Java GenotypesContext.add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
private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniquifySamples) {
    //TODO: should we add a check for cases when the genotypeMergeOption is REQUIRE_UNIQUE
    for ( final Genotype g : oneVC.getGenotypes() ) {
        final String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniquifySamples);
        if ( ! mergedGenotypes.containsSample(name) ) {
            // only add if the name is new
            Genotype newG = g;

            if ( uniquifySamples || alleleMapping.needsRemapping() ) {
                final List<Allele> alleles = alleleMapping.needsRemapping() ? alleleMapping.remap(g.getAlleles()) : g.getAlleles();
                newG = new GenotypeBuilder(g).name(name).alleles(alleles).make();
            }

            mergedGenotypes.add(newG);
        }
    }
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
public static VariantContextBuilder pruneVariantContext(final VariantContextBuilder builder, Collection<String> keysToPreserve ) {
    final VariantContext vc = builder.make();
    if ( keysToPreserve == null ) keysToPreserve = Collections.emptyList();

    // VC info
    final Map<String, Object> attributes = subsetAttributes(vc.getCommonInfo(), keysToPreserve);

    // Genotypes
    final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
    for ( final Genotype g : vc.getGenotypes() ) {
        final GenotypeBuilder gb = new GenotypeBuilder(g);
        // remove AD, DP, PL, and all extended attributes, keeping just GT and GQ
        gb.noAD().noDP().noPL().noAttributes();
        genotypes.add(gb.make());
    }

    return builder.genotypes(genotypes).attributes(attributes);
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set<String> allowedAttributes) {
    if ( allowedAttributes == null )
        return vc;

    final GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
    for ( final Genotype genotype : vc.getGenotypes() ) {
        final Map<String, Object> attrs = new HashMap<>();
        for ( final Map.Entry<String, Object> attr : genotype.getExtendedAttributes().entrySet() ) {
            if ( allowedAttributes.contains(attr.getKey()) )
                attrs.put(attr.getKey(), attr.getValue());
        }
        newGenotypes.add(new GenotypeBuilder(genotype).attributes(attrs).make());
    }

    return new VariantContextBuilder(vc).genotypes(newGenotypes).make();
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
private GenotypesContext annotateGenotypes(final RefMetaDataTracker tracker,
                                           final ReferenceContext ref, final Map<String, AlignmentContext> stratifiedContexts,
                                           final VariantContext vc,
                                           final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
    if (requestedGenotypeAnnotations.isEmpty())
        return vc.getGenotypes();

    final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
    for (final Genotype genotype : vc.getGenotypes()) {
        AlignmentContext context = null;
        PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = null;
        if (stratifiedContexts != null)
            context = stratifiedContexts.get(genotype.getSampleName());
        if (stratifiedPerReadAlleleLikelihoodMap != null)
            perReadAlleleLikelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());


        final GenotypeBuilder gb = new GenotypeBuilder(genotype);
        for (final GenotypeAnnotation annotation : requestedGenotypeAnnotations) {
            annotation.annotate(tracker, walker, ref, context, vc, genotype, gb, perReadAlleleLikelihoodMap);
        }
        genotypes.add(gb.make());
    }

    return genotypes;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
private GenotypesContext annotateGenotypes(final RefMetaDataTracker tracker, final ChromosomeInformationShare ref, final VariantContext vc) {
	if (requestedGenotypeAnnotations.isEmpty())
		return vc.getGenotypes();

	final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
	for (final Genotype genotype : vc.getGenotypes()) {

		final GenotypeBuilder gb = new GenotypeBuilder(genotype);
		for (final GenotypeAnnotation annotation : requestedGenotypeAnnotations) {
			annotation.annotate(tracker, ref,  vc, genotype, gb);
		}
		genotypes.add(gb.make());
	}

	return genotypes;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
public static VariantContextBuilder pruneVariantContext(final VariantContextBuilder builder,
		Collection<String> keysToPreserve) {
	final VariantContext vc = builder.make();
	if (keysToPreserve == null)
		keysToPreserve = Collections.emptyList();

	// VC info
	final Map<String, Object> attributes = subsetAttributes(vc.getCommonInfo(), keysToPreserve);

	// Genotypes
	final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
	for (final Genotype g : vc.getGenotypes()) {
		final GenotypeBuilder gb = new GenotypeBuilder(g);
		// remove AD, DP, PL, and all extended attributes, keeping just GT
		// and GQ
		gb.noAD().noDP().noPL().noAttributes();
		genotypes.add(gb.make());
	}

	return builder.genotypes(genotypes).attributes(attributes);
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set<String> allowedAttributes) {
	if (allowedAttributes == null)
		return vc;

	final GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
	for (final Genotype genotype : vc.getGenotypes()) {
		final Map<String, Object> attrs = new HashMap<>();
		for (final Map.Entry<String, Object> attr : genotype.getExtendedAttributes().entrySet()) {
			if (allowedAttributes.contains(attr.getKey()))
				attrs.put(attr.getKey(), attr.getValue());
		}
		newGenotypes.add(new GenotypeBuilder(genotype).attributes(attrs).make());
	}

	return new VariantContextBuilder(vc).genotypes(newGenotypes).make();
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Subset the samples in VC to reference only information with ref call alleles
 *
 * Preserves DP if present
 *
 * @param vc the variant context to subset down to
 * @param ploidy ploidy to use if a genotype doesn't have any alleles
 * @return a GenotypesContext
 */
public static GenotypesContext subsetToRefOnly(final VariantContext vc, final int ploidy) {
    if ( vc == null ) throw new IllegalArgumentException("vc cannot be null");
    if ( ploidy < 1 ) throw new IllegalArgumentException("ploidy must be >= 1 but got " + ploidy);

    // the genotypes with PLs
    final GenotypesContext oldGTs = vc.getGenotypes();

    // optimization: if no input genotypes, just exit
    if (oldGTs.isEmpty()) return oldGTs;

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

    final Allele ref = vc.getReference();
    final List<Allele> diploidRefAlleles = Arrays.asList(ref, ref);

    // create the new genotypes
    for ( final Genotype g : vc.getGenotypes() ) {
        final int gPloidy = g.getPloidy() == 0 ? ploidy : g.getPloidy();
        final List<Allele> refAlleles = gPloidy == 2 ? diploidRefAlleles : Collections.nCopies(gPloidy, ref);
        final GenotypeBuilder gb = new GenotypeBuilder(g.getSampleName(), refAlleles);
        if ( g.hasDP() ) gb.DP(g.getDP());
        if ( g.hasGQ() ) gb.GQ(g.getGQ());
        newGTs.add(gb.make());
    }

    return newGTs;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
public static GenotypesContext stripPLsAndAD(final GenotypesContext genotypes) {
    final GenotypesContext newGs = GenotypesContext.create(genotypes.size());

    for ( final Genotype g : genotypes ) {
        newGs.add(removePLsAndAD(g));
    }

    return newGs;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
protected static GenotypesContext updateGenotypesWithMappedAlleles(final GenotypesContext originalGenotypes, final AlleleMapper alleleMapper) {
    final GenotypesContext updatedGenotypes = GenotypesContext.create(originalGenotypes.size());

    for ( final Genotype genotype : originalGenotypes ) {
        final List<Allele> updatedAlleles = alleleMapper.remap(genotype.getAlleles());
        updatedGenotypes.add(new GenotypeBuilder(genotype).alleles(updatedAlleles).make());
    }

    return updatedGenotypes;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Merge into the context a new genotype represented by the given VariantContext for the provided list of target alleles.
 * This method assumes that none of the alleles in the VC overlaps with any of the alleles in the set.
 *
 * @param mergedGenotypes   the genotypes context to add to
 * @param VC                the Variant Context for the sample
 * @param remappedAlleles   the list of remapped alleles for the sample
 * @param targetAlleles     the list of target alleles
 */
private static void mergeRefConfidenceGenotypes(final GenotypesContext mergedGenotypes,
                                                final VariantContext VC,
                                                final List<Allele> remappedAlleles,
                                                final List<Allele> targetAlleles) {
    final int maximumPloidy = VC.getMaxPloidy(GATKVariantContextUtils.DEFAULT_PLOIDY);
    // the map is different depending on the ploidy, so in order to keep this method flexible (mixed ploidies)
    // we need to get a map done (lazily inside the loop) for each ploidy, up to the maximum possible.
    final int[][] genotypeIndexMapsByPloidy = new int[maximumPloidy + 1][];
    final int maximumAlleleCount = Math.max(remappedAlleles.size(),targetAlleles.size());
    final int[] indexesOfRelevantAlleles = getIndexesOfRelevantAlleles(remappedAlleles, targetAlleles, VC.getStart());

    for ( final Genotype g : VC.getGenotypes() ) {
        final String name = g.getSampleName();
        if ( mergedGenotypes.containsSample(name) )
            continue;
        final int ploidy = g.getPloidy();
        final GenotypeBuilder genotypeBuilder = new GenotypeBuilder(g).alleles(GATKVariantContextUtils.noCallAlleles(g.getPloidy()));
        if (g.hasPL()) {
            // lazy initialization of the genotype index map by ploidy.
            final int[] genotypeIndexMapByPloidy = genotypeIndexMapsByPloidy[ploidy] == null
                    ? GenotypeLikelihoodCalculators.getInstance(ploidy, maximumAlleleCount).genotypeIndexMap(indexesOfRelevantAlleles)
                    : genotypeIndexMapsByPloidy[ploidy];
            final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
            final int[] AD = g.hasAD() ? generateAD(g.getAD(), indexesOfRelevantAlleles) : null;
            genotypeBuilder.PL(PLs).AD(AD).noGQ();
        }
        mergedGenotypes.add(genotypeBuilder.make());
    }
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * For a particular event described in inputVC, form PL vector for each sample by looking into allele read map and filling likelihood matrix for each allele
 * @param readLikelihoods          Allele map describing mapping from reads to alleles and corresponding likelihoods
 * @param mergedVC               Input VC with event to genotype
 * @return                       GenotypesContext object wrapping genotype objects with PLs
 */
private GenotypesContext calculateGLsForThisEvent( final ReadLikelihoods<Allele> readLikelihoods, final VariantContext mergedVC, final List<Allele> noCallAlleles ) {
    final List<Allele> vcAlleles = mergedVC.getAlleles();
    final AlleleList<Allele> alleleList = readLikelihoods.alleleCount() == vcAlleles.size() ? readLikelihoods : new IndexedAlleleList<>(vcAlleles);
    final GenotypingLikelihoods<Allele> likelihoods = genotypingModel.calculateLikelihoods(alleleList,new GenotypingData<>(ploidyModel,readLikelihoods));
    final int sampleCount = samples.sampleCount();
    final GenotypesContext result = GenotypesContext.create(sampleCount);
    for (int s = 0; s < sampleCount; s++)
        result.add(new GenotypeBuilder(samples.sampleAt(s)).alleles(noCallAlleles).PL(likelihoods.sampleLikelihoods(s).getAsPLs()).make());
    return result;
}
 

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 PLs, ADs and SACs, 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, SACs and AD.
 */
@Override
public GenotypesContext subsetAlleles(final VariantContext vc, final int defaultPloidy,
                                      final List<Allele> allelesToUse,
                                      final boolean assignGenotypes) {

    final GenotypesContext result = GenotypesContext.create();

    // Subset genotypes for each sample
    for (final Genotype g : vc.getGenotypes()) // If it really needs to process order by sample name do so.
        result.add(subsetGenotypeAlleles(g, allelesToUse, vc, defaultPloidy, assignGenotypes));
    return GaeaGvcfVariantContextUtils.fixADFromSubsettedAlleles(result, vc, allelesToUse);
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Subset the samples in VC to reference only information with ref call
 * alleles
 *
 * Preserves DP if present
 *
 * @param vc
 *            the variant context to subset down to
 * @param ploidy
 *            ploidy to use if a genotype doesn't have any alleles
 * @return a GenotypesContext
 */
public static GenotypesContext subsetToRefOnly(final VariantContext vc, final int ploidy) {
	if (vc == null)
		throw new IllegalArgumentException("vc cannot be null");
	if (ploidy < 1)
		throw new IllegalArgumentException("ploidy must be >= 1 but got " + ploidy);

	// the genotypes with PLs
	final GenotypesContext oldGTs = vc.getGenotypes();

	// optimization: if no input genotypes, just exit
	if (oldGTs.isEmpty())
		return oldGTs;

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

	final Allele ref = vc.getReference();
	final List<Allele> diploidRefAlleles = Arrays.asList(ref, ref);

	// create the new genotypes
	for (final Genotype g : vc.getGenotypes()) {
		final int gPloidy = g.getPloidy() == 0 ? ploidy : g.getPloidy();
		final List<Allele> refAlleles = Collections.nCopies(gPloidy, vc.getReference());
		final GenotypeBuilder gb = new GenotypeBuilder(g.getSampleName(), refAlleles);
		if (g.hasDP())
			gb.DP(g.getDP());
		if (g.hasGQ())
			gb.GQ(g.getGQ());
		newGTs.add(gb.make());
	}

	return newGTs;
}