/**
* 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;
}
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)));
}