Examples of GenotypeAlleleCounts

org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeAlleleCounts

Collection of allele counts for a genotype. It encompasses what alleles are present in the genotype and in what number.

Alleles are represented herein by their indices running from 0 to N-1 where N is the number of alleles.

Each allele present in a genotype (count != 0) has a rank, that is the 0-based ordinal of that allele amongst the ones present in the genotype as sorted by their index.

For example:

0/0/2/2 has two alleles with indices 0 and 2, both with count 2. The rank of 0 is 0 whereas the rank of 2 is 1.

2/4/4/7 has three alleles with indices 2, 4 and 7. 2 and 7 have count 1 whereas 4 has count 2. The rank of 2 is 0, the rank of 4 is 1. and the rank of 7 is 2.

In contrast, in both examples above both 3 and 10 (and many others) are absent thus they have no rank (represented by -1 whenever applies).

{@link GenotypeAlleleCounts} instances have themselves their own index (returned by {@link #index() index()}, that indicate their 0-based ordinal within the possible genotype combinations with the same ploidy.

For example, for ploidy 3:

Index	Genotype
0	0/0/0
1	0/0/1
2	0/1/1
3	1/1/1
4	0/0/2
6	0/1/2
7	1/1/2
8	0/2/2
9	1/2/2
10	2/2/2
11	0/0/3
12	0/1/3
13	1/1/3
14	0/2/3
15	1/2/3
16	2/2/3
17	0/3/3
...	...

The total number of possible genotypes is only bounded by the maximum allele index. @author Valentin Ruano-Rubio <valentin@broadinstitute.org>


        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);
            if (alleleIndex == 0) continue; // skip the reference allele.
            final int alleleCount = genotypeAlleleCounts.alleleCountAt(i);
            AC[alleleIndex - 1] = alleleCount;
            AF[alleleIndex - 1] = ((double) alleleCount) / (double) ploidy;
        }
        gb.attribute(VCFConstants.MLE_PER_SAMPLE_ALLELE_COUNT_KEY, Utils.asList(AC));
        gb.attribute(VCFConstants.MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, Utils.asList(AF));

        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)
            gb.noPL();

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Examples of GenotypeAlleleCounts

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

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