/**
  * Add the standard VCF header lines used with VQSR.
  *
  * @param hInfo updated set of VCFHeaderLines
  */
 protected static void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) {
   hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
   hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VQS_LOD_KEY));
   hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.CULPRIT_KEY));
   hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.POSITIVE_LABEL_KEY));
   hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NEGATIVE_LABEL_KEY));
 }
Пример #2
0
 /**
  * Returns the descriptions used for the VCF INFO meta field. Subclasses must ensure that this
  * list is not null and does not contain null.
  */
 public List<VCFInfoHeaderLine> getDescriptions() {
   final List<VCFInfoHeaderLine> lines = new ArrayList<>(getKeyNames().size());
   for (final String key : getKeyNames()) {
     lines.add(GATKVCFHeaderLines.getInfoLine(key));
   }
   return lines;
 }
 /**
  * Add the standard allele-specific VCF header lines used with VQSR.
  *
  * @param hInfo updated set of VCFHeaderLines
  */
 protected static void addAlleleSpecificVQSRHeaderLines(final Set<VCFHeaderLine> hInfo) {
   hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FILTER_STATUS_KEY));
   hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_CULPRIT_KEY));
   hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VQS_LOD_KEY));
 }