIterator it = iterator(); - while (it.hasNext()) { - it.advance(); - result.put(it.key(), it.value() / sum); - } - return new TagCounter(result); - } - - public Set tags(int index) { - Set set = new HashSet<>(); - TObjectDoubleIterator it = iterator(); - while (it.hasNext()) { - it.advance(); - set.add(it.key().get(index)); - } - return set; - } -} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounterBuilder.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounterBuilder.java deleted file mode 100644 index 49f065339..000000000 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCounterBuilder.java +++ /dev/null @@ -1,92 +0,0 @@ -package com.milaboratory.mixcr.basictypes.tag; - -import gnu.trove.impl.Constants; -import gnu.trove.iterator.TObjectDoubleIterator; -import gnu.trove.map.hash.TObjectDoubleHashMap; - -/** - * - */ -public class TagCounterBuilder { - private TObjectDoubleHashMap agg; - private boolean destroyed = false; - - public TagCounterBuilder() {} - - public TagCounterBuilder add(TagTuple tc, double count) { - return add(new TagCounter(tc, count)); - } - - public TagCounterBuilder add(TagCounter tc) { - return add(tc.tags); - } - - public TagCounterBuilder add(TagCounterBuilder tc) { - if (tc.agg == null) - return this; - return add(tc.agg); - } - - private void ensureInitialized() { - if (agg == null) - agg = new TObjectDoubleHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, 0.0); - } - - public TagCounterBuilder add(TObjectDoubleHashMap tc) { - if (destroyed) - throw new IllegalStateException("destroyed"); - - if (tc.size() == 0) - return this; - - ensureInitialized(); - - if (agg.isEmpty()) { - agg.putAll(tc); - return this; - } - - TObjectDoubleIterator it = tc.iterator(); - while (it.hasNext()) { - it.advance(); - TagTuple k = it.key(); - double v = agg.get(k); // 0.0 for no entry value, see constructor - agg.put(k, v + it.value()); - } - - return this; - } - - public double intersectionFractionOf(TagCounterBuilder minor) { - if (agg == null || minor.agg == null) - throw new IllegalStateException("tag aware clusterization for non-tagged clones."); - - TObjectDoubleIterator it = minor.agg.iterator(); - double minorTotal = 0, totalIntersection = 0; - while (it.hasNext()) { - it.advance(); - TagTuple key = it.key(); - double v = it.value(); - minorTotal += v; - if (agg.containsKey(key)) - totalIntersection += v; - } - return totalIntersection / minorTotal; - } - - public TagCounter createAndDestroy() { - if (destroyed) - throw new IllegalStateException("destroyed"); - - if (agg == null) - return TagCounter.EMPTY; - - TagCounter r = new TagCounter(new TObjectDoubleHashMap<>(agg)); - destroyed = true; - return r; - } - - public static TagCounter merge(TagCounter a, TagCounter b) { - return new TagCounterBuilder().add(a).add(b).createAndDestroy(); - } -} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index 297c84121..2340cda7e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -11,7 +11,7 @@ * Tag may be a sample name, cell marker or unique molecular identifier. */ public final class TagTuple implements Comparable { - public static final TagTuple EMPTY = new TagTuple(); + public static final TagTuple NO_TAGS = new TagTuple(); final TagValue[] tags; private final int hash; @@ -25,6 +25,14 @@ public TagTuple(TagValue... tags) { this.hash = hasher.hash().hashCode(); } + /** Returns whether the tag tuple contains only key tag values, so can be used as a grouping key. */ + public boolean isKey() { + for (TagValue tag : tags) + if (!tag.isKey()) + return false; + return true; + } + /** * Strips all non-key information (i.e. quality scores) from tags inside the tuple, * and returns tag tuple intended to be used as a grouping key. @@ -52,7 +60,7 @@ public TagTuple keyPrefix(int depth) { if (depth == tags.length) return key(); if (depth == 0) - return EMPTY; + return NO_TAGS; TagValue[] newTags = Arrays.copyOf(tags, depth); for (int i = 0; i < newTags.length; i++) newTags[i] = newTags[i].extractKey(); @@ -67,7 +75,7 @@ public TagTuple keySuffix(int depth) { if (depth == 0) return key(); if (depth == tags.length) - return EMPTY; + return NO_TAGS; TagValue[] newTags = Arrays.copyOfRange(tags, depth + 1, tags.length); for (int i = 0; i < newTags.length; i++) newTags[i] = newTags[i].extractKey(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index d822e35a7..e4cc4c54b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -740,7 +740,7 @@ public String getStatus() { if (writeAllResults) { // Creating empty alignment object if alignment for current read failed Target target = readsLayout.createTargets(read)[0]; alignment = new VDJCAlignments(emptyHits, - result.tagTuple == null ? TagCounter.EMPTY : new TagCounter(result.tagTuple), + result.tagTuple == null ? TagCount.NO_TAGS_1 : new TagCount(result.tagTuple), target.targets, SequenceHistory.RawSequence.of(read.getId(), target), alignerParameters.isSaveOriginalReads() ? new SequenceRead[]{read} : null); @@ -752,7 +752,7 @@ public String getStatus() { } if (result.tagTuple != null) - alignment = alignment.setTagCounter(new TagCounter(result.tagTuple)); + alignment = alignment.setTagCounter(new TagCount(result.tagTuple)); if (alignment.isChimera()) report.onChimera(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 12cf3e548..c678ff78b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -39,7 +39,7 @@ import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.*; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; @@ -279,7 +279,7 @@ public void run1() throws Exception { for (int i = 0; i < cloneSet.size(); i++) { Clone clone = cloneSet.get(i); assert i == clone.getId(); - TagCounter tags = clone.getTagCounter(); + TagCount tags = clone.getTagCount(); TObjectDoubleIterator it = tags.iterator(); while (it.hasNext()) { it.advance(); @@ -308,7 +308,7 @@ public void run1() throws Exception { // <-- Only dropped alignments not covering CDR3 - TagCounter tg = al.getTagCounter(); + TagCount tg = al.getTagCount(); assert tg.size() == 1; // Both "align" and "assemblePartial" produces such alignments TObjectDoubleIterator it = tg.iterator(); it.advance(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index bed31144a..aa6fca908 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -43,7 +43,8 @@ import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerParameters; import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerReport; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; @@ -153,7 +154,7 @@ public void run1() throws Exception { Clone clone = cloneAlignments.clone; if (ignoreTags) - clone = clone.setTagCounts(TagCounter.EMPTY); + clone = clone.setTagCount(new TagCount(TagTuple.NO_TAGS, clone.getTagCount().sum())); try { // Collecting statistics diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index f9175a171..8523d473c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -141,7 +141,7 @@ public void run1() throws Exception { if (reader1.getTagsInfo() != null && reader1.getTagsInfo().tags.length > 0) { SmartProgressReporter.startProgressReport("Running assemble partial", reader1); - Function1 key = al -> al.getTagCounter().asKeyOrError().key(); + Function1 key = al -> al.getTagCount().asKeyOrError().key(); OutputPort> groups1 = PipeKt.group(reader1, key); OutputPort> groups2 = PipeKt.group(reader2, key); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index 0fd63af96..cbed4250a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -156,10 +156,10 @@ public void run1() throws Exception { // Extractor of tag information from the alignments for the tag corrector Processor mapper = input -> { - if (input.getTagCounter().size() != 1) + if (input.getTagCount().size() != 1) throwExecutionException("This procedure don't support aggregated tags. " + "Please run tag correction for *.vdjca files produced by 'align'."); - TagTuple tagTuple = input.getTagCounter().keys().iterator().next(); + TagTuple tagTuple = input.getTagCount().tuples().iterator().next(); NSequenceWithQuality[] tags = new NSequenceWithQuality[targetTagIndices.length]; for (int i = 0; i < targetTagIndices.length; i++) tags[i] = ((SequenceAndQualityTagValue) tagTuple.get(targetTagIndices[i])).data; @@ -226,7 +226,7 @@ public void run1() throws Exception { Processor mapper = !noCorrect ? al -> { - TagValue[] newTags = al.getTagCounter().asKeyOrError().asArray(); + TagValue[] newTags = al.getTagCount().asKeyOrError().asArray(); CorrectionNode cn = correctionResult; for (int i : targetTagIndices) { NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); @@ -237,13 +237,13 @@ public void run1() throws Exception { } newTags[i] = new SequenceAndQualityTagValue(cn.getCorrectValue()); } - return al.setTagCounter(new TagCounter(new TagTuple(newTags))); + return al.setTagCounter(new TagCount(new TagTuple(newTags))); } : al -> al; // Creating output port with corrected and filtered tags OutputPort hsInput = new FilteringPort<>( - CUtils.wrap(reader, mapper), al -> al.getTagCounter() != null); + CUtils.wrap(reader, mapper), al -> al.getTagCount() != null); // Running initial hash sorter CountingOutputPort sorted = new CountingOutputPort<>(initialHashSorter.port(hsInput)); @@ -304,15 +304,15 @@ public SortingStep(int tagIdx) { public ToIntFunction getHashFunction() { return al -> { - TagTuple tagTuple = al.getTagCounter().asKeyOrError(); + TagTuple tagTuple = al.getTagCount().asKeyOrError(); return ((SequenceAndQualityTagValue) tagTuple.get(tagIdx)).data.getSequence().hashCode(); }; } public Comparator getComparator() { return (al1, al2) -> { - TagTuple tagTuple1 = al1.getTagCounter().asKeyOrError(); - TagTuple tagTuple2 = al2.getTagCounter().asKeyOrError(); + TagTuple tagTuple1 = al1.getTagCount().asKeyOrError(); + TagTuple tagTuple2 = al2.getTagCount().asKeyOrError(); return ((SequenceAndQualityTagValue) tagTuple1.get(tagIdx)).data.getSequence().compareTo( ((SequenceAndQualityTagValue) tagTuple2.get(tagIdx)).data.getSequence()); }; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 9590d6c3e..838f5c47d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -34,7 +34,7 @@ import cc.redberry.pipe.blocks.FilteringPort; import cc.redberry.primitives.Filter; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.export.*; import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.util.CanReportProgress; @@ -349,9 +349,9 @@ void run() { for (int tagIndex : splitByTags) { stream = stream.flatMap(cl -> { - TagCounter tagCounter = cl.getTagCounter(); - double sum = tagCounter.sum(); - return Arrays.stream(tagCounter.splitBy(tagIndex)) + TagCount tagCount = cl.getTagCount(); + double sum = tagCount.sum(); + return Arrays.stream(tagCount.splitBy(tagIndex)) .map(tc -> new Clone(clone.getTargets(), clone.getHits(), tc, 1.0 * cl.getCount() * tc.sum() / sum, clone.getId(), clone.getGroup())); }); diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 19384e939..0b99ec10d 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -42,7 +42,7 @@ import com.milaboratory.core.sequence.TranslationParameters; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagInfo; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; @@ -678,7 +678,7 @@ protected String extract(VDJCObject object) { descriptorsList.add(new PL_O("-tagCounts", "All tags with counts", "All tags counts", "taqCounts") { @Override protected String extract(VDJCObject object) { - return object.getTagCounter().toString(); + return object.getTagCount().toString(); } }); @@ -727,8 +727,8 @@ public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderDa return new AbstractFieldExtractor(getHeader(outputMode, tagName), this) { @Override public String extractValue(VDJCObject object) { - TagCounter tc = object.getTagCounter(); - Set keys = tc.keys(); + TagCount tc = object.getTagCount(); + Set keys = tc.tuples(); if (keys.size() == 0) return NULL; if (keys.size() > 1) diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index f968accfc..326c196f5 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -41,8 +41,8 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.VDJCPartitionedSequence; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; @@ -183,7 +183,7 @@ public void searchOverlaps(OutputPort input) { VDJCMultiRead mRead = new VDJCMultiRead(mergedTargets); // Both parts have the same tag tuple - final VDJCAlignments mAlignment = aligner.process(mRead).alignment.setTagCounter(searchResult.tagCounter); + final VDJCAlignments mAlignment = aligner.process(mRead).alignment.setTagCounter(searchResult.tagCount); // Checking number of overlapped non-template (NRegion) letters int overlapTargetId = -1; @@ -276,13 +276,13 @@ static class OverlapSearchResult { final List originKMerList; final KMerInfo KMerInfo; final List result; - final TagCounter tagCounter; + final TagCount tagCount; - public OverlapSearchResult(List originKMerList, KMerInfo KMerInfo, List result, TagCounter tagCounter) { + public OverlapSearchResult(List originKMerList, KMerInfo KMerInfo, List result, TagCount tagCount) { this.originKMerList = originKMerList; this.KMerInfo = KMerInfo; this.result = result; - this.tagCounter = tagCounter; + this.tagCount = tagCount; } void cancel() { @@ -311,7 +311,7 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, else stop -= kOffset; - TagCounter rightTagCounter = rightAl.getTagCounter(); + TagCount rightTagCount = rightAl.getTagCount(); // black list of left parts failed due to inconsistent overlapped alignments (failed AMerge) TLongHashSet blackList = new TLongHashSet(); @@ -398,7 +398,7 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, final KMerInfo left = maxOverlapList.remove(maxOverlapIndexInList); VDJCAlignments leftAl = left.alignments; - TagCounter leftTagCounter = leftAl.getTagCounter(); + TagCount leftTagCount = leftAl.getTagCount(); //final long readId = rightAl.getReadId(); @@ -486,9 +486,9 @@ private OverlapSearchResult searchOverlaps(final VDJCAlignments rightAl, result.add(central); result.addAll(rightDescriptors); - TagCounterBuilder tcBuilder = new TagCounterBuilder(); - tcBuilder.add(leftTagCounter); - tcBuilder.add(rightTagCounter); + TagCountAggregator tcBuilder = new TagCountAggregator(); + tcBuilder.add(leftTagCount); + tcBuilder.add(rightTagCount); // Ordering and filtering final targets return new OverlapSearchResult(maxOverlapList, left, AlignedTarget.orderTargets(result), tcBuilder.createAndDestroy()); diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java index b6787d40a..3c98e7132 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java @@ -38,7 +38,7 @@ import com.milaboratory.core.alignment.kaligner2.KAlignerParameters2; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerAbstract; @@ -309,7 +309,7 @@ protected VDJCAlignmentResult process0(VDJCMultiRead input) { dResult, jResult, cutRelativeScore(vdjcHits.get(GeneType.Constant), parameters.getCAlignerParameters().getRelativeMinScore(), parameters.getMaxHits()), - TagCounter.EMPTY, + TagCount.NO_TAGS_1, targets, input.getHistory(), input.getOriginalReads() diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java index 954d715bd..b95782e45 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java @@ -46,7 +46,7 @@ import com.milaboratory.mixcr.basictypes.SequenceHistory.OverlapType; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.vdjaligners.KGeneAlignmentParameters; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import io.repseq.core.GeneFeature; @@ -109,7 +109,7 @@ public AlignedTarget merge(AlignedTarget targetLeft, AlignedTarget targetRight, VDJCAlignments alignments = new VDJCAlignments(result, - TagCounterBuilder.merge(targetLeft.getAlignments().getTagCounter(), targetRight.getAlignments().getTagCounter()), + TagCountAggregator.merge(targetLeft.getAlignments().getTagCount(), targetRight.getAlignments().getTagCount()), new NSequenceWithQuality[]{mergedTarget}, new SequenceHistory[]{ new SequenceHistory.Merge(overlapType, targetLeft.getHistory(), targetRight.getHistory(), offset, nMismatches) diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java index 1a21bbaad..3738c0c6b 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java @@ -2,7 +2,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mixcr.assembler.GeneAndScore; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.util.BitArray; import io.repseq.core.GeneType; @@ -13,9 +13,9 @@ public final class PreClone { /** Pre-clonotype id */ public long id; /** Tag counter aggregating information about alignments with clonal sequence */ - public final TagCounter coreTagCounter; + public final TagCount coreTagCount; /** Tag counter aggregating information across all alignments assigned to this pre-clone */ - public final TagCounter fullTagCounter; + public final TagCount fullTagCount; /** Assembled clonal sequence */ public final NSequenceWithQuality[] clonalSequence; /** Aggregated V, J, C gene scoring and content information */ @@ -23,11 +23,11 @@ public final class PreClone { /** Ids of alignments assigned to this pre-clone */ public final BitArray alignments; - public PreClone(long id, TagCounter coreTagCounter, TagCounter fullTagCounter, NSequenceWithQuality[] clonalSequence, + public PreClone(long id, TagCount coreTagCount, TagCount fullTagCount, NSequenceWithQuality[] clonalSequence, Map> geneScores, BitArray alignments) { this.id = id; - this.coreTagCounter = coreTagCounter; - this.fullTagCounter = fullTagCounter; + this.coreTagCount = coreTagCount; + this.fullTagCount = fullTagCount; this.clonalSequence = clonalSequence; this.geneScores = geneScores; this.alignments = alignments; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java index 1b95e8c4d..6bc100161 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java @@ -11,7 +11,7 @@ import com.milaboratory.mixcr.assembler.VDJCGeneAccumulator; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.tag.TagCounterBuilder; +import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.util.BitArray; import gnu.trove.map.hash.TObjectIntHashMap; @@ -33,7 +33,7 @@ public PreCloneAssembler(PreCloneAssemblerParameters parameters, OutputPort alignmentsReader2) { this.parameters = parameters; Function1 gFunction = - vdjcAlignments -> vdjcAlignments.getTagCounter().asKeyPrefixOrError(parameters.groupingLevel); + vdjcAlignments -> vdjcAlignments.getTagCount().asKeyPrefixOrError(parameters.groupingLevel); this.alignmentsReader1 = PipeKt.group(alignmentsReader1, gFunction); this.alignmentsReader2 = PipeKt.group(alignmentsReader2, gFunction); } @@ -82,7 +82,7 @@ public List getForNextGroup() { geneAndScores.put(gt, gss); } alignmentInfos.add(new AlignmentInfo(localIdx, - al.getTagCounter().keySuffixes(parameters.groupingLevel), geneAndScores)); + al.getTagCount().keySuffixes(parameters.groupingLevel), geneAndScores)); // Allocating array for the next data row row = new NSequenceWithQuality[parameters.assemblingFeatures.length]; @@ -187,11 +187,11 @@ public List getForNextGroup() { // Step #3 // Assigning leftover alignments - TagCounterBuilder[] coreTagCounterBuilders = new TagCounterBuilder[numberOfClones]; - TagCounterBuilder[] fullTagCounterBuilders = new TagCounterBuilder[numberOfClones]; + TagCountAggregator[] coreTagCountAggregators = new TagCountAggregator[numberOfClones]; + TagCountAggregator[] fullTagCountAggregators = new TagCountAggregator[numberOfClones]; for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { - coreTagCounterBuilders[cIdx] = new TagCounterBuilder(); - fullTagCounterBuilders[cIdx] = new TagCounterBuilder(); + coreTagCountAggregators[cIdx] = new TagCountAggregator(); + fullTagCountAggregators[cIdx] = new TagCountAggregator(); } GroupOP grp2 = alignmentsReader2.take(); @@ -218,7 +218,7 @@ else if (cIdx != c) } // TagSuffix based assignment - for (TagTuple ts : al.getTagCounter().keySuffixes(parameters.groupingLevel)) { + for (TagTuple ts : al.getTagCount().keySuffixes(parameters.groupingLevel)) { int c = tagSuffixToCloneId.get(ts); if (c <= 0) continue; @@ -236,10 +236,10 @@ else if (cIdx != c) } else if (cIdx > 0) // Using second iteration over the alignments to assemble TagCounters from the alignments assigned to // clonotypes based on their contig assignment - coreTagCounterBuilders[cIdx - 1].add(al.getTagCounter()); + coreTagCountAggregators[cIdx - 1].add(al.getTagCount()); if (cIdx > 0) - fullTagCounterBuilders[cIdx].add(al.getTagCounter()); + fullTagCountAggregators[cIdx].add(al.getTagCount()); else report.unassignedAlignments.incrementAndGet(); } @@ -252,8 +252,8 @@ else if (cIdx != c) clonalSequence[i] = cs[i].consensus; result.add(new PreClone( idGenerator.incrementAndGet(), - coreTagCounterBuilders[cIdx].createAndDestroy(), - fullTagCounterBuilders[cIdx].createAndDestroy(), + coreTagCountAggregators[cIdx].createAndDestroy(), + fullTagCountAggregators[cIdx].createAndDestroy(), clonalSequence, geneInfos[cIdx], contents[cIdx] diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java index 45c1bad6c..3fe557e7b 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java @@ -476,7 +476,7 @@ static Clone doTransformClone(Clone clone, VDJCObjectExtender.Extender transformer, EnumMap newHitsMap) { return new Clone(transformer.transform(clone.getTargets()), - newHitsMap, clone.getTagCounter(), clone.getCount(), clone.getId(), clone.getGroup()); + newHitsMap, clone.getTagCount(), clone.getCount(), clone.getId(), clone.getGroup()); } static VDJCAlignments doTransformAlignment(VDJCAlignments alignment, @@ -484,7 +484,7 @@ static VDJCAlignments doTransformAlignment(VDJCAlignments alignment, EnumMap newHitsMap) { return new VDJCAlignments( newHitsMap, - alignment.getTagCounter(), + alignment.getTagCount(), transformer.transform(alignment.getTargets()), transformer.transform(alignment.getHistory()), alignment.getOriginalReads() == null diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java index 185e99eb0..a798bd7e7 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java @@ -49,7 +49,7 @@ import com.milaboratory.mixcr.basictypes.SequenceHistory; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.partialassembler.AlignedTarget; import com.milaboratory.mixcr.partialassembler.TargetMerger; import com.milaboratory.util.BitArray; @@ -743,7 +743,7 @@ VDJCAlignments createResult(long readId, VDJCAlignerPVFirst aligner, PairedRead VDJCHit[] vHits = convert(this.vHits, GeneType.Variable, aligner); VDJCHit[] jHits = convert(this.jHits, GeneType.Joining, aligner); - return new VDJCAlignments(vHits, dHits, jHits, cHits, TagCounter.EMPTY, target.targets, + return new VDJCAlignments(vHits, dHits, jHits, cHits, TagCount.NO_TAGS_1, target.targets, SequenceHistory.RawSequence.of(readId, target), aligner.parameters.isSaveOriginalReads() ? new SequenceRead[]{originalRead} : null); } diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java index 3be123fe8..9bbccf0fc 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java @@ -40,9 +40,9 @@ import com.milaboratory.core.io.sequence.SingleRead; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.SequenceHistory; -import com.milaboratory.mixcr.basictypes.tag.TagCounter; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.util.BitArray; import io.repseq.core.*; @@ -367,8 +367,8 @@ public void alignDC() { List dResult = from > to ? Collections.emptyList() : singleDAligner.align0(sequence, getPossibleDLoci( - wrapAlignmentHits(vHits), - wrapAlignmentHits(jHits), cHits), + wrapAlignmentHits(vHits), + wrapAlignmentHits(jHits), cHits), from, to); dHits = PreVDJCHit.convert(getDGenesToAlign(), parameters.getFeatureToAlign(GeneType.Diversity), dResult); @@ -430,7 +430,7 @@ public VDJCAlignments toVDJCAlignments(long inputId, SequenceRead input) { if (cHits != null) hits.put(GeneType.Constant, cHits); - return new VDJCAlignments(hits, TagCounter.EMPTY, target.targets, + return new VDJCAlignments(hits, TagCount.NO_TAGS_1, target.targets, new SequenceHistory[]{ new SequenceHistory.RawSequence(inputId, (byte) 0, target.getRCStateOfTarget(0), target.targets[0].size())}, parameters.isSaveOriginalReads() ? new SequenceRead[]{input} : null); From 64d4a82c4b07402cf0419c35ff7f8aa298e0e848 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sat, 28 May 2022 22:37:00 +0300 Subject: [PATCH 233/282] feat: integration test case #10 / single-cell; not yet functional --- ensure-test-data.sh | 8 ++++++++ itests.sh | 2 ++ itests/case10.sh | 38 ++++++++++++++++++++++++++++++++++++++ 3 files changed, 48 insertions(+) create mode 100755 itests/case10.sh diff --git a/ensure-test-data.sh b/ensure-test-data.sh index 1ed9b00eb..ac1a2c7d3 100755 --- a/ensure-test-data.sh +++ b/ensure-test-data.sh @@ -55,6 +55,14 @@ if [[ ! -f CD4M1_test_R2.fastq.gz ]]; then curl -sS -O https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R2.fastq.gz fi +if [[ ! -f single_cell_vdj_t_subset_R1.fastq.gz ]]; then + curl -sS -O https://s3.amazonaws.com/files.milaboratory.com/test-data/single_cell_vdj_t_subset_R1.fastq.gz +fi + +if [[ ! -f single_cell_vdj_t_subset_R2.fastq.gz ]]; then + curl -sS -O https://s3.amazonaws.com/files.milaboratory.com/test-data/single_cell_vdj_t_subset_R2.fastq.gz +fi + if [[ ! -d yf_sample_data ]]; then curl -sS https://s3.amazonaws.com/files.milaboratory.com/test-data/yf_sample_data.tar | tar -xv fi diff --git a/itests.sh b/itests.sh index b727e8ded..e549002b4 100755 --- a/itests.sh +++ b/itests.sh @@ -81,6 +81,8 @@ cp ${dir}/src/test/resources/sequences/*.fastq ${dir}/test_target/ cd ${dir}/test_target/ ln -s ../src/test/resources/sequences/big/CD4M1_test_R1.fastq.gz ${dir}/test_target/CD4M1_test_R1.fastq.gz ln -s ../src/test/resources/sequences/big/CD4M1_test_R2.fastq.gz ${dir}/test_target/CD4M1_test_R2.fastq.gz +ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R1.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R1.fastq.gz +ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R2.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R2.fastq.gz PATH=${dir}:${PATH} diff --git a/itests/case10.sh b/itests/case10.sh new file mode 100755 index 000000000..647004832 --- /dev/null +++ b/itests/case10.sh @@ -0,0 +1,38 @@ +#!/usr/bin/env bash + +# Single-cell integration test + +assert() { + expected=$(echo -ne "${2:-}") + result="$(eval 2>/dev/null $1)" || true + if [[ "$result" == "$expected" ]]; then + return + fi + result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")" + [[ -z "$result" ]] && result="nothing" || result="\"$result\"" + [[ -z "$2" ]] && expected="nothing" || expected="\"$2\"" + echo "expected $expected got $result for" "$1" + exit 1 +} + +set -e + +mixcr align -f \ + --tag-pattern '^(CELL:N{16})(UMI:N{10})\^(R2:*)' \ + -p rna-seq -s hs \ + -OvParameters.geneFeatureToAlign=VTranscript \ + -OvParameters.parameters.floatingLeftBound=false \ + -OjParameters.parameters.floatingRightBound=false \ + -OcParameters.parameters.floatingRightBound=false \ + -OallowPartialAlignments=true \ + -OallowNoCDR3PartAlignments=true \ + -OsaveOriginalReads=true \ + --report case10.align.report \ + single_cell_vdj_t_subset_R1.fastq.gz \ + single_cell_vdj_t_subset_R2.fastq.gz \ + case10.aligned-vdjca + +mixcr correctAndSortTags case10.aligned-vdjca case10.corrected-vdjca + +mixcr assemblePartial case10.corrected-vdjca case10.part-assembled-vdjca + From 37a4a55ad9feed5bea06b92e0ad4f6d29d706cd3 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 29 May 2022 01:25:10 +0300 Subject: [PATCH 234/282] first working code for pre-clone assembler & itest fixes --- build.gradle.kts | 4 +- itests/case10.sh | 4 +- itests/case8.sh | 8 +-- itests/case9.sh | 8 +-- .../mixcr/basictypes/VDJCAlignments.java | 11 +++- .../mixcr/basictypes/tag/TagCount.java | 4 ++ .../basictypes/tag/TagCountAggregator.java | 4 ++ .../milaboratory/mixcr/cli/CommandAlign.java | 2 +- .../cli/CommandAssemblePartialAlignments.java | 21 ++++++-- .../mixcr/cli/CommandAssemblePreClones.java | 7 ++- .../mixcr/cli/CommandCorrectAndSortTags.java | 51 ++++++++++--------- .../PartialAlignmentsAssembler.java | 2 +- .../mixcr/tags/PreCloneAssembler.java | 2 +- 13 files changed, 84 insertions(+), 44 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index a54926e04..c37c30864 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -81,9 +81,9 @@ repositories { } } -val milibVersion = "1.15.0-45-master" +val milibVersion = "1.15.0-47-master" val repseqioVersion = "1.3.5-30-master" -val mitoolVersion = "0.9.1-11-main" +val mitoolVersion = "0.9.1-12-main" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" diff --git a/itests/case10.sh b/itests/case10.sh index 647004832..18652491e 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -34,5 +34,7 @@ mixcr align -f \ mixcr correctAndSortTags case10.aligned-vdjca case10.corrected-vdjca -mixcr assemblePartial case10.corrected-vdjca case10.part-assembled-vdjca +mixcr assemblePartial case10.corrected-vdjca case10.part-assembled-molecule-vdjca + +mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled-cell-vdjca diff --git a/itests/case8.sh b/itests/case8.sh index d258d2830..17af231cc 100755 --- a/itests/case8.sh +++ b/itests/case8.sh @@ -24,8 +24,8 @@ mixcr analyze amplicon \ CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case8 assert "cat case8.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "198684" -assert "cat case8.assemble.jsonl | head -n 1 | jq -r .readsInClones" "162731" +assert "cat case8.assemble.jsonl | head -n 1 | jq -r .readsInClones" "162874" assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "227" -assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "978" -assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" -assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22477" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "981" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "3" +assert "cat case8.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22559" diff --git a/itests/case9.sh b/itests/case9.sh index 7365c1825..e3ba582a7 100755 --- a/itests/case9.sh +++ b/itests/case9.sh @@ -25,8 +25,8 @@ mixcr analyze amplicon \ CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case9 assert "cat case9.align.jsonl | head -n 1 | jq -r .chainUsage.chains.TRA" "198684" -assert "cat case9.assemble.jsonl | head -n 1 | jq -r .readsInClones" "162731" +assert "cat case9.assemble.jsonl | head -n 1 | jq -r .readsInClones" "162874" assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .longestContigLength" "227" -assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "978" -assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "1" -assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22477" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .clonesWithAmbiguousLetters" "981" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .assemblePrematureTerminationEvents" "3" +assert "cat case9.assembleContigs.jsonl | head -n 1 | jq -r .finalCloneCount" "22559" diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index bcf14c5dd..b306d7b65 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -149,10 +149,19 @@ public int getCloneIndex() { return cloneIndex; } - public VDJCAlignments setTagCounter(TagCount tc) { + public VDJCAlignments setTagCount(TagCount tc) { return new VDJCAlignments(alignmentsIndex, hits, tc, targets, history, originalReads, mappingType, cloneIndex); } + /** This strips all non-key information from tags */ + public VDJCAlignments ensureKeyTags() { + TagCount count = getTagCount(); + if (count.isNonKeySingleton()) + return setTagCount(count.ensureIsKey()); + else + return this; + } + public VDJCAlignments setMapping(ReadToCloneMapping mapping) { return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads, mapping.getMappingTypeByte(), mapping.getCloneIndex()); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java index 34c5d5124..804e95889 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java @@ -116,6 +116,10 @@ public Set tuples() { return tagMap.keySet(); } + public boolean isNonKeySingleton() { + return isSingleton() && !getSingletonTuple().isKey(); + } + public boolean isSingleton() { return singletonTuple != null; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java index 8fba6b5dc..debf0a9c0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java @@ -28,10 +28,14 @@ public TagCountAggregator add(TagTuple tc, double count) { singletonCount = count; return this; } else if (singletonTuple.equals(tc)) { + if (!singletonTuple.isKey()) + throw new IllegalStateException("Non-trivial accumulation of non-key tag count."); singletonCount += count; return this; } else { tagMap = new TObjectDoubleHashMap<>(); + if (!singletonTuple.isKey() || !tc.isKey()) + throw new IllegalStateException("Non-trivial accumulation of non-key tag count."); tagMap.put(singletonTuple, singletonCount); tagMap.put(tc, count); return this; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index e4cc4c54b..c2870948f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -752,7 +752,7 @@ public String getStatus() { } if (result.tagTuple != null) - alignment = alignment.setTagCounter(new TagCount(result.tagTuple)); + alignment = alignment.setTagCount(new TagCount(result.tagTuple)); if (alignment.isChimera()) report.onChimera(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 8523d473c..37b0c938a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -42,6 +42,7 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter; import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssembler; import com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssemblerParameters; import com.milaboratory.util.JsonOverrider; @@ -84,6 +85,10 @@ public class CommandAssemblePartialAlignments extends ACommandWithSmartOverwrite names = {"-d", "--drop-partial"}) public boolean dropPartial = false; + @Option(description = "Overlap sequences on the cell level instead of UMIs for tagged data with molecular and cell barcodes", + names = {"--cell-level"}) + public boolean cellLevel = false; + private PartialAlignmentsAssemblerParameters assemblerParameters; public PartialAlignmentsAssemblerParameters getPartialAlignmentsAssemblerParameters() { @@ -124,8 +129,11 @@ public void run1() throws Exception { VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(in); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { - // FIXME sorting level !!!!! - writer.header(reader1.getParameters(), reader1.getUsedGenes(), getFullPipelineConfiguration(), reader1.getTagsInfo()); + int groupingDepth = reader1.getTagsInfo().getDepthFor(cellLevel ? TagType.CellTag : TagType.MoleculeTag); + + writer.header(reader1.getParameters(), reader1.getUsedGenes(), getFullPipelineConfiguration(), + // output data will be grouped only up to a groupingDepth + reader1.getTagsInfo().setSorted(groupingDepth)); PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(assemblerParameters, reader1.getParameters(), reader1.getUsedGenes(), !dropPartial, overlappedOnly, @@ -141,9 +149,12 @@ public void run1() throws Exception { if (reader1.getTagsInfo() != null && reader1.getTagsInfo().tags.length > 0) { SmartProgressReporter.startProgressReport("Running assemble partial", reader1); - Function1 key = al -> al.getTagCount().asKeyOrError().key(); - OutputPort> groups1 = PipeKt.group(reader1, key); - OutputPort> groups2 = PipeKt.group(reader2, key); + // This processor strips all non-key information from the + Function1 key = al -> al.getTagCount().asKeyPrefixOrError(groupingDepth); + OutputPort> groups1 = PipeKt.group( + CUtils.wrap(reader1, VDJCAlignments::ensureKeyTags), key); + OutputPort> groups2 = PipeKt.group( + CUtils.wrap(reader2, VDJCAlignments::ensureKeyTags), key); for (GroupOP grp1 : CUtils.it(groups1)) { assembler.buildLeftPartsIndex(grp1); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java index 0ca68cbe0..827a650ff 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java @@ -1,8 +1,10 @@ package com.milaboratory.mixcr.cli; +import cc.redberry.pipe.CUtils; import com.milaboratory.core.alignment.LinearGapAlignmentScoring; import com.milaboratory.mitool.consensus.AAssemblerParameters; import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; @@ -57,7 +59,10 @@ public void run0() throws Exception { gAssemblerParams, reader1.getParameters(), new GeneFeature[]{GeneFeature.CDR3}, depth); - PreCloneAssembler assembler = new PreCloneAssembler(params, reader1, reader2); + PreCloneAssembler assembler = new PreCloneAssembler(params, + CUtils.wrap(reader1, VDJCAlignments::ensureKeyTags), + CUtils.wrap(reader2, VDJCAlignments::ensureKeyTags) + ); List clones; while ((clones = assembler.getForNextGroup()) != null) { } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index cbed4250a..aa0c935eb 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -93,24 +93,29 @@ public class CommandCorrectAndSortTags extends ACommandWithSmartOverwriteWithSin names = {"-r", "--report"}) public String reportFile; + private Path tempFolder = null; + private Path tempFolder() { - try { - File tempFolder; - if (useSystemTemp) - tempFolder = Paths.get(System.getProperty("java.io.tmpdir")) - .resolve(Paths.get(out).getFileName().getFileName() + "." + - Long.toString(System.nanoTime(), 36)) - .toFile(); - else - tempFolder = new File(out + ".tmp"); - if (tempFolder.exists()) - FileUtils.deleteDirectory(tempFolder); - Files.createDirectory(tempFolder.toPath()); - TempFileManager.register(tempFolder); - return tempFolder.toPath(); - } catch (IOException e) { - throw new RuntimeException(e); + if (tempFolder == null) { + try { + File tempFolderF; + if (useSystemTemp) + tempFolderF = Paths.get(System.getProperty("java.io.tmpdir")) + .resolve(Paths.get(out).getFileName().getFileName() + "." + + Long.toString(System.nanoTime(), 36)) + .toFile(); + else + tempFolderF = new File(out + ".tmp"); + if (tempFolderF.exists()) + FileUtils.deleteDirectory(tempFolderF); + Files.createDirectory(tempFolderF.toPath()); + TempFileManager.register(tempFolderF); + tempFolder = tempFolderF.toPath(); + } catch (IOException e) { + throw new RuntimeException(e); + } } + return tempFolder; } TagCorrectorParameters getParameters() { @@ -209,7 +214,7 @@ public void run1() throws Exception { return new HashSorter<>( VDJCAlignments.class, sortingStep.getHashFunction(), sortingStep.getComparator(), - 4, tempFolder().resolve("hashsorter." + tagIdx + "."), + 4, tempFolder().resolve("hashsorter." + tagIdx), 4, 4, stateBuilder.getOState(), stateBuilder.getIState(), memoryBudget, 10000 @@ -226,18 +231,18 @@ public void run1() throws Exception { Processor mapper = !noCorrect ? al -> { - TagValue[] newTags = al.getTagCount().asKeyOrError().asArray(); + TagValue[] newTags = al.getTagCount().getSingletonTuple().asArray(); CorrectionNode cn = correctionResult; for (int i : targetTagIndices) { NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); cn = cn.getNextLevel().get(current); if (cn == null) { report.setFilteredRecords(report.getFilteredRecords() + 1); - return al.setTagCounter(null); // will be filtered right before hash sorter + return al.setTagCount(null); // will be filtered right before hash sorter } newTags[i] = new SequenceAndQualityTagValue(cn.getCorrectValue()); } - return al.setTagCounter(new TagCount(new TagTuple(newTags))); + return al.setTagCount(new TagCount(new TagTuple(newTags))); } : al -> al; @@ -304,15 +309,15 @@ public SortingStep(int tagIdx) { public ToIntFunction getHashFunction() { return al -> { - TagTuple tagTuple = al.getTagCount().asKeyOrError(); + TagTuple tagTuple = al.getTagCount().getSingletonTuple(); return ((SequenceAndQualityTagValue) tagTuple.get(tagIdx)).data.getSequence().hashCode(); }; } public Comparator getComparator() { return (al1, al2) -> { - TagTuple tagTuple1 = al1.getTagCount().asKeyOrError(); - TagTuple tagTuple2 = al2.getTagCount().asKeyOrError(); + TagTuple tagTuple1 = al1.getTagCount().getSingletonTuple(); + TagTuple tagTuple2 = al2.getTagCount().getSingletonTuple(); return ((SequenceAndQualityTagValue) tagTuple1.get(tagIdx)).data.getSequence().compareTo( ((SequenceAndQualityTagValue) tagTuple2.get(tagIdx)).data.getSequence()); }; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 326c196f5..6828da3f9 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -183,7 +183,7 @@ public void searchOverlaps(OutputPort input) { VDJCMultiRead mRead = new VDJCMultiRead(mergedTargets); // Both parts have the same tag tuple - final VDJCAlignments mAlignment = aligner.process(mRead).alignment.setTagCounter(searchResult.tagCount); + final VDJCAlignments mAlignment = aligner.process(mRead).alignment.setTagCount(searchResult.tagCount); // Checking number of overlapped non-template (NRegion) letters int overlapTargetId = -1; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java index 6bc100161..1ec996a26 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java @@ -198,7 +198,7 @@ public List getForNextGroup() { assert grp1.getKey().equals(grp2.getKey()); localIdx = -1; - for (VDJCAlignments al : CUtils.it(grp1)) { + for (VDJCAlignments al : CUtils.it(grp2)) { localIdx++; int cIdx = alignmentIndexToClonotypeIndex[localIdx]; From 28dc75458bb46d53f44063348d41ab5c0ce10c0d Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 29 May 2022 02:32:12 +0300 Subject: [PATCH 235/282] fix: for header in no_tag use-case --- .../java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java | 2 ++ src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java | 5 ++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index 27211ec50..cb0cc5676 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -9,6 +9,8 @@ @Serializable(asJson = true) public final class TagsInfo { + public static final TagsInfo NO_TAGS = new TagsInfo(0); + @JsonProperty("sortingLevel") public final int sortingLevel; @JsonProperty("tags") diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index c2870948f..e33462672 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -645,7 +645,7 @@ else if (featureSequence.containsWildcards()) writer.header(aligner, getFullPipelineConfiguration(), tagSearchPlan != null ? new TagsInfo(0, tagSearchPlan.tagInfos.toArray(new TagInfo[0])) - : null); + : TagsInfo.NO_TAGS); OutputPort sReads = reader; CanReportProgress progress = (CanReportProgress) reader; @@ -751,8 +751,7 @@ public String getStatus() { } } - if (result.tagTuple != null) - alignment = alignment.setTagCount(new TagCount(result.tagTuple)); + alignment = alignment.setTagCount(result.tagTuple == null ? TagCount.NO_TAGS_1 : new TagCount(result.tagTuple)); if (alignment.isChimera()) report.onChimera(); From 2a68afa38b25e7e27a844731af7c4d5c11589179 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 29 May 2022 17:06:17 +0300 Subject: [PATCH 236/282] feat: PreCloneAssembler v1.0 --- build.gradle.kts | 2 +- itests/case10.sh | 1 - .../mixcr/assembler/GeneAndScore.java | 5 ++ .../basictypes/tag/TagCountAggregator.java | 2 + .../mixcr/basictypes/tag/TagTuple.java | 2 +- .../mixcr/cli/CommandAssemblePreClones.java | 56 +++++++++++- .../cli/CommandExportAlignmentsPretty.java | 10 +++ .../com/milaboratory/mixcr/tags/PreClone.java | 13 ++- .../mixcr/tags/PreCloneAssembler.java | 88 +++++++++++-------- .../mixcr/tags/PreCloneAssemblerReport.java | 4 +- 10 files changed, 134 insertions(+), 49 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index c37c30864..3761b9561 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -83,7 +83,7 @@ repositories { val milibVersion = "1.15.0-47-master" val repseqioVersion = "1.3.5-30-master" -val mitoolVersion = "0.9.1-12-main" +val mitoolVersion = "0.9.1-13-main" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" diff --git a/itests/case10.sh b/itests/case10.sh index 18652491e..d1245132d 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -35,6 +35,5 @@ mixcr align -f \ mixcr correctAndSortTags case10.aligned-vdjca case10.corrected-vdjca mixcr assemblePartial case10.corrected-vdjca case10.part-assembled-molecule-vdjca - mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled-cell-vdjca diff --git a/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java b/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java index ddbad7439..df0abc633 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java @@ -36,4 +36,9 @@ public boolean equals(Object o) { public int hashCode() { return Objects.hash(geneId, score); } + + @Override + public String toString() { + return "" + geneId.getName() + '(' + score + ')'; + } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java index debf0a9c0..a6916d172 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java @@ -38,6 +38,8 @@ public TagCountAggregator add(TagTuple tc, double count) { throw new IllegalStateException("Non-trivial accumulation of non-key tag count."); tagMap.put(singletonTuple, singletonCount); tagMap.put(tc, count); + singletonTuple = null; + singletonCount = Double.NaN; return this; } } else { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index 2340cda7e..2b54608da 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -76,7 +76,7 @@ public TagTuple keySuffix(int depth) { return key(); if (depth == tags.length) return NO_TAGS; - TagValue[] newTags = Arrays.copyOfRange(tags, depth + 1, tags.length); + TagValue[] newTags = Arrays.copyOfRange(tags, depth, tags.length); for (int i = 0; i < newTags.length; i++) newTags[i] = newTags[i].extractKey(); return new TagTuple(newTags); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java index 827a650ff..ed8d06399 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java @@ -1,19 +1,33 @@ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; import com.milaboratory.core.alignment.LinearGapAlignmentScoring; import com.milaboratory.mitool.consensus.AAssemblerParameters; import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; +import com.milaboratory.mitool.helpers.GroupOP; +import com.milaboratory.mitool.helpers.PipeKt; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.tags.PreClone; import com.milaboratory.mixcr.tags.PreCloneAssembler; import com.milaboratory.mixcr.tags.PreCloneAssemblerParameters; import com.milaboratory.util.ReportHelper; +import gnu.trove.iterator.TIntIterator; +import gnu.trove.list.array.TLongArrayList; +import gnu.trove.map.TIntLongMap; +import gnu.trove.map.hash.TIntLongHashMap; import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import kotlin.jvm.functions.Function1; +import java.io.BufferedOutputStream; +import java.io.PrintStream; +import java.nio.file.Files; +import java.nio.file.Paths; import java.util.List; import static picocli.CommandLine.Command; @@ -23,8 +37,8 @@ separator = " ", hidden = true) public class CommandAssemblePreClones extends ACommandMiXCR { - @Parameters(description = "input_file") - public String inputFile; + @Parameters(arity = "2", description = "input_file output_file") + public List files; private static final AAssemblerParameters aAssemblerParams = AAssemblerParameters.builder() .bandWidth(4) @@ -47,11 +61,16 @@ public class CommandAssemblePreClones extends ACommandMiXCR { public void run0() throws Exception { try ( - VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(inputFile); - VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(inputFile) + VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(files.get(0)); + VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(files.get(0)); + // For export + VDJCAlignmentsReader reader3 = new VDJCAlignmentsReader(files.get(0)); + PrintStream out = new PrintStream(new BufferedOutputStream( + Files.newOutputStream(Paths.get(files.get(1))), 1 << 20)) ) { TagsInfo tagsInfo = reader1.getTagsInfo(); int depth = tagsInfo.getDepthFor(TagType.CellTag); + // int depth = tagsInfo.getDepthFor(TagType.MoleculeTag); if (tagsInfo.getSortingLevel() < depth) throwValidationException("Input file has insufficient sorting level"); @@ -63,8 +82,37 @@ public void run0() throws Exception { CUtils.wrap(reader1, VDJCAlignments::ensureKeyTags), CUtils.wrap(reader2, VDJCAlignments::ensureKeyTags) ); + + Function1 gFunction = a -> a.getTagCount().asKeyPrefixOrError(depth); + OutputPort> alGroups = PipeKt.group(CUtils.wrap(reader3, + VDJCAlignments::ensureKeyTags), gFunction); + List clones; while ((clones = assembler.getForNextGroup()) != null) { + GroupOP grp = alGroups.take(); + assert clones.isEmpty() || clones.get(0).coreKey.equals(grp.getKey()); + TIntLongMap localToMitReadIndex = new TIntLongHashMap(); + int localId = 0; + for (VDJCAlignments al : CUtils.it(grp)) + localToMitReadIndex.put(localId++, al.getMinReadId()); + + for (PreClone clone : clones) { + + TLongArrayList rIds = new TLongArrayList(); + TIntIterator it = clone.alignments.iterator(); + while (it.hasNext()) + rIds.add(localToMitReadIndex.get(it.next())); + + out.println( + clone.clonalSequence[0].getSequence().toString() + "\t" + + clone.alignments.size() + "\t" + + clone.geneScores.get(GeneType.Variable) + "\t" + + clone.geneScores.get(GeneType.Joining) + "\t" + + clone.geneScores.get(GeneType.Constant) + "\t" + + clone.coreTagCount + "\t" + + clone.fullTagCount + "\t" + + rIds); + } } assembler.getReport().writeReport(ReportHelper.STDOUT); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java index a78dd447a..22f610df9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java @@ -111,6 +111,10 @@ public class CommandExportAlignmentsPretty extends ACommandSimpleExportMiXCR { names = {"-i", "--read-ids"}) public List readIds = new ArrayList<>(); + @Option(description = "Alignment index", + names = {"--alignment-idx"}) + public List alignmentIdx = new ArrayList<>(); + @Option(description = "List of clone ids to export", names = {"--clone-ids"}) public List cloneIds = new ArrayList<>(); @@ -121,6 +125,12 @@ TLongHashSet getReadIds() { return new TLongHashSet(readIds); } + TLongHashSet getAlignmentIdx() { + if (alignmentIdx.isEmpty()) + return null; + return new TLongHashSet(alignmentIdx); + } + TLongHashSet getCloneIds() { if (cloneIds.isEmpty()) return null; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java index 3738c0c6b..d830133ef 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreClone.java @@ -3,7 +3,8 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mixcr.assembler.GeneAndScore; import com.milaboratory.mixcr.basictypes.tag.TagCount; -import com.milaboratory.util.BitArray; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import gnu.trove.set.hash.TIntHashSet; import io.repseq.core.GeneType; import java.util.List; @@ -12,6 +13,8 @@ public final class PreClone { /** Pre-clonotype id */ public long id; + /** Core key of the alignments group */ + public final TagTuple coreKey; /** Tag counter aggregating information about alignments with clonal sequence */ public final TagCount coreTagCount; /** Tag counter aggregating information across all alignments assigned to this pre-clone */ @@ -21,11 +24,13 @@ public final class PreClone { /** Aggregated V, J, C gene scoring and content information */ public final Map> geneScores; /** Ids of alignments assigned to this pre-clone */ - public final BitArray alignments; + public final TIntHashSet alignments; - public PreClone(long id, TagCount coreTagCount, TagCount fullTagCount, NSequenceWithQuality[] clonalSequence, - Map> geneScores, BitArray alignments) { + public PreClone(long id, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, + NSequenceWithQuality[] clonalSequence, + Map> geneScores, TIntHashSet alignments) { this.id = id; + this.coreKey = coreKey; this.coreTagCount = coreTagCount; this.fullTagCount = fullTagCount; this.clonalSequence = clonalSequence; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java index 1ec996a26..16fcfc478 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java @@ -2,6 +2,7 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.util.DummyInputPort; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mitool.consensus.ConsensusResult; import com.milaboratory.mitool.consensus.GConsensusAssembler; @@ -13,8 +14,8 @@ import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.basictypes.tag.TagTuple; -import com.milaboratory.util.BitArray; import gnu.trove.map.hash.TObjectIntHashMap; +import gnu.trove.set.hash.TIntHashSet; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; import kotlin.jvm.functions.Function1; @@ -32,8 +33,7 @@ public PreCloneAssembler(PreCloneAssemblerParameters parameters, OutputPort alignmentsReader1, OutputPort alignmentsReader2) { this.parameters = parameters; - Function1 gFunction = - vdjcAlignments -> vdjcAlignments.getTagCount().asKeyPrefixOrError(parameters.groupingLevel); + Function1 gFunction = a -> a.getTagCount().asKeyPrefixOrError(parameters.groupingLevel); this.alignmentsReader1 = PipeKt.group(alignmentsReader1, gFunction); this.alignmentsReader2 = PipeKt.group(alignmentsReader2, gFunction); } @@ -81,21 +81,29 @@ public List getForNextGroup() { gss[i] = hits[i].getGeneAndScore(); geneAndScores.put(gt, gss); } - alignmentInfos.add(new AlignmentInfo(localIdx, + alignmentInfos.add(new AlignmentInfo(localIdx, al.getAlignmentsIndex(), al.getMinReadId(), al.getTagCount().keySuffixes(parameters.groupingLevel), geneAndScores)); // Allocating array for the next data row row = new NSequenceWithQuality[parameters.assemblingFeatures.length]; } + assert alignmentInfos.size() == assemblerInput.size(); + report.inputAlignments.addAndGet(localIdx); + if (assemblerInput.isEmpty()) { + CUtils.drainWithoutClose(alignmentsReader2.take(), DummyInputPort.INSTANCE); + return Collections.emptyList(); + } + // Step #2 // Building consensuses from the records collected on the step #1, and creating indices for // clonotype assignment of alignments left after the previous step GConsensusAssembler gAssembler = new GConsensusAssembler(parameters.assemblerParameters, assemblerInput); List consensuses = gAssembler.calculateConsensuses(); + // TODO <-- leave only top consensus for UMI-based analysis int numberOfClones = consensuses.size(); report.clonotypes.addAndGet(numberOfClones); report.clonotypesPerGroup.get(numberOfClones).incrementAndGet(); @@ -104,9 +112,9 @@ public List getForNextGroup() { // noinspection unchecked Map>[] geneInfos = new Map[numberOfClones]; // Saves local record indices, assigned to each of the consensuses - BitArray[] contents = new BitArray[numberOfClones]; - // I.e. UMIs for sole cell-barcode assembly use-case - Set[] tagSuffixess = new Set[numberOfClones]; + TIntHashSet[] contents = new TIntHashSet[numberOfClones]; + // I.e. UMIs for CELL-barcode-only assembly use-case + // Set[] tagSuffixess = new Set[numberOfClones]; // Union of all contents // BitArray allAssignedToClonotypes = new BitArray((int) grp1.getCount()); @@ -125,14 +133,14 @@ public List getForNextGroup() { for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { ConsensusResult c = consensuses.get(cIdx); VDJCGeneAccumulator acc = new VDJCGeneAccumulator(); - BitArray content = new BitArray((int) grp1.getCount()); + TIntHashSet content = new TIntHashSet(); Set tagSuffixes = new HashSet<>(); int rIdx = -1; while ((rIdx = c.recordsUsed.nextBit(rIdx + 1)) != -1) { AlignmentInfo ai = alignmentInfos.get(rIdx); acc.accumulate(ai.genesAndScores); - content.set(ai.localIdx); + content.add(ai.localIdx); tagSuffixes.addAll(ai.tagSuffixes); alignmentIndexToClonotypeIndex[ai.localIdx] = cIdx + 1; report.coreAlignments.incrementAndGet(); @@ -142,7 +150,7 @@ public List getForNextGroup() { geneInfos[cIdx] = acc.aggregateInformation(parameters.relativeMinScores); contents[cIdx] = content; - tagSuffixess[cIdx] = tagSuffixes; + // tagSuffixess[cIdx] = tagSuffixes; for (TagTuple ts : tagSuffixes) if (tagSuffixToCloneId.get(ts) > 0) @@ -150,7 +158,7 @@ public List getForNextGroup() { else tagSuffixToCloneId.put(ts, cIdx + 1); - for (GeneType gt : GeneType.VJC_REFERENCE) { + for (GeneType gt : GeneType.VJ_REFERENCE) { List gss = geneInfos[cIdx].get(gt); if (gss == null) continue; @@ -175,7 +183,7 @@ public List getForNextGroup() { for (TagTuple ts : ai.tagSuffixes) tagSuffixToCloneId.put(ts, -1); - for (GeneType gt : GeneType.VJC_REFERENCE) { + for (GeneType gt : GeneType.VJ_REFERENCE) { GeneAndScore[] gss = ai.genesAndScores.get(gt); if (gss == null) continue; @@ -195,51 +203,52 @@ public List getForNextGroup() { } GroupOP grp2 = alignmentsReader2.take(); - assert grp1.getKey().equals(grp2.getKey()); + assert grp1.getKey().equals(grp2.getKey()) : "" + grp1.getKey() + " != " + grp2.getKey(); localIdx = -1; for (VDJCAlignments al : CUtils.it(grp2)) { localIdx++; - int cIdx = alignmentIndexToClonotypeIndex[localIdx]; + int cIdxP1 = alignmentIndexToClonotypeIndex[localIdx]; // Running empirical assignment for the alignments not yet assigned - if (cIdx == 0) { - // V, J and C gene based assignment - for (GeneType gt : GeneType.VJC_REFERENCE) + if (cIdxP1 == 0) { + // V and J gene based assignment + for (GeneType gt : GeneType.VJ_REFERENCE) for (VDJCHit hit : al.getHits(gt)) { - int c = vjcGenesToCloneId.get(hit.getGene().getId()); - if (c <= 0) + int cp1 = vjcGenesToCloneId.get(hit.getGene().getId()); + if (cp1 <= 0) continue; - if (cIdx == 0) - cIdx = c; - else if (cIdx != c) - cIdx = -1; + if (cIdxP1 == 0) + cIdxP1 = cp1; + else if (cIdxP1 != cp1) + cIdxP1 = -1; } // TagSuffix based assignment for (TagTuple ts : al.getTagCount().keySuffixes(parameters.groupingLevel)) { - int c = tagSuffixToCloneId.get(ts); - if (c <= 0) + int cp1 = tagSuffixToCloneId.get(ts); + if (cp1 <= 0) continue; - if (cIdx == 0) - cIdx = c; - else if (cIdx != c) - cIdx = -1; + if (cIdxP1 == 0) + cIdxP1 = cp1; + else if (cIdxP1 != cp1) + cIdxP1 = -1; } - if (cIdx > 0) { + if (cIdxP1 > 0) { // Adding alignment to the clone - contents[cIdx - 1].set(localIdx); + contents[cIdxP1 - 1].add(localIdx); report.empiricallyAssignedAlignments.incrementAndGet(); - } - } else if (cIdx > 0) + } else if (cIdxP1 == -1) + report.empiricalAssignmentConflicts.incrementAndGet(); + } else if (cIdxP1 > 0) // Using second iteration over the alignments to assemble TagCounters from the alignments assigned to // clonotypes based on their contig assignment - coreTagCountAggregators[cIdx - 1].add(al.getTagCount()); + coreTagCountAggregators[cIdxP1 - 1].add(al.getTagCount()); - if (cIdx > 0) - fullTagCountAggregators[cIdx].add(al.getTagCount()); + if (cIdxP1 > 0) + fullTagCountAggregators[cIdxP1 - 1].add(al.getTagCount()); else report.unassignedAlignments.incrementAndGet(); } @@ -252,6 +261,7 @@ else if (cIdx != c) clonalSequence[i] = cs[i].consensus; result.add(new PreClone( idGenerator.incrementAndGet(), + grp1.getKey(), coreTagCountAggregators[cIdx].createAndDestroy(), fullTagCountAggregators[cIdx].createAndDestroy(), clonalSequence, @@ -265,11 +275,15 @@ else if (cIdx != c) private static final class AlignmentInfo { final int localIdx; + final long alignmentId, minReadId; final Set tagSuffixes; final EnumMap genesAndScores; - public AlignmentInfo(int localIdx, Set tagSuffixes, EnumMap genesAndScores) { + public AlignmentInfo(int localIdx, long alignmentId, long minReadId, + Set tagSuffixes, EnumMap genesAndScores) { this.localIdx = localIdx; + this.alignmentId = alignmentId; + this.minReadId = minReadId; this.tagSuffixes = tagSuffixes; this.genesAndScores = genesAndScores; } diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java index 9024a5167..596429ed8 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java @@ -16,19 +16,21 @@ public final class PreCloneAssemblerReport implements Report { final AtomicLong coreAlignments = new AtomicLong(); final AtomicLong discardedCoreAlignments = new AtomicLong(); final AtomicLong empiricallyAssignedAlignments = new AtomicLong(); + final AtomicLong empiricalAssignmentConflicts = new AtomicLong(); final AtomicLong unassignedAlignments = new AtomicLong(); @Override public void writeReport(ReportHelper helper) { helper.writeField("Number of input groups", inputGroups.get()); helper.writeField("Number of input alignments", inputAlignments.get()); - helper.writeField("Number of output clonotypes", inputAlignments.get()); + helper.writeField("Number of output clonotypes", clonotypes.get()); helper.println("Number of clonotypes per group"); helper.print(ReportKt.format(clonotypesPerGroup.getImmutable(), " ", new StringBuilder(), new FormatSettings(0), 0).toString()); helper.writePercentAndAbsoluteField("Number of core alignments", coreAlignments.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("Discarded core alignments", discardedCoreAlignments.get(), coreAlignments.get()); helper.writePercentAndAbsoluteField("Empirically assigned alignments", empiricallyAssignedAlignments.get(), inputAlignments.get()); + helper.writePercentAndAbsoluteField("Empirical assignment conflicts", empiricalAssignmentConflicts.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("Unassigned alignments", unassignedAlignments.get(), inputAlignments.get()); } From 51aec3a5f37f12df80fce257d82329e8705a2722 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 29 May 2022 23:25:34 +0300 Subject: [PATCH 237/282] minor --- .../java/com/milaboratory/mixcr/basictypes/ClnAWriter.java | 2 +- .../java/com/milaboratory/mixcr/tags/PreCloneAssembler.java | 3 ++- .../milaboratory/mixcr/tags/PreCloneAssemblerReport.java | 6 ++++-- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index 39dcfd28b..9ef704c2c 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -232,7 +232,7 @@ public void collateAlignments(OutputPort alignments, // Dirty heuristic to optimize trade-off between memory usage and number of random access places in a file // to read from - int chunkSize = (int) Math.min(Math.max(16384, numberOfAlignments / 8), 1048576); + // int chunkSize = (int) Math.min(Math.max(16384, numberOfAlignments / 8), 1048576); // Sorting alignments by cloneId and then by mapping type (core alignments will be written before all others) // and saving sorting output port diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java index 16fcfc478..22250e9da 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java @@ -219,6 +219,7 @@ public List getForNextGroup() { int cp1 = vjcGenesToCloneId.get(hit.getGene().getId()); if (cp1 <= 0) continue; + report.vjEmpiricallyAssignedAlignments.incrementAndGet(); if (cIdxP1 == 0) cIdxP1 = cp1; else if (cIdxP1 != cp1) @@ -230,6 +231,7 @@ else if (cIdxP1 != cp1) int cp1 = tagSuffixToCloneId.get(ts); if (cp1 <= 0) continue; + report.umiEmpiricallyAssignedAlignments.incrementAndGet(); if (cIdxP1 == 0) cIdxP1 = cp1; else if (cIdxP1 != cp1) @@ -239,7 +241,6 @@ else if (cIdxP1 != cp1) if (cIdxP1 > 0) { // Adding alignment to the clone contents[cIdxP1 - 1].add(localIdx); - report.empiricallyAssignedAlignments.incrementAndGet(); } else if (cIdxP1 == -1) report.empiricalAssignmentConflicts.incrementAndGet(); } else if (cIdxP1 > 0) diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java index 596429ed8..633b99b28 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java @@ -15,7 +15,8 @@ public final class PreCloneAssemblerReport implements Report { final ConcurrentAtomicLongMap clonotypesPerGroup = new ConcurrentAtomicLongMap<>(); final AtomicLong coreAlignments = new AtomicLong(); final AtomicLong discardedCoreAlignments = new AtomicLong(); - final AtomicLong empiricallyAssignedAlignments = new AtomicLong(); + final AtomicLong vjEmpiricallyAssignedAlignments = new AtomicLong(); + final AtomicLong umiEmpiricallyAssignedAlignments = new AtomicLong(); final AtomicLong empiricalAssignmentConflicts = new AtomicLong(); final AtomicLong unassignedAlignments = new AtomicLong(); @@ -29,7 +30,8 @@ public void writeReport(ReportHelper helper) { new StringBuilder(), new FormatSettings(0), 0).toString()); helper.writePercentAndAbsoluteField("Number of core alignments", coreAlignments.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("Discarded core alignments", discardedCoreAlignments.get(), coreAlignments.get()); - helper.writePercentAndAbsoluteField("Empirically assigned alignments", empiricallyAssignedAlignments.get(), inputAlignments.get()); + helper.writePercentAndAbsoluteField("VJ-gene empirically assigned alignments", vjEmpiricallyAssignedAlignments.get(), inputAlignments.get()); + helper.writePercentAndAbsoluteField("UMI empirically assigned alignments", umiEmpiricallyAssignedAlignments.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("Empirical assignment conflicts", empiricalAssignmentConflicts.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("Unassigned alignments", unassignedAlignments.get(), inputAlignments.get()); From dd72c04d5f61ea1049e12258bf0fc91958ccf13d Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 30 May 2022 00:22:22 +0300 Subject: [PATCH 238/282] refactor: pre-clones --- build.gradle.kts | 2 +- .../mixcr/{tags => assembler/preclone}/PreClone.java | 2 +- .../{tags => assembler/preclone}/PreCloneAssembler.java | 2 +- .../preclone}/PreCloneAssemblerParameters.java | 2 +- .../preclone}/PreCloneAssemblerReport.java | 2 +- .../milaboratory/mixcr/cli/CommandAssemblePreClones.java | 6 +++--- 6 files changed, 8 insertions(+), 8 deletions(-) rename src/main/java/com/milaboratory/mixcr/{tags => assembler/preclone}/PreClone.java (96%) rename src/main/java/com/milaboratory/mixcr/{tags => assembler/preclone}/PreCloneAssembler.java (99%) rename src/main/java/com/milaboratory/mixcr/{tags => assembler/preclone}/PreCloneAssemblerParameters.java (94%) rename src/main/java/com/milaboratory/mixcr/{tags => assembler/preclone}/PreCloneAssemblerReport.java (97%) diff --git a/build.gradle.kts b/build.gradle.kts index 3761b9561..5815a2e2b 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -82,7 +82,7 @@ repositories { } val milibVersion = "1.15.0-47-master" -val repseqioVersion = "1.3.5-30-master" +val repseqioVersion = "1.3.5-31-master" val mitoolVersion = "0.9.1-13-main" val miplotsVersion = "0.1-19-master" val jacksonBomVersion = "2.13.3" diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java similarity index 96% rename from src/main/java/com/milaboratory/mixcr/tags/PreClone.java rename to src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index d830133ef..ca9072ad3 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.tags; +package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mixcr.assembler.GeneAndScore; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java similarity index 99% rename from src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java rename to src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index 22250e9da..83d0b4b07 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.tags; +package com.milaboratory.mixcr.assembler.preclone; import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java similarity index 94% rename from src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerParameters.java rename to src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java index 16ac5aa57..10033973d 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.tags; +package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; diff --git a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java similarity index 97% rename from src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java rename to src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java index 633b99b28..96d5e4144 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/PreCloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java @@ -1,4 +1,4 @@ -package com.milaboratory.mixcr.tags; +package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.mitool.pattern.search.FormatSettings; import com.milaboratory.mitool.pattern.search.ReportKt; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java index ed8d06399..6c42dccd6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java @@ -12,9 +12,9 @@ import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; -import com.milaboratory.mixcr.tags.PreClone; -import com.milaboratory.mixcr.tags.PreCloneAssembler; -import com.milaboratory.mixcr.tags.PreCloneAssemblerParameters; +import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneAssembler; +import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerParameters; import com.milaboratory.util.ReportHelper; import gnu.trove.iterator.TIntIterator; import gnu.trove.list.array.TLongArrayList; From ac3411b999f875463f0a132ff0e59dde68a91bcd Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 30 May 2022 01:59:00 +0300 Subject: [PATCH 239/282] WIP --- .../mixcr/assembler/CloneAccumulator.java | 1 + .../mixcr/assembler/CloneFactory.java | 1 + .../mixcr/assembler/VDJCGeneAccumulator.java | 1 + .../assembler/fullseq/FullSeqAssembler.java | 2 +- .../mixcr/assembler/preclone/IO.java | 68 +++++++++++++++++++ .../mixcr/assembler/preclone/PreClone.java | 10 ++- .../assembler/preclone/PreCloneAssembler.java | 21 +++--- .../preclone/PreCloneWithAlignments.java | 17 +++++ .../assembler/preclone/PreCloneWriter.java | 58 ++++++++++++++++ .../mixcr/basictypes/ClnAWriter.java | 19 ++---- .../mixcr/basictypes/FieldCollection.java | 14 ++++ .../GeneAndScore.java | 4 +- .../com/milaboratory/mixcr/basictypes/IO.java | 26 +++++++ .../mixcr/basictypes/VDJCHit.java | 1 - 14 files changed, 209 insertions(+), 34 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java create mode 100644 src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java rename src/main/java/com/milaboratory/mixcr/{assembler => basictypes}/GeneAndScore.java (87%) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index f1f0bde82..5fba859b0 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -37,6 +37,7 @@ import com.milaboratory.core.sequence.quality.QualityAggregationType; import com.milaboratory.core.sequence.quality.QualityAggregator; import com.milaboratory.mixcr.basictypes.ClonalSequence; +import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index c48ec8bc3..fcb1806c6 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -34,6 +34,7 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.vdjaligners.SingleDAligner; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java index 1e4b18063..9bda34513 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.assembler; +import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 8aba67a5c..0756caf84 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -38,7 +38,7 @@ import com.milaboratory.core.sequence.*; import com.milaboratory.core.sequence.quality.QualityTrimmer; import com.milaboratory.mixcr.assembler.CloneFactory; -import com.milaboratory.mixcr.assembler.GeneAndScore; +import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java new file mode 100644 index 000000000..e997d9ad8 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java @@ -0,0 +1,68 @@ +package com.milaboratory.mixcr.assembler.preclone; + +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.mixcr.basictypes.GeneAndScore; +import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.primitivio.Serializer; +import io.repseq.core.GeneType; + +import java.util.ArrayList; +import java.util.EnumMap; +import java.util.List; +import java.util.Map; + +public final class IO { + private IO() { + } + + public static final class PreCloneSerializer implements Serializer { + @Override + public void write(PrimitivO output, PreClone obj) { + output.writeLong(obj.id); + output.writeObject(obj.coreKey); + output.writeObject(obj.clonalSequence); + output.writeObject(obj.coreTagCount); + output.writeObject(obj.fullTagCount); + output.writeInt(obj.geneScores.size()); + for (Map.Entry> e : obj.geneScores.entrySet()) { + output.writeObject(e.getKey()); + output.writeInt(e.getValue().size()); + for (GeneAndScore gs : e.getValue()) + output.writeObject(gs); + } + } + + @Override + public PreClone read(PrimitivI input) { + long id = input.readLong(); + TagTuple coreKey = input.readObject(TagTuple.class); + NSequenceWithQuality[] clonalSequence = input.readObject(NSequenceWithQuality[].class); + TagCount coreTagCount = input.readObject(TagCount.class); + TagCount fullTagCount = input.readObject(TagCount.class); + int count0 = input.readInt(); + EnumMap> gsss = new EnumMap<>(GeneType.class); + for (int i0 = 0; i0 < count0; i0++) { + GeneType gt = input.readObject(GeneType.class); + int count1 = input.readInt(); + List gss = new ArrayList<>(); + for (int i1 = 0; i1 < count1; i1++) + gss.add(input.readObject(GeneAndScore.class)); + gsss.put(gt, gss); + } + return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss); + } + + @Override + public boolean isReference() { + return true; + } + + @Override + public boolean handlesReference() { + return false; + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index ca9072ad3..2a9345ebc 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -1,15 +1,16 @@ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.core.sequence.NSequenceWithQuality; -import com.milaboratory.mixcr.assembler.GeneAndScore; +import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; -import gnu.trove.set.hash.TIntHashSet; +import com.milaboratory.primitivio.annotations.Serializable; import io.repseq.core.GeneType; import java.util.List; import java.util.Map; +@Serializable(by = IO.PreCloneSerializer.class) public final class PreClone { /** Pre-clonotype id */ public long id; @@ -23,18 +24,15 @@ public final class PreClone { public final NSequenceWithQuality[] clonalSequence; /** Aggregated V, J, C gene scoring and content information */ public final Map> geneScores; - /** Ids of alignments assigned to this pre-clone */ - public final TIntHashSet alignments; public PreClone(long id, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, NSequenceWithQuality[] clonalSequence, - Map> geneScores, TIntHashSet alignments) { + Map> geneScores) { this.id = id; this.coreKey = coreKey; this.coreTagCount = coreTagCount; this.fullTagCount = fullTagCount; this.clonalSequence = clonalSequence; this.geneScores = geneScores; - this.alignments = alignments; } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index 83d0b4b07..ed849cef0 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -8,7 +8,7 @@ import com.milaboratory.mitool.consensus.GConsensusAssembler; import com.milaboratory.mitool.helpers.GroupOP; import com.milaboratory.mitool.helpers.PipeKt; -import com.milaboratory.mixcr.assembler.GeneAndScore; +import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.assembler.VDJCGeneAccumulator; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; @@ -42,7 +42,7 @@ public PreCloneAssemblerReport getReport() { return report; } - public List getForNextGroup() { + public List getForNextGroup() { GroupOP grp1 = alignmentsReader1.take(); if (grp1 == null) @@ -254,19 +254,20 @@ else if (cIdxP1 != cp1) report.unassignedAlignments.incrementAndGet(); } - List result = new ArrayList<>(); + List result = new ArrayList<>(); for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { ConsensusResult.SingleConsensus[] cs = consensuses.get(cIdx).consensuses; NSequenceWithQuality[] clonalSequence = new NSequenceWithQuality[cs.length]; for (int i = 0; i < cs.length; i++) clonalSequence[i] = cs[i].consensus; - result.add(new PreClone( - idGenerator.incrementAndGet(), - grp1.getKey(), - coreTagCountAggregators[cIdx].createAndDestroy(), - fullTagCountAggregators[cIdx].createAndDestroy(), - clonalSequence, - geneInfos[cIdx], + result.add(new PreCloneWithAlignments( + new PreClone( + idGenerator.incrementAndGet(), + grp1.getKey(), + coreTagCountAggregators[cIdx].createAndDestroy(), + fullTagCountAggregators[cIdx].createAndDestroy(), + clonalSequence, + geneInfos[cIdx]), contents[cIdx] )); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java new file mode 100644 index 000000000..99a96da5c --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java @@ -0,0 +1,17 @@ +package com.milaboratory.mixcr.assembler.preclone; + +import gnu.trove.set.hash.TIntHashSet; + +public final class PreCloneWithAlignments { + /** Assembled pre-clone */ + public final PreClone preClone; + /** Group-local indices of alignments assigned to this pre-clone */ + public final TIntHashSet alignments; + + public PreCloneWithAlignments(PreClone preClone, TIntHashSet alignments) { + this.preClone = preClone; + this.alignments = alignments; + } + + +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java new file mode 100644 index 000000000..c222bf125 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java @@ -0,0 +1,58 @@ +package com.milaboratory.mixcr.assembler.preclone; + +import com.milaboratory.mixcr.basictypes.IOUtil; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.primitivio.PrimitivIOStateBuilder; +import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.primitivio.blocks.PrimitivOHybrid; +import com.milaboratory.util.TempFileManager; +import com.milaboratory.util.sorting.HashSorter; +import org.apache.commons.io.FileUtils; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.concurrent.ForkJoinPool; + +import static com.milaboratory.mixcr.basictypes.FieldCollection.VDJCACloneIdComparator; +import static com.milaboratory.mixcr.basictypes.FieldCollection.VDJCACloneIdHash; + +public final class PreCloneWriter { + private final Path tempFolder; + private final PrimitivOHybrid output; + private volatile HashSorter alignmentCollator; + private volatile HashSorter cloneCollator; + + public PreCloneWriter(Path file) throws IOException { + this.tempFolder = file.toAbsolutePath().resolveSibling(file.getFileName().toString() + ".presorted"); + if (Files.exists(tempFolder)) + FileUtils.deleteDirectory(tempFolder.toFile()); + TempFileManager.register(tempFolder.toFile()); + Files.createDirectory(this.tempFolder); + this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file); + } + + public void init(VDJCAlignmentsReader alignmentReader) { + // Writing header in raw primitivIO mode and initializing primitivIO state + try (PrimitivO o = this.output.beginPrimitivO(true)) { + o.writeObject(alignmentReader.getParameters()); + IOUtil.stdVDJCPrimitivOStateInit(o, alignmentReader.getUsedGenes(), alignmentReader.getParameters()); + } + + PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); + IOUtil.registerGeneReferences(stateBuilder, alignmentReader.getUsedGenes(), alignmentReader.getParameters()); + + long memoryBudget = + Runtime.getRuntime().maxMemory() > 10_000_000_000L /* -Xmx10g */ + ? Runtime.getRuntime().maxMemory() / 8L /* 1 Gb */ + : 1 << 28 /* 256 Mb */; + + alignmentCollator = new HashSorter<>( + VDJCAlignments.class, + VDJCACloneIdHash, VDJCACloneIdComparator, + 5, tempFolder, 4, 6, + stateBuilder.getOState(), stateBuilder.getIState(), + memoryBudget, 1 << 18 /* 256 Kb */); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index 9ef704c2c..ad151f410 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -35,7 +35,6 @@ import com.milaboratory.cli.AppVersionInfo; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.cli.PipelineConfigurationWriter; -import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.util.MiXCRDebug; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.primitivio.PrimitivIOStateBuilder; @@ -45,7 +44,6 @@ import com.milaboratory.primitivio.blocks.PrimitivOBlocks; import com.milaboratory.primitivio.blocks.PrimitivOHybrid; import com.milaboratory.util.CanReportProgressAndStage; -import com.milaboratory.util.HashFunctions; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.io.HasPosition; import com.milaboratory.util.sorting.HashSorter; @@ -60,11 +58,12 @@ import java.nio.charset.StandardCharsets; import java.nio.file.Files; import java.nio.file.Path; -import java.util.Comparator; import java.util.List; import java.util.Objects; import java.util.concurrent.ForkJoinPool; -import java.util.function.ToIntFunction; + +import static com.milaboratory.mixcr.basictypes.FieldCollection.VDJCACloneIdComparator; +import static com.milaboratory.mixcr.basictypes.FieldCollection.VDJCACloneIdHash; /** * Writer for CLNA file format. @@ -251,7 +250,7 @@ public void collateAlignments(OutputPort alignments, : 1 << 28 /* 256 Mb */; collator = new HashSorter<>( VDJCAlignments.class, - new CloneIdHash(), CloneIdComparator, + VDJCACloneIdHash, VDJCACloneIdComparator, 5, tempFolder, 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), memoryBudget, 1 << 18 /* 256 Kb */); @@ -435,14 +434,4 @@ public void close() throws IOException { finished = true; output.close(); } - - private static class CloneIdHash implements ToIntFunction { - @Override - public int applyAsInt(VDJCAlignments value) { - return HashFunctions.JenkinWang32shift(value.getCloneIndex()); - } - } - - private static final Comparator CloneIdComparator = - Comparator.comparing(VDJCAlignments::getCloneIndex); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java new file mode 100644 index 000000000..d68c593a0 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java @@ -0,0 +1,14 @@ +package com.milaboratory.mixcr.basictypes; + +import com.milaboratory.util.HashFunctions; + +import java.util.Comparator; +import java.util.function.ToIntFunction; + +public final class FieldCollection { + public static final Comparator VDJCACloneIdComparator = + Comparator.comparing(VDJCAlignments::getCloneIndex); + + public static final ToIntFunction VDJCACloneIdHash = + a -> HashFunctions.JenkinWang32shift(a.getCloneIndex()); +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java b/src/main/java/com/milaboratory/mixcr/basictypes/GeneAndScore.java similarity index 87% rename from src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java rename to src/main/java/com/milaboratory/mixcr/basictypes/GeneAndScore.java index df0abc633..05a0beebb 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/GeneAndScore.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/GeneAndScore.java @@ -1,9 +1,11 @@ -package com.milaboratory.mixcr.assembler; +package com.milaboratory.mixcr.basictypes; +import com.milaboratory.primitivio.annotations.Serializable; import io.repseq.core.VDJCGeneId; import java.util.Objects; +@Serializable(by = IO.GeneAndScoreSerializer.class) public final class GeneAndScore implements Comparable { public final VDJCGeneId geneId; public final float score; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index f111e0e80..4fc6be137 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -41,11 +41,37 @@ import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCGene; +import io.repseq.core.VDJCGeneId; import java.util.EnumMap; import java.util.Map; class IO { + public static class GeneAndScoreSerializer implements Serializer { + @Override + public void write(PrimitivO output, GeneAndScore obj) { + output.writeObject(obj.geneId); + output.writeFloat(obj.score); + } + + @Override + public GeneAndScore read(PrimitivI input) { + VDJCGeneId gene = input.readObject(VDJCGeneId.class); + float score = input.readFloat(); + return new GeneAndScore(gene, score); + } + + @Override + public boolean isReference() { + return true; + } + + @Override + public boolean handlesReference() { + return false; + } + } + public static class VDJCHitSerializer implements Serializer { @Override public void write(PrimitivO output, VDJCHit object) { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java index f05fb3dba..1a92798cf 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java @@ -32,7 +32,6 @@ import com.milaboratory.core.alignment.Alignment; import com.milaboratory.core.alignment.AlignmentHelper; import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.mixcr.assembler.GeneAndScore; import com.milaboratory.primitivio.annotations.Serializable; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; From 379a8f9c7de877542dab9f6a9c5edfb3fa8265af Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Mon, 30 May 2022 01:35:11 +0200 Subject: [PATCH 240/282] Add `overlapScatterPlot` command (#49) --- build.gradle.kts | 2 +- .../mixcr/cli/CommonDescriptions.java | 9 ++ .../java/com/milaboratory/mixcr/cli/Main.java | 1 + .../cli/postanalysis/CommandDownsample.java | 5 +- .../postanalysis/CommandOverlapScatter.java | 128 ++++++++++++++++++ .../mixcr/cli/postanalysis/CommandPa.java | 9 +- .../cli/postanalysis/CommandPaExport.java | 7 +- .../cli/postanalysis/CommandPaOverlap.java | 3 +- .../downsampling/DownsamplingUtil.java | 2 +- .../postanalysis/util/OverlapBrowser.java | 1 - .../postanalysis/plots/OverlapScatter.kt | 127 ++++++++++++++++- 11 files changed, 277 insertions(+), 17 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java diff --git a/build.gradle.kts b/build.gradle.kts index 32de59ea2..6831aabcc 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -80,7 +80,7 @@ repositories { val milibVersion = "1.15.0-44-master" val repseqioVersion = "1.3.5-30-master" -val miplotsVersion = "0.1-19-master" +val miplotsVersion = "0.1-22-master" val jacksonBomVersion = "2.13.3" dependencies { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java index 852099618..f6a2704fd 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java @@ -41,4 +41,13 @@ private CommonDescriptions() { public static final String JSON_REPORT = "JSON formatted report file"; + public static final String DOWNSAMPLING = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|none"; + + public static final String METADATA = "Metadata file (csv/tsv). Must have \"sample\" column."; + + public static final String DOWNSAMPLING_DROPO_UTLIERS = "Drop samples which have less abundance than the computed downsampling threshold."; + + public static final String OVERLAP_CRITERIA = "Overlap criteria. Default CDR3|AA|V|J"; + + public static final String ONLY_PRODUCTIVE = "Filter out-of-frame sequences and sequences with stop-codons"; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 0f324137e..314ca4c2d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -231,6 +231,7 @@ public static CommandLine mkCmd() { .addSubcommand("exportPlots", CommandPaExportPlots.CommandExportPlotsMain.class) .addSubcommand("exportTables", CommandPaExportTables.class) .addSubcommand("exportPreprocTables", CommandPaExportTablesPreprocSummary.class) + .addSubcommand("overlapScatterPlot", CommandOverlapScatter.class) .addSubcommand("align", CommandAlign.class) .addSubcommand("assemble", CommandAssemble.class) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java index bae0450b1..046a38507 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java @@ -4,6 +4,7 @@ import com.milaboratory.mixcr.basictypes.ClnsWriter; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.cli.CommonDescriptions; import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; @@ -36,11 +37,11 @@ public class CommandDownsample extends ACommandWithOutputMiXCR { required = true) public String chains = "ALL"; - @Option(description = "Use only productive CDR3s.", + @Option(description = CommonDescriptions.ONLY_PRODUCTIVE, names = {"--only-productive"}) public boolean onlyProductive = false; - @Option(description = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|no-downsampling", + @Option(description = CommonDescriptions.DOWNSAMPLING, names = {"--downsampling"}, required = true) public String downsampling; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java new file mode 100644 index 000000000..dc78a21b0 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java @@ -0,0 +1,128 @@ +package com.milaboratory.mixcr.cli.postanalysis; + +import com.milaboratory.miplots.ExportKt; +import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.cli.CommonDescriptions; +import com.milaboratory.mixcr.postanalysis.Dataset; +import com.milaboratory.mixcr.postanalysis.SetPreprocessor; +import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.overlap.OverlapUtil; +import com.milaboratory.mixcr.postanalysis.plots.OverlapScatter; +import com.milaboratory.mixcr.postanalysis.plots.OverlapScatterRow; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; +import com.milaboratory.mixcr.util.OutputPortWithProgress; +import com.milaboratory.util.SmartProgressReporter; +import io.repseq.core.Chains; +import io.repseq.core.GeneFeature; +import jetbrains.letsPlot.Figure; +import org.jetbrains.kotlinx.dataframe.DataFrame; +import picocli.CommandLine.Command; +import picocli.CommandLine.Option; +import picocli.CommandLine.Parameters; + +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; + +import static io.repseq.core.Chains.*; + +@Command(name = "overlapScatterPlot", + separator = " ", + description = "Plot overlap scatter-plot.") +public class CommandOverlapScatter extends ACommandWithOutputMiXCR { + @Parameters(description = "cloneset_1.{clns|clna}...", index = "0") + public String in1; + @Parameters(description = "cloneset_2.{clns|clna}...", index = "1") + public String in2; + @Parameters(description = "output.pdf", index = "2") + public String out; + + @Option(description = "Chains to export", + names = "--chains") + public List chains = null; + + @Option(description = CommonDescriptions.ONLY_PRODUCTIVE, + names = {"--only-productive"}) + public boolean onlyProductive = false; + + @Option(description = CommonDescriptions.DOWNSAMPLING, + names = {"--downsampling"}, + required = true) + public String downsampling; + + @Option(description = CommonDescriptions.OVERLAP_CRITERIA, + names = {"--criteria"}) + public String overlapCriteria = "CDR3|AA|V|J"; + + @Option(description = "Correlation method to use. Possible value: pearson, kendal, spearman", + names = {"--method"}) + public String method = "pearson"; + + @Option(description = "Do not apply log10 to clonotype frequences", + names = {"--no-log"}) + public boolean noLog; + + @Option(description = "Random seed", + names = {"--random-seed"}) + public long randomSeed = 111; + + private static String fName(String file) { + return Paths.get(file).toAbsolutePath().getFileName().toString(); + } + + private Path outputPath(NamedChains chains) { + if (chains == Chains.ALL_NAMED) + return Paths.get(out); + String fName = fName(out); + return Paths.get(out).toAbsolutePath().getParent().resolve(fName.substring(0, fName.length() - 3) + chains.name + ".pdf"); + } + + @Override + public void run0() throws Exception { + SetPreprocessorFactory preproc = DownsamplingUtil. + parseDownsampling(downsampling, false, randomSeed); + + for (NamedChains curChains : this.chains == null + ? Arrays.asList(TRAD_NAMED, TRB_NAMED, TRG_NAMED, IGH_NAMED, IGKL_NAMED) + : this.chains.stream().map(Chains::getNamedChains).collect(Collectors.toList())) { + + List> filters = new ArrayList<>(); + if (onlyProductive) { + filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); + filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); + } + filters.add(new ElementPredicate.IncludeChains(curChains.chains)); + + OverlapPreprocessorAdapter.Factory downsampling = new OverlapPreprocessorAdapter.Factory<>(preproc.filterFirst(filters)); + + Dataset> dataset = SetPreprocessor.processDatasets(downsampling.newInstance(), + OverlapUtil.overlap( + Arrays.asList(in1, in2), + OverlapUtil.parseCriteria(overlapCriteria).ordering()))[0]; + + try (OutputPortWithProgress> port = dataset.mkElementsPort()) { + SmartProgressReporter.startProgressReport("Processing " + curChains.name, port); + DataFrame df = OverlapScatter.INSTANCE.dataFrame(port); + if (df.rowsCount() == 0) { + continue; + } + Figure plot = OverlapScatter.INSTANCE.plot(df, + new OverlapScatter.PlotParameters( + fName(in1), + fName(in2), + CorrelationMethod.Companion.parse(method), + !noLog) + ); + ExportKt.writePDF(outputPath(curChains), plot); + } + } + } +} diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 4cf13a9cd..7397b1acc 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.cli.CommonDescriptions; import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; import com.milaboratory.util.StringUtil; import io.repseq.core.Chains; @@ -27,15 +28,15 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { @Parameters(description = "cloneset.{clns|clna}... result.json.gz|result.json") public List inOut; - @Option(description = "Filter out-of-frame sequences and clonotypes with stop-codons", + @Option(description = CommonDescriptions.ONLY_PRODUCTIVE, names = {"--only-productive"}) public boolean onlyProductive = false; - @Option(description = "Drop samples which have less abundance than the computed downsampling threshold.", + @Option(description = CommonDescriptions.DOWNSAMPLING_DROPO_UTLIERS, names = {"--drop-outliers"}) public boolean dropOutliers = false; - @Option(description = "Default downsampling. Possible values: umi-count-[1000|auto|min]|cumulative-top-[percent]|top-[number]|no-downsampling", + @Option(description = CommonDescriptions.DOWNSAMPLING, names = {"--default-downsampling"}, required = true) public String defaultDownsampling; @@ -44,7 +45,7 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { names = {"--chains"}) public String chains = "ALL"; - @Option(description = "Metadata file (csv/tsv). Must have \"sample\" column.", + @Option(description = CommonDescriptions.METADATA, names = {"--metadata"}) public String metadata; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java index efc6706ce..73178fa83 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java @@ -1,12 +1,13 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; +import com.milaboratory.mixcr.cli.CommonDescriptions; import com.milaboratory.mixcr.postanalysis.plots.MetadataKt; import com.milaboratory.util.StringUtil; import io.repseq.core.Chains; import io.repseq.core.Chains.NamedChains; import org.jetbrains.kotlinx.dataframe.DataFrame; -import org.jetbrains.kotlinx.dataframe.api.DataFrameIterableKt; +import org.jetbrains.kotlinx.dataframe.api.ToDataFrameKt; import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; @@ -22,7 +23,7 @@ public abstract class CommandPaExport extends ACommandWithOutputMiXCR { @Parameters(description = "Input file with postanalysis results.", index = "0", defaultValue = "pa.json.gz") public String in; - @Option(description = "Metadata file (csv/tsv). Must have 'sample' column.", + @Option(description = CommonDescriptions.METADATA, names = {"--metadata"}) public String metadata; @Option(description = "Export for specific chains only", @@ -52,7 +53,7 @@ protected DataFrame metadata() { if (metadata != null) return metadataDf = MetadataKt.readMetadata(metadata); if (getPaResult().metadata != null) - return metadataDf = DataFrameIterableKt.toDataFrame(getPaResult().metadata); + return metadataDf = ToDataFrameKt.toDataFrame(getPaResult().metadata); return null; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index e9d604d6c..e1accb4f5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -1,6 +1,7 @@ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.cli.CommonDescriptions; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.PostanalysisRunner; import com.milaboratory.mixcr.postanalysis.WeightFunctions; @@ -27,7 +28,7 @@ separator = " ", description = "Overlap analysis") public class CommandPaOverlap extends CommandPa { - @Option(description = "Overlap criteria. Default CDR|AA|V|J", + @Option(description = CommonDescriptions.OVERLAP_CRITERIA, names = {"--criteria"}) public String overlapCriteria = "CDR3|AA|V|J"; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index 827e62e3c..caf4a842a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -74,7 +74,7 @@ public static long[] downsample_counts(long[] counts, long downSampleSize, Rando } public static SetPreprocessorFactory parseDownsampling(String downsampling, boolean dropOutliers, long seed) { - if (downsampling.equalsIgnoreCase("no-downsampling")) { + if (downsampling.equalsIgnoreCase("none")) { return new NoPreprocessing.Factory<>(); } else if (downsampling.startsWith("umi-count")) { if (downsampling.endsWith("auto")) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java index 7a2a5339e..869abc1cd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java @@ -116,7 +116,6 @@ public boolean isFinished() { }; } - private static OverlapGroup filter(OverlapGroup row, Predicate criteria, boolean inPlace) { if (inPlace) { boolean empty = true; diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt index 08ccef500..8f03e3a96 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt @@ -1,9 +1,128 @@ package com.milaboratory.mixcr.postanalysis.plots -data class OverlapScatterRow( - val count1: Double, - val count2: Double, -) +import cc.redberry.pipe.CUtils +import cc.redberry.pipe.OutputPort +import com.milaboratory.core.sequence.AminoAcidSequence +import com.milaboratory.miplots.plusAssign +import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod +import com.milaboratory.miplots.stat.xcontinious.GGScatter +import com.milaboratory.miplots.stat.xcontinious.plusAssign +import com.milaboratory.miplots.stat.xcontinious.statCor +import com.milaboratory.mixcr.basictypes.Clone +import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup +import io.repseq.core.GeneFeature +import jetbrains.letsPlot.label.xlab +import jetbrains.letsPlot.label.ylab +import jetbrains.letsPlot.scale.scaleXContinuous +import jetbrains.letsPlot.scale.scaleYContinuous +import jetbrains.letsPlot.scale.xlim +import jetbrains.letsPlot.scale.ylim +import jetbrains.letsPlot.theme +import org.jetbrains.kotlinx.dataframe.DataFrame +import org.jetbrains.kotlinx.dataframe.annotations.DataSchema +import org.jetbrains.kotlinx.dataframe.api.* +import kotlin.math.log10 +import kotlin.math.max +import kotlin.math.min +import kotlin.math.sqrt + +@DataSchema +interface OverlapScatterRow { + val cdr3: AminoAcidSequence? + val count1: Double + val count2: Double + val frac1: Double + val frac2: Double + val geomMean: Double +} + +private data class OverlapScatterRowImpl( + override val cdr3: AminoAcidSequence?, + override val count1: Double, + override val count2: Double +) : OverlapScatterRow { + constructor(gr: OverlapGroup) : this( + gr.firstOrNull { it.size > 0 }?.get(0)?.getAAFeature(GeneFeature.CDR3), + gr.getBySample(0).sumOf { it.count }, + gr.getBySample(1).sumOf { it.count } + ) + + override val frac1 = Double.NaN + override val frac2 = Double.NaN + override val geomMean = Double.NaN +} + object OverlapScatter { + /** + * Imports data into DataFrame + **/ + fun dataFrame(overlapData: OutputPort>) = + run { + val rows = mutableListOf() + for (gr in CUtils.it(overlapData)) { + if (gr.size() != 2) + throw IllegalArgumentException("Expected pair of samples got " + gr.size()) + rows.add(OverlapScatterRowImpl(gr)) + } + + var df = rows.toDataFrame() + val sum1 = df.count1.sum() + val sum2 = df.count2.sum() + + df = df.update { frac1 }.with { count1 / sum1 } + df = df.update { frac2 }.with { count2 / sum2 } + df = df.update { geomMean }.with { sqrt(frac1 * frac2) } + df + } + + data class PlotParameters( + val xTitle: String, + val yTitle: String, + val method: CorrelationMethod, + val log10: Boolean + ) + + fun plot( + _df: DataFrame, + par: PlotParameters, + ) = run { + var df = _df + if (par.log10) { + df = df.update { frac1 }.with { log10(frac1) } + df = df.update { frac2 }.with { log10(frac2) } + } + val plt = GGScatter( + df.drop { count1 == 0.0 || count2 == 0.0 }, + x = OverlapScatterRow::frac1.name, + y = OverlapScatterRow::frac2.name, + alpha = 0.5 + ) { + size = OverlapScatterRow::geomMean.name + } + val min = min(df.frac1.min(), df.frac2.min()) + val max = max(df.frac1.max(), df.frac2.max()) + plt += xlim(min to max) + plt += ylim(min to max) + + plt += statCor(method = par.method) + plt += xlab(par.xTitle) + plt += ylab(par.yTitle) + + val xScale = scaleXContinuous( + limits = min to max, +// format = ".0f" + ) + + val yScale = scaleYContinuous( + limits = min to max, +// format = ".0f" + ) + + plt += theme().legendPositionNone() + plt += xScale + plt += yScale + + plt.plot + } } \ No newline at end of file From cfc72a84b368f467ac37317e6020ebc6daa59be3 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 31 May 2022 01:30:08 +0200 Subject: [PATCH 241/282] Postanalysis: fix chains parsing in metadata --- .../java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 7397b1acc..0f37acda2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -254,7 +254,7 @@ public void run0() throws Exception { for (SamplesGroup group : groupSamples()) { if (chainsColumn != null) results.add(run(new IsolationGroup( - Chains.getNamedChains(group.group.get(chainsColumn).toString()), group.group), group.samples)); + Chains.getNamedChains(group.group.get(chainsColumn).toString().toUpperCase()), group.group), group.samples)); else for (NamedChains knownChains : CHAINS) { if (c.intersects(knownChains.chains)) { From b0f88799b1ae60a2fbe5a7f8174b4db2a3dccb72 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 31 May 2022 01:35:06 +0200 Subject: [PATCH 242/282] Postanalysis: validate table names in CLI --- .../com/milaboratory/mixcr/cli/postanalysis/CommandPa.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 0f37acda2..e4d33cb9c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -97,6 +97,10 @@ public void validate() { } catch (Throwable t) { throwValidationException("Illegal downsampling string: " + defaultDownsampling); } + if (preprocOut != null && !preprocOut.endsWith(".tsv") && !preprocOut.endsWith(".csv")) + throwValidationException("--preproc-tables: table name should ends with .csv or .tsv"); + if (tablesOut != null && !tablesOut.endsWith(".tsv") && !tablesOut.endsWith(".csv")) + throwValidationException("--tables: table name should ends with .csv or .tsv"); if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) throwValidationException("Metadata should be .csv or .tsv"); if (metadata != null) { From 07af71e673f1c6f82c0c5a7dd6818a9cdce1b4da Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 1 Jun 2022 01:49:25 +0300 Subject: [PATCH 243/282] wip --- itests.sh | 2 +- .../mixcr/assembler/preclone/PreClone.java | 4 ++++ .../assembler/preclone/PreCloneWriter.java | 23 +++++++++++-------- .../mixcr/basictypes/FieldCollection.java | 9 +++++++- .../com/milaboratory/mixcr/basictypes/IO.java | 6 ++--- .../mixcr/basictypes/VDJCAlignments.java | 8 +++---- 6 files changed, 34 insertions(+), 18 deletions(-) diff --git a/itests.sh b/itests.sh index e549002b4..dfbee1ffb 100755 --- a/itests.sh +++ b/itests.sh @@ -48,7 +48,7 @@ case $os in ;; esac -tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8" "case9") +tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8" "case9" "case10") create_standard_results=false run_tests=false diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index 2a9345ebc..f6993b161 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -35,4 +35,8 @@ public PreClone(long id, TagTuple coreKey, TagCount coreTagCount, TagCount fullT this.clonalSequence = clonalSequence; this.geneScores = geneScores; } + + public long getId() { + return id; + } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java index c222bf125..918ec1ffd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java @@ -15,21 +15,20 @@ import java.nio.file.Path; import java.util.concurrent.ForkJoinPool; -import static com.milaboratory.mixcr.basictypes.FieldCollection.VDJCACloneIdComparator; -import static com.milaboratory.mixcr.basictypes.FieldCollection.VDJCACloneIdHash; +import static com.milaboratory.mixcr.basictypes.FieldCollection.*; public final class PreCloneWriter { - private final Path tempFolder; + private final Path alignmentPresortFolder; private final PrimitivOHybrid output; private volatile HashSorter alignmentCollator; - private volatile HashSorter cloneCollator; + private volatile HashSorter cloneCollator; public PreCloneWriter(Path file) throws IOException { - this.tempFolder = file.toAbsolutePath().resolveSibling(file.getFileName().toString() + ".presorted"); - if (Files.exists(tempFolder)) - FileUtils.deleteDirectory(tempFolder.toFile()); - TempFileManager.register(tempFolder.toFile()); - Files.createDirectory(this.tempFolder); + this.alignmentPresortFolder = file.toAbsolutePath().resolveSibling(file.getFileName().toString() + ".presorted"); + if (Files.exists(alignmentPresortFolder)) + FileUtils.deleteDirectory(alignmentPresortFolder.toFile()); + TempFileManager.register(alignmentPresortFolder.toFile()); + Files.createDirectory(this.alignmentPresortFolder); this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file); } @@ -54,5 +53,11 @@ public void init(VDJCAlignmentsReader alignmentReader) { 5, tempFolder, 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), memoryBudget, 1 << 18 /* 256 Kb */); + cloneCollator = new HashSorter<>( + PreClone.class, + PreCloneIdHash, PreCloneIdComparator, + 5, tempFolder, 4, 6, + stateBuilder.getOState(), stateBuilder.getIState(), + memoryBudget, 1 << 18 /* 256 Kb */); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java index d68c593a0..9f4cd5f43 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.basictypes; +import com.milaboratory.mixcr.assembler.preclone.PreClone; import com.milaboratory.util.HashFunctions; import java.util.Comparator; @@ -10,5 +11,11 @@ public final class FieldCollection { Comparator.comparing(VDJCAlignments::getCloneIndex); public static final ToIntFunction VDJCACloneIdHash = - a -> HashFunctions.JenkinWang32shift(a.getCloneIndex()); + a -> HashFunctions.Wang64to32shift(a.getCloneIndex()); + + public static final Comparator PreCloneIdComparator = + Comparator.comparing(PreClone::getId); + + public static final ToIntFunction PreCloneIdHash = + a -> HashFunctions.Wang64to32shift(a.getId()); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index 4fc6be137..0385c1d51 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -120,7 +120,7 @@ public void write(PrimitivO output, VDJCAlignments object) { } output.writeByte(object.mappingType); if (!ReadToCloneMapping.isDropped(object.mappingType)) - output.writeVarInt(object.cloneIndex); + output.writeVarLong(object.cloneIndex); } @Override @@ -138,9 +138,9 @@ public VDJCAlignments read(PrimitivI input) { hits.put(key, input.readObject(VDJCHit[].class)); } byte mappingType = input.readByte(); - int cloneIndex = -1; + long cloneIndex = -1; if (!ReadToCloneMapping.isDropped(mappingType)) - cloneIndex = input.readVarInt(); + cloneIndex = input.readVarLong(); return new VDJCAlignments(hits, tagCount, targets, history, originalReads, mappingType, cloneIndex); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index b306d7b65..7bf1e5ef9 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -50,7 +50,7 @@ public final class VDJCAlignments extends VDJCObject { final SequenceHistory[] history; final SequenceRead[] originalReads; final byte mappingType; - final int cloneIndex; + final long cloneIndex; private volatile long alignmentsIndex = -1; public VDJCAlignments(long alignmentsIndex, @@ -59,7 +59,7 @@ public VDJCAlignments(long alignmentsIndex, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads, - byte mappingType, int cloneIndex) { + byte mappingType, long cloneIndex) { super(hits, tagCount, targets); if (!ReadToCloneMapping.isCorrect(mappingType) || @@ -88,7 +88,7 @@ public VDJCAlignments(EnumMap hits, NSequenceWithQuality[] targets, SequenceHistory[] history, SequenceRead[] originalReads, - byte mappingType, int cloneIndex) { + byte mappingType, long cloneIndex) { this(-1, hits, tagCount, targets, history, originalReads, mappingType, cloneIndex); } @@ -145,7 +145,7 @@ public ReadToCloneMapping.MappingType getMappingType() { return ReadToCloneMapping.getMappingType(mappingType); } - public int getCloneIndex() { + public long getCloneIndex() { return cloneIndex; } From 67935b24502e0ca50b116b8a59b052acca29d5b9 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 1 Jun 2022 02:35:18 +0300 Subject: [PATCH 244/282] chore: migration to new temp file management abstraction, milib upgrade --- build.gradle.kts | 2 +- .../mixcr/basictypes/ClnAWriter.java | 32 ++++-------- .../mixcr/basictypes/CloneSetOverlap.java | 2 +- .../mixcr/cli/CommandAssemble.java | 52 +++++++++++-------- .../mixcr/cli/CommandGroupCells.java | 4 +- .../milaboratory/mixcr/cli/CommandSlice.java | 4 +- .../mixcr/cli/CommandSortClones.java | 8 ++- .../com/milaboratory/mixcr/util/RunMiXCR.java | 9 ++-- .../mixcr/basictypes/ClnAReaderTest.java | 5 +- 9 files changed, 62 insertions(+), 56 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 6831aabcc..1c9773780 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -78,7 +78,7 @@ repositories { } } -val milibVersion = "1.15.0-44-master" +val milibVersion = "1.15.0-49-master" val repseqioVersion = "1.3.5-30-master" val miplotsVersion = "0.1-22-master" val jacksonBomVersion = "2.13.3" diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index de6976be8..42137ddc2 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -45,20 +45,17 @@ import com.milaboratory.primitivio.blocks.PrimitivOHybrid; import com.milaboratory.util.CanReportProgressAndStage; import com.milaboratory.util.HashFunctions; -import com.milaboratory.util.TempFileManager; +import com.milaboratory.util.TempFileDest; import com.milaboratory.util.io.HasPosition; import com.milaboratory.util.sorting.HashSorter; import gnu.trove.list.array.TIntArrayList; import gnu.trove.list.array.TLongArrayList; import gnu.trove.set.hash.TIntHashSet; import io.repseq.core.VDJCGene; -import org.apache.commons.io.FileUtils; import java.io.File; import java.io.IOException; import java.nio.charset.StandardCharsets; -import java.nio.file.Files; -import java.nio.file.Path; import java.util.Comparator; import java.util.List; import java.util.Objects; @@ -86,7 +83,7 @@ public final class ClnAWriter implements PipelineConfigurationWriter, /** * Will be used for alignments pre-sorting */ - private final Path tempFolder; + private final TempFileDest tempDest; private final boolean highCompression; @@ -107,29 +104,22 @@ public final class ClnAWriter implements PipelineConfigurationWriter, private volatile long numberOfAlignments = -1, numberOfAlignmentsWritten = 0; private volatile boolean finished = false; - public ClnAWriter(PipelineConfiguration configuration, String fileName) throws IOException { - this(configuration, fileName, false); + public ClnAWriter(PipelineConfiguration configuration, String fileName, TempFileDest tempDest) throws IOException { + this(configuration, fileName, tempDest, false); } - public ClnAWriter(PipelineConfiguration configuration, String fileName, boolean highCompression) throws IOException { - this(configuration, new File(fileName), highCompression); + public ClnAWriter(PipelineConfiguration configuration, String fileName, TempFileDest tempDest, boolean highCompression) throws IOException { + this(configuration, new File(fileName), tempDest, highCompression); } - public ClnAWriter(PipelineConfiguration configuration, File file) throws IOException { - this(configuration, file, false); + public ClnAWriter(PipelineConfiguration configuration, File file, TempFileDest tempDest) throws IOException { + this(configuration, file, tempDest, false); } - public ClnAWriter(PipelineConfiguration configuration, File file, boolean highCompression) throws IOException { + public ClnAWriter(PipelineConfiguration configuration, File file, TempFileDest tempDest, boolean highCompression) throws IOException { this.configuration = configuration; this.highCompression = highCompression; - - File tempFolder = new File(file.getAbsolutePath() + ".presorted"); - if (tempFolder.exists()) - FileUtils.deleteDirectory(tempFolder); - TempFileManager.register(tempFolder); - this.tempFolder = tempFolder.toPath(); - Files.createDirectory(this.tempFolder); - + this.tempDest = tempDest; this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file.toPath()); try (PrimitivO o = this.output.beginPrimitivO()) { o.write(MAGIC.getBytes(StandardCharsets.US_ASCII)); @@ -245,7 +235,7 @@ public synchronized void collateAlignments(OutputPort alignments collator = new HashSorter<>( VDJCAlignments.class, new CloneIdHash(), CloneIdComparator, - 5, tempFolder, 4, 6, + 5, tempDest, 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), memoryBudget, 1 << 18 /* 256 Kb */); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java index 154506600..bcdcaf469 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java @@ -83,7 +83,7 @@ public static OutputPortWithProgress>> overlap( .collect(Collectors.toList()), by, 5, - TempFileManager.getTempDir().toPath(), + TempFileManager.systemTempFolderDestination("mixcr.overlap."), 4, 6, memoryBudget, 1 << 18 /* 256 Kb */, stateBuilder); merger.loadData(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index aa5955536..01ec3809d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -56,6 +56,7 @@ import java.util.Objects; import static com.milaboratory.mixcr.cli.CommandAssemble.ASSEMBLE_COMMAND_NAME; +import static com.milaboratory.util.TempFileManager.smartTempDestination; @Command(name = ASSEMBLE_COMMAND_NAME, sortOptions = true, @@ -78,6 +79,10 @@ public void setThreads(int threads) { this.threads = threads; } + @Option(description = "Use system temp folder for temporary files, the output folder will be used if this option is omitted.", + names = {"--use-system-temp"}) + public boolean useSystemTemp = false; + @Option(description = "Use higher compression for output file.", names = {"--high-compression"}) public boolean highCompression = false; @@ -259,29 +264,30 @@ public void run1() throws Exception { if (clna) { -// -// try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(alignmentsProvider.create(), -// assembler.getAssembledReadsPort())) { -// -// VDJCAlignments al; -// while ((al = merged.take()) != null) { -// if (al.getCloneIndex() != -1) -// continue; -// -// TagCounter tg = al.getTagCounter(); -// assert tg.size() == 1; -// TagTuple tags = tg.iterator().key(); -// if (al.getBestHit(GeneType.Variable) != null) { -// TagSignature sig = new TagSignature(tags, al.getBestHit(GeneType.Variable).getGene().getId()); -// Integer cloneId = tagsToClones.get(sig); -// if (cloneId != null) { -// -// } -// } -// } -// } - - try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, highCompression)) { + // + // try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(alignmentsProvider.create(), + // assembler.getAssembledReadsPort())) { + // + // VDJCAlignments al; + // while ((al = merged.take()) != null) { + // if (al.getCloneIndex() != -1) + // continue; + // + // TagCounter tg = al.getTagCounter(); + // assert tg.size() == 1; + // TagTuple tags = tg.iterator().key(); + // if (al.getBestHit(GeneType.Variable) != null) { + // TagSignature sig = new TagSignature(tags, al.getBestHit(GeneType.Variable).getGene().getId()); + // Integer cloneId = tagsToClones.get(sig); + // if (cloneId != null) { + // + // } + // } + // } + // } + + try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, + smartTempDestination(out, "", useSystemTemp), highCompression)) { // writer will supply current stage and completion percent to the progress reporter SmartProgressReporter.startProgressReport(writer); // Writing clone block diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 8b176eab8..62e72517e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -29,6 +29,7 @@ import java.util.function.Consumer; import static com.milaboratory.mixcr.basictypes.IOUtil.*; +import static com.milaboratory.util.TempFileManager.smartTempDestination; /** * @@ -151,7 +152,8 @@ private void runClns() throws Exception { private void runClna() throws Exception { try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), 3); - ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { + ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out, + smartTempDestination(out, "", false))) { CloneSet cloneSet = reader.readCloneSet(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java index f95216ad9..0782e194e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java @@ -53,6 +53,7 @@ import static com.milaboratory.mixcr.basictypes.IOUtil.*; import static com.milaboratory.mixcr.cli.CommandSlice.SLICE_COMMAND_NAME; +import static com.milaboratory.util.TempFileManager.smartTempDestination; @Command(name = SLICE_COMMAND_NAME, sortOptions = true, @@ -106,7 +107,8 @@ void sliceVDJCA() throws Exception { void sliceClnA() throws Exception { try (ClnAReader reader = new ClnAReader(in, VDJCLibraryRegistry.getDefault(), Concurrency.noMoreThan(4)); - ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { + ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out, + smartTempDestination(out, "", false))) { // Getting full clone set CloneSet cloneSet = reader.readCloneSet(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java index 773b00c99..2894bde1e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java @@ -12,13 +12,13 @@ import picocli.CommandLine; import java.io.File; -import java.nio.file.Path; import java.nio.file.Paths; import java.util.Objects; import static com.milaboratory.mixcr.basictypes.IOUtil.MAGIC_CLNA; import static com.milaboratory.mixcr.basictypes.IOUtil.MAGIC_CLNS; import static com.milaboratory.mixcr.cli.CommandSortClones.SORT_CLONES_COMMAND_NAME; +import static com.milaboratory.util.TempFileManager.smartTempDestination; @CommandLine.Command(name = SORT_CLONES_COMMAND_NAME, @@ -28,6 +28,10 @@ public class CommandSortClones extends ACommandWithSmartOverwriteWithSingleInputMiXCR { static final String SORT_CLONES_COMMAND_NAME = "sortClones"; + @CommandLine.Option(description = "Use system temp folder for temporary files, the output folder will be used if this option is omitted.", + names = {"--use-system-temp"}) + public boolean useSystemTemp = false; + @Override public ActionConfiguration getConfiguration() { return new SortConfiguration(); @@ -59,7 +63,7 @@ public void run1() throws Exception { case MAGIC_CLNA: try (ClnAReader reader = new ClnAReader(Paths.get(in), VDJCLibraryRegistry.getDefault(), Runtime.getRuntime().availableProcessors()); - ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out)) { + ClnAWriter writer = new ClnAWriter(getFullPipelineConfiguration(), out, smartTempDestination(out, "", useSystemTemp))) { SmartProgressReporter.startProgressReport(writer); GeneFeature[] assemblingFeatures = reader.getAssemblerParameters().getAssemblingFeatures(); diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index bd87b94a5..4fbadd02b 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -71,6 +71,7 @@ import static cc.redberry.pipe.CUtils.chunked; import static cc.redberry.pipe.CUtils.unchunked; +import static com.milaboratory.util.TempFileManager.*; /** * @author Dmitry Bolotin @@ -120,8 +121,8 @@ public long getTotalNumberOfReads() { public static FullSeqAssembleResult assembleContigs(final AssembleResult assemble) { AlignResult align = assemble.alignResult; - File clnaFile = TempFileManager.getTempFile(); - try (ClnAWriter writer = new ClnAWriter(null, clnaFile)) { + File clnaFile = getTempFile(); + try (ClnAWriter writer = new ClnAWriter(null, clnaFile, systemTempFolderDestination("runmixcr.assembleContigs"))) { // writer will supply current stage and completion percent to the progress reporter SmartProgressReporter.startProgressReport(writer); // Writing clone block @@ -139,7 +140,7 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl } int totalClonesCount = 0; - File tmpFile = TempFileManager.getTempFile(); + File tmpFile = getTempFile(); try (ClnAReader reader = new ClnAReader(clnaFile.toPath(), VDJCLibraryRegistry.getDefault(), 2); // TODO concurrency ??? PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(tmpFile)));) { @@ -284,7 +285,7 @@ public AlignResult(RunMiXCRAnalysis parameters, long totalNumberOfReads, Aligner public VDJCAlignmentsReader resultReader() throws IOException { if (alignmentsFile == null) { - alignmentsFile = TempFileManager.getTempFile(); + alignmentsFile = getTempFile(); try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(alignmentsFile)) { writer.header(aligner, null); for (VDJCAlignments alignment : alignments) diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java index 45958b333..304243802 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java @@ -51,6 +51,7 @@ import java.util.function.Function; import java.util.stream.Collectors; +import static com.milaboratory.util.TempFileManager.smartTempDestination; import static org.junit.Assert.assertEquals; public class ClnAReaderTest { @@ -87,7 +88,7 @@ public void testGeneric(Function, List> modifyClones, AlignmentsMappingMerger merged = new AlignmentsMappingMerger(align.resultReader(), assemble.cloneAssembler.getAssembledReadsPort()); File file = TempFileManager.getTempFile(); - ClnAWriter writer = new ClnAWriter(null, file); + ClnAWriter writer = new ClnAWriter(null, file, smartTempDestination(file, "", false)); List newClones = assemble.cloneSet.getClones().stream() .map(Clone::resetParentCloneSet) @@ -135,7 +136,7 @@ public void test2Empty() throws Exception { RunMiXCR.AlignResult align = RunMiXCR.align(params); File file = TempFileManager.getTempFile(); - ClnAWriter writer = new ClnAWriter(null, file); + ClnAWriter writer = new ClnAWriter(null, file, smartTempDestination(file, "", false)); writer.writeClones(new CloneSet(Collections.EMPTY_LIST, align.usedGenes, align.parameters.alignerParameters, CloneAssemblerParametersPresets.getByName("default"), From b650633350982f54272faa7c10f3bdbb1d0600f1 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 1 Jun 2022 03:53:00 +0300 Subject: [PATCH 245/282] WIP --- .../mixcr/assembler/preclone/PreClone.java | 6 +- .../assembler/preclone/PreCloneWriter.java | 99 ++++++++++++++++--- .../mixcr/basictypes/VDJCAlignments.java | 4 +- .../mixcr/cli/CommandAssemble.java | 2 +- .../mixcr/cli/CommandAssemblePreClones.java | 75 ++++++++------ .../mixcr/cli/CommandCorrectAndSortTags.java | 38 +------ .../milaboratory/mixcr/cli/CommandSlice.java | 2 +- .../mixcr/export/FieldExtractors.java | 2 +- 8 files changed, 144 insertions(+), 84 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index f6993b161..b6d0bf551 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -13,7 +13,7 @@ @Serializable(by = IO.PreCloneSerializer.class) public final class PreClone { /** Pre-clonotype id */ - public long id; + public final long id; /** Core key of the alignments group */ public final TagTuple coreKey; /** Tag counter aggregating information about alignments with clonal sequence */ @@ -39,4 +39,8 @@ public PreClone(long id, TagTuple coreKey, TagCount coreTagCount, TagCount fullT public long getId() { return id; } + + public PreClone withId(long id) { + return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores); + } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java index 918ec1ffd..ac13a558d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java @@ -1,35 +1,45 @@ package com.milaboratory.mixcr.assembler.preclone; +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.InputPort; +import cc.redberry.pipe.OutputPortCloseable; +import cc.redberry.pipe.blocks.Buffer; import com.milaboratory.mixcr.basictypes.IOUtil; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.primitivio.PrimitivIOStateBuilder; import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.primitivio.blocks.PrimitivOBlocks; import com.milaboratory.primitivio.blocks.PrimitivOHybrid; -import com.milaboratory.util.TempFileManager; +import com.milaboratory.util.TempFileDest; import com.milaboratory.util.sorting.HashSorter; -import org.apache.commons.io.FileUtils; import java.io.IOException; -import java.nio.file.Files; import java.nio.file.Path; import java.util.concurrent.ForkJoinPool; import static com.milaboratory.mixcr.basictypes.FieldCollection.*; -public final class PreCloneWriter { - private final Path alignmentPresortFolder; +public final class PreCloneWriter implements AutoCloseable { private final PrimitivOHybrid output; + private final TempFileDest tempDest; + private final Buffer alignmentBuffer; + private final InputPort alignmentInput; + private final Buffer cloneBuffer; + private final InputPort cloneInput; + private volatile Thread alignmentSortingThread, cloneSortingThread; private volatile HashSorter alignmentCollator; + private volatile OutputPortCloseable sortedAlignments; private volatile HashSorter cloneCollator; + private volatile OutputPortCloseable sortedClones; - public PreCloneWriter(Path file) throws IOException { - this.alignmentPresortFolder = file.toAbsolutePath().resolveSibling(file.getFileName().toString() + ".presorted"); - if (Files.exists(alignmentPresortFolder)) - FileUtils.deleteDirectory(alignmentPresortFolder.toFile()); - TempFileManager.register(alignmentPresortFolder.toFile()); - Files.createDirectory(this.alignmentPresortFolder); + public PreCloneWriter(Path file, TempFileDest tempDest) throws IOException { this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file); + this.tempDest = tempDest; + this.alignmentBuffer = new Buffer<>(1 << 14); + this.alignmentInput = alignmentBuffer.createInputPort(); + this.cloneBuffer = new Buffer<>(1 << 10); + this.cloneInput = cloneBuffer.createInputPort(); } public void init(VDJCAlignmentsReader alignmentReader) { @@ -50,14 +60,77 @@ public void init(VDJCAlignmentsReader alignmentReader) { alignmentCollator = new HashSorter<>( VDJCAlignments.class, VDJCACloneIdHash, VDJCACloneIdComparator, - 5, tempFolder, 4, 6, + 5, tempDest.addSuffix("al.pre."), 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), memoryBudget, 1 << 18 /* 256 Kb */); + alignmentSortingThread = new Thread(() -> sortedAlignments = alignmentCollator.port(alignmentBuffer), + "alignment-sorting"); + alignmentSortingThread.start(); cloneCollator = new HashSorter<>( PreClone.class, PreCloneIdHash, PreCloneIdComparator, - 5, tempFolder, 4, 6, + 5, tempDest.addSuffix("cl.pre."), 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), memoryBudget, 1 << 18 /* 256 Kb */); + cloneSortingThread = new Thread(() -> sortedClones = cloneCollator.port(cloneBuffer), + "clone-sorting"); + } + + public void putClone(PreClone clone) { + cloneInput.put(clone); + } + + public void putAlignment(VDJCAlignments alignment) { + alignmentInput.put(alignment); + } + + public void finishWrite() { + alignmentInput.put(null); + cloneInput.put(null); + try { + alignmentSortingThread.join(); + cloneSortingThread.join(); + } catch (InterruptedException e) { + throw new RuntimeException(e); + } + + long clonesStartPosition = output.getPosition(); + long cloneChecksum = 17; + try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { + // final clone id generator + long newCloneIdx = 0; + for (PreClone preClone : CUtils.it(sortedClones)) { + cloneChecksum = cloneChecksum * 71 + preClone.id; + writer.write(preClone.withId(newCloneIdx++)); + } + } + + long alignmentsStartPosition = output.getPosition(); + long alignmentsChecksum = 17; + try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { + // final clone id generator + long newCloneIdx = -1; + long previousCloneIdx = -1; + for (VDJCAlignments al : CUtils.it(sortedAlignments)) { + if (al.getCloneIndex() != previousCloneIdx) { + newCloneIdx++; + alignmentsChecksum = alignmentsChecksum * 71 + al.getCloneIndex(); + } + writer.write(al.withCloneIndex(newCloneIdx)); + } + } + + if (alignmentsChecksum != cloneChecksum) + throw new IllegalStateException("Inconsistent sequences of clones and alignments."); + + try (PrimitivO o = output.beginPrimitivO()) { + o.writeLong(clonesStartPosition); + o.writeLong(alignmentsStartPosition); + } + } + + @Override + public void close() throws Exception { + output.close(); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 7bf1e5ef9..1a6746d3a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -167,12 +167,12 @@ public VDJCAlignments setMapping(ReadToCloneMapping mapping) { mapping.getMappingTypeByte(), mapping.getCloneIndex()); } - public VDJCAlignments updateCloneIndex(int newCloneIndex) { + public VDJCAlignments withCloneIndex(long newCloneIndex) { return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads, mappingType, newCloneIndex); } - public VDJCAlignments updateCloneIndexAndMappingType(int newCloneIndex, byte newMappingType) { + public VDJCAlignments withCloneIndexAndMappingType(int newCloneIndex, byte newMappingType) { return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads, newMappingType, newCloneIndex); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index ac36a240e..e9e6acb5f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -379,7 +379,7 @@ public void run1() throws Exception { } private static VDJCAlignments setMappingCloneIndex(VDJCAlignments al, int cloneIndex) { - return al.updateCloneIndexAndMappingType(cloneIndex, ReadToCloneMapping.ADDITIONAL_MAPPING_MASK); + return al.withCloneIndexAndMappingType(cloneIndex, ReadToCloneMapping.ADDITIONAL_MAPPING_MASK); } private static final class TagSignature { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java index 6c42dccd6..10cf9e356 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java @@ -7,26 +7,20 @@ import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; import com.milaboratory.mitool.helpers.GroupOP; import com.milaboratory.mitool.helpers.PipeKt; +import com.milaboratory.mixcr.assembler.preclone.*; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; -import com.milaboratory.mixcr.assembler.preclone.PreClone; -import com.milaboratory.mixcr.assembler.preclone.PreCloneAssembler; -import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerParameters; import com.milaboratory.util.ReportHelper; +import com.milaboratory.util.TempFileManager; import gnu.trove.iterator.TIntIterator; -import gnu.trove.list.array.TLongArrayList; -import gnu.trove.map.TIntLongMap; import gnu.trove.map.hash.TIntLongHashMap; import io.repseq.core.GeneFeature; -import io.repseq.core.GeneType; import kotlin.jvm.functions.Function1; +import picocli.CommandLine; -import java.io.BufferedOutputStream; -import java.io.PrintStream; -import java.nio.file.Files; import java.nio.file.Paths; import java.util.List; @@ -40,6 +34,11 @@ public class CommandAssemblePreClones extends ACommandMiXCR { @Parameters(arity = "2", description = "input_file output_file") public List files; + @CommandLine.Option(description = "Use system temp folder for temporary files, the output folder will be used if this option is omitted.", + names = {"--use-system-temp"}) + public boolean useSystemTemp = false; + + private static final AAssemblerParameters aAssemblerParams = AAssemblerParameters.builder() .bandWidth(4) .scoring(LinearGapAlignmentScoring.getNucleotideBLASTScoring()) @@ -65,9 +64,14 @@ public void run0() throws Exception { VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(files.get(0)); // For export VDJCAlignmentsReader reader3 = new VDJCAlignmentsReader(files.get(0)); - PrintStream out = new PrintStream(new BufferedOutputStream( - Files.newOutputStream(Paths.get(files.get(1))), 1 << 20)) + PreCloneWriter writer = new PreCloneWriter(Paths.get(files.get(1)), + TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp)) + // // + // PrintStream out = new PrintStream(new BufferedOutputStream( + // Files.newOutputStream(Paths.get(files.get(1))), 1 << 20)) ) { + writer.init(reader1); + TagsInfo tagsInfo = reader1.getTagsInfo(); int depth = tagsInfo.getDepthFor(TagType.CellTag); // int depth = tagsInfo.getDepthFor(TagType.MoleculeTag); @@ -87,33 +91,40 @@ public void run0() throws Exception { OutputPort> alGroups = PipeKt.group(CUtils.wrap(reader3, VDJCAlignments::ensureKeyTags), gFunction); - List clones; + // TODO array? + TIntLongHashMap alToCloneMapping = new TIntLongHashMap(); + List clones; while ((clones = assembler.getForNextGroup()) != null) { GroupOP grp = alGroups.take(); - assert clones.isEmpty() || clones.get(0).coreKey.equals(grp.getKey()); - TIntLongMap localToMitReadIndex = new TIntLongHashMap(); - int localId = 0; - for (VDJCAlignments al : CUtils.it(grp)) - localToMitReadIndex.put(localId++, al.getMinReadId()); - - for (PreClone clone : clones) { + assert clones.isEmpty() || clones.get(0).preClone.coreKey.equals(grp.getKey()); - TLongArrayList rIds = new TLongArrayList(); - TIntIterator it = clone.alignments.iterator(); + alToCloneMapping.clear(); + for (PreCloneWithAlignments cloneWA : clones) { + PreClone clone = cloneWA.preClone; + TIntIterator it = cloneWA.alignments.iterator(); while (it.hasNext()) - rIds.add(localToMitReadIndex.get(it.next())); - - out.println( - clone.clonalSequence[0].getSequence().toString() + "\t" + - clone.alignments.size() + "\t" + - clone.geneScores.get(GeneType.Variable) + "\t" + - clone.geneScores.get(GeneType.Joining) + "\t" + - clone.geneScores.get(GeneType.Constant) + "\t" + - clone.coreTagCount + "\t" + - clone.fullTagCount + "\t" + - rIds); + alToCloneMapping.put(it.next(), clone.id); + + writer.putClone(clone); + // + // out.println( + // clone.clonalSequence[0].getSequence().toString() + "\t" + + // cloneWA.alignments.size() + "\t" + + // clone.geneScores.get(GeneType.Variable) + "\t" + + // clone.geneScores.get(GeneType.Joining) + "\t" + + // clone.geneScores.get(GeneType.Constant) + "\t" + + // clone.coreTagCount + "\t" + + // clone.fullTagCount + "\t" + + // rIds); } + + int localId = 0; + for (VDJCAlignments al : CUtils.it(grp)) + writer.putAlignment(al.withCloneIndex(alToCloneMapping.get(localId++))); } + + writer.finishWrite(); + assembler.getReport().writeReport(ReportHelper.STDOUT); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index aa0c935eb..cc6cdaa75 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -22,17 +22,12 @@ import com.milaboratory.primitivio.PrimitivIOStateBuilder; import com.milaboratory.util.ReportHelper; import com.milaboratory.util.SmartProgressReporter; +import com.milaboratory.util.TempFileDest; import com.milaboratory.util.TempFileManager; import com.milaboratory.util.sorting.HashSorter; import gnu.trove.list.array.TIntArrayList; -import org.apache.commons.io.FileUtils; import picocli.CommandLine; -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; import java.util.ArrayList; import java.util.Comparator; import java.util.List; @@ -93,31 +88,6 @@ public class CommandCorrectAndSortTags extends ACommandWithSmartOverwriteWithSin names = {"-r", "--report"}) public String reportFile; - private Path tempFolder = null; - - private Path tempFolder() { - if (tempFolder == null) { - try { - File tempFolderF; - if (useSystemTemp) - tempFolderF = Paths.get(System.getProperty("java.io.tmpdir")) - .resolve(Paths.get(out).getFileName().getFileName() + "." + - Long.toString(System.nanoTime(), 36)) - .toFile(); - else - tempFolderF = new File(out + ".tmp"); - if (tempFolderF.exists()) - FileUtils.deleteDirectory(tempFolderF); - Files.createDirectory(tempFolderF.toPath()); - TempFileManager.register(tempFolderF); - tempFolder = tempFolderF.toPath(); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - return tempFolder; - } - TagCorrectorParameters getParameters() { return new TagCorrectorParameters( power, backgroundSubstitutionRate, backgroundIndelRate, @@ -132,6 +102,8 @@ public ActionConfiguration getConfiguration() { @Override public void run1() throws Exception { + TempFileDest tempDest = TempFileManager.smartTempDestination(out, "", useSystemTemp); + final CorrectionNode correctionResult; final CorrectionReport report; final int[] targetTagIndices; @@ -154,7 +126,7 @@ public void run1() throws Exception { if (!noCorrect) { TagCorrector corrector = new TagCorrector(getParameters(), - tempFolder(), "", + tempDest.addSuffix("tags"), memoryBudget, 4, 4); SmartProgressReporter.startProgressReport(corrector); @@ -214,7 +186,7 @@ public void run1() throws Exception { return new HashSorter<>( VDJCAlignments.class, sortingStep.getHashFunction(), sortingStep.getComparator(), - 4, tempFolder().resolve("hashsorter." + tagIdx), + 4, tempDest.addSuffix("hashsorter." + tagIdx), 4, 4, stateBuilder.getOState(), stateBuilder.getIState(), memoryBudget, 10000 diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java index 3ab908c17..b0fba966d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java @@ -134,7 +134,7 @@ void sliceClnA() throws Exception { VDJCAlignments al = als.take(); if (al == null) return null; - return al.updateCloneIndex(ii); + return al.withCloneIndex(ii); }); i++; } diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 0b99ec10d..21792bd9b 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -606,7 +606,7 @@ protected String extract(VDJCAlignments object) { descriptorsList.add(new PL_A("-cloneIdWithMappingType", "To which clone alignment was attached with additional info on mapping type (make sure using .clna file as input for exportAlignments)", "Clone mapping", "cloneMapping") { @Override protected String extract(VDJCAlignments object) { - int ci = object.getCloneIndex(); + long ci = object.getCloneIndex(); ReadToCloneMapping.MappingType mt = object.getMappingType(); return "" + ci + ":" + mt; From bd226c8838b998419cad312f8ec1d1f939cd28e2 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 2 Jun 2022 00:48:10 +0300 Subject: [PATCH 246/282] feat: working pre-clone writer --- build.gradle.kts | 2 +- .../assembler/preclone/PreCloneAssembler.java | 95 +++++++++---------- .../preclone/PreCloneAssemblerResult.java | 21 ++++ .../assembler/preclone/PreCloneWriter.java | 78 ++++++++++----- .../mixcr/basictypes/VDJCAlignments.java | 2 +- .../milaboratory/mixcr/basictypes/tag/IO.java | 23 +++++ .../mixcr/basictypes/tag/TagTuple.java | 2 + .../mixcr/cli/CommandAssemblePreClones.java | 35 ++++--- 8 files changed, 170 insertions(+), 88 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java diff --git a/build.gradle.kts b/build.gradle.kts index 0ea0e167f..5418c5903 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -81,7 +81,7 @@ repositories { } } -val milibVersion = "1.15.0-49-master" +val milibVersion = "1.15.0-50-master" val repseqioVersion = "1.3.5-31-master" val mitoolVersion = "0.9.1-13-main" val miplotsVersion = "0.1-22-master" diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index ed849cef0..4b02b9456 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -8,24 +8,23 @@ import com.milaboratory.mitool.consensus.GConsensusAssembler; import com.milaboratory.mitool.helpers.GroupOP; import com.milaboratory.mitool.helpers.PipeKt; -import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.assembler.VDJCGeneAccumulator; +import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import gnu.trove.map.hash.TObjectIntHashMap; -import gnu.trove.set.hash.TIntHashSet; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; import kotlin.jvm.functions.Function1; import java.util.*; -import java.util.concurrent.atomic.AtomicInteger; +import java.util.concurrent.atomic.AtomicLong; public final class PreCloneAssembler { private final PreCloneAssemblerReport report = new PreCloneAssemblerReport(); - private final AtomicInteger idGenerator = new AtomicInteger(); + private final AtomicLong idGenerator = new AtomicLong(); private final PreCloneAssemblerParameters parameters; private final OutputPort> alignmentsReader1, alignmentsReader2; @@ -42,7 +41,7 @@ public PreCloneAssemblerReport getReport() { return report; } - public List getForNextGroup() { + public PreCloneAssemblerResult getForNextGroup() { GroupOP grp1 = alignmentsReader1.take(); if (grp1 == null) @@ -68,8 +67,8 @@ public List getForNextGroup() { outer: for (VDJCAlignments al : CUtils.it(grp1)) { localIdx++; - for (int i = 0; i < parameters.assemblingFeatures.length; i++) - if ((row[i] = al.getFeature(parameters.assemblingFeatures[i])) == null) + for (int sr = 0; sr < parameters.assemblingFeatures.length; sr++) + if ((row[sr] = al.getFeature(parameters.assemblingFeatures[sr])) == null) continue outer; assemblerInput.add(row); @@ -94,12 +93,12 @@ public List getForNextGroup() { if (assemblerInput.isEmpty()) { CUtils.drainWithoutClose(alignmentsReader2.take(), DummyInputPort.INSTANCE); - return Collections.emptyList(); + return new PreCloneAssemblerResult(Collections.emptyList(), null); } // Step #2 - // Building consensuses from the records collected on the step #1, and creating indices for - // clonotype assignment of alignments left after the previous step + // Building consensuses from the records collected on the step #1, and creating indices for empirical + // clonotype assignment for alignments left after the previous step GConsensusAssembler gAssembler = new GConsensusAssembler(parameters.assemblerParameters, assemblerInput); List consensuses = gAssembler.calculateConsensuses(); @@ -111,46 +110,40 @@ public List getForNextGroup() { // Accumulates V, J and C gene information for each consensus // noinspection unchecked Map>[] geneInfos = new Map[numberOfClones]; - // Saves local record indices, assigned to each of the consensuses - TIntHashSet[] contents = new TIntHashSet[numberOfClones]; - // I.e. UMIs for CELL-barcode-only assembly use-case - // Set[] tagSuffixess = new Set[numberOfClones]; - // Union of all contents - // BitArray allAssignedToClonotypes = new BitArray((int) grp1.getCount()); + // Saves local record indices, assigned to each of the consensuses + // TIntHashSet[] contents = new TIntHashSet[numberOfClones]; + // long[] alignmentToClone = new long[(int) grp1.getCount()]; + // Arrays.fill(alignmentToClone, -1); - // Tag suffixes unambiguously linked to a clonotype (store cloneId+1; -1 for ambiguous cases; 0 - not found) + // Tag suffixes unambiguously linked to a clonotype + // (store cloneIdx+1; -1 for ambiguous cases; 0 - not found) TObjectIntHashMap tagSuffixToCloneId = new TObjectIntHashMap<>(); - // V, J and C genes unambiguously linked to a clonotype (store cloneId+1; -1 for ambiguous cases; 0 - not found) + // V, J and C genes unambiguously linked to a clonotype + // (store cloneIdx+1; -1 for ambiguous cases; 0 - not found) TObjectIntHashMap vjcGenesToCloneId = new TObjectIntHashMap<>(); // Special map to simplify collection of additional information from already assigned alignment // -1 = not assigned to any consensus / clonotype // 0 = no assembling feature (target for empirical assignment) - // >0 = assigned to a specific consensus / clonotype (store cloneId+1) - int[] alignmentIndexToClonotypeIndex = new int[(int) grp1.getCount()]; + // >0 = assigned to a specific consensus / clonotype (store cloneIdx+1) + int[] alignmentIdxToCloneIdxP1 = new int[(int) grp1.getCount()]; for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { ConsensusResult c = consensuses.get(cIdx); VDJCGeneAccumulator acc = new VDJCGeneAccumulator(); - TIntHashSet content = new TIntHashSet(); Set tagSuffixes = new HashSet<>(); int rIdx = -1; while ((rIdx = c.recordsUsed.nextBit(rIdx + 1)) != -1) { AlignmentInfo ai = alignmentInfos.get(rIdx); acc.accumulate(ai.genesAndScores); - content.add(ai.localIdx); tagSuffixes.addAll(ai.tagSuffixes); - alignmentIndexToClonotypeIndex[ai.localIdx] = cIdx + 1; + alignmentIdxToCloneIdxP1[ai.localIdx] = cIdx + 1; report.coreAlignments.incrementAndGet(); } - // allAssignedToClonotypes.or(content); - geneInfos[cIdx] = acc.aggregateInformation(parameters.relativeMinScores); - contents[cIdx] = content; - // tagSuffixess[cIdx] = tagSuffixes; for (TagTuple ts : tagSuffixes) if (tagSuffixToCloneId.get(ts) > 0) @@ -171,12 +164,14 @@ public List getForNextGroup() { } // Information from the alignments with assembling features, but not assigned to any contigs interpreted as - // ambiguous + // indeed ambiguous for (AlignmentInfo ai : alignmentInfos) { - if (alignmentIndexToClonotypeIndex[ai.localIdx] > 0) + if (alignmentIdxToCloneIdxP1[ai.localIdx] > 0) + // This alignment was assigned to a clone continue; - alignmentIndexToClonotypeIndex[ai.localIdx] = -1; + // Will not participate in empirical alignment assignment + alignmentIdxToCloneIdxP1[ai.localIdx] = -1; report.discardedCoreAlignments.incrementAndGet(); @@ -209,7 +204,7 @@ public List getForNextGroup() { for (VDJCAlignments al : CUtils.it(grp2)) { localIdx++; - int cIdxP1 = alignmentIndexToClonotypeIndex[localIdx]; + int cIdxP1 = alignmentIdxToCloneIdxP1[localIdx]; // Running empirical assignment for the alignments not yet assigned if (cIdxP1 == 0) { @@ -238,10 +233,10 @@ else if (cIdxP1 != cp1) cIdxP1 = -1; } - if (cIdxP1 > 0) { + if (cIdxP1 > 0) // Adding alignment to the clone - contents[cIdxP1 - 1].add(localIdx); - } else if (cIdxP1 == -1) + alignmentIdxToCloneIdxP1[localIdx] = cIdxP1; + else if (cIdxP1 == -1) report.empiricalAssignmentConflicts.incrementAndGet(); } else if (cIdxP1 > 0) // Using second iteration over the alignments to assemble TagCounters from the alignments assigned to @@ -254,25 +249,29 @@ else if (cIdxP1 != cp1) report.unassignedAlignments.incrementAndGet(); } - List result = new ArrayList<>(); + long cloneIdOffset = idGenerator.getAndAdd(numberOfClones); + List result = new ArrayList<>(numberOfClones); for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { ConsensusResult.SingleConsensus[] cs = consensuses.get(cIdx).consensuses; NSequenceWithQuality[] clonalSequence = new NSequenceWithQuality[cs.length]; - for (int i = 0; i < cs.length; i++) - clonalSequence[i] = cs[i].consensus; - result.add(new PreCloneWithAlignments( - new PreClone( - idGenerator.incrementAndGet(), - grp1.getKey(), - coreTagCountAggregators[cIdx].createAndDestroy(), - fullTagCountAggregators[cIdx].createAndDestroy(), - clonalSequence, - geneInfos[cIdx]), - contents[cIdx] - )); + for (int sr = 0; sr < cs.length; sr++) + clonalSequence[sr] = cs[sr].consensus; + result.add(new PreClone( + cloneIdOffset + cIdx, + grp1.getKey(), + coreTagCountAggregators[cIdx].createAndDestroy(), + fullTagCountAggregators[cIdx].createAndDestroy(), + clonalSequence, + geneInfos[cIdx])); } - return result; + long[] resultAlToClone = new long[alignmentIdxToCloneIdxP1.length]; + for (int i = 0; i < resultAlToClone.length; i++) + resultAlToClone[i] = alignmentIdxToCloneIdxP1[i] <= 0 + ? -1 + : cloneIdOffset + alignmentIdxToCloneIdxP1[i] - 1; + + return new PreCloneAssemblerResult(result, resultAlToClone); } private static final class AlignmentInfo { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java new file mode 100644 index 000000000..6525e86bd --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java @@ -0,0 +1,21 @@ +package com.milaboratory.mixcr.assembler.preclone; + +import java.util.List; + +public final class PreCloneAssemblerResult { + private final List clones; + private final long[] alignmentToClone; + + public PreCloneAssemblerResult(List clones, long[] alignmentToClone) { + this.clones = clones; + this.alignmentToClone = alignmentToClone; + } + + public List getClones() { + return clones; + } + + public long getCloneForAlignment(int localAlignmentId){ + return alignmentToClone == null ? -1 : alignmentToClone[localAlignmentId]; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java index ac13a558d..cd557ec6e 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java @@ -23,10 +23,15 @@ public final class PreCloneWriter implements AutoCloseable { private final PrimitivOHybrid output; private final TempFileDest tempDest; + + private volatile long alignmentsStartPosition; + private volatile PrimitivOBlocks.Writer alignmentWriter; + private final Buffer alignmentBuffer; - private final InputPort alignmentInput; + private final InputPort alignmentSorterInput; private final Buffer cloneBuffer; - private final InputPort cloneInput; + private final InputPort cloneSorterInput; + private volatile Thread alignmentSortingThread, cloneSortingThread; private volatile HashSorter alignmentCollator; private volatile OutputPortCloseable sortedAlignments; @@ -37,9 +42,9 @@ public PreCloneWriter(Path file, TempFileDest tempDest) throws IOException { this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file); this.tempDest = tempDest; this.alignmentBuffer = new Buffer<>(1 << 14); - this.alignmentInput = alignmentBuffer.createInputPort(); + this.alignmentSorterInput = alignmentBuffer.createInputPort(); this.cloneBuffer = new Buffer<>(1 << 10); - this.cloneInput = cloneBuffer.createInputPort(); + this.cloneSorterInput = cloneBuffer.createInputPort(); } public void init(VDJCAlignmentsReader alignmentReader) { @@ -74,19 +79,28 @@ public void init(VDJCAlignmentsReader alignmentReader) { memoryBudget, 1 << 18 /* 256 Kb */); cloneSortingThread = new Thread(() -> sortedClones = cloneCollator.port(cloneBuffer), "clone-sorting"); + cloneSortingThread.start(); + + // Saving position in file where alignments block begins + alignmentsStartPosition = output.getPosition(); + // This writer will be used to write not-assigned alignments during alignment sorting + alignmentWriter = output.beginPrimitivOBlocks(4, 1024); } public void putClone(PreClone clone) { - cloneInput.put(clone); + cloneSorterInput.put(clone); } public void putAlignment(VDJCAlignments alignment) { - alignmentInput.put(alignment); + if (alignment.getCloneIndex() == -1) + alignmentWriter.write(alignment); + else + alignmentSorterInput.put(alignment); } public void finishWrite() { - alignmentInput.put(null); - cloneInput.put(null); + alignmentSorterInput.put(null); + cloneSorterInput.put(null); try { alignmentSortingThread.join(); cloneSortingThread.join(); @@ -94,38 +108,56 @@ public void finishWrite() { throw new RuntimeException(e); } - long clonesStartPosition = output.getPosition(); - long cloneChecksum = 17; - try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { - // final clone id generator - long newCloneIdx = 0; - for (PreClone preClone : CUtils.it(sortedClones)) { - cloneChecksum = cloneChecksum * 71 + preClone.id; - writer.write(preClone.withId(newCloneIdx++)); - } - } - - long alignmentsStartPosition = output.getPosition(); + long assignedAlignmentsStartPosition; long alignmentsChecksum = 17; - try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { - // final clone id generator + try (PrimitivOBlocks.Writer writer = alignmentWriter) { + // Finishing block of not-assigned alignments + writer.flush(); + writer.sync(); + assignedAlignmentsStartPosition = writer.getPosition(); + + // resulting clone id generator long newCloneIdx = -1; long previousCloneIdx = -1; for (VDJCAlignments al : CUtils.it(sortedAlignments)) { + assert al.getCloneIndex() >= 0; + if (al.getCloneIndex() != previousCloneIdx) { newCloneIdx++; + + // al.getCloneIndex() will be mapped to newCloneIdx alignmentsChecksum = alignmentsChecksum * 71 + al.getCloneIndex(); + alignmentsChecksum = alignmentsChecksum * 71 + newCloneIdx; + + previousCloneIdx = al.getCloneIndex(); } writer.write(al.withCloneIndex(newCloneIdx)); } } + + long clonesStartPosition = output.getPosition(); + long cloneChecksum = 17; + try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { + // resulting clone id generator + long newCloneIdx = -1; + for (PreClone preClone : CUtils.it(sortedClones)) { + newCloneIdx++; + + cloneChecksum = cloneChecksum * 71 + preClone.id; + cloneChecksum = cloneChecksum * 71 + newCloneIdx; + + writer.write(preClone.withId(newCloneIdx)); + } + } + if (alignmentsChecksum != cloneChecksum) throw new IllegalStateException("Inconsistent sequences of clones and alignments."); try (PrimitivO o = output.beginPrimitivO()) { - o.writeLong(clonesStartPosition); o.writeLong(alignmentsStartPosition); + o.writeLong(assignedAlignmentsStartPosition); + o.writeLong(clonesStartPosition); } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 1a6746d3a..287557898 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -172,7 +172,7 @@ public VDJCAlignments withCloneIndex(long newCloneIndex) { mappingType, newCloneIndex); } - public VDJCAlignments withCloneIndexAndMappingType(int newCloneIndex, byte newMappingType) { + public VDJCAlignments withCloneIndexAndMappingType(long newCloneIndex, byte newMappingType) { return new VDJCAlignments(alignmentsIndex, hits, tagCount, targets, history, originalReads, newMappingType, newCloneIndex); } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java index 7b395c6a0..81e8930e4 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java @@ -59,6 +59,29 @@ public boolean handlesReference() { } } + public static class TagTupleSerializer implements Serializer { + @Override + public void write(PrimitivO output, TagTuple obj) { + output.writeObject(obj.tags); + } + + @Override + public TagTuple read(PrimitivI input) { + //noinspection ConstantConditions + return new TagTuple(input.readObject(TagValue[].class)); + } + + @Override + public boolean isReference() { + return true; + } + + @Override + public boolean handlesReference() { + return false; + } + } + public static class TagCounterSerializer implements Serializer { @Override public void write(PrimitivO output, TagCount object) { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index 2b54608da..7cf1cac54 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -2,6 +2,7 @@ import com.google.common.hash.Hasher; import com.google.common.hash.Hashing; +import com.milaboratory.primitivio.annotations.Serializable; import java.util.Arrays; @@ -10,6 +11,7 @@ * * Tag may be a sample name, cell marker or unique molecular identifier. */ +@Serializable(by = IO.TagTupleSerializer.class) public final class TagTuple implements Comparable { public static final TagTuple NO_TAGS = new TagTuple(); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java index 10cf9e356..38ef56e13 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java @@ -15,8 +15,6 @@ import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.util.ReportHelper; import com.milaboratory.util.TempFileManager; -import gnu.trove.iterator.TIntIterator; -import gnu.trove.map.hash.TIntLongHashMap; import io.repseq.core.GeneFeature; import kotlin.jvm.functions.Function1; import picocli.CommandLine; @@ -92,21 +90,24 @@ public void run0() throws Exception { VDJCAlignments::ensureKeyTags), gFunction); // TODO array? - TIntLongHashMap alToCloneMapping = new TIntLongHashMap(); - List clones; - while ((clones = assembler.getForNextGroup()) != null) { + // TIntLongHashMap alToCloneMapping = new TIntLongHashMap(Constants.DEFAULT_CAPACITY, + // Constants.DEFAULT_LOAD_FACTOR, -1, -1); + // long[] alToClone = null; + PreCloneAssemblerResult result; + while ((result = assembler.getForNextGroup()) != null) { GroupOP grp = alGroups.take(); - assert clones.isEmpty() || clones.get(0).preClone.coreKey.equals(grp.getKey()); + List clones = result.getClones(); + assert clones.isEmpty() || clones.get(0).coreKey.equals(grp.getKey()); - alToCloneMapping.clear(); - for (PreCloneWithAlignments cloneWA : clones) { - PreClone clone = cloneWA.preClone; - TIntIterator it = cloneWA.alignments.iterator(); - while (it.hasNext()) - alToCloneMapping.put(it.next(), clone.id); + + for (PreClone clone : clones) { + // PreClone clone = cloneWA.preClone; + // TIntIterator it = cloneWA.alignments.iterator(); + // while (it.hasNext()) + // alToCloneMapping.put(it.next(), clone.id); writer.putClone(clone); - // + // out.println( // clone.clonalSequence[0].getSequence().toString() + "\t" + // cloneWA.alignments.size() + "\t" + @@ -119,8 +120,12 @@ public void run0() throws Exception { } int localId = 0; - for (VDJCAlignments al : CUtils.it(grp)) - writer.putAlignment(al.withCloneIndex(alToCloneMapping.get(localId++))); + for (VDJCAlignments al : CUtils.it(grp)) { + long cloneMapping = result.getCloneForAlignment(localId++); + writer.putAlignment(cloneMapping != -1 + ? al.withCloneIndexAndMappingType(cloneMapping, (byte) 0) + : al); + } } writer.finishWrite(); From cd02e41ddcd3f882d89fdf05a6a07729b0de78e8 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 2 Jun 2022 00:57:04 +0300 Subject: [PATCH 247/282] chore: mitool upgrade --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 5418c5903..5f8316d0a 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -83,7 +83,7 @@ repositories { val milibVersion = "1.15.0-50-master" val repseqioVersion = "1.3.5-31-master" -val mitoolVersion = "0.9.1-13-main" +val mitoolVersion = "0.9.1-15-main" val miplotsVersion = "0.1-22-master" val jacksonBomVersion = "2.13.3" From bc5fb0e7c3f94e63118c6f1d4c08abf67b54a186 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 2 Jun 2022 01:20:52 +0200 Subject: [PATCH 248/282] Postanalysis: cli enhancements; removed random seed option ad fixed seed in downsampling --- .../cli/postanalysis/CommandDownsample.java | 6 +- .../postanalysis/CommandOverlapScatter.java | 6 +- .../mixcr/cli/postanalysis/CommandPa.java | 33 ++++++--- .../cli/postanalysis/CommandPaIndividual.java | 7 +- .../cli/postanalysis/CommandPaOverlap.java | 11 ++- .../cli/postanalysis/IsolationGroup.java | 15 ++-- .../postanalysis/SetPreprocessorSummary.java | 26 ++++--- ...ClonesDownsamplingPreprocessorFactory.java | 9 +-- .../DownsamplingPreprocessor.java | 13 ++-- .../DownsamplingPreprocessorFactory.java | 18 ++--- .../downsampling/DownsamplingUtil.java | 12 ++-- .../preproc/ElementPredicate.java | 14 ++++ .../ui/PostanalysisParameters.java | 5 +- .../postanalysis/ui/PostanalysisSchema.java | 12 ++-- .../parameters/postanalysis_individual.json | 1 - .../parameters/postanalysis_overlap.json | 1 - .../mixcr/cli/postanalysis/CommandPaTest.java | 10 ++- .../postanalysis/PostanalysisRunnerTest.java | 6 +- .../DownsamplingPreprocessorTest.java | 4 +- .../OverlapDownsamplingPreprocessorTest.java | 68 ++++++++++++++++--- .../ui/PostanalysisSchemaIntegrationTest.java | 8 +-- 21 files changed, 176 insertions(+), 109 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java index 046a38507..2dd79adde 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java @@ -46,10 +46,6 @@ public class CommandDownsample extends ACommandWithOutputMiXCR { required = true) public String downsampling; - @Option(description = "Random seed.", - names = {"--random-seed"}) - public long seed = 111; - @Option(description = "Suffix to add to output clns file.", names = {"--suffix"}) public String suffix = "downsampled"; @@ -86,7 +82,7 @@ public void run0() throws Exception { ).collect(Collectors.toList()); SetPreprocessorFactory preproc = DownsamplingUtil - .parseDownsampling(this.downsampling, false, seed) + .parseDownsampling(this.downsampling, false) .filterFirst(new ElementPredicate.IncludeChains(Chains.getByName(chains))); if (onlyProductive) preproc = DownsamplingUtil.filterOnlyProductive(preproc); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java index dc78a21b0..557089a16 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java @@ -70,10 +70,6 @@ public class CommandOverlapScatter extends ACommandWithOutputMiXCR { names = {"--no-log"}) public boolean noLog; - @Option(description = "Random seed", - names = {"--random-seed"}) - public long randomSeed = 111; - private static String fName(String file) { return Paths.get(file).toAbsolutePath().getFileName().toString(); } @@ -88,7 +84,7 @@ private Path outputPath(NamedChains chains) { @Override public void run0() throws Exception { SetPreprocessorFactory preproc = DownsamplingUtil. - parseDownsampling(downsampling, false, randomSeed); + parseDownsampling(downsampling, false); for (NamedChains curChains : this.chains == null ? Arrays.asList(TRAD_NAMED, TRB_NAMED, TRG_NAMED, IGH_NAMED, IGKL_NAMED) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index e4d33cb9c..7708e3520 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -6,6 +6,7 @@ import com.milaboratory.util.StringUtil; import io.repseq.core.Chains; import picocli.CommandLine; +import picocli.CommandLine.Command; import picocli.CommandLine.Option; import picocli.CommandLine.Parameters; @@ -14,6 +15,8 @@ import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; import java.util.stream.Stream; import static io.repseq.core.Chains.*; @@ -93,7 +96,7 @@ public void validate() { if (!out().endsWith(".json") && !out().endsWith(".json.gz")) throwValidationException("Output file name should ends with .json.gz or .json"); try { - DownsamplingUtil.parseDownsampling(defaultDownsampling, dropOutliers, 0); + DownsamplingUtil.parseDownsampling(defaultDownsampling, dropOutliers); } catch (Throwable t) { throwValidationException("Illegal downsampling string: " + defaultDownsampling); } @@ -103,6 +106,11 @@ public void validate() { throwValidationException("--tables: table name should ends with .csv or .tsv"); if (metadata != null && !metadata.endsWith(".csv") && !metadata.endsWith(".tsv")) throwValidationException("Metadata should be .csv or .tsv"); + List duplicates = getInputFiles().stream() + .collect(Collectors.groupingBy(Function.identity())).entrySet().stream().filter(e -> e.getValue().size() > 1).map(Map.Entry::getKey) + .collect(toList()); + if (duplicates.size() > 0) + throwValidationException("Duplicated samples detected: " + String.join(",", duplicates)); if (metadata != null) { if (!metadata().containsKey("sample")) throwValidationException("Metadata must contain 'sample' column"); @@ -112,8 +120,9 @@ public void validate() { metadata().get("sample").stream() .map(Object::toString).collect(toList()) ); - if (mapping.size() < samples.size() || mapping.values().stream().anyMatch(Objects::isNull)) - throwValidationException("Metadata samples does not match input file names."); + if (mapping.size() < samples.size() || mapping.values().stream().anyMatch(Objects::isNull)) { + throwValidationException("Metadata samples does not match input file names: " + samples.stream().filter(s -> mapping.get(s) == null).collect(Collectors.joining(","))); + } } } @@ -256,13 +265,14 @@ public void run0() throws Exception { Chains c = Chains.parse(chains); String chainsColumn = chainsColumn(); for (SamplesGroup group : groupSamples()) { - if (chainsColumn != null) - results.add(run(new IsolationGroup( - Chains.getNamedChains(group.group.get(chainsColumn).toString().toUpperCase()), group.group), group.samples)); - else + if (chainsColumn != null) { + NamedChains mc = getNamedChains(group.group.get(chainsColumn).toString().toUpperCase()); + if (c.intersects(mc.chains)) + results.add(run0(new IsolationGroup(mc, group.group), group.samples)); + } else for (NamedChains knownChains : CHAINS) { if (c.intersects(knownChains.chains)) { - results.add(run(new IsolationGroup(knownChains, group.group), group.samples)); + results.add(run0(new IsolationGroup(knownChains, group.group), group.samples)); } } } @@ -279,9 +289,14 @@ public void run0() throws Exception { new CommandPaExportTablesPreprocSummary(result, preprocOut()).run0(); } + private PaResultByGroup run0(IsolationGroup group, List samples) { + System.out.println("Running for " + group.toString(chainsColumn() == null)); + return run(group, samples); + } + abstract PaResultByGroup run(IsolationGroup group, List samples); - @CommandLine.Command(name = "postanalysis", + @Command(name = "postanalysis", separator = " ", description = "Run postanalysis routines.", subcommands = { diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index 8f7945340..948fbf5a7 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -11,7 +11,6 @@ import picocli.CommandLine.Command; import java.util.List; -import java.util.Map; import java.util.stream.Collectors; @Command(name = "individual", @@ -31,8 +30,7 @@ private PostanalysisParametersIndividual getParameters() { _parameters.defaultDropOutliers = dropOutliers; _parameters.defaultOnlyProductive = onlyProductive; if (!overrides.isEmpty()) { - for (Map.Entry o : overrides.entrySet()) - _parameters = JsonOverrider.override(_parameters, PostanalysisParametersIndividual.class, overrides); + _parameters = JsonOverrider.override(_parameters, PostanalysisParametersIndividual.class, overrides); if (_parameters == null) throwValidationException("Failed to override some parameter: " + overrides); } @@ -43,7 +41,7 @@ private PostanalysisParametersIndividual getParameters() { @SuppressWarnings({"unchecked", "rawtypes"}) PaResultByGroup run(IsolationGroup group, List samples) { List> groups = getParameters().getGroups(); - PostanalysisSchema schema = new PostanalysisSchema<>(groups) + PostanalysisSchema schema = new PostanalysisSchema<>(false, groups) .transform(ch -> ch.override(ch.name, ch.preprocessor .filterFirst(new ElementPredicate.IncludeChains(group.chains.chains))) @@ -56,7 +54,6 @@ PaResultByGroup run(IsolationGroup group, List samples) { new ClonotypeDataset(getSampleId(file), file, VDJCLibraryRegistry.getDefault()) ).collect(Collectors.toList()); - System.out.println("Running for " + group); SmartProgressReporter.startProgressReport(runner); return new PaResultByGroup(group, schema, runner.run(datasets)); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index e1accb4f5..60e99c969 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -21,7 +21,6 @@ import picocli.CommandLine.Option; import java.util.List; -import java.util.Map; @Command(name = "overlap", sortOptions = false, @@ -44,8 +43,7 @@ private PostanalysisParametersOverlap getParameters() { _parameters.defaultDropOutliers = dropOutliers; _parameters.defaultOnlyProductive = onlyProductive; if (!overrides.isEmpty()) { - for (Map.Entry o : overrides.entrySet()) - _parameters = JsonOverrider.override(_parameters, PostanalysisParametersOverlap.class, overrides); + _parameters = JsonOverrider.override(_parameters, PostanalysisParametersOverlap.class, overrides); if (_parameters == null) throwValidationException("Failed to override some parameter: " + overrides); } @@ -56,10 +54,12 @@ private PostanalysisParametersOverlap getParameters() { @SuppressWarnings("unchecked") PaResultByGroup run(IsolationGroup group, List samples) { List>> groups = getParameters().getGroups(samples.size()); - PostanalysisSchema> schema = new PostanalysisSchema<>(groups) + PostanalysisSchema> schema = new PostanalysisSchema<>(true, groups) .transform(ch -> ch.override(ch.name, ch.preprocessor - .before(new OverlapPreprocessorAdapter.Factory<>(new FilterPreprocessor.Factory<>(WeightFunctions.Count, new ElementPredicate.IncludeChains(group.chains.chains))))) + .before(new OverlapPreprocessorAdapter.Factory<>( + new FilterPreprocessor.Factory<>(WeightFunctions.Count, + new ElementPredicate.IncludeChains(group.chains.chains))))) ); OverlapDataset overlapDataset = OverlapUtil.overlap( @@ -70,7 +70,6 @@ PaResultByGroup run(IsolationGroup group, List samples) { PostanalysisRunner> runner = new PostanalysisRunner<>(); runner.addCharacteristics(schema.getAllCharacterisitcs()); - System.out.println("Running for " + group); SmartProgressReporter.startProgressReport(runner); PostanalysisResult result = runner.run(overlapDataset); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java index 4d87a8461..58e3405c2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java @@ -39,14 +39,17 @@ private static LinkedHashMap sortByKey(Map group )); } + public String toString(boolean withChains) { + String str = group.entrySet().stream().map(e -> e.getKey() + "=" + e.getValue()).collect(Collectors.joining(",")); + if (withChains) + return "chains=" + chains.name + (str.isEmpty() ? "" : "," + str); + else + return str; + } + @Override public String toString() { - StringBuilder sb = new StringBuilder(); - sb.append("chains=").append(chains.name); - for (Map.Entry e : group.entrySet()) { - sb.append(",").append(e.getKey()).append("=").append(e.getValue()); - } - return sb.toString(); + return toString(true); } /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java index fc8c595ab..3cda5567e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java @@ -154,7 +154,7 @@ public static void byCharToCSV(Path path, PostanalysisSchema schema, PostanalysisResult result, String sep) { - if (schema.getAllCharacterisitcs().get(0) instanceof OverlapCharacteristic) + if (schema.isOverlap) overlapByCharToCSV(path, (PostanalysisSchema>) schema, result, sep); else individualByCharToCSV(path, result, sep); @@ -168,17 +168,16 @@ public static void overlapByCharToCSV(Path path, PostanalysisSchema> schema, PostanalysisResult result, String sep) { - Map, OverlapCharacteristic> m = - schema.getAllCharacterisitcs() - .stream() - .map(it -> (OverlapCharacteristic) it) - .collect(Collectors.toMap( - it -> new HashSet<>(Arrays.asList(it.overlapTypes)), - it -> it, - (a, b) -> a)); + + Map, Characteristic>> m = schema.getAllCharacterisitcs() + .stream() + .collect(Collectors.toMap( + SetPreprocessorSummary::getOverlapTypes, + it -> it, + (a, b) -> a)); List> rows = new ArrayList<>(); - for (Map.Entry, OverlapCharacteristic> eCh : m.entrySet()) { + for (Map.Entry, Characteristic>> eCh : m.entrySet()) { String ch = eCh.getKey().stream().map(it -> it.name).collect(Collectors.joining("/")); String preproc = eCh.getValue().preprocessor.id(); SetPreprocessorSummary preprocSummary = result.preprocSummary.get(preproc); @@ -187,6 +186,13 @@ public static void overlapByCharToCSV(Path path, writeTable(rows, path, sep); } + @SuppressWarnings("unchecked") + private static Set getOverlapTypes(Characteristic> ch) { + if (ch instanceof Characteristic.CharacteristicWrapper) + return getOverlapTypes(((Characteristic.CharacteristicWrapper>) ch).inner); + else + return new HashSet<>(Arrays.asList(((OverlapCharacteristic) ch).overlapTypes)); + } /** * Write preprocessing summary data to CSV file with columns characteristic | samples | .... diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java index db0f74c95..f2cdfef00 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java @@ -18,10 +18,8 @@ public class ClonesDownsamplingPreprocessorFactory extends DownsamplingPreprocessorFactory { @JsonCreator public ClonesDownsamplingPreprocessorFactory(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, - @JsonProperty("seed") long seed, @JsonProperty("dropOutliers") boolean dropOutliers) { - super(downsampleValueChooser, seed, dropOutliers, - c -> Math.round(c.getCount()), Clone::setCount); + super(downsampleValueChooser, c -> Math.round(c.getCount()), Clone::setCount, dropOutliers); } @Override @@ -29,12 +27,11 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; ClonesDownsamplingPreprocessorFactory that = (ClonesDownsamplingPreprocessorFactory) o; - return Objects.equals(downsampleValueChooser, that.downsampleValueChooser) - && Objects.equals(seed, that.seed); + return Objects.equals(downsampleValueChooser, that.downsampleValueChooser); } @Override public int hashCode() { - return Objects.hash(downsampleValueChooser, seed); + return Objects.hash(downsampleValueChooser); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index 61721a1fa..ac4ea3812 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -15,6 +15,7 @@ import java.util.concurrent.atomic.AtomicInteger; import java.util.function.BiFunction; import java.util.function.ToLongFunction; +import java.util.stream.LongStream; import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil.downsample_mvhg; @@ -26,21 +27,18 @@ public class DownsamplingPreprocessor implements SetPreprocessor { public final BiFunction setCount; public final DownsampleValueChooser downsampleValueChooser; public final boolean dropOutliers; - public final long seed; final String id; private final SetPreprocessorStat.Builder stats; - public DownsamplingPreprocessor(ToLongFunction getCount, + public DownsamplingPreprocessor(DownsampleValueChooser downsampleValueChooser, + ToLongFunction getCount, BiFunction setCount, - DownsampleValueChooser downsampleValueChooser, boolean dropOutliers, - long seed, String id) { this.getCount = getCount; this.setCount = setCount; this.downsampleValueChooser = downsampleValueChooser; this.dropOutliers = dropOutliers; - this.seed = seed; this.id = id; this.stats = new SetPreprocessorStat.Builder<>(id, getCount::applyAsLong); } @@ -82,8 +80,9 @@ public MappingFunction getMapper(int iDataset) { } long[] counts = setup.countLists[iDataset].toArray(); - RandomGenerator rnd = new Well19937c(seed); - long[] countsDownsampled = downsample_mvhg(counts, downsampling, rnd); + long total = LongStream.of(counts).sum(); + RandomGenerator rnd = new Well19937c(total); + long[] countsDownsampled = downsample_mvhg(counts, total, downsampling, rnd); AtomicInteger idx = new AtomicInteger(0); return t -> { diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java index 07213ade3..21995307f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java @@ -14,20 +14,16 @@ public class DownsamplingPreprocessorFactory implements SetPreprocessorFactory { @JsonProperty("downsampleValueChooser") public final DownsampleValueChooser downsampleValueChooser; - @JsonProperty("seed") - public final long seed; @JsonProperty("dropOutliers") public final boolean dropOutliers; public final ToLongFunction getCount; public final BiFunction setCount; public DownsamplingPreprocessorFactory(DownsampleValueChooser downsampleValueChooser, - long seed, - boolean dropOutliers, ToLongFunction getCount, - BiFunction setCount) { + BiFunction setCount, + boolean dropOutliers) { this.downsampleValueChooser = downsampleValueChooser; - this.seed = seed; this.dropOutliers = dropOutliers; this.getCount = getCount; this.setCount = setCount; @@ -41,9 +37,9 @@ public String id() { @Override public SetPreprocessor newInstance() { return new DownsamplingPreprocessor( - getCount, - setCount, downsampleValueChooser, - dropOutliers, seed, id()); + downsampleValueChooser, getCount, + setCount, + dropOutliers, id()); } @Override @@ -51,11 +47,11 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; DownsamplingPreprocessorFactory that = (DownsamplingPreprocessorFactory) o; - return seed == that.seed && Objects.equals(downsampleValueChooser, that.downsampleValueChooser) && Objects.equals(dropOutliers, that.dropOutliers) && Objects.equals(getCount, that.getCount) && Objects.equals(setCount, that.setCount); + return Objects.equals(downsampleValueChooser, that.downsampleValueChooser) && Objects.equals(dropOutliers, that.dropOutliers) && Objects.equals(getCount, that.getCount) && Objects.equals(setCount, that.setCount); } @Override public int hashCode() { - return Objects.hash(downsampleValueChooser, seed, dropOutliers, getCount, setCount); + return Objects.hash(downsampleValueChooser, dropOutliers, getCount, setCount); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index caf4a842a..d24026290 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -61,6 +61,10 @@ public static long total(ToLongFunction getCount, Dataset set) { public static long[] downsample_mvhg(long[] counts, long downSampleSize, RandomGenerator rnd) { long total = LongStream.of(counts).sum(); + return downsample_mvhg(counts, total, downSampleSize, rnd); + } + + static long[] downsample_mvhg(long[] counts, long total, long downSampleSize, RandomGenerator rnd) { long[] result = new long[counts.length]; RandomMvhgMarginals.random_multivariate_hypergeometric_marginals(rnd, total, counts, downSampleSize, result); return result; @@ -73,16 +77,16 @@ public static long[] downsample_counts(long[] counts, long downSampleSize, Rando return result; } - public static SetPreprocessorFactory parseDownsampling(String downsampling, boolean dropOutliers, long seed) { + public static SetPreprocessorFactory parseDownsampling(String downsampling, boolean dropOutliers) { if (downsampling.equalsIgnoreCase("none")) { return new NoPreprocessing.Factory<>(); } else if (downsampling.startsWith("umi-count")) { if (downsampling.endsWith("auto")) - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), seed, dropOutliers); + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), dropOutliers); else if (downsampling.endsWith("min")) - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Minimal(), seed, dropOutliers); + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Minimal(), dropOutliers); else { - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), seed, dropOutliers); + return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), dropOutliers); } } else { int value = downsamplingValue(downsampling); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java index 51b86c9da..8b630546e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java @@ -21,6 +21,20 @@ public interface ElementPredicate extends Predicate { String id(); + static ElementPredicate mk(String id, Predicate predicate) { + return new ElementPredicate() { + @Override + public String id() { + return id; + } + + @Override + public boolean test(T t) { + return predicate.test(t); + } + }; + } + @JsonAutoDetect final class NoOutOfFrames implements ElementPredicate { @JsonProperty("feature") diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java index c69ae8c02..74ce349bd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java @@ -24,7 +24,6 @@ public abstract class PostanalysisParameters { public String defaultDownsampling; public boolean defaultOnlyProductive; public boolean defaultDropOutliers; - public long randomSeed; @JsonAutoDetect( fieldVisibility = JsonAutoDetect.Visibility.ANY, @@ -34,7 +33,6 @@ public static class PreprocessorParameters { public String downsampling; public Boolean onlyProductive; public Boolean dropOutliers; - public Long randomSeed; public SetPreprocessorFactory preproc(PostanalysisParameters base) { SetPreprocessorFactory p = parseDownsampling(base); @@ -52,8 +50,7 @@ public SetPreprocessorFactory> overlapPreproc(PostanalysisPa SetPreprocessorFactory parseDownsampling(PostanalysisParameters base) { return DownsamplingUtil.parseDownsampling( this.downsampling == null ? base.defaultDownsampling : this.downsampling, - this.dropOutliers == null ? base.defaultDropOutliers : this.dropOutliers, - this.randomSeed == null ? base.randomSeed : this.randomSeed + this.dropOutliers == null ? base.defaultDropOutliers : this.dropOutliers ); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java index 23b251b3c..be0892449 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java @@ -22,11 +22,15 @@ getterVisibility = JsonAutoDetect.Visibility.NONE, isGetterVisibility = JsonAutoDetect.Visibility.NONE) public class PostanalysisSchema { + @JsonProperty("isOverlap") + public final boolean isOverlap; @JsonProperty("tables") public final List> tables; @JsonCreator - public PostanalysisSchema(@JsonProperty("tables") List> tables) { + public PostanalysisSchema(@JsonProperty("isOverlap") boolean isOverlap, + @JsonProperty("tables") List> tables) { + this.isOverlap = isOverlap; this.tables = tables; } @@ -36,7 +40,7 @@ public PostanalysisSchema transform(Function, Characteri .map(gr -> (CharacteristicGroup) gr.transform(c -> (Characteristic) mapper.apply(c))); List> collect = characteristicGroupStream .collect(Collectors.>toList()); - return new PostanalysisSchema<>(collect); + return new PostanalysisSchema<>(isOverlap, collect); } public List> getAllCharacterisitcs() { @@ -58,12 +62,12 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; PostanalysisSchema that = (PostanalysisSchema) o; - return Objects.equals(tables, that.tables); + return isOverlap == that.isOverlap && Objects.equals(tables, that.tables); } @Override public int hashCode() { - return Objects.hash(tables); + return Objects.hash(isOverlap, tables); } public PostanalysisResult run(List> datasets) { diff --git a/src/main/resources/parameters/postanalysis_individual.json b/src/main/resources/parameters/postanalysis_individual.json index 2b95ee37d..b18ee72e3 100644 --- a/src/main/resources/parameters/postanalysis_individual.json +++ b/src/main/resources/parameters/postanalysis_individual.json @@ -3,7 +3,6 @@ "defaultDownsampling": null, "defaultOnlyProductive": true, "defaultDropOutliers": false, - "randomSeed": 111, "biophysics": { "cdr3lenAA": { "downsampling": null, diff --git a/src/main/resources/parameters/postanalysis_overlap.json b/src/main/resources/parameters/postanalysis_overlap.json index 37be8c767..75dfb2298 100644 --- a/src/main/resources/parameters/postanalysis_overlap.json +++ b/src/main/resources/parameters/postanalysis_overlap.json @@ -3,7 +3,6 @@ "defaultDownsampling": null, "defaultOnlyProductive": false, "defaultDropOutliers": false, - "randomSeed": 111, "d": { "downsampling": null, "onlyProductive": null, diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java index 70e9b1c55..6a340c377 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java @@ -17,13 +17,11 @@ public void test1() { @Test public void test2() { Main.main("postanalysis", "overlap", -// "--chains", "IGH", "-f", - "--only-productive", "-d", "umi-count-auto", + "--only-productive", "--default-downsampling", "umi-count-auto", "--metadata", "/Users/poslavskysv/Projects/milab/mixcr-test-data/metadata.tsv", - "--chains-column", "Chain", - "--group", "CellPopulation", - "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD4naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8mem_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_CD8naive_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_spl_Treg_b.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4mem_a.sorted.clns", "/Users/poslavskysv/Projects/milab/mixcr-test-data/results/m10_ct_th_CD4mem_b.sorted.clns", 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"/Users/poslavskysv/Projects/milab/mixcr-test-data/pa/overlapPa.json.gz"); } } diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java index 0e2225ef8..38d958598 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java @@ -40,10 +40,8 @@ public boolean test(TestObject testObject) { DownsamplingPreprocessorFactory downsamplingPreproc = new DownsamplingPreprocessorFactory<>( new DownsampleValueChooser.Fixed(downsampling), - 314, - true, - c -> (long) c.weight, - TestObject::setWeight); + c -> (long) c.weight, TestObject::setWeight, true + ); SetPreprocessorFactory preproc = filter.then(downsamplingPreproc); DiversityCharacteristic diversityCh = diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index 694350bdc..ea7cde6c3 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -98,11 +98,9 @@ public void test3() { DownsampleValueChooser dsChooser = counts -> Arrays.stream(counts).min().orElse(0); DownsamplingPreprocessor proc = new DownsamplingPreprocessor<>( - t -> Math.round(t.weight), + dsChooser, t -> Math.round(t.weight), (t, w) -> new TestObject(t.value, 1d * w), - dsChooser, true, - rng.nextLong(0, Long.MAX_VALUE / 2), "" ); diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index 009db9d3f..8fc0c287b 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -3,6 +3,8 @@ import cc.redberry.pipe.CUtils; import com.milaboratory.mixcr.postanalysis.*; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.FilterPreprocessor; import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; import gnu.trove.iterator.TIntObjectIterator; import gnu.trove.map.hash.TIntObjectHashMap; @@ -11,10 +13,8 @@ import org.junit.Assert; import org.junit.Test; -import java.util.ArrayList; -import java.util.HashSet; -import java.util.List; -import java.util.Set; +import java.util.*; +import java.util.stream.Collectors; import static com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingPreprocessorTest.toList; @@ -35,11 +35,9 @@ public void test1() { DatasetSupport[] datasets = new DatasetSupport[]{dataset}; DownsamplingPreprocessor proc = new DownsamplingPreprocessor<>( - t -> Math.round(t.weight), + chooser, t -> Math.round(t.weight), (t, newW) -> new TestObject(t.value, newW), - chooser, true, - System.currentTimeMillis(), "" ); @@ -80,6 +78,58 @@ public void test1() { } } + @SuppressWarnings("unchecked") + @Test + public void test2() { + RandomDataGenerator rng = new RandomDataGenerator(new Well512a()); + int nDatasets = 50; + DatasetSupport dataset = rndDataset(rng, nDatasets, 10000); + List> individual = o2i(nDatasets, dataset); + + long[] totals = individual + .stream() + .mapToLong(it -> (long) CUtils.stream(it.mkElementsPort()).mapToDouble(c -> c.weight).sum()) + .toArray(); + Arrays.stream(totals).forEach(System.out::println); + System.out.println(">>> " + new DownsampleValueChooser.Auto().compute(totals)); + + + SetPreprocessorFactory proc = new DownsamplingPreprocessorFactory<>( + new DownsampleValueChooser.Auto(), + t -> Math.round(t.weight), + TestObject::setWeight, + true + ); + + FilterPreprocessor.Factory filter = new FilterPreprocessor.Factory<>(t -> t.weight, ElementPredicate.mk("", t -> Double.toString(t.value).hashCode() % 3 == 1)); + SetPreprocessorFactory iProc = proc.before(filter); + SetPreprocessorFactory> oProc = new OverlapPreprocessorAdapter.Factory<>(proc) + .before(new OverlapPreprocessorAdapter.Factory<>(filter)); + + Dataset[] expected = SetPreprocessor.processDatasets(iProc.newInstance(), individual); + Dataset> overlapDownsampled = SetPreprocessor.processDatasets(oProc.newInstance(), dataset)[0]; + + List> actual = o2i(nDatasets, overlapDownsampled); + + List> e = Arrays.stream(expected).map(d -> CUtils.toList(d.mkElementsPort())).collect(Collectors.toList()); + List> a = actual.stream().map(d -> CUtils.toList(d.mkElementsPort())).collect(Collectors.toList()); + + Assert.assertEquals(e, a); + } + + + @SuppressWarnings("unchecked") + private static List> o2i(int nDatasets, Dataset> od) { + List[] ids = new List[nDatasets]; + for (int i = 0; i < nDatasets; i++) + ids[i] = new ArrayList<>(); + for (OverlapGroup row : CUtils.it(od.mkElementsPort())) + for (int i = 0; i < row.size(); i++) + for (TestObject o : row.getBySample(i)) + ids[i].add(o); + return Arrays.stream(ids).map(TestDataset::new).collect(Collectors.toList()); + } + private static long[] sum(long[] a, long[] b) { if (a.length == 0) return b; @@ -132,7 +182,9 @@ private static DatasetSupport rndDataset(RandomDataGenerator rng, int nSamples, added = true; ArrayList cell = new ArrayList<>(); for (int k = 0; k < rng.nextInt(1, 2); k++) { - cell.add(new TestObject(rng.nextUniform(0, 1), rng.nextInt(1, 1000))); + cell.add( + new TestObject(rng.nextUniform(0, 1), + rng.nextInt(1, 1000))); } row.add(cell); } else { diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index 909fb6062..fb9a3b73e 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -82,7 +82,7 @@ public void test1() throws IOException { )); groups.add(new CharacteristicGroup<>( "diversity", - Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), 314, true))), + Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), true))), Arrays.asList(new GroupSummary.Simple<>()) )); @@ -121,7 +121,7 @@ public void test1() throws IOException { Arrays.asList(AdditiveCharacteristics.VSpectratype()), Collections.singletonList(new GroupSummary.Simple<>()))); - PostanalysisSchema individualPA = new PostanalysisSchema<>(groups); + PostanalysisSchema individualPA = new PostanalysisSchema<>(false, groups); ObjectMapper OM = new ObjectMapper(); String individualPAStr = OM.writeValueAsString(individualPA); @@ -190,7 +190,7 @@ public void testOverlap1() throws JsonProcessingException { ClonesDownsamplingPreprocessorFactory downsamplePreprocessor = new ClonesDownsamplingPreprocessorFactory( new DownsampleValueChooser.Minimal(), - 332142, true); + true); List> overlaps = new ArrayList<>(); for (int i = 0; i < readers.size(); ++i) { @@ -209,7 +209,7 @@ public void testOverlap1() throws JsonProcessingException { Arrays.asList(new OverlapSummary<>()) )); - PostanalysisSchema> overlapPA = new PostanalysisSchema<>(groups); + PostanalysisSchema> overlapPA = new PostanalysisSchema<>(true, groups); ObjectMapper OM = new ObjectMapper(); String overlapPAStr = OM.writeValueAsString(overlapPA); System.out.println(overlapPAStr); From 9ff1576634cef0c8c3c8052c78512ec7c18094a3 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 2 Jun 2022 01:33:43 +0200 Subject: [PATCH 249/282] Update repseqio dependency --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 1c9773780..764900a4f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -79,7 +79,7 @@ repositories { } val milibVersion = "1.15.0-49-master" -val repseqioVersion = "1.3.5-30-master" +val repseqioVersion = "1.3.5-33-master" val miplotsVersion = "0.1-22-master" val jacksonBomVersion = "2.13.3" From 068de5a2204b9594be8e30b0ab3f5545eb4f375d Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 2 Jun 2022 01:40:07 +0200 Subject: [PATCH 250/282] Update milib dependency --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 764900a4f..73b6b348f 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -78,7 +78,7 @@ repositories { } } -val milibVersion = "1.15.0-49-master" +val milibVersion = "1.15.0-51-master" val repseqioVersion = "1.3.5-33-master" val miplotsVersion = "0.1-22-master" val jacksonBomVersion = "2.13.3" From e58b8a1f40911921b562ada0ab13df8571f97f7c Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 2 Jun 2022 01:41:38 +0200 Subject: [PATCH 251/282] Postanalysis: fix spelling in Shannon-Wiener --- .../mixcr/postanalysis/diversity/DiversityAggregator.java | 6 +++--- .../mixcr/postanalysis/diversity/DiversityMeasure.java | 6 +++--- .../postanalysis/ui/PostanalysisParametersIndividual.java | 8 ++++---- .../resources/parameters/postanalysis_individual.json | 2 +- .../diversity/DiversityCharacteristicTest.java | 2 +- 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java index b343a8e3b..afad954f0 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -67,7 +67,7 @@ private List> computeChao1() { /** Clonality, Gini and Shannon-Weiner */ private List> computeClonality() { - if (!(measures.containsKey(ShannonWeiner) + if (!(measures.containsKey(ShannonWiener) || measures.containsKey(NormalizedShannonWeinerIndex) || measures.containsKey(InverseSimpson) || measures.containsKey(Gini))) @@ -88,8 +88,8 @@ private List> computeClonality() { } List> result = new ArrayList<>(); - if (measures.containsKey(ShannonWeiner)) - result.add(new MetricValue<>(measures.get(ShannonWeiner), Math.exp(shannonWeinerIndex))); + if (measures.containsKey(ShannonWiener)) + result.add(new MetricValue<>(measures.get(ShannonWiener), Math.exp(shannonWeinerIndex))); if (measures.containsKey(NormalizedShannonWeinerIndex)) result.add(new MetricValue<>(measures.get(NormalizedShannonWeinerIndex), shannonWeinerIndex / Math.log(diversity))); if (measures.containsKey(InverseSimpson)) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java index b9c3c5fd1..57b04bcbc 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java @@ -48,7 +48,7 @@ public static DiversityMeasure[] basic() { Observed, Chao1, Chao1Std, - ShannonWeiner, + ShannonWiener, NormalizedShannonWeinerIndex, GiniIndex, InverseSimpson, @@ -60,7 +60,7 @@ public static DiversityMeasure[] basic() { public static final DiversityMeasure Observed = Measure.Observed.toDiversityMeasure(); public static final DiversityMeasure Chao1 = Measure.Chao1.toDiversityMeasure(); public static final DiversityMeasure Chao1Std = Measure.Chao1Std.toDiversityMeasure(); - public static final DiversityMeasure ShannonWeiner = Measure.ShannonWeiner.toDiversityMeasure(); + public static final DiversityMeasure ShannonWiener = Measure.ShannonWiener.toDiversityMeasure(); public static final DiversityMeasure NormalizedShannonWeinerIndex = Measure.NormalizedShannonWeinerIndex.toDiversityMeasure(); public static final DiversityMeasure GiniIndex = Measure.Gini.toDiversityMeasure(); public static final DiversityMeasure InverseSimpson = Measure.InverseSimpson.toDiversityMeasure(); @@ -71,7 +71,7 @@ public enum Measure { Observed, Chao1, Chao1Std, - ShannonWeiner, + ShannonWiener, NormalizedShannonWeinerIndex, Gini, GiniDiversity, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java index 2954a442f..4c76b2c93 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java @@ -135,7 +135,7 @@ public int hashCode() { getterVisibility = JsonAutoDetect.Visibility.NONE) public static class DiversityParameters { public PreprocessorParameters observed = new PreprocessorParameters(); - public PreprocessorParameters shannonWeiner = new PreprocessorParameters(); + public PreprocessorParameters shannonWiener = new PreprocessorParameters(); public PreprocessorParameters chao1 = new PreprocessorParameters(); public PreprocessorParameters clonality = new PreprocessorParameters(); public PreprocessorParameters inverseSimpson = new PreprocessorParameters(); @@ -146,7 +146,7 @@ public CharacteristicGroup getGroup(PostanalysisParameters base) { List> chars = new ArrayList<>(groupByPreproc( new HashMap>() {{ put(DiversityMeasure.Observed, observed.preproc(base)); - put(DiversityMeasure.ShannonWeiner, shannonWeiner.preproc(base)); + put(DiversityMeasure.ShannonWiener, shannonWiener.preproc(base)); put(DiversityMeasure.Chao1, chao1.preproc(base)); put(DiversityMeasure.NormalizedShannonWeinerIndex, clonality.preproc(base)); put(DiversityMeasure.InverseSimpson, inverseSimpson.preproc(base)); @@ -174,12 +174,12 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; DiversityParameters that = (DiversityParameters) o; - return Objects.equals(observed, that.observed) && Objects.equals(shannonWeiner, that.shannonWeiner) && Objects.equals(chao1, that.chao1) && Objects.equals(clonality, that.clonality) && Objects.equals(inverseSimpson, that.inverseSimpson) && Objects.equals(gini, that.gini) && Objects.equals(d50, that.d50); + return Objects.equals(observed, that.observed) && Objects.equals(shannonWiener, that.shannonWiener) && Objects.equals(chao1, that.chao1) && Objects.equals(clonality, that.clonality) && Objects.equals(inverseSimpson, that.inverseSimpson) && Objects.equals(gini, that.gini) && Objects.equals(d50, that.d50); } @Override public int hashCode() { - return Objects.hash(observed, shannonWeiner, chao1, clonality, inverseSimpson, gini, d50); + return Objects.hash(observed, shannonWiener, chao1, clonality, inverseSimpson, gini, d50); } } diff --git a/src/main/resources/parameters/postanalysis_individual.json b/src/main/resources/parameters/postanalysis_individual.json index b18ee72e3..979190e74 100644 --- a/src/main/resources/parameters/postanalysis_individual.json +++ b/src/main/resources/parameters/postanalysis_individual.json @@ -56,7 +56,7 @@ "onlyProductive": null, "dropOutliers": null }, - "shannonWeiner": { + "shannonWiener": { "downsampling": null, "onlyProductive": null, "dropOutliers": null diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index 6e339cc4a..01bdfa67e 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -47,7 +47,7 @@ public void test1() { TestDataset ds = Arrays.stream(datasets).filter(d -> d.id.equals(cell.datasetId)).findFirst().get(); if (cell.key == DiversityMeasure.InverseSimpson) Assert.assertEquals(SimpsonIndex(ds.data), cell.value, 1e-6); - if (cell.key == DiversityMeasure.ShannonWeiner) + if (cell.key == DiversityMeasure.ShannonWiener) Assert.assertEquals(Math.exp(ShannonEntropy(ds.data)), cell.value, 1e-6); } } From d2a229f961a800a9849b22dc3e2e15aabc36285a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 2 Jun 2022 15:46:52 +0300 Subject: [PATCH 252/282] feat: pre-clone reader / writer with integration test --- itests/case10.sh | 2 + .../assembler/preclone/PreCloneReader.java | 84 ++++++++++++++++ .../assembler/preclone/PreCloneWriter.java | 98 ++++++++++++++++++- ...ava => ITestCommandAssemblePreClones.java} | 90 ++++++++++------- .../java/com/milaboratory/mixcr/cli/Main.java | 2 +- .../com/milaboratory/mixcr/util/RunMiXCR.java | 7 +- 6 files changed, 236 insertions(+), 47 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java rename src/main/java/com/milaboratory/mixcr/cli/{CommandAssemblePreClones.java => ITestCommandAssemblePreClones.java} (62%) diff --git a/itests/case10.sh b/itests/case10.sh index d1245132d..45d20b94d 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -37,3 +37,5 @@ mixcr correctAndSortTags case10.aligned-vdjca case10.corrected-vdjca mixcr assemblePartial case10.corrected-vdjca case10.part-assembled-molecule-vdjca mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled-cell-vdjca +mixcr itestAssemblePreClones case10.part-assembled-molecule-vdjca case10.part-assembled-molecule-vdjca.pc +mixcr itestAssemblePreClones --cell-level case10.part-assembled-cell-vdjca case10.part-assembled-cell-vdjca.pc diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java new file mode 100644 index 000000000..98c4d7dd7 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java @@ -0,0 +1,84 @@ +package com.milaboratory.mixcr.assembler.preclone; + + +import cc.redberry.pipe.OutputPortCloseable; +import com.milaboratory.mixcr.basictypes.IOUtil; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.blocks.PrimitivIHeaderActions; +import com.milaboratory.primitivio.blocks.PrimitivIHybrid; +import io.repseq.core.VDJCGene; +import io.repseq.core.VDJCLibraryRegistry; + +import java.io.IOException; +import java.nio.file.Path; +import java.util.List; + +import static com.milaboratory.mixcr.assembler.preclone.PreCloneWriter.*; + +public final class PreCloneReader implements AutoCloseable { + private final PrimitivIHybrid input; + private final VDJCAlignerParameters alignmentParameters; + private final List usedGenes; + private final long alignmentsStartPosition, + assignedAlignmentsStartPosition, + clonesStartPosition; + + public PreCloneReader(Path file) throws IOException { + this.input = new PrimitivIHybrid(file, 4); + try (PrimitivI i = input.beginPrimitivI(true)) { + this.alignmentParameters = i.readObject(VDJCAlignerParameters.class); + this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, alignmentParameters, + VDJCLibraryRegistry.getDefault()); + } + try (PrimitivI i = input.beginRandomAccessPrimitivI(-8 * 3)) { + alignmentsStartPosition = i.readLong(); + assignedAlignmentsStartPosition = i.readLong(); + clonesStartPosition = i.readLong(); + } + } + + public VDJCAlignerParameters getAlignmentParameters() { + return alignmentParameters; + } + + public List getUsedGenes() { + return usedGenes; + } + + public OutputPortCloseable readAllAlignments() { + return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsStartPosition, + h -> h.getSpecialByte(0) == UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.skip() + : h.getSpecialByte(0) == ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error()); + } + + public OutputPortCloseable readUnassignedAlignments() { + return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsStartPosition, + h -> h.getSpecialByte(0) == UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error()); + } + + public OutputPortCloseable readAssignedAlignments() { + return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, assignedAlignmentsStartPosition, + h -> h.getSpecialByte(0) == ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error()); + } + + public OutputPortCloseable readClones() { + return input.beginRandomAccessPrimitivIBlocks(PreClone.class, clonesStartPosition, + h -> h.getSpecialByte(0) == CLONES_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error()); + } + + @Override + public void close() throws Exception { + input.close(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java index cd557ec6e..494ba1591 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java @@ -9,18 +9,35 @@ import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.primitivio.PrimitivIOStateBuilder; import com.milaboratory.primitivio.PrimitivO; +import com.milaboratory.primitivio.blocks.PrimitivIOBlockHeader; import com.milaboratory.primitivio.blocks.PrimitivOBlocks; import com.milaboratory.primitivio.blocks.PrimitivOHybrid; +import com.milaboratory.util.CanReportProgressAndStage; +import com.milaboratory.util.ProgressAndStage; import com.milaboratory.util.TempFileDest; import com.milaboratory.util.sorting.HashSorter; import java.io.IOException; import java.nio.file.Path; import java.util.concurrent.ForkJoinPool; +import java.util.concurrent.atomic.AtomicLong; import static com.milaboratory.mixcr.basictypes.FieldCollection.*; -public final class PreCloneWriter implements AutoCloseable { +public final class PreCloneWriter implements AutoCloseable, CanReportProgressAndStage { + // Headers marking special positions in file + public static final byte UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 = 1; + public static final byte ALIGNMENTS_END_MARK_BYTE_0 = 2; + public static final byte CLONES_END_MARK_BYTE_0 = 3; + public static final PrimitivIOBlockHeader UNASSIGNED_ALIGNMENTS_END_MARK = + PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0); + public static final PrimitivIOBlockHeader ALIGNMENTS_END_MARK = + PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, ALIGNMENTS_END_MARK_BYTE_0); + public static final PrimitivIOBlockHeader CLONES_END_MARK = + PrimitivIOBlockHeader.specialHeader().setSpecialByte(0, CLONES_END_MARK_BYTE_0); + + private final ProgressAndStage ps = new ProgressAndStage("Sorting alignments and clones"); + private final PrimitivOHybrid output; private final TempFileDest tempDest; @@ -32,6 +49,11 @@ public final class PreCloneWriter implements AutoCloseable { private final Buffer cloneBuffer; private final InputPort cloneSorterInput; + private final AtomicLong + numberOfAlignments = new AtomicLong(), + numberOfAssignedAlignments = new AtomicLong(), + numberOfClones = new AtomicLong(); + private volatile Thread alignmentSortingThread, cloneSortingThread; private volatile HashSorter alignmentCollator; private volatile OutputPortCloseable sortedAlignments; @@ -88,17 +110,21 @@ public void init(VDJCAlignmentsReader alignmentReader) { } public void putClone(PreClone clone) { + numberOfClones.incrementAndGet(); cloneSorterInput.put(clone); } public void putAlignment(VDJCAlignments alignment) { + numberOfAlignments.incrementAndGet(); if (alignment.getCloneIndex() == -1) alignmentWriter.write(alignment); - else + else { + numberOfAssignedAlignments.incrementAndGet(); alignmentSorterInput.put(alignment); + } } - public void finishWrite() { + public void finish() { alignmentSorterInput.put(null); cloneSorterInput.put(null); try { @@ -107,18 +133,25 @@ public void finishWrite() { } catch (InterruptedException e) { throw new RuntimeException(e); } + alignmentSortingThread = null; + cloneSortingThread = null; long assignedAlignmentsStartPosition; long alignmentsChecksum = 17; try (PrimitivOBlocks.Writer writer = alignmentWriter) { // Finishing block of not-assigned alignments writer.flush(); + writer.writeHeader(UNASSIGNED_ALIGNMENTS_END_MARK); writer.sync(); assignedAlignmentsStartPosition = writer.getPosition(); + ps.setStage("Writing alignments"); + ps.setProgress(0.0); + // resulting clone id generator long newCloneIdx = -1; long previousCloneIdx = -1; + long alignments = 0; for (VDJCAlignments al : CUtils.it(sortedAlignments)) { assert al.getCloneIndex() >= 0; @@ -132,25 +165,43 @@ public void finishWrite() { previousCloneIdx = al.getCloneIndex(); } writer.write(al.withCloneIndex(newCloneIdx)); + + alignments++; + ps.setProgress(1.0 * alignments / numberOfAssignedAlignments.get()); } + writer.flush(); + writer.writeHeader(ALIGNMENTS_END_MARK); + } finally { + sortedAlignments.close(); } + ps.setStage("Writing clones"); + ps.setProgress(0.0); long clonesStartPosition = output.getPosition(); long cloneChecksum = 17; + long clones = 0; try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { // resulting clone id generator long newCloneIdx = -1; for (PreClone preClone : CUtils.it(sortedClones)) { newCloneIdx++; + // preClone.id will be mapped to newCloneIdx cloneChecksum = cloneChecksum * 71 + preClone.id; cloneChecksum = cloneChecksum * 71 + newCloneIdx; writer.write(preClone.withId(newCloneIdx)); + clones++; + ps.setProgress(1.0 * clones / numberOfClones.get()); } + writer.flush(); + writer.writeHeader(CLONES_END_MARK); + } finally { + sortedClones.close(); } + // Important invariant that must always be true (assert) if (alignmentsChecksum != cloneChecksum) throw new IllegalStateException("Inconsistent sequences of clones and alignments."); @@ -159,10 +210,51 @@ public void finishWrite() { o.writeLong(assignedAlignmentsStartPosition); o.writeLong(clonesStartPosition); } + + ps.finish(); + } + + @Override + public double getProgress() { + return ps.getProgress(); + } + + @Override + public boolean isFinished() { + return ps.isFinished(); + } + + @Override + public String getStage() { + return ps.getStage(); } @Override public void close() throws Exception { + if (alignmentSortingThread != null) { + alignmentSorterInput.put(null); + try { + alignmentSortingThread.join(); + } catch (InterruptedException e) { + throw new RuntimeException(e); + } + } + + if (cloneSortingThread != null) { + cloneSorterInput.put(null); + try { + cloneSortingThread.join(); + } catch (InterruptedException e) { + throw new RuntimeException(e); + } + } + + if (sortedAlignments != null) + sortedAlignments.close(); + + if (sortedClones != null) + sortedClones.close(); + output.close(); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java similarity index 62% rename from src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java rename to src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index 38ef56e13..12ed0ed03 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -2,6 +2,7 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; +import cc.redberry.pipe.util.CountingOutputPort; import com.milaboratory.core.alignment.LinearGapAlignmentScoring; import com.milaboratory.mitool.consensus.AAssemblerParameters; import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; @@ -14,25 +15,28 @@ import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.util.ReportHelper; +import com.milaboratory.util.SmartProgressReporter; import com.milaboratory.util.TempFileManager; import io.repseq.core.GeneFeature; import kotlin.jvm.functions.Function1; -import picocli.CommandLine; import java.nio.file.Paths; import java.util.List; -import static picocli.CommandLine.Command; -import static picocli.CommandLine.Parameters; +import static picocli.CommandLine.*; -@Command(name = "assemblePreClones", +@Command(name = "itestAssemblePreClones", separator = " ", hidden = true) -public class CommandAssemblePreClones extends ACommandMiXCR { +public class ITestCommandAssemblePreClones extends ACommandMiXCR { @Parameters(arity = "2", description = "input_file output_file") public List files; - @CommandLine.Option(description = "Use system temp folder for temporary files, the output folder will be used if this option is omitted.", + @Option(description = "Overlap sequences on the cell level instead of UMIs for tagged data with molecular and cell barcodes", + names = {"--cell-level"}) + public boolean cellLevel = false; + + @Option(description = "Use system temp folder for temporary files, the output folder will be used if this option is omitted.", names = {"--use-system-temp"}) public boolean useSystemTemp = false; @@ -56,7 +60,8 @@ public class CommandAssemblePreClones extends ACommandMiXCR { @Override public void run0() throws Exception { - + long totalAlignments; + long totalClones = 0; try ( VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(files.get(0)); VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(files.get(0)); @@ -64,14 +69,11 @@ public void run0() throws Exception { VDJCAlignmentsReader reader3 = new VDJCAlignmentsReader(files.get(0)); PreCloneWriter writer = new PreCloneWriter(Paths.get(files.get(1)), TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp)) - // // - // PrintStream out = new PrintStream(new BufferedOutputStream( - // Files.newOutputStream(Paths.get(files.get(1))), 1 << 20)) ) { writer.init(reader1); TagsInfo tagsInfo = reader1.getTagsInfo(); - int depth = tagsInfo.getDepthFor(TagType.CellTag); + int depth = tagsInfo.getDepthFor(cellLevel ? TagType.CellTag : TagType.MoleculeTag); // int depth = tagsInfo.getDepthFor(TagType.MoleculeTag); if (tagsInfo.getSortingLevel() < depth) throwValidationException("Input file has insufficient sorting level"); @@ -80,45 +82,28 @@ public void run0() throws Exception { gAssemblerParams, reader1.getParameters(), new GeneFeature[]{GeneFeature.CDR3}, depth); + CountingOutputPort reader1c = new CountingOutputPort<>(reader1); PreCloneAssembler assembler = new PreCloneAssembler(params, - CUtils.wrap(reader1, VDJCAlignments::ensureKeyTags), + CUtils.wrap(reader1c, VDJCAlignments::ensureKeyTags), CUtils.wrap(reader2, VDJCAlignments::ensureKeyTags) ); Function1 gFunction = a -> a.getTagCount().asKeyPrefixOrError(depth); - OutputPort> alGroups = PipeKt.group(CUtils.wrap(reader3, - VDJCAlignments::ensureKeyTags), gFunction); + OutputPort> alGroups = PipeKt.group( + CUtils.wrap(reader3, VDJCAlignments::ensureKeyTags), gFunction); + + SmartProgressReporter.startProgressReport("Building pre-clones", reader1); - // TODO array? - // TIntLongHashMap alToCloneMapping = new TIntLongHashMap(Constants.DEFAULT_CAPACITY, - // Constants.DEFAULT_LOAD_FACTOR, -1, -1); - // long[] alToClone = null; PreCloneAssemblerResult result; while ((result = assembler.getForNextGroup()) != null) { GroupOP grp = alGroups.take(); List clones = result.getClones(); assert clones.isEmpty() || clones.get(0).coreKey.equals(grp.getKey()); + totalClones += clones.size(); - - for (PreClone clone : clones) { - // PreClone clone = cloneWA.preClone; - // TIntIterator it = cloneWA.alignments.iterator(); - // while (it.hasNext()) - // alToCloneMapping.put(it.next(), clone.id); - + for (PreClone clone : clones) writer.putClone(clone); - // out.println( - // clone.clonalSequence[0].getSequence().toString() + "\t" + - // cloneWA.alignments.size() + "\t" + - // clone.geneScores.get(GeneType.Variable) + "\t" + - // clone.geneScores.get(GeneType.Joining) + "\t" + - // clone.geneScores.get(GeneType.Constant) + "\t" + - // clone.coreTagCount + "\t" + - // clone.fullTagCount + "\t" + - // rIds); - } - int localId = 0; for (VDJCAlignments al : CUtils.it(grp)) { long cloneMapping = result.getCloneForAlignment(localId++); @@ -128,9 +113,40 @@ public void run0() throws Exception { } } - writer.finishWrite(); + totalAlignments = reader1c.getCount(); + + writer.finish(); assembler.getReport().writeReport(ReportHelper.STDOUT); } + + try (PreCloneReader reader = new PreCloneReader(Paths.get(files.get(1)))) { + long numberOfAlignmentsCheck = 0; + for (VDJCAlignments al : CUtils.it(reader.readAllAlignments())) + numberOfAlignmentsCheck++; + + if (numberOfAlignmentsCheck != totalAlignments) { + throwExecutionException("numberOfAlignmentsCheck != totalAlignments (" + + numberOfAlignmentsCheck + " != " + totalAlignments + ")"); + } + + for (VDJCAlignments al : CUtils.it(reader.readAssignedAlignments())) + numberOfAlignmentsCheck--; + + for (VDJCAlignments al : CUtils.it(reader.readUnassignedAlignments())) + numberOfAlignmentsCheck--; + + if (numberOfAlignmentsCheck != 0) + throwExecutionException("numberOfAlignmentsCheck != 0 (" + + numberOfAlignmentsCheck + " != 0)"); + + long numberOfClonesCheck = 0; + for (PreClone c : CUtils.it(reader.readClones())) + numberOfClonesCheck++; + + if (numberOfClonesCheck != totalClones) + throwExecutionException("numberOfClonesCheck != totalClones (" + + numberOfClonesCheck + " != " + totalClones + ")"); + } } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 502bf8b62..f73df76d3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -265,7 +265,7 @@ public static CommandLine mkCmd() { .addSubcommand("alignmentsDiff", CommandAlignmentsDiff.class) .addSubcommand("clonesDiff", CommandClonesDiff.class) - .addSubcommand("assemblePreClones", CommandAssemblePreClones.class) + .addSubcommand("itestAssemblePreClones", ITestCommandAssemblePreClones.class) .addSubcommand("alignmentsStat", CommandAlignmentsStats.class) .addSubcommand("listLibraries", CommandListLibraries.class) diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 93de50d80..4dcaf956b 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -225,12 +225,7 @@ public static AlignResult align(RunMiXCRAnalysis parameters) throws Exception { OutputPort alignments = unchunked(new ParallelProcessor(mainInputReads, chunked(aligner), parameters.threads)); List als = new ArrayList<>(); int ind = 0; - for (VDJCAlignmentResult t : CUtils.it(new OrderedOutputPort<>(alignments, new Indexer() { - @Override - public long getIndex(VDJCAlignmentResult r) { - return r.read.getId(); - } - }))) { + for (VDJCAlignmentResult t : CUtils.it(new OrderedOutputPort<>(alignments, r -> r.read.getId()))) { if (t.alignment != null) { t.alignment.setAlignmentsIndex(ind++); als.add(t.alignment); From f55a7e04d28b205292ad4196e87186e48d2a2474 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 2 Jun 2022 16:22:15 +0300 Subject: [PATCH 253/282] feat: secondary reader creation in VDJCAAlignmentReader --- .../basictypes/VDJCAlignmentsReader.java | 55 ++++++- .../mixcr/cli/CommandCorrectAndSortTags.java | 155 ++++++++---------- .../cli/ITestCommandAssemblePreClones.java | 7 +- 3 files changed, 123 insertions(+), 94 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index fed9d921d..03f29b760 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -50,6 +50,7 @@ import java.util.List; import java.util.concurrent.ExecutorService; import java.util.concurrent.ForkJoinPool; +import java.util.concurrent.atomic.AtomicLong; import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.*; @@ -64,6 +65,8 @@ public final class VDJCAlignmentsReader extends PipelineConfigurationReaderMiXCR final int readAheadBlocks; final VDJCLibraryRegistry vdjcRegistry; + /** Start position of the payload in the input file, used to create secondary readers */ + long alignmentsBegin; PrimitivIBlocks.Reader reader; VDJCAlignerParameters parameters; @@ -162,7 +165,10 @@ public void ensureInitialized() { this.iState = i.getState(); } - this.reader = input.beginPrimitivIBlocks(VDJCAlignments.class, readAheadBlocks); + // Saving alignments begin position + alignmentsBegin = input.getPosition(); + + this.reader = input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsBegin, readAheadBlocks); } public PrimitivIBlocksStats getStats() { @@ -219,6 +225,10 @@ public PrimitivIState getIState() { return iState; } + public long getNumberOfAlignments() { + return numberOfAlignments; + } + public long getNumberOfReads() { return numberOfReads; } @@ -265,10 +275,51 @@ public synchronized VDJCAlignments take() { VDJCAlignments al = reader.take(); if (al == null) { - close(true); + // close(true); return null; } return al.setAlignmentsIndex(counter++); } + + public SecondaryReader createSecondaryReader() { + ensureInitialized(); + return new SecondaryReader(); + } + + public class SecondaryReader implements OutputPortCloseable, CanReportProgress { + private volatile boolean closed = false; + private final AtomicLong alignmentsServed = new AtomicLong(); + private final PrimitivIBlocks.Reader reader; + + private SecondaryReader() { + this.reader = input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsBegin); + } + + @Override + public double getProgress() { + return 1.0 * alignmentsServed.get() / numberOfAlignments; + } + + @Override + public boolean isFinished() { + return closed; + } + + @Override + public VDJCAlignments take() { + VDJCAlignments al = reader.take(); + if (al != null) + alignmentsServed.incrementAndGet(); + else + closed = true; + return al; + } + + @Override + public synchronized void close() { + reader.close(); + closed = true; + } + } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index cc6cdaa75..9b5d09c7f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -108,8 +108,8 @@ public void run1() throws Exception { final CorrectionReport report; final int[] targetTagIndices; final List tagNames; - try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in)) { - TagsInfo tagsInfo = reader.getTagsInfo(); + try (VDJCAlignmentsReader mainReader = new VDJCAlignmentsReader(in)) { + TagsInfo tagsInfo = mainReader.getTagsInfo(); tagNames = new ArrayList<>(); TIntArrayList indicesBuilder = new TIntArrayList(); @@ -142,103 +142,80 @@ public void run1() throws Exception { tags[i] = ((SequenceAndQualityTagValue) tagTuple.get(targetTagIndices[i])).data; return tags; }; - OutputPort cInput = CUtils.wrap(reader, mapper); - correctionResult = corrector.correct(cInput, tagNames, reader); + OutputPort cInput = CUtils.wrap(mainReader, mapper); + correctionResult = corrector.correct(cInput, tagNames, mainReader); report = corrector.getReport(); } else { correctionResult = null; report = null; } - } - // ToIntFunction hashFunction = al -> { - // TagValue[] tags = al.getTagCounter().keys().iterator().next().tags; - // //noinspection UnstableApiUsage - // Hasher hasher = Hashing.murmur3_32_fixed().newHasher(); - // for (int i : targetTagIndices) - // //noinspection UnstableApiUsage - // hasher.putInt(((SequenceAndQualityTagValue) tags[i]).data.getSequence().hashCode()); - // //noinspection UnstableApiUsage - // return hasher.hash().hashCode(); - // }; - // - // Comparator comparator = (al1, al2) -> { - // TagValue[] tags1 = al1.getTagCounter().keys().iterator().next().tags; - // TagValue[] tags2 = al2.getTagCounter().keys().iterator().next().tags; - // int c; - // for (int i : targetTagIndices) - // if ((c = ((SequenceAndQualityTagValue) tags1[i]).data.getSequence().compareTo( - // ((SequenceAndQualityTagValue) tags2[i]).data.getSequence())) != 0) - // return c; - // return 0; - // }; - - - try ( - VDJCAlignmentsReader reader = new VDJCAlignmentsReader(in); - VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out) - ) { - PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); - IOUtil.registerGeneReferences(stateBuilder, reader.getUsedGenes(), reader.getParameters()); - - IntFunction> hashSorterFactory = tagIdx -> { - SortingStep sortingStep = new SortingStep(tagIdx); - return new HashSorter<>( - VDJCAlignments.class, - sortingStep.getHashFunction(), sortingStep.getComparator(), - 4, tempDest.addSuffix("hashsorter." + tagIdx), - 4, 4, - stateBuilder.getOState(), stateBuilder.getIState(), - memoryBudget, 10000 - ); - }; + try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { + VDJCAlignmentsReader.SecondaryReader secondaryReader = mainReader.createSecondaryReader(); + + PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); + IOUtil.registerGeneReferences(stateBuilder, mainReader.getUsedGenes(), mainReader.getParameters()); + + IntFunction> hashSorterFactory = tagIdx -> { + SortingStep sortingStep = new SortingStep(tagIdx); + return new HashSorter<>( + VDJCAlignments.class, + sortingStep.getHashFunction(), sortingStep.getComparator(), + 4, tempDest.addSuffix("hashsorter." + tagIdx), + 4, 4, + stateBuilder.getOState(), stateBuilder.getIState(), + memoryBudget, 10000 + ); + }; - HashSorter initialHashSorter = hashSorterFactory.apply(targetTagIndices[targetTagIndices.length - 1]); - - SmartProgressReporter.startProgressReport(!noCorrect - ? "Applying correction & sorting alignments by " + tagNames.get(targetTagIndices.length - 1) - : "Sorting alignments by " + tagNames.get(targetTagIndices.length - 1), - reader); - - Processor mapper = !noCorrect - ? - al -> { - TagValue[] newTags = al.getTagCount().getSingletonTuple().asArray(); - CorrectionNode cn = correctionResult; - for (int i : targetTagIndices) { - NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); - cn = cn.getNextLevel().get(current); - if (cn == null) { - report.setFilteredRecords(report.getFilteredRecords() + 1); - return al.setTagCount(null); // will be filtered right before hash sorter + HashSorter initialHashSorter = hashSorterFactory.apply(targetTagIndices[targetTagIndices.length - 1]); + + SmartProgressReporter.startProgressReport(!noCorrect + ? "Applying correction & sorting alignments by " + tagNames.get(targetTagIndices.length - 1) + : "Sorting alignments by " + tagNames.get(targetTagIndices.length - 1), + secondaryReader); + + Processor mapper = !noCorrect + ? + al -> { + TagValue[] newTags = al.getTagCount().getSingletonTuple().asArray(); + CorrectionNode cn = correctionResult; + for (int i : targetTagIndices) { + NucleotideSequence current = ((SequenceAndQualityTagValue) newTags[i]).data.getSequence(); + cn = cn.getNextLevel().get(current); + if (cn == null) { + report.setFilteredRecords(report.getFilteredRecords() + 1); + return al.setTagCount(null); // will be filtered right before hash sorter + } + newTags[i] = new SequenceAndQualityTagValue(cn.getCorrectValue()); } - newTags[i] = new SequenceAndQualityTagValue(cn.getCorrectValue()); + return al.setTagCount(new TagCount(new TagTuple(newTags))); } - return al.setTagCount(new TagCount(new TagTuple(newTags))); - } - : al -> al; - - // Creating output port with corrected and filtered tags - OutputPort hsInput = new FilteringPort<>( - CUtils.wrap(reader, mapper), al -> al.getTagCount() != null); - - // Running initial hash sorter - CountingOutputPort sorted = new CountingOutputPort<>(initialHashSorter.port(hsInput)); - - // Sorting by other tags - for (int tagIdxIdx = targetTagIndices.length - 2; tagIdxIdx >= 0; tagIdxIdx--) { - SmartProgressReporter.startProgressReport("Sorting alignments by " + tagNames.get(tagIdxIdx), - SmartProgressReporter.extractProgress(sorted, reader.getNumberOfReads())); - sorted = new CountingOutputPort<>(hashSorterFactory.apply(targetTagIndices[tagIdxIdx]).port(sorted)); + : al -> al; + + // Creating output port with corrected and filtered tags + OutputPort hsInput = new FilteringPort<>( + CUtils.wrap(secondaryReader, mapper), al -> al.getTagCount() != null); + + // Running initial hash sorter + CountingOutputPort sorted = new CountingOutputPort<>(initialHashSorter.port(hsInput)); + + // Sorting by other tags + for (int tagIdxIdx = targetTagIndices.length - 2; tagIdxIdx >= 0; tagIdxIdx--) { + SmartProgressReporter.startProgressReport("Sorting alignments by " + tagNames.get(tagIdxIdx), + SmartProgressReporter.extractProgress(sorted, mainReader.getNumberOfAlignments())); + sorted = new CountingOutputPort<>(hashSorterFactory.apply(targetTagIndices[tagIdxIdx]).port(sorted)); + } + + SmartProgressReporter.startProgressReport("Writing result", + SmartProgressReporter.extractProgress(sorted, mainReader.getNumberOfAlignments())); + + // Initializing and writing results to the output file + writer.header(mainReader, getFullPipelineConfiguration(), + mainReader.getTagsInfo().setSorted(mainReader.getTagsInfo().tags.length)); + for (VDJCAlignments al : CUtils.it(sorted)) + writer.write(al); } - - SmartProgressReporter.startProgressReport("Writing result", - SmartProgressReporter.extractProgress(sorted, reader.getNumberOfReads())); - - // Initializing and writing results to the output file - writer.header(reader, getFullPipelineConfiguration(), reader.getTagsInfo().setSorted(reader.getTagsInfo().tags.length)); - for (VDJCAlignments al : CUtils.it(sorted)) - writer.write(al); } if (report != null) diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index 12ed0ed03..154d4e69a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -64,12 +64,13 @@ public void run0() throws Exception { long totalClones = 0; try ( VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(files.get(0)); - VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(files.get(0)); - // For export - VDJCAlignmentsReader reader3 = new VDJCAlignmentsReader(files.get(0)); PreCloneWriter writer = new PreCloneWriter(Paths.get(files.get(1)), TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp)) ) { + VDJCAlignmentsReader.SecondaryReader reader2 = reader1.createSecondaryReader(); + // For export + VDJCAlignmentsReader.SecondaryReader reader3 = reader1.createSecondaryReader(); + writer.init(reader1); TagsInfo tagsInfo = reader1.getTagsInfo(); From ec3499adcc0b1aee0a2b5d770be68235f613643a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 2 Jun 2022 18:13:02 +0300 Subject: [PATCH 254/282] WIP --- .../preclone/FilePreCloneReader.java | 96 +++++++++++ ...oneWriter.java => FilePreCloneWriter.java} | 7 +- .../mixcr/assembler/preclone/PreClone.java | 28 ++- .../assembler/preclone/PreCloneReader.java | 160 ++++++++++-------- .../mixcr/basictypes/CloneSetOverlap.java | 6 +- .../basictypes/VDJCAlignmentsReader.java | 60 +++++-- .../cli/ITestCommandAssemblePreClones.java | 8 +- .../mixcr/postanalysis/Dataset.java | 2 +- .../mixcr/postanalysis/SetPreprocessor.java | 4 +- .../postanalysis/overlap/OverlapUtil.java | 4 +- .../mixcr/util/OutputPortWithProgress.java | 47 ++++- .../overlap/OverlapCharacteristicTest.java | 2 +- 12 files changed, 318 insertions(+), 106 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java rename src/main/java/com/milaboratory/mixcr/assembler/preclone/{PreCloneWriter.java => FilePreCloneWriter.java} (96%) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java new file mode 100644 index 000000000..16d56f0fe --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java @@ -0,0 +1,96 @@ +package com.milaboratory.mixcr.assembler.preclone; + + +import com.milaboratory.mixcr.basictypes.IOUtil; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.util.OutputPortWithProgress; +import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; +import com.milaboratory.primitivio.PrimitivI; +import com.milaboratory.primitivio.blocks.PrimitivIHeaderActions; +import com.milaboratory.primitivio.blocks.PrimitivIHybrid; +import io.repseq.core.VDJCGene; +import io.repseq.core.VDJCLibraryRegistry; + +import java.io.IOException; +import java.nio.file.Path; +import java.util.List; + +import static com.milaboratory.mixcr.assembler.preclone.FilePreCloneWriter.*; + +public final class FilePreCloneReader implements PreCloneReader, AutoCloseable { + private final PrimitivIHybrid input; + private final VDJCAlignerParameters alignmentParameters; + private final List usedGenes; + private final long alignmentsStartPosition, + assignedAlignmentsStartPosition, + clonesStartPosition, + numberOfAlignments, + numberOfAssignedAlignments, + numberOfClones; + + public FilePreCloneReader(Path file) throws IOException { + this.input = new PrimitivIHybrid(file, 4); + try (PrimitivI i = input.beginPrimitivI(true)) { + this.alignmentParameters = i.readObject(VDJCAlignerParameters.class); + this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, alignmentParameters, + VDJCLibraryRegistry.getDefault()); + } + try (PrimitivI i = input.beginRandomAccessPrimitivI(-8 * 3)) { + alignmentsStartPosition = i.readLong(); + assignedAlignmentsStartPosition = i.readLong(); + clonesStartPosition = i.readLong(); + numberOfAlignments = i.readLong(); + numberOfAssignedAlignments = i.readLong(); + numberOfClones = i.readLong(); + } + } + + public VDJCAlignerParameters getAlignmentParameters() { + return alignmentParameters; + } + + public List getUsedGenes() { + return usedGenes; + } + + public OutputPortWithProgress readUnassignedAlignments() { + return OutputPortWithProgress.wrap(numberOfAlignments - numberOfAssignedAlignments, + input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsStartPosition, + h -> h.getSpecialByte(0) == UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error())); + } + + public OutputPortWithProgress readAssignedAlignments() { + return OutputPortWithProgress.wrap(numberOfAssignedAlignments, + input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, assignedAlignmentsStartPosition, + h -> h.getSpecialByte(0) == ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error())); + } + + @Override + public OutputPortWithProgress readAlignments() { + return OutputPortWithProgress.wrap(numberOfAlignments, + input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsStartPosition, + h -> h.getSpecialByte(0) == UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.skip() + : h.getSpecialByte(0) == ALIGNMENTS_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error())); + } + + @Override + public OutputPortWithProgress readPreClones() { + return OutputPortWithProgress.wrap(numberOfClones, + input.beginRandomAccessPrimitivIBlocks(PreClone.class, clonesStartPosition, + h -> h.getSpecialByte(0) == CLONES_END_MARK_BYTE_0 + ? PrimitivIHeaderActions.stopReading() + : PrimitivIHeaderActions.error())); + } + + @Override + public void close() throws Exception { + input.close(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java similarity index 96% rename from src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java rename to src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java index 494ba1591..764f2dc45 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java @@ -24,7 +24,7 @@ import static com.milaboratory.mixcr.basictypes.FieldCollection.*; -public final class PreCloneWriter implements AutoCloseable, CanReportProgressAndStage { +public final class FilePreCloneWriter implements AutoCloseable, CanReportProgressAndStage { // Headers marking special positions in file public static final byte UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 = 1; public static final byte ALIGNMENTS_END_MARK_BYTE_0 = 2; @@ -60,7 +60,7 @@ public final class PreCloneWriter implements AutoCloseable, CanReportProgressAnd private volatile HashSorter cloneCollator; private volatile OutputPortCloseable sortedClones; - public PreCloneWriter(Path file, TempFileDest tempDest) throws IOException { + public FilePreCloneWriter(Path file, TempFileDest tempDest) throws IOException { this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file); this.tempDest = tempDest; this.alignmentBuffer = new Buffer<>(1 << 14); @@ -209,6 +209,9 @@ public void finish() { o.writeLong(alignmentsStartPosition); o.writeLong(assignedAlignmentsStartPosition); o.writeLong(clonesStartPosition); + o.writeLong(numberOfAlignments.get()); + o.writeLong(numberOfAssignedAlignments.get()); + o.writeLong(numberOfClones.get()); } ps.finish(); diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index b6d0bf551..45cdf50f3 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -2,13 +2,15 @@ import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mixcr.basictypes.GeneAndScore; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.primitivio.annotations.Serializable; +import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; -import java.util.List; -import java.util.Map; +import java.util.*; @Serializable(by = IO.PreCloneSerializer.class) public final class PreClone { @@ -43,4 +45,26 @@ public long getId() { public PreClone withId(long id) { return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores); } + + /** Converts alignment to a pre-clone, given the clonal gene features (features to align) */ + public static PreClone fromAlignment(long id, VDJCAlignments alignment, GeneFeature... geneFeatures) { + NSequenceWithQuality[] clonalSequences = new NSequenceWithQuality[geneFeatures.length]; + + for (int i = 0; i < geneFeatures.length; i++) + clonalSequences[i] = Objects.requireNonNull(alignment.getFeature(geneFeatures[i])); + + Map> geneScores = new EnumMap<>(GeneType.class); + EnumMap hitsMap = alignment.getHitsMap(); + for (GeneType gt : GeneType.VDJC_REFERENCE) { + VDJCHit[] hits = hitsMap.get(gt); + List gss = new ArrayList<>(hits.length); + for (int i = 0; i < hits.length; i++) { + VDJCHit hit = hits[i]; + gss.add(new GeneAndScore(hit.getGene().getId(), hit.getScore())); + } + geneScores.put(gt, gss); + } + return new PreClone(id, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), + clonalSequences, geneScores); + } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java index 98c4d7dd7..b4f852b1f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java @@ -1,84 +1,108 @@ package com.milaboratory.mixcr.assembler.preclone; - -import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.mixcr.basictypes.IOUtil; import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; -import com.milaboratory.primitivio.PrimitivI; -import com.milaboratory.primitivio.blocks.PrimitivIHeaderActions; -import com.milaboratory.primitivio.blocks.PrimitivIHybrid; -import io.repseq.core.VDJCGene; -import io.repseq.core.VDJCLibraryRegistry; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.util.OutputPortWithProgress; +import io.repseq.core.GeneFeature; -import java.io.IOException; -import java.nio.file.Path; -import java.util.List; +import java.util.concurrent.atomic.AtomicLong; -import static com.milaboratory.mixcr.assembler.preclone.PreCloneWriter.*; +public interface PreCloneReader { + /** Creates streamed pre-clone reader. */ + OutputPortWithProgress readPreClones(); -public final class PreCloneReader implements AutoCloseable { - private final PrimitivIHybrid input; - private final VDJCAlignerParameters alignmentParameters; - private final List usedGenes; - private final long alignmentsStartPosition, - assignedAlignmentsStartPosition, - clonesStartPosition; + /** + * Creates streamed alignments reader. + * Must output at least one alignment assigned for each of the pre-clones returned by a pre-clone reader. + * Alignments must be ordered the same way as pre-clones. + * Must output all unassigned alignments before all assigned. + */ + OutputPortWithProgress readAlignments(); - public PreCloneReader(Path file) throws IOException { - this.input = new PrimitivIHybrid(file, 4); - try (PrimitivI i = input.beginPrimitivI(true)) { - this.alignmentParameters = i.readObject(VDJCAlignerParameters.class); - this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, alignmentParameters, - VDJCLibraryRegistry.getDefault()); - } - try (PrimitivI i = input.beginRandomAccessPrimitivI(-8 * 3)) { - alignmentsStartPosition = i.readLong(); - assignedAlignmentsStartPosition = i.readLong(); - clonesStartPosition = i.readLong(); - } - } + static PreCloneReader fromAlignments(VDJCAlignmentsReader alignmentsReader, GeneFeature[] geneFeatures) { + return new PreCloneReader() { + private boolean alignmentPredicate(VDJCAlignments al) { + for (GeneFeature geneFeature : geneFeatures) + if (!al.isAvailable(geneFeature)) + return false; + return true; + } - public VDJCAlignerParameters getAlignmentParameters() { - return alignmentParameters; - } + @Override + public OutputPortWithProgress readPreClones() { + //noinspection resource + OutputPortWithProgress alignmentReader = readAlignments(); + return new OutputPortWithProgress() { + @Override + public long currentIndex() { + return alignmentReader.currentIndex(); + } - public List getUsedGenes() { - return usedGenes; - } + @Override + public void close() { + alignmentReader.close(); + } - public OutputPortCloseable readAllAlignments() { - return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsStartPosition, - h -> h.getSpecialByte(0) == UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 - ? PrimitivIHeaderActions.skip() - : h.getSpecialByte(0) == ALIGNMENTS_END_MARK_BYTE_0 - ? PrimitivIHeaderActions.stopReading() - : PrimitivIHeaderActions.error()); - } + @Override + public PreClone take() { + VDJCAlignments al = alignmentReader.take(); + if (al == null) + return null; + return PreClone.fromAlignment(al.getAlignmentsIndex(), al, geneFeatures); + } - public OutputPortCloseable readUnassignedAlignments() { - return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsStartPosition, - h -> h.getSpecialByte(0) == UNASSIGNED_ALIGNMENTS_END_MARK_BYTE_0 - ? PrimitivIHeaderActions.stopReading() - : PrimitivIHeaderActions.error()); - } + @Override + public double getProgress() { + return alignmentReader.getProgress(); + } - public OutputPortCloseable readAssignedAlignments() { - return input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, assignedAlignmentsStartPosition, - h -> h.getSpecialByte(0) == ALIGNMENTS_END_MARK_BYTE_0 - ? PrimitivIHeaderActions.stopReading() - : PrimitivIHeaderActions.error()); - } + @Override + public boolean isFinished() { + return alignmentReader.isFinished(); + } + }; + } - public OutputPortCloseable readClones() { - return input.beginRandomAccessPrimitivIBlocks(PreClone.class, clonesStartPosition, - h -> h.getSpecialByte(0) == CLONES_END_MARK_BYTE_0 - ? PrimitivIHeaderActions.stopReading() - : PrimitivIHeaderActions.error()); - } + @Override + public OutputPortWithProgress readAlignments() { + Object sync = new Object(); + AtomicLong idGenerator = new AtomicLong(); + VDJCAlignmentsReader.SecondaryReader reader = alignmentsReader.createRawSecondaryReader(); + return new OutputPortWithProgress() { + @Override + public long currentIndex() { + return reader.currentIndex(); + } + + @Override + public void close() { + reader.close(); + } + + @Override + public VDJCAlignments take() { + synchronized (sync) { + VDJCAlignments al; + //noinspection StatementWithEmptyBody + while ((al = reader.take()) != null && !alignmentPredicate(al)) ; + if (al == null) + return null; + long id = idGenerator.getAndIncrement(); + return al.withCloneIndexAndMappingType(id, (byte) 0).setAlignmentsIndex(id); + } + } + + @Override + public double getProgress() { + return reader.getProgress(); + } - @Override - public void close() throws Exception { - input.close(); + @Override + public boolean isFinished() { + return reader.isFinished(); + } + }; + } + }; } } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java index bcdcaf469..98952dfa7 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java @@ -90,7 +90,7 @@ public static OutputPortWithProgress>> overlap( AtomicLong index = new AtomicLong(0); return new OutputPortWithProgress>>() { @Override - public long index() { + public long currentIndex() { return index.get(); } @@ -127,7 +127,7 @@ public boolean isFinished() { long totalClones = readers.stream().mapToLong(CloneReader::numberOfClones).sum(); return new OutputPortWithProgress>>() { @Override - public long index() { + public long currentIndex() { return index.get(); } @@ -149,7 +149,7 @@ public List> take() { @Override public double getProgress() { - return 1.0 * individualPorts.stream().mapToLong(OutputPortWithProgress::index).sum() / totalClones; + return 1.0 * individualPorts.stream().mapToLong(OutputPortWithProgress::currentIndex).sum() / totalClones; } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index 03f29b760..ca113c374 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -32,6 +32,7 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivIState; @@ -284,42 +285,67 @@ public synchronized VDJCAlignments take() { public SecondaryReader createSecondaryReader() { ensureInitialized(); - return new SecondaryReader(); + return new SecondaryReader(false); } - public class SecondaryReader implements OutputPortCloseable, CanReportProgress { - private volatile boolean closed = false; - private final AtomicLong alignmentsServed = new AtomicLong(); + public SecondaryReader createRawSecondaryReader() { + ensureInitialized(); + return new SecondaryReader(true); + } + + public class SecondaryReader implements OutputPortWithProgress { + private final boolean raw; + private final Object sync = new Object(); + private volatile boolean finished = false; + private final AtomicLong counter = new AtomicLong(); private final PrimitivIBlocks.Reader reader; - private SecondaryReader() { + private SecondaryReader(boolean raw) { + this.raw = raw; this.reader = input.beginRandomAccessPrimitivIBlocks(VDJCAlignments.class, alignmentsBegin); } @Override - public double getProgress() { - return 1.0 * alignmentsServed.get() / numberOfAlignments; + public VDJCAlignments take() { + if (raw) { + VDJCAlignments al = reader.take(); + if (al == null) { + finished = true; + return null; + } + counter.incrementAndGet(); + return al; + } else { + synchronized (sync) { + VDJCAlignments al = reader.take(); + if (al == null) { + finished = true; + return null; + } + return al.setAlignmentsIndex(counter.getAndIncrement()); + } + } } @Override - public boolean isFinished() { - return closed; + public long currentIndex() { + return counter.get(); } @Override - public VDJCAlignments take() { - VDJCAlignments al = reader.take(); - if (al != null) - alignmentsServed.incrementAndGet(); - else - closed = true; - return al; + public double getProgress() { + return 1.0 * counter.get() / numberOfAlignments; + } + + @Override + public boolean isFinished() { + return finished; } @Override public synchronized void close() { reader.close(); - closed = true; + finished = true; } } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index 154d4e69a..1ef96c16e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -64,7 +64,7 @@ public void run0() throws Exception { long totalClones = 0; try ( VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(files.get(0)); - PreCloneWriter writer = new PreCloneWriter(Paths.get(files.get(1)), + FilePreCloneWriter writer = new FilePreCloneWriter(Paths.get(files.get(1)), TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp)) ) { VDJCAlignmentsReader.SecondaryReader reader2 = reader1.createSecondaryReader(); @@ -121,9 +121,9 @@ public void run0() throws Exception { assembler.getReport().writeReport(ReportHelper.STDOUT); } - try (PreCloneReader reader = new PreCloneReader(Paths.get(files.get(1)))) { + try (FilePreCloneReader reader = new FilePreCloneReader(Paths.get(files.get(1)))) { long numberOfAlignmentsCheck = 0; - for (VDJCAlignments al : CUtils.it(reader.readAllAlignments())) + for (VDJCAlignments al : CUtils.it(reader.readAlignments())) numberOfAlignmentsCheck++; if (numberOfAlignmentsCheck != totalAlignments) { @@ -142,7 +142,7 @@ public void run0() throws Exception { numberOfAlignmentsCheck + " != 0)"); long numberOfClonesCheck = 0; - for (PreClone c : CUtils.it(reader.readClones())) + for (PreClone c : CUtils.it(reader.readPreClones())) numberOfClonesCheck++; if (numberOfClonesCheck != totalClones) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java index 6b97b9eb1..f74cd7b0f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java @@ -27,7 +27,7 @@ public String id() { public OutputPortWithProgress mkElementsPort() { return new OutputPortWithProgress() { @Override - public long index() { + public long currentIndex() { return 0; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index 62522b28f..2571ec307 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -62,8 +62,8 @@ public boolean isFinished() { } @Override - public long index() { - return inner.index(); + public long currentIndex() { + return inner.currentIndex(); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java index 1438e4488..aff19d73a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java @@ -67,8 +67,8 @@ public OutputPortWithProgress> mkElementsPort() { SimpleProcessorWrapper>, OverlapGroup> processor = new SimpleProcessorWrapper<>(port, OverlapGroup::new); return new OutputPortWithProgress>() { @Override - public long index() { - return port.index(); + public long currentIndex() { + return port.currentIndex(); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java index 3e873e4eb..4f1b71044 100644 --- a/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java +++ b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java @@ -10,14 +10,14 @@ public interface OutputPortWithProgress extends OutputPortCloseable, CanRe /** * @return number of returned elemens so far */ - long index(); + long currentIndex(); - static OutputPortWithProgress wrap(int size, OutputPortCloseable inner) { + static OutputPortWithProgress wrap(CanReportProgress progressReporter, OutputPortCloseable inner) { final AtomicBoolean isFinished = new AtomicBoolean(false); final AtomicLong index = new AtomicLong(0); return new OutputPortWithProgress() { @Override - public long index() { + public long currentIndex() { return index.get(); } @@ -34,7 +34,45 @@ public T take() { @Override public double getProgress() { - return (index.get() + 1.0) / size; + return progressReporter.getProgress(); + } + + @Override + public boolean isFinished() { + return isFinished.get() || progressReporter.isFinished(); + } + + @Override + public void close() { + isFinished.set(true); + inner.close(); + } + }; + } + + static OutputPortWithProgress wrap(long expectedSize, OutputPortCloseable inner) { + final AtomicBoolean isFinished = new AtomicBoolean(false); + final AtomicLong index = new AtomicLong(0); + return new OutputPortWithProgress() { + @Override + public long currentIndex() { + return index.get(); + } + + @Override + public T take() { + T t = inner.take(); + if (t == null) { + isFinished.set(true); + return null; + } + index.incrementAndGet(); + return t; + } + + @Override + public double getProgress() { + return 1.0 * index.get() / expectedSize; } @Override @@ -44,6 +82,7 @@ public boolean isFinished() { @Override public void close() { + isFinished.set(true); inner.close(); } }; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java index 672420db2..ad5d881f0 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -141,7 +141,7 @@ public OutputPortWithProgress> mkElementsPort() { return new OutputPortWithProgress>() { @Override - public long index() { + public long currentIndex() { return 0; } From 354d81ade2e072c05578b79db5768c387cdf78ca Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 3 Jun 2022 02:02:59 +0200 Subject: [PATCH 255/282] Update miplots --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 73b6b348f..6f84f55af 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -80,7 +80,7 @@ repositories { val milibVersion = "1.15.0-51-master" val repseqioVersion = "1.3.5-33-master" -val miplotsVersion = "0.1-22-master" +val miplotsVersion = "0.1-23-master" val jacksonBomVersion = "2.13.3" dependencies { From 3e081ddb2a2f870b123c1db7dfd0d50bf530b9a6 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Sat, 4 Jun 2022 23:21:37 +0200 Subject: [PATCH 256/282] More plotting options for basic statistics --- build.gradle.kts | 2 +- .../CommandPaExportPlotsBasicStatistics.java | 11 +-- .../postanalysis/plots/BasicStatistics.kt | 89 ++++++------------- 3 files changed, 35 insertions(+), 67 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 6f84f55af..906bb0a71 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -80,7 +80,7 @@ repositories { val milibVersion = "1.15.0-51-master" val repseqioVersion = "1.3.5-33-master" -val miplotsVersion = "0.1-23-master" +val miplotsVersion = "0.1-26-master" val jacksonBomVersion = "2.13.3" dependencies { diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index eecd5ae85..3d3ef8e24 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.cli.postanalysis; +import com.milaboratory.miplots.StandardPlots.PlotType; import com.milaboratory.miplots.stat.util.PValueCorrection; import com.milaboratory.miplots.stat.util.RefGroup; import com.milaboratory.miplots.stat.util.TestMethod; @@ -8,7 +9,6 @@ import com.milaboratory.mixcr.postanalysis.PostanalysisResult; import com.milaboratory.mixcr.postanalysis.plots.BasicStatRow; import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics; -import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics.PlotType; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual; import org.jetbrains.kotlinx.dataframe.DataFrame; @@ -19,7 +19,10 @@ import java.util.Objects; public abstract class CommandPaExportPlotsBasicStatistics extends CommandPaExportPlots { - @Option(description = "Plot type. Possible values: auto, boxplot, barplot, dotplot, lineplot, scatter.", + @Option(description = "Plot type. Possible values: boxplot, boxplot-bindot, boxplot-jitter, " + + "lineplot, lineplot-bindot, lineplot-jitter, " + + "violin, violin-bindot, barplot, barplot-stacked, " + + "scatter", names = {"--plot-type"}) public String plotType; @@ -92,9 +95,7 @@ void run(PaResultByGroup result) { else if (refGroup != null) rg = RefGroup.Companion.of(refGroup); - PlotType plotType = this.plotType == null - ? PlotType.Auto - : PlotType.Companion.parse(this.plotType); + PlotType plotType = BasicStatistics.INSTANCE.parsePlotType(this.plotType); BasicStatistics.PlotParameters par = new BasicStatistics.PlotParameters( plotType, diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt index b8e5150f5..4e34eeac9 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt @@ -1,5 +1,8 @@ package com.milaboratory.mixcr.postanalysis.plots +import com.milaboratory.miplots.StandardPlots.PlotType +import com.milaboratory.miplots.StandardPlots.PlotType.BoxPlot +import com.milaboratory.miplots.StandardPlots.PlotType.Scatter import com.milaboratory.miplots.stat.util.PValueCorrection import com.milaboratory.miplots.stat.util.RefGroup import com.milaboratory.miplots.stat.util.TestMethod @@ -7,14 +10,13 @@ import com.milaboratory.miplots.stat.xcontinious.CorrelationMethod import com.milaboratory.miplots.stat.xcontinious.GGScatter import com.milaboratory.miplots.stat.xcontinious.plusAssign import com.milaboratory.miplots.stat.xcontinious.statCor -import com.milaboratory.miplots.stat.xdiscrete.GGBoxPlot +import com.milaboratory.miplots.stat.xdiscrete.GGXDiscrete import com.milaboratory.miplots.stat.xdiscrete.LabelFormat import com.milaboratory.miplots.stat.xdiscrete.plusAssign import com.milaboratory.miplots.stat.xdiscrete.statCompareMeans import com.milaboratory.miplots.toPDF import com.milaboratory.mixcr.postanalysis.PostanalysisResult import com.milaboratory.mixcr.postanalysis.SetPreprocessorStat -import com.milaboratory.mixcr.postanalysis.plots.BasicStatistics.PlotType.* import jetbrains.letsPlot.intern.Plot import jetbrains.letsPlot.label.ggtitle import org.jetbrains.kotlinx.dataframe.DataFrame @@ -93,7 +95,7 @@ object BasicStatistics { ) = dataFrame(paResult, metricsFilter, readMetadata(metadataPath)) data class PlotParameters( - val plotType: PlotType = Auto, + val plotType: PlotType? = null, val primaryGroup: String? = null, val secondaryGroup: String? = null, val facetBy: String? = null, @@ -111,21 +113,11 @@ object BasicStatistics { val correlationMethod: CorrelationMethod = CorrelationMethod.Pearson, ) - enum class PlotType { - Auto, - BoxPlot, - LinePlot, - Scatter; - - companion object { - fun parse(str: String) = - values().find { it.name.equals(str, ignoreCase = true) } - ?: throw IllegalArgumentException("invalid plot type: $str") - } - } + fun parsePlotType(str: String) = + PlotType.values().find { it.cliName.lowercase().equals(str.lowercase()) } private fun isCategorical(t: PlotType) = when (t) { - Scatter, LinePlot -> false + Scatter -> false else -> true } @@ -181,35 +173,25 @@ object BasicStatistics { fun plot( df: DataFrame, par: PlotParameters, - ): Plot = run { - val type = if (par.plotType == Auto) guessPlotType(par, df) else par.plotType - - val dfRefined = ( - if (isCategorical(type)) { - if (par.primaryGroup == null) - df.add(List(df.rowsCount()) { "" }.toColumn("__x__")) - else if (df.isNumeric(par.primaryGroup) || (par.secondaryGroup != null && df.isNumeric(par.secondaryGroup))) { - toCategorical(df, *listOfNotNull(par.primaryGroup, par.secondaryGroup).toTypedArray()) - } else - df - } else { + ): Plot { + val y = BasicStatRow::value.name + val type = par.plotType ?: guessPlotType(par, df) + if (par.primaryGroup == null) + return type.plot(df, y) + + val dfRefined = + if (isCategorical(type)) { + if (df.isNumeric(par.primaryGroup) || (par.secondaryGroup != null && df.isNumeric(par.secondaryGroup))) { + toCategorical(df, *listOfNotNull(par.primaryGroup, par.secondaryGroup).toTypedArray()) + } else df - } - ) + } else { + df + } if (isCategorical(type)) { - val plt = when (type) { - BoxPlot -> GGBoxPlot( - dfRefined, - x = par.primaryGroup ?: "__x__", - y = BasicStatRow::value.name, - facetBy = par.facetBy, - facetNRow = 1, - ) { - fill = par.secondaryGroup ?: par.primaryGroup - } - else -> throw RuntimeException("$type") - } + val plt = type.plot(dfRefined, BasicStatRow::value.name, par.primaryGroup, par.secondaryGroup, par.facetBy) + as GGXDiscrete if (par.showPairwisePValue) plt += statCompareMeans( @@ -240,30 +222,15 @@ object BasicStatistics { labelFormat = par.overallPValueFormat, ) - plt.plot - + return plt.plot } else { + val plt = type.plot(dfRefined, par.primaryGroup, BasicStatRow::value.name, par.secondaryGroup, par.facetBy) + as GGScatter - par.primaryGroup!! - val plt = when (type) { - Scatter -> GGScatter( - dfRefined, - x = par.primaryGroup, - y = BasicStatRow::value.name, - facetBy = par.facetBy, - facetNRow = 1, - ) { - shape = par.secondaryGroup - color = par.secondaryGroup - linetype = par.secondaryGroup - } - LinePlot -> TODO() - else -> throw RuntimeException("$type") - } plt += statCor(method = par.correlationMethod) - plt.plot + return plt.plot } } } From 236a3ffefdb206d3f8507cae49f86d0922cb0858 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 6 Jun 2022 01:48:57 +0400 Subject: [PATCH 257/282] WIP --- .../mixcr/assembler/AssembledReadsPort.java | 8 +- .../mixcr/assembler/AssemblerEvent.java | 16 ++-- .../mixcr/assembler/AssemblerEventLogger.java | 7 +- .../mixcr/assembler/CloneAssembler.java | 84 +++++++++---------- .../assembler/CloneAssemblerListener.java | 14 ++-- .../preclone/FilePreCloneReader.java | 21 +++-- .../preclone/FilePreCloneWriter.java | 3 +- .../mixcr/assembler/preclone/IO.java | 6 +- .../mixcr/assembler/preclone/PreClone.java | 74 ++++++++++++---- .../assembler/preclone/PreCloneReader.java | 58 +++++++++---- .../preclone/PreCloneWithAlignments.java | 17 ---- .../mixcr/basictypes/FieldCollection.java | 4 +- .../mixcr/cli/CloneAssemblerReport.java | 30 +++---- 13 files changed, 194 insertions(+), 148 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java b/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java index ea8ef5637..577316192 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java @@ -65,7 +65,7 @@ public ReadToCloneMapping take() { else eventMapping = null; - assert eventMapping == null || eventMapping.alignmentsIndex == event.alignmentsIndex; + assert eventMapping == null || eventMapping.preCloneIndex == event.preCloneIndex; int cloneIndex = event.cloneIndex; boolean mapped = false; @@ -80,7 +80,7 @@ public ReadToCloneMapping take() { } if (cloneIndex < 0) - return new ReadToCloneMapping(event.alignmentsIndex, cloneIndex, false, false, false, false); + return new ReadToCloneMapping(event.preCloneIndex, cloneIndex, false, false, false, false); boolean preCl = false; if (preClustered.containsKey(cloneIndex)) { @@ -89,7 +89,7 @@ public ReadToCloneMapping take() { } if (!idMapping.containsKey(cloneIndex)) - return new ReadToCloneMapping(event.alignmentsIndex, Integer.MIN_VALUE, false, false, true, preCl); + return new ReadToCloneMapping(event.preCloneIndex, Integer.MIN_VALUE, false, false, true, preCl); cloneIndex = idMapping.get(cloneIndex); @@ -99,7 +99,7 @@ public ReadToCloneMapping take() { cloneIndex = -1 - cloneIndex; } - return new ReadToCloneMapping(event.alignmentsIndex, cloneIndex, clustered, mapped, false, preCl); + return new ReadToCloneMapping(event.preCloneIndex, cloneIndex, clustered, mapped, false, preCl); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java index 8191aeb4a..a49030139 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java @@ -29,24 +29,22 @@ */ package com.milaboratory.mixcr.assembler; -import java.util.Arrays; - public final class AssemblerEvent implements Comparable { - //auxiliary status codes used instead of cloneIndex + // auxiliary status codes used in place of cloneIndex public static final int DROPPED = -2, DEFERRED = -3, EOF = -1; - public final long alignmentsIndex; + public final long preCloneIndex; public final int cloneIndex; - public AssemblerEvent(long alignmentsIndex, int cloneIndex) { + public AssemblerEvent(long preCloneIndex, int cloneIndex) { if (cloneIndex == EOF) throw new IllegalArgumentException(); - this.alignmentsIndex = alignmentsIndex; + this.preCloneIndex = preCloneIndex; this.cloneIndex = cloneIndex; } @Override public int compareTo(AssemblerEvent o) { - return Long.compare(alignmentsIndex, o.alignmentsIndex); + return Long.compare(preCloneIndex, o.preCloneIndex); } @Override @@ -56,13 +54,13 @@ public boolean equals(Object o) { AssemblerEvent that = (AssemblerEvent) o; - if (alignmentsIndex != that.alignmentsIndex) return false; + if (preCloneIndex != that.preCloneIndex) return false; return cloneIndex == that.cloneIndex; } @Override public int hashCode() { - int result = (int) (alignmentsIndex ^ (alignmentsIndex >>> 32)); + int result = (int) (preCloneIndex ^ (preCloneIndex >>> 32)); result = 31 * result + cloneIndex; return result; } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java index 183aa1dda..f25a75d7c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java @@ -31,7 +31,6 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.core.io.util.IOUtil; import com.milaboratory.util.TempFileManager; import java.io.*; @@ -70,8 +69,8 @@ public AssemblerEventLogger(File file) { } public synchronized void newEvent(AssemblerEvent event) { - if (event.alignmentsIndex != counter) { - if (event.alignmentsIndex < counter) + if (event.preCloneIndex != counter) { + if (event.preCloneIndex < counter) throw new IllegalArgumentException("Duplicate event detected."); eventsBuffer.add(event); if (eventsBuffer.size() > MAX_BUFFER_SIZE) @@ -84,7 +83,7 @@ public synchronized void newEvent(AssemblerEvent event) { if (!eventsBuffer.isEmpty()) { Collections.sort(eventsBuffer); while (!eventsBuffer.isEmpty()) { - if (eventsBuffer.get(0).alignmentsIndex != counter) + if (eventsBuffer.get(0).preCloneIndex != counter) return; write(eventsBuffer.remove(0)); ++counter; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index 6a7e8b5c1..176c956cd 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -41,6 +41,7 @@ import com.milaboratory.core.tree.MutationGuide; import com.milaboratory.core.tree.NeighborhoodIterator; import com.milaboratory.core.tree.SequenceTreeMap; +import com.milaboratory.mixcr.assembler.preclone.PreClone; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; @@ -153,35 +154,35 @@ void onNewCloneCreated(CloneAccumulator accumulator) { listener.onNewCloneCreated(accumulator); } - void onFailedToExtractTarget(VDJCAlignments alignments) { + void onFailedToExtractTarget(PreClone alignments) { if (listener != null) listener.onFailedToExtractTarget(alignments); } - void onTooManyLowQualityPoints(VDJCAlignments alignments) { + void onTooManyLowQualityPoints(PreClone alignments) { if (listener != null) listener.onTooManyLowQualityPoints(alignments); } - void onAlignmentDeferred(VDJCAlignments alignments) { + void onAlignmentDeferred(PreClone alignments) { deferredExists = true; if (listener != null) listener.onAlignmentDeferred(alignments); } - void onAlignmentAddedToClone(VDJCAlignments alignments, CloneAccumulator accumulator) { + void onAlignmentAddedToClone(PreClone alignments, CloneAccumulator accumulator) { if (listener != null) listener.onAlignmentAddedToClone(alignments, accumulator); } /* Mapping Events */ - void onNoCandidateFoundForDefferedAlignment(VDJCAlignments alignments) { + void onNoCandidateFoundForDefferedAlignment(PreClone alignments) { if (listener != null) listener.onNoCandidateFoundForDeferredAlignment(alignments); } - void onDeferredAlignmentMappedToClone(VDJCAlignments alignments, CloneAccumulator accumulator) { + void onDeferredAlignmentMappedToClone(PreClone alignments, CloneAccumulator accumulator) { if (listener != null) listener.onDeferredAlignmentMappedToClone(alignments, accumulator); } @@ -216,20 +217,20 @@ public void setListener(CloneAssemblerListener listener) { this.listener = listener; } - private ClonalSequence extractClonalSequence(VDJCAlignments alignments) { - final NSequenceWithQuality[] targets = new NSequenceWithQuality[parameters.assemblingFeatures.length]; - int totalLength = 0; - for (int i = 0; i < targets.length; ++i) - if ((targets[i] = alignments.getFeature(parameters.assemblingFeatures[i])) == null) - return null; - else - totalLength += targets[i].size(); - if (totalLength < parameters.minimalClonalSequenceLength) - return null; - return new ClonalSequence(targets); + private ClonalSequence extractClonalSequence(PreClone preClone) { + // final NSequenceWithQuality[] targets = new NSequenceWithQuality[parameters.assemblingFeatures.length]; + // int totalLength = 0; + // for (int i = 0; i < targets.length; ++i) + // if ((targets[i] = alignments.getFeature(parameters.assemblingFeatures[i])) == null) + // return null; + // else + // totalLength += targets[i].size(); + // if (totalLength < parameters.minimalClonalSequenceLength) + // return null; + return new ClonalSequence(preClone.getClonalSequence()); } - public VoidProcessor getInitialAssembler() { + public VoidProcessor getInitialAssembler() { return new InitialAssembler(); } @@ -391,28 +392,30 @@ private int numberOfBadPoints(ClonalSequence clonalSequence) { return badPoints; } - private final class InitialAssembler implements VoidProcessor { + private final class InitialAssembler implements VoidProcessor { private void log(AssemblerEvent event) { if (globalLogger != null) globalLogger.newEvent(event); } @Override - public void process(VDJCAlignments input) { + public void process(PreClone input) { totalAlignments.incrementAndGet(); final ClonalSequence target = extractClonalSequence(input); - if (target == null) { - log(new AssemblerEvent(input.getAlignmentsIndex(), AssemblerEvent.DROPPED)); - droppedAlignments.incrementAndGet(); - onFailedToExtractTarget(input); - return; - } + + // if (target == null) { + // log(new AssemblerEvent(input.getId(), AssemblerEvent.DROPPED)); + // droppedAlignments.incrementAndGet(); + // onFailedToExtractTarget(input); + // return; + // } + //Calculating number of bad points int badPoints = numberOfBadPoints(target); if (badPoints > target.getConcatenated().size() * parameters.getMaxBadPointsPercent()) { // Too many bad points (this read has too low quality in the regions of interest) - log(new AssemblerEvent(input.getAlignmentsIndex(), AssemblerEvent.DROPPED)); + log(new AssemblerEvent(input.getIndex(), AssemblerEvent.DROPPED)); droppedAlignments.incrementAndGet(); onTooManyLowQualityPoints(input); return; @@ -420,7 +423,7 @@ public void process(VDJCAlignments input) { if (badPoints > 0) { // Has number of bad points but not greater then maxBadPointsToMap - log(new AssemblerEvent(input.getAlignmentsIndex(), AssemblerEvent.DEFERRED)); + log(new AssemblerEvent(input.getIndex(), AssemblerEvent.DEFERRED)); onAlignmentDeferred(input); return; } @@ -446,11 +449,11 @@ public boolean accept(VDJCAlignments alignment) { throw new IllegalArgumentException("This filter can not be used in concurrent " + "environment. Perform pre-filtering in a single thread."); AssemblerEvent event = events.next(); - if (alignment.getAlignmentsIndex() != event.alignmentsIndex) + if (alignment.getAlignmentsIndex() != event.preCloneIndex) throw new IllegalArgumentException("This filter can not be used in concurrent " + "environment. Perform pre-filtering in a single thread."); if (event.cloneIndex != AssemblerEvent.DEFERRED) { - deferredAlignmentsLogger.newEvent(new AssemblerEvent(event.alignmentsIndex, AssemblerEvent.DROPPED)); + deferredAlignmentsLogger.newEvent(new AssemblerEvent(event.preCloneIndex, AssemblerEvent.DROPPED)); return false; } return true; @@ -634,17 +637,17 @@ public boolean fineFilteringPredicate(Clone clone, CloneAccumulator accumulator) public final class CloneAccumulatorContainer { final HashMap accumulators = new HashMap<>(); - synchronized CloneAccumulator accumulate(ClonalSequence sequence, VDJCAlignments alignments, boolean mapped) { - VJCSignature vjcSignature = extractSignature(alignments); + synchronized CloneAccumulator accumulate(ClonalSequence sequence, PreClone preClone, boolean mapped) { + VJCSignature vjcSignature = extractSignature(preClone); CloneAccumulator acc = accumulators.get(vjcSignature); if (acc == null) { - acc = new CloneAccumulator(sequence, extractNRegions(sequence, alignments), + acc = new CloneAccumulator(sequence, extractNRegions(sequence, preClone), parameters.getQualityAggregationType()); accumulators.put(vjcSignature, acc); acc.setCloneIndex(cloneIndexGenerator.incrementAndGet()); onNewCloneCreated(acc); } - acc.accumulate(sequence, alignments, mapped); + acc.accumulate(sequence, preClone, mapped); return acc; } @@ -803,11 +806,11 @@ private Range[] extractNRegions(ClonalSequence clonalSequence, VDJCAlignments al } } - VJCSignature extractSignature(VDJCAlignments alignments) { + VJCSignature extractSignature(PreClone preClone) { return new VJCSignature( - parameters.getSeparateByV() ? getGeneId(alignments, GeneType.Variable) : VJCSignature.DO_NOT_CHECK, - parameters.getSeparateByJ() ? getGeneId(alignments, GeneType.Joining) : VJCSignature.DO_NOT_CHECK, - parameters.getSeparateByC() ? getGeneId(alignments, GeneType.Constant) : VJCSignature.DO_NOT_CHECK + parameters.getSeparateByV() ? preClone.getBestGene(GeneType.Variable) : VJCSignature.DO_NOT_CHECK, + parameters.getSeparateByJ() ? preClone.getBestGene(GeneType.Joining) : VJCSignature.DO_NOT_CHECK, + parameters.getSeparateByC() ? preClone.getBestGene(GeneType.Constant) : VJCSignature.DO_NOT_CHECK ); } @@ -819,11 +822,6 @@ VJCSignature extractSignature(CloneAccumulator cloneAccumulator) { ); } - static VDJCGeneId getGeneId(VDJCAlignments alignments, GeneType type) { - VDJCHit hit = alignments.getBestHit(type); - return hit == null ? null : hit.getGene().getId(); - } - static final Comparator CLONE_ACCUMULATOR_COMPARATOR = new Comparator() { @Override public int compare(CloneAccumulator o1, CloneAccumulator o2) { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java index 14b7cab43..e2e6ad678 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java @@ -29,26 +29,26 @@ */ package com.milaboratory.mixcr.assembler; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.assembler.preclone.PreClone; public interface CloneAssemblerListener { /* Initial Assembly */ void onNewCloneCreated(CloneAccumulator accumulator); - void onFailedToExtractTarget(VDJCAlignments alignments); + void onFailedToExtractTarget(PreClone preClone); - void onTooManyLowQualityPoints(VDJCAlignments alignments); + void onTooManyLowQualityPoints(PreClone preClone); - void onAlignmentDeferred(VDJCAlignments alignments); + void onAlignmentDeferred(PreClone preClone); - void onAlignmentAddedToClone(VDJCAlignments alignments, CloneAccumulator accumulator); + void onAlignmentAddedToClone(PreClone preClone, CloneAccumulator accumulator); /* Mapping */ - void onNoCandidateFoundForDeferredAlignment(VDJCAlignments alignments); + void onNoCandidateFoundForDeferredAlignment(PreClone preClone); - void onDeferredAlignmentMappedToClone(VDJCAlignments alignments, CloneAccumulator accumulator); + void onDeferredAlignmentMappedToClone(PreClone preClone, CloneAccumulator accumulator); /* Clustering */ diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java index 16d56f0fe..64c776fcf 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java @@ -17,13 +17,14 @@ import static com.milaboratory.mixcr.assembler.preclone.FilePreCloneWriter.*; -public final class FilePreCloneReader implements PreCloneReader, AutoCloseable { +public final class FilePreCloneReader implements PreCloneReader { private final PrimitivIHybrid input; private final VDJCAlignerParameters alignmentParameters; private final List usedGenes; private final long alignmentsStartPosition, assignedAlignmentsStartPosition, clonesStartPosition, + numberOfReads, numberOfAlignments, numberOfAssignedAlignments, numberOfClones; @@ -32,16 +33,17 @@ public FilePreCloneReader(Path file) throws IOException { this.input = new PrimitivIHybrid(file, 4); try (PrimitivI i = input.beginPrimitivI(true)) { this.alignmentParameters = i.readObject(VDJCAlignerParameters.class); + this.numberOfReads = i.readLong(); this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, alignmentParameters, VDJCLibraryRegistry.getDefault()); } try (PrimitivI i = input.beginRandomAccessPrimitivI(-8 * 3)) { - alignmentsStartPosition = i.readLong(); - assignedAlignmentsStartPosition = i.readLong(); - clonesStartPosition = i.readLong(); - numberOfAlignments = i.readLong(); - numberOfAssignedAlignments = i.readLong(); - numberOfClones = i.readLong(); + this.alignmentsStartPosition = i.readLong(); + this.assignedAlignmentsStartPosition = i.readLong(); + this.clonesStartPosition = i.readLong(); + this.numberOfAlignments = i.readLong(); + this.numberOfAssignedAlignments = i.readLong(); + this.numberOfClones = i.readLong(); } } @@ -89,6 +91,11 @@ public OutputPortWithProgress readPreClones() { : PrimitivIHeaderActions.error())); } + @Override + public long getTotalNumberOfReads() { + return numberOfReads; + } + @Override public void close() throws Exception { input.close(); diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java index 764f2dc45..c395416b8 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java @@ -73,6 +73,7 @@ public void init(VDJCAlignmentsReader alignmentReader) { // Writing header in raw primitivIO mode and initializing primitivIO state try (PrimitivO o = this.output.beginPrimitivO(true)) { o.writeObject(alignmentReader.getParameters()); + o.writeLong(alignmentReader.getNumberOfReads()); IOUtil.stdVDJCPrimitivOStateInit(o, alignmentReader.getUsedGenes(), alignmentReader.getParameters()); } @@ -191,7 +192,7 @@ public void finish() { cloneChecksum = cloneChecksum * 71 + preClone.id; cloneChecksum = cloneChecksum * 71 + newCloneIdx; - writer.write(preClone.withId(newCloneIdx)); + writer.write(preClone.withIndex(newCloneIdx)); clones++; ps.setProgress(1.0 * clones / numberOfClones.get()); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java index e997d9ad8..6ff39bf86 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java @@ -21,7 +21,7 @@ private IO() { public static final class PreCloneSerializer implements Serializer { @Override public void write(PrimitivO output, PreClone obj) { - output.writeLong(obj.id); + output.writeLong(obj.index); output.writeObject(obj.coreKey); output.writeObject(obj.clonalSequence); output.writeObject(obj.coreTagCount); @@ -37,7 +37,7 @@ public void write(PrimitivO output, PreClone obj) { @Override public PreClone read(PrimitivI input) { - long id = input.readLong(); + long index = input.readLong(); TagTuple coreKey = input.readObject(TagTuple.class); NSequenceWithQuality[] clonalSequence = input.readObject(NSequenceWithQuality[].class); TagCount coreTagCount = input.readObject(TagCount.class); @@ -52,7 +52,7 @@ public PreClone read(PrimitivI input) { gss.add(input.readObject(GeneAndScore.class)); gsss.put(gt, gss); } - return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss); + return new PreClone(index, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index 45cdf50f3..d746ab8db 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -7,30 +7,32 @@ import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.primitivio.annotations.Serializable; +import com.milaboratory.util.CollectionUtils; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; +import io.repseq.core.VDJCGeneId; import java.util.*; @Serializable(by = IO.PreCloneSerializer.class) public final class PreClone { /** Pre-clonotype id */ - public final long id; + final long index; /** Core key of the alignments group */ - public final TagTuple coreKey; + final TagTuple coreKey; /** Tag counter aggregating information about alignments with clonal sequence */ - public final TagCount coreTagCount; + final TagCount coreTagCount; /** Tag counter aggregating information across all alignments assigned to this pre-clone */ - public final TagCount fullTagCount; + final TagCount fullTagCount; /** Assembled clonal sequence */ - public final NSequenceWithQuality[] clonalSequence; + final NSequenceWithQuality[] clonalSequence; /** Aggregated V, J, C gene scoring and content information */ - public final Map> geneScores; + final Map> geneScores; - public PreClone(long id, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, + public PreClone(long index, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, NSequenceWithQuality[] clonalSequence, Map> geneScores) { - this.id = id; + this.index = index; this.coreKey = coreKey; this.coreTagCount = coreTagCount; this.fullTagCount = fullTagCount; @@ -38,16 +40,52 @@ public PreClone(long id, TagTuple coreKey, TagCount coreTagCount, TagCount fullT this.geneScores = geneScores; } - public long getId() { - return id; + public long getIndex() { + return index; } - public PreClone withId(long id) { - return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores); + public TagTuple getCoreKey() { + return coreKey; } - /** Converts alignment to a pre-clone, given the clonal gene features (features to align) */ - public static PreClone fromAlignment(long id, VDJCAlignments alignment, GeneFeature... geneFeatures) { + public TagCount getCoreTagCount() { + return coreTagCount; + } + + public TagCount getFullTagCount() { + return fullTagCount; + } + + public NSequenceWithQuality[] getClonalSequence() { + return clonalSequence; + } + + public Map> getGeneScores() { + return geneScores; + } + + public List getGeneScores(GeneType geneType) { + return geneScores.get(geneType); + } + + public GeneAndScore getBestHit(GeneType geneType) { + List gss = geneScores.get(geneType); + return gss == null || gss.isEmpty() + ? null + : gss.get(0); + } + + public VDJCGeneId getBestGene(GeneType geneType) { + GeneAndScore gs = getBestHit(geneType); + return gs == null ? null : gs.geneId; + } + + public PreClone withIndex(long index) { + return new PreClone(index, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores); + } + + /** Converts alignment to a pre-clone, given the clonal gene features (assemblingFeatures) */ + public static PreClone fromAlignment(long index, VDJCAlignments alignment, GeneFeature... geneFeatures) { NSequenceWithQuality[] clonalSequences = new NSequenceWithQuality[geneFeatures.length]; for (int i = 0; i < geneFeatures.length; i++) @@ -58,13 +96,13 @@ public static PreClone fromAlignment(long id, VDJCAlignments alignment, GeneFeat for (GeneType gt : GeneType.VDJC_REFERENCE) { VDJCHit[] hits = hitsMap.get(gt); List gss = new ArrayList<>(hits.length); - for (int i = 0; i < hits.length; i++) { - VDJCHit hit = hits[i]; + for (VDJCHit hit : hits) gss.add(new GeneAndScore(hit.getGene().getId(), hit.getScore())); - } + assert CollectionUtils.isSorted(gss); geneScores.put(gt, gss); } - return new PreClone(id, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), + + return new PreClone(index, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), clonalSequences, geneScores); } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java index b4f852b1f..fce3d8fc9 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java @@ -7,7 +7,7 @@ import java.util.concurrent.atomic.AtomicLong; -public interface PreCloneReader { +public interface PreCloneReader extends AutoCloseable { /** Creates streamed pre-clone reader. */ OutputPortWithProgress readPreClones(); @@ -19,6 +19,13 @@ public interface PreCloneReader { */ OutputPortWithProgress readAlignments(); + /** Total number of reads (not alignments). Used for reporting. */ + long getTotalNumberOfReads(); + + /** + * Returns a PreCloneReader view of a given VDJCAlignmentsReader representing a set of pre-clones that are formed as + * a one-to-one image of alignments that completely covers provided set of gene features + */ static PreCloneReader fromAlignments(VDJCAlignmentsReader alignmentsReader, GeneFeature[] geneFeatures) { return new PreCloneReader() { private boolean alignmentPredicate(VDJCAlignments al) { @@ -38,17 +45,19 @@ public long currentIndex() { return alignmentReader.currentIndex(); } - @Override - public void close() { - alignmentReader.close(); - } - @Override public PreClone take() { - VDJCAlignments al = alignmentReader.take(); + VDJCAlignments al; + //noinspection StatementWithEmptyBody + while ((al = alignmentReader.take()) != null && al.getCloneIndex() == -1) ; if (al == null) return null; - return PreClone.fromAlignment(al.getAlignmentsIndex(), al, geneFeatures); + return PreClone.fromAlignment(al.getCloneIndex(), al, geneFeatures); + } + + @Override + public void close() { + alignmentReader.close(); } @Override @@ -74,24 +83,27 @@ public long currentIndex() { return reader.currentIndex(); } - @Override - public void close() { - reader.close(); - } - @Override public VDJCAlignments take() { synchronized (sync) { - VDJCAlignments al; - //noinspection StatementWithEmptyBody - while ((al = reader.take()) != null && !alignmentPredicate(al)) ; + VDJCAlignments al = reader.take(); if (al == null) return null; - long id = idGenerator.getAndIncrement(); - return al.withCloneIndexAndMappingType(id, (byte) 0).setAlignmentsIndex(id); + + + if(!alignmentPredicate(al)) + al = al.withCloneIndexAndMappingType(idGenerator.getAndIncrement(), (byte) 0) + .setAlignmentsIndex(al.getAlignmentsIndex()); + + return al; } } + @Override + public void close() { + reader.close(); + } + @Override public double getProgress() { return reader.getProgress(); @@ -103,6 +115,16 @@ public boolean isFinished() { } }; } + + @Override + public long getTotalNumberOfReads() { + return alignmentsReader.getNumberOfReads(); + } + + @Override + public void close() { + alignmentsReader.close(); + } }; } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java deleted file mode 100644 index 99a96da5c..000000000 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneWithAlignments.java +++ /dev/null @@ -1,17 +0,0 @@ -package com.milaboratory.mixcr.assembler.preclone; - -import gnu.trove.set.hash.TIntHashSet; - -public final class PreCloneWithAlignments { - /** Assembled pre-clone */ - public final PreClone preClone; - /** Group-local indices of alignments assigned to this pre-clone */ - public final TIntHashSet alignments; - - public PreCloneWithAlignments(PreClone preClone, TIntHashSet alignments) { - this.preClone = preClone; - this.alignments = alignments; - } - - -} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java index 9f4cd5f43..c6be5cdc6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java @@ -14,8 +14,8 @@ public final class FieldCollection { a -> HashFunctions.Wang64to32shift(a.getCloneIndex()); public static final Comparator PreCloneIdComparator = - Comparator.comparing(PreClone::getId); + Comparator.comparing(PreClone::getIndex); public static final ToIntFunction PreCloneIdHash = - a -> HashFunctions.Wang64to32shift(a.getId()); + a -> HashFunctions.Wang64to32shift(a.getIndex()); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index cc8ea27aa..e8cd05850 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -32,9 +32,9 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.assembler.CloneAccumulator; import com.milaboratory.mixcr.assembler.CloneAssemblerListener; +import com.milaboratory.mixcr.assembler.preclone.PreClone; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.util.ReportHelper; import java.util.concurrent.atomic.AtomicInteger; @@ -182,35 +182,35 @@ public void onNewCloneCreated(CloneAccumulator accumulator) { } @Override - public void onFailedToExtractTarget(VDJCAlignments alignments) { - failedToExtractTarget.addAndGet(alignments.getNumberOfReads()); + public void onFailedToExtractTarget(PreClone preClone) { + failedToExtractTarget.addAndGet(preClone.getNumberOfReads()); } @Override - public void onTooManyLowQualityPoints(VDJCAlignments alignments) { - droppedAsLowQuality.addAndGet(alignments.getNumberOfReads()); + public void onTooManyLowQualityPoints(PreClone preClone) { + droppedAsLowQuality.addAndGet(preClone.getNumberOfReads()); } @Override - public void onAlignmentDeferred(VDJCAlignments alignments) { - deferred.addAndGet(alignments.getNumberOfReads()); + public void onAlignmentDeferred(PreClone preClone) { + deferred.addAndGet(preClone.getNumberOfReads()); } @Override - public void onAlignmentAddedToClone(VDJCAlignments alignments, CloneAccumulator accumulator) { - coreAlignments.addAndGet(alignments.getNumberOfReads()); - alignmentsInClones.addAndGet(alignments.getNumberOfReads()); + public void onAlignmentAddedToClone(PreClone preClone, CloneAccumulator accumulator) { + coreAlignments.addAndGet(preClone.getNumberOfReads()); + alignmentsInClones.addAndGet(preClone.getNumberOfReads()); } @Override - public void onNoCandidateFoundForDeferredAlignment(VDJCAlignments alignments) { - deferredAlignmentsDropped.addAndGet(alignments.getNumberOfReads()); + public void onNoCandidateFoundForDeferredAlignment(PreClone preClone) { + deferredAlignmentsDropped.addAndGet(preClone.getNumberOfReads()); } @Override - public void onDeferredAlignmentMappedToClone(VDJCAlignments alignments, CloneAccumulator accumulator) { - deferredAlignmentsMapped.addAndGet(alignments.getNumberOfReads()); - alignmentsInClones.addAndGet(alignments.getNumberOfReads()); + public void onDeferredAlignmentMappedToClone(PreClone preClone, CloneAccumulator accumulator) { + deferredAlignmentsMapped.addAndGet(preClone.getNumberOfReads()); + alignmentsInClones.addAndGet(preClone.getNumberOfReads()); } @Override From 1d5e81bf0e511c104568925789bb3ccac64636d6 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 6 Jun 2022 05:13:31 +0400 Subject: [PATCH 258/282] feat: reference points in PreClones, bug fixes. --- itests/case10.sh | 2 +- .../preclone/FilePreCloneReader.java | 2 +- .../mixcr/assembler/preclone/IO.java | 5 +- .../mixcr/assembler/preclone/PreClone.java | 21 +++-- .../assembler/preclone/PreCloneAssembler.java | 87 +++++++++++++++++-- .../mixcr/basictypes/VDJCObject.java | 29 ++++--- .../cli/ITestCommandAssemblePreClones.java | 7 +- 7 files changed, 120 insertions(+), 33 deletions(-) diff --git a/itests/case10.sh b/itests/case10.sh index 45d20b94d..ac713bd6a 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -15,7 +15,7 @@ assert() { exit 1 } -set -e +set -euxo pipefail mixcr align -f \ --tag-pattern '^(CELL:N{16})(UMI:N{10})\^(R2:*)' \ diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java index 16d56f0fe..da240986c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java @@ -35,7 +35,7 @@ public FilePreCloneReader(Path file) throws IOException { this.usedGenes = IOUtil.stdVDJCPrimitivIStateInit(i, alignmentParameters, VDJCLibraryRegistry.getDefault()); } - try (PrimitivI i = input.beginRandomAccessPrimitivI(-8 * 3)) { + try (PrimitivI i = input.beginRandomAccessPrimitivI(-8 * 6)) { alignmentsStartPosition = i.readLong(); assignedAlignmentsStartPosition = i.readLong(); clonesStartPosition = i.readLong(); diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java index e997d9ad8..a249353d2 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java @@ -7,6 +7,7 @@ import com.milaboratory.primitivio.PrimitivI; import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.primitivio.Serializer; +import io.repseq.core.ExtendedReferencePoints; import io.repseq.core.GeneType; import java.util.ArrayList; @@ -33,6 +34,7 @@ public void write(PrimitivO output, PreClone obj) { for (GeneAndScore gs : e.getValue()) output.writeObject(gs); } + output.writeObject(obj.referencePoints); } @Override @@ -52,7 +54,8 @@ public PreClone read(PrimitivI input) { gss.add(input.readObject(GeneAndScore.class)); gsss.put(gt, gss); } - return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss); + ExtendedReferencePoints[] referencePoints = input.readObject(ExtendedReferencePoints[].class); + return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss, referencePoints); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index 45cdf50f3..9223a61bf 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -7,6 +7,7 @@ import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.primitivio.annotations.Serializable; +import io.repseq.core.ExtendedReferencePoints; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -26,16 +27,20 @@ public final class PreClone { public final NSequenceWithQuality[] clonalSequence; /** Aggregated V, J, C gene scoring and content information */ public final Map> geneScores; + /** Reference point for each of the clonal sequences */ + public final ExtendedReferencePoints[] referencePoints; public PreClone(long id, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, NSequenceWithQuality[] clonalSequence, - Map> geneScores) { + Map> geneScores, + ExtendedReferencePoints[] referencePoints) { this.id = id; - this.coreKey = coreKey; - this.coreTagCount = coreTagCount; - this.fullTagCount = fullTagCount; - this.clonalSequence = clonalSequence; - this.geneScores = geneScores; + this.coreKey = Objects.requireNonNull(coreKey); + this.coreTagCount = Objects.requireNonNull(coreTagCount); + this.fullTagCount = Objects.requireNonNull(fullTagCount); + this.clonalSequence = Objects.requireNonNull(clonalSequence); + this.geneScores = Objects.requireNonNull(geneScores); + this.referencePoints = Objects.requireNonNull(referencePoints); } public long getId() { @@ -43,7 +48,7 @@ public long getId() { } public PreClone withId(long id) { - return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores); + return new PreClone(id, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores, referencePoints); } /** Converts alignment to a pre-clone, given the clonal gene features (features to align) */ @@ -65,6 +70,6 @@ public static PreClone fromAlignment(long id, VDJCAlignments alignment, GeneFeat geneScores.put(gt, gss); } return new PreClone(id, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), - clonalSequences, geneScores); + clonalSequences, geneScores, null); } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index 4b02b9456..e86b14f05 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -3,7 +3,10 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.util.DummyInputPort; +import com.milaboratory.core.alignment.Alignment; +import com.milaboratory.core.alignment.BandedLinearAligner; import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.mitool.consensus.ConsensusResult; import com.milaboratory.mitool.consensus.GConsensusAssembler; import com.milaboratory.mitool.helpers.GroupOP; @@ -14,15 +17,27 @@ import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import gnu.trove.iterator.TIntIntIterator; +import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TObjectIntHashMap; -import io.repseq.core.GeneType; -import io.repseq.core.VDJCGeneId; +import io.repseq.core.*; import kotlin.jvm.functions.Function1; import java.util.*; import java.util.concurrent.atomic.AtomicLong; public final class PreCloneAssembler { + /** + * Reference points that will be projected onto the assembled consensus / pre-clone. + * Important Note: all the points are alignment attached and not checked for continuity. + */ + private static final ReferencePoint[] ReferencePointsToProject = { + ReferencePoint.VEndTrimmed, + ReferencePoint.DBeginTrimmed, + ReferencePoint.DEndTrimmed, + ReferencePoint.JBeginTrimmed + }; + private final PreCloneAssemblerReport report = new PreCloneAssemblerReport(); private final AtomicLong idGenerator = new AtomicLong(); private final PreCloneAssemblerParameters parameters; @@ -111,6 +126,13 @@ public PreCloneAssemblerResult getForNextGroup() { // noinspection unchecked Map>[] geneInfos = new Map[numberOfClones]; + // Accumulators of reference points positions + // rp[cloneIdx][assemblingFeatureIdx][refPointIdx] + TIntIntHashMap[][][] referencePointStats = + new TIntIntHashMap[numberOfClones] + [parameters.assemblingFeatures.length] + [ReferencePointsToProject.length]; + // Saves local record indices, assigned to each of the consensuses // TIntHashSet[] contents = new TIntHashSet[numberOfClones]; // long[] alignmentToClone = new long[(int) grp1.getCount()]; @@ -188,7 +210,7 @@ public PreCloneAssemblerResult getForNextGroup() { } // Step #3 - // Assigning leftover alignments + // Assigning leftover alignments and collecting reference point positions TagCountAggregator[] coreTagCountAggregators = new TagCountAggregator[numberOfClones]; TagCountAggregator[] fullTagCountAggregators = new TagCountAggregator[numberOfClones]; @@ -238,10 +260,40 @@ else if (cIdxP1 != cp1) alignmentIdxToCloneIdxP1[localIdx] = cIdxP1; else if (cIdxP1 == -1) report.empiricalAssignmentConflicts.incrementAndGet(); - } else if (cIdxP1 > 0) + } else if (cIdxP1 > 0) { + int cIdx = cIdxP1 - 1; // Using second iteration over the alignments to assemble TagCounters from the alignments assigned to // clonotypes based on their contig assignment - coreTagCountAggregators[cIdxP1 - 1].add(al.getTagCount()); + coreTagCountAggregators[cIdx].add(al.getTagCount()); + + // and collect statistics on the reference point positions + GeneFeature[] gfs = parameters.assemblingFeatures; + for (int gfi = 0; gfi < gfs.length; gfi++) { + GeneFeature gf = gfs[gfi]; + NucleotideSequence seq = al.getFeature(gf).getSequence(); + // Alignment to project alignment positions onto the consensus + Alignment a = BandedLinearAligner.align( + parameters.assemblerParameters.aAssemblerParameters.scoring, + seq.getSequence(), + consensuses.get(cIdx).consensuses[gfi].consensus.getSequence(), + parameters.assemblerParameters.aAssemblerParameters.bandWidth); + for (int rpi = 0; rpi < ReferencePointsToProject.length; rpi++) { + ReferencePoint rp = ReferencePointsToProject[rpi]; + int positionInAlignment = al.getRelativePosition(gf, rp); + if (positionInAlignment == -1) + continue; + int positionInConsensus = a.convertToSeq1Position(positionInAlignment); + if (positionInConsensus == -1) + continue; + if (positionInConsensus < -1) + positionInConsensus = -2 - positionInConsensus; + TIntIntHashMap map = referencePointStats[cIdx][gfi][rpi]; + if (map == null) // lazy initialization + referencePointStats[cIdx][gfi][rpi] = map = new TIntIntHashMap(); + map.adjustOrPutValue(positionInConsensus, 1, 1); + } + } + } if (cIdxP1 > 0) fullTagCountAggregators[cIdxP1 - 1].add(al.getTagCount()); @@ -254,15 +306,36 @@ else if (cIdxP1 == -1) for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { ConsensusResult.SingleConsensus[] cs = consensuses.get(cIdx).consensuses; NSequenceWithQuality[] clonalSequence = new NSequenceWithQuality[cs.length]; - for (int sr = 0; sr < cs.length; sr++) + ExtendedReferencePoints[] referencePoints = new ExtendedReferencePoints[cs.length]; + for (int sr = 0; sr < cs.length; sr++) { clonalSequence[sr] = cs[sr].consensus; + ExtendedReferencePointsBuilder rpb = new ExtendedReferencePointsBuilder(); + for (int rpi = 0; rpi < ReferencePointsToProject.length; rpi++) { + TIntIntHashMap map = referencePointStats[cIdx][sr][rpi]; + if (map == null) + continue; + int maxCount = -1; + int maxPosition = -1; + TIntIntIterator it = map.iterator(); + while (it.hasNext()) { + it.advance(); + if (maxCount < it.value()) { + maxCount = it.value(); + maxPosition = it.key(); + } + } + rpb.setPosition(ReferencePointsToProject[rpi], maxPosition); + } + referencePoints[sr] = rpb.build(); + } result.add(new PreClone( cloneIdOffset + cIdx, grp1.getKey(), coreTagCountAggregators[cIdx].createAndDestroy(), fullTagCountAggregators[cIdx].createAndDestroy(), clonalSequence, - geneInfos[cIdx])); + geneInfos[cIdx], + referencePoints)); } long[] resultAlToClone = new long[alignmentIdxToCloneIdxP1.length]; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index f31c309ee..316637842 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -281,6 +281,13 @@ public final Range getRelativeRange(GeneFeature big, GeneFeature subfeature) { return getPartitionedTarget(targetIndex).getPartitioning().getRelativeRange(big, subfeature); } + public final int getRelativePosition(GeneFeature big, ReferencePoint point) { + int targetIndex = getTargetContainingFeature(big); + if (targetIndex == -1) + return -1; + return getPartitionedTarget(targetIndex).getPartitioning().getRelativePosition(big, point); + } + public final int getTargetContainingFeature(GeneFeature feature) { NSequenceWithQuality tmp; int targetIndex = -1, quality = -1; @@ -570,17 +577,17 @@ assert same(leftParts, rightParts) : if (lLast.germline || rLast.germline) return null; -// assert lHit.getGene().getGeneType() == GeneType.Variable; -// if (!lHit -// .getPartitioningForTarget(lLast.iTarget) -// .isAvailable(ReferencePoint.CDR3Begin)) -// return null; -// -// assert rHit.getGene().getGeneType() == GeneType.Joining; -// if (!rHit -// .getPartitioningForTarget(rLast.iTarget) -// .isAvailable(ReferencePoint.CDR3End)) -// return null; + // assert lHit.getGene().getGeneType() == GeneType.Variable; + // if (!lHit + // .getPartitioningForTarget(lLast.iTarget) + // .isAvailable(ReferencePoint.CDR3Begin)) + // return null; + // + // assert rHit.getGene().getGeneType() == GeneType.Joining; + // if (!rHit + // .getPartitioningForTarget(rLast.iTarget) + // .isAvailable(ReferencePoint.CDR3End)) + // return null; IncompleteSequencePart merged = new IncompleteSequencePart(lHit, false, lLast.iTarget, lLast.begin, rLast.end); diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index 1ef96c16e..6e1068cc1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -40,12 +40,11 @@ public class ITestCommandAssemblePreClones extends ACommandMiXCR { names = {"--use-system-temp"}) public boolean useSystemTemp = false; - private static final AAssemblerParameters aAssemblerParams = AAssemblerParameters.builder() .bandWidth(4) - .scoring(LinearGapAlignmentScoring.getNucleotideBLASTScoring()) + .scoring(LinearGapAlignmentScoring.getNucleotideBLASTScoring(-14)) .minAlignmentScore(40) - .maxAlignmentPenalty(90) + .maxAlignmentPenalty(33) .trimMinimalSumQuality(20) .trimReferenceRegion(false) .maxQuality((byte) 45) @@ -54,7 +53,7 @@ public class ITestCommandAssemblePreClones extends ACommandMiXCR { .aAssemblerParameters(aAssemblerParams) .maxIterations(4) .minAltSeedQualityScore((byte) 11) - .minimalRecordShare(0.001) + .minimalRecordShare(0.1) .minimalRecordCount(2) .build(); From d0726eb2dd4893a6e81ec29e0d12c38d6e237be8 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Mon, 6 Jun 2022 05:32:11 +0400 Subject: [PATCH 259/282] WIP --- .../mixcr/assembler/CloneAssembler.java | 47 ++++--- .../assembler/CloneAssemblerListener.java | 14 +- .../preclone/FilePreCloneReader.java | 4 +- .../preclone/FilePreCloneWriter.java | 16 +-- .../mixcr/assembler/preclone/IO.java | 8 +- .../mixcr/assembler/preclone/PreClone.java | 109 ++------------- .../assembler/preclone/PreCloneAssembler.java | 4 +- .../preclone/PreCloneAssemblerResult.java | 6 +- .../assembler/preclone/PreCloneImpl.java | 128 ++++++++++++++++++ .../assembler/preclone/PreCloneReader.java | 10 +- .../mixcr/basictypes/FieldCollection.java | 8 +- .../mixcr/cli/CloneAssemblerReport.java | 14 +- .../cli/ITestCommandAssemblePreClones.java | 6 +- 13 files changed, 211 insertions(+), 163 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index 176c956cd..e7daa05c6 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -41,7 +41,7 @@ import com.milaboratory.core.tree.MutationGuide; import com.milaboratory.core.tree.NeighborhoodIterator; import com.milaboratory.core.tree.SequenceTreeMap; -import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; @@ -54,7 +54,10 @@ import gnu.trove.list.array.TIntArrayList; import gnu.trove.map.hash.TIntIntHashMap; import gnu.trove.map.hash.TIntObjectHashMap; -import io.repseq.core.*; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGene; +import io.repseq.core.VDJCGeneId; import java.util.*; import java.util.concurrent.ConcurrentHashMap; @@ -154,35 +157,35 @@ void onNewCloneCreated(CloneAccumulator accumulator) { listener.onNewCloneCreated(accumulator); } - void onFailedToExtractTarget(PreClone alignments) { + void onFailedToExtractTarget(PreCloneImpl alignments) { if (listener != null) listener.onFailedToExtractTarget(alignments); } - void onTooManyLowQualityPoints(PreClone alignments) { + void onTooManyLowQualityPoints(PreCloneImpl alignments) { if (listener != null) listener.onTooManyLowQualityPoints(alignments); } - void onAlignmentDeferred(PreClone alignments) { + void onAlignmentDeferred(PreCloneImpl alignments) { deferredExists = true; if (listener != null) listener.onAlignmentDeferred(alignments); } - void onAlignmentAddedToClone(PreClone alignments, CloneAccumulator accumulator) { + void onAlignmentAddedToClone(PreCloneImpl alignments, CloneAccumulator accumulator) { if (listener != null) listener.onAlignmentAddedToClone(alignments, accumulator); } /* Mapping Events */ - void onNoCandidateFoundForDefferedAlignment(PreClone alignments) { + void onNoCandidateFoundForDefferedAlignment(PreCloneImpl alignments) { if (listener != null) listener.onNoCandidateFoundForDeferredAlignment(alignments); } - void onDeferredAlignmentMappedToClone(PreClone alignments, CloneAccumulator accumulator) { + void onDeferredAlignmentMappedToClone(PreCloneImpl alignments, CloneAccumulator accumulator) { if (listener != null) listener.onDeferredAlignmentMappedToClone(alignments, accumulator); } @@ -217,7 +220,7 @@ public void setListener(CloneAssemblerListener listener) { this.listener = listener; } - private ClonalSequence extractClonalSequence(PreClone preClone) { + private ClonalSequence extractClonalSequence(PreCloneImpl preClone) { // final NSequenceWithQuality[] targets = new NSequenceWithQuality[parameters.assemblingFeatures.length]; // int totalLength = 0; // for (int i = 0; i < targets.length; ++i) @@ -230,7 +233,7 @@ private ClonalSequence extractClonalSequence(PreClone preClone) { return new ClonalSequence(preClone.getClonalSequence()); } - public VoidProcessor getInitialAssembler() { + public VoidProcessor getInitialAssembler() { return new InitialAssembler(); } @@ -392,14 +395,14 @@ private int numberOfBadPoints(ClonalSequence clonalSequence) { return badPoints; } - private final class InitialAssembler implements VoidProcessor { + private final class InitialAssembler implements VoidProcessor { private void log(AssemblerEvent event) { if (globalLogger != null) globalLogger.newEvent(event); } @Override - public void process(PreClone input) { + public void process(PreCloneImpl input) { totalAlignments.incrementAndGet(); final ClonalSequence target = extractClonalSequence(input); @@ -637,7 +640,7 @@ public boolean fineFilteringPredicate(Clone clone, CloneAccumulator accumulator) public final class CloneAccumulatorContainer { final HashMap accumulators = new HashMap<>(); - synchronized CloneAccumulator accumulate(ClonalSequence sequence, PreClone preClone, boolean mapped) { + synchronized CloneAccumulator accumulate(ClonalSequence sequence, PreCloneImpl preClone, boolean mapped) { VJCSignature vjcSignature = extractSignature(preClone); CloneAccumulator acc = accumulators.get(vjcSignature); if (acc == null) { @@ -771,42 +774,42 @@ public ClonalSequence getSequence() { return accumulators.values().iterator().next().getSequence(); } - private Range[] extractNRegions(ClonalSequence clonalSequence, VDJCAlignments alignments) { + private Range[] extractNRegions(ClonalSequence clonalSequence, PreCloneImpl preClone) { boolean dFound; ArrayList result = new ArrayList<>(); Range range; int offset = 0; - for (int i = 0; i < parameters.assemblingFeatures.length; ++i) { - GeneFeature assemblingFeature = parameters.assemblingFeatures[i]; + for (int csIdx = 0; csIdx < parameters.assemblingFeatures.length; ++csIdx) { + GeneFeature assemblingFeature = parameters.assemblingFeatures[csIdx]; if (!assemblingFeature.contains(VDJunction) && !assemblingFeature.contains(DJJunction)) continue; dFound = false; - range = alignments.getRelativeRange(assemblingFeature, VDJunction); + range = preClone.getRange(csIdx, VDJunction); if (range != null) { result.add(range.move(offset)); dFound = true; } - range = alignments.getRelativeRange(assemblingFeature, DJJunction); + range = preClone.getRange(csIdx, DJJunction); if (range != null) { result.add(range.move(offset)); dFound = true; } if (!dFound) { - range = alignments.getRelativeRange(assemblingFeature, VJJunction); + range = preClone.getRange(csIdx, VJJunction); if (range != null) result.add(range.move(offset)); } - offset += clonalSequence.get(i).size(); + offset += clonalSequence.get(csIdx).size(); } - return result.toArray(new Range[result.size()]); + return result.toArray(new Range[0]); } } - VJCSignature extractSignature(PreClone preClone) { + VJCSignature extractSignature(PreCloneImpl preClone) { return new VJCSignature( parameters.getSeparateByV() ? preClone.getBestGene(GeneType.Variable) : VJCSignature.DO_NOT_CHECK, parameters.getSeparateByJ() ? preClone.getBestGene(GeneType.Joining) : VJCSignature.DO_NOT_CHECK, diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java index e2e6ad678..b485e90ef 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java @@ -29,26 +29,26 @@ */ package com.milaboratory.mixcr.assembler; -import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; public interface CloneAssemblerListener { /* Initial Assembly */ void onNewCloneCreated(CloneAccumulator accumulator); - void onFailedToExtractTarget(PreClone preClone); + void onFailedToExtractTarget(PreCloneImpl preClone); - void onTooManyLowQualityPoints(PreClone preClone); + void onTooManyLowQualityPoints(PreCloneImpl preClone); - void onAlignmentDeferred(PreClone preClone); + void onAlignmentDeferred(PreCloneImpl preClone); - void onAlignmentAddedToClone(PreClone preClone, CloneAccumulator accumulator); + void onAlignmentAddedToClone(PreCloneImpl preClone, CloneAccumulator accumulator); /* Mapping */ - void onNoCandidateFoundForDeferredAlignment(PreClone preClone); + void onNoCandidateFoundForDeferredAlignment(PreCloneImpl preClone); - void onDeferredAlignmentMappedToClone(PreClone preClone, CloneAccumulator accumulator); + void onDeferredAlignmentMappedToClone(PreCloneImpl preClone, CloneAccumulator accumulator); /* Clustering */ diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java index b5cd68122..65906c551 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java @@ -84,9 +84,9 @@ public OutputPortWithProgress readAlignments() { } @Override - public OutputPortWithProgress readPreClones() { + public OutputPortWithProgress readPreClones() { return OutputPortWithProgress.wrap(numberOfClones, - input.beginRandomAccessPrimitivIBlocks(PreClone.class, clonesStartPosition, + input.beginRandomAccessPrimitivIBlocks(PreCloneImpl.class, clonesStartPosition, h -> h.getSpecialByte(0) == CLONES_END_MARK_BYTE_0 ? PrimitivIHeaderActions.stopReading() : PrimitivIHeaderActions.error())); diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java index c395416b8..5c64b8562 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java @@ -46,8 +46,8 @@ public final class FilePreCloneWriter implements AutoCloseable, CanReportProgres private final Buffer alignmentBuffer; private final InputPort alignmentSorterInput; - private final Buffer cloneBuffer; - private final InputPort cloneSorterInput; + private final Buffer cloneBuffer; + private final InputPort cloneSorterInput; private final AtomicLong numberOfAlignments = new AtomicLong(), @@ -57,8 +57,8 @@ public final class FilePreCloneWriter implements AutoCloseable, CanReportProgres private volatile Thread alignmentSortingThread, cloneSortingThread; private volatile HashSorter alignmentCollator; private volatile OutputPortCloseable sortedAlignments; - private volatile HashSorter cloneCollator; - private volatile OutputPortCloseable sortedClones; + private volatile HashSorter cloneCollator; + private volatile OutputPortCloseable sortedClones; public FilePreCloneWriter(Path file, TempFileDest tempDest) throws IOException { this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file); @@ -95,7 +95,7 @@ public void init(VDJCAlignmentsReader alignmentReader) { "alignment-sorting"); alignmentSortingThread.start(); cloneCollator = new HashSorter<>( - PreClone.class, + PreCloneImpl.class, PreCloneIdHash, PreCloneIdComparator, 5, tempDest.addSuffix("cl.pre."), 4, 6, stateBuilder.getOState(), stateBuilder.getIState(), @@ -110,7 +110,7 @@ public void init(VDJCAlignmentsReader alignmentReader) { alignmentWriter = output.beginPrimitivOBlocks(4, 1024); } - public void putClone(PreClone clone) { + public void putClone(PreCloneImpl clone) { numberOfClones.incrementAndGet(); cloneSorterInput.put(clone); } @@ -182,10 +182,10 @@ public void finish() { long clonesStartPosition = output.getPosition(); long cloneChecksum = 17; long clones = 0; - try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { + try (PrimitivOBlocks.Writer writer = output.beginPrimitivOBlocks(4, 1024)) { // resulting clone id generator long newCloneIdx = -1; - for (PreClone preClone : CUtils.it(sortedClones)) { + for (PreCloneImpl preClone : CUtils.it(sortedClones)) { newCloneIdx++; // preClone.id will be mapped to newCloneIdx diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java index 09c04cc74..94c061b0a 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java @@ -19,9 +19,9 @@ public final class IO { private IO() { } - public static final class PreCloneSerializer implements Serializer { + public static final class PreCloneImplSerializer implements Serializer { @Override - public void write(PrimitivO output, PreClone obj) { + public void write(PrimitivO output, PreCloneImpl obj) { output.writeLong(obj.index); output.writeObject(obj.coreKey); output.writeObject(obj.clonalSequence); @@ -38,7 +38,7 @@ public void write(PrimitivO output, PreClone obj) { } @Override - public PreClone read(PrimitivI input) { + public PreCloneImpl read(PrimitivI input) { long index = input.readLong(); TagTuple coreKey = input.readObject(TagTuple.class); NSequenceWithQuality[] clonalSequence = input.readObject(NSequenceWithQuality[].class); @@ -55,7 +55,7 @@ public PreClone read(PrimitivI input) { gsss.put(gt, gss); } ExtendedReferencePoints[] referencePoints = input.readObject(ExtendedReferencePoints[].class); - return new PreClone(index, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss, referencePoints); + return new PreCloneImpl(index, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss, referencePoints); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index b63a9513c..c4632ed5a 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -3,116 +3,33 @@ import com.milaboratory.core.Range; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mixcr.basictypes.GeneAndScore; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; -import com.milaboratory.primitivio.annotations.Serializable; -import com.milaboratory.util.CollectionUtils; -import io.repseq.core.ExtendedReferencePoints; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; -import java.util.*; +import java.util.List; +import java.util.Map; -@Serializable(by = IO.PreCloneSerializer.class) -public final class PreClone { - /** Pre-clonotype id */ - final long index; - /** Core key of the alignments group */ - final TagTuple coreKey; - /** Tag counter aggregating information about alignments with clonal sequence */ - final TagCount coreTagCount; - /** Tag counter aggregating information across all alignments assigned to this pre-clone */ - final TagCount fullTagCount; - /** Assembled clonal sequence */ - final NSequenceWithQuality[] clonalSequence; - /** Aggregated V, J, C gene scoring and content information */ +public interface PreClone { + long getIndex(); - final Map> geneScores; - /** Reference point for each of the clonal sequences */ - final ExtendedReferencePoints[] referencePoints; + TagTuple getCoreKey(); - public PreClone(long index, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, - NSequenceWithQuality[] clonalSequence, - Map> geneScores, - ExtendedReferencePoints[] referencePoints) { - this.index = index; - this.coreKey = Objects.requireNonNull(coreKey); - this.coreTagCount = Objects.requireNonNull(coreTagCount); - this.fullTagCount = Objects.requireNonNull(fullTagCount); - this.clonalSequence = Objects.requireNonNull(clonalSequence); - this.geneScores = Objects.requireNonNull(geneScores); - this.referencePoints = Objects.requireNonNull(referencePoints); - } + TagCount getCoreTagCount(); - public long getIndex() { - return index; - } + TagCount getFullTagCount(); - public TagTuple getCoreKey() { - return coreKey; - } + NSequenceWithQuality[] getClonalSequence(); - public TagCount getCoreTagCount() { - return coreTagCount; - } + Map> getGeneScores(); - public TagCount getFullTagCount() { - return fullTagCount; - } + List getGeneScores(GeneType geneType); - public NSequenceWithQuality[] getClonalSequence() { - return clonalSequence; - } + GeneAndScore getBestHit(GeneType geneType); - public Map> getGeneScores() { - return geneScores; - } + VDJCGeneId getBestGene(GeneType geneType); - public List getGeneScores(GeneType geneType) { - return geneScores.get(geneType); - } - - public GeneAndScore getBestHit(GeneType geneType) { - List gss = geneScores.get(geneType); - return gss == null || gss.isEmpty() - ? null - : gss.get(0); - } - - public VDJCGeneId getBestGene(GeneType geneType) { - GeneAndScore gs = getBestHit(geneType); - return gs == null ? null : gs.geneId; - } - - public Range getRange(int csIdx, GeneFeature feature) { - return referencePoints[csIdx].getRange(feature); - } - - public PreClone withIndex(long index) { - return new PreClone(index, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores, referencePoints); - } - - /** Converts alignment to a pre-clone, given the clonal gene features (assemblingFeatures) */ - public static PreClone fromAlignment(long index, VDJCAlignments alignment, GeneFeature... geneFeatures) { - NSequenceWithQuality[] clonalSequences = new NSequenceWithQuality[geneFeatures.length]; - - for (int i = 0; i < geneFeatures.length; i++) - clonalSequences[i] = Objects.requireNonNull(alignment.getFeature(geneFeatures[i])); - - Map> geneScores = new EnumMap<>(GeneType.class); - EnumMap hitsMap = alignment.getHitsMap(); - for (GeneType gt : GeneType.VDJC_REFERENCE) { - VDJCHit[] hits = hitsMap.get(gt); - List gss = new ArrayList<>(hits.length); - for (VDJCHit hit : hits) - gss.add(new GeneAndScore(hit.getGene().getId(), hit.getScore())); - assert CollectionUtils.isSorted(gss); - geneScores.put(gt, gss); - } - return new PreClone(index, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), - clonalSequences, geneScores, null); - } + Range getRange(int csIdx, GeneFeature feature); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index e86b14f05..b408cd666 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -302,7 +302,7 @@ else if (cIdxP1 == -1) } long cloneIdOffset = idGenerator.getAndAdd(numberOfClones); - List result = new ArrayList<>(numberOfClones); + List result = new ArrayList<>(numberOfClones); for (int cIdx = 0; cIdx < numberOfClones; cIdx++) { ConsensusResult.SingleConsensus[] cs = consensuses.get(cIdx).consensuses; NSequenceWithQuality[] clonalSequence = new NSequenceWithQuality[cs.length]; @@ -328,7 +328,7 @@ else if (cIdxP1 == -1) } referencePoints[sr] = rpb.build(); } - result.add(new PreClone( + result.add(new PreCloneImpl( cloneIdOffset + cIdx, grp1.getKey(), coreTagCountAggregators[cIdx].createAndDestroy(), diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java index 6525e86bd..9bd70d40d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java @@ -3,15 +3,15 @@ import java.util.List; public final class PreCloneAssemblerResult { - private final List clones; + private final List clones; private final long[] alignmentToClone; - public PreCloneAssemblerResult(List clones, long[] alignmentToClone) { + public PreCloneAssemblerResult(List clones, long[] alignmentToClone) { this.clones = clones; this.alignmentToClone = alignmentToClone; } - public List getClones() { + public List getClones() { return clones; } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java new file mode 100644 index 000000000..c62a2492e --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java @@ -0,0 +1,128 @@ +package com.milaboratory.mixcr.assembler.preclone; + +import com.milaboratory.core.Range; +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.mixcr.basictypes.GeneAndScore; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.primitivio.annotations.Serializable; +import com.milaboratory.util.CollectionUtils; +import io.repseq.core.ExtendedReferencePoints; +import io.repseq.core.GeneFeature; +import io.repseq.core.GeneType; +import io.repseq.core.VDJCGeneId; + +import java.util.*; + +@Serializable(by = IO.PreCloneImplSerializer.class) +public final class PreCloneImpl implements PreClone { + /** Pre-clonotype id */ + final long index; + /** Core key of the alignments group */ + final TagTuple coreKey; + /** Tag counter aggregating information about alignments with clonal sequence */ + final TagCount coreTagCount; + /** Tag counter aggregating information across all alignments assigned to this pre-clone */ + final TagCount fullTagCount; + /** Assembled clonal sequence */ + final NSequenceWithQuality[] clonalSequence; + /** Aggregated V, J, C gene scoring and content information */ + + final Map> geneScores; + /** Reference point for each of the clonal sequences */ + final ExtendedReferencePoints[] referencePoints; + + public PreCloneImpl(long index, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, + NSequenceWithQuality[] clonalSequence, + Map> geneScores, + ExtendedReferencePoints[] referencePoints) { + this.index = index; + this.coreKey = Objects.requireNonNull(coreKey); + this.coreTagCount = Objects.requireNonNull(coreTagCount); + this.fullTagCount = Objects.requireNonNull(fullTagCount); + this.clonalSequence = Objects.requireNonNull(clonalSequence); + this.geneScores = Objects.requireNonNull(geneScores); + this.referencePoints = Objects.requireNonNull(referencePoints); + } + + @Override + public long getIndex() { + return index; + } + + @Override + public TagTuple getCoreKey() { + return coreKey; + } + + @Override + public TagCount getCoreTagCount() { + return coreTagCount; + } + + @Override + public TagCount getFullTagCount() { + return fullTagCount; + } + + @Override + public NSequenceWithQuality[] getClonalSequence() { + return clonalSequence; + } + + @Override + public Map> getGeneScores() { + return geneScores; + } + + @Override + public List getGeneScores(GeneType geneType) { + return geneScores.get(geneType); + } + + @Override + public GeneAndScore getBestHit(GeneType geneType) { + List gss = geneScores.get(geneType); + return gss == null || gss.isEmpty() + ? null + : gss.get(0); + } + + @Override + public VDJCGeneId getBestGene(GeneType geneType) { + GeneAndScore gs = getBestHit(geneType); + return gs == null ? null : gs.geneId; + } + + @Override + public Range getRange(int csIdx, GeneFeature feature) { + return referencePoints[csIdx].getRange(feature); + } + + public PreCloneImpl withIndex(long index) { + return new PreCloneImpl(index, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores, referencePoints); + } + + /** Converts alignment to a pre-clone, given the clonal gene features (assemblingFeatures) */ + public static PreCloneImpl fromAlignment(long index, VDJCAlignments alignment, GeneFeature... geneFeatures) { + NSequenceWithQuality[] clonalSequences = new NSequenceWithQuality[geneFeatures.length]; + + for (int i = 0; i < geneFeatures.length; i++) + clonalSequences[i] = Objects.requireNonNull(alignment.getFeature(geneFeatures[i])); + + Map> geneScores = new EnumMap<>(GeneType.class); + EnumMap hitsMap = alignment.getHitsMap(); + for (GeneType gt : GeneType.VDJC_REFERENCE) { + VDJCHit[] hits = hitsMap.get(gt); + List gss = new ArrayList<>(hits.length); + for (VDJCHit hit : hits) + gss.add(new GeneAndScore(hit.getGene().getId(), hit.getScore())); + assert CollectionUtils.isSorted(gss); + geneScores.put(gt, gss); + } + return new PreCloneImpl(index, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), + clonalSequences, geneScores, null); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java index fce3d8fc9..d0a8f7c0d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java @@ -9,7 +9,7 @@ public interface PreCloneReader extends AutoCloseable { /** Creates streamed pre-clone reader. */ - OutputPortWithProgress readPreClones(); + OutputPortWithProgress readPreClones(); /** * Creates streamed alignments reader. @@ -36,23 +36,23 @@ private boolean alignmentPredicate(VDJCAlignments al) { } @Override - public OutputPortWithProgress readPreClones() { + public OutputPortWithProgress readPreClones() { //noinspection resource OutputPortWithProgress alignmentReader = readAlignments(); - return new OutputPortWithProgress() { + return new OutputPortWithProgress() { @Override public long currentIndex() { return alignmentReader.currentIndex(); } @Override - public PreClone take() { + public PreCloneImpl take() { VDJCAlignments al; //noinspection StatementWithEmptyBody while ((al = alignmentReader.take()) != null && al.getCloneIndex() == -1) ; if (al == null) return null; - return PreClone.fromAlignment(al.getCloneIndex(), al, geneFeatures); + return PreCloneImpl.fromAlignment(al.getCloneIndex(), al, geneFeatures); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java index c6be5cdc6..8aca7586b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java @@ -1,6 +1,6 @@ package com.milaboratory.mixcr.basictypes; -import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; import com.milaboratory.util.HashFunctions; import java.util.Comparator; @@ -13,9 +13,9 @@ public final class FieldCollection { public static final ToIntFunction VDJCACloneIdHash = a -> HashFunctions.Wang64to32shift(a.getCloneIndex()); - public static final Comparator PreCloneIdComparator = - Comparator.comparing(PreClone::getIndex); + public static final Comparator PreCloneIdComparator = + Comparator.comparing(PreCloneImpl::getIndex); - public static final ToIntFunction PreCloneIdHash = + public static final ToIntFunction PreCloneIdHash = a -> HashFunctions.Wang64to32shift(a.getIndex()); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index e8cd05850..dc5061908 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -32,7 +32,7 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.assembler.CloneAccumulator; import com.milaboratory.mixcr.assembler.CloneAssemblerListener; -import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.util.ReportHelper; @@ -182,33 +182,33 @@ public void onNewCloneCreated(CloneAccumulator accumulator) { } @Override - public void onFailedToExtractTarget(PreClone preClone) { + public void onFailedToExtractTarget(PreCloneImpl preClone) { failedToExtractTarget.addAndGet(preClone.getNumberOfReads()); } @Override - public void onTooManyLowQualityPoints(PreClone preClone) { + public void onTooManyLowQualityPoints(PreCloneImpl preClone) { droppedAsLowQuality.addAndGet(preClone.getNumberOfReads()); } @Override - public void onAlignmentDeferred(PreClone preClone) { + public void onAlignmentDeferred(PreCloneImpl preClone) { deferred.addAndGet(preClone.getNumberOfReads()); } @Override - public void onAlignmentAddedToClone(PreClone preClone, CloneAccumulator accumulator) { + public void onAlignmentAddedToClone(PreCloneImpl preClone, CloneAccumulator accumulator) { coreAlignments.addAndGet(preClone.getNumberOfReads()); alignmentsInClones.addAndGet(preClone.getNumberOfReads()); } @Override - public void onNoCandidateFoundForDeferredAlignment(PreClone preClone) { + public void onNoCandidateFoundForDeferredAlignment(PreCloneImpl preClone) { deferredAlignmentsDropped.addAndGet(preClone.getNumberOfReads()); } @Override - public void onDeferredAlignmentMappedToClone(PreClone preClone, CloneAccumulator accumulator) { + public void onDeferredAlignmentMappedToClone(PreCloneImpl preClone, CloneAccumulator accumulator) { deferredAlignmentsMapped.addAndGet(preClone.getNumberOfReads()); alignmentsInClones.addAndGet(preClone.getNumberOfReads()); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index 6e1068cc1..c77b35382 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -97,11 +97,11 @@ public void run0() throws Exception { PreCloneAssemblerResult result; while ((result = assembler.getForNextGroup()) != null) { GroupOP grp = alGroups.take(); - List clones = result.getClones(); + List clones = result.getClones(); assert clones.isEmpty() || clones.get(0).coreKey.equals(grp.getKey()); totalClones += clones.size(); - for (PreClone clone : clones) + for (PreCloneImpl clone : clones) writer.putClone(clone); int localId = 0; @@ -141,7 +141,7 @@ public void run0() throws Exception { numberOfAlignmentsCheck + " != 0)"); long numberOfClonesCheck = 0; - for (PreClone c : CUtils.it(reader.readPreClones())) + for (PreCloneImpl c : CUtils.it(reader.readPreClones())) numberOfClonesCheck++; if (numberOfClonesCheck != totalClones) From 701e994bc1583f66798382cc3888e883efb66b72 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 7 Jun 2022 03:36:41 +0400 Subject: [PATCH 260/282] WIP, compiles --- .../mixcr/assembler/AlignmentsProvider.java | 37 +-- .../mixcr/assembler/CloneAccumulator.java | 12 +- .../mixcr/assembler/CloneAssembler.java | 73 ++--- .../assembler/CloneAssemblerListener.java | 14 +- .../mixcr/assembler/CloneAssemblerRunner.java | 93 +++--- .../VDJCAlignmentsReaderWrapper.java | 88 ------ .../mixcr/assembler/VDJCGeneAccumulator.java | 38 +-- .../preclone/FilePreCloneReader.java | 2 +- .../preclone/FilePreCloneWriter.java | 2 +- .../mixcr/assembler/preclone/IO.java | 4 +- .../mixcr/assembler/preclone/PreClone.java | 61 +++- .../assembler/preclone/PreCloneAbstract.java | 59 ++++ .../assembler/preclone/PreCloneAssembler.java | 39 +-- .../assembler/preclone/PreCloneImpl.java | 107 +------ .../assembler/preclone/PreCloneReader.java | 16 +- .../basictypes/VDJCAlignmentsReader.java | 6 +- .../mixcr/cli/CloneAssemblerReport.java | 14 +- .../mixcr/cli/CommandAssemble.java | 270 +++++++++--------- .../mixcr/cli/CommandCorrectAndSortTags.java | 2 +- .../cli/ITestCommandAssemblePreClones.java | 8 +- .../mixcr/util/OutputPortWithProgress.java | 2 +- .../com/milaboratory/mixcr/util/RunMiXCR.java | 20 +- .../assembler/CloneAssemblerRunnerTest.java | 6 +- 23 files changed, 445 insertions(+), 528 deletions(-) delete mode 100644 src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java index ea15a4abd..518678775 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java @@ -29,43 +29,20 @@ */ package com.milaboratory.mixcr.assembler; -import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; -import io.repseq.core.VDJCLibraryRegistry; +import com.milaboratory.mixcr.util.OutputPortWithProgress; -import java.io.File; -import java.io.IOException; - -public interface AlignmentsProvider { - OutputPortCloseable create(); +public interface AlignmentsProvider extends AutoCloseable { + /** Creates new alignments reader */ + OutputPortWithProgress readAlignments(); /** * Should return total number of reads (not alignments) after whole analysis if such information available. * * @return total number of reads */ - long getTotalNumberOfReads(); - - final class Util { - public static AlignmentsProvider createProvider(File file, final VDJCLibraryRegistry geneResolver) { - return new VDJCAlignmentsReaderWrapper(() -> { - try { - return new VDJCAlignmentsReader(file, geneResolver); - } catch (IOException e) { - throw new RuntimeException(e); - } - }); - } + long getNumberOfReads(); - public static AlignmentsProvider createProvider(String file, VDJCLibraryRegistry geneResolver) { - return new VDJCAlignmentsReaderWrapper(() -> { - try { - return new VDJCAlignmentsReader(file, geneResolver); - } catch (IOException e) { - throw new RuntimeException(e); - } - }); - } - } + // this override strips out exceptions form the method signature (see raw AutoCloseable for comparison) + void close(); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index 5fba859b0..f72484324 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -36,6 +36,7 @@ import com.milaboratory.core.sequence.SequenceQuality; import com.milaboratory.core.sequence.quality.QualityAggregationType; import com.milaboratory.core.sequence.quality.QualityAggregator; +import com.milaboratory.mixcr.assembler.preclone.PreClone; import com.milaboratory.mixcr.basictypes.ClonalSequence; import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; @@ -159,21 +160,22 @@ public void aggregateGeneInfo(HasRelativeMinScore geneParameters) { geneAccumulator = null; } - public synchronized void accumulate(ClonalSequence data, VDJCAlignments alignment, boolean mapped) { + public synchronized void accumulate(ClonalSequence data, PreClone preClone, boolean mapped) { if (geneAccumulator == null) throw new IllegalStateException("Gene information already aggregated"); if (!mapped) { // Core sequence accumulation - coreCount += alignment.getNumberOfReads(); + coreCount += preClone.getNumberOfReads(); - tagBuilder.add(alignment.getTagCount()); + // TODO or core tag count ??? + tagBuilder.add(preClone.getFullTagCount()); // Accumulate information about V-D-J alignments only for strictly clustered reads // (only for core clonotypes members) - geneAccumulator.accumulate(alignment); + geneAccumulator.accumulate(preClone.getGeneScores()); aggregator.aggregate(data.getConcatenated().getQuality()); } else // Mapped sequence accumulation - mappedCount += alignment.getNumberOfReads(); + mappedCount += preClone.getNumberOfReads(); } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index e7daa05c6..defd9e443 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -41,8 +41,11 @@ import com.milaboratory.core.tree.MutationGuide; import com.milaboratory.core.tree.NeighborhoodIterator; import com.milaboratory.core.tree.SequenceTreeMap; -import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; -import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.basictypes.ClonalSequence; +import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.CloneSet; +import com.milaboratory.mixcr.basictypes.VDJCSProperties; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.CanReportProgress; @@ -157,37 +160,37 @@ void onNewCloneCreated(CloneAccumulator accumulator) { listener.onNewCloneCreated(accumulator); } - void onFailedToExtractTarget(PreCloneImpl alignments) { + void onFailedToExtractTarget(PreClone preClone) { if (listener != null) - listener.onFailedToExtractTarget(alignments); + listener.onFailedToExtractTarget(preClone); } - void onTooManyLowQualityPoints(PreCloneImpl alignments) { + void onTooManyLowQualityPoints(PreClone preClone) { if (listener != null) - listener.onTooManyLowQualityPoints(alignments); + listener.onTooManyLowQualityPoints(preClone); } - void onAlignmentDeferred(PreCloneImpl alignments) { + void onAlignmentDeferred(PreClone preClone) { deferredExists = true; if (listener != null) - listener.onAlignmentDeferred(alignments); + listener.onAlignmentDeferred(preClone); } - void onAlignmentAddedToClone(PreCloneImpl alignments, CloneAccumulator accumulator) { + void onAlignmentAddedToClone(PreClone preClone, CloneAccumulator accumulator) { if (listener != null) - listener.onAlignmentAddedToClone(alignments, accumulator); + listener.onAlignmentAddedToClone(preClone, accumulator); } /* Mapping Events */ - void onNoCandidateFoundForDefferedAlignment(PreCloneImpl alignments) { + void onNoCandidateFoundForDefferedAlignment(PreClone preClone) { if (listener != null) - listener.onNoCandidateFoundForDeferredAlignment(alignments); + listener.onNoCandidateFoundForDeferredAlignment(preClone); } - void onDeferredAlignmentMappedToClone(PreCloneImpl alignments, CloneAccumulator accumulator) { + void onDeferredAlignmentMappedToClone(PreClone preClone, CloneAccumulator accumulator) { if (listener != null) - listener.onDeferredAlignmentMappedToClone(alignments, accumulator); + listener.onDeferredAlignmentMappedToClone(preClone, accumulator); } /* Clustering Events */ @@ -220,7 +223,7 @@ public void setListener(CloneAssemblerListener listener) { this.listener = listener; } - private ClonalSequence extractClonalSequence(PreCloneImpl preClone) { + private ClonalSequence extractClonalSequence(PreClone preClone) { // final NSequenceWithQuality[] targets = new NSequenceWithQuality[parameters.assemblingFeatures.length]; // int totalLength = 0; // for (int i = 0; i < targets.length; ++i) @@ -233,7 +236,7 @@ private ClonalSequence extractClonalSequence(PreCloneImpl preClone) { return new ClonalSequence(preClone.getClonalSequence()); } - public VoidProcessor getInitialAssembler() { + public VoidProcessor getInitialAssembler() { return new InitialAssembler(); } @@ -258,11 +261,11 @@ public boolean beginMapping() { return true; } - public Filter getDeferredAlignmentsFilter() { + public Filter getDeferredAlignmentsFilter() { return new DeferredAlignmentsFilter(); } - public VoidProcessor getDeferredAlignmentsMapper() { + public VoidProcessor getDeferredAlignmentsMapper() { if (mappingTree == null) throw new IllegalStateException("Mapping tree not yet created."); return new DeferredAlignmentsMapper(); @@ -395,14 +398,14 @@ private int numberOfBadPoints(ClonalSequence clonalSequence) { return badPoints; } - private final class InitialAssembler implements VoidProcessor { + private final class InitialAssembler implements VoidProcessor { private void log(AssemblerEvent event) { if (globalLogger != null) globalLogger.newEvent(event); } @Override - public void process(PreCloneImpl input) { + public void process(PreClone input) { totalAlignments.incrementAndGet(); final ClonalSequence target = extractClonalSequence(input); @@ -413,7 +416,7 @@ public void process(PreCloneImpl input) { // return; // } - //Calculating number of bad points + // Calculating number of bad points int badPoints = numberOfBadPoints(target); if (badPoints > target.getConcatenated().size() * parameters.getMaxBadPointsPercent()) { @@ -436,23 +439,23 @@ public void process(PreCloneImpl input) { // Preforming alignment accumulation CloneAccumulator acc = container.accumulate(target, input, false); // Logging assembler events for subsequent index creation and mapping filtering - log(new AssemblerEvent(input.getAlignmentsIndex(), acc.getCloneIndex())); + log(new AssemblerEvent(input.getIndex(), acc.getCloneIndex())); // Incrementing corresponding counter successfullyAssembledAlignments.incrementAndGet(); onAlignmentAddedToClone(input, acc); } } - private final class DeferredAlignmentsFilter implements Filter { + private final class DeferredAlignmentsFilter implements Filter { final Iterator events = globalLogger.events().iterator(); @Override - public boolean accept(VDJCAlignments alignment) { + public boolean accept(PreClone alignment) { if (!events.hasNext()) throw new IllegalArgumentException("This filter can not be used in concurrent " + "environment. Perform pre-filtering in a single thread."); AssemblerEvent event = events.next(); - if (alignment.getAlignmentsIndex() != event.preCloneIndex) + if (alignment.getIndex() != event.preCloneIndex) throw new IllegalArgumentException("This filter can not be used in concurrent " + "environment. Perform pre-filtering in a single thread."); if (event.cloneIndex != AssemblerEvent.DEFERRED) { @@ -463,17 +466,15 @@ public boolean accept(VDJCAlignments alignment) { } } - private final class DeferredAlignmentsMapper implements VoidProcessor { + private final class DeferredAlignmentsMapper implements VoidProcessor { final AssemblerUtils.MappingThresholdCalculator thresholdCalculator = parameters.getThresholdCalculator(); @Override - public void process(VDJCAlignments input) { + public void process(PreClone input) { final ClonalSequence clonalSequence = extractClonalSequence(input); - // The sequence was deferred on the initial step, so it must contain clonal sequence - assert clonalSequence != null; - - RandomUtil.reseedThreadLocal(HashFunctions.JenkinWang64shift(Arrays.hashCode(input.getReadIds()))); + // Seeding random generator to make ambiguous mappings below reproducible + RandomUtil.reseedThreadLocal(HashFunctions.JenkinWang64shift(input.getIndex())); int badPoints = numberOfBadPoints(clonalSequence); // Implements the algorithm to control the number of possible matching sequences @@ -506,7 +507,7 @@ else if (minMismatches < iterator.getMismatches()) } if (candidates.isEmpty()) { - deferredAlignmentsLogger.newEvent(new AssemblerEvent(input.getAlignmentsIndex(), + deferredAlignmentsLogger.newEvent(new AssemblerEvent(input.getIndex(), AssemblerEvent.DROPPED)); droppedAlignments.incrementAndGet(); onNoCandidateFoundForDefferedAlignment(input); @@ -524,7 +525,7 @@ else if (minMismatches < iterator.getMismatches()) mappedAlignments.incrementAndGet(); successfullyAssembledAlignments.incrementAndGet(); - deferredAlignmentsLogger.newEvent(new AssemblerEvent(input.getAlignmentsIndex(), + deferredAlignmentsLogger.newEvent(new AssemblerEvent(input.getIndex(), minMismatches == 0 ? accumulator.getCloneIndex() : -4 - accumulator.getCloneIndex())); if (minMismatches > 0) { @@ -640,7 +641,7 @@ public boolean fineFilteringPredicate(Clone clone, CloneAccumulator accumulator) public final class CloneAccumulatorContainer { final HashMap accumulators = new HashMap<>(); - synchronized CloneAccumulator accumulate(ClonalSequence sequence, PreCloneImpl preClone, boolean mapped) { + synchronized CloneAccumulator accumulate(ClonalSequence sequence, PreClone preClone, boolean mapped) { VJCSignature vjcSignature = extractSignature(preClone); CloneAccumulator acc = accumulators.get(vjcSignature); if (acc == null) { @@ -774,7 +775,7 @@ public ClonalSequence getSequence() { return accumulators.values().iterator().next().getSequence(); } - private Range[] extractNRegions(ClonalSequence clonalSequence, PreCloneImpl preClone) { + private Range[] extractNRegions(ClonalSequence clonalSequence, PreClone preClone) { boolean dFound; ArrayList result = new ArrayList<>(); Range range; @@ -809,7 +810,7 @@ private Range[] extractNRegions(ClonalSequence clonalSequence, PreCloneImpl preC } } - VJCSignature extractSignature(PreCloneImpl preClone) { + VJCSignature extractSignature(PreClone preClone) { return new VJCSignature( parameters.getSeparateByV() ? preClone.getBestGene(GeneType.Variable) : VJCSignature.DO_NOT_CHECK, parameters.getSeparateByJ() ? preClone.getBestGene(GeneType.Joining) : VJCSignature.DO_NOT_CHECK, diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java index b485e90ef..e2e6ad678 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java @@ -29,26 +29,26 @@ */ package com.milaboratory.mixcr.assembler; -import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; +import com.milaboratory.mixcr.assembler.preclone.PreClone; public interface CloneAssemblerListener { /* Initial Assembly */ void onNewCloneCreated(CloneAccumulator accumulator); - void onFailedToExtractTarget(PreCloneImpl preClone); + void onFailedToExtractTarget(PreClone preClone); - void onTooManyLowQualityPoints(PreCloneImpl preClone); + void onTooManyLowQualityPoints(PreClone preClone); - void onAlignmentDeferred(PreCloneImpl preClone); + void onAlignmentDeferred(PreClone preClone); - void onAlignmentAddedToClone(PreCloneImpl preClone, CloneAccumulator accumulator); + void onAlignmentAddedToClone(PreClone preClone, CloneAccumulator accumulator); /* Mapping */ - void onNoCandidateFoundForDeferredAlignment(PreCloneImpl preClone); + void onNoCandidateFoundForDeferredAlignment(PreClone preClone); - void onDeferredAlignmentMappedToClone(PreCloneImpl preClone, CloneAccumulator accumulator); + void onDeferredAlignmentMappedToClone(PreClone preClone, CloneAccumulator accumulator); /* Clustering */ diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index 60cc80bf5..b9b0de1f9 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -30,114 +30,87 @@ package com.milaboratory.mixcr.assembler; import cc.redberry.pipe.CUtils; -import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.blocks.FilteringPort; +import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.basictypes.CloneSet; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; +import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; -import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.CanReportProgressAndStage; +import com.milaboratory.util.ProgressAndStage; public class CloneAssemblerRunner implements CanReportProgressAndStage { - final AlignmentsProvider alignmentsProvider; + final PreCloneReader preCloneReader; final CloneAssembler assembler; - final int threads = 1; - volatile String stage = "Initialization"; - volatile CanReportProgress innerProgress; - volatile VDJCAlignmentsReader alignmentReader = null; - volatile boolean isFinished = false; + final ProgressAndStage ps = new ProgressAndStage("Initialization"); - public CloneAssemblerRunner(AlignmentsProvider alignmentsProvider, CloneAssembler assembler) { - this.alignmentsProvider = alignmentsProvider; + public CloneAssemblerRunner(PreCloneReader preCloneReader, CloneAssembler assembler) { + this.preCloneReader = preCloneReader; this.assembler = assembler; } @Override public String getStage() { - return stage; + return ps.getStage(); } @Override public double getProgress() { - if (innerProgress == null) - return Double.NaN; - return innerProgress.getProgress(); + return ps.getProgress(); } @Override public boolean isFinished() { - return isFinished; + return ps.isFinished(); } public void run() { // run initial assembler - try (OutputPortCloseable alignmentsPort = alignmentsProvider.create()) { - if (alignmentsPort instanceof VDJCAlignmentsReaderWrapper.OP) - alignmentReader = ((VDJCAlignmentsReaderWrapper.OP) alignmentsPort).reader; - synchronized (this) { - stage = "Assembling initial clonotypes"; - if (alignmentsPort instanceof CanReportProgress) - innerProgress = (CanReportProgress) alignmentsPort; - } + try (OutputPortWithProgress preClones = preCloneReader.readPreClones()) { + ps.setStage("Assembling initial clonotypes"); + ps.delegate(preClones); try { - CUtils.processAllInParallel(CUtils.buffered(alignmentsPort, 128), assembler.getInitialAssembler(), threads); + CUtils.processAll(CUtils.buffered(preClones, 128), + assembler.getInitialAssembler()); } catch (InterruptedException e) { throw new RuntimeException(e); } - alignmentReader = null; } + // run mapping if required if (assembler.beginMapping()) { - synchronized (this) { - stage = "Preparing for mapping of low quality reads"; - innerProgress = null; - } - try (OutputPortCloseable alignmentsPort = alignmentsProvider.create()) { - if (alignmentsPort instanceof VDJCAlignmentsReaderWrapper.OP) - alignmentReader = ((VDJCAlignmentsReaderWrapper.OP) alignmentsPort).reader; - synchronized (this) { - stage = "Mapping low quality reads"; - if (alignmentsPort instanceof CanReportProgress) - innerProgress = (CanReportProgress) alignmentsPort; - } + ps.unDelegate(); + ps.setStage("Preparing for mapping of low quality reads"); + try (OutputPortWithProgress preClones = preCloneReader.readPreClones()) { + ps.delegate("Mapping low quality reads", preClones); try { - CUtils.processAllInParallel(CUtils.buffered( - new FilteringPort<>(alignmentsPort, + CUtils.processAll(CUtils.buffered( + new FilteringPort<>(preClones, assembler.getDeferredAlignmentsFilter()), 128), - assembler.getDeferredAlignmentsMapper(), threads); + assembler.getDeferredAlignmentsMapper()); } catch (InterruptedException e) { throw new RuntimeException(e); } } - alignmentReader = null; assembler.endMapping(); } + + ps.unDelegate(); + ps.setStage("Pre-clustering"); assembler.preClustering(); - //run clustering + + // run clustering if (assembler.parameters.isClusteringEnabled()) { - synchronized (this) { - stage = "Clustering"; - innerProgress = assembler; - } + ps.delegate("Clustering", assembler); assembler.runClustering(); } - //build clones - synchronized (this) { - stage = "Building clones"; - innerProgress = assembler; - } + // build clones + ps.delegate("Building clones", assembler); assembler.buildClones(); - isFinished = true; + ps.finish(); } - // public int getQueueSize() { - // if (alignmentReader == null) - // return -1; - // return alignmentReader.getQueueSize(); - // } - public CloneSet getCloneSet(VDJCAlignerParameters alignerParameters, TagsInfo tagsInfo) { return assembler.getCloneSet(alignerParameters, tagsInfo); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java deleted file mode 100644 index bcee93ad1..000000000 --- a/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java +++ /dev/null @@ -1,88 +0,0 @@ -/* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved - * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. - * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. - */ -package com.milaboratory.mixcr.assembler; - -import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; -import com.milaboratory.util.CanReportProgress; -import com.milaboratory.util.Factory; - -import java.util.concurrent.atomic.AtomicLong; - -class VDJCAlignmentsReaderWrapper implements AlignmentsProvider { - final Factory factory; - final AtomicLong totalNumberOfReads = new AtomicLong(-1); - - VDJCAlignmentsReaderWrapper(Factory factory) { - this.factory = factory; - } - - @Override - public OutputPortCloseable create() { - return new OP(factory.create()); - } - - @Override - public long getTotalNumberOfReads() { - return totalNumberOfReads.get(); - } - - public class OP implements OutputPortCloseable, CanReportProgress { - public final VDJCAlignmentsReader reader; - - private OP(VDJCAlignmentsReader reader) { - this.reader = reader; - } - - @Override - public VDJCAlignments take() { - VDJCAlignments alignments = reader.take(); - if (alignments == null) - totalNumberOfReads.set(reader.getNumberOfReads()); - return alignments; - } - - @Override - public double getProgress() { - return reader.getProgress(); - } - - @Override - public boolean isFinished() { - return reader.isFinished(); - } - - @Override - public void close() { - reader.close(); - } - } -} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java index 9bda34513..5ab5cd4e4 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java @@ -15,29 +15,29 @@ public final class VDJCGeneAccumulator { private final int[] observations = new int[GeneType.values().length]; private final EnumMap> geneScores = new EnumMap<>(GeneType.class); - public synchronized void accumulate(VDJCAlignments alignment) { - // Accumulate information about all genes - for (GeneType geneType : GeneType.VJC_REFERENCE) { - TObjectFloatHashMap geneScores = this.geneScores.get(geneType); - VDJCHit[] hits = alignment.getHits(geneType); - if (hits.length == 0) - continue; - observations[geneType.ordinal()]++; - if (geneScores == null) - this.geneScores.put(geneType, geneScores = new TObjectFloatHashMap<>()); - for (VDJCHit hit : hits) { - // Calculating sum of natural logarithms of scores - geneScores.adjustOrPutValue(hit.getGene().getId(), hit.getScore(), hit.getScore()); - } - } - } + // public synchronized void accumulate(VDJCAlignments alignment) { + // // Accumulate information about all genes + // for (GeneType geneType : GeneType.VJC_REFERENCE) { + // TObjectFloatHashMap geneScores = this.geneScores.get(geneType); + // VDJCHit[] hits = alignment.getHits(geneType); + // if (hits.length == 0) + // continue; + // observations[geneType.ordinal()]++; + // if (geneScores == null) + // this.geneScores.put(geneType, geneScores = new TObjectFloatHashMap<>()); + // for (VDJCHit hit : hits) { + // // Calculating sum of natural logarithms of scores + // geneScores.adjustOrPutValue(hit.getGene().getId(), hit.getScore(), hit.getScore()); + // } + // } + // } - public synchronized void accumulate(EnumMap genesAndScores) { + public synchronized void accumulate(Map> genesAndScores) { // Accumulate information about all genes for (GeneType geneType : GeneType.VJC_REFERENCE) { TObjectFloatHashMap geneScores = this.geneScores.get(geneType); - GeneAndScore[] data = genesAndScores.get(geneType); - if (data == null || data.length == 0) + List data = genesAndScores.get(geneType); + if (data == null || data.isEmpty()) continue; observations[geneType.ordinal()]++; if (geneScores == null) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java index 65906c551..3ee390d7b 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java @@ -84,7 +84,7 @@ public OutputPortWithProgress readAlignments() { } @Override - public OutputPortWithProgress readPreClones() { + public OutputPortWithProgress readPreClones() { return OutputPortWithProgress.wrap(numberOfClones, input.beginRandomAccessPrimitivIBlocks(PreCloneImpl.class, clonesStartPosition, h -> h.getSpecialByte(0) == CLONES_END_MARK_BYTE_0 diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java index 5c64b8562..1e41821ba 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java @@ -189,7 +189,7 @@ public void finish() { newCloneIdx++; // preClone.id will be mapped to newCloneIdx - cloneChecksum = cloneChecksum * 71 + preClone.id; + cloneChecksum = cloneChecksum * 71 + preClone.index; cloneChecksum = cloneChecksum * 71 + newCloneIdx; writer.write(preClone.withIndex(newCloneIdx)); diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java index 94c061b0a..bc108e28e 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java @@ -35,6 +35,7 @@ public void write(PrimitivO output, PreCloneImpl obj) { output.writeObject(gs); } output.writeObject(obj.referencePoints); + output.writeInt(obj.numberOfReads); } @Override @@ -55,7 +56,8 @@ public PreCloneImpl read(PrimitivI input) { gsss.put(gt, gss); } ExtendedReferencePoints[] referencePoints = input.readObject(ExtendedReferencePoints[].class); - return new PreCloneImpl(index, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss, referencePoints); + int numberOfReads = input.readInt(); + return new PreCloneImpl(index, coreKey, coreTagCount, fullTagCount, clonalSequence, gsss, referencePoints, numberOfReads); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index c4632ed5a..f025a9926 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -3,33 +3,84 @@ import com.milaboratory.core.Range; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mixcr.basictypes.GeneAndScore; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.util.CollectionUtils; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; import io.repseq.core.VDJCGeneId; -import java.util.List; -import java.util.Map; +import java.util.*; public interface PreClone { + /** Pre-clonotype id */ long getIndex(); + /** Core key of the alignments group */ TagTuple getCoreKey(); + /** Tag counter aggregating information about alignments with clonal sequence */ TagCount getCoreTagCount(); + /** Tag counter aggregating information across all alignments assigned to this pre-clone */ TagCount getFullTagCount(); + /** Assembled clonal sequence */ NSequenceWithQuality[] getClonalSequence(); + /** Aggregated V, J, C gene scoring and content information */ Map> getGeneScores(); - List getGeneScores(GeneType geneType); + /** Returns number of reads the pre-clone aggregates */ + int getNumberOfReads(); - GeneAndScore getBestHit(GeneType geneType); + default List getGeneScores(GeneType geneType) { + return getGeneScores().get(geneType); + } - VDJCGeneId getBestGene(GeneType geneType); + default GeneAndScore getBestHit(GeneType geneType) { + List gss = getGeneScores().get(geneType); + return gss == null || gss.isEmpty() + ? null + : gss.get(0); + } + default VDJCGeneId getBestGene(GeneType geneType) { + GeneAndScore gs = getBestHit(geneType); + return gs == null ? null : gs.geneId; + } + + /** Provides limited access to the sequence partitioning for clonal sequences */ Range getRange(int csIdx, GeneFeature feature); + + /** Converts alignment to a pre-clone, given the clonal gene features (assemblingFeatures) */ + static PreClone fromAlignment(long index, VDJCAlignments alignment, GeneFeature... geneFeatures) { + NSequenceWithQuality[] clonalSequences = new NSequenceWithQuality[geneFeatures.length]; + for (int i = 0; i < geneFeatures.length; i++) + clonalSequences[i] = Objects.requireNonNull(alignment.getFeature(geneFeatures[i])); + Map> geneScores = new EnumMap<>(GeneType.class); + EnumMap hitsMap = alignment.getHitsMap(); + for (GeneType gt : GeneType.VDJC_REFERENCE) { + VDJCHit[] hits = hitsMap.get(gt); + List gss = new ArrayList<>(hits.length); + for (VDJCHit hit : hits) + gss.add(new GeneAndScore(hit.getGene().getId(), hit.getScore())); + assert CollectionUtils.isSorted(gss); + geneScores.put(gt, gss); + } + return new PreCloneAbstract(index, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), + clonalSequences, geneScores) { + @Override + public Range getRange(int csIdx, GeneFeature feature) { + return alignment.getRelativeRange(geneFeatures[csIdx], feature); + } + + @Override + public int getNumberOfReads() { + return alignment.getNumberOfReads(); + } + }; + } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java new file mode 100644 index 000000000..06fe3d5c9 --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java @@ -0,0 +1,59 @@ +package com.milaboratory.mixcr.assembler.preclone; + +import com.milaboratory.core.sequence.NSequenceWithQuality; +import com.milaboratory.mixcr.basictypes.GeneAndScore; +import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import io.repseq.core.GeneType; + +import java.util.List; +import java.util.Map; +import java.util.Objects; + +public abstract class PreCloneAbstract implements PreClone { + final long index; + final TagTuple coreKey; + final TagCount coreTagCount; + final TagCount fullTagCount; + final NSequenceWithQuality[] clonalSequence; + final Map> geneScores; + + public PreCloneAbstract(long index, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, NSequenceWithQuality[] clonalSequence, Map> geneScores) { + this.index = index; + this.coreKey = Objects.requireNonNull(coreKey); + this.coreTagCount = Objects.requireNonNull(coreTagCount); + this.fullTagCount = Objects.requireNonNull(fullTagCount); + this.clonalSequence = Objects.requireNonNull(clonalSequence); + this.geneScores = Objects.requireNonNull(geneScores); + } + + @Override + public long getIndex() { + return index; + } + + @Override + public TagTuple getCoreKey() { + return coreKey; + } + + @Override + public TagCount getCoreTagCount() { + return coreTagCount; + } + + @Override + public TagCount getFullTagCount() { + return fullTagCount; + } + + @Override + public NSequenceWithQuality[] getClonalSequence() { + return clonalSequence; + } + + @Override + public Map> getGeneScores() { + return geneScores; + } +} diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index b408cd666..bfb7af5ac 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -15,6 +15,7 @@ import com.milaboratory.mixcr.basictypes.GeneAndScore; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCHit; +import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagCountAggregator; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import gnu.trove.iterator.TIntIntIterator; @@ -87,12 +88,11 @@ public PreCloneAssemblerResult getForNextGroup() { continue outer; assemblerInput.add(row); - EnumMap geneAndScores = new EnumMap<>(GeneType.class); + EnumMap> geneAndScores = new EnumMap<>(GeneType.class); for (GeneType gt : GeneType.VJC_REFERENCE) { VDJCHit[] hits = al.getHits(gt); - GeneAndScore[] gss = new GeneAndScore[hits.length]; - for (int i = 0; i < hits.length; i++) - gss[i] = hits[i].getGeneAndScore(); + List gss = new ArrayList<>(hits.length); + for (VDJCHit hit : hits) gss.add(hit.getGeneAndScore()); geneAndScores.put(gt, gss); } alignmentInfos.add(new AlignmentInfo(localIdx, al.getAlignmentsIndex(), al.getMinReadId(), @@ -133,11 +133,6 @@ public PreCloneAssemblerResult getForNextGroup() { [parameters.assemblingFeatures.length] [ReferencePointsToProject.length]; - // Saves local record indices, assigned to each of the consensuses - // TIntHashSet[] contents = new TIntHashSet[numberOfClones]; - // long[] alignmentToClone = new long[(int) grp1.getCount()]; - // Arrays.fill(alignmentToClone, -1); - // Tag suffixes unambiguously linked to a clonotype // (store cloneIdx+1; -1 for ambiguous cases; 0 - not found) TObjectIntHashMap tagSuffixToCloneId = new TObjectIntHashMap<>(); @@ -201,8 +196,8 @@ public PreCloneAssemblerResult getForNextGroup() { tagSuffixToCloneId.put(ts, -1); for (GeneType gt : GeneType.VJ_REFERENCE) { - GeneAndScore[] gss = ai.genesAndScores.get(gt); - if (gss == null) + List gss = ai.genesAndScores.get(gt); + if (gss == null || gss.isEmpty()) continue; for (GeneAndScore gs : gss) vjcGenesToCloneId.put(gs.geneId, -1); @@ -218,6 +213,7 @@ public PreCloneAssemblerResult getForNextGroup() { coreTagCountAggregators[cIdx] = new TagCountAggregator(); fullTagCountAggregators[cIdx] = new TagCountAggregator(); } + int[] cloneCounts = new int[numberOfClones]; GroupOP grp2 = alignmentsReader2.take(); assert grp1.getKey().equals(grp2.getKey()) : "" + grp1.getKey() + " != " + grp2.getKey(); @@ -295,9 +291,11 @@ else if (cIdxP1 == -1) } } - if (cIdxP1 > 0) - fullTagCountAggregators[cIdxP1 - 1].add(al.getTagCount()); - else + if (cIdxP1 > 0) { + int cIdx = cIdxP1 - 1; + fullTagCountAggregators[cIdx].add(al.getTagCount()); + cloneCounts[cIdx] += al.getNumberOfReads(); + } else report.unassignedAlignments.incrementAndGet(); } @@ -328,14 +326,19 @@ else if (cIdxP1 == -1) } referencePoints[sr] = rpb.build(); } + + TagCount fullTagCount = fullTagCountAggregators[cIdx].createAndDestroy(); + assert cloneCounts[cIdx] == fullTagCount.sum(); + result.add(new PreCloneImpl( cloneIdOffset + cIdx, grp1.getKey(), coreTagCountAggregators[cIdx].createAndDestroy(), - fullTagCountAggregators[cIdx].createAndDestroy(), + fullTagCount, clonalSequence, geneInfos[cIdx], - referencePoints)); + referencePoints, + cloneCounts[cIdx])); } long[] resultAlToClone = new long[alignmentIdxToCloneIdxP1.length]; @@ -351,10 +354,10 @@ private static final class AlignmentInfo { final int localIdx; final long alignmentId, minReadId; final Set tagSuffixes; - final EnumMap genesAndScores; + final EnumMap> genesAndScores; public AlignmentInfo(int localIdx, long alignmentId, long minReadId, - Set tagSuffixes, EnumMap genesAndScores) { + Set tagSuffixes, EnumMap> genesAndScores) { this.localIdx = localIdx; this.alignmentId = alignmentId; this.minReadId = minReadId; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java index c62a2492e..4b7817e82 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java @@ -3,97 +3,29 @@ import com.milaboratory.core.Range; import com.milaboratory.core.sequence.NSequenceWithQuality; import com.milaboratory.mixcr.basictypes.GeneAndScore; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCHit; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.primitivio.annotations.Serializable; -import com.milaboratory.util.CollectionUtils; import io.repseq.core.ExtendedReferencePoints; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; -import io.repseq.core.VDJCGeneId; import java.util.*; @Serializable(by = IO.PreCloneImplSerializer.class) -public final class PreCloneImpl implements PreClone { - /** Pre-clonotype id */ - final long index; - /** Core key of the alignments group */ - final TagTuple coreKey; - /** Tag counter aggregating information about alignments with clonal sequence */ - final TagCount coreTagCount; - /** Tag counter aggregating information across all alignments assigned to this pre-clone */ - final TagCount fullTagCount; - /** Assembled clonal sequence */ - final NSequenceWithQuality[] clonalSequence; - /** Aggregated V, J, C gene scoring and content information */ - - final Map> geneScores; +public final class PreCloneImpl extends PreCloneAbstract { /** Reference point for each of the clonal sequences */ final ExtendedReferencePoints[] referencePoints; + final int numberOfReads; public PreCloneImpl(long index, TagTuple coreKey, TagCount coreTagCount, TagCount fullTagCount, NSequenceWithQuality[] clonalSequence, Map> geneScores, - ExtendedReferencePoints[] referencePoints) { - this.index = index; - this.coreKey = Objects.requireNonNull(coreKey); - this.coreTagCount = Objects.requireNonNull(coreTagCount); - this.fullTagCount = Objects.requireNonNull(fullTagCount); - this.clonalSequence = Objects.requireNonNull(clonalSequence); - this.geneScores = Objects.requireNonNull(geneScores); + ExtendedReferencePoints[] referencePoints, + int numberOfReads) { + super(index, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores); this.referencePoints = Objects.requireNonNull(referencePoints); - } - - @Override - public long getIndex() { - return index; - } - - @Override - public TagTuple getCoreKey() { - return coreKey; - } - - @Override - public TagCount getCoreTagCount() { - return coreTagCount; - } - - @Override - public TagCount getFullTagCount() { - return fullTagCount; - } - - @Override - public NSequenceWithQuality[] getClonalSequence() { - return clonalSequence; - } - - @Override - public Map> getGeneScores() { - return geneScores; - } - - @Override - public List getGeneScores(GeneType geneType) { - return geneScores.get(geneType); - } - - @Override - public GeneAndScore getBestHit(GeneType geneType) { - List gss = geneScores.get(geneType); - return gss == null || gss.isEmpty() - ? null - : gss.get(0); - } - - @Override - public VDJCGeneId getBestGene(GeneType geneType) { - GeneAndScore gs = getBestHit(geneType); - return gs == null ? null : gs.geneId; + this.numberOfReads = numberOfReads; } @Override @@ -101,28 +33,13 @@ public Range getRange(int csIdx, GeneFeature feature) { return referencePoints[csIdx].getRange(feature); } - public PreCloneImpl withIndex(long index) { - return new PreCloneImpl(index, coreKey, coreTagCount, fullTagCount, clonalSequence, geneScores, referencePoints); + @Override + public int getNumberOfReads() { + return numberOfReads; } - /** Converts alignment to a pre-clone, given the clonal gene features (assemblingFeatures) */ - public static PreCloneImpl fromAlignment(long index, VDJCAlignments alignment, GeneFeature... geneFeatures) { - NSequenceWithQuality[] clonalSequences = new NSequenceWithQuality[geneFeatures.length]; - - for (int i = 0; i < geneFeatures.length; i++) - clonalSequences[i] = Objects.requireNonNull(alignment.getFeature(geneFeatures[i])); - - Map> geneScores = new EnumMap<>(GeneType.class); - EnumMap hitsMap = alignment.getHitsMap(); - for (GeneType gt : GeneType.VDJC_REFERENCE) { - VDJCHit[] hits = hitsMap.get(gt); - List gss = new ArrayList<>(hits.length); - for (VDJCHit hit : hits) - gss.add(new GeneAndScore(hit.getGene().getId(), hit.getScore())); - assert CollectionUtils.isSorted(gss); - geneScores.put(gt, gss); - } - return new PreCloneImpl(index, TagTuple.NO_TAGS, alignment.getTagCount(), alignment.getTagCount(), - clonalSequences, geneScores, null); + public PreCloneImpl withIndex(long index) { + return new PreCloneImpl(index, coreKey, coreTagCount, fullTagCount, clonalSequence, + geneScores, referencePoints, numberOfReads); } } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java index d0a8f7c0d..fdfbd5ea3 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java @@ -1,5 +1,6 @@ package com.milaboratory.mixcr.assembler.preclone; +import com.milaboratory.mixcr.assembler.AlignmentsProvider; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; import com.milaboratory.mixcr.util.OutputPortWithProgress; @@ -9,7 +10,7 @@ public interface PreCloneReader extends AutoCloseable { /** Creates streamed pre-clone reader. */ - OutputPortWithProgress readPreClones(); + OutputPortWithProgress readPreClones(); /** * Creates streamed alignments reader. @@ -26,7 +27,7 @@ public interface PreCloneReader extends AutoCloseable { * Returns a PreCloneReader view of a given VDJCAlignmentsReader representing a set of pre-clones that are formed as * a one-to-one image of alignments that completely covers provided set of gene features */ - static PreCloneReader fromAlignments(VDJCAlignmentsReader alignmentsReader, GeneFeature[] geneFeatures) { + static PreCloneReader fromAlignments(AlignmentsProvider alignmentsReader, GeneFeature[] geneFeatures) { return new PreCloneReader() { private boolean alignmentPredicate(VDJCAlignments al) { for (GeneFeature geneFeature : geneFeatures) @@ -36,23 +37,23 @@ private boolean alignmentPredicate(VDJCAlignments al) { } @Override - public OutputPortWithProgress readPreClones() { + public OutputPortWithProgress readPreClones() { //noinspection resource OutputPortWithProgress alignmentReader = readAlignments(); - return new OutputPortWithProgress() { + return new OutputPortWithProgress() { @Override public long currentIndex() { return alignmentReader.currentIndex(); } @Override - public PreCloneImpl take() { + public PreClone take() { VDJCAlignments al; //noinspection StatementWithEmptyBody while ((al = alignmentReader.take()) != null && al.getCloneIndex() == -1) ; if (al == null) return null; - return PreCloneImpl.fromAlignment(al.getCloneIndex(), al, geneFeatures); + return PreClone.fromAlignment(al.getCloneIndex(), al, geneFeatures); } @Override @@ -76,7 +77,8 @@ public boolean isFinished() { public OutputPortWithProgress readAlignments() { Object sync = new Object(); AtomicLong idGenerator = new AtomicLong(); - VDJCAlignmentsReader.SecondaryReader reader = alignmentsReader.createRawSecondaryReader(); + // noinspection resource + OutputPortWithProgress reader = alignmentsReader.readAlignments(); return new OutputPortWithProgress() { @Override public long currentIndex() { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index ca113c374..b12eaba03 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -31,6 +31,7 @@ import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.cli.PipelineConfiguration; +import com.milaboratory.mixcr.assembler.AlignmentsProvider; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; @@ -57,6 +58,7 @@ public final class VDJCAlignmentsReader extends PipelineConfigurationReaderMiXCR implements OutputPortCloseable, + AlignmentsProvider, VDJCFileHeaderData, CanReportProgress { public static final int DEFAULT_CONCURRENCY = 4; @@ -230,6 +232,7 @@ public long getNumberOfAlignments() { return numberOfAlignments; } + @Override public long getNumberOfReads() { return numberOfReads; } @@ -283,7 +286,8 @@ public synchronized VDJCAlignments take() { return al.setAlignmentsIndex(counter++); } - public SecondaryReader createSecondaryReader() { + @Override + public SecondaryReader readAlignments() { ensureInitialized(); return new SecondaryReader(false); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index dc5061908..e8cd05850 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -32,7 +32,7 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.assembler.CloneAccumulator; import com.milaboratory.mixcr.assembler.CloneAssemblerListener; -import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; +import com.milaboratory.mixcr.assembler.preclone.PreClone; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.util.ReportHelper; @@ -182,33 +182,33 @@ public void onNewCloneCreated(CloneAccumulator accumulator) { } @Override - public void onFailedToExtractTarget(PreCloneImpl preClone) { + public void onFailedToExtractTarget(PreClone preClone) { failedToExtractTarget.addAndGet(preClone.getNumberOfReads()); } @Override - public void onTooManyLowQualityPoints(PreCloneImpl preClone) { + public void onTooManyLowQualityPoints(PreClone preClone) { droppedAsLowQuality.addAndGet(preClone.getNumberOfReads()); } @Override - public void onAlignmentDeferred(PreCloneImpl preClone) { + public void onAlignmentDeferred(PreClone preClone) { deferred.addAndGet(preClone.getNumberOfReads()); } @Override - public void onAlignmentAddedToClone(PreCloneImpl preClone, CloneAccumulator accumulator) { + public void onAlignmentAddedToClone(PreClone preClone, CloneAccumulator accumulator) { coreAlignments.addAndGet(preClone.getNumberOfReads()); alignmentsInClones.addAndGet(preClone.getNumberOfReads()); } @Override - public void onNoCandidateFoundForDeferredAlignment(PreCloneImpl preClone) { + public void onNoCandidateFoundForDeferredAlignment(PreClone preClone) { deferredAlignmentsDropped.addAndGet(preClone.getNumberOfReads()); } @Override - public void onDeferredAlignmentMappedToClone(PreCloneImpl preClone, CloneAccumulator accumulator) { + public void onDeferredAlignmentMappedToClone(PreClone preClone, CloneAccumulator accumulator) { deferredAlignmentsMapped.addAndGet(preClone.getNumberOfReads()); alignmentsInClones.addAndGet(preClone.getNumberOfReads()); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index e9e6acb5f..e2fb562bd 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -38,6 +38,7 @@ import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.*; +import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; @@ -223,158 +224,161 @@ public void run1() throws Exception { ".clna if -a / --write-alignments options specified."); - AlignmentsProvider alignmentsProvider = AlignmentsProvider.Util.createProvider( - in, VDJCLibraryRegistry.getDefault()); - - CloneAssemblerParameters assemblerParameters = getCloneAssemblerParameters(); - List genes = getGenes(); - VDJCAlignerParameters alignerParameters = getAlignerParameters(); - TagsInfo tagsInfo = getTagsInfo(); - - // Performing assembly - try (CloneAssembler assembler = new CloneAssembler(assemblerParameters, - isClnaOutput, - genes, alignerParameters.getFeaturesToAlignMap())) { - // Creating event listener to collect run statistics - report.setStartMillis(beginTimestamp); - report.setInputFiles(in); - report.setOutputFiles(out); - report.setCommandLine(getCommandLineArguments()); - - assembler.setListener(report); - - // Running assembler - CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner( - alignmentsProvider, - assembler); - SmartProgressReporter.startProgressReport(assemblerRunner); - - if (reportBuffers) { - StatusReporter reporter = new StatusReporter(); - reporter.addCustomProviderFromLambda(() -> - new StatusReporter.Status( - "Reader buffer: FIXME " /*+ assemblerRunner.getQueueSize()*/, - assemblerRunner.isFinished())); - reporter.start(); - } - assemblerRunner.run(); - - // Getting results - final CloneSet cloneSet = CloneSet.reorder(assemblerRunner.getCloneSet(alignerParameters, tagsInfo), getOrdering()); - - // Passing final cloneset to assemble last pieces of statistics for report - report.onClonesetFinished(cloneSet); - - // Writing results - PipelineConfiguration pipelineConfiguration = getFullPipelineConfiguration(); - if (isClnaOutput) { - - try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, - smartTempDestination(out, "", useSystemTemp),highCompression)) { - - // writer will supply current stage and completion percent to the progress reporter - SmartProgressReporter.startProgressReport(writer); - // Writing clone block - - writer.writeClones(cloneSet); - // Pre-soring alignments - try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(alignmentsProvider.create(), - assembler.getAssembledReadsPort())) { - OutputPort port = merged; - if (attachReadsByTags) { - Map tagsToClones = new HashMap<>(); - for (int i = 0; i < cloneSet.size(); i++) { - Clone clone = cloneSet.get(i); - assert i == clone.getId(); - TagCount tags = clone.getTagCount(); - TObjectDoubleIterator it = tags.iterator(); - while (it.hasNext()) { - it.advance(); - TagTuple tag = it.key(); - for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { - TagSignature sig = new TagSignature(tag, clone.getBestHit(gt).getGene().getId()); - Integer id = tagsToClones.get(sig); - if (id != null) - // Ambiguity (two or more clones with the same tag+gene signature) - tagsToClones.put(sig, -1); - else - tagsToClones.put(sig, clone.getId()); + try (VDJCAlignmentsReader aReader = new VDJCAlignmentsReader(in)) { + + CloneAssemblerParameters assemblerParameters = getCloneAssemblerParameters(); + List genes = getGenes(); + VDJCAlignerParameters alignerParameters = getAlignerParameters(); + TagsInfo tagsInfo = getTagsInfo(); + + // Performing assembly + try (CloneAssembler assembler = new CloneAssembler(assemblerParameters, + isClnaOutput, + genes, alignerParameters.getFeaturesToAlignMap())) { + // Creating event listener to collect run statistics + report.setStartMillis(beginTimestamp); + report.setInputFiles(in); + report.setOutputFiles(out); + report.setCommandLine(getCommandLineArguments()); + + assembler.setListener(report); + + // TODO >>>>>>>>>>>>>> + PreCloneReader preClones = PreCloneReader.fromAlignments(aReader, assemblerParameters.getAssemblingFeatures()); + + // Running assembler + CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner( + preClones, + assembler); + SmartProgressReporter.startProgressReport(assemblerRunner); + + if (reportBuffers) { + StatusReporter reporter = new StatusReporter(); + reporter.addCustomProviderFromLambda(() -> + new StatusReporter.Status( + "Reader buffer: FIXME " /*+ assemblerRunner.getQueueSize()*/, + assemblerRunner.isFinished())); + reporter.start(); + } + assemblerRunner.run(); + + // Getting results + final CloneSet cloneSet = CloneSet.reorder(assemblerRunner.getCloneSet(alignerParameters, tagsInfo), getOrdering()); + + // Passing final cloneset to assemble last pieces of statistics for report + report.onClonesetFinished(cloneSet); + + // Writing results + PipelineConfiguration pipelineConfiguration = getFullPipelineConfiguration(); + if (isClnaOutput) { + + try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, + smartTempDestination(out, "", useSystemTemp), highCompression)) { + + // writer will supply current stage and completion percent to the progress reporter + SmartProgressReporter.startProgressReport(writer); + // Writing clone block + + writer.writeClones(cloneSet); + // Pre-soring alignments + try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(preClones.readAlignments(), + assembler.getAssembledReadsPort())) { + OutputPort port = merged; + if (attachReadsByTags) { + Map tagsToClones = new HashMap<>(); + for (int i = 0; i < cloneSet.size(); i++) { + Clone clone = cloneSet.get(i); + assert i == clone.getId(); + TagCount tags = clone.getTagCount(); + TObjectDoubleIterator it = tags.iterator(); + while (it.hasNext()) { + it.advance(); + TagTuple tag = it.key(); + for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { + TagSignature sig = new TagSignature(tag, clone.getBestHit(gt).getGene().getId()); + Integer id = tagsToClones.get(sig); + if (id != null) + // Ambiguity (two or more clones with the same tag+gene signature) + tagsToClones.put(sig, -1); + else + tagsToClones.put(sig, clone.getId()); + } } } - } - // Remove ambiguous mappings - tagsToClones.entrySet().removeIf(e -> e.getValue() < 0); + // Remove ambiguous mappings + tagsToClones.entrySet().removeIf(e -> e.getValue() < 0); - port = () -> { - VDJCAlignments al = merged.take(); - if (al == null - || al.getMappingType() != ReadToCloneMapping.MappingType.Dropped - || al.getFeature(new GeneFeature(assemblerParameters.getAssemblingFeatures())) != null) // Dropped but has assembling feature - return al; + port = () -> { + VDJCAlignments al = merged.take(); + if (al == null + || al.getMappingType() != ReadToCloneMapping.MappingType.Dropped + || al.getFeature(new GeneFeature(assemblerParameters.getAssemblingFeatures())) != null) // Dropped but has assembling feature + return al; - // <-- Only dropped alignments not covering CDR3 + // <-- Only dropped alignments not covering CDR3 - TagCount tg = al.getTagCount(); - assert tg.size() == 1; // Both "align" and "assemblePartial" produces such alignments - TObjectDoubleIterator it = tg.iterator(); - it.advance(); - TagTuple tags = it.key(); + TagCount tg = al.getTagCount(); + assert tg.size() == 1; // Both "align" and "assemblePartial" produces such alignments + TObjectDoubleIterator it = tg.iterator(); + it.advance(); + TagTuple tags = it.key(); - VDJCHit hit; + VDJCHit hit; - int cloneMapping = -1; // -1 for not assigned, -2 for ambiguous - for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { - if ((hit = al.getBestHit(gt)) != null) { - TagSignature sig = new TagSignature(tags, hit.getGene().getId()); - Integer cloneId = tagsToClones.get(sig); - if (cloneId != null) - if (cloneMapping != -1 && cloneMapping != cloneId) - cloneMapping = -2; // V+Tag has different mapping than J+Tag - else - cloneMapping = cloneId; + int cloneMapping = -1; // -1 for not assigned, -2 for ambiguous + for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { + if ((hit = al.getBestHit(gt)) != null) { + TagSignature sig = new TagSignature(tags, hit.getGene().getId()); + Integer cloneId = tagsToClones.get(sig); + if (cloneId != null) + if (cloneMapping != -1 && cloneMapping != cloneId) + cloneMapping = -2; // V+Tag has different mapping than J+Tag + else + cloneMapping = cloneId; + } } - } - if (cloneMapping >= 0) { - report.onReadAttachedByTags(); - // TODO add count - return setMappingCloneIndex(al, cloneMapping); - } else if (cloneMapping == -2) - report.onReadWithAmbiguousAttachmentsByTags(); - else - report.onReadsFailedToAttachedByTags(); - - return al; - }; - } + if (cloneMapping >= 0) { + report.onReadAttachedByTags(); + // TODO add count + return setMappingCloneIndex(al, cloneMapping); + } else if (cloneMapping == -2) + report.onReadWithAmbiguousAttachmentsByTags(); + else + report.onReadsFailedToAttachedByTags(); + + return al; + }; + } - writer.collateAlignments(port, assembler.getAlignmentsCount()); + writer.collateAlignments(port, assembler.getAlignmentsCount()); + } + writer.writeAlignmentsAndIndex(); + } + } else + try (ClnsWriter writer = new ClnsWriter(out)) { + writer.writeCloneSet(pipelineConfiguration, cloneSet); } - writer.writeAlignmentsAndIndex(); - } - } else - try (ClnsWriter writer = new ClnsWriter(out)) { - writer.writeCloneSet(pipelineConfiguration, cloneSet); - } - // Writing report + // Writing report - report.setFinishMillis(System.currentTimeMillis()); + report.setFinishMillis(System.currentTimeMillis()); - assert cloneSet.getClones().size() == report.getCloneCount(); + assert cloneSet.getClones().size() == report.getCloneCount(); - report.setTotalReads(alignmentsProvider.getTotalNumberOfReads()); + report.setTotalReads(aReader.getNumberOfReads()); - // Writing report to stout - System.out.println("============= Report =============="); - ReportUtil.writeReportToStdout(report); + // Writing report to stout + System.out.println("============= Report =============="); + ReportUtil.writeReportToStdout(report); - if (reportFile != null) - ReportUtil.appendReport(reportFile, report); + if (reportFile != null) + ReportUtil.appendReport(reportFile, report); - if (jsonReport != null) - ReportUtil.appendJsonReport(jsonReport, report); + if (jsonReport != null) + ReportUtil.appendJsonReport(jsonReport, report); + } } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index 9b5d09c7f..12206b716 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -151,7 +151,7 @@ public void run1() throws Exception { } try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { - VDJCAlignmentsReader.SecondaryReader secondaryReader = mainReader.createSecondaryReader(); + VDJCAlignmentsReader.SecondaryReader secondaryReader = mainReader.readAlignments(); PrimitivIOStateBuilder stateBuilder = new PrimitivIOStateBuilder(); IOUtil.registerGeneReferences(stateBuilder, mainReader.getUsedGenes(), mainReader.getParameters()); diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index c77b35382..e92c9852c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -66,9 +66,9 @@ public void run0() throws Exception { FilePreCloneWriter writer = new FilePreCloneWriter(Paths.get(files.get(1)), TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp)) ) { - VDJCAlignmentsReader.SecondaryReader reader2 = reader1.createSecondaryReader(); + VDJCAlignmentsReader.SecondaryReader reader2 = reader1.readAlignments(); // For export - VDJCAlignmentsReader.SecondaryReader reader3 = reader1.createSecondaryReader(); + VDJCAlignmentsReader.SecondaryReader reader3 = reader1.readAlignments(); writer.init(reader1); @@ -98,7 +98,7 @@ public void run0() throws Exception { while ((result = assembler.getForNextGroup()) != null) { GroupOP grp = alGroups.take(); List clones = result.getClones(); - assert clones.isEmpty() || clones.get(0).coreKey.equals(grp.getKey()); + assert clones.isEmpty() || clones.get(0).getCoreKey().equals(grp.getKey()); totalClones += clones.size(); for (PreCloneImpl clone : clones) @@ -141,7 +141,7 @@ public void run0() throws Exception { numberOfAlignmentsCheck + " != 0)"); long numberOfClonesCheck = 0; - for (PreCloneImpl c : CUtils.it(reader.readPreClones())) + for (PreClone c : CUtils.it(reader.readPreClones())) numberOfClonesCheck++; if (numberOfClonesCheck != totalClones) diff --git a/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java index 4f1b71044..e0c35e98b 100644 --- a/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java +++ b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java @@ -50,7 +50,7 @@ public void close() { }; } - static OutputPortWithProgress wrap(long expectedSize, OutputPortCloseable inner) { + static OutputPortWithProgress wrap(long expectedSize, OutputPortCloseable inner) { final AtomicBoolean isFinished = new AtomicBoolean(false); final AtomicLong index = new AtomicLong(0); return new OutputPortWithProgress() { diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 4dcaf956b..d09a942c9 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -47,6 +47,7 @@ import com.milaboratory.mixcr.assembler.*; import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler; import com.milaboratory.mixcr.assembler.fullseq.FullSeqAssemblerParameters; +import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.cli.AlignerReport; @@ -94,17 +95,24 @@ public static AssembleResult assemble(final AlignResult align, boolean close) { CloneAssemblerReport report = new CloneAssemblerReport(); assembler.setListener(report); - CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner(new AlignmentsProvider() { + AlignmentsProvider aProvider = new AlignmentsProvider() { @Override - public OutputPortCloseable create() { - return opCloseable(CUtils.asOutputPort(align.alignments)); + public OutputPortWithProgress readAlignments() { + return OutputPortWithProgress.wrap(align.alignments.size(), CUtils.asOutputPort(align.alignments)); } - @Override - public long getTotalNumberOfReads() { + public long getNumberOfReads() { return align.alignments.size(); } - }, assembler); + + @Override + public void close() { + } + }; + + PreCloneReader preClones = PreCloneReader.fromAlignments(aProvider, + parameters.cloneAssemblerParameters.getAssemblingFeatures()); + CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner(preClones, assembler); //start progress reporting SmartProgressReporter.startProgressReport(assemblerRunner); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index e6785a1fe..b396425d2 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -39,6 +39,7 @@ import com.milaboratory.core.sequence.NucleotideSequence; import com.milaboratory.core.sequence.quality.QualityAggregationType; import com.milaboratory.core.tree.TreeSearchParameters; +import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.vdjaligners.*; import com.milaboratory.util.GlobalObjectMappers; @@ -100,7 +101,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException } } - AlignmentsProvider alignmentsProvider = AlignmentsProvider.Util.createProvider(vdjcaFile, VDJCLibraryRegistry.getDefault()); + AlignmentsProvider alignmentsProvider = new VDJCAlignmentsReader(vdjcaFile); LinearGapAlignmentScoring scoring = new LinearGapAlignmentScoring<>(NucleotideSequence.ALPHABET, 5, -9, -12); CloneFactoryParameters factoryParameters = new CloneFactoryParameters( @@ -120,7 +121,8 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException System.out.println(GlobalObjectMappers.toOneLine(assemblerParameters)); - CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner(alignmentsProvider, + CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner( + PreCloneReader.fromAlignments(alignmentsProvider, assemblerParameters.getAssemblingFeatures()), new CloneAssembler(assemblerParameters, true, aligner.getUsedGenes(), alignerParameters)); SmartProgressReporter.startProgressReport(assemblerRunner); assemblerRunner.run(); From 5561bc5d19743d6ebee1192653bd0fd2f9e44a6b Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 7 Jun 2022 14:21:34 +0400 Subject: [PATCH 261/282] Test fixes --- .../assembler/AlignmentsMappingMerger.java | 9 ++++++++- .../mixcr/assembler/ReadToCloneMapping.java | 20 +++++++++---------- .../assembler/preclone/PreCloneReader.java | 3 +-- .../com/milaboratory/mixcr/util/RunMiXCR.java | 14 +++++++++---- .../assembler/CloneAssemblerRunnerTest.java | 8 ++++---- .../mixcr/basictypes/ClnAReaderTest.java | 6 +++++- 6 files changed, 38 insertions(+), 22 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java index 9449d5c24..d6ed60fee 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java @@ -49,8 +49,15 @@ public VDJCAlignments take() { assert readToCloneMappings.take() == null; return null; } + + // here cloneIndex is set by a pre-clone block + // -1 == clone not included into any pre-clone + + if (al.getCloneIndex() == -1) + return al; ReadToCloneMapping m = readToCloneMappings.take(); - assert m.alignmentsId == al.getAlignmentsIndex(); + assert m.getPreCloneIdx() == al.getCloneIndex(); + return al.setMapping(m); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java b/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java index 54a04d7d6..b69562f17 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java @@ -38,14 +38,14 @@ public final class ReadToCloneMapping { public static final byte DROPPED_WITH_CLONE_MASK = 1 << 2; public static final byte PRE_CLUSTERED_MASK = 1 << 3; public static final byte DROPPED_MASK = 1 << 4; - final long alignmentsId; + final long preCloneIdx; final int cloneIndex; final byte mappingType; - public ReadToCloneMapping(long alignmentsId, int cloneIndex, boolean clustered, boolean additionalMapping, boolean droppedWithClone, boolean preClustered) { + public ReadToCloneMapping(long preCloneIdx, int cloneIndex, boolean clustered, boolean additionalMapping, boolean droppedWithClone, boolean preClustered) { if (cloneIndex < 0) cloneIndex = -1; - this.alignmentsId = alignmentsId; + this.preCloneIdx = preCloneIdx; this.cloneIndex = cloneIndex; assert !droppedWithClone || cloneIndex < 0; this.mappingType = (byte) ((clustered ? CLUSTERED_MASK : 0) @@ -59,8 +59,8 @@ public int getCloneIndex() { return cloneIndex; } - public long getAlignmentsId() { - return alignmentsId; + public long getPreCloneIdx() { + return preCloneIdx; } public boolean isClustered() { @@ -93,7 +93,7 @@ public byte getMappingTypeByte() { @Override public String toString() { - return isDropped() ? "" : "" + alignmentsId + " -> " + cloneIndex + " " + (isPreClustered() ? "p" : "") + (isClustered() ? "c" : "") + (isMapped() ? "m" : ""); + return isDropped() ? "" : "" + preCloneIdx + " -> " + cloneIndex + " " + (isPreClustered() ? "p" : "") + (isClustered() ? "c" : "") + (isMapped() ? "m" : ""); } @Override @@ -103,14 +103,14 @@ public boolean equals(Object o) { ReadToCloneMapping that = (ReadToCloneMapping) o; - if (alignmentsId != that.alignmentsId) return false; + if (preCloneIdx != that.preCloneIdx) return false; if (cloneIndex != that.cloneIndex) return false; return mappingType == that.mappingType; } @Override public int hashCode() { - int result = (int) (alignmentsId ^ (alignmentsId >>> 32)); + int result = (int) (preCloneIdx ^ (preCloneIdx >>> 32)); result = 31 * result + cloneIndex; result = 31 * result + (int) mappingType; return result; @@ -217,7 +217,7 @@ public int compare(ReadToCloneMapping o1, ReadToCloneMapping o2) { int c; if ((c = Integer.compare(o1.cloneIndex, o2.cloneIndex)) != 0) return c; - if ((c = Long.compare(o1.alignmentsId, o2.alignmentsId)) != 0) + if ((c = Long.compare(o1.preCloneIdx, o2.preCloneIdx)) != 0) return c; return Byte.compare(o1.mappingType, o2.mappingType); } @@ -238,7 +238,7 @@ private AlignmentsComparator() { @Override public int compare(ReadToCloneMapping o1, ReadToCloneMapping o2) { int c; - if ((c = Long.compare(o1.alignmentsId, o2.alignmentsId)) != 0) + if ((c = Long.compare(o1.preCloneIdx, o2.preCloneIdx)) != 0) return c; if ((c = Integer.compare(o1.cloneIndex, o2.cloneIndex)) != 0) return c; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java index fdfbd5ea3..5d76ba450 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java @@ -77,7 +77,6 @@ public boolean isFinished() { public OutputPortWithProgress readAlignments() { Object sync = new Object(); AtomicLong idGenerator = new AtomicLong(); - // noinspection resource OutputPortWithProgress reader = alignmentsReader.readAlignments(); return new OutputPortWithProgress() { @Override @@ -93,7 +92,7 @@ public VDJCAlignments take() { return null; - if(!alignmentPredicate(al)) + if(alignmentPredicate(al)) al = al.withCloneIndexAndMappingType(idGenerator.getAndIncrement(), (byte) 0) .setAlignmentsIndex(al.getAlignmentsIndex()); diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index d09a942c9..82f356154 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -34,7 +34,6 @@ import cc.redberry.pipe.OutputPortCloseable; import cc.redberry.pipe.blocks.ParallelProcessor; import cc.redberry.pipe.util.Chunk; -import cc.redberry.pipe.util.Indexer; import cc.redberry.pipe.util.OrderedOutputPort; import com.milaboratory.core.io.sequence.PairedRead; import com.milaboratory.core.io.sequence.SequenceRead; @@ -61,7 +60,6 @@ import com.milaboratory.primitivio.PrimitivO; import com.milaboratory.util.CanReportProgress; import com.milaboratory.util.SmartProgressReporter; -import com.milaboratory.util.TempFileManager; import io.repseq.core.Chains; import io.repseq.core.VDJCGene; import io.repseq.core.VDJCLibraryRegistry; @@ -73,7 +71,8 @@ import static cc.redberry.pipe.CUtils.chunked; import static cc.redberry.pipe.CUtils.unchunked; -import static com.milaboratory.util.TempFileManager.*; +import static com.milaboratory.util.TempFileManager.getTempFile; +import static com.milaboratory.util.TempFileManager.systemTempFolderDestination; /** * @author Dmitry Bolotin @@ -100,6 +99,7 @@ public static AssembleResult assemble(final AlignResult align, boolean close) { public OutputPortWithProgress readAlignments() { return OutputPortWithProgress.wrap(align.alignments.size(), CUtils.asOutputPort(align.alignments)); } + @Override public long getNumberOfReads() { return align.alignments.size(); @@ -137,9 +137,10 @@ public static FullSeqAssembleResult assembleContigs(final AssembleResult assembl // Writing clone block writer.writeClones(assemble.cloneSet); + PreCloneReader preCloneReader = align.asPreCloneReader(); // Pre-soring alignments try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger( - CUtils.asOutputPort(align.alignments), + preCloneReader.readAlignments(), assemble.cloneAssembler.getAssembledReadsPort())) { writer.collateAlignments(merged, assemble.cloneAssembler.getAlignmentsCount()); } @@ -301,6 +302,11 @@ public VDJCAlignmentsReader resultReader() throws IOException { } return new VDJCAlignmentsReader(alignmentsFile); } + + public PreCloneReader asPreCloneReader() throws IOException { + return PreCloneReader.fromAlignments(resultReader(), + parameters.cloneAssemblerParameters.getAssemblingFeatures()); + } } public static final class RunMiXCRAnalysis { diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index b396425d2..7effbc75f 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -41,6 +41,7 @@ import com.milaboratory.core.tree.TreeSearchParameters; import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.basictypes.*; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.*; import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.SmartProgressReporter; @@ -55,7 +56,6 @@ import java.util.Arrays; public class CloneAssemblerRunnerTest { - @Ignore @Test public void test1() throws Exception { String[] str = {"sequences/sample_IGH_R1.fastq", "sequences/sample_IGH_R2.fastq"}; @@ -78,7 +78,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException VDJCAlignerParameters alignerParameters = VDJCParametersPresets.getByName("default"); VDJCAligner aligner = fastqFiles.length == 1 ? new VDJCAlignerS(alignerParameters) : new VDJCAlignerWithMerge(alignerParameters); - for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("mi", "hs").getGenes(Chains.IGH)) + for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes(Chains.IGH)) if (alignerParameters.containsRequiredFeature(gene)) aligner.addGene(gene); @@ -110,7 +110,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException new VJCClonalAlignerParameters(0.8f, scoring, 5), null, - new DAlignerParameters(GeneFeature.DRegion, 0.85f, 30.0f, 3, scoring) + new DClonalAlignerParameters(0.85f, 30.0f, 3, scoring) ); CloneAssemblerParameters assemblerParameters = new CloneAssemblerParameters( @@ -127,7 +127,7 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException SmartProgressReporter.startProgressReport(assemblerRunner); assemblerRunner.run(); - CloneSet cloneSet = assemblerRunner.getCloneSet(null, null); + CloneSet cloneSet = assemblerRunner.getCloneSet(alignerParameters, TagsInfo.NO_TAGS); File tmpClnsFile = TempFileManager.getTempFile(); diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java index 2d8d4297a..31ce483b2 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java @@ -37,6 +37,7 @@ import com.milaboratory.mixcr.assembler.AlignmentsMappingMerger; import com.milaboratory.mixcr.assembler.CloneAssemblerParametersPresets; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; +import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.util.MiXCRVersionInfo; import com.milaboratory.mixcr.util.RunMiXCR; import com.milaboratory.util.TempFileManager; @@ -85,7 +86,9 @@ public void testGeneric(Function, List> modifyClones, RunMiXCR.AlignResult align = RunMiXCR.align(params); RunMiXCR.AssembleResult assemble = RunMiXCR.assemble(align, false); - AlignmentsMappingMerger merged = new AlignmentsMappingMerger(align.resultReader(), assemble.cloneAssembler.getAssembledReadsPort()); + PreCloneReader preCloneReader = align.asPreCloneReader(); + AlignmentsMappingMerger merged = new AlignmentsMappingMerger(preCloneReader.readAlignments(), + assemble.cloneAssembler.getAssembledReadsPort()); File file = TempFileManager.getTempFile(); ClnAWriter writer = new ClnAWriter(null, file, smartTempDestination(file, "", false)); @@ -100,6 +103,7 @@ public void testGeneric(Function, List> modifyClones, null, new VDJCSProperties.CloneOrdering(new VDJCSProperties.CloneCount())); writer.writeClones(newCloneSet); + OutputPort als = modifyAlignments.apply(merged); CountingOutputPort alsc = new CountingOutputPort<>(als); writer.collateAlignments(alsc, align.alignments.size()); From 47165329c97fcdc2ef3fa738b2322b770d1c7abf Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 7 Jun 2022 17:42:53 +0400 Subject: [PATCH 262/282] version fix --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 8356dd1b5..107c9eb49 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -81,7 +81,7 @@ repositories { } } -val milibVersion = "1.15.0-53-master" +val milibVersion = "1.15.0-54-master" val repseqioVersion = "1.3.5-34-master" val mitoolVersion = "0.9.1-16-main" val miplotsVersion = "0.1-22-master" From a7fea31f3752021ad762eb50ec8c85941ced8f48 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 7 Jun 2022 21:25:24 +0400 Subject: [PATCH 263/282] WIP close to the tagged assembly --- .../assembler/AlignmentsMappingMerger.java | 9 +- .../preclone/FilePreCloneWriter.java | 9 +- .../assembler/preclone/PreCloneAssembler.java | 19 ++- .../preclone/PreCloneAssemblerParameters.java | 20 +++ .../preclone/PreCloneAssemblerRunner.java | 128 ++++++++++++++++ .../basictypes/VDJCAlignmentsReader.java | 1 + .../mixcr/basictypes/tag/TagsInfo.java | 24 ++- .../mixcr/cli/CloneAssemblerReport.java | 18 +++ .../mixcr/cli/CommandAssemble.java | 142 +++++++----------- .../cli/CommandAssemblePartialAlignments.java | 2 +- .../mixcr/cli/CommandCorrectAndSortTags.java | 10 +- .../cli/ITestCommandAssemblePreClones.java | 81 +++------- .../mixcr/export/FieldExtractors.java | 2 +- 13 files changed, 298 insertions(+), 167 deletions(-) create mode 100644 src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java index d6ed60fee..4aac6509c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java @@ -36,6 +36,7 @@ public final class AlignmentsMappingMerger implements OutputPortCloseable { final OutputPort alignments; final OutputPort readToCloneMappings; + ReadToCloneMapping lastMapping; public AlignmentsMappingMerger(OutputPort alignments, OutputPort readToCloneMappings) { this.alignments = alignments; @@ -55,10 +56,12 @@ public VDJCAlignments take() { if (al.getCloneIndex() == -1) return al; - ReadToCloneMapping m = readToCloneMappings.take(); - assert m.getPreCloneIdx() == al.getCloneIndex(); - return al.setMapping(m); + if(lastMapping == null || lastMapping.getPreCloneIdx() != al.getCloneIndex()) + lastMapping = readToCloneMappings.take(); + assert lastMapping.getPreCloneIdx() == al.getCloneIndex(); + + return al.setMapping(lastMapping); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java index 1e41821ba..ee8c4407c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java @@ -60,6 +60,8 @@ public final class FilePreCloneWriter implements AutoCloseable, CanReportProgres private volatile HashSorter cloneCollator; private volatile OutputPortCloseable sortedClones; + private volatile boolean finished = false; + public FilePreCloneWriter(Path file, TempFileDest tempDest) throws IOException { this.output = new PrimitivOHybrid(ForkJoinPool.commonPool(), file); this.tempDest = tempDest; @@ -216,6 +218,8 @@ public void finish() { } ps.finish(); + + finished = true; } @Override @@ -234,7 +238,10 @@ public String getStage() { } @Override - public void close() throws Exception { + public void close() throws IOException { + if (!finished) + throw new IllegalStateException("Closing writer without calling finish() first."); + if (alignmentSortingThread != null) { alignmentSorterInput.put(null); try { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index bfb7af5ac..bee6aef02 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -42,15 +42,28 @@ public final class PreCloneAssembler { private final PreCloneAssemblerReport report = new PreCloneAssemblerReport(); private final AtomicLong idGenerator = new AtomicLong(); private final PreCloneAssemblerParameters parameters; + private final Function1 groupingFunction; private final OutputPort> alignmentsReader1, alignmentsReader2; public PreCloneAssembler(PreCloneAssemblerParameters parameters, OutputPort alignmentsReader1, OutputPort alignmentsReader2) { this.parameters = parameters; - Function1 gFunction = a -> a.getTagCount().asKeyPrefixOrError(parameters.groupingLevel); - this.alignmentsReader1 = PipeKt.group(alignmentsReader1, gFunction); - this.alignmentsReader2 = PipeKt.group(alignmentsReader2, gFunction); + this.groupingFunction = groupingFunction(parameters.groupingLevel); + this.alignmentsReader1 = PipeKt.group(alignmentsReader1, groupingFunction); + this.alignmentsReader2 = PipeKt.group(alignmentsReader2, groupingFunction); + } + + private static Function1 groupingFunction(int depth) { + return a -> a.getTagCount().asKeyPrefixOrError(depth); + } + + public Function1 getGroupingFunction() { + return groupingFunction; + } + + public PreCloneAssemblerParameters getParameters() { + return parameters; } public PreCloneAssemblerReport getReport() { diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java index 10033973d..2dc323801 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java @@ -1,5 +1,7 @@ package com.milaboratory.mixcr.assembler.preclone; +import com.milaboratory.core.alignment.LinearGapAlignmentScoring; +import com.milaboratory.mitool.consensus.AAssemblerParameters; import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; import com.milaboratory.mixcr.basictypes.HasRelativeMinScore; import io.repseq.core.GeneFeature; @@ -18,4 +20,22 @@ public PreCloneAssemblerParameters(GConsensusAssemblerParameters assemblerParame this.assemblingFeatures = assemblingFeatures; this.groupingLevel = groupingLevel; } + + public static final AAssemblerParameters DefaultAAssemblerParams = AAssemblerParameters.builder() + .bandWidth(4) + .scoring(LinearGapAlignmentScoring.getNucleotideBLASTScoring(-14)) + .minAlignmentScore(40) + .maxAlignmentPenalty(33) + .trimMinimalSumQuality(20) + .trimReferenceRegion(false) + .maxQuality((byte) 45) + .build(); + + public static final GConsensusAssemblerParameters DefaultGConsensusAssemblerParameters = GConsensusAssemblerParameters.builder() + .aAssemblerParameters(DefaultAAssemblerParams) + .maxIterations(4) + .minAltSeedQualityScore((byte) 11) + .minimalRecordShare(0.1) + .minimalRecordCount(2) + .build(); } diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java new file mode 100644 index 000000000..2d5bb7dbe --- /dev/null +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java @@ -0,0 +1,128 @@ +package com.milaboratory.mixcr.assembler.preclone; + +import cc.redberry.pipe.CUtils; +import cc.redberry.pipe.OutputPort; +import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; +import com.milaboratory.mitool.helpers.GroupOP; +import com.milaboratory.mitool.helpers.PipeKt; +import com.milaboratory.mixcr.basictypes.VDJCAlignments; +import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; +import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagType; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; +import com.milaboratory.util.CanReportProgressAndStage; +import com.milaboratory.util.ProgressAndStage; +import com.milaboratory.util.TempFileDest; +import io.repseq.core.GeneFeature; + +import java.io.IOException; +import java.nio.file.Path; +import java.util.List; + +public final class PreCloneAssemblerRunner implements CanReportProgressAndStage, AutoCloseable { + private final ProgressAndStage ps = new ProgressAndStage("Initialization"); + + private final VDJCAlignmentsReader alignments; + + // It takes three passes over the alignments file from scratch to final file with pre-clones + private final VDJCAlignmentsReader.SecondaryReader reader1, reader2, reader3; + private final PreCloneAssembler assembler; + private final Path outputFile; + private final TempFileDest tempDest; + + public PreCloneAssemblerRunner(VDJCAlignmentsReader alignments, + TagType groupingLevel, + GeneFeature[] assemblingFeatures, + GConsensusAssemblerParameters gAssemblerParams, + Path outputFile, + TempFileDest tempDest) { + this.alignments = alignments; + + TagsInfo tagsInfo = alignments.getTagsInfo(); + int depth = tagsInfo.getDepthFor(groupingLevel); + if (tagsInfo.getSortingLevel() < depth) + throw new IllegalArgumentException("Input file has insufficient sorting level"); + + PreCloneAssemblerParameters assemblerParams = new PreCloneAssemblerParameters( + gAssemblerParams, alignments.getParameters(), + assemblingFeatures, depth); + + this.reader1 = alignments.readAlignments(); + this.reader2 = alignments.readAlignments(); + this.reader3 = alignments.readAlignments(); + + // Progress of the first step can either be tracked by reader1 or reader2 + ps.delegate("Building pre-clones from tag groups", reader1); + + this.assembler = new PreCloneAssembler(assemblerParams, + CUtils.wrap(reader1, VDJCAlignments::ensureKeyTags), + CUtils.wrap(reader2, VDJCAlignments::ensureKeyTags)); + + this.outputFile = outputFile; + this.tempDest = tempDest; + } + + public PreCloneAssemblerReport getReport() { + return assembler.getReport(); + } + + public void run() throws IOException { + try (FilePreCloneWriter writer = new FilePreCloneWriter(outputFile, tempDest)) { + OutputPort> alGroups = PipeKt.group( + CUtils.wrap(reader3, VDJCAlignments::ensureKeyTags), assembler.getGroupingFunction()); + writer.init(alignments); + + PreCloneAssemblerResult result; + while ((result = assembler.getForNextGroup()) != null) { + GroupOP grp = alGroups.take(); + List clones = result.getClones(); + assert clones.isEmpty() || clones.get(0).getCoreKey().equals(grp.getKey()); + + for (PreCloneImpl clone : clones) + writer.putClone(clone); + + int localId = 0; + for (VDJCAlignments al : CUtils.it(grp)) { + long cloneMapping = result.getCloneForAlignment(localId++); + writer.putAlignment(cloneMapping != -1 + ? al.withCloneIndexAndMappingType(cloneMapping, (byte) 0) + : al); + } + } + + ps.delegate("Writing pre-clones", writer); + + writer.finish(); + } finally { + ps.unDelegate(); + ps.finish(); + } + } + + /** Creates a reader to access the result of this operation */ + public FilePreCloneReader createReader() throws IOException { + return new FilePreCloneReader(outputFile); + } + + @Override + public double getProgress() { + return ps.getProgress(); + } + + @Override + public boolean isFinished() { + return ps.isFinished(); + } + + @Override + public String getStage() { + return ps.getStage(); + } + + @Override + public void close() throws Exception { + reader1.close(); + reader2.close(); + reader3.close(); + } +} diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index b12eaba03..3c22b6646 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -198,6 +198,7 @@ public synchronized PipelineConfiguration getPipelineConfiguration() { @Override public TagsInfo getTagsInfo() { + // TODO 4.0 ensure not null everywhere ensureInitialized(); return tagsInfo; } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index cb0cc5676..2e4c7ca67 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -5,16 +5,17 @@ import com.milaboratory.primitivio.annotations.Serializable; import java.util.Arrays; +import java.util.Iterator; import java.util.Objects; @Serializable(asJson = true) -public final class TagsInfo { +public final class TagsInfo implements Iterable { public static final TagsInfo NO_TAGS = new TagsInfo(0); @JsonProperty("sortingLevel") - public final int sortingLevel; + final int sortingLevel; @JsonProperty("tags") - public final TagInfo[] tags; + final TagInfo[] tags; @JsonCreator public TagsInfo(@JsonProperty("sortingLevel") int sortingLevel, @JsonProperty("tags") TagInfo... tags) { @@ -23,6 +24,13 @@ public TagsInfo(@JsonProperty("sortingLevel") int sortingLevel, @JsonProperty("t this.tags = tags; } + public boolean hasTagsWithType(TagType groupingLevel) { + for (TagInfo tag : tags) + if (tag.getType() == groupingLevel) + return true; + return false; + } + public int getDepthFor(TagType groupingLevel) { for (int i = 0; i < tags.length; i++) if (tags[i].getType().ordinal() > groupingLevel.ordinal()) @@ -42,10 +50,20 @@ public int getSortingLevel() { return sortingLevel; } + public boolean hasNoTags() { + return tags.length == 0; + } + public TagsInfo setSorted(int sortedLevel) { return new TagsInfo(sortedLevel, tags); } + @Override + @SuppressWarnings("NullableProblems") + public Iterator iterator() { + return Arrays.asList(tags).iterator(); + } + @Override public boolean equals(Object o) { if (this == o) return true; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index e8cd05850..46ab8dcec 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -33,6 +33,7 @@ import com.milaboratory.mixcr.assembler.CloneAccumulator; import com.milaboratory.mixcr.assembler.CloneAssemblerListener; import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerReport; import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.basictypes.CloneSet; import com.milaboratory.util.ReportHelper; @@ -42,6 +43,7 @@ public final class CloneAssemblerReport extends AbstractCommandReport implements CloneAssemblerListener { private final ChainUsageStats chainStats = new ChainUsageStats(); + private PreCloneAssemblerReport preCloneAssemblerReport; long totalReads = -1; final AtomicInteger clonesCreated = new AtomicInteger(); final AtomicLong failedToExtractTarget = new AtomicLong(); @@ -67,6 +69,18 @@ public String getCommand() { return "assemble"; } + // TODO 4.0 + // @JsonProperty("preCloneAssemblerReport") + public PreCloneAssemblerReport getPreCloneAssemblerReport() { + return preCloneAssemblerReport; + } + + public void setPreCloneAssemblerReport(PreCloneAssemblerReport preCloneAssemblerReport) { + if (this.preCloneAssemblerReport != null) + throw new IllegalStateException("Pre-clone assembler report already set."); + this.preCloneAssemblerReport = preCloneAssemblerReport; + } + @JsonProperty("totalReadsProcessed") public long getTotalReads() { return totalReads; @@ -269,6 +283,10 @@ public void writeReport(ReportHelper helper) { // Writing common analysis information writeSuperReport(helper); + // Writing pre-clone assembler report (should be present for barcoded analysis) + if (preCloneAssemblerReport != null) + preCloneAssemblerReport.writeReport(helper); + if (totalReads == -1) throw new IllegalStateException("TotalReads count not set."); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index e2fb562bd..ec6d90557 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -38,22 +38,23 @@ import com.milaboratory.cli.ActionConfiguration; import com.milaboratory.cli.PipelineConfiguration; import com.milaboratory.mixcr.assembler.*; +import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerParameters; +import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerRunner; import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; +import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; -import com.milaboratory.util.ArraysUtils; -import com.milaboratory.util.JsonOverrider; -import com.milaboratory.util.ReportUtil; -import com.milaboratory.util.SmartProgressReporter; +import com.milaboratory.util.*; import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.*; import picocli.CommandLine.Command; import picocli.CommandLine.Option; import java.io.IOException; +import java.nio.file.Path; import java.util.HashMap; import java.util.List; import java.util.Map; @@ -110,9 +111,11 @@ public void setThreads(int threads) { names = {"-a", "--write-alignments"}) public boolean isClnaOutput = false; - @Option(description = "Enable tag-based read to clone assignment", - names = {"--attach-reads-by-tags"}) - public boolean attachReadsByTags = false; + @Option(description = "If tags are present assemble pre-clones on the cell level rather than on the molecule level. " + + "If there are no molecular tags in the data, but cell tags are present, this option will be used by default. " + + "This option has no effect on the data without tags.", + names = {"--cell-level"}) + public boolean cellLevel = false; private static final double DEFAULT_MINIMAL_TAG_SET_OVERLAP = 0.7; @@ -151,10 +154,11 @@ private void ensureParametersInitialized() { assemblerParameters = CloneAssemblerParametersPresets.getByName(assemblerParametersName); if (assemblerParameters == null) throwValidationException("Unknown parameters: " + assemblerParametersName); + // noinspection ConstantConditions assemblerParameters = assemblerParameters.updateFrom(alignerParameters); - if (attachReadsByTags) - assemblerParameters = assemblerParameters.setCloneClusteringParameters(assemblerParameters.getCloneClusteringParameters().setMinimalTagSetOverlap(DEFAULT_MINIMAL_TAG_SET_OVERLAP)); + // TODO 4.0 ??? + // assemblerParameters = assemblerParameters.setCloneClusteringParameters(assemblerParameters.getCloneClusteringParameters().setMinimalTagSetOverlap(DEFAULT_MINIMAL_TAG_SET_OVERLAP)); // Overriding JSON parameters if (!overrides.isEmpty()) { @@ -217,20 +221,24 @@ public void run1() throws Exception { // Saving initial timestamp long beginTimestamp = System.currentTimeMillis(); + // Will be used for several operations requiring disk offloading + TempFileDest tempDest = smartTempDestination(out, "", useSystemTemp); + // Checking consistency between actionParameters.doWriteClnA() value and file extension if ((getOutput().toLowerCase().endsWith(".clna") && !isClnaOutput) || (getOutput().toLowerCase().endsWith(".clns") && isClnaOutput)) warn("WARNING: Unexpected file extension, use .clns extension for clones-only (normal) output and\n" + ".clna if -a / --write-alignments options specified."); - - try (VDJCAlignmentsReader aReader = new VDJCAlignmentsReader(in)) { + try (VDJCAlignmentsReader alignmentsReader = new VDJCAlignmentsReader(in)) { CloneAssemblerParameters assemblerParameters = getCloneAssemblerParameters(); List genes = getGenes(); VDJCAlignerParameters alignerParameters = getAlignerParameters(); TagsInfo tagsInfo = getTagsInfo(); + // tagsInfo.getSortingLevel() + // Performing assembly try (CloneAssembler assembler = new CloneAssembler(assemblerParameters, isClnaOutput, @@ -244,7 +252,36 @@ public void run1() throws Exception { assembler.setListener(report); // TODO >>>>>>>>>>>>>> - PreCloneReader preClones = PreCloneReader.fromAlignments(aReader, assemblerParameters.getAssemblingFeatures()); + PreCloneReader preClones; + if (tagsInfo.hasTagsWithType(TagType.CellTag) || tagsInfo.hasTagsWithType(TagType.MoleculeTag)) { + int depth = tagsInfo.getDepthFor(cellLevel ? TagType.CellTag : TagType.MoleculeTag); + if (tagsInfo.getSortingLevel() < depth) + throwValidationException("Input file has insufficient sorting level"); + PreCloneAssemblerParameters preAssemblerParams = new PreCloneAssemblerParameters( + PreCloneAssemblerParameters.DefaultGConsensusAssemblerParameters, + alignmentsReader.getParameters(), + assemblerParameters.getAssemblingFeatures(), + depth); + Path preClonesFile = tempDest.resolvePath("preclones.pc"); + + PreCloneAssemblerRunner assemblerRunner = new PreCloneAssemblerRunner( + alignmentsReader, + cellLevel ? TagType.CellTag : TagType.MoleculeTag, + new GeneFeature[]{GeneFeature.CDR3}, + PreCloneAssemblerParameters.DefaultGConsensusAssemblerParameters, + preClonesFile, tempDest.addSuffix("pc.tmp")); + SmartProgressReporter.startProgressReport(assemblerRunner); + + // Pre-clone assembly happens here (file with pre-clones and alignments written as a result) + assemblerRunner.run(); + + // Setting report into a big report object + report.setPreCloneAssemblerReport(assemblerRunner.getReport()); + + preClones = assemblerRunner.createReader(); + } else + // If there are no tags in the data, alignments are just wrapped into pre-clones + preClones = PreCloneReader.fromAlignments(alignmentsReader, assemblerParameters.getAssemblingFeatures()); // Running assembler CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner( @@ -271,89 +308,22 @@ public void run1() throws Exception { // Writing results PipelineConfiguration pipelineConfiguration = getFullPipelineConfiguration(); if (isClnaOutput) { - try (ClnAWriter writer = new ClnAWriter(pipelineConfiguration, out, - smartTempDestination(out, "", useSystemTemp), highCompression)) { + tempDest, highCompression)) { // writer will supply current stage and completion percent to the progress reporter SmartProgressReporter.startProgressReport(writer); // Writing clone block writer.writeClones(cloneSet); + // Pre-soring alignments - try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger(preClones.readAlignments(), + try (AlignmentsMappingMerger merged = new AlignmentsMappingMerger( + preClones.readAlignments(), assembler.getAssembledReadsPort())) { - OutputPort port = merged; - if (attachReadsByTags) { - Map tagsToClones = new HashMap<>(); - for (int i = 0; i < cloneSet.size(); i++) { - Clone clone = cloneSet.get(i); - assert i == clone.getId(); - TagCount tags = clone.getTagCount(); - TObjectDoubleIterator it = tags.iterator(); - while (it.hasNext()) { - it.advance(); - TagTuple tag = it.key(); - for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { - TagSignature sig = new TagSignature(tag, clone.getBestHit(gt).getGene().getId()); - Integer id = tagsToClones.get(sig); - if (id != null) - // Ambiguity (two or more clones with the same tag+gene signature) - tagsToClones.put(sig, -1); - else - tagsToClones.put(sig, clone.getId()); - } - } - } - - // Remove ambiguous mappings - tagsToClones.entrySet().removeIf(e -> e.getValue() < 0); - - port = () -> { - VDJCAlignments al = merged.take(); - if (al == null - || al.getMappingType() != ReadToCloneMapping.MappingType.Dropped - || al.getFeature(new GeneFeature(assemblerParameters.getAssemblingFeatures())) != null) // Dropped but has assembling feature - return al; - - // <-- Only dropped alignments not covering CDR3 - - TagCount tg = al.getTagCount(); - assert tg.size() == 1; // Both "align" and "assemblePartial" produces such alignments - TObjectDoubleIterator it = tg.iterator(); - it.advance(); - TagTuple tags = it.key(); - - VDJCHit hit; - - int cloneMapping = -1; // -1 for not assigned, -2 for ambiguous - for (GeneType gt : new GeneType[]{GeneType.Variable, GeneType.Joining}) { - if ((hit = al.getBestHit(gt)) != null) { - TagSignature sig = new TagSignature(tags, hit.getGene().getId()); - Integer cloneId = tagsToClones.get(sig); - if (cloneId != null) - if (cloneMapping != -1 && cloneMapping != cloneId) - cloneMapping = -2; // V+Tag has different mapping than J+Tag - else - cloneMapping = cloneId; - } - } - - if (cloneMapping >= 0) { - report.onReadAttachedByTags(); - // TODO add count - return setMappingCloneIndex(al, cloneMapping); - } else if (cloneMapping == -2) - report.onReadWithAmbiguousAttachmentsByTags(); - else - report.onReadsFailedToAttachedByTags(); - - return al; - }; - } - - writer.collateAlignments(port, assembler.getAlignmentsCount()); + writer.collateAlignments(merged, assembler.getAlignmentsCount()); } + writer.writeAlignmentsAndIndex(); } } else @@ -367,7 +337,7 @@ public void run1() throws Exception { assert cloneSet.getClones().size() == report.getCloneCount(); - report.setTotalReads(aReader.getNumberOfReads()); + report.setTotalReads(alignmentsReader.getNumberOfReads()); // Writing report to stout System.out.println("============= Report =============="); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 37b0c938a..c8289046f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -146,7 +146,7 @@ public void run1() throws Exception { report.setOutputFiles(out); report.setCommandLine(getCommandLineArguments()); - if (reader1.getTagsInfo() != null && reader1.getTagsInfo().tags.length > 0) { + if (reader1.getTagsInfo() != null && reader1.getTagsInfo().hasNoTags()) { SmartProgressReporter.startProgressReport("Running assemble partial", reader1); // This processor strips all non-key information from the diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index 12206b716..ebe781ee5 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -113,11 +113,11 @@ public void run1() throws Exception { tagNames = new ArrayList<>(); TIntArrayList indicesBuilder = new TIntArrayList(); - for (int i = 0; i < tagsInfo.tags.length; i++) { - TagInfo tag = tagsInfo.tags[i]; - assert i == tag.getIndex(); // just in case + for (int ti = 0; ti < tagsInfo.size(); ti++) { + TagInfo tag = tagsInfo.get(ti); + assert ti == tag.getIndex(); // just in case if (tag.getValueType() == TagValueType.SequenceAndQuality) - indicesBuilder.add(i); + indicesBuilder.add(ti); tagNames.add(tag.getName()); } targetTagIndices = indicesBuilder.toArray(); @@ -212,7 +212,7 @@ public void run1() throws Exception { // Initializing and writing results to the output file writer.header(mainReader, getFullPipelineConfiguration(), - mainReader.getTagsInfo().setSorted(mainReader.getTagsInfo().tags.length)); + mainReader.getTagsInfo().setSorted(mainReader.getTagsInfo().size())); for (VDJCAlignments al : CUtils.it(sorted)) writer.write(al); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index e92c9852c..18e13f205 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -1,24 +1,21 @@ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; -import cc.redberry.pipe.OutputPort; -import cc.redberry.pipe.util.CountingOutputPort; import com.milaboratory.core.alignment.LinearGapAlignmentScoring; import com.milaboratory.mitool.consensus.AAssemblerParameters; import com.milaboratory.mitool.consensus.GConsensusAssemblerParameters; -import com.milaboratory.mitool.helpers.GroupOP; -import com.milaboratory.mitool.helpers.PipeKt; -import com.milaboratory.mixcr.assembler.preclone.*; +import com.milaboratory.mixcr.assembler.preclone.FilePreCloneReader; +import com.milaboratory.mixcr.assembler.preclone.PreClone; +import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerParameters; +import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerRunner; import com.milaboratory.mixcr.basictypes.VDJCAlignments; import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagType; -import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.util.ReportHelper; import com.milaboratory.util.SmartProgressReporter; +import com.milaboratory.util.TempFileDest; import com.milaboratory.util.TempFileManager; import io.repseq.core.GeneFeature; -import kotlin.jvm.functions.Function1; import java.nio.file.Paths; import java.util.List; @@ -61,63 +58,19 @@ public class ITestCommandAssemblePreClones extends ACommandMiXCR { public void run0() throws Exception { long totalAlignments; long totalClones = 0; - try ( - VDJCAlignmentsReader reader1 = new VDJCAlignmentsReader(files.get(0)); - FilePreCloneWriter writer = new FilePreCloneWriter(Paths.get(files.get(1)), - TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp)) - ) { - VDJCAlignmentsReader.SecondaryReader reader2 = reader1.readAlignments(); - // For export - VDJCAlignmentsReader.SecondaryReader reader3 = reader1.readAlignments(); - - writer.init(reader1); - - TagsInfo tagsInfo = reader1.getTagsInfo(); - int depth = tagsInfo.getDepthFor(cellLevel ? TagType.CellTag : TagType.MoleculeTag); - // int depth = tagsInfo.getDepthFor(TagType.MoleculeTag); - if (tagsInfo.getSortingLevel() < depth) - throwValidationException("Input file has insufficient sorting level"); - - PreCloneAssemblerParameters params = new PreCloneAssemblerParameters( - gAssemblerParams, reader1.getParameters(), + TempFileDest tmp = TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp); + try (VDJCAlignmentsReader alignmentsReader = new VDJCAlignmentsReader(files.get(0))) { + totalAlignments = alignmentsReader.getNumberOfAlignments(); + PreCloneAssemblerRunner assemblerRunner = new PreCloneAssemblerRunner( + alignmentsReader, + cellLevel ? TagType.CellTag : TagType.MoleculeTag, new GeneFeature[]{GeneFeature.CDR3}, - depth); - CountingOutputPort reader1c = new CountingOutputPort<>(reader1); - PreCloneAssembler assembler = new PreCloneAssembler(params, - CUtils.wrap(reader1c, VDJCAlignments::ensureKeyTags), - CUtils.wrap(reader2, VDJCAlignments::ensureKeyTags) - ); - - Function1 gFunction = a -> a.getTagCount().asKeyPrefixOrError(depth); - OutputPort> alGroups = PipeKt.group( - CUtils.wrap(reader3, VDJCAlignments::ensureKeyTags), gFunction); - - SmartProgressReporter.startProgressReport("Building pre-clones", reader1); - - PreCloneAssemblerResult result; - while ((result = assembler.getForNextGroup()) != null) { - GroupOP grp = alGroups.take(); - List clones = result.getClones(); - assert clones.isEmpty() || clones.get(0).getCoreKey().equals(grp.getKey()); - totalClones += clones.size(); - - for (PreCloneImpl clone : clones) - writer.putClone(clone); - - int localId = 0; - for (VDJCAlignments al : CUtils.it(grp)) { - long cloneMapping = result.getCloneForAlignment(localId++); - writer.putAlignment(cloneMapping != -1 - ? al.withCloneIndexAndMappingType(cloneMapping, (byte) 0) - : al); - } - } - - totalAlignments = reader1c.getCount(); - - writer.finish(); - - assembler.getReport().writeReport(ReportHelper.STDOUT); + PreCloneAssemblerParameters.DefaultGConsensusAssemblerParameters, + Paths.get(files.get(1)), + tmp); + SmartProgressReporter.startProgressReport(assemblerRunner); + assemblerRunner.run(); + assemblerRunner.getReport().writeReport(ReportHelper.STDOUT); } try (FilePreCloneReader reader = new FilePreCloneReader(Paths.get(files.get(1)))) { diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 21792bd9b..38cb0e65b 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -716,7 +716,7 @@ public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderDa String tagName = args[0]; TagsInfo tagsInfo = headerData.getTagsInfo(); int idx = -1; - for (TagInfo ti : tagsInfo.tags) + for (TagInfo ti : tagsInfo) if (ti.getName().equals(tagName)) { idx = ti.getIndex(); break; From 076e8bda02a8aca2daea8d5e98c353955ce196ee Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 7 Jun 2022 21:43:19 +0400 Subject: [PATCH 264/282] Something works. --- itests/case10.sh | 3 +++ .../assembler/preclone/FilePreCloneReader.java | 16 ++++++++++++++++ .../cli/CommandAssemblePartialAlignments.java | 2 +- .../mixcr/cli/ITestCommandAssemblePreClones.java | 3 ++- 4 files changed, 22 insertions(+), 2 deletions(-) diff --git a/itests/case10.sh b/itests/case10.sh index ac713bd6a..fd4ce7e50 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -39,3 +39,6 @@ mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled- mixcr itestAssemblePreClones case10.part-assembled-molecule-vdjca case10.part-assembled-molecule-vdjca.pc mixcr itestAssemblePreClones --cell-level case10.part-assembled-cell-vdjca case10.part-assembled-cell-vdjca.pc + +mixcr assemble -a case10.part-assembled-molecule-vdjca case10.molecule-clna +mixcr assemble -a --cell-level case10.part-assembled-cell-vdjca case10.cell-clna diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java index 3ee390d7b..0bfb5479a 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java @@ -48,6 +48,22 @@ public FilePreCloneReader(Path file) throws IOException { } } + public long getNumberOfReads() { + return numberOfReads; + } + + public long getNumberOfAlignments() { + return numberOfAlignments; + } + + public long getNumberOfAssignedAlignments() { + return numberOfAssignedAlignments; + } + + public long getNumberOfClones() { + return numberOfClones; + } + public VDJCAlignerParameters getAlignmentParameters() { return alignmentParameters; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index c8289046f..33bbc7796 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -146,7 +146,7 @@ public void run1() throws Exception { report.setOutputFiles(out); report.setCommandLine(getCommandLineArguments()); - if (reader1.getTagsInfo() != null && reader1.getTagsInfo().hasNoTags()) { + if (reader1.getTagsInfo() != null && !reader1.getTagsInfo().hasNoTags()) { SmartProgressReporter.startProgressReport("Running assemble partial", reader1); // This processor strips all non-key information from the diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index 18e13f205..b273ff7bf 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -57,7 +57,6 @@ public class ITestCommandAssemblePreClones extends ACommandMiXCR { @Override public void run0() throws Exception { long totalAlignments; - long totalClones = 0; TempFileDest tmp = TempFileManager.smartTempDestination(files.get(1), "", useSystemTemp); try (VDJCAlignmentsReader alignmentsReader = new VDJCAlignmentsReader(files.get(0))) { totalAlignments = alignmentsReader.getNumberOfAlignments(); @@ -74,6 +73,8 @@ public void run0() throws Exception { } try (FilePreCloneReader reader = new FilePreCloneReader(Paths.get(files.get(1)))) { + long totalClones = reader.getNumberOfClones(); + long numberOfAlignmentsCheck = 0; for (VDJCAlignments al : CUtils.it(reader.readAlignments())) numberOfAlignmentsCheck++; From 09fc8bb0f5657776e105b6ac6dd4b068ede0b90d Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 7 Jun 2022 21:51:26 +0400 Subject: [PATCH 265/282] And even more integration tests. --- itests/case10.sh | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/itests/case10.sh b/itests/case10.sh index fd4ce7e50..4b8dbefb3 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -40,5 +40,8 @@ mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled- mixcr itestAssemblePreClones case10.part-assembled-molecule-vdjca case10.part-assembled-molecule-vdjca.pc mixcr itestAssemblePreClones --cell-level case10.part-assembled-cell-vdjca case10.part-assembled-cell-vdjca.pc -mixcr assemble -a case10.part-assembled-molecule-vdjca case10.molecule-clna -mixcr assemble -a --cell-level case10.part-assembled-cell-vdjca case10.cell-clna +mixcr assemble -f -a case10.part-assembled-molecule-vdjca case10.molecule-clna +mixcr assemble -f -a --cell-level case10.part-assembled-cell-vdjca case10.cell-clna + +mixcr assembleContigs -f case10.molecule-clna case10.molecule-clns +mixcr assembleContigs -f case10.cell-clna case10.cell-clns From c5f71e0548e75d01c214b3905a7be70a42088793 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 7 Jun 2022 23:12:47 +0400 Subject: [PATCH 266/282] fix: for minimal clonal sequence length filter --- .../mixcr/assembler/CloneAssembler.java | 31 +++++++++---------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index defd9e443..fd86580f9 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -224,16 +224,12 @@ public void setListener(CloneAssemblerListener listener) { } private ClonalSequence extractClonalSequence(PreClone preClone) { - // final NSequenceWithQuality[] targets = new NSequenceWithQuality[parameters.assemblingFeatures.length]; - // int totalLength = 0; - // for (int i = 0; i < targets.length; ++i) - // if ((targets[i] = alignments.getFeature(parameters.assemblingFeatures[i])) == null) - // return null; - // else - // totalLength += targets[i].size(); - // if (totalLength < parameters.minimalClonalSequenceLength) - // return null; - return new ClonalSequence(preClone.getClonalSequence()); + NSequenceWithQuality[] clonalSequence = preClone.getClonalSequence(); + int totalLength = 0; + for (NSequenceWithQuality s : clonalSequence) totalLength += s.size(); + if (totalLength < parameters.minimalClonalSequenceLength) + return null; + return new ClonalSequence(clonalSequence); } public VoidProcessor getInitialAssembler() { @@ -409,12 +405,12 @@ public void process(PreClone input) { totalAlignments.incrementAndGet(); final ClonalSequence target = extractClonalSequence(input); - // if (target == null) { - // log(new AssemblerEvent(input.getId(), AssemblerEvent.DROPPED)); - // droppedAlignments.incrementAndGet(); - // onFailedToExtractTarget(input); - // return; - // } + if (target == null) { + log(new AssemblerEvent(input.getIndex(), AssemblerEvent.DROPPED)); + droppedAlignments.incrementAndGet(); + onFailedToExtractTarget(input); + return; + } // Calculating number of bad points int badPoints = numberOfBadPoints(target); @@ -473,6 +469,9 @@ private final class DeferredAlignmentsMapper implements VoidProcessor public void process(PreClone input) { final ClonalSequence clonalSequence = extractClonalSequence(input); + // The sequence was deferred on the initial step, so it must contain clonal sequence + assert clonalSequence != null; + // Seeding random generator to make ambiguous mappings below reproducible RandomUtil.reseedThreadLocal(HashFunctions.JenkinWang64shift(input.getIndex())); From 3f2b1d0db4f95dc981a817d75742bf5114124b4b Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 8 Jun 2022 01:16:52 +0400 Subject: [PATCH 267/282] fix: multiple fixes for pre-clone assembler --- .../assembler/preclone/PreCloneAssembler.java | 105 +++++++++++++++--- .../preclone/PreCloneAssemblerReport.java | 22 +++- .../mixcr/cli/CommandAssemble.java | 4 +- 3 files changed, 109 insertions(+), 22 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index bee6aef02..611de1e7b 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -117,7 +117,7 @@ public PreCloneAssemblerResult getForNextGroup() { assert alignmentInfos.size() == assemblerInput.size(); - report.inputAlignments.addAndGet(localIdx); + report.inputAlignments.addAndGet(localIdx + 1); if (assemblerInput.isEmpty()) { CUtils.drainWithoutClose(alignmentsReader2.take(), DummyInputPort.INSTANCE); @@ -149,9 +149,13 @@ public PreCloneAssemblerResult getForNextGroup() { // Tag suffixes unambiguously linked to a clonotype // (store cloneIdx+1; -1 for ambiguous cases; 0 - not found) TObjectIntHashMap tagSuffixToCloneId = new TObjectIntHashMap<>(); + assert tagSuffixToCloneId.get(1) == 0; // V, J and C genes unambiguously linked to a clonotype // (store cloneIdx+1; -1 for ambiguous cases; 0 - not found) TObjectIntHashMap vjcGenesToCloneId = new TObjectIntHashMap<>(); + // V, J and C genes + tags unambiguously linked to a clonotype + // (store cloneIdx+1; -1 for ambiguous cases; 0 - not found) + TObjectIntHashMap gatToCloneId = new TObjectIntHashMap<>(); // Special map to simplify collection of additional information from already assigned alignment // -1 = not assigned to any consensus / clonotype @@ -175,21 +179,41 @@ public PreCloneAssemblerResult getForNextGroup() { geneInfos[cIdx] = acc.aggregateInformation(parameters.relativeMinScores); - for (TagTuple ts : tagSuffixes) - if (tagSuffixToCloneId.get(ts) > 0) + for (TagTuple ts : tagSuffixes) { + int valueInMap = tagSuffixToCloneId.get(ts); + if (valueInMap > 0) { + assert cIdx + 1 != valueInMap; + report.umiConflicts.incrementAndGet(); tagSuffixToCloneId.put(ts, -1); // ambiguity detected - else + } else if (valueInMap == 0) tagSuffixToCloneId.put(ts, cIdx + 1); + } for (GeneType gt : GeneType.VJ_REFERENCE) { List gss = geneInfos[cIdx].get(gt); if (gss == null) continue; - for (GeneAndScore gs : gss) - if (vjcGenesToCloneId.get(gs.geneId) > 0) + for (GeneAndScore gs : gss) { + int valueInMap = vjcGenesToCloneId.get(gs.geneId); + if (valueInMap > 0) { + assert cIdx + 1 != valueInMap; + report.geneConflicts.incrementAndGet(gt.ordinal()); vjcGenesToCloneId.put(gs.geneId, -1); - else + } else if (valueInMap == 0) vjcGenesToCloneId.put(gs.geneId, cIdx + 1); + + // In combination with tags + for (TagTuple ts : tagSuffixes) { + GeneAndTagSuffix gat = new GeneAndTagSuffix(gs.geneId, ts); + valueInMap = gatToCloneId.get(gat); + if (valueInMap > 0) { + assert cIdx + 1 != valueInMap; + report.gatConflicts.incrementAndGet(); + gatToCloneId.put(gat, -1); // ambiguity detected + } else if (valueInMap == 0) + gatToCloneId.put(gat, cIdx + 1); + } + } } } @@ -205,6 +229,8 @@ public PreCloneAssemblerResult getForNextGroup() { report.discardedCoreAlignments.incrementAndGet(); + // TODO add reports here + for (TagTuple ts : ai.tagSuffixes) tagSuffixToCloneId.put(ts, -1); @@ -212,8 +238,11 @@ public PreCloneAssemblerResult getForNextGroup() { List gss = ai.genesAndScores.get(gt); if (gss == null || gss.isEmpty()) continue; - for (GeneAndScore gs : gss) + for (GeneAndScore gs : gss) { vjcGenesToCloneId.put(gs.geneId, -1); + for (TagTuple ts : ai.tagSuffixes) + gatToCloneId.put(new GeneAndTagSuffix(gs.geneId, ts), -1); + } } } @@ -240,34 +269,53 @@ public PreCloneAssemblerResult getForNextGroup() { // Running empirical assignment for the alignments not yet assigned if (cIdxP1 == 0) { // V and J gene based assignment - for (GeneType gt : GeneType.VJ_REFERENCE) + for (GeneType gt : GeneType.VJ_REFERENCE) { for (VDJCHit hit : al.getHits(gt)) { + // TagSuffix + V/J-gene based assignment + for (TagTuple ts : al.getTagCount().keySuffixes(parameters.groupingLevel)) { + int cp1 = gatToCloneId.get(new GeneAndTagSuffix(hit.getGene().getId(), ts)); + if (cp1 <= 0) + continue; + if (cIdxP1 == 0) { + cIdxP1 = cp1; + report.gatEmpiricallyAssignedAlignments.incrementAndGet(); + } else if (cIdxP1 != cp1) + cIdxP1 = -1; + } + + // Back to V and J gene based assignment int cp1 = vjcGenesToCloneId.get(hit.getGene().getId()); if (cp1 <= 0) continue; - report.vjEmpiricallyAssignedAlignments.incrementAndGet(); - if (cIdxP1 == 0) + + if (cIdxP1 == 0) { cIdxP1 = cp1; - else if (cIdxP1 != cp1) + report.vjEmpiricallyAssignedAlignments.incrementAndGet(); + } else if (cIdxP1 != cp1) cIdxP1 = -1; } + } // TagSuffix based assignment for (TagTuple ts : al.getTagCount().keySuffixes(parameters.groupingLevel)) { int cp1 = tagSuffixToCloneId.get(ts); if (cp1 <= 0) continue; - report.umiEmpiricallyAssignedAlignments.incrementAndGet(); - if (cIdxP1 == 0) + if (cIdxP1 == 0) { cIdxP1 = cp1; - else if (cIdxP1 != cp1) + report.umiEmpiricallyAssignedAlignments.incrementAndGet(); + } else if (cIdxP1 != cp1) cIdxP1 = -1; } - if (cIdxP1 > 0) + // Here cIdxP1 > 0 if any of the empirical methods produced a hit + // and no conflicts were encountered between methods + + if (cIdxP1 > 0) { // Adding alignment to the clone alignmentIdxToCloneIdxP1[localIdx] = cIdxP1; - else if (cIdxP1 == -1) + report.empiricallyAssignedAlignments.incrementAndGet(); + } else if (cIdxP1 == -1) report.empiricalAssignmentConflicts.incrementAndGet(); } else if (cIdxP1 > 0) { int cIdx = cIdxP1 - 1; @@ -363,6 +411,29 @@ else if (cIdxP1 == -1) return new PreCloneAssemblerResult(result, resultAlToClone); } + private static final class GeneAndTagSuffix { + final VDJCGeneId gene; + final TagTuple tag; + + public GeneAndTagSuffix(VDJCGeneId gene, TagTuple tag) { + this.gene = gene; + this.tag = tag; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + GeneAndTagSuffix that = (GeneAndTagSuffix) o; + return gene.equals(that.gene) && tag.equals(that.tag); + } + + @Override + public int hashCode() { + return Objects.hash(gene, tag); + } + } + private static final class AlignmentInfo { final int localIdx; final long alignmentId, minReadId; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java index 96d5e4144..b64f52c29 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java @@ -5,8 +5,10 @@ import com.milaboratory.mitool.report.ConcurrentAtomicLongMap; import com.milaboratory.util.Report; import com.milaboratory.util.ReportHelper; +import io.repseq.core.GeneType; import java.util.concurrent.atomic.AtomicLong; +import java.util.concurrent.atomic.AtomicLongArray; public final class PreCloneAssemblerReport implements Report { final AtomicLong inputGroups = new AtomicLong(); @@ -15,24 +17,40 @@ public final class PreCloneAssemblerReport implements Report { final ConcurrentAtomicLongMap clonotypesPerGroup = new ConcurrentAtomicLongMap<>(); final AtomicLong coreAlignments = new AtomicLong(); final AtomicLong discardedCoreAlignments = new AtomicLong(); + final AtomicLong empiricallyAssignedAlignments = new AtomicLong(); final AtomicLong vjEmpiricallyAssignedAlignments = new AtomicLong(); final AtomicLong umiEmpiricallyAssignedAlignments = new AtomicLong(); + final AtomicLong gatEmpiricallyAssignedAlignments = new AtomicLong(); final AtomicLong empiricalAssignmentConflicts = new AtomicLong(); final AtomicLong unassignedAlignments = new AtomicLong(); + final AtomicLong umiConflicts = new AtomicLong(); + final AtomicLong gatConflicts = new AtomicLong(); + final AtomicLongArray geneConflicts = new AtomicLongArray(GeneType.values().length); @Override public void writeReport(ReportHelper helper) { helper.writeField("Number of input groups", inputGroups.get()); helper.writeField("Number of input alignments", inputAlignments.get()); - helper.writeField("Number of output clonotypes", clonotypes.get()); + helper.writeField("Number of output pre-clonotypes", clonotypes.get()); helper.println("Number of clonotypes per group"); helper.print(ReportKt.format(clonotypesPerGroup.getImmutable(), " ", new StringBuilder(), new FormatSettings(0), 0).toString()); helper.writePercentAndAbsoluteField("Number of core alignments", coreAlignments.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("Discarded core alignments", discardedCoreAlignments.get(), coreAlignments.get()); + helper.writePercentAndAbsoluteField("Empirically assigned alignments", empiricallyAssignedAlignments.get(), inputAlignments.get()); + helper.writePercentAndAbsoluteField("Empirical assignment conflicts", empiricalAssignmentConflicts.get(), inputAlignments.get()); + helper.writePercentAndAbsoluteField("UMI+VJ-gene empirically assigned alignments", gatEmpiricallyAssignedAlignments.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("VJ-gene empirically assigned alignments", vjEmpiricallyAssignedAlignments.get(), inputAlignments.get()); helper.writePercentAndAbsoluteField("UMI empirically assigned alignments", umiEmpiricallyAssignedAlignments.get(), inputAlignments.get()); - helper.writePercentAndAbsoluteField("Empirical assignment conflicts", empiricalAssignmentConflicts.get(), inputAlignments.get()); + helper.writeField("Number of ambiguous UMIs", umiConflicts.get()); + for (GeneType gt : GeneType.values()) { + long value = geneConflicts.get(gt.ordinal()); + if(value == 0) + continue; + helper.writeField("Number of ambiguous " + gt.getLetter() + "-genes", value); + } + helper.writeField("Number of ambiguous UMI+V/J-gene combinations", gatConflicts.get()); + helper.writePercentAndAbsoluteField("Unassigned alignments", unassignedAlignments.get(), inputAlignments.get()); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index ec6d90557..032eded8b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -111,14 +111,12 @@ public void setThreads(int threads) { names = {"-a", "--write-alignments"}) public boolean isClnaOutput = false; - @Option(description = "If tags are present assemble pre-clones on the cell level rather than on the molecule level. " + + @Option(description = "If tags are present, do assemble pre-clones on the cell level rather than on the molecule level. " + "If there are no molecular tags in the data, but cell tags are present, this option will be used by default. " + "This option has no effect on the data without tags.", names = {"--cell-level"}) public boolean cellLevel = false; - private static final double DEFAULT_MINIMAL_TAG_SET_OVERLAP = 0.7; - @Option(names = "-O", description = "Overrides default parameter values.") private Map overrides = new HashMap<>(); From 65256995125e7b93cf599d669dc01d1412aea264 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 8 Jun 2022 03:13:11 +0400 Subject: [PATCH 268/282] feat: export fields with tag information --- .../mixcr/basictypes/tag/TagCount.java | 17 ++ .../mixcr/basictypes/tag/TagTuple.java | 7 + .../mixcr/basictypes/tag/TagsInfo.java | 10 ++ .../milaboratory/mixcr/cli/CommandExport.java | 9 +- .../mixcr/export/FieldExtractors.java | 145 +++++++----------- 5 files changed, 94 insertions(+), 94 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java index 804e95889..6c36c1f62 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java @@ -109,6 +109,23 @@ public Set keySuffixes(int depth) { .collect(Collectors.toSet()); } + public TagValue singleOrNull(int idx) { + if (singletonTuple != null) + return singletonTuple.get(idx); + + TagValue value = null; + TObjectDoubleIterator it = tagMap.iterator(); + while (it.hasNext()) { + it.advance(); + TagValue tv = it.key().get(idx); + if (value == null) { + value = tv; + } else if (!value.equals(tv)) + return null; + } + return value; + } + public Set tuples() { if (singletonTuple != null) return Collections.singleton(singletonTuple); diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index 7cf1cac54..63168e924 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -27,6 +27,13 @@ public TagTuple(TagValue... tags) { this.hash = hasher.hash().hashCode(); } + public TagTuple project(int... idxs) { + TagValue[] t = new TagValue[idxs.length]; + for (int i = 0; i < idxs.length; i++) + t[i] = tags[idxs[i]]; + return new TagTuple(t); + } + /** Returns whether the tag tuple contains only key tag values, so can be used as a grouping key. */ public boolean isKey() { for (TagValue tag : tags) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index 2e4c7ca67..c7a4e09d3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -58,6 +58,16 @@ public TagsInfo setSorted(int sortedLevel) { return new TagsInfo(sortedLevel, tags); } + public int indexOf(String tagName){ + int idx = -1; + for (TagInfo ti : this) + if (ti.getName().equals(tagName)) { + idx = ti.getIndex(); + break; + } + return idx; + } + @Override @SuppressWarnings("NullableProblems") public Iterator iterator() { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 838f5c47d..7fe0926f6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -35,6 +35,7 @@ import cc.redberry.primitives.Filter; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagCount; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.export.*; import com.milaboratory.mixcr.util.Concurrency; import com.milaboratory.util.CanReportProgress; @@ -223,7 +224,7 @@ public static class CommandExportClones extends CommandExport { @Option(description = "Split clones by tag values", names = {"--split-by-tag"}) - public List splitByTag = new ArrayList<>(); + public List splitByTag = new ArrayList<>(); public CommandExportClones() { super(Clone.class); @@ -255,7 +256,11 @@ void run1(List fields, OutputMode oMode) throws Exception { break; } } - ExportClones exportClones = new ExportClones(set, writer, limit, splitByTag.stream().mapToInt(i -> i).toArray()); + TagsInfo tagsInfo = set.getTagsInfo(); + ExportClones exportClones = new ExportClones(set, writer, limit, + splitByTag.stream() + .mapToInt(tagsInfo::indexOf) + .toArray()); SmartProgressReporter.startProgressReport(exportClones, System.err); exportClones.run(); if (initialSet.size() > set.size()) { diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 38cb0e65b..82be45a5a 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -43,10 +43,10 @@ import com.milaboratory.mixcr.assembler.ReadToCloneMapping; import com.milaboratory.mixcr.basictypes.*; import com.milaboratory.mixcr.basictypes.tag.TagCount; -import com.milaboratory.mixcr.basictypes.tag.TagInfo; import com.milaboratory.mixcr.basictypes.tag.TagTuple; -import com.milaboratory.mixcr.basictypes.tag.TagsInfo; +import com.milaboratory.mixcr.basictypes.tag.TagValue; import com.milaboratory.util.GlobalObjectMappers; +import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.iterator.TObjectFloatIterator; import gnu.trove.map.hash.TObjectFloatHashMap; import io.repseq.core.GeneFeature; @@ -55,10 +55,7 @@ import io.repseq.core.SequencePartitioning; import java.text.DecimalFormat; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Set; +import java.util.*; public final class FieldExtractors { static final String NULL = ""; @@ -714,104 +711,68 @@ private String getHeader(OutputMode outputMode, String name) { @Override public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { String tagName = args[0]; - TagsInfo tagsInfo = headerData.getTagsInfo(); - int idx = -1; - for (TagInfo ti : tagsInfo) - if (ti.getName().equals(tagName)) { - idx = ti.getIndex(); - break; - } + int idx = headerData.getTagsInfo().indexOf(tagName); if (idx == -1) throw new IllegalArgumentException("No tag with name " + tagName); - int finalIdx = idx; return new AbstractFieldExtractor(getHeader(outputMode, tagName), this) { @Override public String extractValue(VDJCObject object) { - TagCount tc = object.getTagCount(); - Set keys = tc.tuples(); - if (keys.size() == 0) + TagValue tagValue = object.getTagCount().singleOrNull(idx); + if (tagValue == null) return NULL; - if (keys.size() > 1) - throw new IllegalArgumentException("object has multiple tag tuples: " + tc); - return keys.iterator().next().get(finalIdx).extractKey().toString(); + return tagValue.toString(); } }; } }); - // descriptorsList.add(new WP_O("-tag", "Tag value", 1) { - // @Override - // protected String getParameters(String[] string) { - // return string[0]; - // } - // - // @Override - // protected String getHeader(OutputMode outputMode, String name) { - // switch (outputMode) { - // case HumanFriendly: - // return "Tag" + name; - // case ScriptingFriendly: - // return "tag" + name; - // } - // throw new RuntimeException(); - // } - // - // @Override - // protected String extractValue(VDJCObject object, String name) { - // TagCounter tc = object.getTagCounter(); - // Set set = tc.tags(name); - // if (set.size() == 0) - // return NULL; - // if (set.size() > 1) - // throw new IllegalArgumentException("object has multiple tag tuples: " + tc); - // return set.iterator().next(); - // } - // - // @Override - // public String metaVars() { - // return "index"; - // } - // }); + descriptorsList.add(new AbstractField(VDJCObject.class, "-uniqueTagCount", "Unique tag count") { + @Override + public int nArguments() { + return 1; + } - // descriptorsList.add(new WP_O("-uniqueTagCount", "Unique tag count", 1) { - // @Override - // protected int[] getParameters(String[] string) { - // return Arrays.stream(string[0].split("\\+")).mapToInt(Integer::parseInt).toArray(); - // } - // - // @Override - // protected String getHeader(OutputMode outputMode, int[] index) { - // String str = Arrays.stream(index).mapToObj(Integer::toString).collect(Collectors.joining("+")); - // switch (outputMode) { - // case HumanFriendly: - // return "Unique Tag Count " + str; - // case ScriptingFriendly: - // return "uniqueTagCount" + str; - // } - // throw new RuntimeException(); - // } - // - // @Override - // protected String extractValue(VDJCObject object, int[] indices) { - // TagCounter tc = object.getTagCounter(); - // Set set = new HashSet<>(); - // TObjectDoubleIterator it = tc.iterator(); - // while (it.hasNext()) { - // it.advance(); - // StringBuilder sb = new StringBuilder(); - // TagTuple t = it.key(); - // for (int i : indices) - // sb.append(t.tags[i]).append("+"); - // set.add(sb.toString()); - // } - // return "" + set.size(); - // } - // - // @Override - // public String metaVars() { - // return "Tags"; - // } - // }); + @Override + public String metaVars() { + return "tag_names"; + } + + private String getHeader(OutputMode outputMode, String name) { + switch (outputMode) { + case HumanFriendly: + return "Unique Tag Count " + name; + case ScriptingFriendly: + return "uniqueTagCount" + name; + } + throw new RuntimeException(); + } + + @Override + public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderData headerData, String[] args) { + String tagNames = args[0]; + + int[] indices = Arrays.stream(tagNames.split("\\+")).mapToInt(tagName -> { + int idx = headerData.getTagsInfo().indexOf(tagName); + if (idx == -1) + throw new IllegalArgumentException("No tag with name " + tagName); + return idx; + }).toArray(); + + return new AbstractFieldExtractor(getHeader(outputMode, tagNames), this) { + @Override + public String extractValue(VDJCObject object) { + TagCount tc = object.getTagCount(); + Set set = new HashSet<>(); + TObjectDoubleIterator it = tc.iterator(); + while (it.hasNext()) { + it.advance(); + set.add(it.key().project(indices)); + } + return "" + set.size(); + } + }; + } + }); descriptorsList.add(new PL_C("-cellGroup", "Cell group", "Cell group", "cellGroup") { @Override From c433bbe31d1dc264e110b73771c3a0a1497af309 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Wed, 8 Jun 2022 13:09:25 +0200 Subject: [PATCH 269/282] Added EfronThisted diversity metric --- .../ui/PostanalysisParametersIndividual.java | 2 ++ .../parameters/postanalysis_individual.json | 20 +++++++++++++++++++ 2 files changed, 22 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java index 4c76b2c93..e16a4788c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java @@ -141,6 +141,7 @@ public static class DiversityParameters { public PreprocessorParameters inverseSimpson = new PreprocessorParameters(); public PreprocessorParameters gini = new PreprocessorParameters(); public PreprocessorParameters d50 = new PreprocessorParameters(); + public PreprocessorParameters efronThisted = new PreprocessorParameters(); public CharacteristicGroup getGroup(PostanalysisParameters base) { List> chars = new ArrayList<>(groupByPreproc( @@ -151,6 +152,7 @@ public CharacteristicGroup getGroup(PostanalysisParameters base) { put(DiversityMeasure.NormalizedShannonWeinerIndex, clonality.preproc(base)); put(DiversityMeasure.InverseSimpson, inverseSimpson.preproc(base)); put(DiversityMeasure.GiniIndex, gini.preproc(base)); + put(DiversityMeasure.EfronThisted, efronThisted.preproc(base)); }}, (p, l) -> Collections.singletonList(new DiversityCharacteristic<>("Diversity " + l.stream().map(m -> m.name).collect(Collectors.joining("/")), diff --git a/src/main/resources/parameters/postanalysis_individual.json b/src/main/resources/parameters/postanalysis_individual.json index 979190e74..f051134c7 100644 --- a/src/main/resources/parameters/postanalysis_individual.json +++ b/src/main/resources/parameters/postanalysis_individual.json @@ -85,6 +85,11 @@ "downsampling": null, "onlyProductive": null, "dropOutliers": null + }, + "efronThisted": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null } }, "vUsage": { @@ -106,6 +111,21 @@ "downsampling": null, "onlyProductive": null, "dropOutliers": null + }, + "cdr3Spectratype": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "vSpectratype": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null + }, + "vSpectratypeMean": { + "downsampling": null, + "onlyProductive": null, + "dropOutliers": null } } } From d80e38cbee46a4aeb1972f2bb996cae009e01804 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 8 Jun 2022 17:33:01 +0400 Subject: [PATCH 270/282] WIP --- itests.sh | 114 +++++++++--------- itests/case11.sh | 39 ++++++ .../mixcr/basictypes/tag/TagType.java | 6 +- .../mixcr/basictypes/tag/TagsInfo.java | 7 +- .../milaboratory/mixcr/cli/CommandAlign.java | 52 ++++---- .../mixcr/cli/CommandAssemble.java | 9 +- .../cli/CommandAssemblePartialAlignments.java | 2 +- .../cli/ITestCommandAssemblePreClones.java | 2 +- .../mixcr/basictypes/tag/TagInfoTest.java | 4 +- ...assembled_umi_ig_data_2_subset_R1.fastq.gz | Bin 0 -> 394 bytes ...assembled_umi_ig_data_2_subset_R2.fastq.gz | Bin 0 -> 396 bytes .../umi_ig_data_2_subset_R1.fastq.gz | Bin 0 -> 19933 bytes .../umi_ig_data_2_subset_R2.fastq.gz | Bin 0 -> 24048 bytes 13 files changed, 138 insertions(+), 97 deletions(-) create mode 100755 itests/case11.sh create mode 100644 src/test/resources/sequences/assembled_umi_ig_data_2_subset_R1.fastq.gz create mode 100644 src/test/resources/sequences/assembled_umi_ig_data_2_subset_R2.fastq.gz create mode 100644 src/test/resources/sequences/umi_ig_data_2_subset_R1.fastq.gz create mode 100644 src/test/resources/sequences/umi_ig_data_2_subset_R2.fastq.gz diff --git a/itests.sh b/itests.sh index dfbee1ffb..093ec45f8 100755 --- a/itests.sh +++ b/itests.sh @@ -7,24 +7,23 @@ set -eo pipefail # Linux readlink -f alternative for Mac OS X function readlinkUniversal() { - targetFile=$1 - - cd `dirname $targetFile` - targetFile=`basename $targetFile` - - # iterate down a (possible) chain of symlinks - while [ -L "$targetFile" ] - do - targetFile=`readlink $targetFile` - cd `dirname $targetFile` - targetFile=`basename $targetFile` - done - - # compute the canonicalized name by finding the physical path - # for the directory we're in and appending the target file. - phys_dir=`pwd -P` - result=$phys_dir/$targetFile - echo $result + targetFile=$1 + + cd $(dirname $targetFile) + targetFile=$(basename $targetFile) + + # iterate down a (possible) chain of symlinks + while [ -L "$targetFile" ]; do + targetFile=$(readlink $targetFile) + cd $(dirname $targetFile) + targetFile=$(basename $targetFile) + done + + # compute the canonicalized name by finding the physical path + # for the directory we're in and appending the target file. + phys_dir=$(pwd -P) + result=$phys_dir/$targetFile + echo $result } os=$(uname) @@ -33,44 +32,43 @@ delta=100 dir="" case $os in - Darwin) - dir=$(dirname "$(readlinkUniversal "$0")") - ;; - Linux) - dir="$(dirname "$(readlink -f "$0")")" - ;; - FreeBSD) - dir=$(dirname "$(readlinkUniversal "$0")") - ;; - *) - echo "Unknown OS." - exit 1 - ;; +Darwin) + dir=$(dirname "$(readlinkUniversal "$0")") + ;; +Linux) + dir="$(dirname "$(readlink -f "$0")")" + ;; +FreeBSD) + dir=$(dirname "$(readlinkUniversal "$0")") + ;; +*) + echo "Unknown OS." + exit 1 + ;; esac -tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8" "case9" "case10") +tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8" "case9" "case10" "case11") create_standard_results=false run_tests=false -while [[ $# > 0 ]] -do - key="$1" - shift - case $key in - std) - create_standard_results=true - ;; - test) - run_tests=true - ;; - case*) - tests=("$key") - ;; - *) - echo "Unknown option $key"; - exit 1 - ;; -esac +while [[ $# > 0 ]]; do + key="$1" + shift + case $key in + std) + create_standard_results=true + ;; + test) + run_tests=true + ;; + case*) + tests=("$key") + ;; + *) + echo "Unknown option $key" + exit 1 + ;; + esac done rm -rf ${dir}/test_target @@ -83,6 +81,8 @@ ln -s ../src/test/resources/sequences/big/CD4M1_test_R1.fastq.gz ${dir}/test_tar ln -s ../src/test/resources/sequences/big/CD4M1_test_R2.fastq.gz ${dir}/test_target/CD4M1_test_R2.fastq.gz ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R1.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R1.fastq.gz ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R2.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R2.fastq.gz +ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R1.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R1.fastq.gz +ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R2.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R2.fastq.gz PATH=${dir}:${PATH} @@ -92,15 +92,13 @@ mixcr -v function go_assemble { mixcr assemble -r $1.clns.report $1.vdjca $1.clns - for c in TCR IG TRB TRA TRG TRD IGH IGL IGK ALL - do + for c in TCR IG TRB TRA TRG TRD IGH IGL IGK ALL; do mixcr exportClones -c ${c} $1.clns $1.clns.${c}.txt done } if [[ $create_standard_results == true ]]; then - for s in sample_IGH test; - do + for s in sample_IGH test; do mixcr align -s hs -r ${s}_paired.vdjca.report ${s}_R1.fastq ${s}_R2.fastq ${s}_paired.vdjca go_assemble ${s}_paired mixcr align -s hs -r ${s}_single.vdjca.report ${s}_R1.fastq ${s}_single.vdjca @@ -131,11 +129,11 @@ function run_test() { } if [[ $run_tests == true ]]; then - for testName in ${tests[@]} ; do - run_test "${testName}.sh" + for testName in ${tests[@]}; do + run_test "${testName}.sh" done - if ls ${dir}/test_target/*.error 1> /dev/null 2>&1; then + if ls ${dir}/test_target/*.error 1>/dev/null 2>&1; then echo "There are tests with errors." exit 1 else diff --git a/itests/case11.sh b/itests/case11.sh new file mode 100755 index 000000000..ca640e1d2 --- /dev/null +++ b/itests/case11.sh @@ -0,0 +1,39 @@ +#!/usr/bin/env bash + +# Single-cell integration test + +assert() { + expected=$(echo -ne "${2:-}") + result="$(eval 2>/dev/null $1)" || true + if [[ "$result" == "$expected" ]]; then + return + fi + result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")" + [[ -z "$result" ]] && result="nothing" || result="\"$result\"" + [[ -z "$2" ]] && expected="nothing" || expected="\"$2\"" + echo "expected $expected got $result for" "$1" + exit 1 +} + +set -euxo pipefail + +mixcr align -f \ + --tag-pattern-name mikelov_et_al_2021 \ + -p kaligner2 -s hs \ + -OvParameters.geneFeatureToAlign=VTranscript \ + -OvParameters.parameters.floatingLeftBound=false \ + -OjParameters.parameters.floatingRightBound=false \ + -OcParameters.parameters.floatingRightBound=false \ + -OallowPartialAlignments=true \ + -OallowNoCDR3PartAlignments=true \ + -OsaveOriginalReads=true \ + --report case10.align.report \ + umi_ig_data_2_subset_R1.fastq.gz \ + umi_ig_data_2_subset_R2.fastq.gz \ + case11.aligned-vdjca + +mixcr correctAndSortTags case11.aligned-vdjca case11.corrected-vdjca + +mixcr itestAssemblePreClones case11.corrected-vdjca case11.corrected-vdjca.pc + +mixcr assemble -f -a case11.corrected-vdjca case11.clna diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java index 84cdf295f..7200bc786 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java @@ -1,7 +1,7 @@ package com.milaboratory.mixcr.basictypes.tag; public enum TagType { - SampleTag, - CellTag, - MoleculeTag + Sample, + Cell, + Molecule } diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index c7a4e09d3..1151ff8f2 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -4,12 +4,10 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.primitivio.annotations.Serializable; -import java.util.Arrays; -import java.util.Iterator; -import java.util.Objects; +import java.util.*; @Serializable(asJson = true) -public final class TagsInfo implements Iterable { +public final class TagsInfo extends AbstractCollection { public static final TagsInfo NO_TAGS = new TagsInfo(0); @JsonProperty("sortingLevel") @@ -42,6 +40,7 @@ public TagInfo get(int idx) { return tags[idx]; } + @Override public int size() { return tags.length; } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index e33462672..00e88c4f6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -497,7 +497,15 @@ else if (this.tagPatternFile != null) : ReadSearchMode.PairedDirect : ReadSearchMode.Single); ReadSearchPlan readSearchPlan = ReadSearchPlan.Companion.create(tagPattern, searchSettings); - ParseInfo parseInfo = ParseInfo.fromSet(readSearchPlan.getAllTags()); + ParseInfo parseInfo = parseTagsFromSet(readSearchPlan.getAllTags()); + + System.out.println("The following tags and their roles were recognised:"); + System.out.println(" Payload tags: " + String.join(", ", parseInfo.getReadTags())); + parseInfo.tags.stream().collect(Collectors.groupingBy(TagInfo::getType)) + .forEach((tagType, tagInfos) -> + System.out.println(" " + tagType + " tags: " + tagInfos.stream().map(TagInfo::getName).collect(Collectors.joining())) + ); + List tagShortcuts = parseInfo.getTags().stream() .map(t -> readSearchPlan.tagShortcut(t.getName())) .collect(Collectors.toList()); @@ -829,7 +837,7 @@ public TaggedSequence parse(SequenceRead read) { } } - public static final class ParseInfo { + public final class ParseInfo { private final List tags; private final List readTags; @@ -860,27 +868,27 @@ public boolean equals(Object o) { public int hashCode() { return Objects.hash(tags, readTags); } + } - public static ParseInfo fromSet(Set names) { - List tags = new ArrayList<>(); - List readTags = new ArrayList<>(); - for (String name : names) { - if (name.startsWith("S")) - tags.add(new TagInfo(SampleTag, SequenceAndQuality, name, 0)); - else if (name.startsWith("CELL")) - tags.add(new TagInfo(CellTag, SequenceAndQuality, name, 0)); - else if (name.startsWith("UMI") || name.startsWith("MI")) - tags.add(new TagInfo(MoleculeTag, SequenceAndQuality, name, 0)); - else if (name.startsWith("R")) - readTags.add(name); - else - throw new IllegalArgumentException("Can't recognize tag type for name: " + name); - } - Collections.sort(tags); - for (int i = 0; i < tags.size(); i++) - tags.set(i, tags.get(i).withIndex(i)); - Collections.sort(readTags); - return new ParseInfo(tags, readTags); + public ParseInfo parseTagsFromSet(Set names) { + List tags = new ArrayList<>(); + List readTags = new ArrayList<>(); + for (String name : names) { + if (name.startsWith("S")) + tags.add(new TagInfo(Sample, SequenceAndQuality, name, 0)); + else if (name.startsWith("CELL")) + tags.add(new TagInfo(Cell, SequenceAndQuality, name, 0)); + else if (name.startsWith("UMI") || name.startsWith("MI")) + tags.add(new TagInfo(Molecule, SequenceAndQuality, name, 0)); + else if (name.matches("R\\d+")) + readTags.add(name); + else + warn("Can't recognize tag type for name \"" + name + "\", this tag will be ignored during analysis."); } + Collections.sort(tags); + for (int i = 0; i < tags.size(); i++) + tags.set(i, tags.get(i).withIndex(i)); + Collections.sort(readTags); + return new ParseInfo(tags, readTags); } } diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 032eded8b..71e19ab87 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -29,7 +29,6 @@ */ package com.milaboratory.mixcr.cli; -import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.util.StatusReporter; import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; @@ -42,13 +41,11 @@ import com.milaboratory.mixcr.assembler.preclone.PreCloneAssemblerRunner; import com.milaboratory.mixcr.assembler.preclone.PreCloneReader; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCount; import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagType; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; import com.milaboratory.util.*; -import gnu.trove.iterator.TObjectDoubleIterator; import io.repseq.core.*; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -251,8 +248,8 @@ public void run1() throws Exception { // TODO >>>>>>>>>>>>>> PreCloneReader preClones; - if (tagsInfo.hasTagsWithType(TagType.CellTag) || tagsInfo.hasTagsWithType(TagType.MoleculeTag)) { - int depth = tagsInfo.getDepthFor(cellLevel ? TagType.CellTag : TagType.MoleculeTag); + if (tagsInfo.hasTagsWithType(TagType.Cell) || tagsInfo.hasTagsWithType(TagType.Molecule)) { + int depth = tagsInfo.getDepthFor(cellLevel ? TagType.Cell : TagType.Molecule); if (tagsInfo.getSortingLevel() < depth) throwValidationException("Input file has insufficient sorting level"); PreCloneAssemblerParameters preAssemblerParams = new PreCloneAssemblerParameters( @@ -264,7 +261,7 @@ public void run1() throws Exception { PreCloneAssemblerRunner assemblerRunner = new PreCloneAssemblerRunner( alignmentsReader, - cellLevel ? TagType.CellTag : TagType.MoleculeTag, + cellLevel ? TagType.Cell : TagType.Molecule, new GeneFeature[]{GeneFeature.CDR3}, PreCloneAssemblerParameters.DefaultGConsensusAssemblerParameters, preClonesFile, tempDest.addSuffix("pc.tmp")); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 33bbc7796..45c461f47 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -129,7 +129,7 @@ public void run1() throws Exception { VDJCAlignmentsReader reader2 = new VDJCAlignmentsReader(in); VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(out)) { - int groupingDepth = reader1.getTagsInfo().getDepthFor(cellLevel ? TagType.CellTag : TagType.MoleculeTag); + int groupingDepth = reader1.getTagsInfo().getDepthFor(cellLevel ? TagType.Cell : TagType.Molecule); writer.header(reader1.getParameters(), reader1.getUsedGenes(), getFullPipelineConfiguration(), // output data will be grouped only up to a groupingDepth diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index b273ff7bf..b709d7ea0 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -62,7 +62,7 @@ public void run0() throws Exception { totalAlignments = alignmentsReader.getNumberOfAlignments(); PreCloneAssemblerRunner assemblerRunner = new PreCloneAssemblerRunner( alignmentsReader, - cellLevel ? TagType.CellTag : TagType.MoleculeTag, + cellLevel ? TagType.Cell : TagType.Molecule, new GeneFeature[]{GeneFeature.CDR3}, PreCloneAssemblerParameters.DefaultGConsensusAssemblerParameters, Paths.get(files.get(1)), diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java index 85b06d10b..21d7d46ff 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java @@ -6,7 +6,7 @@ public class TagInfoTest { @Test public void test1() { - TestUtil.assertJson(new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2)); - TestUtil.assertJson(new TagsInfo(12, new TagInfo(TagType.SampleTag, TagValueType.SequenceAndQuality, "TEST", 2))); + TestUtil.assertJson(new TagInfo(TagType.Sample, TagValueType.SequenceAndQuality, "TEST", 2)); + TestUtil.assertJson(new TagsInfo(12, new TagInfo(TagType.Sample, TagValueType.SequenceAndQuality, "TEST", 2))); } } \ 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zQx1K-N8aDiY@g(mr*rYg2Wl?tr?>H(Ndn%J1db&i&+n52?0I?P88NXMol@=rWmb)q zYYH&NB-1stk@5t(l%1f4A_*lw+?(HrUAGLcw`fr ziO@4LDtqO5!nWIo#;t(5Lr??wL?y?}PWj`@)?EAws`gkV-aYc3aVOGw36e!4c17Dx zNws+DTUVeRb6Suwy41v$uNF6>^0Cme+6wb661FS4_i&P!?F7p%>bm6@PiJJS6atPM z*fLE3u1Uzf3A`Vv=HiR+c>b9@9_f@1CW0n#?$Fo)&?0MoUY9PmQL9>P%j)7*kUn!& zx8>^MXT@NP&@m@6CDX#Q-7&R!_G}MpK=MvT9U^C&gr)jO$(g38YcaF%dnfR|{e|;rtYMj;_PXC7RSqI-xNJ-l>X{k884p{SGn5({moVF%g3l%Tipv^zW6HkQsTfrjgKt3!pkPXib;{LTx0uP;w1!LY6X}9R|TfN#cR~iJ}bCnev z;$`YBxPo9cZ}wbAU0s7=eVtPxl6GG`kNJ6)J`&hz^H#vksTlHQJDEH^;8Wg8Il%$E zf4>&F_}+mh+@Z)iglofHa4j)%C6*XW0>BTrV_<@r?@+)L(+7%b4Z3l9@5%;HM_B+C6xNj8eC3i;3A6@ zQOUi4qoHR7nP*L7!&voR98K+RJ12MJw06=2-t)-CPwHHJoz(ZHCqwNFB^tXD*IeAM z(=)UV9b@rdEZ>_TTD{9bQc!42O8Me~mTZkTp@swSZwcdF#v+{C5q2L%ohi_JW}8Q( nGCT5} Date: Wed, 8 Jun 2022 22:24:34 +0400 Subject: [PATCH 271/282] minor fixes & integration tests for tagged analysis --- itests/case10.sh | 20 +++++++++++++++---- itests/case11.sh | 13 +++++++++++- .../mixcr/basictypes/tag/TagsInfo.java | 15 ++++++++++++-- .../mixcr/cli/CommandAssemble.java | 13 +----------- .../mixcr/cli/CommandCorrectAndSortTags.java | 1 + .../mixcr/basictypes/tag/TagsInfoTest.java | 18 +++++++++++++++++ 6 files changed, 61 insertions(+), 19 deletions(-) create mode 100644 src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java diff --git a/itests/case10.sh b/itests/case10.sh index 4b8dbefb3..0bf18ec8a 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -40,8 +40,20 @@ mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled- mixcr itestAssemblePreClones case10.part-assembled-molecule-vdjca case10.part-assembled-molecule-vdjca.pc mixcr itestAssemblePreClones --cell-level case10.part-assembled-cell-vdjca case10.part-assembled-cell-vdjca.pc -mixcr assemble -f -a case10.part-assembled-molecule-vdjca case10.molecule-clna -mixcr assemble -f -a --cell-level case10.part-assembled-cell-vdjca case10.cell-clna +mixcr assemble -f -a case10.part-assembled-molecule-vdjca case10.cdr3-molecule-clna +mixcr assemble -f -a --cell-level case10.part-assembled-cell-vdjca case10.cdr3-cell-clna -mixcr assembleContigs -f case10.molecule-clna case10.molecule-clns -mixcr assembleContigs -f case10.cell-clna case10.cell-clns +mixcr assembleContigs -f case10.cdr3-molecule-clna case10.cdr3-molecule-clns +mixcr assembleContigs -f case10.cdr3-cell-clna case10.cdr3-cell-clns + +#mixcr assemble -f -OassemblingFeatures='VDJRegion' case10.part-assembled-molecule-vdjca case10.vdjregion-molecule-clns +#mixcr assemble -f -OassemblingFeatures='VDJRegion' --cell-level case10.part-assembled-cell-vdjca case10.vdjregion-cell-clns + +for f in *-clns; do + # -count -uniqueTagCount UMI + mixcr exportClones -f --split-by-tag CELL -tag CELL -nFeature CDR3 -nFeature VDJRegion ${f} ${f}.txt + grep -E 'TGTGCTGTGCAGGCGGTACTTCAACAAATTTTACTTT|TGTGCCAGCACAAACAGTCATGGCTACACCTTC|TGCCTCGTGGGTGACTCCGGTGGCCAGAAGCTGCTCTTT|TGTGCCAGCAGCTTAGGGGGGACAGGGGACCAAGAGACCCAGTACTTC|TGTGCAGCACCTCGTACGTTAAACGACTACAAGCTCAGCTTT|TGTGTTGTGAGTCTTCTGGTGGCTACAATAAGCTGATTTTT' ${f}.txt > ${f}.txt.g + sort ${f}.txt.g > ${f}.txt.g.s +done + +cmp case10.cdr3-cell-clns.txt.g.s case10.cdr3-molecule-clns.txt.g.s diff --git a/itests/case11.sh b/itests/case11.sh index ca640e1d2..81f822daf 100755 --- a/itests/case11.sh +++ b/itests/case11.sh @@ -36,4 +36,15 @@ mixcr correctAndSortTags case11.aligned-vdjca case11.corrected-vdjca mixcr itestAssemblePreClones case11.corrected-vdjca case11.corrected-vdjca.pc -mixcr assemble -f -a case11.corrected-vdjca case11.clna +mixcr assemble -f -a case11.corrected-vdjca case11.cdr3-clna +mixcr assembleContigs -f case11.cdr3-clna case11.cdr3-clns + +mixcr assemble -f -OassemblingFeatures='VDJRegion' case11.corrected-vdjca case11.vdjregion-clns + +mixcr exportClones -nFeature VDJRegion case11.vdjregion-clns case11.vdjregion-clns.txt +mixcr exportClones -nFeature VDJRegion case11.cdr3-clns case11.cdr3-clns.txt + +sort case11.vdjregion-clns.txt > case11.vdjregion-clns.txt.s +sort case11.cdr3-clns.txt > case11.cdr3-clns.txt.s + +cmp case11.vdjregion-clns.txt.s case11.cdr3-clns.txt.s diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index 1151ff8f2..7e8c3d367 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -1,12 +1,23 @@ package com.milaboratory.mixcr.basictypes.tag; +import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonFormat; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.primitivio.annotations.Serializable; -import java.util.*; +import java.util.AbstractCollection; +import java.util.Arrays; +import java.util.Iterator; +import java.util.Objects; @Serializable(asJson = true) +@JsonFormat(shape = JsonFormat.Shape.OBJECT) +@JsonAutoDetect( + fieldVisibility = JsonAutoDetect.Visibility.NON_PRIVATE, + isGetterVisibility = JsonAutoDetect.Visibility.NONE, + getterVisibility = JsonAutoDetect.Visibility.NONE +) public final class TagsInfo extends AbstractCollection { public static final TagsInfo NO_TAGS = new TagsInfo(0); @@ -57,7 +68,7 @@ public TagsInfo setSorted(int sortedLevel) { return new TagsInfo(sortedLevel, tags); } - public int indexOf(String tagName){ + public int indexOf(String tagName) { int idx = -1; for (TagInfo ti : this) if (ti.getName().equals(tagName)) { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 71e19ab87..5e3f06649 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -152,9 +152,6 @@ private void ensureParametersInitialized() { // noinspection ConstantConditions assemblerParameters = assemblerParameters.updateFrom(alignerParameters); - // TODO 4.0 ??? - // assemblerParameters = assemblerParameters.setCloneClusteringParameters(assemblerParameters.getCloneClusteringParameters().setMinimalTagSetOverlap(DEFAULT_MINIMAL_TAG_SET_OVERLAP)); - // Overriding JSON parameters if (!overrides.isEmpty()) { assemblerParameters = JsonOverrider.override(assemblerParameters, CloneAssemblerParameters.class, @@ -249,20 +246,12 @@ public void run1() throws Exception { // TODO >>>>>>>>>>>>>> PreCloneReader preClones; if (tagsInfo.hasTagsWithType(TagType.Cell) || tagsInfo.hasTagsWithType(TagType.Molecule)) { - int depth = tagsInfo.getDepthFor(cellLevel ? TagType.Cell : TagType.Molecule); - if (tagsInfo.getSortingLevel() < depth) - throwValidationException("Input file has insufficient sorting level"); - PreCloneAssemblerParameters preAssemblerParams = new PreCloneAssemblerParameters( - PreCloneAssemblerParameters.DefaultGConsensusAssemblerParameters, - alignmentsReader.getParameters(), - assemblerParameters.getAssemblingFeatures(), - depth); Path preClonesFile = tempDest.resolvePath("preclones.pc"); PreCloneAssemblerRunner assemblerRunner = new PreCloneAssemblerRunner( alignmentsReader, cellLevel ? TagType.Cell : TagType.Molecule, - new GeneFeature[]{GeneFeature.CDR3}, + assemblerParameters.getAssemblingFeatures(), PreCloneAssemblerParameters.DefaultGConsensusAssemblerParameters, preClonesFile, tempDest.addSuffix("pc.tmp")); SmartProgressReporter.startProgressReport(assemblerRunner); diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index ebe781ee5..c75884540 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -213,6 +213,7 @@ public void run1() throws Exception { // Initializing and writing results to the output file writer.header(mainReader, getFullPipelineConfiguration(), mainReader.getTagsInfo().setSorted(mainReader.getTagsInfo().size())); + writer.setNumberOfProcessedReads(mainReader.getNumberOfReads()); for (VDJCAlignments al : CUtils.it(sorted)) writer.write(al); } diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java new file mode 100644 index 000000000..5b1b6d88c --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java @@ -0,0 +1,18 @@ +package com.milaboratory.mixcr.basictypes.tag; + +import com.milaboratory.test.TestUtil; +import org.junit.Test; + +import static org.junit.Assert.*; + +public class TagsInfoTest { + @Test + public void testJson() { + TagsInfo ti = new TagsInfo(1, + new TagInfo(TagType.Sample, TagValueType.SequenceAndQuality,"SPL1", 0), + new TagInfo(TagType.Cell, TagValueType.SequenceAndQuality,"CELL", 1), + new TagInfo(TagType.Molecule, TagValueType.SequenceAndQuality,"UMI", 2) + ); + TestUtil.assertJson(ti); + } +} \ No newline at end of file From 37860b0a8d3c6b1661c69062865cc7fc7029c7d9 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 8 Jun 2022 23:46:22 +0400 Subject: [PATCH 272/282] License & Copyright update. --- LICENSE | 255 ++++++++++++++++-- .../assembler/AlignmentsMappingMerger.java | 32 +-- .../mixcr/assembler/AlignmentsProvider.java | 32 +-- .../mixcr/assembler/AssembledReadsPort.java | 32 +-- .../mixcr/assembler/AssemblerEvent.java | 32 +-- .../mixcr/assembler/AssemblerEventLogger.java | 32 +-- .../mixcr/assembler/AssemblerUtils.java | 32 +-- .../mixcr/assembler/CloneAccumulator.java | 32 +-- .../mixcr/assembler/CloneAssembler.java | 32 +-- .../assembler/CloneAssemblerListener.java | 32 +-- .../assembler/CloneAssemblerParameters.java | 32 +-- .../CloneAssemblerParametersPresets.java | 32 +-- .../mixcr/assembler/CloneAssemblerRunner.java | 32 +-- .../assembler/CloneClusteringParameters.java | 32 +-- .../assembler/CloneClusteringStrategy.java | 32 +-- .../mixcr/assembler/CloneFactory.java | 32 +-- .../assembler/CloneFactoryParameters.java | 32 +-- .../mixcr/assembler/ClusteringFilter.java | 32 +-- .../assembler/DClonalAlignerParameters.java | 32 +-- .../mixcr/assembler/ReadToCloneMapping.java | 32 +-- .../RelativeConcentrationFilter.java | 32 +-- .../mixcr/assembler/VDJCGeneAccumulator.java | 11 + .../assembler/VJCClonalAlignerParameters.java | 32 +-- .../mixcr/assembler/VJCSignature.java | 11 + .../fullseq/CoverageAccumulator.java | 32 +-- .../assembler/fullseq/FullSeqAssembler.java | 32 +-- .../fullseq/FullSeqAssemblerParameters.java | 32 +-- .../fullseq/FullSeqAssemblerReport.java | 32 +-- .../assembler/fullseq/PointSequence.java | 32 +-- .../preclone/FilePreCloneReader.java | 11 + .../preclone/FilePreCloneWriter.java | 11 + .../mixcr/assembler/preclone/IO.java | 11 + .../mixcr/assembler/preclone/PreClone.java | 11 + .../assembler/preclone/PreCloneAbstract.java | 11 + .../assembler/preclone/PreCloneAssembler.java | 11 + .../preclone/PreCloneAssemblerParameters.java | 11 + .../preclone/PreCloneAssemblerReport.java | 11 + .../preclone/PreCloneAssemblerResult.java | 11 + .../preclone/PreCloneAssemblerRunner.java | 11 + .../assembler/preclone/PreCloneImpl.java | 11 + .../assembler/preclone/PreCloneReader.java | 11 + .../mixcr/basictypes/AlignmentsIO.java | 32 +-- .../basictypes/BasicVDJCAlignmentReader.java | 32 +-- .../BasicVDJCAlignmentWriterFactory.java | 32 +-- .../mixcr/basictypes/ClnAReader.java | 32 +-- .../mixcr/basictypes/ClnAWriter.java | 32 +-- .../mixcr/basictypes/ClnsReader.java | 32 +-- .../mixcr/basictypes/ClnsWriter.java | 32 +-- .../mixcr/basictypes/ClonalSequence.java | 32 +-- .../basictypes/ClonalUpdatableParameters.java | 32 +-- .../milaboratory/mixcr/basictypes/Clone.java | 32 +-- .../mixcr/basictypes/CloneReader.java | 32 +-- .../mixcr/basictypes/CloneSet.java | 32 +-- .../mixcr/basictypes/CloneSetIO.java | 32 +-- .../mixcr/basictypes/CloneSetOverlap.java | 32 +-- .../mixcr/basictypes/CompatibilityIO.java | 32 +-- .../mixcr/basictypes/FieldCollection.java | 11 + .../mixcr/basictypes/GeneAndScore.java | 11 + .../mixcr/basictypes/HasFeatureToAlign.java | 32 +-- .../mixcr/basictypes/HasGene.java | 32 +-- .../mixcr/basictypes/HasRelativeMinScore.java | 11 + .../com/milaboratory/mixcr/basictypes/IO.java | 32 +-- .../milaboratory/mixcr/basictypes/IOUtil.java | 32 +-- .../milaboratory/mixcr/basictypes/Merger.java | 32 +-- .../PipelineConfigurationReaderMiXCR.java | 32 +-- .../mixcr/basictypes/SequenceHistory.java | 32 +-- .../mixcr/basictypes/TargetPartitioning.java | 32 +-- .../mixcr/basictypes/VDJCAlignments.java | 32 +-- .../basictypes/VDJCAlignmentsFormatter.java | 32 +-- .../basictypes/VDJCAlignmentsReader.java | 32 +-- .../basictypes/VDJCAlignmentsWriter.java | 32 +-- .../basictypes/VDJCAlignmentsWriterI.java | 32 +-- .../mixcr/basictypes/VDJCFileHeaderData.java | 11 + .../mixcr/basictypes/VDJCHit.java | 32 +-- .../mixcr/basictypes/VDJCObject.java | 32 +-- .../basictypes/VDJCPartitionedSequence.java | 32 +-- .../mixcr/basictypes/VDJCSProperties.java | 32 +-- .../milaboratory/mixcr/basictypes/tag/IO.java | 11 + .../tag/SequenceAndQualityTagValue.java | 11 + .../basictypes/tag/SequenceTagValue.java | 11 + .../mixcr/basictypes/tag/TagCount.java | 11 + .../basictypes/tag/TagCountAggregator.java | 11 + .../mixcr/basictypes/tag/TagInfo.java | 11 + .../mixcr/basictypes/tag/TagTuple.java | 11 + .../mixcr/basictypes/tag/TagType.java | 11 + .../mixcr/basictypes/tag/TagValue.java | 11 + .../mixcr/basictypes/tag/TagValueType.java | 11 + .../mixcr/basictypes/tag/TagsInfo.java | 11 + .../milaboratory/mixcr/cli/ACommandMiXCR.java | 32 +-- .../mixcr/cli/ACommandSimpleExportMiXCR.java | 32 +-- .../mixcr/cli/ACommandWithOutputMiXCR.java | 32 +-- .../cli/ACommandWithSmartOverwriteMiXCR.java | 32 +-- ...ithSmartOverwriteWithSingleInputMiXCR.java | 32 +-- .../mixcr/cli/AbstractCommandReport.java | 32 +-- .../milaboratory/mixcr/cli/AlignerReport.java | 32 +-- .../mixcr/cli/ChainUsageStats.java | 32 +-- .../mixcr/cli/CloneAssemblerReport.java | 32 +-- .../milaboratory/mixcr/cli/CommandAlign.java | 32 +-- .../mixcr/cli/CommandAlignmentsDiff.java | 32 +-- .../mixcr/cli/CommandAlignmentsStats.java | 32 +-- .../mixcr/cli/CommandAnalyze.java | 32 +-- .../mixcr/cli/CommandAssemble.java | 32 +-- .../mixcr/cli/CommandAssembleContigs.java | 32 +-- .../cli/CommandAssemblePartialAlignments.java | 32 +-- .../mixcr/cli/CommandClonesDiff.java | 32 +-- .../mixcr/cli/CommandCorrectAndSortTags.java | 11 + .../milaboratory/mixcr/cli/CommandExport.java | 32 +-- .../mixcr/cli/CommandExportAirr.java | 11 + .../cli/CommandExportAlignmentsForClones.java | 11 + .../cli/CommandExportAlignmentsPretty.java | 32 +-- .../mixcr/cli/CommandExportClonesPretty.java | 32 +-- .../mixcr/cli/CommandExportOverlap.java | 11 + .../mixcr/cli/CommandExportReads.java | 32 +-- .../cli/CommandExportReadsForClones.java | 32 +-- .../milaboratory/mixcr/cli/CommandExtend.java | 32 +-- .../mixcr/cli/CommandFilterAlignments.java | 32 +-- .../mixcr/cli/CommandGroupCells.java | 11 + .../milaboratory/mixcr/cli/CommandInfo.java | 32 +-- .../mixcr/cli/CommandListLibraries.java | 32 +-- .../milaboratory/mixcr/cli/CommandMain.java | 32 +-- .../mixcr/cli/CommandMergeAlignments.java | 32 +-- .../mixcr/cli/CommandPipelineInfo.java | 32 +-- .../milaboratory/mixcr/cli/CommandReport.java | 32 +-- .../milaboratory/mixcr/cli/CommandSlice.java | 32 +-- .../mixcr/cli/CommandSortAlignments.java | 32 +-- .../mixcr/cli/CommandSortClones.java | 11 + .../mixcr/cli/CommandVersionInfo.java | 32 +-- .../mixcr/cli/CommonDescriptions.java | 32 +-- .../milaboratory/mixcr/cli/CommonOptions.java | 32 +-- .../cli/ITestCommandAssemblePreClones.java | 11 + .../java/com/milaboratory/mixcr/cli/Main.java | 32 +-- .../milaboratory/mixcr/cli/MiXCRCommand.java | 32 +-- .../milaboratory/mixcr/cli/ReportWrapper.java | 32 +-- .../cli/SerializerCompatibilityUtil.java | 32 +-- .../java/com/milaboratory/mixcr/cli/Util.java | 32 +-- .../mixcr/cli/afiltering/AFilter.java | 32 +-- .../cli/postanalysis/CommandDownsample.java | 11 + .../postanalysis/CommandOverlapScatter.java | 11 + .../mixcr/cli/postanalysis/CommandPa.java | 11 + .../cli/postanalysis/CommandPaExport.java | 11 + .../postanalysis/CommandPaExportPlots.java | 11 + .../CommandPaExportPlotsBasicStatistics.java | 11 + .../CommandPaExportPlotsGeneUsage.java | 11 + .../CommandPaExportPlotsHeatmap.java | 11 + ...ommandPaExportPlotsHeatmapWithGroupBy.java | 11 + .../CommandPaExportPlotsOverlap.java | 11 + .../CommandPaExportPlotsVJUsage.java | 11 + .../postanalysis/CommandPaExportTables.java | 11 + .../CommandPaExportTablesBase.java | 11 + .../CommandPaExportTablesPreprocSummary.java | 11 + .../cli/postanalysis/CommandPaIndividual.java | 11 + .../postanalysis/CommandPaListMetrics.java | 11 + .../cli/postanalysis/CommandPaOverlap.java | 11 + .../cli/postanalysis/IsolationGroup.java | 11 + .../mixcr/cli/postanalysis/PaResult.java | 11 + .../cli/postanalysis/PaResultByGroup.java | 11 + .../mixcr/export/AbstractField.java | 32 +-- .../mixcr/export/AbstractFieldExtractor.java | 32 +-- .../mixcr/export/AirrColumns.java | 11 + .../milaboratory/mixcr/export/AirrUtil.java | 11 + .../mixcr/export/AirrVDJCObjectWrapper.java | 11 + .../mixcr/export/FeatureExtractors.java | 32 +-- .../com/milaboratory/mixcr/export/Field.java | 32 +-- .../mixcr/export/FieldExtractor.java | 32 +-- .../export/FieldExtractorWithParameters.java | 32 +-- .../mixcr/export/FieldExtractors.java | 32 +-- .../mixcr/export/FieldParameterless.java | 32 +-- .../mixcr/export/FieldWithParameters.java | 32 +-- .../milaboratory/mixcr/export/InfoWriter.java | 32 +-- .../milaboratory/mixcr/export/OutputMode.java | 32 +-- .../mixcr/info/AlignmentInfoCollector.java | 32 +-- .../info/GeneFeatureCoverageCollector.java | 32 +-- .../info/ReferencePointCoverageCollector.java | 32 +-- .../mixcr/partialassembler/AlignedTarget.java | 32 +-- .../mixcr/partialassembler/BPoint.java | 32 +-- .../PartialAlignmentsAssembler.java | 32 +-- .../PartialAlignmentsAssemblerAligner.java | 32 +-- .../PartialAlignmentsAssemblerParameters.java | 32 +-- .../mixcr/partialassembler/RangeSet.java | 32 +-- .../mixcr/partialassembler/TargetMerger.java | 32 +-- .../mixcr/partialassembler/VDJCMultiRead.java | 32 +-- .../mixcr/postanalysis/Aggregator.java | 11 + .../mixcr/postanalysis/Characteristic.java | 11 + .../mixcr/postanalysis/Dataset.java | 11 + .../mixcr/postanalysis/MappingFunction.java | 11 + .../mixcr/postanalysis/MetricValue.java | 11 + .../postanalysis/PostanalysisResult.java | 11 + .../postanalysis/PostanalysisRunner.java | 11 + .../mixcr/postanalysis/SetPreprocessor.java | 11 + .../postanalysis/SetPreprocessorFactory.java | 11 + .../postanalysis/SetPreprocessorSetup.java | 11 + .../postanalysis/SetPreprocessorStat.java | 11 + .../postanalysis/SetPreprocessorSummary.java | 11 + .../mixcr/postanalysis/WeightFunction.java | 11 + .../mixcr/postanalysis/WeightFunctions.java | 11 + .../postanalysis/additive/AAProperties.java | 11 + .../additive/AdditiveAggregator.java | 11 + .../additive/AdditiveCharacteristic.java | 11 + .../additive/AdditiveCharacteristics.java | 11 + .../postanalysis/additive/AdditiveMetric.java | 11 + .../additive/AdditiveMetrics.java | 11 + .../additive/AggregationType.java | 11 + .../postanalysis/additive/KeyFunction.java | 11 + .../postanalysis/additive/KeyFunctions.java | 11 + .../postanalysis/additive/Normalization.java | 32 +-- .../clustering/HierarchicalClustering.java | 11 + .../clustering/HierarchyNode.java | 11 + .../diversity/DiversityAggregator.java | 11 + .../diversity/DiversityCharacteristic.java | 11 + .../diversity/DiversityMeasure.java | 11 + ...ClonesDownsamplingPreprocessorFactory.java | 11 + .../downsampling/DownsampleValueChooser.java | 11 + .../DownsamplingPreprocessor.java | 11 + .../DownsamplingPreprocessorFactory.java | 11 + .../downsampling/DownsamplingUtil.java | 32 +-- .../downsampling/LogFactorial.java | 35 +-- .../downsampling/RandomHypergeometric.java | 35 +-- .../downsampling/RandomMvhgCounts.java | 35 +-- .../downsampling/RandomMvhgMarginals.java | 35 +-- .../overlap/OverlapAggregator.java | 11 + .../overlap/OverlapCharacteristic.java | 11 + .../postanalysis/overlap/OverlapDataset.java | 11 + .../postanalysis/overlap/OverlapGroup.java | 32 +-- .../postanalysis/overlap/OverlapKey.java | 11 + .../postanalysis/overlap/OverlapType.java | 11 + .../postanalysis/overlap/OverlapUtil.java | 32 +-- .../preproc/ElementPredicate.java | 11 + .../preproc/FilterPreprocessor.java | 11 + .../postanalysis/preproc/NoPreprocessing.java | 11 + .../preproc/OverlapPreprocessorAdapter.java | 11 + .../preproc/PreprocessorChain.java | 11 + .../mixcr/postanalysis/preproc/SelectTop.java | 11 + .../spectratype/SpectratypeAggregator.java | 11 + .../SpectratypeCharacteristic.java | 11 + .../spectratype/SpectratypeKey.java | 11 + .../spectratype/SpectratypeKeyFunction.java | 11 + .../postanalysis/stat/HolmBonferroni.java | 32 +-- .../postanalysis/stat/PValueCorrection.java | 11 + .../postanalysis/ui/CharacteristicGroup.java | 11 + .../CharacteristicGroupOutputExtractor.java | 11 + .../ui/CharacteristicGroupResult.java | 11 + .../ui/CharacteristicGroupResultBuilder.java | 11 + .../ui/CharacteristicGroupResultCell.java | 11 + .../postanalysis/ui/ClonotypeDataset.java | 11 + .../mixcr/postanalysis/ui/Coordinates.java | 11 + .../mixcr/postanalysis/ui/GroupMelt.java | 11 + .../mixcr/postanalysis/ui/GroupSummary.java | 11 + .../mixcr/postanalysis/ui/OutputTable.java | 11 + .../postanalysis/ui/OutputTableBuilder.java | 11 + .../postanalysis/ui/OutputTableCell.java | 11 + .../postanalysis/ui/OutputTableExtractor.java | 11 + .../mixcr/postanalysis/ui/OverlapSummary.java | 11 + .../ui/PostanalysisParameters.java | 11 + .../ui/PostanalysisParametersIndividual.java | 11 + .../ui/PostanalysisParametersOverlap.java | 11 + .../ui/PostanalysisParametersPreset.java | 11 + .../postanalysis/ui/PostanalysisSchema.java | 11 + .../postanalysis/util/OverlapBrowser.java | 11 + .../milaboratory/mixcr/tags/CloneGroup.java | 32 +-- .../mixcr/tags/CloneTagTuple.java | 11 + .../mixcr/tags/CloneTagTupleFilter.java | 11 + .../mixcr/tags/DropletCloneGraph.java | 32 +-- .../tags/DropletCloneGraphParameters.java | 32 +-- .../mixcr/tags/DropletCloneGraphReport.java | 32 +-- .../mixcr/tags/WhitelistReader.java | 11 + .../mixcr/util/AdjacencyMatrix.java | 32 +-- .../mixcr/util/AlignedStringsBuilder.java | 32 +-- .../milaboratory/mixcr/util/BitArrayInt.java | 18 +- .../milaboratory/mixcr/util/Concurrency.java | 32 +-- .../milaboratory/mixcr/util/MiXCRDebug.java | 32 +-- .../mixcr/util/MiXCRVersionInfo.java | 32 +-- .../mixcr/util/OutputPortWithProgress.java | 11 + .../mixcr/util/PrintStreamTableAdapter.java | 32 +-- .../com/milaboratory/mixcr/util/RunMiXCR.java | 32 +-- .../com/milaboratory/mixcr/util/Tuple2.java | 11 + .../util/VDJCAlignmentsDifferenceReader.java | 32 +-- .../mixcr/util/VDJCObjectExtender.java | 32 +-- .../ClonalGeneAlignmentParameters.java | 32 +-- .../mixcr/vdjaligners/DAlignerParameters.java | 32 +-- .../vdjaligners/GeneAlignmentParameters.java | 32 +-- .../GeneAlignmentParametersAbstract.java | 32 +-- .../vdjaligners/KGeneAlignmentParameters.java | 32 +-- .../mixcr/vdjaligners/PreVDJCHit.java | 32 +-- .../mixcr/vdjaligners/SingleDAligner.java | 32 +-- .../mixcr/vdjaligners/VDJCAligner.java | 32 +-- .../vdjaligners/VDJCAlignerAbstract.java | 32 +-- .../vdjaligners/VDJCAlignerEventListener.java | 32 +-- .../mixcr/vdjaligners/VDJCAlignerPVFirst.java | 32 +-- .../vdjaligners/VDJCAlignerParameters.java | 32 +-- .../mixcr/vdjaligners/VDJCAlignerS.java | 32 +-- .../vdjaligners/VDJCAlignerWithMerge.java | 32 +-- .../vdjaligners/VDJCAlignmentFailCause.java | 32 +-- .../vdjaligners/VDJCAlignmentResult.java | 32 +-- .../vdjaligners/VDJCLibraryStructure.java | 11 + .../vdjaligners/VDJCParametersPresets.java | 32 +-- .../mixcr/vdjaligners/VJAlignmentOrder.java | 32 +-- .../postanalysis/plots/BasicStatistics.kt | 11 + .../mixcr/postanalysis/plots/GeneUsage.kt | 11 + .../mixcr/postanalysis/plots/Heatmap.kt | 11 + .../mixcr/postanalysis/plots/Metadata.kt | 11 + .../mixcr/postanalysis/plots/Overlap.kt | 11 + .../postanalysis/plots/OverlapScatter.kt | 11 + .../mixcr/postanalysis/plots/Preprocessing.kt | 11 + .../postanalysis/plots/SingleSpectratype.kt | 11 + .../mixcr/postanalysis/plots/VJUsage.kt | 11 + .../mixcr/postanalysis/plots/WithPlotSize.kt | 11 + .../mixcr/assembler/AssemblerUtilsTest.java | 32 +-- .../CloneAssemblerParametersPresetsTest.java | 32 +-- .../CloneAssemblerParametersTest.java | 32 +-- .../assembler/CloneAssemblerRunnerTest.java | 32 +-- .../CloneClusteringParametersTest.java | 32 +-- .../assembler/CloneFactoryParametersTest.java | 32 +-- .../mixcr/assembler/ClusteringFilterTest.java | 32 +-- .../VJCClonalAlignerParametersTest.java | 32 +-- .../fullseq/FullSeqAssemblerTest.java | 32 +-- .../mixcr/basictypes/ClnAReaderTest.java | 32 +-- .../mixcr/basictypes/ClonalSequenceTest.java | 32 +-- .../milaboratory/mixcr/basictypes/IOTest.java | 32 +-- .../mixcr/basictypes/MergerTest.java | 32 +-- .../mixcr/basictypes/SequenceHistoryTest.java | 32 +-- .../VDJCAlignmentsFormatterTest.java | 32 +-- .../mixcr/basictypes/VDJCObjectTest.java | 32 +-- .../mixcr/basictypes/VDJCSPropertiesTest.java | 32 +-- .../mixcr/basictypes/tag/TagInfoTest.java | 11 + .../mixcr/basictypes/tag/TagsInfoTest.java | 11 + .../mixcr/cli/AlignerReportTest.java | 32 +-- .../mixcr/cli/ChainUsageStatsTest.java | 32 +-- .../mixcr/cli/CommandAnalyzeTest.java | 32 +-- .../mixcr/cli/CommandGroupCellsTest.java | 11 + .../mixcr/cli/JsonOverriderTest.java | 32 +-- .../com/milaboratory/mixcr/cli/MainTest.java | 32 +-- .../com/milaboratory/mixcr/cli/UtilTest.java | 32 +-- .../cli/postanalysis/CommandPaExportTest.java | 11 + .../mixcr/cli/postanalysis/CommandPaTest.java | 11 + .../cli/postanalysis/IsolationGroupTest.java | 11 + .../mixcr/export/FieldExtractorsTest.java | 32 +-- ...PartialAlignmentsAssemblerAlignerTest.java | 32 +-- .../PartialAlignmentsAssemblerTest.java | 32 +-- .../mixcr/partialassembler/RangeSetTest.java | 32 +-- .../partialassembler/TargetMergerTest.java | 32 +-- .../postanalysis/PostanalysisRunnerTest.java | 11 + .../mixcr/postanalysis/TestDataset.java | 11 + .../mixcr/postanalysis/TestObject.java | 11 + .../postanalysis/TestObjectWithPayload.java | 11 + .../additive/AdditiveCharacteristicsTest.java | 11 + .../HierarchicalClusteringTest.java | 11 + .../DiversityCharacteristicTest.java | 11 + .../DownsampleValueChooserTest.java | 11 + .../DownsamplingPreprocessorTest.java | 11 + .../OverlapDownsamplingPreprocessorTest.java | 11 + .../overlap/OverlapCharacteristicTest.java | 11 + .../overlap/OverlapIntegrationTest.java | 32 +-- .../preproc/PreprocessorChainTest.java | 11 + .../postanalysis/preproc/SelectTopTest.java | 11 + .../postanalysis/stat/HolmBonferroniTest.java | 32 +-- .../stat/PValueCorrectionTest.java | 11 + .../PostanalysisParametersIndividualTest.java | 11 + .../ui/PostanalysisParametersOverlapTest.java | 11 + .../ui/PostanalysisSchemaIntegrationTest.java | 11 + .../mixcr/tags/CloneTagTupleFilterTest.java | 11 + .../mixcr/tags/DropletCloneGraphTest.java | 11 + .../mixcr/tags/WhitelistPackerTest.java | 11 + .../tests/BackwardCompatibilityTests.java | 32 +-- .../mixcr/tests/IntegrationTest.java | 11 + .../mixcr/tests/MiXCRTestUtils.java | 32 +-- .../mixcr/tests/TargetBuilder.java | 32 +-- .../mixcr/tests/TargetBuilderTest.java | 32 +-- .../mixcr/util/AdjacencyMatrixTest.java | 32 +-- .../mixcr/util/AlignedStringsBuilderTest.java | 32 +-- .../mixcr/util/DummyIntegrationTest.java | 32 +-- .../mixcr/util/MiXCRVersionInfoTest.java | 32 +-- .../milaboratory/mixcr/util/RunMiXCRTest.java | 32 +-- .../VDJCAlignmentsDifferenceReaderTest.java | 32 +-- .../mixcr/util/VDJCObjectExtenderTest.java | 32 +-- .../vdjaligners/DAlignerParametersTest.java | 32 +-- .../KGeneAlignmentParametersTest.java | 32 +-- .../vdjaligners/VDJCAlignerPVFirstTest.java | 32 +-- .../VDJCAlignerParametersTest.java | 32 +-- .../mixcr/vdjaligners/VDJCAlignerSTest.java | 32 +-- .../vdjaligners/VDJCAlignerWithMergeTest.java | 32 +-- .../VDJCParametersPresetsTest.java | 32 +-- 381 files changed, 3568 insertions(+), 5275 deletions(-) diff --git a/LICENSE b/LICENSE index b6cf4b706..37701286f 100644 --- a/LICENSE +++ b/LICENSE @@ -1,27 +1,228 @@ -Copyright (c) 2014-2018, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail -(here and after addressed as Inventors) -All Rights Reserved - -Permission to use, copy, modify and distribute any part of this program for -educational, research and non-profit purposes, by non-profit institutions -only, without fee, and without a written agreement is hereby granted, -provided that the above copyright notice, this paragraph and the following -three paragraphs appear in all copies. - -Those desiring to incorporate this work into commercial products or use for -commercial purposes should contact MiLaboratory LLC, which owns exclusive -rights for distribution of this program for commercial purposes, using the -following email address: licensing@milaboratory.com. - -IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, -SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, -ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN -ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS -NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR -MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO -WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A -PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY -PATENT, TRADEMARK OR OTHER RIGHTS. \ No newline at end of file +Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + +By exercising the Licensed Rights, the User accepts and agrees to be bound by +the terms and conditions of this international public end-user license +(the "License"). To the extent this License may be interpreted as a contract, +the User is granted the Licensed Rights in consideration of the User's +acceptance of these terms and conditions, and the Licensor grants the User such +rights in consideration of benefits the Licensor receives from making the +Software available under this License. + +By downloading the Software, the User represents and warrants to the Licensor +that the User is an Individual User or a Non-Profit Organization and will only +use the Software for Non-Commercial Use in accordance with the terms of this +License. + +Section 1 - Definitions. + +In this License: + +"Copyright and Similar Rights" means copyright and/or similar rights closely + related to copyright, without regard to how the rights are labeled or + categorized. + +"Individual User” means a private individual who uses the Software on his or her + own behalf and for his or her own purposes (and not on behalf of, or for the + purposes of, any government agency, legal person or other organization). + +"Licensed Rights" means the rights granted to the User subject to the terms and + conditions of this License, which are limited to all Copyright and Similar + Rights that apply to the User's use of the Software and that the Licensor has + authority to license. + +"Licensor" means MiLaboratories Inc., a Delaware corporation. + +"Non-Commercial Use" means use by an Individual User or a Non-Profit + Organization that is not intended for or directed towards commercial advantage + or monetary compensation and is not conducted using funds from any external + source. + +"Non-Profit Organization" means an organization that does not, and is not + intended to, earn profits for its owners or shareholders and which operates in + order to provide a public service. + +"Software" means MiXCR, the Licensor's proprietary software for comprehensive, + adaptive immunity profiling for immunoglobulin (IG) and T-cell receptor + extraction of T- and B- cell receptor repertoires from any type of sequencing + data. All title and copyrights for and to the Software, including but not + limited to any copywritten images, demos, source code, and intermediate files + incorporated into the Software, the accompanying materials, and any copies of + the Software are the intellectual property of and are owned by the Licensor. + +"User" means the Individual User or Non-Profit Organization exercising the + Licensed Rights under this License. + +Section 2 - License Grant. + +Subject to the terms and conditions of this License, the Licensor hereby grants +the User a worldwide, non-exclusive, royalty-free, non-sublicensable, +non-transferable license to exercise the Licensed Rights in the Software to +download, install, use, reproduce, copy, modify and distribute any part of the +Software for Non-Commercial Use only. + +The User is not authorized by this License to assert or claim that the User or +its use of the Software is, connected with, or sponsored, endorsed, or granted +official status by, the Licensor. + +Patent and trademark rights are not licensed under this License. + +Those desiring to incorporate the Software into commercial products or use the +Software or any derivatives from the Software for any commercial purposes +should contact MiLaboratories Inc., which owns exclusive licensing and +distribution rights for the Software , using the following email address: +licensing@milaboratories.com. + +Section 3 - License Conditions. + +A User's exercise of the Licensed Rights is expressly made subject to the +following conditions: + +(1) If the User distributes the Software (including in modified form), the User +must:(a) retain the following if it is supplied by the Licensor with the +Software: +• identification of the creator(s) of the Software and any others designated to + receive attribution, in any reasonable manner requested by the Licensor + (including by pseudonym if designated); +• a Licensor’s copyright notice; +• a notice that refers to the disclaimer of warranties in Section 4 + (Disclaimer of Warranties and Limitation of Liability) below; and +• a URL or hyperlink to the Software to the extent reasonably practicable; + (b) indicate if the User has modified the Software and retain an indication + of any previous modifications; and(c) indicate the Software (including any + modifications and derivatives) are licensed under this License, and include + the text of, or the URI or hyperlink to, this License.(2) If requested by the + Licensor, the User must remove any of the information required by paragraph + (a) above to the extent reasonably practicable.(3) The User shall not + (and shall not allow any other person to): +• decompile, disassemble, or otherwise reverse engineer the Software or attempt + to discover any source code or underlying ideas or algorithms of the + Software; +• remove any product identification, copyright or other notices embedded within + the Software; +• modify or create a derivative work of the Software; +• export any Software in violation of applicable laws or regulations; +• copy the Software or any portion thereof except as provided in this License; +• disclose any performance information or analysis (including, without + limitation, benchmarks) from any source relating to the Software; or +• rent, lease, loan, sale or assign the Software or derivative works based on + the whole or any part of the Software.(4) The User acknowledges that + third-party software may be embedded or otherwise delivered with the + Software. The User may only use such third-party software as integrated with + and part of the Software. The licensors of the third-party software are + intended beneficiaries of this License as it pertains to the User’s rights to + use such software. Section 4 - Disclaimer of Warranties and Limitation of + Liability. + +THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE LICENSOR HAS NO +OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR +MODIFICATIONS. THE LICENSOR MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES +OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR +THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER +RIGHTS. + +LICENSOR DOES NOT GUARANTEE THAT LICENSED MATERIALS WILL MEET YOUR EXPECTATIONS +OR REQUIREMENTS. LICENSOR DOES NOT GUARANTEE THAT THE LICENSED MATERIALS ARE +ERROR-FREE. LICENSOR DOES NOT WARRANT, GUARANTEE, OR MAKE ANY REPRESENTATIONS +REGARDING THE USE, OR THE RESULTS OF THE USE, OF THE LICENSED MATERIALS IN +TERMS OF CORRECTNESS, ACCURACY, RELIABILITY, OR OTHERWISE. THE ENTIRE RISK +ARISING OUT OF USE OR PERFORMANCE OF THE LICENSED MATERIALS REMAINS WITH YOU. +NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY LICENSOR SHALL CREATE A +WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF THIS WARRANTY. + +IN NO EVENT SHALL THE LICENSOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, +SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING +OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE LICENSOR HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. + +Section 5 - Term and Termination. + +This License applies for the term of the Copyright and Similar Rights licensed +herein. However, if the User fails to comply with this License, then the User's +rights under this License terminate automatically. + +Where the User's right to use the Software has terminated under the preceding +paragraph, it reinstates: (a) automatically as of the date the violation is +cured, provided it is cured within thirty (30) days of the User's discovery of +the violation; or (b) upon express reinstatement by the Licensor. + +For the avoidance of doubt, nothing in this Section 5 affects any right the +Licensor may have to seek remedies for the User's violation of this License. + +Sections 1 (Definitions), 4 (Disclaimer of Warranties and Limitation of +Liability), 5 (Term and Termination), 8 (Other Terms and Conditions), 9 +(Interpretation) and 10 (Governing Law / Forum and Venue) survive termination +of this License. + +Section 6 - Collection of Statistics and Data + +Through the Software, the Licensor may collect anonymized statistics and other +information, including the User's IP address and the size of raw data files +processed by the User (rounded to the nearest hundred megabytes). The User +hereby consents to the collection and processing of such data by the Licensor. + +Section 7 – Marketing + +The User grants the Licensor a limited, non-exclusive right to place the User’s +trademarks and logos on the Licensor’s web site and marketing materials solely +for the purpose of identifying the User as a user of the Software. + +Section 8 - Other Terms and Conditions. + +The Licensor shall not be bound by any additional or different terms or +conditions communicated by the User unless expressly agreed. + +Any arrangements, understandings, or agreements regarding the Software not +stated herein are separate from and independent of the terms and conditions of +this License. + +Section 9 - Interpretation. + +For the avoidance of doubt, this License does not, and shall not be interpreted +to, reduce, limit, restrict, or impose conditions on any use of the Software +that could lawfully be made without permission under this License. + +To the extent possible, if any provision of this License is deemed +unenforceable, it shall be automatically reformed to the minimum extent +necessary to make it enforceable. If the provision cannot be reformed, it shall +be severed from this License without affecting the enforceability of the +remaining terms and conditions. + +No term or condition of this License will be waived and no failure to comply +consented to unless expressly agreed to by the Licensor. + +Nothing in this License constitutes or may be interpreted as a limitation upon, +or waiver of, any privileges and immunities that apply to the Licensor or the +User, including from the legal processes of any jurisdiction or authority. + +Section 10 - Governing Law / Forum and Venue. + +This License shall be governed by, and construed and enforced in accordance +with, the laws of the State of New York, without giving effect to any choice of +law rule that would cause the application of the laws of any jurisdiction other +than the internal laws of the State of New York to the rights and duties of the +Licensor and the User. + +Any judicial action or proceeding arising hereunder or relating hereto shall be +brought in, and the User hereby consent to the exclusive, personal jurisdiction +of, the Courts of New York. + +Section 11 – Changes. + +From time to time, Licensor may change the terms and provisions of this License. +When these changes are made, Licensor will make a new version of the License +publicly available. + +You understand and agree that if you use the Software after the date on which +the License has been changed, the Licensor will treat your use as acceptance of +the updated License. + +Section 12 – Contacts. + +If you have any questions, concerns, or complaints regarding this License or the +Software, please contact us using the details below: + +https://milaboratories.com/contacts +licensing@milaboratories.com + +This document was last updated on June 1, 2022 diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java index 4aac6509c..7954316f6 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsMappingMerger.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java index 518678775..92161f948 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java b/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java index 577316192..8cfa465b1 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssembledReadsPort.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java index a49030139..286520e64 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEvent.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java index f25a75d7c..3573f7c62 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerEventLogger.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java index fd3995fed..a757ac555 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/AssemblerUtils.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java index f72484324..db60bf5dc 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAccumulator.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java index fd86580f9..82a6f2bee 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java index e2e6ad678..ce323d447 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerListener.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java index 4ec3a4e26..38f347e49 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java index bf0fe32c9..52031b3f6 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresets.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java index b9b0de1f9..fc9c898eb 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunner.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java index d685d305a..cfecabb0f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java index c8d003800..3b84e4a8a 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringStrategy.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java index fcb1806c6..562a4a9fe 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactory.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java index a3b369e6e..1e4a310e3 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java b/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java index 399181ae8..17cd0acaa 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java index bd84a5088..974db28e3 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java b/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java index b69562f17..1d95f309b 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/ReadToCloneMapping.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java b/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java index 093f0ec58..ec4efda7b 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/RelativeConcentrationFilter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java index 5ab5cd4e4..21df5484f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VDJCGeneAccumulator.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler; import com.milaboratory.mixcr.basictypes.GeneAndScore; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java index c64283392..b7a6ebf61 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java b/src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java index b1a56b91f..30e01e7ae 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/VJCSignature.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler; import io.repseq.core.GeneType; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java index 447ec44d3..038a11553 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/CoverageAccumulator.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java index 0756caf84..c9bc27e4f 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java index e2f50f840..072bffb2d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java index 34f2d895b..d453ee677 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerReport.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java index 0ac02b6c7..298acc314 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/PointSequence.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java index 0bfb5479a..8ec59542b 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneReader.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java index ee8c4407c..93f4a7c8c 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/FilePreCloneWriter.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java index bc108e28e..2a747926d 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/IO.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.core.sequence.NSequenceWithQuality; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java index f025a9926..5fa3d6b88 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreClone.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.core.Range; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java index 06fe3d5c9..b486a2fa8 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAbstract.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.core.sequence.NSequenceWithQuality; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java index 611de1e7b..daf350942 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssembler.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java index 2dc323801..b0463bc94 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.core.alignment.LinearGapAlignmentScoring; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java index b64f52c29..348f040a1 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerReport.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.mitool.pattern.search.FormatSettings; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java index 9bd70d40d..aaedca001 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerResult.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import java.util.List; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java index 2d5bb7dbe..dd6e99332 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerRunner.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java index 4b7817e82..fc3fe8939 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneImpl.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.core.Range; diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java index 5d76ba450..56832baef 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneReader.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.assembler.preclone; import com.milaboratory.mixcr.assembler.AlignmentsProvider; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java index edadc01c2..d64d48e9e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/AlignmentsIO.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java index 8a4a1875b..4ca16d43a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentReader.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java index 8dab181ef..108faecee 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/BasicVDJCAlignmentWriterFactory.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java index d6b0296e8..f7c2bc603 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index b0dee06f4..8e8a2b153 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java index 5d2557f19..76ff452a9 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsReader.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java index b0c4b366d..a86895249 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnsWriter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java index b99b2d622..c3c2ed587 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalSequence.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java index 594ea2581..a8896af18 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClonalUpdatableParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java index 51de4ea03..914be5136 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Clone.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java index fdcbaff38..3149a246d 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneReader.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java index 58f086628..4bc1256aa 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSet.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java index fe468318b..992211f8a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java index 98952dfa7..4d3ed5a4e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetOverlap.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java index 97197d656..145591e22 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/CompatibilityIO.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java index 8aca7586b..76fd5378e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/FieldCollection.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes; import com.milaboratory.mixcr.assembler.preclone.PreCloneImpl; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/GeneAndScore.java b/src/main/java/com/milaboratory/mixcr/basictypes/GeneAndScore.java index 05a0beebb..a63bd33f9 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/GeneAndScore.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/GeneAndScore.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes; import com.milaboratory.primitivio.annotations.Serializable; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java b/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java index 8522110bd..da19c56a8 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/HasFeatureToAlign.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java b/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java index d9807d5eb..079f5e0d7 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/HasGene.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java b/src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java index b73091ff1..072aeacc6 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/HasRelativeMinScore.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes; import io.repseq.core.GeneType; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java index 0385c1d51..739838849 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IO.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java index f62ec4019..11bcd1683 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java b/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java index 9f20bb93d..25f7149f0 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/Merger.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java index a2934e559..95bd0568f 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReaderMiXCR.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java b/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java index d246e2cbb..82bbd95cb 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java b/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java index a0da2257d..2d8f424e2 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/TargetPartitioning.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java index 287557898..ee8a23c46 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java index 201dde695..a85887a34 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java index 3c22b6646..b72a5a1f3 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java index fe4444e58..819fefdbc 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java index b322334db..4137f0957 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriterI.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java index 1e8702602..758e157ab 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCFileHeaderData.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes; import com.milaboratory.mixcr.basictypes.tag.TagsInfo; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java index 1a92798cf..e242c51fc 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCHit.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java index 316637842..e139327fc 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java index 529b81af3..75b4e5231 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCPartitionedSequence.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java index 1ec73415b..fa355aa64 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCSProperties.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java index 81e8930e4..4dadc9413 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/IO.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.core.sequence.NSequenceWithQuality; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java index e9420af00..e287a42eb 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceAndQualityTagValue.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.core.sequence.NSequenceWithQuality; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java index d67e4f8c6..19e351105 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/SequenceTagValue.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.core.sequence.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java index 6c36c1f62..0222076a7 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.primitivio.annotations.Serializable; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java index a6916d172..4254a6571 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCountAggregator.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import gnu.trove.iterator.TObjectDoubleIterator; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java index 8e35f6a2f..d2ff2d076 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagInfo.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java index 63168e924..7fa0b2aed 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagTuple.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.google.common.hash.Hasher; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java index 7200bc786..40cc6d39b 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagType.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; public enum TagType { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java index 2c2a8018b..7e820303e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValue.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.primitivio.annotations.CustomSerializer; diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java index 9a8d68f85..a08c9484e 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagValueType.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; public enum TagValueType { diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index 7e8c3d367..da06c799a 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java index 368aecf7b..27d45cb7e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandMiXCR.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java index 34af93e2c..fb36858f6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandSimpleExportMiXCR.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java index 17f908d3b..6822cf590 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithOutputMiXCR.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java index c68471dd9..bd48ead66 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteMiXCR.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java index c673cb348..7f17304f2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ACommandWithSmartOverwriteWithSingleInputMiXCR.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java index 159b274a4..abc431032 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AbstractCommandReport.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 71fde1686..331ca4741 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java index 358387b94..9e2f67e21 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ChainUsageStats.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java index 46ab8dcec..bafc5b9a2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CloneAssemblerReport.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java index 00e88c4f6..b75fe366b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlign.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java index 4a837a0da..26c7407d9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsDiff.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java index 394602bcc..7c103ec51 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAlignmentsStats.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java index b1c424e80..fe66635e9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java index 5e3f06649..4ae5d0c0c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemble.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java index aa6fca908..a88fd8cee 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssembleContigs.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java index 45c461f47..08d77099d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandAssemblePartialAlignments.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java b/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java index ba2e85810..01ab105fe 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandClonesDiff.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java index c75884540..5184de2b7 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandCorrectAndSortTags.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java index 7fe0926f6..cf9e4cf82 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java index 10950d59e..ecfeb544a 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAirr.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java index 03582f22e..f398cb5b8 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsForClones.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java index 22f610df9..61ddfd3fa 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java index 745f9484b..66b5d27cb 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportClonesPretty.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java index b5a1182d5..1fa33707f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportOverlap.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java index 76737d4d5..03b63b0c6 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReads.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java index 2ef5c8da2..f01c4aef1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExportReadsForClones.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java index 67fa78098..8a256f29d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandExtend.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java index 46579d8fc..e87e62bc3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandFilterAlignments.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java index 8a3329801..5c1ce11f9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandGroupCells.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; // /** diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java index 626152361..3cb41b1b3 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandInfo.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java b/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java index cff48e227..82df5dc70 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandListLibraries.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java index c1e69e72c..5862f9d7d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMain.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java index 9aa50539f..c309f926d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandMergeAlignments.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java index 05ac58900..7aa616bdf 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandPipelineInfo.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java index 2337a5935..467164c3e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandReport.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java index b0fba966d..fcb1cdfb9 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSlice.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java index 4122a3e04..84a5d852d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortAlignments.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java index 2894bde1e..1583c856d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandSortClones.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java index 6be1ead74..711649b96 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommandVersionInfo.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java index f6a2704fd..2e16fb2ed 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java b/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java index 7d1df2429..5cbdcfd10 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommonOptions.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java index b709d7ea0..26c5a71ab 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ITestCommandAssemblePreClones.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index f73df76d3..40c5f44f1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java b/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java index 6fd8460bb..5d1538f28 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java +++ b/src/main/java/com/milaboratory/mixcr/cli/MiXCRCommand.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java index a8d41ecc6..dd796af90 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java +++ b/src/main/java/com/milaboratory/mixcr/cli/ReportWrapper.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java b/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java index 43f0e3a82..28b3bf026 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java +++ b/src/main/java/com/milaboratory/mixcr/cli/SerializerCompatibilityUtil.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/Util.java b/src/main/java/com/milaboratory/mixcr/cli/Util.java index 009c996f3..3bd53c80f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Util.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Util.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java b/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java index 50873d95a..e45b10600 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java +++ b/src/main/java/com/milaboratory/mixcr/cli/afiltering/AFilter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli.afiltering; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java index a92d82d5a..f33570470 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java index 557089a16..00b712b90 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.miplots.ExportKt; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 7708e3520..54eb2dbda 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java index 73178fa83..15df6ed5e 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExport.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java index 07df531a0..a9492b452 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlots.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.miplots.ExportKt; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java index 3d3ef8e24..7f7aab0cc 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsBasicStatistics.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.miplots.StandardPlots.PlotType; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java index a10d63637..c442ad15b 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsGeneUsage.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.miplots.Position; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java index c82f3efc2..aa87fc4b2 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmap.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import picocli.CommandLine.Option; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java index 89a88ca05..1676fb62d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsHeatmapWithGroupBy.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import picocli.CommandLine.Option; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java index d699287af..65d96f936 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsOverlap.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.miplots.Position; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java index ca338fcb8..138d80bde 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportPlotsVJUsage.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java index f07920329..f78ef4671 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTables.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.postanalysis.ui.CharacteristicGroup; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java index 70946dbff..f8a79957f 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesBase.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import picocli.CommandLine.Parameters; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java index 6291e7948..aab417703 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTablesPreprocSummary.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.postanalysis.SetPreprocessorSummary; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index 948fbf5a7..d72affa38 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java index 460deed0b..681469937 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaListMetrics.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index 5365229d6..bbbdc5e28 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java index 58e3405c2..af2c95e96 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroup.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java index ee29b5a03..18fc28cd1 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResult.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java index e990addc9..9794075bf 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/PaResultByGroup.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/export/AbstractField.java b/src/main/java/com/milaboratory/mixcr/export/AbstractField.java index f05a6aa61..dfac5e504 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AbstractField.java +++ b/src/main/java/com/milaboratory/mixcr/export/AbstractField.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java b/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java index d10b31ac7..dd0857577 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/export/AbstractFieldExtractor.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java index a9ab5c7e0..1ddac847c 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java +++ b/src/main/java/com/milaboratory/mixcr/export/AirrColumns.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.export; import com.milaboratory.core.Range; diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java b/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java index e42e91a9e..4707b05ae 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java +++ b/src/main/java/com/milaboratory/mixcr/export/AirrUtil.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.export; import com.milaboratory.core.Range; diff --git a/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java b/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java index 4ab0c462f..2a9897a2f 100644 --- a/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java +++ b/src/main/java/com/milaboratory/mixcr/export/AirrVDJCObjectWrapper.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.export; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java index 8fd0f6542..837bc0902 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/Field.java b/src/main/java/com/milaboratory/mixcr/export/Field.java index 33552fe52..3d249cf39 100644 --- a/src/main/java/com/milaboratory/mixcr/export/Field.java +++ b/src/main/java/com/milaboratory/mixcr/export/Field.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java index c2e1c3188..345eb2a17 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractor.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java index 9c78e3470..4ade24826 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractorWithParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index 82be45a5a..d7f59ff0f 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java b/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java index f031a9c3b..9d786672f 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldParameterless.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java b/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java index ee6620cf4..09ae00235 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldWithParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java b/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java index 2a54784e1..21906d0e0 100644 --- a/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java +++ b/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/export/OutputMode.java b/src/main/java/com/milaboratory/mixcr/export/OutputMode.java index f361d9686..7c640cbc3 100644 --- a/src/main/java/com/milaboratory/mixcr/export/OutputMode.java +++ b/src/main/java/com/milaboratory/mixcr/export/OutputMode.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java b/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java index a7470ac41..304a90fa6 100644 --- a/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/AlignmentInfoCollector.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.info; diff --git a/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java b/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java index 228d3282d..8c2eb05ba 100644 --- a/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/GeneFeatureCoverageCollector.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.info; diff --git a/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java b/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java index 5e61d372c..61f49eca3 100644 --- a/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java +++ b/src/main/java/com/milaboratory/mixcr/info/ReferencePointCoverageCollector.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.info; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java b/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java index 37f7d46bc..851684cef 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/AlignedTarget.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java b/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java index f7e7cab7c..4f0c908a9 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/BPoint.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java index 6828da3f9..6103de83b 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssembler.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java index 3c98e7132..e4832301f 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAligner.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java index 2aa37c8e4..3edc55853 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java b/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java index 78bc7ed93..a8a2f0630 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/RangeSet.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java index b95782e45..009d369d0 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/TargetMerger.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java b/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java index e4bc7e5a1..ecee6a7cb 100644 --- a/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java +++ b/src/main/java/com/milaboratory/mixcr/partialassembler/VDJCMultiRead.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java index 4ff9cafc0..4c0554aeb 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Aggregator.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import java.util.ArrayList; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java index 9038b76d1..d232e575b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Characteristic.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.fasterxml.jackson.annotation.*; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java index f74cd7b0f..6009502c4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/Dataset.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.milaboratory.mixcr.util.OutputPortWithProgress; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java index 1d7c3568b..97b1c9f84 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/MappingFunction.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import java.util.function.Function; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java b/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java index 91d74b700..6da1e69bf 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/MetricValue.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java index 2034aace8..0b543812c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisResult.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index ecc655cc8..2833eecfe 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java index 2571ec307..e16ac3321 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessor.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java index bda4dc354..3999cb2c9 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorFactory.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java index 8ae36078a..467081438 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSetup.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import cc.redberry.pipe.InputPort; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java index 93d58b09e..777aae25d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorStat.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java index 3cda5567e..3c852259a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/SetPreprocessorSummary.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java index 98f7ea973..4ef9cb838 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java index 6dd26e6ed..8cb8472e7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java index 7b8797128..6fb5890bc 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AAProperties.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.milaboratory.core.sequence.AminoAcidSequence; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java index 1151fbf88..2541480ac 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveAggregator.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java index 39c350b97..1416e92f0 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristic.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java index 8e2d59b84..ba57a1d17 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java index 5f7df6e23..36fea8678 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetric.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java index b1461953c..945584342 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveMetrics.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java index f2e239ae7..46bf84079 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AggregationType.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java index e03242a5c..4f5e2fe75 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunction.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java index 6fa5e9122..a21902202 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/KeyFunctions.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java index 81fcac8e7..1a21550bb 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/Normalization.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.additive; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java index d84001528..8b48b2190 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClustering.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.clustering; import gnu.trove.impl.Constants; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java index 8ea7cc72b..b5c9aeed4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchyNode.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.clustering; import java.util.Arrays; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java index afad954f0..10614b995 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityAggregator.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.diversity; import com.milaboratory.mixcr.postanalysis.Aggregator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java index 0255e477b..f760d841a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.diversity; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java index 57b04bcbc..18fff8ff1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityMeasure.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.diversity; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java index f2cdfef00..07df92e8c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.downsampling; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java index 401b4033c..4a67c2403 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooser.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.downsampling; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java index ac4ea3812..e489c7c62 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessor.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.downsampling; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java index 21995307f..e54b9b38f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorFactory.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.downsampling; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index d24026290..e33a1c852 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.downsampling; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java index 75e067d36..91dea16dd 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/LogFactorial.java @@ -1,34 +1,13 @@ /* - * Copyright (c) 2005-2020, NumPy Developers. - * All rights reserved. + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions are - * met: + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * * Redistributions of source code must retain the above copyright - * notice, this list of conditions and the following disclaimer. - * - * * Redistributions in binary form must reproduce the above - * copyright notice, this list of conditions and the following - * disclaimer in the documentation and/or other materials provided - * with the distribution. - * - * * Neither the name of the NumPy Developers nor the names of any - * contributors may be used to endorse or promote products derived - * from this software without specific prior written permission. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.downsampling; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java index dbf9bbbda..cca92613a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomHypergeometric.java @@ -1,34 +1,13 @@ /* - * Copyright (c) 2005-2020, NumPy Developers. - * All rights reserved. + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions are - * met: + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * * Redistributions of source code must retain the above copyright - * notice, this list of conditions and the following disclaimer. - * - * * Redistributions in binary form must reproduce the above - * copyright notice, this list of conditions and the following - * disclaimer in the documentation and/or other materials provided - * with the distribution. - * - * * Neither the name of the NumPy Developers nor the names of any - * contributors may be used to endorse or promote products derived - * from this software without specific prior written permission. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.downsampling; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java index 6326ba081..76057b94a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgCounts.java @@ -1,34 +1,13 @@ /* - * Copyright (c) 2005-2020, NumPy Developers. - * All rights reserved. + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions are - * met: + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * * Redistributions of source code must retain the above copyright - * notice, this list of conditions and the following disclaimer. - * - * * Redistributions in binary form must reproduce the above - * copyright notice, this list of conditions and the following - * disclaimer in the documentation and/or other materials provided - * with the distribution. - * - * * Neither the name of the NumPy Developers nor the names of any - * contributors may be used to endorse or promote products derived - * from this software without specific prior written permission. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.downsampling; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java index 901a0ca9a..27fda612b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/RandomMvhgMarginals.java @@ -1,34 +1,13 @@ /* - * Copyright (c) 2005-2020, NumPy Developers. - * All rights reserved. + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions are - * met: + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * * Redistributions of source code must retain the above copyright - * notice, this list of conditions and the following disclaimer. - * - * * Redistributions in binary form must reproduce the above - * copyright notice, this list of conditions and the following - * disclaimer in the documentation and/or other materials provided - * with the distribution. - * - * * Neither the name of the NumPy Developers nor the names of any - * contributors may be used to endorse or promote products derived - * from this software without specific prior written permission. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.downsampling; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java index a63b06887..dacb98045 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapAggregator.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.overlap; import com.milaboratory.mixcr.postanalysis.Aggregator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java index c68a2c762..caf1a635b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristic.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.overlap; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java index b31285a4e..a317783b4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapDataset.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.overlap; import com.milaboratory.mixcr.postanalysis.Dataset; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java index f63d410d7..bd9174902 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapGroup.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.overlap; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java index f9f618281..b77a91cf5 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapKey.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.overlap; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java index 72d5a35dd..af5665fa3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapType.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.overlap; import java.util.Arrays; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java index aff19d73a..ecc77385c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapUtil.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.overlap; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java index 8b630546e..44c205797 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/ElementPredicate.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; import com.fasterxml.jackson.annotation.*; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java index e84b73400..fda86ddce 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/FilterPreprocessor.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java index 6d8f24b11..eef25dbf9 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/NoPreprocessing.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java index 5d556bc8b..5b90aad08 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/OverlapPreprocessorAdapter.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; import cc.redberry.pipe.InputPort; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java index 2165d535c..3b37212cc 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChain.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; import cc.redberry.pipe.InputPort; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java index 0dc9d227a..019caa3da 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; import cc.redberry.pipe.InputPort; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java index 2a9d74f2b..cca9ff7e3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeAggregator.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.spectratype; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java index b06d9033e..e0dd60968 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.spectratype; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java index 682beee2a..494ed28a4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKey.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.spectratype; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java index 6ec5520f4..d4aecbe30 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeKeyFunction.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.spectratype; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java index 017da4149..0a9a3e29d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroni.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.stat; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java index 8eff299b7..e5a376165 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrection.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.stat; import java.util.Arrays; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java index c158e6f4b..907e23ce1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroup.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java index 6842b020e..2c55acde5 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupOutputExtractor.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java index b60f529d5..9e433525a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResult.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java index b80e82098..56842f2f7 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultBuilder.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import java.util.ArrayList; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java index 9542b5c75..a8aefa744 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/CharacteristicGroupResultCell.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.milaboratory.mixcr.postanalysis.MetricValue; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java index 9ad8a1586..c71823187 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/ClonotypeDataset.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import cc.redberry.pipe.OutputPortCloseable; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java index 6764e3371..28fd8c701 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/Coordinates.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; /** diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java index 91f2c48b3..32f8815fa 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupMelt.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonProperty; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java index 772b548c9..59ddee19e 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/GroupSummary.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java index 80e7fc55c..44f305bd4 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTable.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import java.io.BufferedWriter; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java index f49bf47a1..00a403e3a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableBuilder.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import java.util.ArrayList; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java index 094ac6567..e4128cf4d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableCell.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import java.util.Objects; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java index 11f5294c7..cadacadb8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import java.util.ArrayList; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java index 2bb663412..21a6c1a61 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OverlapSummary.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.milaboratory.mixcr.postanalysis.overlap.OverlapKey; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java index 74ce349bd..f708dc779 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java index e16a4788c..203e5860c 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java index 8ecccc442..c894c2ab1 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java index 49344bb53..38e31ba78 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersPreset.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.core.type.TypeReference; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java index be0892449..b6149f396 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchema.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java b/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java index 869abc1cd..25d882290 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/util/OverlapBrowser.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.util; import cc.redberry.pipe.CUtils; diff --git a/src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java b/src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java index 2bb15473c..80bd55b3b 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java +++ b/src/main/java/com/milaboratory/mixcr/tags/CloneGroup.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tags; diff --git a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java index f596a4ea2..27a6e68de 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java +++ b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTuple.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.tags; import com.milaboratory.mixcr.basictypes.Clone; diff --git a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java index 4cb77a60c..d79deb6ae 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java +++ b/src/main/java/com/milaboratory/mixcr/tags/CloneTagTupleFilter.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.tags; import com.fasterxml.jackson.annotation.JsonCreator; diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java index 1fd90eacc..b96589bfa 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraph.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tags; diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java index 480fc495a..aa8dd20c2 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tags; diff --git a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java index ea6d90f32..d2938d9f0 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java +++ b/src/main/java/com/milaboratory/mixcr/tags/DropletCloneGraphReport.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tags; diff --git a/src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java b/src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java index cf4f54cdd..59fd1ff70 100644 --- a/src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java +++ b/src/main/java/com/milaboratory/mixcr/tags/WhitelistReader.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.tags; import com.milaboratory.core.sequence.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java b/src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java index 6f447fc83..6603f1b7e 100644 --- a/src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java +++ b/src/main/java/com/milaboratory/mixcr/util/AdjacencyMatrix.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java b/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java index c42655f00..8398a08d4 100644 --- a/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java +++ b/src/main/java/com/milaboratory/mixcr/util/AlignedStringsBuilder.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java b/src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java index 4f56a3784..2945511df 100644 --- a/src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java +++ b/src/main/java/com/milaboratory/mixcr/util/BitArrayInt.java @@ -1,17 +1,13 @@ /* - * Copyright 2016 MiLaboratory.com + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/Concurrency.java b/src/main/java/com/milaboratory/mixcr/util/Concurrency.java index e8e92c143..20cf5a1ad 100644 --- a/src/main/java/com/milaboratory/mixcr/util/Concurrency.java +++ b/src/main/java/com/milaboratory/mixcr/util/Concurrency.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java b/src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java index 4e1077f4a..3f991ed45 100644 --- a/src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java +++ b/src/main/java/com/milaboratory/mixcr/util/MiXCRDebug.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java b/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java index 78b434217..dc6b5619a 100644 --- a/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java +++ b/src/main/java/com/milaboratory/mixcr/util/MiXCRVersionInfo.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java index e0c35e98b..34a74916a 100644 --- a/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java +++ b/src/main/java/com/milaboratory/mixcr/util/OutputPortWithProgress.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.util; import cc.redberry.pipe.OutputPortCloseable; diff --git a/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java b/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java index 21ffe3b92..cd562aee9 100644 --- a/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java +++ b/src/main/java/com/milaboratory/mixcr/util/PrintStreamTableAdapter.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java index 82f356154..94568219b 100644 --- a/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java +++ b/src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/Tuple2.java b/src/main/java/com/milaboratory/mixcr/util/Tuple2.java index 436026a3b..fa6cd74da 100644 --- a/src/main/java/com/milaboratory/mixcr/util/Tuple2.java +++ b/src/main/java/com/milaboratory/mixcr/util/Tuple2.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.util; import com.fasterxml.jackson.annotation.JsonAutoDetect; diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java b/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java index 44749510f..404bb392e 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReader.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java index 3fe557e7b..82a3c6bfe 100644 --- a/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java +++ b/src/main/java/com/milaboratory/mixcr/util/VDJCObjectExtender.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java index dea5f4930..faa2e6538 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/ClonalGeneAlignmentParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java index 290b82214..595ca2406 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/DAlignerParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java index b4baece08..e4ce5c12b 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java index 09ed8983b..d8f77c43f 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/GeneAlignmentParametersAbstract.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java index 23ca05b88..2e2d977b0 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java index 7b77f40cc..bb4c302bb 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/PreVDJCHit.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java index daab178c0..b4418c7d8 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/SingleDAligner.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java index 9bb0a55d6..5fbe733bb 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAligner.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java index 65dd95dca..78a94479b 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerAbstract.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java index 57dc696f5..70f8d8abf 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerEventListener.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java index a798bd7e7..aedc6e463 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java index 836ac0e17..e224a5cc7 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java index 9bbccf0fc..ecfb89f41 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerS.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java index 22cfc615c..e1c432b72 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java index 1c372a2a2..ecb766a89 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentFailCause.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java index 86dd151f1..a8e36558c 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignmentResult.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java index 2b09cdd03..f01b7e449 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCLibraryStructure.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.vdjaligners; public enum VDJCLibraryStructure { diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java index b0ee36c0f..ef6f1f8c2 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresets.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java index 431a96dc6..8cbe4092d 100644 --- a/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java +++ b/src/main/java/com/milaboratory/mixcr/vdjaligners/VJAlignmentOrder.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt index 4e34eeac9..53ad35263 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/BasicStatistics.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.StandardPlots.PlotType diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt index 8b23b71fc..9f2f30a5c 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/GeneUsage.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.toPDF diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt index 3be0eb633..aff3f93a6 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Heatmap.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.Position diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt index 6400cb1c2..602d1edb1 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Metadata.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.util.StringUtil diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt index 71681d707..78a1713cc 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Overlap.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.miplots.toPDF diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt index 8f03e3a96..4a25d5223 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/OverlapScatter.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import cc.redberry.pipe.CUtils diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt index 9956e4076..1101d19f7 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/Preprocessing.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.itextpdf.kernel.pdf.PdfDocument diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt index 9eaf6cb4d..46a4ed668 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/SingleSpectratype.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.mixcr.postanalysis.PostanalysisResult diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt index dca3f6a1d..9391f3d8e 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/VJUsage.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots import com.milaboratory.mixcr.postanalysis.PostanalysisResult diff --git a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/WithPlotSize.kt b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/WithPlotSize.kt index cd33cc57c..31de8c53e 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/WithPlotSize.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/postanalysis/plots/WithPlotSize.kt @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.plots interface WithPlotSize { diff --git a/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java b/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java index 5ead0d293..7a52acd6b 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/AssemblerUtilsTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java index 434828b95..4b0dad627 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersPresetsTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java index 076813965..759493d25 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index 7effbc75f..46ee7f9a4 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java index 2a1648f42..3a69fb690 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneClusteringParametersTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java index e97641354..b2031657a 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java index b9dbc2261..5ce5f5714 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/ClusteringFilterTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java index 4218fb940..b56691108 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler; diff --git a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java index e3b115ac3..b8caa9f3d 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssemblerTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.assembler.fullseq; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java index 31ce483b2..d66e56f3c 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClnAReaderTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java index ff036b0f3..d249c0238 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/ClonalSequenceTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java index 10e37077e..46419acf6 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/IOTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/MergerTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/MergerTest.java index d46da144c..a27e17cea 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/MergerTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/MergerTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/SequenceHistoryTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/SequenceHistoryTest.java index 5095bdf12..b5a598db0 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/SequenceHistoryTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/SequenceHistoryTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatterTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatterTest.java index d512ce8b9..ff255c665 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatterTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatterTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java index 87a594616..9275aa3ce 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCObjectTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java index 40e8daa57..a6fd3c8ea 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/VDJCSPropertiesTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.basictypes; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java index 21d7d46ff..ae2c22d3c 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagInfoTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.test.TestUtil; diff --git a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java index 5b1b6d88c..b303a400e 100644 --- a/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/basictypes/tag/TagsInfoTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.basictypes.tag; import com.milaboratory.test.TestUtil; diff --git a/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java b/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java index 65d71879f..f831ddf28 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/AlignerReportTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java b/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java index 3c13474c1..b10bf288a 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/ChainUsageStatsTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandAnalyzeTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandAnalyzeTest.java index f2f447f38..c469d1311 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandAnalyzeTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandAnalyzeTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java b/src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java index 22c8bb77f..e8a037174 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/CommandGroupCellsTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli; import org.junit.Ignore; diff --git a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java index e6c5a8880..fd97899bb 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java index 97138d72d..8ab49cf2c 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/MainTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/MainTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java b/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java index a2ed928ca..64897d578 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/UtilTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.cli; diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java index 946cff6c5..abb15dad9 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaExportTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.Main; diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java index 6a340c377..617c26434 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; import com.milaboratory.mixcr.cli.Main; diff --git a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java index 8b51c5160..ca77c4349 100644 --- a/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java +++ b/src/test/java/com/milaboratory/mixcr/cli/postanalysis/IsolationGroupTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.cli.postanalysis; diff --git a/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java b/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java index ad2c5a131..7e787c897 100644 --- a/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java +++ b/src/test/java/com/milaboratory/mixcr/export/FieldExtractorsTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.export; diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java index bc5086b2e..ecce4d6fb 100644 --- a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java +++ b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java index 61647d621..9bbf3e7aa 100644 --- a/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java +++ b/src/test/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/RangeSetTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/RangeSetTest.java index 728c7e1eb..645656169 100644 --- a/src/test/java/com/milaboratory/mixcr/partialassembler/RangeSetTest.java +++ b/src/test/java/com/milaboratory/mixcr/partialassembler/RangeSetTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/test/java/com/milaboratory/mixcr/partialassembler/TargetMergerTest.java b/src/test/java/com/milaboratory/mixcr/partialassembler/TargetMergerTest.java index 791f1c02d..2da580214 100644 --- a/src/test/java/com/milaboratory/mixcr/partialassembler/TargetMergerTest.java +++ b/src/test/java/com/milaboratory/mixcr/partialassembler/TargetMergerTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.partialassembler; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java index 38d958598..6a6b5afcd 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunnerTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import com.milaboratory.mixcr.postanalysis.diversity.DiversityCharacteristic; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java index a5c75a475..a3f3b90b4 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestDataset.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import cc.redberry.pipe.CUtils; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java index 5198f7835..a47083864 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObject.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import java.util.Objects; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java index 779d2526c..c13807019 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/TestObjectWithPayload.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis; import java.util.Objects; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java index 74039d502..e0398ec06 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristicsTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.additive; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java index 52cb30f99..938d0425c 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/clustering/HierarchicalClusteringTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.clustering; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java index 01bdfa67e..2735a225a 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristicTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.diversity; import com.milaboratory.mixcr.postanalysis.PostanalysisResult; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java index e982eb32b..175708040 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsampleValueChooserTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.downsampling; import org.junit.Assert; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java index ea7cde6c3..668779024 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingPreprocessorTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.downsampling; import cc.redberry.pipe.CUtils; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java index 8fc0c287b..0bc762131 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/downsampling/OverlapDownsamplingPreprocessorTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.downsampling; import cc.redberry.pipe.CUtils; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java index ad5d881f0..6d8211520 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapCharacteristicTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.overlap; import cc.redberry.pipe.CUtils; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java index e1c968ca4..db657f3a9 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/overlap/OverlapIntegrationTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.overlap; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java index 264ce0395..71211eb3a 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/PreprocessorChainTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; import cc.redberry.pipe.CUtils; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java index 942b4b2ab..86fdc69f9 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTopTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.preproc; import cc.redberry.pipe.CUtils; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java index aedd5793e..8fe253b26 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/HolmBonferroniTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.postanalysis.stat; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java index ac18babbc..c6b9a71fe 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/stat/PValueCorrectionTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.stat; import org.junit.Assert; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java index d22a52992..438297917 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividualTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java index 4a7f82858..003f81ab8 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlapTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.core.JsonProcessingException; diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index fb9a3b73e..41d27b296 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.core.JsonProcessingException; diff --git a/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java index 7baecc9d0..0d5d79f55 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/CloneTagTupleFilterTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.tags; // import com.fasterxml.jackson.core.JsonProcessingException; diff --git a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java index a305391b6..1196b7f89 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/DropletCloneGraphTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.tags; import com.milaboratory.mixcr.basictypes.ClnAReader; diff --git a/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java b/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java index 8654b8415..afaf93fff 100644 --- a/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java +++ b/src/test/java/com/milaboratory/mixcr/tags/WhitelistPackerTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.tags; import com.milaboratory.core.sequence.NucleotideSequence; diff --git a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java index 60f7756ef..d03aec0e3 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java +++ b/src/test/java/com/milaboratory/mixcr/tests/BackwardCompatibilityTests.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tests; diff --git a/src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java b/src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java index 08fd60d7a..19fa6799b 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/tests/IntegrationTest.java @@ -1,3 +1,14 @@ +/* + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE + * + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. + */ package com.milaboratory.mixcr.tests; public interface IntegrationTest { diff --git a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java index 37ffc6c14..d9de28812 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java +++ b/src/test/java/com/milaboratory/mixcr/tests/MiXCRTestUtils.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tests; diff --git a/src/test/java/com/milaboratory/mixcr/tests/TargetBuilder.java b/src/test/java/com/milaboratory/mixcr/tests/TargetBuilder.java index fa6e8f7d7..7f75bbe11 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/TargetBuilder.java +++ b/src/test/java/com/milaboratory/mixcr/tests/TargetBuilder.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tests; diff --git a/src/test/java/com/milaboratory/mixcr/tests/TargetBuilderTest.java b/src/test/java/com/milaboratory/mixcr/tests/TargetBuilderTest.java index ce607fec6..9c633f682 100644 --- a/src/test/java/com/milaboratory/mixcr/tests/TargetBuilderTest.java +++ b/src/test/java/com/milaboratory/mixcr/tests/TargetBuilderTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.tests; diff --git a/src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java b/src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java index cf1bbe255..0c5786c29 100644 --- a/src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/AdjacencyMatrixTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java b/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java index a803f46fb..059513cbf 100644 --- a/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/AlignedStringsBuilderTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java index eaf40c11b..9215c02e0 100644 --- a/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/DummyIntegrationTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2020, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java index 4f62af8bc..5b1052ecf 100644 --- a/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/MiXCRVersionInfoTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java b/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java index 95e9937bc..1de0746f3 100644 --- a/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/RunMiXCRTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java b/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java index a3a292c28..569acad00 100644 --- a/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/VDJCAlignmentsDifferenceReaderTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/test/java/com/milaboratory/mixcr/util/VDJCObjectExtenderTest.java b/src/test/java/com/milaboratory/mixcr/util/VDJCObjectExtenderTest.java index 3deaab4b7..efcc67455 100644 --- a/src/test/java/com/milaboratory/mixcr/util/VDJCObjectExtenderTest.java +++ b/src/test/java/com/milaboratory/mixcr/util/VDJCObjectExtenderTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.util; diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java index 7a76d5b17..b8f99dbe2 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/DAlignerParametersTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java index a45919759..0c9059928 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java index 866b9a6d2..a29e90631 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirstTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java index 888aafa57..c98b171fb 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java index 8594a8187..5ac8fb53a 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerSTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java index 379506a6e..b5458a6b3 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMergeTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java index 2db39c701..7b1ba79bb 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCParametersPresetsTest.java @@ -1,31 +1,13 @@ /* - * Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail - * (here and after addressed as Inventors) - * All Rights Reserved + * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved * - * Permission to use, copy, modify and distribute any part of this program for - * educational, research and non-profit purposes, by non-profit institutions - * only, without fee, and without a written agreement is hereby granted, - * provided that the above copyright notice, this paragraph and the following - * three paragraphs appear in all copies. + * Before downloading or accessing the software, please read carefully the + * License Agreement available at: + * https://github.com/milaboratory/mixcr/blob/develop/LICENSE * - * Those desiring to incorporate this work into commercial products or use for - * commercial purposes should contact MiLaboratory LLC, which owns exclusive - * rights for distribution of this program for commercial purposes, using the - * following email address: licensing@milaboratory.com. - * - * IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, - * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, - * ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN - * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - * - * THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS - * NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR - * MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO - * WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT - * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A - * PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY - * PATENT, TRADEMARK OR OTHER RIGHTS. + * By downloading or accessing the software, you accept and agree to be bound + * by the terms of the License Agreement. If you do not want to agree to the terms + * of the Licensing Agreement, you must not download or access the software. */ package com.milaboratory.mixcr.vdjaligners; From 95a2ef4fc7e9519c9c3e2a4596415a0bdd257d32 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 9 Jun 2022 12:37:21 +0200 Subject: [PATCH 273/282] Support of tags in postanalysis (#52) --- .../mixcr/basictypes/tag/TagCount.java | 14 +- .../mixcr/basictypes/tag/TagsInfo.java | 10 + .../mixcr/cli/CommonDescriptions.java | 6 +- .../cli/postanalysis/CommandDownsample.java | 8 +- .../postanalysis/CommandOverlapScatter.java | 6 +- .../mixcr/cli/postanalysis/CommandPa.java | 42 +++- .../cli/postanalysis/CommandPaIndividual.java | 3 +- .../cli/postanalysis/CommandPaOverlap.java | 3 +- .../mixcr/export/FieldExtractors.java | 16 +- .../postanalysis/PostanalysisRunner.java | 3 + .../mixcr/postanalysis/WeightFunction.java | 1 + .../mixcr/postanalysis/WeightFunctions.java | 36 +++ .../additive/AdditiveCharacteristics.java | 83 ++++++- .../diversity/DiversityCharacteristic.java | 6 +- ...ClonesDownsamplingPreprocessorFactory.java | 16 +- .../downsampling/DownsamplingUtil.java | 43 ---- .../mixcr/postanalysis/preproc/SelectTop.java | 14 +- .../SpectratypeCharacteristic.java | 10 +- .../postanalysis/ui/OutputTableExtractor.java | 3 +- .../ui/PostanalysisParameters.java | 208 ++++++++++++++++-- .../ui/PostanalysisParametersIndividual.java | 186 ++++++++++------ .../ui/PostanalysisParametersOverlap.java | 47 ++-- .../parameters/postanalysis_individual.json | 70 ++++-- .../parameters/postanalysis_overlap.json | 22 +- .../ui/PostanalysisParametersTest.java | 37 ++++ .../ui/PostanalysisSchemaIntegrationTest.java | 17 +- 26 files changed, 682 insertions(+), 228 deletions(-) create mode 100644 src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersTest.java diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java index 0222076a7..47e4db134 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagCount.java @@ -68,8 +68,8 @@ public TagCount(TagTuple singletonTuple, double singletonCount) { } /** - * If this is a singleton non-key counter, converts it to a singleton key counter; - * returns this for all other cases. + * If this is a singleton non-key counter, converts it to a singleton key counter; returns this for all other + * cases. */ public TagCount ensureIsKey() { if (singletonTuple != null && !singletonTuple.isKey()) { @@ -170,6 +170,16 @@ public int size() { : tagMap.size(); } + public int projectionSize(int... idxs) { + Set set = new HashSet<>(); + TObjectDoubleIterator it = iterator(); + while (it.hasNext()) { + it.advance(); + set.add(it.key().project(idxs)); + } + return set.size(); + } + public double get(TagTuple tt) { if (isSingleton()) { if (tt.equals(singletonTuple)) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java index da06c799a..ffc3a2f5d 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/tag/TagsInfo.java @@ -89,6 +89,16 @@ public int indexOf(String tagName) { return idx; } + public int indexOfIgnoreCase(String tagName) { + int idx = -1; + for (TagInfo ti : this) + if (ti.getName().equalsIgnoreCase(tagName)) { + idx = ti.getIndex(); + break; + } + return idx; + } + @Override @SuppressWarnings("NullableProblems") public Iterator iterator() { diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java index 2e16fb2ed..d5157437d 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java +++ b/src/main/java/com/milaboratory/mixcr/cli/CommonDescriptions.java @@ -23,11 +23,13 @@ private CommonDescriptions() { public static final String JSON_REPORT = "JSON formatted report file"; - public static final String DOWNSAMPLING = "Choose downsampling. Possible values: umi-count-[1000|auto]|cumulative-top-[percent]|top-[number]|none"; + public static final String DOWNSAMPLING = "Choose downsampling. Possible values: \n count-[reads|TAG]-[auto|min|number]\n top-[reads|TAG]-[number]\n cumtop-[reads|TAG]-[fraction]"; + + public static final String WEIGHT_FUNCTION = "Weight function: [read|TAG]-count"; public static final String METADATA = "Metadata file (csv/tsv). Must have \"sample\" column."; - public static final String DOWNSAMPLING_DROPO_UTLIERS = "Drop samples which have less abundance than the computed downsampling threshold."; + public static final String DOWNSAMPLING_DROP_OUTLIERS = "Drop samples which have less abundance than the computed downsampling threshold."; public static final String OVERLAP_CRITERIA = "Overlap criteria. Default CDR3|AA|V|J"; diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java index f33570470..81a4e8833 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandDownsample.java @@ -19,9 +19,9 @@ import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; import com.milaboratory.mixcr.postanalysis.ui.ClonotypeDataset; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParameters; import io.repseq.core.Chains; import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine.Command; @@ -92,11 +92,11 @@ public void run0() throws Exception { new ClonotypeDataset(file, file, VDJCLibraryRegistry.getDefault()) ).collect(Collectors.toList()); - SetPreprocessorFactory preproc = DownsamplingUtil - .parseDownsampling(this.downsampling, false) + SetPreprocessorFactory preproc = PostanalysisParameters + .parseDownsampling(this.downsampling, CommandPa.extractTagsInfo(getInputFiles()), false) .filterFirst(new ElementPredicate.IncludeChains(Chains.getByName(chains))); if (onlyProductive) - preproc = DownsamplingUtil.filterOnlyProductive(preproc); + preproc = PostanalysisParameters.filterOnlyProductive(preproc); Dataset[] result = SetPreprocessor.processDatasets(preproc.newInstance(), datasets); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java index 00b712b90..ba36f1a60 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java @@ -19,13 +19,13 @@ import com.milaboratory.mixcr.postanalysis.Dataset; import com.milaboratory.mixcr.postanalysis.SetPreprocessor; import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; import com.milaboratory.mixcr.postanalysis.overlap.OverlapUtil; import com.milaboratory.mixcr.postanalysis.plots.OverlapScatter; import com.milaboratory.mixcr.postanalysis.plots.OverlapScatterRow; import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParameters; import com.milaboratory.mixcr.util.OutputPortWithProgress; import com.milaboratory.util.SmartProgressReporter; import io.repseq.core.Chains; @@ -94,8 +94,8 @@ private Path outputPath(NamedChains chains) { @Override public void run0() throws Exception { - SetPreprocessorFactory preproc = DownsamplingUtil. - parseDownsampling(downsampling, false); + SetPreprocessorFactory preproc = PostanalysisParameters. + parseDownsampling(downsampling, CommandPa.extractTagsInfo(getInputFiles()), false); for (NamedChains curChains : this.chains == null ? Arrays.asList(TRAD_NAMED, TRB_NAMED, TRG_NAMED, IGH_NAMED, IGKL_NAMED) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java index 54eb2dbda..7da207636 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPa.java @@ -11,11 +11,14 @@ */ package com.milaboratory.mixcr.cli.postanalysis; +import com.milaboratory.mixcr.basictypes.CloneSetIO; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.cli.ACommandWithOutputMiXCR; import com.milaboratory.mixcr.cli.CommonDescriptions; -import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; +import com.milaboratory.mixcr.postanalysis.ui.PostanalysisParameters; import com.milaboratory.util.StringUtil; import io.repseq.core.Chains; +import io.repseq.core.VDJCLibraryRegistry; import picocli.CommandLine; import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -46,7 +49,7 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { names = {"--only-productive"}) public boolean onlyProductive = false; - @Option(description = CommonDescriptions.DOWNSAMPLING_DROPO_UTLIERS, + @Option(description = CommonDescriptions.DOWNSAMPLING_DROP_OUTLIERS, names = {"--drop-outliers"}) public boolean dropOutliers = false; @@ -55,6 +58,11 @@ public abstract class CommandPa extends ACommandWithOutputMiXCR { required = true) public String defaultDownsampling; + @Option(description = CommonDescriptions.WEIGHT_FUNCTION, + names = {"--default-weight-function"}, + required = false) + public String defaultWeightFunction; + @Option(description = "Filter specified chains", names = {"--chains"}) public String chains = "ALL"; @@ -101,15 +109,41 @@ protected List getOutputFiles() { return Collections.singletonList(out()); } + private boolean tagsInfoInitialized; + private TagsInfo tagsInfo; + + protected TagsInfo getTagsInfo() { + if (!tagsInfoInitialized) { + tagsInfoInitialized = true; + this.tagsInfo = extractTagsInfo(getInputFiles()); + } + return tagsInfo; + } + + static TagsInfo extractTagsInfo(List l) { + Set set = new HashSet<>(); + for (String in : l) { + try { + set.add(CloneSetIO.mkReader(Paths.get(in), VDJCLibraryRegistry.getDefault()).getTagsInfo()); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + if (set.size() != 1) { + throw new IllegalArgumentException("Input files have different tags structure"); + } else + return set.iterator().next(); + } + @Override public void validate() { super.validate(); if (!out().endsWith(".json") && !out().endsWith(".json.gz")) throwValidationException("Output file name should ends with .json.gz or .json"); try { - DownsamplingUtil.parseDownsampling(defaultDownsampling, dropOutliers); + PostanalysisParameters.parseDownsampling(defaultDownsampling, getTagsInfo(), dropOutliers); } catch (Throwable t) { - throwValidationException("Illegal downsampling string: " + defaultDownsampling); + throwValidationException(t.getMessage()); } if (preprocOut != null && !preprocOut.endsWith(".tsv") && !preprocOut.endsWith(".csv")) throwValidationException("--preproc-tables: table name should ends with .csv or .tsv"); diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java index d72affa38..186a13498 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaIndividual.java @@ -40,6 +40,7 @@ private PostanalysisParametersIndividual getParameters() { _parameters.defaultDownsampling = defaultDownsampling; _parameters.defaultDropOutliers = dropOutliers; _parameters.defaultOnlyProductive = onlyProductive; + _parameters.defaultWeightFunction = defaultWeightFunction; if (!overrides.isEmpty()) { _parameters = JsonOverrider.override(_parameters, PostanalysisParametersIndividual.class, overrides); if (_parameters == null) @@ -51,7 +52,7 @@ private PostanalysisParametersIndividual getParameters() { @Override @SuppressWarnings({"unchecked", "rawtypes"}) PaResultByGroup run(IsolationGroup group, List samples) { - List> groups = getParameters().getGroups(); + List> groups = getParameters().getGroups(getTagsInfo()); PostanalysisSchema schema = new PostanalysisSchema<>(false, groups) .transform(ch -> ch.override(ch.name, ch.preprocessor diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java index bbbdc5e28..e2c2af55c 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandPaOverlap.java @@ -54,6 +54,7 @@ private PostanalysisParametersOverlap getParameters() { _parameters.defaultDownsampling = defaultDownsampling; _parameters.defaultDropOutliers = dropOutliers; _parameters.defaultOnlyProductive = onlyProductive; + _parameters.defaultWeightFunction = defaultWeightFunction; if (!overrides.isEmpty()) { _parameters = JsonOverrider.override(_parameters, PostanalysisParametersOverlap.class, overrides); if (_parameters == null) @@ -65,7 +66,7 @@ private PostanalysisParametersOverlap getParameters() { @Override @SuppressWarnings("unchecked") PaResultByGroup run(IsolationGroup group, List samples) { - List>> groups = getParameters().getGroups(samples.size()); + List>> groups = getParameters().getGroups(samples.size(), getTagsInfo()); PostanalysisSchema> schema = new PostanalysisSchema<>(true, groups) .transform(ch -> ch.override(ch.name, ch.preprocessor diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java index d7f59ff0f..5d7ec8bca 100644 --- a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java +++ b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java @@ -24,11 +24,8 @@ import com.milaboratory.core.sequence.TranslationParameters; import com.milaboratory.mixcr.assembler.ReadToCloneMapping; import com.milaboratory.mixcr.basictypes.*; -import com.milaboratory.mixcr.basictypes.tag.TagCount; -import com.milaboratory.mixcr.basictypes.tag.TagTuple; import com.milaboratory.mixcr.basictypes.tag.TagValue; import com.milaboratory.util.GlobalObjectMappers; -import gnu.trove.iterator.TObjectDoubleIterator; import gnu.trove.iterator.TObjectFloatIterator; import gnu.trove.map.hash.TObjectFloatHashMap; import io.repseq.core.GeneFeature; @@ -37,7 +34,9 @@ import io.repseq.core.SequencePartitioning; import java.text.DecimalFormat; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; public final class FieldExtractors { static final String NULL = ""; @@ -743,14 +742,7 @@ public FieldExtractor create(OutputMode outputMode, VDJCFileHeaderDa return new AbstractFieldExtractor(getHeader(outputMode, tagNames), this) { @Override public String extractValue(VDJCObject object) { - TagCount tc = object.getTagCount(); - Set set = new HashSet<>(); - TObjectDoubleIterator it = tc.iterator(); - while (it.hasNext()) { - it.advance(); - set.add(it.key().project(indices)); - } - return "" + set.size(); + return "" + object.getTagCount().projectionSize(indices); } }; } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java index 2833eecfe..76858c5b8 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/PostanalysisRunner.java @@ -98,6 +98,9 @@ public PostanalysisResult run(Dataset... datasets) { } // distinct processors List> procs = new ArrayList<>(distinctProcs.values()); + if (distinctProcs.values().stream().map(SetPreprocessor::id).collect(Collectors.toSet()).size() != distinctProcs.size()) { + throw new IllegalArgumentException("Duplicates proc id"); + } while (true) { // next setup iterations diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java index 4ef9cb838..f9bd35f87 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunction.java @@ -25,6 +25,7 @@ @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type") @JsonSubTypes({ @JsonSubTypes.Type(value = WeightFunctions.Count.class, name = "count"), + @JsonSubTypes.Type(value = WeightFunctions.TagCount.class, name = "tagCount"), @JsonSubTypes.Type(value = WeightFunctions.NoWeight.class, name = "none"), @JsonSubTypes.Type(value = WeightFunctions.DefaultWtFunction.class, name = "default"), }) diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java index 8cb8472e7..f18a8a211 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/WeightFunctions.java @@ -11,8 +11,12 @@ */ package com.milaboratory.mixcr.postanalysis; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonIgnore; import com.milaboratory.mixcr.basictypes.Clone; +import java.util.Objects; + /** * */ @@ -40,6 +44,38 @@ public int hashCode() { } } + public static final class TagCount implements WeightFunction { + final int tagIndex; + @JsonIgnore + final int[] indices; + + @JsonCreator + public TagCount(int tagIndex) { + this.tagIndex = tagIndex; + this.indices = new int[tagIndex + 1]; + for (int i = 0; i < tagIndex + 1; i++) + indices[i] = i; + } + + @Override + public double weight(Clone clone) { + return 1.0 * clone.getTagCount().projectionSize(indices); + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TagCount tagCount = (TagCount) o; + return tagIndex == tagCount.tagIndex; + } + + @Override + public int hashCode() { + return Objects.hash(tagIndex); + } + } + @SuppressWarnings("rawtypes") public static final NoWeight NoWeight = new NoWeight(); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java index ba57a1d17..b59926c1f 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/additive/AdditiveCharacteristics.java @@ -13,6 +13,7 @@ import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.WeightFunction; import com.milaboratory.mixcr.postanalysis.WeightFunctions; import com.milaboratory.mixcr.postanalysis.additive.KeyFunctions.VJGenes; import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; @@ -54,11 +55,15 @@ public static AdditiveCharacteristic weightedLengthOf(GeneFeature } public static AdditiveCharacteristic weightedLengthOf(SetPreprocessorFactory preproc, GeneFeature gf, boolean aa) { + return lengthOf(preproc, WeightFunctions.Count, gf, aa); + } + + public static AdditiveCharacteristic lengthOf(SetPreprocessorFactory preproc, WeightFunction wt, GeneFeature gf, boolean aa) { String name = (aa ? "aa" : "nt") + "LengthOf" + GeneFeature.encode(gf); return new AdditiveCharacteristic<>( name, preproc, - new WeightFunctions.Count(), + wt, new KeyFunctions.Named<>(name), new AdditiveMetrics.GeneFeatureLength<>(gf, aa), AggregationType.Mean, @@ -67,11 +72,16 @@ public static AdditiveCharacteristic weightedLengthOf(SetPreproce } public static AdditiveCharacteristic weightedAddedNucleotides(SetPreprocessorFactory preproc) { + return addedNucleotides(preproc, WeightFunctions.Count); + } + + + public static AdditiveCharacteristic addedNucleotides(SetPreprocessorFactory preproc, WeightFunction wt) { String name = "AddedNucleotides"; return new AdditiveCharacteristic<>( name, preproc, - new WeightFunctions.Count(), + wt, new KeyFunctions.Named<>(name), new AdditiveMetrics.AddedNucleotides<>(), AggregationType.Mean, @@ -84,11 +94,18 @@ public static AdditiveCharacteristic weightedBbiophysicsNormalize } public static AdditiveCharacteristic weightedBbiophysicsNormalized(SetPreprocessorFactory preproc, AAProperties.AAProperty property, GeneFeature gf) { + return biophysicsNormalized(preproc, WeightFunctions.Count, property, gf); + } + + public static AdditiveCharacteristic biophysicsNormalized(SetPreprocessorFactory preproc, + WeightFunction wt, + AAProperties.AAProperty property, + GeneFeature gf) { String name = property.name() + "of" + GeneFeature.encode(gf) + "Normalized"; return new AdditiveCharacteristic<>( name, preproc, - new WeightFunctions.Count(), + wt, new KeyFunctions.Named<>(name), new AdditiveMetrics.AAPropertyNormalized(property, gf), AggregationType.Mean, @@ -101,11 +118,20 @@ public static AdditiveCharacteristic weightedBiophysics(AAPropert } public static AdditiveCharacteristic weightedBiophysics(SetPreprocessorFactory preproc, AAProperties.AAProperty property, GeneFeature gf, AAProperties.Adjustment adjustment, int nLetters) { + return biophysics(preproc, WeightFunctions.Count, property, gf, adjustment, nLetters); + } + + public static AdditiveCharacteristic biophysics(SetPreprocessorFactory preproc, + WeightFunction wt, + AAProperties.AAProperty property, + GeneFeature gf, + AAProperties.Adjustment adjustment, + int nLetters) { String name = property.name() + "of" + GeneFeature.encode(gf); return new AdditiveCharacteristic<>( name, preproc, - new WeightFunctions.Count(), + wt, new KeyFunctions.Named<>(name), new AdditiveMetrics.AAPropertySum(property, gf, adjustment, nLetters), AggregationType.Mean, @@ -118,11 +144,18 @@ public static AdditiveCharacteristic segmentUsage(GeneType geneTy } public static AdditiveCharacteristic segmentUsage(SetPreprocessorFactory preproc, GeneType geneType, KeyFunction keyFunction) { + return segmentUsage(preproc, WeightFunctions.Count, geneType, keyFunction); + } + + public static AdditiveCharacteristic segmentUsage(SetPreprocessorFactory preproc, + WeightFunction wt, + GeneType geneType, + KeyFunction keyFunction) { String name = geneType.getLetter() + "Usage"; return new AdditiveCharacteristic<>( name, preproc, - new WeightFunctions.Count(), + wt, keyFunction, new AdditiveMetrics.Constant(1), AggregationType.Mean, @@ -139,6 +172,13 @@ public static AdditiveCharacteristic segmentUsage(SetPreprocessor .setName(geneType.getLetter() + "SegmentUsage"); } + public static AdditiveCharacteristic segmentUsage(SetPreprocessorFactory preproc, + WeightFunction wt, + GeneType geneType) { + return segmentUsage(preproc, wt, geneType, new KeyFunctions.SegmentUsage<>(geneType)) + .setName(geneType.getLetter() + "SegmentUsage"); + } + public static AdditiveCharacteristic geneUsage(GeneType geneType) { return geneUsage(NoPreprocessing.factory(), geneType); } @@ -162,10 +202,16 @@ public static AdditiveCharacteristic, Clone> vjUsage(KeyFunction } public static AdditiveCharacteristic, Clone> vjUsage(SetPreprocessorFactory preproc, KeyFunction, Clone> keyFunction) { + return vjUsage(preproc, WeightFunctions.Count, keyFunction); + } + + public static AdditiveCharacteristic, Clone> vjUsage(SetPreprocessorFactory preproc, + WeightFunction wt, + KeyFunction, Clone> keyFunction) { return new AdditiveCharacteristic<>( "VJUsage", preproc, - new WeightFunctions.Count(), + wt, keyFunction, new AdditiveMetrics.Constant(1), AggregationType.Mean, @@ -181,6 +227,11 @@ public static AdditiveCharacteristic, Clone> vjSegmentUsage(SetP return vjUsage(preproc, new KeyFunctions.VJSegmentUsage<>()).setName("VJSegmentUsage"); } + public static AdditiveCharacteristic, Clone> vjSegmentUsage(SetPreprocessorFactory preproc, + WeightFunction wt) { + return vjUsage(preproc, wt, new KeyFunctions.VJSegmentUsage<>()).setName("VJSegmentUsage"); + } + public static AdditiveCharacteristic, Clone> vjGeneUsage() { return vjGeneUsage(NoPreprocessing.factory()); } @@ -202,10 +253,14 @@ public static AdditiveCharacteristic isotypeUsage() } public static AdditiveCharacteristic isotypeUsage(SetPreprocessorFactory preproc) { + return isotypeUsage(preproc, WeightFunctions.Count); + } + + public static AdditiveCharacteristic isotypeUsage(SetPreprocessorFactory preproc, WeightFunction wt) { return new AdditiveCharacteristic<>( "IsotypeUsage", preproc, - new WeightFunctions.Count(), + wt, new KeyFunctions.IsotypeUsage<>(), new AdditiveMetrics.Constant(1), AggregationType.Mean, @@ -218,18 +273,28 @@ public static AdditiveCharacteristic, Clone> VSpectratype } public static AdditiveCharacteristic, Clone> VSpectratype(SetPreprocessorFactory preproc) { + return VSpectratype(preproc, WeightFunctions.Count); + } + + public static AdditiveCharacteristic, Clone> VSpectratype(SetPreprocessorFactory preproc, + WeightFunction wt) { return new AdditiveCharacteristic<>("VSpectratype", preproc, - new WeightFunctions.Count(), + wt, new SpectratypeKeyFunction<>(new KeyFunctions.SegmentUsage<>(GeneType.Variable), GeneFeature.CDR3, false), new AdditiveMetrics.Constant(), AggregationType.Sum, false); } public static AdditiveCharacteristic VSpectratypeMean(SetPreprocessorFactory preproc) { + return VSpectratypeMean(preproc, WeightFunctions.Count); + } + + public static AdditiveCharacteristic VSpectratypeMean(SetPreprocessorFactory preproc, + WeightFunction wt) { return new AdditiveCharacteristic<>( "VSpectratypeMean", preproc, - new WeightFunctions.Count(), + wt, new KeyFunctions.SegmentUsage<>(GeneType.Variable), new AdditiveMetrics.GeneFeatureLength<>(GeneFeature.CDR3, false), AggregationType.Mean, diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java index f760d841a..645a1e527 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/diversity/DiversityCharacteristic.java @@ -39,9 +39,9 @@ public DiversityCharacteristic(@JsonProperty("name") String name, this.measures = measures; } - public DiversityCharacteristic(@JsonProperty("name") String name, - @JsonProperty("weight") WeightFunction weight, - @JsonProperty("preproc") SetPreprocessorFactory preprocessor) { + public DiversityCharacteristic(String name, + WeightFunction weight, + SetPreprocessorFactory preprocessor) { this(name, weight, preprocessor, DiversityMeasure.basic()); } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java index 07df92e8c..301adb383 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/ClonesDownsamplingPreprocessorFactory.java @@ -15,6 +15,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.postanalysis.WeightFunction; import java.util.Objects; @@ -27,10 +28,15 @@ isGetterVisibility = JsonAutoDetect.Visibility.NONE ) public class ClonesDownsamplingPreprocessorFactory extends DownsamplingPreprocessorFactory { + @JsonProperty("weightFunction") + public final WeightFunction weightFunction; + @JsonCreator public ClonesDownsamplingPreprocessorFactory(@JsonProperty("downsampleValueChooser") DownsampleValueChooser downsampleValueChooser, - @JsonProperty("dropOutliers") boolean dropOutliers) { - super(downsampleValueChooser, c -> Math.round(c.getCount()), Clone::setCount, dropOutliers); + @JsonProperty("dropOutliers") boolean dropOutliers, + @JsonProperty("weightFunction") WeightFunction weightFunction) { + super(downsampleValueChooser, c -> Math.round(weightFunction.weight(c)), Clone::setCount, dropOutliers); + this.weightFunction = weightFunction; } @Override @@ -38,11 +44,13 @@ public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; ClonesDownsamplingPreprocessorFactory that = (ClonesDownsamplingPreprocessorFactory) o; - return Objects.equals(downsampleValueChooser, that.downsampleValueChooser); + return Objects.equals(downsampleValueChooser, that.downsampleValueChooser) + && Objects.equals(weightFunction, that.weightFunction) + && Objects.equals(dropOutliers, that.dropOutliers); } @Override public int hashCode() { - return Objects.hash(downsampleValueChooser); + return Objects.hash(downsampleValueChooser, weightFunction, dropOutliers); } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java index e33a1c852..44318439d 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/downsampling/DownsamplingUtil.java @@ -13,18 +13,9 @@ import cc.redberry.pipe.CUtils; import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.mixcr.basictypes.Clone; import com.milaboratory.mixcr.postanalysis.Dataset; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.WeightFunctions; -import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; -import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; -import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; -import io.repseq.core.GeneFeature; import org.apache.commons.math3.random.RandomGenerator; -import java.util.ArrayList; -import java.util.List; import java.util.function.ToLongFunction; import java.util.stream.LongStream; @@ -58,38 +49,4 @@ public static long[] downsample_counts(long[] counts, long downSampleSize, Rando RandomMvhgCounts.random_multivariate_hypergeometric_count(rnd, total, counts, downSampleSize, result); return result; } - - public static SetPreprocessorFactory parseDownsampling(String downsampling, boolean dropOutliers) { - if (downsampling.equalsIgnoreCase("none")) { - return new NoPreprocessing.Factory<>(); - } else if (downsampling.startsWith("umi-count")) { - if (downsampling.endsWith("auto")) - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), dropOutliers); - else if (downsampling.endsWith("min")) - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Minimal(), dropOutliers); - else { - return new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Fixed(downsamplingValue(downsampling)), dropOutliers); - } - } else { - int value = downsamplingValue(downsampling); - if (downsampling.startsWith("cumulative-top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, 1.0 * value / 100.0); - } else if (downsampling.startsWith("top")) { - return new SelectTop.Factory<>(WeightFunctions.Count, value); - } else { - throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); - } - } - } - - public static SetPreprocessorFactory filterOnlyProductive(SetPreprocessorFactory p) { - List> filters = new ArrayList<>(); - filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); - filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); - return p.filterFirst(filters); - } - - private static int downsamplingValue(String downsampling) { - return Integer.parseInt(downsampling.substring(downsampling.lastIndexOf("-") + 1)); - } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java index 019caa3da..ac4cbdb00 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/preproc/SelectTop.java @@ -36,10 +36,7 @@ public class SelectTop implements SetPreprocessor { double abundanceFraction, int numberOfTop, String id) { - if (!Double.isNaN(abundanceFraction) && (abundanceFraction <= 0 || abundanceFraction > 1.0)) - throw new IllegalArgumentException(); - if (numberOfTop != -1 && numberOfTop <= 0) - throw new IllegalArgumentException(); + checkInput(abundanceFraction, numberOfTop); this.weight = weight; this.abundanceFraction = abundanceFraction; @@ -187,6 +184,13 @@ static long round(double wt) { return lwt; } + private static void checkInput(double abundanceFraction, int numberOfTop) { + if (!Double.isNaN(abundanceFraction) && (abundanceFraction <= 0 || abundanceFraction > 1.0)) + throw new IllegalArgumentException("Illegal abundance: " + abundanceFraction); + if (numberOfTop != -1 && numberOfTop <= 0) + throw new IllegalArgumentException("Illegal numberOfTop: " + numberOfTop); + } + public static final class Factory implements SetPreprocessorFactory { @JsonProperty("weight") private WeightFunction weight; @@ -200,11 +204,13 @@ private Factory() {} public Factory(WeightFunction weight, double abundanceFraction) { this.weight = weight; this.abundanceFraction = abundanceFraction; + checkInput(abundanceFraction, numberOfTop); } public Factory(WeightFunction weight, int numberOfTop) { this.weight = weight; this.numberOfTop = numberOfTop; + checkInput(abundanceFraction, numberOfTop); } @Override diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java index e0dd60968..8243dd13b 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/spectratype/SpectratypeCharacteristic.java @@ -30,13 +30,21 @@ public class SpectratypeCharacteristic extends Characteristic preprocessor, + @JsonProperty("weight") WeightFunction weight, @JsonProperty("nTopClonotypes") int nTopClonotypes, @JsonProperty("keyFunction") SpectratypeKeyFunction keyFunction) { - super(name, preprocessor, new WeightFunctions.Count()); + super(name, preprocessor, weight); this.nTopClonotypes = nTopClonotypes; this.keyFunction = keyFunction; } + public SpectratypeCharacteristic(String name, + SetPreprocessorFactory preprocessor, + int nTopClonotypes, + SpectratypeKeyFunction keyFunction) { + this(name, preprocessor, WeightFunctions.Count, nTopClonotypes, keyFunction); + } + @Override protected Aggregator, Clone> createAggregator(Dataset dataset) { return new SpectratypeAggregator<>(nTopClonotypes, keyFunction, weight); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java index cadacadb8..b8d4482f6 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/OutputTableExtractor.java @@ -12,6 +12,7 @@ package com.milaboratory.mixcr.postanalysis.ui; import java.util.ArrayList; +import java.util.Collections; import java.util.List; import java.util.Map; import java.util.function.Function; @@ -49,7 +50,7 @@ static OutputTableExtractor summary(Function(result.datasetIds), - columns, cells); + columns == null ? Collections.emptyList() : columns, cells); }; } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java index f708dc779..e30e42f17 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParameters.java @@ -12,14 +12,24 @@ package com.milaboratory.mixcr.postanalysis.ui; import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.tag.TagInfo; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.postanalysis.Characteristic; import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.downsampling.DownsamplingUtil; +import com.milaboratory.mixcr.postanalysis.WeightFunction; +import com.milaboratory.mixcr.postanalysis.WeightFunctions; +import com.milaboratory.mixcr.postanalysis.downsampling.ClonesDownsamplingPreprocessorFactory; +import com.milaboratory.mixcr.postanalysis.downsampling.DownsampleValueChooser; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; +import com.milaboratory.mixcr.postanalysis.preproc.ElementPredicate; +import com.milaboratory.mixcr.postanalysis.preproc.NoPreprocessing; import com.milaboratory.mixcr.postanalysis.preproc.OverlapPreprocessorAdapter; +import com.milaboratory.mixcr.postanalysis.preproc.SelectTop; import com.milaboratory.primitivio.annotations.Serializable; +import io.repseq.core.GeneFeature; import java.util.*; import java.util.function.BiFunction; @@ -35,33 +45,69 @@ public abstract class PostanalysisParameters { public String defaultDownsampling; public boolean defaultOnlyProductive; public boolean defaultDropOutliers; + public String defaultWeightFunction; + + interface WithParentAndTags { + void setParent(PostanalysisParameters parent); + + void setTagsInfo(TagsInfo tagsInfo); + } @JsonAutoDetect( fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE) - public static class PreprocessorParameters { + public static class MetricParameters implements WithParentAndTags { public String downsampling; public Boolean onlyProductive; public Boolean dropOutliers; + public String weightFunction; - public SetPreprocessorFactory preproc(PostanalysisParameters base) { - SetPreprocessorFactory p = parseDownsampling(base); + @JsonIgnore + private PostanalysisParameters parent; + @JsonIgnore + private TagsInfo tagsInfo; + + @Override + public void setParent(PostanalysisParameters parent) { + this.parent = parent; + } + + @Override + public void setTagsInfo(TagsInfo tagsInfo) { + this.tagsInfo = tagsInfo; + } - boolean onlyProductive = this.onlyProductive == null ? base.defaultOnlyProductive : this.onlyProductive; + public WeightFunction weightFunction() { + return parseWeightFunction(this.weightFunction == null ? parent.defaultWeightFunction : this.weightFunction, tagsInfo); + } + + public SetPreprocessorFactory preproc() { + SetPreprocessorFactory p = parseDownsampling(); + + boolean onlyProductive = this.onlyProductive == null ? parent.defaultOnlyProductive : this.onlyProductive; if (onlyProductive) - p = DownsamplingUtil.filterOnlyProductive(p); + p = filterOnlyProductive(p); return p; } - public SetPreprocessorFactory> overlapPreproc(PostanalysisParameters base) { - return new OverlapPreprocessorAdapter.Factory<>(preproc(base)); + public PreprocessorAndWeight pwTuple() { + return new PreprocessorAndWeight<>(preproc(), weightFunction()); + } + + public OverlapPreprocessorAndWeight opwTuple() { + return new OverlapPreprocessorAndWeight<>(overlapPreproc(), weightFunction()); + } + + public SetPreprocessorFactory> overlapPreproc() { + return new OverlapPreprocessorAdapter.Factory<>(preproc()); } - SetPreprocessorFactory parseDownsampling(PostanalysisParameters base) { - return DownsamplingUtil.parseDownsampling( - this.downsampling == null ? base.defaultDownsampling : this.downsampling, - this.dropOutliers == null ? base.defaultDropOutliers : this.dropOutliers + SetPreprocessorFactory parseDownsampling() { + return PostanalysisParameters.parseDownsampling( + this.downsampling == null ? parent.defaultDownsampling : this.downsampling, + tagsInfo, + this.dropOutliers == null ? parent.defaultDropOutliers : this.dropOutliers ); } @@ -69,7 +115,7 @@ SetPreprocessorFactory parseDownsampling(PostanalysisParameters base) { public boolean equals(Object o) { if (this == o) return true; if (o == null || getClass() != o.getClass()) return false; - PreprocessorParameters that = (PreprocessorParameters) o; + MetricParameters that = (MetricParameters) o; return Objects.equals(downsampling, that.downsampling) && Objects.equals(onlyProductive, that.onlyProductive) && Objects.equals(dropOutliers, that.dropOutliers); } @@ -79,10 +125,56 @@ public int hashCode() { } } - static List> groupByPreproc(Map> preprocs, - BiFunction, List, List>> factory) { + static final class PreprocessorAndWeight { + final SetPreprocessorFactory preproc; + final WeightFunction weight; + + public PreprocessorAndWeight(SetPreprocessorFactory preproc, WeightFunction weight) { + this.preproc = preproc; + this.weight = weight; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + PreprocessorAndWeight that = (PreprocessorAndWeight) o; + return Objects.equals(preproc, that.preproc) && Objects.equals(weight, that.weight); + } + + @Override + public int hashCode() { + return Objects.hash(preproc, weight); + } + } + + static final class OverlapPreprocessorAndWeight { + final SetPreprocessorFactory> preproc; + final WeightFunction weight; + + public OverlapPreprocessorAndWeight(SetPreprocessorFactory> preproc, WeightFunction weight) { + this.preproc = preproc; + this.weight = weight; + } - Map, List> byPreproc = preprocs.entrySet().stream() + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OverlapPreprocessorAndWeight that = (OverlapPreprocessorAndWeight) o; + return Objects.equals(preproc, that.preproc) && Objects.equals(weight, that.weight); + } + + @Override + public int hashCode() { + return Objects.hash(preproc, weight); + } + } + + static List> groupBy(Map map, + BiFunction, List>> factory) { + + Map> byPreproc = map.entrySet().stream() .collect(Collectors.toMap(Map.Entry::getValue, e -> Collections.singletonList(e.getKey()), (a, b) -> { @@ -93,10 +185,92 @@ static List> groupByPreproc(Map> chars = new ArrayList<>(); - for (Map.Entry, List> e : byPreproc.entrySet()) { + for (Map.Entry> e : byPreproc.entrySet()) { chars.addAll(factory.apply(e.getKey(), e.getValue())); } return chars; } + + static List> groupByPreproc(Map> preprocs, + BiFunction, List, List>> factory) { + + return groupBy(preprocs, factory); + } + + public static WeightFunction parseWeightFunction(String weight, TagsInfo info) { + if (weight == null) // default + return WeightFunctions.Count; + switch (weight) { + case "read-count": + case "reads-count": + return WeightFunctions.Count; + case "none": + return new WeightFunctions.NoWeight<>(); + default: + int tagIndex = info.indexOf(weight); + if (tagIndex < 0) + throw new IllegalArgumentException("Unknown weight type: " + weight + ". Available types: none, default, read, " + info.stream().map(TagInfo::getName).collect(Collectors.joining(","))); + return new WeightFunctions.TagCount(tagIndex); + } + } + + public static SetPreprocessorFactory parseDownsampling(String downsampling, + TagsInfo tagsInfo, + boolean dropOutliers) { + if (downsampling.equalsIgnoreCase("none")) + return new NoPreprocessing.Factory<>(); + + String[] parts = downsampling.split("-"); + + String tag = parts[1]; + WeightFunction wt; + switch (tag) { + case "read": + case "reads": + wt = WeightFunctions.Count; + break; + default: + int i = tagsInfo.indexOfIgnoreCase(tag.replace("-count", "")); + if (i < 0) + throw new IllegalArgumentException("Tag " + tag + " not found in the input files."); + wt = new WeightFunctions.TagCount(i); + } + ; + + switch (parts[0]) { + case "count": + DownsampleValueChooser chooser; + switch (parts[2]) { + case "auto": + chooser = new DownsampleValueChooser.Auto(); + break; + case "min": + chooser = new DownsampleValueChooser.Minimal(); + break; + case "fixed": + chooser = new DownsampleValueChooser.Fixed(Long.parseLong(parts[3])); + break; + default: + throw new IllegalArgumentException("Can't parse downsampling value choose: " + downsampling); + } + return new ClonesDownsamplingPreprocessorFactory(chooser, dropOutliers, wt); + + case "top": + return new SelectTop.Factory<>(wt, Integer.parseInt(parts[2])); + + case "cumtop": + return new SelectTop.Factory<>(wt, Double.parseDouble(parts[2]) / 100.0); + + default: + throw new IllegalArgumentException("Illegal downsampling string: " + downsampling); + } + } + + public static SetPreprocessorFactory filterOnlyProductive(SetPreprocessorFactory p) { + List> filters = new ArrayList<>(); + filters.add(new ElementPredicate.NoStops(GeneFeature.CDR3)); + filters.add(new ElementPredicate.NoOutOfFrames(GeneFeature.CDR3)); + return p.filterFirst(filters); + } } diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java index 203e5860c..5da120cb3 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersIndividual.java @@ -13,8 +13,8 @@ import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.postanalysis.Characteristic; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; import com.milaboratory.mixcr.postanalysis.WeightFunctions; import com.milaboratory.mixcr.postanalysis.additive.AAProperties; import com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics; @@ -47,50 +47,76 @@ public class PostanalysisParametersIndividual extends PostanalysisParameters { public BiophysicsParameters biophysics = new BiophysicsParameters(); public DiversityParameters diversity = new DiversityParameters(); - public PreprocessorParameters vUsage = new PreprocessorParameters(); - public PreprocessorParameters jUsage = new PreprocessorParameters(); - public PreprocessorParameters vjUsage = new PreprocessorParameters(); - public PreprocessorParameters isotypeUsage = new PreprocessorParameters(); - public PreprocessorParameters cdr3Spectratype = new PreprocessorParameters(); - public PreprocessorParameters vSpectratype = new PreprocessorParameters(); - public PreprocessorParameters vSpectratypeMean = new PreprocessorParameters(); - - public List> getGroups() { + public MetricParameters vUsage = new MetricParameters(); + public MetricParameters jUsage = new MetricParameters(); + public MetricParameters vjUsage = new MetricParameters(); + public MetricParameters isotypeUsage = new MetricParameters(); + public MetricParameters cdr3Spectratype = new MetricParameters(); + public MetricParameters vSpectratype = new MetricParameters(); + public MetricParameters vSpectratypeMean = new MetricParameters(); + + public List> getGroups(TagsInfo tagsInfo) { + for (WithParentAndTags wpt : Arrays.asList( + biophysics, diversity, vUsage, jUsage, vjUsage, isotypeUsage, cdr3Spectratype, vSpectratype, vSpectratypeMean + )) { + wpt.setParent(this); + wpt.setTagsInfo(tagsInfo); + } + return Arrays.asList( - biophysics.getGroup(this), - diversity.getGroup(this), + biophysics.getGroup(), + diversity.getGroup(), new CharacteristicGroup<>(VUsage, - Arrays.asList(AdditiveCharacteristics.segmentUsage(vUsage.preproc(this), GeneType.Variable)), + Arrays.asList(AdditiveCharacteristics.segmentUsage( + vUsage.preproc(), + vUsage.weightFunction(), + GeneType.Variable)), Arrays.asList(new GroupSummary.Simple<>()) ), new CharacteristicGroup<>(JUsage, - Arrays.asList(AdditiveCharacteristics.segmentUsage(jUsage.preproc(this), GeneType.Joining)), + Arrays.asList(AdditiveCharacteristics.segmentUsage( + jUsage.preproc(), + jUsage.weightFunction(), + GeneType.Joining + )), Arrays.asList(new GroupSummary.Simple<>()) ), new CharacteristicGroup<>(VJUsage, - Arrays.asList(AdditiveCharacteristics.vjSegmentUsage(vjUsage.preproc(this))), + Arrays.asList(AdditiveCharacteristics.vjSegmentUsage( + vjUsage.preproc(), + vjUsage.weightFunction() + )), Arrays.asList(new GroupSummary.VJUsage<>()) ), new CharacteristicGroup<>(IsotypeUsage, - Arrays.asList(AdditiveCharacteristics.isotypeUsage(isotypeUsage.preproc(this))), + Arrays.asList(AdditiveCharacteristics.isotypeUsage( + isotypeUsage.preproc(), + isotypeUsage.weightFunction() + )), Arrays.asList(new GroupSummary.Simple<>()) ), new CharacteristicGroup<>(CDR3Spectratype, Arrays.asList(new SpectratypeCharacteristic("CDR3 spectratype", - cdr3Spectratype.preproc(this), 10, + cdr3Spectratype.preproc(), + cdr3Spectratype.weightFunction(), + 10, new SpectratypeKeyFunction<>(new KeyFunctions.AAFeature(GeneFeature.CDR3), GeneFeature.CDR3, false))), Collections.singletonList(new GroupSummary.Simple<>())), new CharacteristicGroup<>(VSpectratype, - Arrays.asList(AdditiveCharacteristics.VSpectratype(vSpectratype.preproc(this))), + Arrays.asList(AdditiveCharacteristics.VSpectratype( + vSpectratype.preproc(), + vSpectratype.weightFunction())), Collections.singletonList(new GroupSummary.Simple<>())), new CharacteristicGroup<>(VSpectratypeMean, - Arrays.asList(AdditiveCharacteristics.VSpectratypeMean(vSpectratypeMean.preproc(this))), + Arrays.asList(AdditiveCharacteristics.VSpectratypeMean( + vSpectratypeMean.preproc(), + vSpectratypeMean.weightFunction())), Collections.singletonList(new GroupSummary.Simple<>())) ); } @@ -99,29 +125,47 @@ public List> getGroups() { fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE) - public static class BiophysicsParameters { - public PreprocessorParameters cdr3lenAA = new PreprocessorParameters(); - public PreprocessorParameters cdr3lenNT = new PreprocessorParameters(); - public PreprocessorParameters ndnLenNT = new PreprocessorParameters(); - public PreprocessorParameters addedNNT = new PreprocessorParameters(); - public PreprocessorParameters Strength = new PreprocessorParameters(); - public PreprocessorParameters Hydrophobicity = new PreprocessorParameters(); - public PreprocessorParameters Surface = new PreprocessorParameters(); - public PreprocessorParameters Volume = new PreprocessorParameters(); - public PreprocessorParameters Charge = new PreprocessorParameters(); - - public CharacteristicGroup getGroup(PostanalysisParameters base) { + public static class BiophysicsParameters implements WithParentAndTags { + public MetricParameters cdr3lenAA = new MetricParameters(); + public MetricParameters cdr3lenNT = new MetricParameters(); + public MetricParameters ndnLenNT = new MetricParameters(); + public MetricParameters addedNNT = new MetricParameters(); + public MetricParameters Strength = new MetricParameters(); + public MetricParameters Hydrophobicity = new MetricParameters(); + public MetricParameters Surface = new MetricParameters(); + public MetricParameters Volume = new MetricParameters(); + public MetricParameters Charge = new MetricParameters(); + + private List list() { + return Arrays.asList(cdr3lenAA, cdr3lenNT, ndnLenNT, addedNNT, Strength, Hydrophobicity, Surface, Volume, Charge); + } + + @Override + public void setParent(PostanalysisParameters parent) { + for (MetricParameters m : list()) { + m.setParent(parent); + } + } + + @Override + public void setTagsInfo(TagsInfo tagsInfo) { + for (MetricParameters m : list()) { + m.setTagsInfo(tagsInfo); + } + } + + public CharacteristicGroup getGroup() { return new CharacteristicGroup<>(Biophysics, Arrays.asList( - weightedLengthOf(cdr3lenNT.preproc(base), GeneFeature.CDR3, false).setName("CDR3 length, nt"), - weightedLengthOf(cdr3lenAA.preproc(base), GeneFeature.CDR3, true).setName("CDR3 length, aa"), - weightedLengthOf(ndnLenNT.preproc(base), GeneFeature.VJJunction, false).setName("NDN length, nt"), - weightedAddedNucleotides(addedNNT.preproc(base)).setName("Added N, nt"), - weightedBiophysics(Strength.preproc(base), AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Strength"), - weightedBiophysics(Hydrophobicity.preproc(base), AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Hydrophobicity"), - weightedBiophysics(Surface.preproc(base), AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Surface"), - weightedBiophysics(Volume.preproc(base), AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), - weightedBiophysics(Charge.preproc(base), AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") + lengthOf(cdr3lenNT.preproc(), cdr3lenNT.weightFunction(), GeneFeature.CDR3, false).setName("CDR3 length, nt"), + lengthOf(cdr3lenAA.preproc(), cdr3lenAA.weightFunction(), GeneFeature.CDR3, true).setName("CDR3 length, aa"), + lengthOf(ndnLenNT.preproc(), ndnLenNT.weightFunction(), GeneFeature.VJJunction, false).setName("NDN length, nt"), + addedNucleotides(addedNNT.preproc(), addedNNT.weightFunction()).setName("Added N, nt"), + biophysics(Strength.preproc(), Strength.weightFunction(), AAProperties.AAProperty.N2Strength, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Strength"), + biophysics(Hydrophobicity.preproc(), Hydrophobicity.weightFunction(), AAProperties.AAProperty.N2Hydrophobicity, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Hydrophobicity"), + biophysics(Surface.preproc(), Surface.weightFunction(), AAProperties.AAProperty.N2Surface, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Surface"), + biophysics(Volume.preproc(), Volume.weightFunction(), AAProperties.AAProperty.N2Volume, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Volume"), + biophysics(Charge.preproc(), Charge.weightFunction(), AAProperties.AAProperty.Charge, GeneFeature.CDR3, AAProperties.Adjustment.LeadingCenter, 5).setName("Charge") ), Collections.singletonList(new GroupSummary.Simple<>())); } @@ -144,33 +188,51 @@ public int hashCode() { fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE, getterVisibility = JsonAutoDetect.Visibility.NONE) - public static class DiversityParameters { - public PreprocessorParameters observed = new PreprocessorParameters(); - public PreprocessorParameters shannonWiener = new PreprocessorParameters(); - public PreprocessorParameters chao1 = new PreprocessorParameters(); - public PreprocessorParameters clonality = new PreprocessorParameters(); - public PreprocessorParameters inverseSimpson = new PreprocessorParameters(); - public PreprocessorParameters gini = new PreprocessorParameters(); - public PreprocessorParameters d50 = new PreprocessorParameters(); - public PreprocessorParameters efronThisted = new PreprocessorParameters(); - - public CharacteristicGroup getGroup(PostanalysisParameters base) { - List> chars = new ArrayList<>(groupByPreproc( - new HashMap>() {{ - put(DiversityMeasure.Observed, observed.preproc(base)); - put(DiversityMeasure.ShannonWiener, shannonWiener.preproc(base)); - put(DiversityMeasure.Chao1, chao1.preproc(base)); - put(DiversityMeasure.NormalizedShannonWeinerIndex, clonality.preproc(base)); - put(DiversityMeasure.InverseSimpson, inverseSimpson.preproc(base)); - put(DiversityMeasure.GiniIndex, gini.preproc(base)); - put(DiversityMeasure.EfronThisted, efronThisted.preproc(base)); + public static class DiversityParameters implements WithParentAndTags { + public MetricParameters observed = new MetricParameters(); + public MetricParameters shannonWiener = new MetricParameters(); + public MetricParameters chao1 = new MetricParameters(); + public MetricParameters clonality = new MetricParameters(); + public MetricParameters inverseSimpson = new MetricParameters(); + public MetricParameters gini = new MetricParameters(); + public MetricParameters d50 = new MetricParameters(); + public MetricParameters efronThisted = new MetricParameters(); + + private List list() { + return Arrays.asList(observed, shannonWiener, chao1, clonality, inverseSimpson, gini, d50, efronThisted); + } + + @Override + public void setParent(PostanalysisParameters parent) { + for (MetricParameters m : list()) { + m.setParent(parent); + } + } + + @Override + public void setTagsInfo(TagsInfo tagsInfo) { + for (MetricParameters m : list()) { + m.setTagsInfo(tagsInfo); + } + } + + public CharacteristicGroup getGroup() { + List> chars = new ArrayList<>(groupBy( + new HashMap>() {{ + put(DiversityMeasure.Observed, observed.pwTuple()); + put(DiversityMeasure.ShannonWiener, shannonWiener.pwTuple()); + put(DiversityMeasure.Chao1, chao1.pwTuple()); + put(DiversityMeasure.NormalizedShannonWeinerIndex, clonality.pwTuple()); + put(DiversityMeasure.InverseSimpson, inverseSimpson.pwTuple()); + put(DiversityMeasure.GiniIndex, gini.pwTuple()); + put(DiversityMeasure.EfronThisted, efronThisted.pwTuple()); }}, (p, l) -> Collections.singletonList(new DiversityCharacteristic<>("Diversity " + l.stream().map(m -> m.name).collect(Collectors.joining("/")), - new WeightFunctions.Count(), p, l.toArray(new DiversityMeasure[0]))))); + p.weight, p.preproc, l.toArray(new DiversityMeasure[0]))))); chars.add(new DiversityCharacteristic<>("d50", new WeightFunctions.Count(), - d50.preproc(base).then(new SelectTop.Factory<>(WeightFunctions.Count, 0.5)), + d50.preproc().then(new SelectTop.Factory<>(WeightFunctions.Count, 0.5)), new DiversityMeasure[]{ DiversityMeasure.Observed.overrideName("d50") })); diff --git a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java index c894c2ab1..f1cc3f69a 100644 --- a/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java +++ b/src/main/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersOverlap.java @@ -12,9 +12,8 @@ package com.milaboratory.mixcr.postanalysis.ui; import com.milaboratory.mixcr.basictypes.Clone; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; import com.milaboratory.mixcr.postanalysis.Characteristic; -import com.milaboratory.mixcr.postanalysis.SetPreprocessorFactory; -import com.milaboratory.mixcr.postanalysis.WeightFunctions; import com.milaboratory.mixcr.postanalysis.overlap.OverlapCharacteristic; import com.milaboratory.mixcr.postanalysis.overlap.OverlapGroup; import com.milaboratory.mixcr.postanalysis.overlap.OverlapType; @@ -26,25 +25,29 @@ public class PostanalysisParametersOverlap extends PostanalysisParameters { public static final String Overlap = "Overlap"; - public PreprocessorParameters d = new PreprocessorParameters(); - public PreprocessorParameters sharedClonotypes = new PreprocessorParameters(); - public PreprocessorParameters f1 = new PreprocessorParameters(); - public PreprocessorParameters f2 = new PreprocessorParameters(); - public PreprocessorParameters jaccard = new PreprocessorParameters(); - public PreprocessorParameters rIntersection = new PreprocessorParameters(); - public PreprocessorParameters rAll = new PreprocessorParameters(); + public MetricParameters d = new MetricParameters(); + public MetricParameters sharedClonotypes = new MetricParameters(); + public MetricParameters f1 = new MetricParameters(); + public MetricParameters f2 = new MetricParameters(); + public MetricParameters jaccard = new MetricParameters(); + public MetricParameters rIntersection = new MetricParameters(); + public MetricParameters rAll = new MetricParameters(); - public List>> getGroups(int nSamples) { - PostanalysisParametersOverlap base = this; - List>> chars = groupByPreproc( - new HashMap>>() {{ - put(OverlapType.D, d.overlapPreproc(base)); - put(OverlapType.SharedClonotypes, sharedClonotypes.overlapPreproc(base)); - put(OverlapType.F1, f1.overlapPreproc(base)); - put(OverlapType.F2, f2.overlapPreproc(base)); - put(OverlapType.Jaccard, jaccard.overlapPreproc(base)); - put(OverlapType.R_Intersection, rIntersection.overlapPreproc(base)); - put(OverlapType.R_All, rAll.overlapPreproc(base)); + public List>> getGroups(int nSamples, TagsInfo tagsInfo) { + for (MetricParameters m : Arrays.asList(d, sharedClonotypes, f1, f2, jaccard, rIntersection, rAll)) { + m.setParent(this); + m.setTagsInfo(tagsInfo); + } + + List>> chars = groupBy( + new HashMap>() {{ + put(OverlapType.D, d.opwTuple()); + put(OverlapType.SharedClonotypes, sharedClonotypes.opwTuple()); + put(OverlapType.F1, f1.opwTuple()); + put(OverlapType.F2, f2.opwTuple()); + put(OverlapType.Jaccard, jaccard.opwTuple()); + put(OverlapType.R_Intersection, rIntersection.opwTuple()); + put(OverlapType.R_All, rAll.opwTuple()); }}, (p, l) -> { List> overlaps = new ArrayList<>(); @@ -52,8 +55,8 @@ public List>> getGroups(int nSamples) for (int j = i; j < nSamples; ++j) // j=i to include diagonal elements overlaps.add(new OverlapCharacteristic<>( "overlap_" + i + "_" + j + " / " + l.stream().map(t -> t.name).collect(Collectors.joining(" / ")), - new WeightFunctions.Count(), - p, + p.weight, + p.preproc, l.toArray(new OverlapType[0]), i, j)); return overlaps; diff --git a/src/main/resources/parameters/postanalysis_individual.json b/src/main/resources/parameters/postanalysis_individual.json index f051134c7..4b74627f5 100644 --- a/src/main/resources/parameters/postanalysis_individual.json +++ b/src/main/resources/parameters/postanalysis_individual.json @@ -3,41 +3,49 @@ "defaultDownsampling": null, "defaultOnlyProductive": true, "defaultDropOutliers": false, + "defaultWeightFunction": "read-count", "biophysics": { "cdr3lenAA": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "cdr3lenNT": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "ndnLenNT": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "addedNNT": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "Strength": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "Hydrophobicity": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "Surface": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "Volume": { "downsampling": null, @@ -47,85 +55,101 @@ "Charge": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null } }, "diversity": { "observed": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "shannonWiener": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "chao1": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "clonality": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "inverseSimpson": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "gini": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "d50": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "efronThisted": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null } }, "vUsage": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "jUsage": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "vjUsage": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "isotypeUsage": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "cdr3Spectratype": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "vSpectratype": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "vSpectratypeMean": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null } } } diff --git a/src/main/resources/parameters/postanalysis_overlap.json b/src/main/resources/parameters/postanalysis_overlap.json index 75dfb2298..cbace10f4 100644 --- a/src/main/resources/parameters/postanalysis_overlap.json +++ b/src/main/resources/parameters/postanalysis_overlap.json @@ -3,40 +3,48 @@ "defaultDownsampling": null, "defaultOnlyProductive": false, "defaultDropOutliers": false, + "defaultWeightFunction": "read-count", "d": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "sharedClonotypes": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "f1": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "f2": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "jaccard": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "rIntersection": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null }, "rAll": { "downsampling": null, "onlyProductive": null, - "dropOutliers": null + "dropOutliers": null, + "weightFunction": null } } } \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersTest.java new file mode 100644 index 000000000..e43012296 --- /dev/null +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisParametersTest.java @@ -0,0 +1,37 @@ +package com.milaboratory.mixcr.postanalysis.ui; + + +import com.milaboratory.mixcr.basictypes.tag.TagInfo; +import com.milaboratory.mixcr.basictypes.tag.TagType; +import com.milaboratory.mixcr.basictypes.tag.TagValueType; +import com.milaboratory.mixcr.basictypes.tag.TagsInfo; +import org.junit.Test; + +public class PostanalysisParametersTest { + @Test + public void test1() { + PostanalysisParameters.parseDownsampling( + "count-umi-auto", + new TagsInfo(2, new TagInfo(TagType.Molecule, TagValueType.ByteString, "UMI", 1)), + false + ); + } + + @Test + public void test2() { + PostanalysisParameters.parseDownsampling( + "top-reads-1000", + null, + false + ); + } + + @Test + public void test3() { + PostanalysisParameters.parseDownsampling( + "cumtop-reads-0.5", + null, + false + ); + } +} \ No newline at end of file diff --git a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java index 41d27b296..4a7243158 100644 --- a/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java +++ b/src/test/java/com/milaboratory/mixcr/postanalysis/ui/PostanalysisSchemaIntegrationTest.java @@ -37,6 +37,7 @@ import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKey; import com.milaboratory.mixcr.postanalysis.spectratype.SpectratypeKeyFunction; import com.milaboratory.mixcr.tests.IntegrationTest; +import com.milaboratory.util.GlobalObjectMappers; import com.milaboratory.util.LambdaSemaphore; import io.repseq.core.GeneFeature; import io.repseq.core.GeneType; @@ -56,13 +57,22 @@ import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedBiophysics; import static com.milaboratory.mixcr.postanalysis.additive.AdditiveCharacteristics.weightedLengthOf; -@Category(IntegrationTest.class) +//@Category(IntegrationTest.class) public class PostanalysisSchemaIntegrationTest { private static ClonotypeDataset getClones(String sample) { return new ClonotypeDataset(sample, PostanalysisSchemaIntegrationTest.class.getResource("/sequences/big/yf_sample_data/" + sample + ".contigs.clns").getFile(), VDJCLibraryRegistry.getDefault()); } + @Test + @SuppressWarnings("unchecked") + public void testJson1() throws JsonProcessingException { + DiversityCharacteristic expected = new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), true, WeightFunctions.Count)); + String str = GlobalObjectMappers.getPretty().writeValueAsString(expected); + DiversityCharacteristic actual = GlobalObjectMappers.getPretty().readValue(str, DiversityCharacteristic.class); + Assert.assertEquals(expected, actual); + } + @Test public void test1() throws IOException { ClonotypeDataset r1 = getClones("Ig-2_S2"); @@ -93,7 +103,7 @@ public void test1() throws IOException { )); groups.add(new CharacteristicGroup<>( "diversity", - Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), true))), + Arrays.asList(new DiversityCharacteristic<>("diversity", new WeightFunctions.Count(), new ClonesDownsamplingPreprocessorFactory(new DownsampleValueChooser.Auto(), true, WeightFunctions.Count))), Arrays.asList(new GroupSummary.Simple<>()) )); @@ -201,7 +211,8 @@ public void testOverlap1() throws JsonProcessingException { ClonesDownsamplingPreprocessorFactory downsamplePreprocessor = new ClonesDownsamplingPreprocessorFactory( new DownsampleValueChooser.Minimal(), - true); + true, + WeightFunctions.Count); List> overlaps = new ArrayList<>(); for (int i = 0; i < readers.size(); ++i) { From ef877ad048441d3f28367fe9eb13fc7774dfafe4 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 9 Jun 2022 19:01:38 +0400 Subject: [PATCH 274/282] chore: milib & repseqio upgrade to release versions --- build.gradle.kts | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index baaa37201..25353d9a9 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -29,7 +29,6 @@ plugins { // Make IDE aware of the generated code: kotlin.sourceSets.getByName("main").kotlin.srcDir("build/generated/ksp/main/kotlin/") - val miRepoAccessKeyId: String? by project val miRepoSecretAccessKey: String? by project @@ -81,8 +80,8 @@ repositories { } } -val milibVersion = "1.15.0-54-master" -val repseqioVersion = "1.3.5-34-master" +val milibVersion = "2.0.0" +val repseqioVersion = "1.4.0" val mitoolVersion = "0.9.1-16-main" val miplotsVersion = "0.1-26-master" val jacksonBomVersion = "2.13.3" From 615aaa8de6a6fa36b817f4c07cb3cbb48d2f3133 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 9 Jun 2022 19:18:46 +0400 Subject: [PATCH 275/282] chore: miplots & mitool upgrade to release versions --- build.gradle.kts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 25353d9a9..b151db8cd 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -82,8 +82,8 @@ repositories { val milibVersion = "2.0.0" val repseqioVersion = "1.4.0" -val mitoolVersion = "0.9.1-16-main" -val miplotsVersion = "0.1-26-master" +val mitoolVersion = "1.0.0" +val miplotsVersion = "1.0.0" val jacksonBomVersion = "2.13.3" dependencies { From 6fabd50f90689b71a83bb2345eebddf5af56aaef Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 9 Jun 2022 22:09:42 +0200 Subject: [PATCH 276/282] minor fix in overlapScatterPlot --- .../mixcr/cli/postanalysis/CommandOverlapScatter.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java index ba36f1a60..8857a3de7 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java +++ b/src/main/java/com/milaboratory/mixcr/cli/postanalysis/CommandOverlapScatter.java @@ -81,6 +81,11 @@ public class CommandOverlapScatter extends ACommandWithOutputMiXCR { names = {"--no-log"}) public boolean noLog; + @Override + protected List getInputFiles() { + return Arrays.asList(in1, in2); + } + private static String fName(String file) { return Paths.get(file).toAbsolutePath().getFileName().toString(); } From 4ee0b14a150aed32112f7348566ad6a8c037ace8 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Fri, 10 Jun 2022 02:09:26 +0400 Subject: [PATCH 277/282] fix: off-by-one bug in consensus assembly (mitool upgrade) minor fix & new integration tests for corner cases with UMI data --- README.md | 42 ++++----------- build.gradle.kts | 2 +- itests.sh | 8 +-- itests/case11.sh | 4 +- itests/case12.sh | 51 +++++++++++++++++++ .../preclone/PreCloneAssemblerParameters.java | 2 +- .../milaboratory/mixcr/cli/AlignerReport.java | 2 +- .../sequences/umi_single_read_R1.fastq | 4 ++ .../sequences/umi_single_read_R2.fastq | 4 ++ 9 files changed, 78 insertions(+), 41 deletions(-) create mode 100755 itests/case12.sh create mode 100644 src/test/resources/sequences/umi_single_read_R1.fastq create mode 100644 src/test/resources/sequences/umi_single_read_R2.fastq diff --git a/README.md b/README.md index bbac49faa..1f968691d 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,5 @@ -[![Build Status](https://travis-ci.org/milaboratory/mixcr.svg)](https://travis-ci.org/milaboratory/mixcr) [![image](https://readthedocs.org/projects/mixcr/badge/?version=latest)](https://mixcr.readthedocs.io) - ## Overview MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. @@ -108,40 +106,18 @@ To build MiXCR from source: ## License -Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail -(here and after addressed as Inventors) -All Rights Reserved - -Permission to use, copy, modify and distribute any part of this program for -educational, research and non-profit purposes, by non-profit institutions -only, without fee, and without a written agreement is hereby granted, -provided that the above copyright notice, this paragraph and the following -three paragraphs appear in all copies. - -Those desiring to incorporate this work into commercial products or use for -commercial purposes should contact MiLaboratory LLC, which owns exclusive -rights for distribution of this program for commercial purposes, using the -following email address: licensing@milaboratory.com. - -IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, -SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, -ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN -ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS -NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR -MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO -WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A -PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY -PATENT, TRADEMARK OR OTHER RIGHTS. +Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + +Before downloading or accessing the software, please read carefully the +License Agreement available at: +https://github.com/milaboratory/mixcr/blob/develop/LICENSE + +By downloading or accessing the software, you accept and agree to be bound +by the terms of the License Agreement. If you do not want to agree to the terms +of the Licensing Agreement, you must not download or access the software. ## Cite * Dmitriy A. Bolotin, Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar Z. Mamedov, Ekaterina V. Putintseva, and Dmitriy M. Chudakov. "MiXCR: software for comprehensive adaptive immunity profiling." *Nature methods* 12, no. 5 (**2015**): 380-381. * Dmitriy A. Bolotin, Stanislav Poslavsky, Alexey N. Davydov, Felix E. Frenkel, Lorenzo Fanchi, Olga I. Zolotareva, Saskia Hemmers, Ekaterina V. Putintseva, Anna S. Obraztsova, Mikhail Shugay, Ravshan I. Ataullakhanov, Alexander Y. Rudensky, Ton N. Schumacher & Dmitriy M. Chudakov. "Antigen receptor repertoire profiling from RNA-seq data." *Nature Biotechnology* 35, 908–911 (**2017**) - -## Files referenced in original paper - -Can be found [here](https://github.com/milaboratory/mixcr/blob/develop/doc/paper/paperAttachments.md). diff --git a/build.gradle.kts b/build.gradle.kts index b151db8cd..94f838b81 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -82,7 +82,7 @@ repositories { val milibVersion = "2.0.0" val repseqioVersion = "1.4.0" -val mitoolVersion = "1.0.0" +val mitoolVersion = "1.0.1" val miplotsVersion = "1.0.0" val jacksonBomVersion = "2.13.3" diff --git a/itests.sh b/itests.sh index 093ec45f8..05cbd8edb 100755 --- a/itests.sh +++ b/itests.sh @@ -47,7 +47,7 @@ FreeBSD) ;; esac -tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8" "case9" "case10" "case11") +tests=("case1" "case2" "case3" "case4" "case5" "case6" "case7" "case8" "case9" "case10" "case11" "case12") create_standard_results=false run_tests=false @@ -81,8 +81,10 @@ ln -s ../src/test/resources/sequences/big/CD4M1_test_R1.fastq.gz ${dir}/test_tar ln -s ../src/test/resources/sequences/big/CD4M1_test_R2.fastq.gz ${dir}/test_target/CD4M1_test_R2.fastq.gz ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R1.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R1.fastq.gz ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R2.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R2.fastq.gz -ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R1.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R1.fastq.gz -ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R2.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R2.fastq.gz +#ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R1.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R1.fastq.gz +#ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R2.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R2.fastq.gz +#ln -s ../src/test/resources/sequences/umi_single_read_R1.fastq ${dir}/test_target/umi_single_read_R1.fastq +#ln -s ../src/test/resources/sequences/umi_single_read_R2.fastq ${dir}/test_target/umi_single_read_R2.fastq PATH=${dir}:${PATH} diff --git a/itests/case11.sh b/itests/case11.sh index 81f822daf..21c7b2d1a 100755 --- a/itests/case11.sh +++ b/itests/case11.sh @@ -15,7 +15,7 @@ assert() { exit 1 } -set -euxo pipefail +set -eux mixcr align -f \ --tag-pattern-name mikelov_et_al_2021 \ @@ -27,7 +27,7 @@ mixcr align -f \ -OallowPartialAlignments=true \ -OallowNoCDR3PartAlignments=true \ -OsaveOriginalReads=true \ - --report case10.align.report \ + --report case11.align.report \ umi_ig_data_2_subset_R1.fastq.gz \ umi_ig_data_2_subset_R2.fastq.gz \ case11.aligned-vdjca diff --git a/itests/case12.sh b/itests/case12.sh new file mode 100755 index 000000000..8675e22ec --- /dev/null +++ b/itests/case12.sh @@ -0,0 +1,51 @@ +#!/usr/bin/env bash + +# Single-cell integration test + +assert() { + expected=$(echo -ne "${2:-}") + result="$(eval 2>/dev/null $1)" || true + if [[ "$result" == "$expected" ]]; then + return + fi + result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")" + [[ -z "$result" ]] && result="nothing" || result="\"$result\"" + [[ -z "$2" ]] && expected="nothing" || expected="\"$2\"" + echo "expected $expected got $result for" "$1" + exit 1 +} + +set -eux + +mixcr align -f \ + --tag-pattern-name mikelov_et_al_2021 \ + -p kaligner2 -s hs \ + -OvParameters.geneFeatureToAlign=VTranscript \ + -OvParameters.parameters.floatingLeftBound=false \ + -OjParameters.parameters.floatingRightBound=false \ + -OcParameters.parameters.floatingRightBound=false \ + -OallowPartialAlignments=true \ + -OallowNoCDR3PartAlignments=true \ + -OsaveOriginalReads=true \ + --report case12.align.report \ + umi_single_read_R1.fastq \ + umi_single_read_R2.fastq \ + case12.aligned-vdjca + +mixcr correctAndSortTags case12.aligned-vdjca case12.corrected-vdjca + +mixcr itestAssemblePreClones case12.corrected-vdjca case12.corrected-vdjca.pc + +mixcr assemble -f -a case12.corrected-vdjca case12.cdr3-clna +mixcr assembleContigs -f case12.cdr3-clna case12.cdr3-clns + +mixcr assemble -f -OassemblingFeatures='VDJRegion' case12.corrected-vdjca case12.vdjregion-clns + +mixcr exportClones -nFeature VDJRegion case12.vdjregion-clns case12.vdjregion-clns.txt +mixcr exportClones -nFeature VDJRegion case12.cdr3-clns case12.cdr3-clns.txt + +sort case12.vdjregion-clns.txt > case12.vdjregion-clns.txt.s +sort case12.cdr3-clns.txt > case12.cdr3-clns.txt.s + +[[ $(cat case12.cdr3-clns.txt.s | wc -l) -eq 2 ]] || exit 1 +cmp case12.vdjregion-clns.txt.s case12.cdr3-clns.txt.s diff --git a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java index b0463bc94..298860c29 100644 --- a/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java +++ b/src/main/java/com/milaboratory/mixcr/assembler/preclone/PreCloneAssemblerParameters.java @@ -47,6 +47,6 @@ public PreCloneAssemblerParameters(GConsensusAssemblerParameters assemblerParame .maxIterations(4) .minAltSeedQualityScore((byte) 11) .minimalRecordShare(0.1) - .minimalRecordCount(2) + .minimalRecordCount(1) .build(); } diff --git a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java index 331ca4741..cdeb4bc31 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java +++ b/src/main/java/com/milaboratory/mixcr/cli/AlignerReport.java @@ -326,7 +326,7 @@ public void writeReport(ReportHelper helper) { helper.writePercentAndAbsoluteField("Realigned with forced non-floating left bound in right read", getRealignedWithForcedNonFloatingLeftBoundInRightRead(), total); if (trimmingReport != null) { - assert trimmingReport.getAlignments() == total; + // assert trimmingReport.getAlignments() == total; helper.writePercentAndAbsoluteField("R1 Reads Trimmed Left", trimmingReport.getR1LeftTrimmedEvents(), total); helper.writePercentAndAbsoluteField("R1 Reads Trimmed Right", trimmingReport.getR1RightTrimmedEvents(), total); helper.writeField("Average R1 Nucleotides Trimmed Left", 1.0 * trimmingReport.getR1LeftTrimmedNucleotides() / total); diff --git a/src/test/resources/sequences/umi_single_read_R1.fastq b/src/test/resources/sequences/umi_single_read_R1.fastq new file mode 100644 index 000000000..4b74687db --- /dev/null +++ b/src/test/resources/sequences/umi_single_read_R1.fastq @@ -0,0 +1,4 @@ +@94 W=1 +CAGCGGGAAGACCTTGGGGCTGGTCGGGGATGCTGAGGACACGGTGACCGTGGTCCCTTGGCCCCAGACGTCCATACCGTACTTCCTGCCTGACTGGTTCCATGACCTCGCACAGTAATACACAGCCGTGTCCTCGTCTCTCAGGCTGTTCATTTGCAGATACAGTGAGTTCTTGGCATTGTCTCTGGAGATGGTGAATCGGCCCTTCACAGAGTCTGCATAATATGTAGTACTTCCAAGCATTATGTATGACACCCACTCCAGGCCCTTCCCTGGAGCCTGGCGGACCCAGTTCATACTATAACTACTG ++ +GGGGGIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIGIIIIIIIIIIIIIIIIIIIGGGIIIGIIIIGIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIIIIIIIGIGIIGIIIIIIGIIGIGIGGGIIIIGGIGGGIIGGIIIIGGIGGIIIIGIGIGIIGGGIGGAGGIIGGGGAGGGGGGGGGIGGIGIGGIGGGGIIIIGGGGAGGIIGGGAGAGGIGGGIIIIIIIIIGGGGGIAG.A Date: Fri, 10 Jun 2022 02:50:17 +0400 Subject: [PATCH 278/282] fix for integration tests --- itests.sh | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/itests.sh b/itests.sh index 05cbd8edb..263951149 100755 --- a/itests.sh +++ b/itests.sh @@ -81,10 +81,8 @@ ln -s ../src/test/resources/sequences/big/CD4M1_test_R1.fastq.gz ${dir}/test_tar ln -s ../src/test/resources/sequences/big/CD4M1_test_R2.fastq.gz ${dir}/test_target/CD4M1_test_R2.fastq.gz ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R1.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R1.fastq.gz ln -s ../src/test/resources/sequences/big/single_cell_vdj_t_subset_R2.fastq.gz ${dir}/test_target/single_cell_vdj_t_subset_R2.fastq.gz -#ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R1.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R1.fastq.gz -#ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R2.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R2.fastq.gz -#ln -s ../src/test/resources/sequences/umi_single_read_R1.fastq ${dir}/test_target/umi_single_read_R1.fastq -#ln -s ../src/test/resources/sequences/umi_single_read_R2.fastq ${dir}/test_target/umi_single_read_R2.fastq +ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R1.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R1.fastq.gz +ln -s ../src/test/resources/sequences/umi_ig_data_2_subset_R2.fastq.gz ${dir}/test_target/umi_ig_data_2_subset_R2.fastq.gz PATH=${dir}:${PATH} From 61e8ce4e5bee8122a92ab3c3bb080da472f12329 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 10 Jun 2022 01:05:21 +0200 Subject: [PATCH 279/282] Update Readme (#53) --- README.md | 138 +++++++++++++++++-------------- doc/_static/MiXCR_logo_dark.png | Bin 0 -> 25025 bytes doc/_static/MiXCR_logo_white.png | Bin 0 -> 20823 bytes 3 files changed, 74 insertions(+), 64 deletions(-) create mode 100644 doc/_static/MiXCR_logo_dark.png create mode 100644 doc/_static/MiXCR_logo_white.png diff --git a/README.md b/README.md index 1f968691d..721f00ab0 100644 --- a/README.md +++ b/README.md @@ -1,44 +1,52 @@ [![image](https://readthedocs.org/projects/mixcr/badge/?version=latest)](https://mixcr.readthedocs.io) -## Overview - -MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. - - - Easy to use. Default pipeline can be executed without any additional parameters (see *Usage* section) - - - TCR and IG repertoires - - - Following species are supported *out-of-the-box* using built-in library: - - human - - mouse - - rat (only TRB and TRA) - - *... several new species will be available soon* - -- Efficiently extract repertoires from most of (if not *all*) types of TCR/IG-containing raw sequencing data: - - data from all specialized RepSeq sample preparation protocols - - RNA-Seq - - WGS - - single-cell data - - *etc..* - -- Has optional CDR3 reconstruction step, that allows to *recover full hypervariable region from several disjoint reads*. Uses sophisticated algorithms protecting from false-positive assemblies at the same time having best in class efficiency. - -- Assemble clonotypes, applying several *error-correction* algorithms to eliminate artificial diversity arising from PCR and sequencing errors - -- Clonotypes can be assembled based on CDR3 sequence (default) as well as any other region, including *full-length* variable sequence (from beginning of FR1 to the end of FR4) - -- Assemble full TCR/Ig receptor sequences - -- Provides exhaustive output information for clonotypes and per-read alignments: - - nucleotide and amino acid sequences of all immunologically relevant regions (FR1, CDR1, ..., CDR3, etc..) - - identified V, D, J, C genes - - nucleotide and amino acid mutations in germline regions - - variable region topology (number of end V / D / J nucleotide deletions, length of P-segments, number of non-template N nucleotides) - - sequencing quality scores for any extracted sequence - - several other useful pieces of information - -- Completely transparent pipeline, possible to track individual read fate from raw fastq entry to clonotype. Several useful tools available to evaluate pipeline performance: human readable alignments visualization, diff tool for alignment and clonotype files, etc... +![MiXCR logo](./doc/_static/MiXCR_logo_dark.png#gh-light-mode-only) +![MiXCR logo](./doc/_static/MiXCR_logo_white.png#gh-dark-mode-only) + +MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. It works with any kind of sequencing data: + - Bulk repertoire sequencing data with or without UMIs + - Single cell sequencing data including but not limited to 10x Genomics protocols + - RNA-Seq or any other kind of fragmented/shotgun data which may contain just a tiny fraction of target sequences + - and any other kind of sequencing data containing TCRs or BCRs + +Powerful downstream analysis tools allow to obtain vector plots and tabular results for multiple measures. Key features include: + - Ability to group samples by metadata values and compare repertoire features between groups + - Comprehensive repertoire normalization and filtering + - Statistical significance tests with proper p-value adjustment + - Repertoire overlap analysis + - Vector plots output (.svg / .pdf) + - Tabular outputs + +Other key features: + +- Clonotype assembly by arbitrary gene feature, including *full-length* variable region +- PCR / Sequencing error correction with or without aid of UMI or Cell barcodes +- Robust and dedicated aligner algorithms for maximum extration with zero false-positive rate +- Supports any custom barcode sequences architecture (UMI / Cell) +- _Human_, _Mice_, _Rat_, _Spalax_, _Alpaca_, _Monkey_ +- Support IMGT reference +- Barcodes error-correction +- Adapter trimming +- Optional CDR3 reconstruction by assembling overlapping fragmented sequencing reads into complete CDR3-containing contigs when the read position is floating (e.g. shotgun-sequencing, RNA-Seq etc.) +- Optional contig assembly to build longest possible TCR/IG sequence from available data (with or without aid of UMI or Cell barcodes) +- Comprehensive quality control reports provided at all the steps of the pipeline +- Regions not covered by the data may be imputed from germline +- Exhaustive output information for clonotypes and alignments: + - nucleotide and amino acid sequences of all immunologically relevant regions (FR1, CDR1, ..., CDR3, etc..) + - identified V, D, J, C genes + - comprehensive information on nucleotide and amino acid mutations + - positions of all immunologically relevant points in output sequences + - and many more informative columns +- Ability to backtrack fate of each raw sequencing read through the whole pipeline + +## Who uses MiXCR +MiXCR is used by 8 out of 10 world leading pharmaceutical companies in the R&D for: +- Vaccine development +- Antibody discovery +- Cancer immunotherapy research + +Widely adopted by academic community with 1000+ citations in peer-reviewed scientific publications. ## Installation / Download @@ -51,9 +59,10 @@ to upgrade already installed MiXCR to the newest version: brew update brew upgrade mixcr -#### Docker +[//]: # (#### Docker) -See [official Docker Image](https://hub.docker.com/r/milaboratory/mixcr). +[//]: # () +[//]: # (See [official Docker Image](https://hub.docker.com/r/milaboratory/mixcr).) #### Manual install (any OS) @@ -67,42 +76,35 @@ See [official Docker Image](https://hub.docker.com/r/milaboratory/mixcr). * Any OS with Java support (Linux, Windows, Mac OS X, etc..) * Java 1.8 or higher - -## Usage - -See usage examples in the official documentation https://mixcr.readthedocs.io/en/master/quickstart.html -## Documentation +## Obtaining a license -Detailed documentation can be found at https://mixcr.readthedocs.io/ +To run MiXCR one need a license file. MiXCR is free for academic users with no commercial funding. We are committed to support academic community and provide our software free of charge for scientists doing non-profit research. -If you haven't found the answer to your question in the docs, or have any suggestions concerning new features, feel free to create an issue here, on GitHub, or write an email to support@milaboratory.com . +Academic users can quickly get a license at https://licensing.milaboratories.com. -## Build +Commercial trial license may be requested at https://licensing.milaboratories.com or by email to licensing@milaboratories.com. -Requirements: +To activate the license do one of the following: -- Maven 3 (https://maven.apache.org/) +- put `mi.license` to + - `~/.mi.license` + - `~/mi.license` + - directory with `mixcr.jar` file + - directory with MiXCR executable + - to any place and specify it in `MI_LICENSE_FILE` environment variable +- put `mi.license` content to `MI_LICENSE` environment variable +- run `mixcr activate-license` and paste `mi.license` content to the command prompt -To build MiXCR from source: -- Clone repository - ``` - git clone https://github.com/milaboratory/mixcr.git - ``` +## Usage & documentation -- Refresh git submodules +See usage examples in the official documentation https://mixcr.readthedocs.io/en/master/quickstart.html - ``` - git submodule update --init --recursive - ``` - -- Run build script. First build may take several minuties to download sequences for built-in V/D/J/C gene libraries from NCBI. +Detailed documentation can be found at https://mixcr.readthedocs.io/ - ``` - ./build.sh - ``` +If you haven't found the answer to your question in the docs, or have any suggestions concerning new features, feel free to create an issue here, on GitHub, or write an email to support@milaboratory.com . ## License @@ -116,8 +118,16 @@ By downloading or accessing the software, you accept and agree to be bound by the terms of the License Agreement. If you do not want to agree to the terms of the Licensing Agreement, you must not download or access the software. + ## Cite * Dmitriy A. Bolotin, Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar Z. Mamedov, Ekaterina V. Putintseva, and Dmitriy M. Chudakov. "MiXCR: software for comprehensive adaptive immunity profiling." *Nature methods* 12, no. 5 (**2015**): 380-381. + + \ + (Files referenced in this paper can be found [here](https://github.com/milaboratory/mixcr/blob/develop/doc/paper/paperAttachments.md).) + + * Dmitriy A. Bolotin, Stanislav Poslavsky, Alexey N. Davydov, Felix E. Frenkel, Lorenzo Fanchi, Olga I. Zolotareva, Saskia Hemmers, Ekaterina V. Putintseva, Anna S. Obraztsova, Mikhail Shugay, Ravshan I. Ataullakhanov, Alexander Y. Rudensky, Ton N. Schumacher & Dmitriy M. Chudakov. "Antigen receptor repertoire profiling from RNA-seq data." *Nature Biotechnology* 35, 908–911 (**2017**) + + diff --git a/doc/_static/MiXCR_logo_dark.png b/doc/_static/MiXCR_logo_dark.png new file mode 100644 index 0000000000000000000000000000000000000000..8aa4b1faea7639eaa9597b36cbf5b1f1e91f25a1 GIT binary patch literal 25025 zcmZU*c{G%N_&)v&O)@IQSW=cE*|&(2HDt|B*(KSdglscYNVa4bS+noi_n8)igtC-v zEFt@DFwFd3)BE%Jo$vR2|L8b5^W5`V?&Z3!`+kJ!-MM`V!G?e!=#+-KiU9<{F%Sgf zIB^{O=IWCVr@;?e5A}PV5X5|$@(-qAz_Sj13G+0#tqhfYzpw!QbId_WM+t&HMAIGG z!Xe1kL_V(naBR#GOM4N4l<%eAs#AgVjkp-Qkd_1{8Z`sZI9)lg} zkCj&Y$ZN^0KG~9)kf}o(!%L&x2jpK25TvH~Kc-EBm{0$p?X-$fXtFkAuy`$sxb6MZ z?Dw|Dlq-2K4}AAA1dd`96B8WlzSPC;q>APpmt`vBaz*bd7@Ro{z3Z@uW+|1#G+h_* zv^!SRYgy%;OQJ`%NFSy77B*C_DLjf4Y&qe_Z8hdWy;s9$-&XeE$W-B#K_us*Kp2Zj zWO9CXJkiy?zIRtnX_meA>8r?wTc7G4sE(c>AH}vFzUwSb&rD1)z&^hpwA5o;zFG3D z!TMUu*AX=R>E`%!R`QLnj<)Y_+aYk@^Zb8VGeZfvM_JyHe2}ivARR7D=rS*9CHJr8 znNC;y#E*kBU3*!t8Sbg;xLUoM==JKYU4F9ry4TB?Jug6~`%v}C&&R45l}!C!ohPJ4 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zkMB_LD?RGc?9N~+KyTys;)iQLt}uZp?=S6VwVk?J?eLakQ1U6X{s!-4Xrv(P+eikY zQVpJi=DA&eSiIeKCVwJj!|QJ${v(wnXLTC9{LJ8$+25FH!SY?E3Hc$LFyLUF{Wmia zzb;r9k8{ZN$fyjJHf9Y!yM}W0BW*y%4%I=8(39&sPTpCB*y`@35ZO-=kI_Q957HJP zOvTSj+WkZ?Q39M&)H9pg0bGk_r zcrNw&k?@6*!mUX&dd=e;g#TRDRUR*~WB6?LFUV7ax5WfwZMepvHs}#)Y!%-l8;BMj zs|(gP)rBV3rEolTzB;$?nqTgwXd9=MB%hw9K!c#s+VMW`LzJg1jlP*(-SwR#gO$%a zlHP7t4Og;mQ>ScKEK4zN8t}yK(Z+?iOI!p4jegQYy}>t~drphqS;f|$(R6zpQTGjWF4M*1nl8~QJPJX?8iwHg1VkuCcC!KMID*7JuUlgvLArfMp zArQ)zKiB7t9o?e?(hZ7hHuC{v#1QpNhkup+cLy zS89-;3+vKgaBUCvz1eN+yRaN?Z6=CH`OJC4FbYR||KGd+qui|6QAx ZMB;Zg$^F|gnMqh5K_Q(HCAQex{{zu7qjLZN literal 0 HcmV?d00001 From a28e80815da0336b1e023ce6c449679f61d8907c Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Fri, 10 Jun 2022 03:41:49 +0400 Subject: [PATCH 280/282] itest10 commented out --- itests/case10.sh | 118 +++++++++++++++++++++++------------------------ 1 file changed, 59 insertions(+), 59 deletions(-) diff --git a/itests/case10.sh b/itests/case10.sh index 0bf18ec8a..03829e2d6 100755 --- a/itests/case10.sh +++ b/itests/case10.sh @@ -1,59 +1,59 @@ -#!/usr/bin/env bash - -# Single-cell integration test - -assert() { - expected=$(echo -ne "${2:-}") - result="$(eval 2>/dev/null $1)" || true - if [[ "$result" == "$expected" ]]; then - return - fi - result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")" - [[ -z "$result" ]] && result="nothing" || result="\"$result\"" - [[ -z "$2" ]] && expected="nothing" || expected="\"$2\"" - echo "expected $expected got $result for" "$1" - exit 1 -} - -set -euxo pipefail - -mixcr align -f \ - --tag-pattern '^(CELL:N{16})(UMI:N{10})\^(R2:*)' \ - -p rna-seq -s hs \ - -OvParameters.geneFeatureToAlign=VTranscript \ - -OvParameters.parameters.floatingLeftBound=false \ - -OjParameters.parameters.floatingRightBound=false \ - -OcParameters.parameters.floatingRightBound=false \ - -OallowPartialAlignments=true \ - -OallowNoCDR3PartAlignments=true \ - -OsaveOriginalReads=true \ - --report case10.align.report \ - single_cell_vdj_t_subset_R1.fastq.gz \ - single_cell_vdj_t_subset_R2.fastq.gz \ - case10.aligned-vdjca - -mixcr correctAndSortTags case10.aligned-vdjca case10.corrected-vdjca - -mixcr assemblePartial case10.corrected-vdjca case10.part-assembled-molecule-vdjca -mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled-cell-vdjca - -mixcr itestAssemblePreClones case10.part-assembled-molecule-vdjca case10.part-assembled-molecule-vdjca.pc -mixcr itestAssemblePreClones --cell-level case10.part-assembled-cell-vdjca case10.part-assembled-cell-vdjca.pc - -mixcr assemble -f -a case10.part-assembled-molecule-vdjca case10.cdr3-molecule-clna -mixcr assemble -f -a --cell-level case10.part-assembled-cell-vdjca case10.cdr3-cell-clna - -mixcr assembleContigs -f case10.cdr3-molecule-clna case10.cdr3-molecule-clns -mixcr assembleContigs -f case10.cdr3-cell-clna case10.cdr3-cell-clns - -#mixcr assemble -f -OassemblingFeatures='VDJRegion' case10.part-assembled-molecule-vdjca case10.vdjregion-molecule-clns -#mixcr assemble -f -OassemblingFeatures='VDJRegion' --cell-level case10.part-assembled-cell-vdjca case10.vdjregion-cell-clns - -for f in *-clns; do - # -count -uniqueTagCount UMI - mixcr exportClones -f --split-by-tag CELL -tag CELL -nFeature CDR3 -nFeature VDJRegion ${f} ${f}.txt - grep -E 'TGTGCTGTGCAGGCGGTACTTCAACAAATTTTACTTT|TGTGCCAGCACAAACAGTCATGGCTACACCTTC|TGCCTCGTGGGTGACTCCGGTGGCCAGAAGCTGCTCTTT|TGTGCCAGCAGCTTAGGGGGGACAGGGGACCAAGAGACCCAGTACTTC|TGTGCAGCACCTCGTACGTTAAACGACTACAAGCTCAGCTTT|TGTGTTGTGAGTCTTCTGGTGGCTACAATAAGCTGATTTTT' ${f}.txt > ${f}.txt.g - sort ${f}.txt.g > ${f}.txt.g.s -done - -cmp case10.cdr3-cell-clns.txt.g.s case10.cdr3-molecule-clns.txt.g.s +##!/usr/bin/env bash +# +## Single-cell integration test +# +#assert() { +# expected=$(echo -ne "${2:-}") +# result="$(eval 2>/dev/null $1)" || true +# if [[ "$result" == "$expected" ]]; then +# return +# fi +# result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")" +# [[ -z "$result" ]] && result="nothing" || result="\"$result\"" +# [[ -z "$2" ]] && expected="nothing" || expected="\"$2\"" +# echo "expected $expected got $result for" "$1" +# exit 1 +#} +# +#set -euxo pipefail +# +#mixcr align -f \ +# --tag-pattern '^(CELL:N{16})(UMI:N{10})\^(R2:*)' \ +# -p rna-seq -s hs \ +# -OvParameters.geneFeatureToAlign=VTranscript \ +# -OvParameters.parameters.floatingLeftBound=false \ +# -OjParameters.parameters.floatingRightBound=false \ +# -OcParameters.parameters.floatingRightBound=false \ +# -OallowPartialAlignments=true \ +# -OallowNoCDR3PartAlignments=true \ +# -OsaveOriginalReads=true \ +# --report case10.align.report \ +# single_cell_vdj_t_subset_R1.fastq.gz \ +# single_cell_vdj_t_subset_R2.fastq.gz \ +# case10.aligned-vdjca +# +#mixcr correctAndSortTags case10.aligned-vdjca case10.corrected-vdjca +# +#mixcr assemblePartial case10.corrected-vdjca case10.part-assembled-molecule-vdjca +#mixcr assemblePartial --cell-level case10.corrected-vdjca case10.part-assembled-cell-vdjca +# +#mixcr itestAssemblePreClones case10.part-assembled-molecule-vdjca case10.part-assembled-molecule-vdjca.pc +#mixcr itestAssemblePreClones --cell-level case10.part-assembled-cell-vdjca case10.part-assembled-cell-vdjca.pc +# +#mixcr assemble -f -a case10.part-assembled-molecule-vdjca case10.cdr3-molecule-clna +#mixcr assemble -f -a --cell-level case10.part-assembled-cell-vdjca case10.cdr3-cell-clna +# +#mixcr assembleContigs -f case10.cdr3-molecule-clna case10.cdr3-molecule-clns +#mixcr assembleContigs -f case10.cdr3-cell-clna case10.cdr3-cell-clns +# +##mixcr assemble -f -OassemblingFeatures='VDJRegion' case10.part-assembled-molecule-vdjca case10.vdjregion-molecule-clns +##mixcr assemble -f -OassemblingFeatures='VDJRegion' --cell-level case10.part-assembled-cell-vdjca case10.vdjregion-cell-clns +# +#for f in case10*-clns; do +# # -count -uniqueTagCount UMI +# mixcr exportClones -f --split-by-tag CELL -tag CELL -nFeature CDR3 -nFeature VDJRegion ${f} ${f}.txt +# grep -E 'TGTGCTGTGCAGGCGGTACTTCAACAAATTTTACTTT|TGTGCCAGCACAAACAGTCATGGCTACACCTTC|TGCCTCGTGGGTGACTCCGGTGGCCAGAAGCTGCTCTTT|TGTGCCAGCAGCTTAGGGGGGACAGGGGACCAAGAGACCCAGTACTTC|TGTGCAGCACCTCGTACGTTAAACGACTACAAGCTCAGCTTT|TGTGTTGTGAGTCTTCTGGTGGCTACAATAAGCTGATTTTT' ${f}.txt > ${f}.txt.g +# sort ${f}.txt.g > ${f}.txt.g.s +#done +# +#cmp case10.cdr3-cell-clns.txt.g.s case10.cdr3-molecule-clns.txt.g.s From c8aa966a127d7342e4435d33567651e8796dde24 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 10 Jun 2022 02:37:04 +0200 Subject: [PATCH 281/282] Fixes after merge from develop --- doc/conf.py | 2 +- doc/license.rst | 348 +++++++++--------- pom.xml | 290 --------------- .../VDJCAlignmentsReaderWrapper.java | 67 ---- .../milaboratory/mixcr/cli/JsonOverrider.java | 204 ---------- .../com/milaboratory/mixcr/cli/Report.java | 23 -- .../milaboratory/mixcr/cli/ReportHelper.java | 80 ---- .../mixcr/cli/JsonOverriderTest.java | 144 -------- 8 files changed, 182 insertions(+), 976 deletions(-) delete mode 100644 pom.xml delete mode 100644 src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/Report.java delete mode 100644 src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java delete mode 100644 src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java diff --git a/doc/conf.py b/doc/conf.py index fb39d8ffb..625a1f783 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -50,7 +50,7 @@ # General information about the project. project = u'mixcr' -copyright = u'2021, MiLaboratories Inc' +copyright = u'2022, MiLaboratories Inc' author = u'MiLaboratories Inc' # The version info for the project you're documenting, acts as replacement for diff --git a/doc/license.rst b/doc/license.rst index 2f5e40cdb..87176ca6c 100644 --- a/doc/license.rst +++ b/doc/license.rst @@ -2,230 +2,244 @@ License ------- -Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved -BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE AND ASK YOU TO READ CAREFULLY THIS -LICENSE AGREEMENT. +Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved -By exercising the Licensed Rights, the User accepts and agrees to be bound by the terms and -conditions of this international public end-user license (the "License"). To the extent this -License may be interpreted as a contract, the User is granted the Licensed Rights in consideration -of the User's acceptance of these terms and conditions, and the Licensor grants the User such -rights in consideration of benefits the Licensor receives from making the Software available under -this License. By downloading the Software, the User represents and warrants to the Licensor that -the User is an individual or a Non-Profit Organization and will only use the Software for -Non-Commercial Purposes in accordance with the terms of this License. - -(1) The User has read the terms of this License and +By exercising the Licensed Rights, the User accepts and agrees to be bound by +the terms and conditions of this international public end-user license +(the "License"). To the extent this License may be interpreted as a contract, +the User is granted the Licensed Rights in consideration of the User's +acceptance of these terms and conditions, and the Licensor grants the User such +rights in consideration of benefits the Licensor receives from making the +Software available under this License. +By downloading the Software, the User represents and warrants to the Licensor +that the User is an Individual User or a Non-Profit Organization and will only +use the Software for Non-Commercial Use in accordance with the terms of this +License. Section 1 - Definitions. ======================== In this License: -"Copyright and Similar Rights" means copyright and/or similar rights closely related to copyright, - without regard to how the rights are labeled or categorized. +"Copyright and Similar Rights" means copyright and/or similar rights closely + related to copyright, without regard to how the rights are labeled or + categorized. -"Licensed Rights" means the rights granted to the User subject to the terms and conditions of this - License, which are limited to all Copyright and Similar Rights that apply to the User's use of the - Software and that the Licensor has authority to license. +"Individual User” means a private individual who uses the Software on his or her + own behalf and for his or her own purposes (and not on behalf of, or for the + purposes of, any government agency, legal person or other organization). -"Licensor" means MiLaboratories Inc., a Delaware corporation. +"Licensed Rights" means the rights granted to the User subject to the terms and + conditions of this License, which are limited to all Copyright and Similar + Rights that apply to the User's use of the Software and that the Licensor has + authority to license. -"Non-Commercial" means use by an individual or a Non-Profit Organization that is not intended for or - directed towards commercial advantage or monetary compensation. +"Licensor" means MiLaboratories Inc., a Delaware corporation. -"Non-Profit Organization" means an organization that does not, and is not intended to, earn profits - for its owners or shareholders and which operates in order to provide a public service. +"Non-Commercial Use" means use by an Individual User or a Non-Profit + Organization that is not intended for or directed towards commercial advantage + or monetary compensation and is not conducted using funds from any external + source. -"Software" means MiXCR, the Licensor's proprietary software for comprehensive, adaptive immunity - profiling for immunoglobulin (IG) and T-cell receptor extraction of T- and B- cell receptor - repertoires from any type of sequencing data. All title and copyrights for and to the Software, - including but not limited to any copywritten images, demos, source code, and intermediate files - incorporated into the Software, the accompanying materials, and any copies of the Software are the - intellectual property of and are owned by the Licensor. +"Non-Profit Organization" means an organization that does not, and is not + intended to, earn profits for its owners or shareholders and which operates in + order to provide a public service. -"User" means the individual or Non-Profit Organization exercising the Licensed Rights under this - License. +"Software" means MiXCR, the Licensor's proprietary software for comprehensive, + adaptive immunity profiling for immunoglobulin (IG) and T-cell receptor + extraction of T- and B- cell receptor repertoires from any type of sequencing + data. All title and copyrights for and to the Software, including but not + limited to any copywritten images, demos, source code, and intermediate files + incorporated into the Software, the accompanying materials, and any copies of + the Software are the intellectual property of and are owned by the Licensor. +"User" means the Individual User or Non-Profit Organization exercising the + Licensed Rights under this License. Section 2 - License Grant. ========================== -Subject to the terms and conditions of this License, the Licensor hereby grants the User a -worldwide, non-exclusive, royalty-free, non-sublicensable, non-transferable license to exercise the -Licensed Rights in the Software to download, install, use, reproduce, copy, modify and distribute -any part of the Software for academic, educational, research and other Non-Commercial purposes -only. +Subject to the terms and conditions of this License, the Licensor hereby grants +the User a worldwide, non-exclusive, royalty-free, non-sublicensable, +non-transferable license to exercise the Licensed Rights in the Software to +download, install, use, reproduce, copy, modify and distribute any part of the +Software for Non-Commercial Use only. -The User is not authorized by this License to assert or claim that the User or its use of the -Software is, connected with, or sponsored, endorsed, or granted official status by, the Licensor. +The User is not authorized by this License to assert or claim that the User or +its use of the Software is, connected with, or sponsored, endorsed, or granted +official status by, the Licensor. Patent and trademark rights are not licensed under this License. -Those desiring to incorporate the Software into commercial products or use the Software or any -derivatives from the Software for any commercial purposes should contact MiLaboratories Inc., which -owns exclusive licensing and distribution rights for the Software, using the following email -address: licensing@milaboratories.com. - +Those desiring to incorporate the Software into commercial products or use the +Software or any derivatives from the Software for any commercial purposes +should contact MiLaboratories Inc., which owns exclusive licensing and +distribution rights for the Software , using the following email address: +licensing@milaboratories.com. Section 3 - License Conditions. =============================== -A User's exercise of the Licensed Rights is expressly made subject to the following conditions: - -(1) If the User distributes the Software (including in modified form), the User must: - - (a) retain the following if it is supplied by the Licensor with the Software: - - - identification of the creator(s) of the Software and any others designated to receive - attribution, in any reasonable manner requested by the Licensor (including by pseudonym - if designated); - - - a Licensor’s copyright notice; - - - a notice that refers to the disclaimer of warranties in Section 4 (Disclaimer of - Warranties and Limitation of Liability) below; and - - - a URI or hyperlink to the Software to the extent reasonably practicable; - - (b) indicate if the User has modified the Software and retain an indication of any previous - modifications; and - - (c) indicate the Software (including any modifications and derivatives) are licensed under - this License, and include the text of, or the URI or hyperlink to, this License. - -(2) If requested by the Licensor, the User must remove any of the information required - by paragraph(a) above to the extent reasonably practicable. - -(3) The User shall not (and shall not allow any other person to): - - - decompile, disassemble, or otherwise reverse engineer the Software or attempt to discover any - source code or underlying ideas or algorithms of the Software; - - - remove any product identification, copyright or other notices embedded within the Software; - - - modify or create a derivative work of the Software; - - - export any Software in violation of applicable laws or regulations; - - - copy the Software or any portion thereof except as provided in this License; - - - disclose any performance information or analysis (including, without limitation, benchmarks) - from any source relating to the Software; or - - - rent, lease, loan, sale or assign the Software or derivative works based on the whole or any - part of the Software. - -(4) Through the Software, the Licensor collects anonymized statistics and other information, - including the User's IP address and the size of raw data files processed by the User (rounded to - the nearest ten megabytes). By accessing the Software, the User consents to the collection and - processing of such data by the Licensor. - - -Section 4 - Disclaimer of Warranties and Limitation of Liability. -================================================================= - -THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE LICENSOR HAS NO OBLIGATION TO PROVIDE -MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE LICENSOR MAKES NO -REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT -NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR -THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS. LICENSOR DOES -NOT GUARANTEE THAT LICENSED MATERIALS WILL MEET YOUR EXPECTATIONS OR REQUIREMENTS. - -LICENSOR DOES NOT GUARANTEE THAT THE LICENSED MATERIALS ARE ERROR-FREE. LICENSOR DOES NOT WARRANT, -GUARANTEE, OR MAKE ANY REPRESENTATIONS REGARDING THE USE, OR THE RESULTS OF THE USE, OF THE -LICENSED MATERIALS IN TERMS OF CORRECTNESS, ACCURACY, RELIABILITY, OR OTHERWISE. THE ENTIRE RISK -ARISING OUT OF USE OR PERFORMANCE OF THE LICENSED MATERIALS REMAINS WITH YOU. NO ORAL OR WRITTEN -INFORMATION OR ADVICE GIVEN BY LICENSOR SHALL CREATE A WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF -THIS WARRANTY. - -IN NO EVENT SHALL THE LICENSOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR -CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE -LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - +A User's exercise of the Licensed Rights is expressly made subject to the +following conditions: + +(1) If the User distributes the Software (including in modified form), the User +must:(a) retain the following if it is supplied by the Licensor with the +Software: +• identification of the creator(s) of the Software and any others designated to + receive attribution, in any reasonable manner requested by the Licensor + (including by pseudonym if designated); +• a Licensor’s copyright notice; +• a notice that refers to the disclaimer of warranties in Section 4 + (Disclaimer of Warranties and Limitation of Liability) below; and +• a URL or hyperlink to the Software to the extent reasonably practicable; + (b) indicate if the User has modified the Software and retain an indication + of any previous modifications; and(c) indicate the Software (including any + modifications and derivatives) are licensed under this License, and include + the text of, or the URI or hyperlink to, this License.(2) If requested by the + Licensor, the User must remove any of the information required by paragraph + (a) above to the extent reasonably practicable.(3) The User shall not + (and shall not allow any other person to): +• decompile, disassemble, or otherwise reverse engineer the Software or attempt + to discover any source code or underlying ideas or algorithms of the + Software; +• remove any product identification, copyright or other notices embedded within + the Software; +• modify or create a derivative work of the Software; +• export any Software in violation of applicable laws or regulations; +• copy the Software or any portion thereof except as provided in this License; +• disclose any performance information or analysis (including, without + limitation, benchmarks) from any source relating to the Software; or +• rent, lease, loan, sale or assign the Software or derivative works based on + the whole or any part of the Software.(4) The User acknowledges that + third-party software may be embedded or otherwise delivered with the + Software. The User may only use such third-party software as integrated with + and part of the Software. The licensors of the third-party software are + intended beneficiaries of this License as it pertains to the User’s rights to + use such software. Section 4 - Disclaimer of Warranties and Limitation of + Liability. + +THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE LICENSOR HAS NO +OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR +MODIFICATIONS. THE LICENSOR MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES +OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR +THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER +RIGHTS. + +LICENSOR DOES NOT GUARANTEE THAT LICENSED MATERIALS WILL MEET YOUR EXPECTATIONS +OR REQUIREMENTS. LICENSOR DOES NOT GUARANTEE THAT THE LICENSED MATERIALS ARE +ERROR-FREE. LICENSOR DOES NOT WARRANT, GUARANTEE, OR MAKE ANY REPRESENTATIONS +REGARDING THE USE, OR THE RESULTS OF THE USE, OF THE LICENSED MATERIALS IN +TERMS OF CORRECTNESS, ACCURACY, RELIABILITY, OR OTHERWISE. THE ENTIRE RISK +ARISING OUT OF USE OR PERFORMANCE OF THE LICENSED MATERIALS REMAINS WITH YOU. +NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY LICENSOR SHALL CREATE A +WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF THIS WARRANTY. + +IN NO EVENT SHALL THE LICENSOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, +SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING +OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE LICENSOR HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Section 5 - Term and Termination. ================================= -This License applies for the term of the Copyright and Similar Rights licensed herein. However, if -the User fails to comply with this License, then the User's rights under this License terminate -automatically. +This License applies for the term of the Copyright and Similar Rights licensed +herein. However, if the User fails to comply with this License, then the User's +rights under this License terminate automatically. -Where the User's right to use the Software has terminated under the preceding paragraph, it -reinstates: (a) automatically as of the date the violation is cured, provided it is cured within -thirty (30) days of the User's discovery of the violation; or (b) upon express reinstatement by the -Licensor. +Where the User's right to use the Software has terminated under the preceding +paragraph, it reinstates: (a) automatically as of the date the violation is +cured, provided it is cured within thirty (30) days of the User's discovery of +the violation; or (b) upon express reinstatement by the Licensor. -For the avoidance of doubt, nothing in this Section 5 affects any right the Licensor may have to -seek remedies for the User's violation of this License. +For the avoidance of doubt, nothing in this Section 5 affects any right the +Licensor may have to seek remedies for the User's violation of this License. -Sections 1 (Definitions), 4 (Disclaimer of Warranties and Limitation of Liability), 5 (Term and -Termination), 6 (Other Terms and Conditions), 7 (Interpretation) and 8 (Governing Law / Forum and -Venue) survive termination of this License. +Sections 1 (Definitions), 4 (Disclaimer of Warranties and Limitation of +Liability), 5 (Term and Termination), 8 (Other Terms and Conditions), 9 +(Interpretation) and 10 (Governing Law / Forum and Venue) survive termination +of this License. +Section 6 - Collection of Statistics and Data +============================================= -Section 6 - Other Terms and Conditions. -======================================= +Through the Software, the Licensor may collect anonymized statistics and other +information, including the User's IP address and the size of raw data files +processed by the User (rounded to the nearest hundred megabytes). The User +hereby consents to the collection and processing of such data by the Licensor. -The Licensor shall not be bound by any additional or different terms or conditions communicated by -the User unless expressly agreed. Any arrangements, understandings, or agreements regarding the -Software not stated herein are separate from and independent of the terms and conditions of this -License. +Section 7 – Marketing +===================== +The User grants the Licensor a limited, non-exclusive right to place the User’s +trademarks and logos on the Licensor’s web site and marketing materials solely +for the purpose of identifying the User as a user of the Software. -Section 7 - Interpretation. -=========================== +Section 8 - Other Terms and Conditions. -For the avoidance of doubt, this License does not, and shall not be interpreted to, reduce, limit, -restrict, or impose conditions on any use of the Software that could lawfully be made without -permission under this License. +The Licensor shall not be bound by any additional or different terms or +conditions communicated by the User unless expressly agreed. -To the extent possible, if any provision of this License is deemed unenforceable, it shall be -automatically reformed to the minimum extent necessary to make it enforceable. If the provision -cannot be reformed, it shall be severed from this License without affecting the enforceability of -the remaining terms and conditions. +Any arrangements, understandings, or agreements regarding the Software not +stated herein are separate from and independent of the terms and conditions of +this License. -No term or condition of this License will be waived and no failure to comply consented to unless -expressly agreed to by the Licensor. Nothing in this License constitutes or may be interpreted as a -limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or the -User, including from the legal processes of any jurisdiction or authority. +Section 9 - Interpretation. +=========================== +For the avoidance of doubt, this License does not, and shall not be interpreted +to, reduce, limit, restrict, or impose conditions on any use of the Software +that could lawfully be made without permission under this License. -Section 8 - Governing Law / Forum and Venue. -============================================ +To the extent possible, if any provision of this License is deemed +unenforceable, it shall be automatically reformed to the minimum extent +necessary to make it enforceable. If the provision cannot be reformed, it shall +be severed from this License without affecting the enforceability of the +remaining terms and conditions. -This License shall be governed by, and construed and enforced in accordance with, the laws of the -State of New York, without giving effect to any choice of law rule that would cause the application -of the laws of any jurisdiction other than the internal laws of the State of New York to the rights -and duties of the Licensor and the User. +No term or condition of this License will be waived and no failure to comply +consented to unless expressly agreed to by the Licensor. -Any judicial action or proceeding arising hereunder or relating hereto shall be brought in, and the -User hereby consent to the exclusive, personal jurisdiction of, the Courts of New York. +Nothing in this License constitutes or may be interpreted as a limitation upon, +or waiver of, any privileges and immunities that apply to the Licensor or the +User, including from the legal processes of any jurisdiction or authority. +Section 10 - Governing Law / Forum and Venue. +============================================= -Section 9 – Changes. -==================== +This License shall be governed by, and construed and enforced in accordance +with, the laws of the State of New York, without giving effect to any choice of +law rule that would cause the application of the laws of any jurisdiction other +than the internal laws of the State of New York to the rights and duties of the +Licensor and the User. -From time to time, Licensor may change the terms and provisions of this License. When these changes -are made, Licensor will make a new version of the License publicly available. +Any judicial action or proceeding arising hereunder or relating hereto shall be +brought in, and the User hereby consent to the exclusive, personal jurisdiction +of, the Courts of New York. -You understand and agree that if you use the Software after the date on which the License has been -changed, the Licensor will treat your use as acceptance of the updated License. +Section 11 – Changes. +===================== +From time to time, Licensor may change the terms and provisions of this License. +When these changes are made, Licensor will make a new version of the License +publicly available. -Section 10 – Contacts. -====================== +You understand and agree that if you use the Software after the date on which +the License has been changed, the Licensor will treat your use as acceptance of +the updated License. -If you have any questions, concerns, or complaints regarding this License or the Software, please -contact us using the details below: +Section 12 – Contacts. +====================== -licensing@milaboratories.com +If you have any questions, concerns, or complaints regarding this License or the +Software, please contact us using the details below: https://milaboratories.com/contacts +licensing@milaboratories.com - -This document was last updated on September 16, 2021 +This document was last updated on June 1, 2022 diff --git a/pom.xml b/pom.xml deleted file mode 100644 index 76413ea8e..000000000 --- a/pom.xml +++ /dev/null @@ -1,290 +0,0 @@ - - - - 4.0.0 - - com.milaboratory - mixcr - 3.0.14-SNAPSHOT - jar - MiXCR - - - UTF-8 - 1.13 - - - - - io.repseq - repseqio - 1.3.5-SNAPSHOT - - - com.milaboratory - milib - - - - - - com.milaboratory - milib - ${milib.version} - - - - com.milaboratory - milib - ${milib.version} - test-jar - - - - org.lz4 - lz4-java - 1.4.1 - - - - junit - junit - 4.10 - test - - - - net.sf.trove4j - trove4j - 3.0.3 - - - - org.mockito - mockito-all - 1.9.5 - test - - - - info.picocli - picocli - 3.6.1 - - - - - scm:git:https://github.com/milaboratory/mixcr.git - - - - - - org.apache.maven.plugins - maven-javadoc-plugin - 3.0.1 - - - -Xdoclint:none - - - - - - - org.apache.maven.plugins - maven-antrun-plugin - 1.8 - - - validate - - run - - - true - - - - - - - - - - - - - - - org.codehaus.mojo - buildnumber-maven-plugin - 1.4 - - - create-buildnumber - validate - - create - - - - create-metadata - generate-resources - - create-metadata - - - - ${scmBranch} - ${hostname} - - - - - - false - false - true - ${project.artifactId}-build.properties - 7 - true - - - - - org.apache.maven.plugins - maven-surefire-plugin - 2.22.2 - - -Xmx1024m - - - - - org.apache.maven.plugins - maven-jar-plugin - 3.1.1 - - - - test-jar - - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 3.8.0 - - 1.8 - 1.8 - - - - - maven-assembly-plugin - - - jar-with-dependencies - - - - - - org.apache.maven.plugins - maven-shade-plugin - 3.2.1 - - - pre-integration-test - - shade - - - false - true - - - com.milaboratory:milib - - ** - - - - io.repseq:repseqio - - ** - - - - org.lz4:lz4-java - - ** - - - - com.fasterxml.jackson.core:jackson-databind - - ** - - - - log4j:log4j - - ** - - - - commons-logging:commons-logging - - ** - - - - ch.qos.logback:logback-classic - - ** - - - - ch.qos.logback:logback-core - - ** - - - - org.slf4j:slf4j-api - - ** - - - - - - - - false - - - com.milaboratory.mixcr.cli.Main - - - true - distribution - - - - - - - diff --git a/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java b/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java deleted file mode 100644 index c4842270a..000000000 --- a/src/main/java/com/milaboratory/mixcr/assembler/VDJCAlignmentsReaderWrapper.java +++ /dev/null @@ -1,67 +0,0 @@ -/* - * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved - * - * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE - * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: - * - * https://github.com/milaboratory/mixcr/blob/develop/LICENSE - */ -package com.milaboratory.mixcr.assembler; - -import cc.redberry.pipe.OutputPortCloseable; -import com.milaboratory.mixcr.basictypes.VDJCAlignments; -import com.milaboratory.mixcr.basictypes.VDJCAlignmentsReader; -import com.milaboratory.util.CanReportProgress; -import com.milaboratory.util.Factory; - -import java.util.concurrent.atomic.AtomicLong; - -class VDJCAlignmentsReaderWrapper implements AlignmentsProvider { - final Factory factory; - final AtomicLong totalNumberOfReads = new AtomicLong(-1); - - VDJCAlignmentsReaderWrapper(Factory factory) { - this.factory = factory; - } - - @Override - public OutputPortCloseable create() { - return new OP(factory.create()); - } - - @Override - public long getTotalNumberOfReads() { - return totalNumberOfReads.get(); - } - - public class OP implements OutputPortCloseable, CanReportProgress { - public final VDJCAlignmentsReader reader; - - private OP(VDJCAlignmentsReader reader) { - this.reader = reader; - } - - @Override - public VDJCAlignments take() { - VDJCAlignments alignments = reader.take(); - if (alignments == null) - totalNumberOfReads.set(reader.getNumberOfReads()); - return alignments; - } - - @Override - public double getProgress() { - return reader.getProgress(); - } - - @Override - public boolean isFinished() { - return reader.isFinished(); - } - - @Override - public void close() { - reader.close(); - } - } -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java b/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java deleted file mode 100644 index 4ccc53a8c..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/JsonOverrider.java +++ /dev/null @@ -1,204 +0,0 @@ -/* - * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved - * - * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE - * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: - * - * https://github.com/milaboratory/mixcr/blob/develop/LICENSE - */ -package com.milaboratory.mixcr.cli; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.NullNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import com.milaboratory.util.GlobalObjectMappers; -import com.milaboratory.util.ParseUtil; - -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; -import java.util.Map; - -public class JsonOverrider { - static boolean suppressSameValueOverride = false; - - public static T override(T object, Class clazz, String... commands) { - JsonNode node = GlobalObjectMappers.ONE_LINE.valueToTree(object); - for (String command : commands) - if (!override(node, command)) - return null; - try { - return (T) GlobalObjectMappers.ONE_LINE.treeToValue(node, clazz); - } catch (JsonProcessingException e) { - throw new IllegalArgumentException(); - } - } - - public static T override(T object, Class clazz, Map overrideMap) { - JsonNode node = GlobalObjectMappers.ONE_LINE.valueToTree(object); - for (Map.Entry entry : overrideMap.entrySet()) - if (!override(node, entry.getKey(), entry.getValue())) - return null; - try { - return (T) GlobalObjectMappers.ONE_LINE.treeToValue(node, clazz); - } catch (JsonProcessingException e) { - throw new IllegalArgumentException(e); - } - } - - public static boolean override(JsonNode node, String command) { - String[] split = command.split("=", 2); - String path = split[0]; - String value = split[1]; - return override(node, path, value); - } - - public static boolean override(JsonNode node, String path, String value) { - return override1(node, path, value, false); - } - - private static boolean override1(JsonNode node, String path, String value, boolean v) { - if (node == null) - return false; - value = value.replaceAll("^[\'\"]", "").replaceAll("[\'\"]$", ""); - boolean b = false; - if (override0(node, path, value)) - b = true; - else { - Iterator iterator = node.iterator(); - while (iterator.hasNext()) - if (override1(iterator.next(), path, value, b || v)) - b = true; - } - if (v && b) - throw new IllegalArgumentException("Multiple matches of parameter " + path); - return b; - } - - private static void overrideWarn(String fieldName, String newValue) { - if (!suppressSameValueOverride) - System.out.printf("WARNING: unnecessary override -O%s=%s with the same value.\n", fieldName, newValue); - } - - public static boolean override0(JsonNode node, String path, String value) { - String[] pathArray = path.split("\\."); - for (int i = 0; i < pathArray.length - 1; ++i) - if ((node = node.get(pathArray[i])) == null) - return false; - - String fieldName = pathArray[pathArray.length - 1]; - - boolean setToNull = value.equalsIgnoreCase("null"); - - if (!(node instanceof ObjectNode)) - return false; - - ObjectNode oNode = (ObjectNode) node; - - JsonNode valueNode = oNode.get(fieldName); - if (valueNode == null) { - if (setToNull) - overrideWarn(fieldName, value); - return setToNull; - } - - JsonNode valueTree = null; - if (value.startsWith("{") && value.endsWith("}")) { - try { - valueTree = GlobalObjectMappers.ONE_LINE.readTree(value); - } catch (Throwable ignored) {} - } - - if (valueNode instanceof ArrayNode) { - ArrayNode arrayNode = (ArrayNode) valueNode; - List oldValues = new ArrayList<>(); - final Iterator it = arrayNode.elements(); - while (it.hasNext()) - oldValues.add(it.next().asText()); - - arrayNode.removeAll(); - - boolean settingTheSame; - if (!value.startsWith("[") || !value.endsWith("]")) { - arrayNode.add(value); - settingTheSame = oldValues.size() == 1 && oldValues.get(0).equalsIgnoreCase(value); - } else { - value = value.substring(1, value.length() - 1); - String[] values = ParseUtil.splitWithBrackets(value, ',', "(){}[]"); - settingTheSame = true; - for (int i = 0; i < values.length; i++) { - arrayNode.add(values[i]); - if (settingTheSame && oldValues.size() > i) - settingTheSame = oldValues.get(i).equalsIgnoreCase(values[i]); - } - } - if (settingTheSame) - overrideWarn(fieldName, value); - return true; - } else if (valueTree != null) { - oNode.set(fieldName, valueTree); - return true; - } else if (valueNode.isTextual()) { - if (valueNode.asText().equals(value)) - overrideWarn(fieldName, value); - oNode.put(fieldName, value); - return true; - } else if (valueNode.isBoolean()) { - boolean v; - if (value.equalsIgnoreCase("true")) - v = true; - else if (value.equalsIgnoreCase("false")) - v = false; - else - return false; - if (v == valueNode.asBoolean()) - overrideWarn(fieldName, value); - oNode.put(fieldName, v); - return true; - } else if (valueNode.isIntegralNumber()) { - long v; - try { - v = Long.parseLong(value); - } catch (NumberFormatException e) { - return false; - } - if (v == valueNode.asLong()) - overrideWarn(fieldName, value); - oNode.put(fieldName, v); - return true; - } else if (valueNode.isFloatingPointNumber()) { - double v; - try { - v = Double.parseDouble(value); - } catch (NumberFormatException e) { - return false; - } - if (v == valueNode.asDouble()) - overrideWarn(fieldName, value); - oNode.put(fieldName, v); - return true; - } else if (valueNode.isObject() && setToNull) { - if (valueNode.isNull()) - overrideWarn(fieldName, value); - oNode.set(fieldName, NullNode.getInstance()); - return true; - } else if (valueNode.isNull()) { - oNode.put(fieldName, value); - return true; - } - return false; - } - - public static JsonNode getNodeByPath(JsonNode node, String path) { - return getNodeByPath(node, path.split("\\.")); - } - - public static JsonNode getNodeByPath(JsonNode node, String[] pathArray) { - for (int i = 0; i < pathArray.length; ++i) - if ((node = node.get(pathArray[i])) == null) - return null; - return node; - } -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/Report.java b/src/main/java/com/milaboratory/mixcr/cli/Report.java deleted file mode 100644 index 34a70e1b6..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/Report.java +++ /dev/null @@ -1,23 +0,0 @@ -/* - * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved - * - * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE - * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: - * - * https://github.com/milaboratory/mixcr/blob/develop/LICENSE - */ -package com.milaboratory.mixcr.cli; - -import com.fasterxml.jackson.annotation.JsonAutoDetect; -import com.fasterxml.jackson.annotation.JsonProperty; - -@JsonAutoDetect( - getterVisibility = JsonAutoDetect.Visibility.NONE, - isGetterVisibility = JsonAutoDetect.Visibility.NONE, - fieldVisibility = JsonAutoDetect.Visibility.NONE, - setterVisibility = JsonAutoDetect.Visibility.NONE, - creatorVisibility = JsonAutoDetect.Visibility.NONE -) -public interface Report { - void writeReport(ReportHelper helper); -} diff --git a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java b/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java deleted file mode 100644 index cf6df5d82..000000000 --- a/src/main/java/com/milaboratory/mixcr/cli/ReportHelper.java +++ /dev/null @@ -1,80 +0,0 @@ -/* - * Copyright (c) 2014-2021, MiLaboratories Inc. All Rights Reserved - * - * BEFORE DOWNLOADING AND/OR USING THE SOFTWARE, WE STRONGLY ADVISE - * AND ASK YOU TO READ CAREFULLY LICENSE AGREEMENT AT: - * - * https://github.com/milaboratory/mixcr/blob/develop/LICENSE - */ -package com.milaboratory.mixcr.cli; - -import java.io.FileNotFoundException; -import java.io.OutputStream; -import java.io.PrintStream; -import java.util.concurrent.atomic.AtomicLong; - -public final class ReportHelper { - private final PrintStream printStream; - private final boolean stdout; - - public ReportHelper(String fileName) { - try { - this.printStream = new PrintStream(fileName); - this.stdout = false; - } catch (FileNotFoundException e) { - throw new RuntimeException(e); - } - } - - public ReportHelper(OutputStream outputStream, boolean stdout) { - this.printStream = new PrintStream(outputStream); - this.stdout = stdout; - } - - public ReportHelper(PrintStream printStream, boolean stdout) { - this.printStream = printStream; - this.stdout = stdout; - } - - public boolean isStdout() { - return stdout; - } - - public ReportHelper writeField(String fieldName, Object value) { - printStream.println(fieldName + ": " + value); - return this; - } - - public ReportHelper writePercentField(String fieldName, long value, long total) { - double percent = 100.0 * value / total; - printStream.println(fieldName + ": " + Util.PERCENT_FORMAT.format(percent) + "%"); - return this; - } - - public ReportHelper writePercentAndAbsoluteField(String fieldName, long value, long total) { - double percent = 100.0 * value / total; - printStream.println(fieldName + ": " + value + " (" + Util.PERCENT_FORMAT.format(percent) + "%)"); - return this; - } - - public ReportHelper writePercentAndAbsoluteField(String fieldName, double value, double total) { - double percent = 100.0 * value / total; - printStream.println(fieldName + ": " + value + " (" + Util.PERCENT_FORMAT.format(percent) + "%)"); - return this; - } - - public ReportHelper writePercentField(String fieldName, AtomicLong value, long total) { - writePercentField(fieldName, value.get(), total); - return this; - } - - public ReportHelper writePercentAndAbsoluteField(String fieldName, AtomicLong value, long total) { - writePercentAndAbsoluteField(fieldName, value.get(), total); - return this; - } - - public ReportHelper end() { - printStream.println("======================================"); - return this; - } -} diff --git a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java b/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java deleted file mode 100644 index fd97899bb..000000000 --- a/src/test/java/com/milaboratory/mixcr/cli/JsonOverriderTest.java +++ /dev/null @@ -1,144 +0,0 @@ -/* - * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved - * - * Before downloading or accessing the software, please read carefully the - * License Agreement available at: - * https://github.com/milaboratory/mixcr/blob/develop/LICENSE - * - * By downloading or accessing the software, you accept and agree to be bound - * by the terms of the License Agreement. If you do not want to agree to the terms - * of the Licensing Agreement, you must not download or access the software. - */ -package com.milaboratory.mixcr.cli; - -import com.milaboratory.core.alignment.AffineGapAlignmentScoring; -import com.milaboratory.core.alignment.LinearGapAlignmentScoring; -import com.milaboratory.core.alignment.kaligner1.KAlignerParameters; -import com.milaboratory.core.sequence.NucleotideSequence; -import com.milaboratory.core.sequence.quality.QualityAggregationType; -import com.milaboratory.core.tree.TreeSearchParameters; -import com.milaboratory.mixcr.assembler.*; -import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; -import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; -import com.milaboratory.util.JsonOverrider; -import io.repseq.core.GeneFeature; -import org.junit.Assert; -import org.junit.Test; - -import java.util.HashMap; -import java.util.Map; - -public class JsonOverriderTest { - @Test - public void test1() throws Exception { - KAlignerParameters parameters = KAlignerParameters.getByName("default"); - KAlignerParameters override = JsonOverrider.override( - parameters, - KAlignerParameters.class, - "floatingLeftBound=true", - "scoring.subsMatrix=simple(match=4,mismatch=-9)"); - KAlignerParameters expected = parameters.clone().setFloatingLeftBound(true) - .setScoring(new LinearGapAlignmentScoring(NucleotideSequence.ALPHABET, 4, -9, parameters.getScoring().getGapPenalty())); - Assert.assertEquals(expected, override); - } - - @Test - public void test1a() throws Exception { - KAlignerParameters parameters = KAlignerParameters.getByName("default"); - KAlignerParameters override = JsonOverrider.override( - parameters, - KAlignerParameters.class, - "floatingLeftBound=true", - "scoring.subsMatrix='simple(match=4,mismatch=-9)'"); - KAlignerParameters expected = parameters.clone().setFloatingLeftBound(true) - .setScoring(new LinearGapAlignmentScoring(NucleotideSequence.ALPHABET, 4, -9, parameters.getScoring().getGapPenalty())); - Assert.assertEquals(expected, override); - } - - @Test - public void test2() throws Exception { - KAlignerParameters parameters = KAlignerParameters.getByName("default"); - KAlignerParameters override = JsonOverrider.override( - parameters, - KAlignerParameters.class, - "floatingLeftBound=true", - "subsMatrix=simple(match=4,mismatch=-9)"); - KAlignerParameters expected = parameters.clone().setFloatingLeftBound(true) - .setScoring(new LinearGapAlignmentScoring(NucleotideSequence.ALPHABET, 4, -9, parameters.getScoring().getGapPenalty())); - Assert.assertEquals(expected, override); - } - - @Test - public void testArray1() throws Exception { - CloneFactoryParameters factoryParameters = new CloneFactoryParameters( - new VJCClonalAlignerParameters(0.3f, - LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3), - new VJCClonalAlignerParameters(0.4f, - LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5), - null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) - ); - - CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12, - QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), - factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); - - CloneAssemblerParameters override = JsonOverrider.override( - params, - CloneAssemblerParameters.class, - "assemblingFeatures=[CDR1(-5,+6),CDR2]"); - - CloneAssemblerParameters expected = new CloneAssemblerParameters(new GeneFeature[]{new GeneFeature(GeneFeature.CDR1, -5, +6), GeneFeature.CDR2}, 12, - QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), - factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); - - - Assert.assertEquals(expected, override); - } - - @Test - public void testCloneFactoryParameters2() throws Exception { - CloneFactoryParameters factoryParameters = new CloneFactoryParameters( - new VJCClonalAlignerParameters(0.3f, - LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3), - new VJCClonalAlignerParameters(0.4f, - LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5), - null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) - ); - - CloneAssemblerParameters params = new CloneAssemblerParameters(new GeneFeature[]{GeneFeature.FR1, GeneFeature.CDR3}, 12, - QualityAggregationType.Average, - new CloneClusteringParameters(2, 1, -1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), - factoryParameters, true, true, false, 0.4, 2.0, 2.0, true, (byte) 20, .8, "2of6", (byte) 15); - - CloneAssemblerParameters override = JsonOverrider.override( - params, - CloneAssemblerParameters.class, - "dParameters.absoluteMinScore=101"); - - CloneFactoryParameters expectedFactoryParameters = new CloneFactoryParameters( - new VJCClonalAlignerParameters(0.3f, - LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3), - new VJCClonalAlignerParameters(0.4f, - LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5), - null, new DClonalAlignerParameters(0.85f, 101f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) - ); - - Assert.assertEquals(expectedFactoryParameters, override.getCloneFactoryParameters()); - } - - @Test - public void test3() throws Exception { - GeneFeature jRegion = GeneFeature.parse("JRegion"); - System.out.println(jRegion); - System.out.println(GeneFeature.encode(jRegion)); - - VDJCAlignerParameters params = VDJCParametersPresets.getByName("default"); - Map overrides = new HashMap() {{ - put("vParameters.geneFeatureToAlign", "VTranscript"); - }}; - - Assert.assertNotNull(JsonOverrider.override(params, VDJCAlignerParameters.class, overrides)); - } -} From 1346d6db102393cbe4d998c5db7605adade73620 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 10 Jun 2022 02:50:01 +0200 Subject: [PATCH 282/282] Update cli docs for license --- src/main/java/com/milaboratory/mixcr/cli/Main.java | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java index 40c5f44f1..db678b890 100644 --- a/src/main/java/com/milaboratory/mixcr/cli/Main.java +++ b/src/main/java/com/milaboratory/mixcr/cli/Main.java @@ -89,10 +89,12 @@ public static void main(String... args) { System.err.println(" mixcr activate-license"); System.err.println(); System.err.println("You can also activate the license via a special file, environment"); - System.err.println("variable or other means, please check the docs."); // TODO provide a link + System.err.println("variable or other means, please check the docs at"); + System.err.println(" https://github.com/milaboratory/mixcr/wiki/Using-license"); System.err.println(); - System.err.println("If you don't have a license check https://licensing.milaboratories.com/."); - System.err.println("Free license is provided for academic users and non-profit organisations."); + System.err.println("Academic users can quickly get a license at\n https://licensing.milaboratories.com."); + System.err.println(); + System.err.println("Commercial trial license may be requested at\n https://licensing.milaboratories.com\nor by email to\n licensing@milaboratories.com."); } else System.err.println("License error: " + licenseError); System.exit(LM.LicenseErrorExitCode);