private static void addGenotypesAndGTests() { // for ( final int ploidy : Arrays.asList(2)) { for (final int ploidy : Arrays.asList(1, 2, 3, 4, 5)) { final List<List<String>> alleleCombinations = Arrays.asList( Arrays.asList("A"), Arrays.asList("A", "C"), Arrays.asList("A", "C", "G"), Arrays.asList("A", "C", "G", "T")); for (final List<String> alleles : alleleCombinations) { final VariantContextBuilder vcb = builder().alleles(alleles); final VariantContext site = vcb.make(); final int nAlleles = site.getNAlleles(); final Allele ref = site.getReference(); // base genotype is ref/.../ref up to ploidy final List<Allele> baseGenotype = new ArrayList<Allele>(ploidy); for (int i = 0; i < ploidy; i++) baseGenotype.add(ref); final int nPLs = GenotypeLikelihoods.numLikelihoods(nAlleles, ploidy); // ada is 0, 1, ..., nAlleles - 1 final List<Integer> ada = new ArrayList<Integer>(nAlleles); for (int i = 0; i < nAlleles - 1; i++) ada.add(i); // pl is 0, 1, ..., up to nPLs (complex calc of nAlleles and ploidy) final int[] pl = new int[nPLs]; for (int i = 0; i < pl.length; i++) pl[i] = i; final GenotypeBuilder gb = new GenotypeBuilder("ADA_PL_SAMPLE"); gb.alleles(baseGenotype); gb.PL(pl); gb.attribute("ADA", nAlleles == 2 ? ada.get(0) : ada); vcb.genotypes(gb.make()); add(vcb); } } }