Merge branch 'TASK-5564' into TASK-5387

.github/workflows/pull-request-approved.yml

@@ -0,0 +1,15 @@
+name: Pull request approve workflow
+
+on:
+  pull_request_review:
+    types: [ submitted ]
+
+jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+
+  test:
+    name: "Test analysis"
+    uses: ./.github/workflows/test-analysis.yml
+    needs: build
+    secrets: inherit

.github/workflows/test-analysis.yml

@@ -10,11 +10,11 @@ jobs:
     name: Test and push Sonar analysis
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: '0'
       - name: Set up JDK 11
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '11'

biodata-external/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>3.2.0-SNAPSHOT</version>
+        <version>3.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-formats/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.2.0-SNAPSHOT</version>
+        <version>3.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-models/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.2.0-SNAPSHOT</version>
+        <version>3.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-models/src/main/java/org/opencb/biodata/models/core/Snp.java

@@ -0,0 +1,147 @@
+/*
+ * <!--
+ *   ~ Copyright 2015-2017 OpenCB
+ *   ~
+ *   ~ 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 org.opencb.biodata.models.core;
+
+import java.util.List;
+
+public class Snp {
+    private String id;
+    private String chromosome;
+    private int position;
+    private String reference;
+    private List<String> alternates;
+    private String type;
+    private String source;
+    private String version;
+    private SnpAnnotation annotation;
+
+    public Snp() {
+    }
+
+    public Snp(String id, String chromosome, int position, String reference, List<String> alternates, String type,
+               String source, String version, SnpAnnotation annotation) {
+        this.id = id;
+        this.chromosome = chromosome;
+        this.position = position;
+        this.reference = reference;
+        this.alternates = alternates;
+        this.type = type;
+        this.source = source;
+        this.version = version;
+        this.annotation = annotation;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("Snp{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", chromosome='").append(chromosome).append('\'');
+        sb.append(", position=").append(position);
+        sb.append(", reference='").append(reference).append('\'');
+        sb.append(", alternates=").append(alternates);
+        sb.append(", type='").append(type).append('\'');
+        sb.append(", source='").append(source).append('\'');
+        sb.append(", version='").append(version).append('\'');
+        sb.append(", annotation=").append(annotation);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public Snp setId(String id) {
+        this.id = id;
+        return this;
+    }
+
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    public Snp setChromosome(String chromosome) {
+        this.chromosome = chromosome;
+        return this;
+    }
+
+    public int getPosition() {
+        return position;
+    }
+
+    public Snp setPosition(int position) {
+        this.position = position;
+        return this;
+    }
+
+    public String getReference() {
+        return reference;
+    }
+
+    public Snp setReference(String reference) {
+        this.reference = reference;
+        return this;
+    }
+
+    public List<String> getAlternates() {
+        return alternates;
+    }
+
+    public Snp setAlternates(List<String> alternates) {
+        this.alternates = alternates;
+        return this;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public Snp setType(String type) {
+        this.type = type;
+        return this;
+    }
+
+    public String getSource() {
+        return source;
+    }
+
+    public Snp setSource(String source) {
+        this.source = source;
+        return this;
+    }
+
+    public String getVersion() {
+        return version;
+    }
+
+    public Snp setVersion(String version) {
+        this.version = version;
+        return this;
+    }
+
+    public SnpAnnotation getAnnotation() {
+        return annotation;
+    }
+
+    public Snp setAnnotation(SnpAnnotation annotation) {
+        this.annotation = annotation;
+        return this;
+    }
+}

biodata-models/src/main/java/org/opencb/biodata/models/core/SnpAnnotation.java

@@ -0,0 +1,79 @@
+/*
+ * <!--
+ *   ~ Copyright 2015-2017 OpenCB
+ *   ~
+ *   ~ 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 org.opencb.biodata.models.core;
+
+import org.opencb.biodata.models.variant.avro.PopulationFrequency;
+
+import java.util.List;
+import java.util.Map;
+
+public class SnpAnnotation {
+
+    private List<String> flags;
+    private String gene;
+    private List<PopulationFrequency> populationFrequencies;
+    private Map<String, Object> additionalAttributes;
+
+    public SnpAnnotation() {
+    }
+
+    public SnpAnnotation(List<String> flags, String gene, List<PopulationFrequency> populationFrequencies, Map<String, Object> additionalAttributes) {
+        this.flags = flags;
+        this.gene = gene;
+        this.populationFrequencies = populationFrequencies;
+        this.additionalAttributes = additionalAttributes;
+    }
+
+    public List<String> getFlags() {
+        return flags;
+    }
+
+    public SnpAnnotation setFlags(List<String> flags) {
+        this.flags = flags;
+        return this;
+    }
+
+    public String getGene() {
+        return gene;
+    }
+
+    public SnpAnnotation setGene(String gene) {
+        this.gene = gene;
+        return this;
+    }
+
+    public List<PopulationFrequency> getPopulationFrequencies() {
+        return populationFrequencies;
+    }
+
+    public SnpAnnotation setPopulationFrequencies(List<PopulationFrequency> populationFrequencies) {
+        this.populationFrequencies = populationFrequencies;
+        return this;
+    }
+
+    public Map<String, Object> getAdditionalAttributes() {
+        return additionalAttributes;
+    }
+
+    public SnpAnnotation setAdditionalAttributes(Map<String, Object> additionalAttributes) {
+        this.additionalAttributes = additionalAttributes;
+        return this;
+    }
+}

biodata-tools/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.2.0-SNAPSHOT</version>
+        <version>3.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -53,6 +53,12 @@
         <dependency>
             <groupId>com.databricks</groupId>
             <artifactId>SnpEff</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>distlib</groupId>
+                    <artifactId>distlib</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.rocksdb</groupId>

biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/BamManager.java

@@ -49,6 +49,7 @@
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -62,7 +63,7 @@ public class BamManager implements AutoCloseable {
 
     public static final int DEFAULT_WINDOW_SIZE = 1;
     public static final int MAX_NUM_RECORDS = 50000;
-    public static final int MAX_REGION_COVERAGE = 100000;
+    public static final int MAX_REGION_COVERAGE = 500000;
     public static final String COVERAGE_BIGWIG_EXTENSION = ".bw";
 
     private Logger logger;
@@ -191,7 +192,10 @@ public Path calculateBigWigCoverage(Path bigWigPath, int windowSize) throws IOEx
         return bigWigPath;
     }
 
-
+    /**
+     * @deprecated (since getFileHeader().getTextHeader() is deprecated !)
+     */
+    @Deprecated
     public String header() {
         return samReader.getFileHeader().getTextHeader();
     }
@@ -338,7 +342,7 @@ public List<Chunk> getChunks(Region region) {
             BAMIndex index = samReader.indexing().getIndex();
             return index.getSpanOverlapping(sequenceIndex, start, end).getChunks();
         }
-        return null;
+        return Collections.emptyList();
     }
 
     public List<String> getBreakpoints(Region region) throws IOException {
@@ -378,7 +382,7 @@ public List<String> getBreakpoints(Region region) throws IOException {
                 }
             }
         }
-        return null;
+        return Collections.emptyList();
     }
 
     /**
@@ -445,7 +449,7 @@ public AlignmentGlobalStats stats(Region region, AlignmentFilters<SAMRecord> fil
         return calculateGlobalStats(iterator(region, filters, options));
     }
 
-    private AlignmentGlobalStats calculateGlobalStats(BamIterator<SAMRecord> iterator) throws IOException {
+    private AlignmentGlobalStats calculateGlobalStats(BamIterator<SAMRecord> iterator) {
         AlignmentGlobalStats alignmentGlobalStats = new AlignmentGlobalStats();
         SamRecordAlignmentGlobalStatsCalculator calculator = new SamRecordAlignmentGlobalStatsCalculator();
         while (iterator.hasNext()) {

biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java

@@ -1394,6 +1394,8 @@ private Variant newVariant(Variant variant, VariantKeyFields keyFields, Structur
                 normalizedVariant.getSv().setCiStartRight(sv.getCiStartRight());
                 normalizedVariant.getSv().setCiEndLeft(sv.getCiEndLeft());
                 normalizedVariant.getSv().setCiEndRight(sv.getCiEndRight());
+                normalizedVariant.getSv().setLeftSvInsSeq(sv.getLeftSvInsSeq());
+                normalizedVariant.getSv().setRightSvInsSeq(sv.getRightSvInsSeq());
 
                 // Variant will never have CopyNumber, because the Alternate is normalized from <CNxx> to <CNV>
                 normalizedVariant.getSv().setCopyNumber(keyFields.getCopyNumber());

biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java

@@ -784,6 +784,14 @@ public void testNormalizeSvToIndel() throws NonStandardCompliantSampleField {
 
     }
 
+    @Test
+    public void testNormalizeWithInsSeq() throws NonStandardCompliantSampleField {
+        Variant variant = new Variant("1:799984<800001<800022:-:ACCACACCCACACAACACACA...TGTGGTGTGTGTGGTGTG");
+        Variant normVar = new VariantNormalizer().normalize(Collections.singletonList(variant), false).get(0);
+        assertEquals(variant, normVar);
+        assertEquals(variant.toString(), normVar.toString());
+    }
+
     @Test
     public void testNormalizeBND() throws NonStandardCompliantSampleField {
         normalizeBnd(newVariant(101, 100, "", ".[9:10["),  newVariant(100, 99, "A", "A[chr9:10["));