private double log10PLFromSamples(
final VariantContext vc, final String sample, boolean calcRefP) {
Genotype g = vc.getGenotype(sample);
double log10pSample = -1000;
if (!g.isNoCall()) {
final double[] gLikelihoods = MathUtils.normalizeFromLog10(g.getLikelihoods().getAsVector());
log10pSample = Math.log10(calcRefP ? gLikelihoods[0] : 1 - gLikelihoods[0]);
log10pSample = Double.isInfinite(log10pSample) ? -10000 : log10pSample;
}
return log10pSample;
}
