Updated header writing

broadinstitute · Dec 13, 2024 · 0ab56eb · 0ab56eb
1 parent 726144d
commit 0ab56eb
Show file tree

Hide file tree

Showing 3 changed files with 2 additions and 20 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVReviseMultiallelicCnvs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVReviseMultiallelicCnvs.java
@@ -81,10 +81,8 @@ protected void afterNthPass(int n) {}
 
     @Override
     public void onTraversalStart() {
-        final VCFHeader header = getHeaderForVariants();
-        header.addMetaDataLine(new VCFFormatHeaderLine(GATKSVVCFConstants.EV, 1, VCFHeaderLineType.String, "Classes of evidence supporting final genotype"));
         vcfWriter = createVCFWriter(outputVcf);
-        vcfWriter.writeHeader(header);
+        vcfWriter.writeHeader(getHeaderForVariants());
     }
 
     @Override

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVReviseOverlappingCnvCns.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVReviseOverlappingCnvCns.java
@@ -85,9 +85,7 @@ public class SVReviseOverlappingCnvCns extends MultiplePassVariantWalker {
     @Override
     public void onTraversalStart() {
         vcfWriter = createVCFWriter(outputVcf);
-        final VCFHeader header = getHeaderForVariants();
-        header.addMetaDataLine(new VCFInfoHeaderLine(GATKSVVCFConstants.MULTI_CNV, 0, VCFHeaderLineType.Flag, "Variant is a multiallelic CNV"));
-        vcfWriter.writeHeader(header);
+        vcfWriter.writeHeader(getHeaderForVariants());
     }
 
     @Override

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
@@ -282,20 +282,6 @@ private void processCnvs(final VariantContextBuilder builder, final VariantConte
         }
     }
 
-    private Map<String, Set<String>> getSupportForVariant(final VariantContext variant) {
-        Map<String, Set<String>> supportMap = new HashMap<>();
-        for (String sample : variant.getSampleNames()) {
-            Genotype genotype = variant.getGenotype(sample);
-            String supportStr = genotype.hasExtendedAttribute(GATKSVVCFConstants.EV) ? genotype.getExtendedAttribute(GATKSVVCFConstants.EV).toString() : "";
-            Set<String> supportSet = new HashSet<>();
-            if (!supportStr.isEmpty()) {
-                supportSet.addAll(Arrays.asList(supportStr.split(",")));
-            }
-            supportMap.put(sample, supportSet);
-        }
-        return supportMap;
-    }
-
     private boolean isDelDup(final VariantContext variant) {
         String svType = variant.getAttributeAsString(GATKSVVCFConstants.SVTYPE, "");
         return svType.equals(GATKSVVCFConstants.SYMB_ALT_STRING_DEL) || svType.equals(GATKSVVCFConstants.SYMB_ALT_STRING_DUP);