SVCallRecord add CPX_TYPE if exists, not just if SVTYPE==CPX

broadinstitute · Jun 28, 2024 · 36448cb · 36448cb
1 parent 0b779dd
commit 36448cb
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/sv/SVCallRecordUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/sv/SVCallRecordUtils.java
@@ -329,8 +329,7 @@ public static SVCallRecord create(final VariantContext variant, boolean keepVari
         final int positionA = variant.getStart();
 
         final GATKSVVCFConstants.StructuralVariantAnnotationType type = inferStructuralVariantType(variant);
-        final GATKSVVCFConstants.ComplexVariantSubtype cpxSubtype =
-                type == GATKSVVCFConstants.StructuralVariantAnnotationType.CPX ? getComplexSubtype(variant) : null;
+        final GATKSVVCFConstants.ComplexVariantSubtype cpxSubtype = getComplexSubtype(variant);
         final List<String> algorithms = getAlgorithms(variant);
 
         final String strands;