private VariantCallContext generateEmptyContext(
RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, AlignmentContext> stratifiedContexts,
AlignmentContext rawContext) {
VariantContext vc;
if (UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
VariantContext vcInput =
UnifiedGenotyperEngine.getVCFromAllelesRod(
tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
if (vcInput == null) return null;
vc =
new VariantContextBuilder(
"UG_call",
ref.getLocus().getContig(),
vcInput.getStart(),
vcInput.getEnd(),
vcInput.getAlleles())
.make();
} else {
// deal with bad/non-standard reference bases
if (!Allele.acceptableAlleleBases(new byte[] {ref.getBase()})) return null;
Set<Allele> alleles = new HashSet<Allele>();
alleles.add(Allele.create(ref.getBase(), true));
vc =
new VariantContextBuilder(
"UG_call",
ref.getLocus().getContig(),
ref.getLocus().getStart(),
ref.getLocus().getStart(),
alleles)
.make();
}
if (annotationEngine != null) {
// Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
final ReadBackedPileup pileup = rawContext.getBasePileup();
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
vc = annotationEngine.annotateContext(tracker, ref, stratifiedContexts, vc);
}
return new VariantCallContext(vc, false);
}
