protected final void printCallInfo(
final VariantContext vc,
final double[] log10AlleleFrequencyPriors,
final long runtimeNano,
final AFCalcResult result) {
printCallElement(vc, "type", "ignore", vc.getType());
int allelei = 0;
for (final Allele a : vc.getAlleles())
printCallElement(vc, "allele", allelei++, a.getDisplayString());
for (final Genotype g : vc.getGenotypes())
printCallElement(vc, "PL", g.getSampleName(), g.getLikelihoodsString());
for (int priorI = 0; priorI < log10AlleleFrequencyPriors.length; priorI++)
printCallElement(vc, "priorI", priorI, log10AlleleFrequencyPriors[priorI]);
printCallElement(vc, "runtime.nano", "ignore", runtimeNano);
printCallElement(vc, "log10PosteriorOfAFEq0", "ignore", result.getLog10PosteriorOfAFEq0());
printCallElement(vc, "log10PosteriorOfAFGt0", "ignore", result.getLog10PosteriorOfAFGT0());
for (final Allele allele : result.getAllelesUsedInGenotyping()) {
if (allele.isNonReference()) {
printCallElement(vc, "MLE", allele, result.getAlleleCountAtMLE(allele));
printCallElement(
vc, "pNonRefByAllele", allele, result.getLog10PosteriorOfAFGt0ForAllele(allele));
}
}
callReport.flush();
}
static boolean someSampleHasDoubleNonReferenceAllele(VariantContext vc1, VariantContext vc2) {
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(); // this is OK, since allSamplesAreMergeable()
if (all1.isNonReference() && all2.isNonReference()) // corresponding alleles are alternate
return true;
}
}
return false;
}