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); }