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);
}
}
}
