Java GenotypesContext.getSampleNamesOrderedByName方法代码示例

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Fix the AD for the GenotypesContext of a VariantContext that has been subset
 *
 * @param originalGs       the original GenotypesContext
 * @param originalVC       the original VariantContext
 * @param allelesToUse     the new (sub)set of alleles to use
 * @return a new non-null GenotypesContext
 */
static private GenotypesContext fixADFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List<Allele> allelesToUse) {

    // the bitset representing the allele indexes we want to keep
    final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);

    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());

    // the samples
    final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();

    // create the new genotypes
    for ( int k = 0; k < originalGs.size(); k++ ) {
        final Genotype g = originalGs.get(sampleIndices.get(k));
        newGTs.add(fixAD(g, alleleIndexesToUse, allelesToUse.size()));
    }

    return newGTs;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Fix the AD for the GenotypesContext of a VariantContext that has been
 * subset
 *
 * @param originalGs
 *            the original GenotypesContext
 * @param originalVC
 *            the original VariantContext
 * @param allelesToUse
 *            the new (sub)set of alleles to use
 * @return a new non-null GenotypesContext
 */
public static GenotypesContext fixADFromSubsettedAlleles(final GenotypesContext originalGs,
		final VariantContext originalVC, final List<Allele> allelesToUse) {
	if (originalGs == null)
		throw new IllegalArgumentException("the original Gs cannot be null");
	if (originalVC == null)
		throw new IllegalArgumentException("the original VC cannot be null");
	if (allelesToUse == null)
		throw new IllegalArgumentException("the alleles to use list cannot be null");

	// the bitset representing the allele indexes we want to keep
	final BitSet alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);

	// the new genotypes to create
	final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());

	// the samples
	final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();

	// create the new genotypes
	for (int k = 0; k < originalGs.size(); k++) {
		final Genotype g = originalGs.get(sampleIndices.get(k));
		newGTs.add(fixAD(g, alleleIndexesToUse));
	}

	return newGTs;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
public static void assertEquals(final GenotypesContext actual, final GenotypesContext expected) {
    if (expected == null) {
        Assert.assertNull(actual);
        return;
    }
    Assert.assertEquals(actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "Sample names differ");

    for (final String name : expected.getSampleNamesOrderedByName()) {
        Assert.assertEquals(actual.get(name).getAlleles(), expected.get(name).getAlleles(), "Alleles differ for sample " + name);
        Assert.assertEquals(actual.get(name).getAD(), expected.get(name).getAD());
        Assert.assertEquals(actual.get(name).getPL(), expected.get(name).getPL());
    }
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Create the new GenotypesContext with the subsetted PLs and ADs
 *
 * @param originalGs               the original GenotypesContext
 * @param vc                       the original VariantContext
 * @param allelesToUse             the actual alleles to use with the new Genotypes
 * @param likelihoodIndexesToUse   the indexes in the PL to use given the allelesToUse (@see #determineLikelihoodIndexesToUse())
 * @param assignGenotypes          assignment strategy for the (subsetted) PLs
 * @return a new non-null GenotypesContext
 */
private static GenotypesContext createGenotypesWithSubsettedLikelihoods(final GenotypesContext originalGs,
                                                                        final VariantContext vc,
                                                                        final List<Allele> allelesToUse,
                                                                        final List<Integer> likelihoodIndexesToUse,
                                                                        final GenotypeAssignmentMethod assignGenotypes) {
    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());

    // make sure we are seeing the expected number of likelihoods per sample
    final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), 2);

    // the samples
    final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();

    // create the new genotypes
    for ( int k = 0; k < originalGs.size(); k++ ) {
        final Genotype g = originalGs.get(sampleIndices.get(k));
        final GenotypeBuilder gb = new GenotypeBuilder(g);

        // create the new likelihoods array from the alleles we are allowed to use
        double[] newLikelihoods;
        if ( !g.hasLikelihoods() ) {
            // we don't have any likelihoods, so we null out PLs and make G ./.
            newLikelihoods = null;
            gb.noPL();
        } else {
            final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
            if ( likelihoodIndexesToUse == null ) {
                newLikelihoods = originalLikelihoods;
            } else if ( originalLikelihoods.length != expectedNumLikelihoods ) {
                newLikelihoods = null;
            } else {
                newLikelihoods = new double[likelihoodIndexesToUse.size()];
                int newIndex = 0;
                for ( final int oldIndex : likelihoodIndexesToUse )
                    newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];

                // might need to re-normalize
                newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
            }

            if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) )
                gb.noPL();
            else
                gb.PL(newLikelihoods);
        }

        updateGenotypeAfterSubsetting(g.getAlleles(), gb, assignGenotypes, newLikelihoods, allelesToUse);
        newGTs.add(gb.make());
    }

    return fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * From a given variant context, extract a given subset of alleles, and update genotype context accordingly,
 * including updating the PL's, and assign genotypes accordingly
 *
 * @param vc              variant context with alleles and genotype likelihoods
 * @param defaultPloidy   ploidy to assume in case that {@code vc} does not contain that information
 *                        for a sample.
 * @param allelesToUse    alleles to subset
 * @param assignGenotypes true: assign hard genotypes, false: leave as no-call
 * @return GenotypesContext with new PLs
 */
public GenotypesContext subsetAlleles(final VariantContext vc, final int defaultPloidy,
                                      final List<Allele> allelesToUse,
                                      final boolean assignGenotypes) {
    // the genotypes with PLs
    final GenotypesContext oldGTs = vc.getGenotypes();

    // samples
    final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();

    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create();

    // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
    final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
    final int numNewAltAlleles = allelesToUse.size() - 1;


    // create the new genotypes
    for (int k = 0; k < oldGTs.size(); k++) {
        final Genotype g = oldGTs.get(sampleIndices.get(k));
        final int declaredPloidy = g.getPloidy();
        final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
        if (!g.hasLikelihoods()) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy)));
            continue;
        }

        // create the new likelihoods array from the alleles we are allowed to use
        final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
        double[] newLikelihoods;

        // Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
        // and subsetting
        if (numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
            newLikelihoods = originalLikelihoods;
        } else {
            newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);

            // might need to re-normalize
            newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
        }

        // if there is no mass on the (new) likelihoods, then just no-call the sample
        if (MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy)));
        } else {
            final GenotypeBuilder gb = new GenotypeBuilder(g);

            if (numNewAltAlleles == 0)
                gb.noPL();
            else
                gb.PL(newLikelihoods);

            // if we weren't asked to assign a genotype, then just no-call the sample
            if (!assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL)
                gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy));
            else
                assignGenotype(gb, newLikelihoods, allelesToUse, ploidy);
            newGTs.add(gb.make());
        }
    }

    return newGTs;

}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
@Override
@Requires("vc != null && allelesToUse != null")
public GenotypesContext subsetAlleles(VariantContext vc, int defaultPloidy, List<Allele> allelesToUse, boolean assignGenotypes) {
    // the genotypes with PLs
    final GenotypesContext oldGTs = vc.getGenotypes();

    // samples
    final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();

    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create();

    // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
    final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
    final int numNewAltAlleles = allelesToUse.size() - 1;


    // create the new genotypes
    for ( int k = 0; k < oldGTs.size(); k++ ) {
        final Genotype g = oldGTs.get(sampleIndices.get(k));
        final int declaredPloidy = g.getPloidy();
        final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
        if ( !g.hasLikelihoods() ) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(),GaeaGvcfVariantContextUtils.noCallAlleles(ploidy)));
            continue;
        }

        // create the new likelihoods array from the alleles we are allowed to use
        final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
        double[] newLikelihoods;

        // Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
        // and subsetting
        if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
            newLikelihoods = originalLikelihoods;
        } else {
            newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);

            // might need to re-normalize
            newLikelihoods = GvcfMathUtils.normalizeFromLog10(newLikelihoods, false, true);
        }

        // if there is no mass on the (new) likelihoods, then just no-call the sample
        if ( GvcfMathUtils.sum(newLikelihoods) > GaeaGvcfVariantContextUtils.SUM_GL_THRESH_NOCALL ) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(), GaeaGvcfVariantContextUtils.noCallAlleles(ploidy)));
        } else {
            final GenotypeBuilder gb = new GenotypeBuilder(g);
            final String sampleName = g.getSampleName();

            if ( numNewAltAlleles == 0 )
                gb.noPL();
            else
                gb.PL(newLikelihoods);

            // if we weren't asked to assign a genotype, then just no-call the sample
            if ( !assignGenotypes || GvcfMathUtils.sum(newLikelihoods) > GaeaGvcfVariantContextUtils.SUM_GL_THRESH_NOCALL )
                gb.alleles(GaeaGvcfVariantContextUtils.noCallAlleles(ploidy));
            else
                assignGenotype(gb, vc, sampleName, newLikelihoods, allelesToUse, ploidy);
            newGTs.add(gb.make());
        }
    }

    return GaeaGvcfVariantContextUtils.fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
}