Examples of AFCalculationResult

org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult
Describes the results of the AFCalc Only the bare essentials are represented here, as all AFCalc models must return meaningful results for all of these fields. Note that all of the values -- i.e. priors -- are checked now that they are meaningful, which means that users of this code can rely on the values coming out of these functions.

Examples of org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult

            return emptyCallContext(tracker,refContext,rawContext);


        final int defaultPloidy = configuration.genotypeArgs.samplePloidy;
        final int maxAltAlleles = configuration.genotypeArgs.MAX_ALTERNATE_ALLELES;
        final AFCalculator afCalculator = afCalculatorProvider.getInstance(vc,defaultPloidy,maxAltAlleles);
        final AFCalculationResult AFresult = afCalculator.getLog10PNonRef(vc, defaultPloidy,maxAltAlleles, getAlleleFrequencyPriors(vc,defaultPloidy,model));


        final OutputAlleleSubset outputAlternativeAlleles = calculateOutputAlleleSubset(AFresult);


        final double PoFGT0 = Math.pow(10, AFresult.getLog10PosteriorOfAFGT0());


        // note the math.abs is necessary because -10 * 0.0 => -0.0 which isn't nice
        double log10Confidence =
                ! outputAlternativeAlleles.siteIsMonomorphic ||
                    configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES || configuration.annotateAllSitesWithPLs
                        ? AFresult.getLog10PosteriorOfAFEq0() + 0.0
                        : AFresult.getLog10PosteriorOfAFGT0() + 0.0 ;




        // Add 0.0 removes -0.0 occurrences.
        final double phredScaledConfidence = (-10.0 * log10Confidence) + 0.0;

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult

        // do we want to apply a prior? maybe user-spec?
        if ( flatPriors == null ) {
            flatPriors = new double[1+2*samples.size()];
            afCalculator = AFCalculatorFactory.createCalculator(samples.size(), MAX_ALT_ALLELES, HomoSapiensConstants.DEFAULT_PLOIDY);
        }
        final AFCalculationResult result = afCalculator.getLog10PNonRef(subContext, HomoSapiensConstants.DEFAULT_PLOIDY, MAX_ALT_ALLELES,  flatPriors);
        // do we want to let this qual go up or down?
        if ( result.getLog10LikelihoodOfAFEq0() < referenceLikelihood ) {
            return true;
        }


        return false;
    }

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult

        //double overallLog10PofNull = AFresult.log10AlleleFrequencyPosteriors[0];
        final double overallLog10PofF = AFresult.getLog10LikelihoodOfAFGT0();
        //if ( DEBUG_SLOD ) System.out.println("overallLog10PofF=" + overallLog10PofF);


        // the forward lod
        final AFCalculationResult forwardAFresult = getDirectionalAfCalcResult(AlignmentContextUtils.ReadOrientation.FORWARD,stratifiedContexts, tracker, refContext, allAllelesToUse, model, perReadAlleleLikelihoodMap);
        final double forwardLog10PofNull = forwardAFresult.getLog10LikelihoodOfAFEq0();
        final double forwardLog10PofF = forwardAFresult.getLog10LikelihoodOfAFGT0();
        //if ( DEBUG_SLOD ) System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF);


        // the reverse lod
        final AFCalculationResult reverseAFresult = getDirectionalAfCalcResult(AlignmentContextUtils.ReadOrientation.REVERSE,stratifiedContexts, tracker, refContext, allAllelesToUse, model, perReadAlleleLikelihoodMap);
        final double reverseLog10PofNull = reverseAFresult.getLog10LikelihoodOfAFEq0();
        final double reverseLog10PofF = reverseAFresult.getLog10LikelihoodOfAFGT0();
        //if ( DEBUG_SLOD ) System.out.println("reverseLog10PofNull=" + reverseLog10PofNull + ", reverseLog10PofF=" + reverseLog10PofF);


        final double forwardLod = forwardLog10PofF + reverseLog10PofNull - overallLog10PofF;
        final double reverseLod = reverseLog10PofF + forwardLog10PofNull - overallLog10PofF;
        //if ( DEBUG_SLOD ) System.out.println("forward lod=" + forwardLod + ", reverse lod=" + reverseLod);

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