/**
* Function that process a set of statuses into strings
*
* @param statuses the set of statuses to be converted
* @return a matching set of strings
*/
private List<String> statusToStrings(
Iterable<CallableStatus> statuses, final boolean isInfoField) {
List<String> output = new LinkedList<>();
for (CallableStatus status : statuses)
if (isInfoField || status != CallableStatus.PASS) output.add(status.name());
return output;
}
/**
* 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;
}