static boolean alleleSegregationIsKnown(Genotype gt1, Genotype gt2) {
if (gt1.getPloidy() != gt2.getPloidy()) return false;
/* If gt2 is phased or hom, then could even be MERGED with gt1 [This is standard].
HOWEVER, EVEN if this is not the case, but gt1.isHom(),
it is trivially known that each of gt2's alleles segregate with the single allele type present in gt1.
*/
return (gt2.isPhased() || gt2.isHom() || gt1.isHom());
}
public static void assertEquals(final Genotype actual, final Genotype expected) {
Assert.assertEquals(actual.getSampleName(), expected.getSampleName(), "Genotype names");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "Genotype alleles");
Assert.assertEquals(
actual.getGenotypeString(), expected.getGenotypeString(), "Genotype string");
Assert.assertEquals(actual.getType(), expected.getType(), "Genotype type");
// filters are the same
Assert.assertEquals(actual.getFilters(), expected.getFilters(), "Genotype fields");
Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "Genotype isFiltered");
// inline attributes
Assert.assertEquals(actual.getDP(), expected.getDP(), "Genotype dp");
Assert.assertTrue(Arrays.equals(actual.getAD(), expected.getAD()));
Assert.assertEquals(actual.getGQ(), expected.getGQ(), "Genotype gq");
Assert.assertEquals(actual.hasPL(), expected.hasPL(), "Genotype hasPL");
Assert.assertEquals(actual.hasAD(), expected.hasAD(), "Genotype hasAD");
Assert.assertEquals(actual.hasGQ(), expected.hasGQ(), "Genotype hasGQ");
Assert.assertEquals(actual.hasDP(), expected.hasDP(), "Genotype hasDP");
Assert.assertEquals(
actual.hasLikelihoods(), expected.hasLikelihoods(), "Genotype haslikelihoods");
Assert.assertEquals(
actual.getLikelihoodsString(),
expected.getLikelihoodsString(),
"Genotype getlikelihoodsString");
Assert.assertEquals(
actual.getLikelihoods(), expected.getLikelihoods(), "Genotype getLikelihoods");
Assert.assertTrue(Arrays.equals(actual.getPL(), expected.getPL()));
Assert.assertEquals(
actual.getPhredScaledQual(), expected.getPhredScaledQual(), "Genotype phredScaledQual");
assertAttributesEquals(actual.getExtendedAttributes(), expected.getExtendedAttributes());
Assert.assertEquals(actual.isPhased(), expected.isPhased(), "Genotype isPhased");
Assert.assertEquals(actual.getPloidy(), expected.getPloidy(), "Genotype getPloidy");
}
