/**
* Gets the header fields from all VCF rods input by the user
*
* @param toolkit GATK engine
* @param rodNames names of rods to use, or null if we should use all possible ones
* @return a set of all fields
*/
public static Set<VCFHeaderLine> getHeaderFields(
GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
// keep a map of sample name to occurrences encountered
TreeSet<VCFHeaderLine> fields = new TreeSet<VCFHeaderLine>();
// iterate to get all of the sample names
List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
for (ReferenceOrderedDataSource source : dataSources) {
// ignore the rod if it's not in our list
if (rodNames != null && !rodNames.contains(source.getName())) continue;
if (source.getRecordType().equals(VariantContext.class)) {
VCFHeader header = (VCFHeader) source.getHeader();
if (header != null) fields.addAll(header.getMetaDataInSortedOrder());
}
}
return fields;
}
public void initialize() {
for (final Tranche t : Tranche.readTranches(TRANCHES_FILE)) {
if (t.ts >= TS_FILTER_LEVEL) {
tranches.add(t);
}
logger.info(String.format("Read tranche " + t));
}
Collections.reverse(
tranches); // this algorithm wants the tranches ordered from best (lowest truth sensitivity)
// to worst (highest truth sensitivity)
for (final RodBinding rod : input) {
inputNames.add(rod.getName());
}
if (IGNORE_INPUT_FILTERS != null) {
ignoreInputFilterSet.addAll(Arrays.asList(IGNORE_INPUT_FILTERS));
}
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
addVQSRStandardHeaderLines(hInfo);
final TreeSet<String> samples = new TreeSet<String>();
samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
if (tranches.size() >= 2) {
for (int iii = 0; iii < tranches.size() - 1; iii++) {
final Tranche t = tranches.get(iii);
hInfo.add(
new VCFFilterHeaderLine(
t.name,
String.format(
"Truth sensitivity tranche level for "
+ t.model.toString()
+ " model at VQS Lod: "
+ t.minVQSLod
+ " <= x < "
+ tranches.get(iii + 1).minVQSLod)));
}
}
if (tranches.size() >= 1) {
hInfo.add(
new VCFFilterHeaderLine(
tranches.get(0).name + "+",
String.format(
"Truth sensitivity tranche level for "
+ tranches.get(0).model.toString()
+ " model at VQS Lod < "
+ tranches.get(0).minVQSLod)));
} else {
throw new UserException(
"No tranches were found in the file or were above the truth sensitivity filter level "
+ TS_FILTER_LEVEL);
}
logger.info("Keeping all variants in tranche " + tranches.get(tranches.size() - 1));
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader);
}
