@Test
public void testCompHetAutosomalRecessiveIndividualWithFrequencyThreshold() {

    List<Allele> alleles = buildAlleles("A", "T", "C");
    Genotype proband = buildUnPhasedSampleGenotype("Cain", alleles.get(1), alleles.get(2));
    VariantContext variantContext = buildVariantContext(1, 12345, alleles, proband);
    VariantEvaluation alleleOne = filteredVariant(1, 12345, "A", "T", FilterResult.pass(FilterType.FREQUENCY_FILTER), variantContext);
    alleleOne.setFrequencyData(FrequencyData.of(Frequency.of(FrequencySource.LOCAL, 1f)));
    VariantEvaluation alleleTwo = filteredVariant(1, 12345, "A", "C", FilterResult.pass(FilterType.FREQUENCY_FILTER), variantContext);
    alleleTwo.setFrequencyData(FrequencyData.of(Frequency.of(FrequencySource.LOCAL, 1f)));
    Pedigree pedigree = singleAffectedSample("Cain");
    InheritanceModeAnnotator instance = new InheritanceModeAnnotator(pedigree, InheritanceModeOptions.defaults());
    Map<ModeOfInheritance, List<VariantEvaluation>> results = instance.computeCompatibleInheritanceModes(ImmutableList.of(alleleOne, alleleTwo));
    //Both alleles are potentially dominant, but they are deemed too common in the population to be causative of a rare disease
    Map<ModeOfInheritance, List<VariantEvaluation>> expected = ImmutableMap.of(
            ModeOfInheritance.AUTOSOMAL_RECESSIVE, ImmutableList.of(alleleOne, alleleTwo)
    );
    assertThat(results, equalTo(expected));
}