/**
* Helper method to subset a VC record, modifying some metadata stored in the INFO field (i.e. AN,
* AC, AF).
*
* @param vc the VariantContext record to subset
* @param samples the samples to extract
* @return the subsetted VariantContext
*/
private VariantContext subsetRecord(VariantContext vc, Set<String> samples) {
if (samples == null || samples.isEmpty()) return vc;
ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
for (Map.Entry<String, Genotype> genotypePair : vc.getGenotypes().entrySet()) {
if (samples.contains(genotypePair.getKey())) genotypes.add(genotypePair.getValue());
}
VariantContext sub = vc.subContextFromGenotypes(genotypes, vc.getAlleles());
// if we have fewer alternate alleles in the selected VC than in the original VC, we need to
// strip out the GL/PLs (because they are no longer accurate)
if (vc.getAlleles().size() != sub.getAlleles().size())
sub = VariantContext.modifyGenotypes(sub, VariantContextUtils.stripPLs(vc.getGenotypes()));
HashMap<String, Object> attributes = new HashMap<String, Object>(sub.getAttributes());
int depth = 0;
for (String sample : sub.getSampleNames()) {
Genotype g = sub.getGenotype(sample);
if (g.isNotFiltered() && g.isCalled()) {
String dp = (String) g.getAttribute("DP");
if (dp != null
&& !dp.equals(VCFConstants.MISSING_DEPTH_v3)
&& !dp.equals(VCFConstants.MISSING_VALUE_v4)) {
depth += Integer.valueOf(dp);
}
}
}
if (KEEP_ORIGINAL_CHR_COUNTS) {
if (attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY))
attributes.put("AC_Orig", attributes.get(VCFConstants.ALLELE_COUNT_KEY));
if (attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY))
attributes.put("AF_Orig", attributes.get(VCFConstants.ALLELE_FREQUENCY_KEY));
if (attributes.containsKey(VCFConstants.ALLELE_NUMBER_KEY))
attributes.put("AN_Orig", attributes.get(VCFConstants.ALLELE_NUMBER_KEY));
}
VariantContextUtils.calculateChromosomeCounts(sub, attributes, false);
attributes.put("DP", depth);
sub = VariantContext.modifyAttributes(sub, attributes);
return sub;
}
