From cf82c5ddca85df40d417bbb39fa817d7dc9a5f9f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 8 Jul 2024 16:43:25 +0200 Subject: [PATCH 1/6] exclude distlib dependency --- biodata-tools/pom.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 826ca18f..d63983d3 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -53,6 +53,12 @@ com.databricks SnpEff + + + distlib + distlib + + org.rocksdb From b3d21ca549639a2c8c5398fbac33d9b637a6e87a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 8 Jul 2024 16:43:25 +0200 Subject: [PATCH 2/6] pom: exclude distlib dependency #TASK-6481 --- biodata-tools/pom.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 826ca18f..d63983d3 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -53,6 +53,12 @@ com.databricks SnpEff + + + distlib + distlib + + org.rocksdb From 6d83ad3706c1d9c62cbd18fa933d77da368161da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 25 Apr 2024 15:53:04 +0100 Subject: [PATCH 3/6] tools: Fix normalization of variants wiht ins seq. (cherry-pick from 941cb51e) #TASK-6266 --- .../opencb/biodata/tools/variant/VariantNormalizer.java | 2 ++ .../biodata/tools/variant/VariantNormalizerTest.java | 8 ++++++++ 2 files changed, 10 insertions(+) diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java index 990d61e8..e3bb3d6e 100644 --- a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java +++ b/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 to normalizedVariant.getSv().setCopyNumber(keyFields.getCopyNumber()); diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java index 95265190..a4a62f06 100644 --- a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java +++ b/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[")); From 2b43895bc954d33afa2bf48348c08696a10a5cf7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jul 2024 10:41:39 +0200 Subject: [PATCH 4/6] Prepare release 3.2.0 --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index c27bf0eb..12a6b4f5 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index e84416eb..bfef3117 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index c7d21a5f..887ce92d 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index d63983d3..03bfa0e2 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/pom.xml b/pom.xml index e35210e0..c1c07dc3 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 pom Biodata @@ -38,7 +38,7 @@ - 5.2.0-SNAPSHOT + 5.2.0 2.14.3 4.4 From 234ebdb3cb48496360151d0ef1995c369176ce58 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jul 2024 10:42:13 +0200 Subject: [PATCH 5/6] Prepare new development branch release-3.2.x --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 12a6b4f5..d6d1acdd 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index bfef3117..c3332c2e 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 887ce92d..7325a383 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 03bfa0e2..e8d90ada 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index c1c07dc3..faf0f65b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.2.0 + 5.3.0-SNAPSHOT 2.14.3 4.4 From b4c2afb5bd4659e3d90a11446935797d595685bb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jul 2024 10:42:33 +0200 Subject: [PATCH 6/6] Prepare new development branch release-3.2.x --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index d6d1acdd..bb85a556 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index c3332c2e..238588ca 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 7325a383..f9cf2628 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index e8d90ada..c7c32361 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index faf0f65b..cee50cbd 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT 2.14.3 4.4