Merge branch 'release-3.2.x'

opencb · Jul 17, 2024 · 65f6eff · 65f6eff
2 parents afa87fc + 2b43895
commit 65f6eff
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Showing 9 changed files with 39 additions and 8 deletions.
diff --git a/.github/workflows/pull-request-approved.yml b/.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
diff --git a/.github/workflows/test-analysis.yml b/.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'

diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>3.1.0</version>
+        <version>3.2.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.1.0</version>
+        <version>3.2.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.1.0</version>
+        <version>3.2.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>3.1.0</version>
+        <version>3.2.0</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>

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
@@ -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());

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
@@ -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["));

diff --git a/pom.xml b/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>org.opencb.biodata</groupId>
     <artifactId>biodata</artifactId>
-    <version>3.1.0</version>
+    <version>3.2.0</version>
     <packaging>pom</packaging>
 
     <name>Biodata</name>
@@ -38,7 +38,7 @@
 
     <properties>
         <!-- All dependency versions must be defined here -->
-        <java-common-libs.version>5.1.0</java-common-libs.version>
+        <java-common-libs.version>5.2.0</java-common-libs.version>
 
         <jackson.version>2.14.3</jackson.version>
         <collections.version>4.4</collections.version>