/** * 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)); }