/**
  * 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));
 }
  /**
   * Gets the header lines for the VCF writer
   *
   * @return A set of VCF header lines
   */
  private static Set<VCFHeaderLine> getHeaderInfo() {
    Set<VCFHeaderLine> headerLines = new HashSet<>();

    // INFO fields for overall data
    headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
    headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AVG_INTERVAL_DP_KEY));
    headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY));
    headerLines.add(
        new VCFInfoHeaderLine(
            "Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));

    // FORMAT fields for each genotype
    headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
    headerLines.add(
        GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY));
    headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.LOW_COVERAGE_LOCI));
    headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.ZERO_COVERAGE_LOCI));

    // FILTER fields
    for (CallableStatus stat : CallableStatus.values())
      headerLines.add(new VCFFilterHeaderLine(stat.name(), stat.description));

    return headerLines;
  }
Beispiel #3
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 public List<VCFInfoHeaderLine> getDescriptions() {
   return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)));
 }