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());
}
static PhaseAndQuality calcPhaseForMergedGenotypes(Genotype gt1, Genotype gt2) {
if (gt2.isPhased() || gt2.isHom()) return new PhaseAndQuality(gt1); // maintain the phase of gt1
if (!gt1.isHom())
throw new ReviewedStingException(
"alleleSegregationIsKnown(gt1, gt2) implies: gt2.genotypesArePhased() || gt2.isHom() || gt1.isHom()");
/* We're dealing with: gt1.isHom(), gt2.isHet(), !gt2.genotypesArePhased(); so, the merged (het) Genotype is not phased relative to the previous Genotype
For example, if we're merging the third Genotype with the second one:
0/1
1|1
0/1
Then, we want to output:
0/1
1/2
*/
return new PhaseAndQuality(gt2); // maintain the phase of gt2 [since !gt2.genotypesArePhased()]
}