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); }