public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null || !BaseUtils.isRegularBase(ref.getBase())) return 0;
Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
for (VariantContext vc : contexts) {
VariantContextBuilder builder = new VariantContextBuilder(vc);
// set the appropriate sample name if necessary
if (sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName())) {
Genotype g =
new GenotypeBuilder(vc.getGenotype(variants.getName())).name(sampleName).make();
builder.genotypes(g);
}
final VariantContext withID = variantOverlapAnnotator.annotateRsID(tracker, builder.make());
writeRecord(withID, tracker, ref.getLocus());
}
return 1;
}
