/**
* 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));
}
/**
* 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));
}