Concatenated overlapping cnv tasks into one

broadinstitute · Jan 17, 2025 · a40b193 · a40b193
1 parent 8fbd27e
commit a40b193
Show file tree

Hide file tree

Showing 2 changed files with 523 additions and 1 deletion.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVReviseOverlappingCnvGts.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVReviseOverlappingCnvGts.java
@@ -259,7 +259,7 @@ private void processRevisedEvent(final VariantContextBuilder builder, final Vari
                 if (newVal != -1) {
                     final GenotypeBuilder gb = new GenotypeBuilder(oldGenotype);
                     gb.alleles(Arrays.asList(variant.getReference(), variant.getAlternateAllele(0)));
-//                    if (!oldGenotype.hasExtendedAttribute(GATKSVVCFConstants.RD_CN)) continue;
+                    if (!oldGenotype.hasExtendedAttribute(GATKSVVCFConstants.RD_CN)) continue;
 
                     final int rdCn = Integer.parseInt(oldGenotype.getExtendedAttribute(GATKSVVCFConstants.RD_CN).toString());
                     gb.GQ(rdCn);