tools: Fix normalization of variants wiht ins seq. (cherry-pick from 9…

…41cb51) #TASK-6266
opencb · Jul 11, 2024 · 6d83ad3 · 6d83ad3
1 parent 228e478
commit 6d83ad3
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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["));