Java Genotype.isHetNonRef方法代码示例

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
private String getZygosityType(Genotype gt){
    if(gt.isHet())
        return "het-ref";
    else if(gt.isHomVar())
        return "hom-alt";
    else if(gt.isHetNonRef())
        return  "het-alt";
    return ".";
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
/**
 * Get the genotype counts for A/A, A/B, and B/B where A is the reference and B is any alternate allele
 * @param vc
 * @param genotypes may be subset to just founders if a pedigree file is provided
 * @return may be null, otherwise length-3 double[] representing homRef, het, and homVar counts
 */
public double[] getGenotypeCountsForRefVsAllAlts(final VariantContext vc, final GenotypesContext genotypes) {
    if (genotypes == null || !vc.isVariant())
        return null;

    final boolean doMultiallelicMapping = !vc.isBiallelic();

    int idxAA = 0, idxAB = 1, idxBB = 2;

    double refCount = 0;
    double hetCount = 0;
    double homCount = 0;

    sampleCount = 0;
    for (final Genotype g : genotypes) {
        if (g.isCalled() && g.hasLikelihoods() && g.getPloidy() == 2)  // only work for diploid samples
            sampleCount++;
        else
            continue;

        //Need to round the likelihoods to deal with small numerical deviations due to normalizing
        final double[] normalizedLikelihoodsUnrounded = GvcfMathUtils.normalizeFromLog10(g.getLikelihoods().getAsVector());
        double[] normalizedLikelihoods = new double[normalizedLikelihoodsUnrounded.length];
        if (returnRounded) {
            for (int i = 0; i < normalizedLikelihoodsUnrounded.length; i++) {
                normalizedLikelihoods[i] = Math.round(normalizedLikelihoodsUnrounded[i]);
            }
        } else {
            normalizedLikelihoods = normalizedLikelihoodsUnrounded;
        }

        if (doMultiallelicMapping) {
            if (g.isHetNonRef()) {
                //all likelihoods go to homCount
                homCount++;
                continue;
            }

            if (!g.isHomRef()) {
                //get alternate allele for each sample
                final Allele a1 = g.getAllele(0);
                final Allele a2 = g.getAllele(1);
                final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a2.isNonReference() ? a2 : a1);
                idxAA = idxVector[0];
                idxAB = idxVector[1];
                idxBB = idxVector[2];
            }
        }

        refCount += normalizedLikelihoods[idxAA];
        hetCount += normalizedLikelihoods[idxAB];
        homCount += normalizedLikelihoods[idxBB];
    }
    return new double[]{refCount, hetCount, homCount};
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
/**
 * Check if any of the genotypes is heterozygous, non-reference (i.e. 1/2)
 *
 * @param genotypesContext
 *            genotype information
 * @return true if any of the genotypes are heterozygous, non-reference,
 *         false otherwise
 */
private static boolean hasHetNonRef(final GenotypesContext genotypesContext) {
	for (final Genotype gt : genotypesContext) {
		if (gt.isHetNonRef())
			return true;
	}
	return false;
}