private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError) { return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).log10PError(log10pError).make(); }
private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError, int... pls) { return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).log10PError(log10pError).PL(pls).make(); }
gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
.log10PError(log10Error) .attributes(genotypeAttributes) .phased(phasedGenotype.isPhased()).make();
gb = new GenotypeBuilder(g).noPL().noGQ().alleles(DIPLOID_NO_CALL); } else { gb = new GenotypeBuilder(g).PL(newPLs).log10PError(newLog10GQ); final List<Integer> originalDiploidAlleles = GenotypeLikelihoods.getAlleles(MathUtil.indexOfMin(newPLs), 2); gb.alleles(originalDiploidAlleles.stream().map(allelesToKeep::get).collect(Collectors.toList()));
gb = new GenotypeBuilder(g).noPL().noGQ().alleles(DIPLOID_NO_CALL); } else { gb = new GenotypeBuilder(g).PL(newPLs).log10PError(newLog10GQ); final List<Integer> originalDiploidAlleles = GenotypeLikelihoods.getAlleles(MathUtil.indexOfMin(newPLs), 2); gb.alleles(originalDiploidAlleles.stream().map(allelesToKeep::get).collect(Collectors.toList()));
gb.PL(newLikelihoods); final int PLindex = MathUtils.maxElementIndex(newLikelihoods); gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
final Genotype mergedGt = new GenotypeBuilder(gt1.getSampleName(), mergedAllelesForSample).log10PError(mergedGQ).attributes(mergedGtAttribs).phased(isPhased).make(); mergedGenotypes.add(mergedGt);