Examples of GenotypeLikelihoodCalculator

            return;


        final int bestLikelihoodIndex = MathUtils.minElementIndex(PL);
        final int numberOfAlleles = vc.getNAlleles();
        final int ploidy = g.getPloidy();
        final GenotypeLikelihoodCalculator calculator = GenotypeLikelihoodCalculators.getInstance(ploidy, numberOfAlleles);
        final GenotypeAlleleCounts genotypeAlleleCounts = calculator.genotypeAlleleCountsAt(bestLikelihoodIndex);
        final int[] AC = new int[numberOfAlleles - 1];
        final double[] AF = new double[numberOfAlleles - 1];
        final int allelesPresentCount = genotypeAlleleCounts.distinctAlleleCount();
        for (int i = 0; i < allelesPresentCount; i++) {
            final int alleleIndex = genotypeAlleleCounts.alleleIndexAt(i);

Examples of org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator

                                final int numChromosomes) {
        final int numNewAltAlleles = allelesToUse.size() - 1;


        // find the genotype with maximum likelihoods
        final int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods);
        final GenotypeLikelihoodCalculator calculator = GenotypeLikelihoodCalculators.getInstance(numChromosomes,allelesToUse.size());
        final GenotypeAlleleCounts alleleCounts = calculator.genotypeAlleleCountsAt(PLindex);


        gb.alleles(alleleCounts.asAlleleList(allelesToUse));


        // remove PLs if necessary
        if (newLikelihoods.length > MAX_LENGTH_FOR_POOL_PL_LOGGING)

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.