@Test
public void testCompHetAutosomalRecessiveFamilyTwoAlts() {

    List<Allele> alleles = buildAlleles("A", "T", "C");
    Genotype proband = buildUnPhasedSampleGenotype("Cain", alleles.get(1), alleles.get(2));
    Genotype brother = buildUnPhasedSampleGenotype("Abel", alleles.get(0), alleles.get(2));
    Genotype mother = buildUnPhasedSampleGenotype("Eve", alleles.get(0), alleles.get(1));
    Genotype father = buildUnPhasedSampleGenotype("Adam", alleles.get(0), alleles.get(2));
    VariantContext variantContext = buildVariantContext(1, 12345, alleles, proband, brother, mother, father);
    //Test A T allele
    Map<String, SampleGenotype> allele1Result = VariantContextSampleGenotypeConverter.createAlleleSampleGenotypes(variantContext, 0);
    System.out.println(allele1Result);
    Map<String, SampleGenotype> expected1 = ImmutableMap.of(
            "Cain", SampleGenotype.of(AlleleCall.ALT, AlleleCall.OTHER_ALT),
            "Abel", SampleGenotype.of(AlleleCall.REF, AlleleCall.OTHER_ALT),
            "Eve", SampleGenotype.of(AlleleCall.REF, AlleleCall.ALT),
            "Adam", SampleGenotype.of(AlleleCall.REF, AlleleCall.OTHER_ALT)
    );
    assertThat(allele1Result, equalTo(expected1));
    //Test A C allele
    Map<String, SampleGenotype> allele2Result = VariantContextSampleGenotypeConverter.createAlleleSampleGenotypes(variantContext, 1);
    System.out.println(allele2Result);
    Map<String, SampleGenotype> expected2 = ImmutableMap.of(
            "Cain", SampleGenotype.of(AlleleCall.ALT, AlleleCall.OTHER_ALT),
            "Abel", SampleGenotype.of(AlleleCall.REF, AlleleCall.ALT),
            "Eve", SampleGenotype.of(AlleleCall.REF, AlleleCall.OTHER_ALT),
            "Adam", SampleGenotype.of(AlleleCall.REF, AlleleCall.ALT)
    );
    assertThat(allele2Result, equalTo(expected2));
}