private VariantCallContext estimateReferenceConfidence(
VariantContext vc,
Map<String, AlignmentContext> contexts,
double theta,
boolean ignoreCoveredSamples,
double initialPofRef) {
if (contexts == null) return null;
double P_of_ref = initialPofRef;
// for each sample that we haven't examined yet
for (String sample : samples) {
boolean isCovered = contexts.containsKey(sample);
if (ignoreCoveredSamples && isCovered) continue;
int depth = 0;
if (isCovered) {
depth = contexts.get(sample).getBasePileup().depthOfCoverage();
}
P_of_ref *= 1.0 - (theta / 2.0) * getRefBinomialProb(depth);
}
return new VariantCallContext(
vc,
QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING,
false);
}
protected boolean confidentlyCalled(double conf, double PofF) {
return conf >= UAC.STANDARD_CONFIDENCE_FOR_CALLING
|| (UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
&& QualityUtils.phredScaleErrorRate(PofF) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING);
}