code: private void addHomozygousGenotype(Variant variant, int numAllele, String[] alternateAlleles, VariantStats stats, String[] homCounts) {
          if (homCounts.length == alternateAlleles.length) {
              for (int i = 0; i < homCounts.length; i++) {
                  Integer alleles[] = new Integer[2];
                  getHomozygousGenotype(i + 1, alleles);
                  String gt = VariantVcfFactory.mapToMultiallelicIndex(alleles[0], numAllele) + "/" + VariantVcfFactory.mapToMultiallelicIndex(alleles[1], numAllele);
                  Genotype genotype = new Genotype(gt, variant.getReference(), alternateAlleles[numAllele]);
                  stats.addGenotype(genotype, Integer.parseInt(homCounts[i]));
              }
          }
      }
docs: Adds the homozygous genotypes to a variant stats. Those are (in this order):
  1/1, 2/2, 3/3...
  @param variant
  @param numAllele
  @param alternateAlleles
  @param stats
  @param homCounts parsed string