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();
}
@Override
public String toString() {
return String.format(
"ExactCall %s:%d alleles=%s nSamples=%s orig.pNonRef=%.2f orig.runtime=%s",
vc.getChr(),
vc.getStart(),
vc.getAlleles(),
vc.getNSamples(),
originalCall.getLog10PosteriorOfAFGT0(),
new AutoFormattingTime(runtime / 1e9).toString());
}