static boolean doubleAllelesSegregatePerfectlyAmongSamples(
VariantContext vc1, VariantContext vc2) {
// Check that Alleles at vc1 and at vc2 always segregate together in all samples (including
// reference):
Map<Allele, Allele> allele1ToAllele2 = new HashMap<Allele, Allele>();
Map<Allele, Allele> allele2ToAllele1 = new HashMap<Allele, Allele>();
// Note the segregation of the alleles for the reference genome:
allele1ToAllele2.put(vc1.getReference(), vc2.getReference());
allele2ToAllele1.put(vc2.getReference(), vc1.getReference());
// Note the segregation of the alleles for each sample (and check that it is consistent with the
// reference and all previous samples).
for (final Genotype gt1 : vc1.getGenotypes()) {
Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
List<Allele> site1Alleles = gt1.getAlleles();
List<Allele> site2Alleles = gt2.getAlleles();
Iterator<Allele> all2It = site2Alleles.iterator();
for (Allele all1 : site1Alleles) {
Allele all2 = all2It.next();
Allele all1To2 = allele1ToAllele2.get(all1);
if (all1To2 == null) allele1ToAllele2.put(all1, all2);
else if (!all1To2.equals(all2)) // all1 segregates with two different alleles at site 2
return false;
Allele all2To1 = allele2ToAllele1.get(all2);
if (all2To1 == null) allele2ToAllele1.put(all2, all1);
else if (!all2To1.equals(all1)) // all2 segregates with two different alleles at site 1
return false;
}
}
return true;
}
@Requires({"eval != null", "comp != null"})
private EvalCompMatchType doEvalAndCompMatch(
final VariantContext eval, final VariantContext comp, boolean requireStrictAlleleMatch) {
// find all of the matching comps
if (comp.getType() != eval.getType()) return EvalCompMatchType.NO_MATCH;
// find the comp which matches both the reference allele and alternate allele from eval
final Allele altEval =
eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
final Allele altComp =
comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
if ((altEval == null && altComp == null)
|| (altEval != null
&& altEval.equals(altComp)
&& eval.getReference().equals(comp.getReference()))) return EvalCompMatchType.STRICT;
else return requireStrictAlleleMatch ? EvalCompMatchType.NO_MATCH : EvalCompMatchType.LENIENT;
}