List of forTotalPloidy() Examples

Examples of forTotalPloidy()

org.broadinstitute.gatk.tools.walkers.genotyper.AFPriorProvider.forTotalPloidy()
Returns the priors given a total-ploidy (the total number of genome copies across all samples).
For performance sake the returned value is a direct reference ot the cached prior, so the client code must not modify its content.
@param totalPloidy the requested total ploidy. @return never {@code null}, please do not modify its content. An array of {@code totalPloidy + 1} positions wherethe ith position is the log10(prior) probability of the an alternative allele AC to be exactly i copies in a draw of {@code totalPloidy} elements.
org.broadinstitute.gatk.tools.walkers.genotyper.CustomAFPriorProvider.forTotalPloidy()
org.broadinstitute.gatk.tools.walkers.genotyper.HeterozygosityAFPriorProvider.forTotalPloidy()

Examples of org.broadinstitute.gatk.tools.walkers.genotyper.AFPriorProvider.forTotalPloidy()

            plodies[i] = rdn.nextInt(maxPloidy - minPloidy + 1) + minPloidy;


        final AFPriorProvider provider = new HeterozygosityAFPriorProvider(het);
        for (int i = 0; i < useCount; i++) {
            final int ploidy = plodies[i];
            double[] priors = provider.forTotalPloidy(ploidy);
            Assert.assertNotNull(priors);
            Assert.assertEquals(priors.length, ploidy + 1);
            Assert.assertEquals(MathUtils.approximateLog10SumLog10(priors),0,TOLERANCE);
            for (int j = 0; j < priors.length; j++) {
                Assert.assertTrue(!Double.isNaN(priors[j]));

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.AFPriorProvider.forTotalPloidy()

            priorsList.add(priors[i]);
        }


        final AFPriorProvider provider = new CustomAFPriorProvider(priorsList);


        final double[] providedPriors = provider.forTotalPloidy(ploidy);
        Assert.assertNotNull(providedPriors);
        Assert.assertEquals(providedPriors.length, priors.length + 1);
        for (int i = 0; i < priors.length; i++)
            Assert.assertEquals(providedPriors[i+1],Math.log10(priors[i]),TOLERANCE);
        Assert.assertEquals(MathUtils.approximateLog10SumLog10(providedPriors),0,TOLERANCE);

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.CustomAFPriorProvider.forTotalPloidy()

            priorsList.add(priors[i]);
        }


        final AFPriorProvider provider = new CustomAFPriorProvider(priorsList);


        final double[] providedPriors = provider.forTotalPloidy(ploidy);
        Assert.assertNotNull(providedPriors);
        Assert.assertEquals(providedPriors.length, priors.length + 1);
        for (int i = 0; i < priors.length; i++)
            Assert.assertEquals(providedPriors[i+1],Math.log10(priors[i]),TOLERANCE);
        Assert.assertEquals(MathUtils.approximateLog10SumLog10(providedPriors),0,TOLERANCE);

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.HeterozygosityAFPriorProvider.forTotalPloidy()

            plodies[i] = rdn.nextInt(maxPloidy - minPloidy + 1) + minPloidy;


        final AFPriorProvider provider = new HeterozygosityAFPriorProvider(het);
        for (int i = 0; i < useCount; i++) {
            final int ploidy = plodies[i];
            double[] priors = provider.forTotalPloidy(ploidy);
            Assert.assertNotNull(priors);
            Assert.assertEquals(priors.length, ploidy + 1);
            Assert.assertEquals(MathUtils.approximateLog10SumLog10(priors),0,TOLERANCE);
            for (int j = 0; j < priors.length; j++) {
                Assert.assertTrue(!Double.isNaN(priors[j]));

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