Java Genotype.hasDP方法代码示例

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
public int getNumOfReads(final VariantContext vc) {
	// don't use the full depth because we don't calculate MQ for reference
	// blocks
	int numOfReads = 0;
	if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) {
		numOfReads += Integer.parseInt(vc.getAttributeAsString(VCFConstants.DEPTH_KEY, "-1"));
		if (vc.hasGenotypes()) {
			for (Genotype gt : vc.getGenotypes()) {
				if (gt.isHomRef()) {
					// site-level DP contribution will come from MIN_DP for
					// gVCF-called reference variants or DP for BP
					// resolution
					if (gt.hasExtendedAttribute("MIN_DP"))
						numOfReads -= Integer.parseInt(gt.getExtendedAttribute("MIN_DP").toString());
					else if (gt.hasDP())
						numOfReads -= gt.getDP();
				}

			}
		}
		return numOfReads;
	}
	return -1;
}
 

import htsjdk.variant.variantcontext.Genotype; //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.Genotype; //导入方法依赖的package包/类
protected int getDepth(final GenotypesContext genotypes) {
    int standardDepth = 0;
    int ADrestrictedDepth = 0;

    for ( final Genotype genotype : genotypes ) {

        // we care only about variant calls with likelihoods
        if ( !genotype.isHet() && !genotype.isHomVar() )
            continue;

        // if we have the AD values for this sample, let's make sure that the variant depth is greater than 1!
        if ( genotype.hasAD() ) {
            final int[] AD = genotype.getAD();
            final int totalADdepth = (int)GvcfMathUtils.sum(AD);
            if ( totalADdepth - AD[0] > 1 )
                ADrestrictedDepth += totalADdepth;
            standardDepth += totalADdepth;
            continue;
        }
        
        if ( genotype.hasDP() )
        	standardDepth += genotype.getDP();
    }

    // if the AD-restricted depth is a usable value (i.e. not zero), then we should use that one going forward
    if ( ADrestrictedDepth > 0 )
        standardDepth = ADrestrictedDepth;

    return standardDepth;
}
 

import htsjdk.variant.variantcontext.Genotype; //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;
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
/**
 * Cleans up genotype-level annotations that need to be updated.
 * 1. move MIN_DP to DP if present
 * 2. propagate DP to AD if not present
 * 3. remove SB if present
 * 4. change the PGT value from "0|1" to "1|1" for homozygous variant genotypes
 *
 * @param VC            the VariantContext with the Genotypes to fix
 * @param createRefGTs  if true we will also create proper hom ref genotypes since we assume the site is monomorphic
 * @return a new set of Genotypes
 */
private List<Genotype> cleanupGenotypeAnnotations(final VariantContext VC, final boolean createRefGTs) {
    final GenotypesContext oldGTs = VC.getGenotypes();
    final List<Genotype> recoveredGs = new ArrayList<>(oldGTs.size());
    for ( final Genotype oldGT : oldGTs ) {
        final Map<String, Object> attrs = new HashMap<>(oldGT.getExtendedAttributes());

        final GenotypeBuilder builder = new GenotypeBuilder(oldGT);
        int depth = oldGT.hasDP() ? oldGT.getDP() : 0;

        // move the MIN_DP to DP
        if ( oldGT.hasExtendedAttribute("MIN_DP") ) {
            depth = Integer.parseInt((String)oldGT.getAnyAttribute("MIN_DP"));
            builder.DP(depth);
            attrs.remove("MIN_DP");
        }

        // remove SB
        attrs.remove("SB");

        // update PGT for hom vars
        if ( oldGT.isHomVar() && oldGT.hasExtendedAttribute(HaplotypeCaller.HAPLOTYPE_CALLER_PHASING_GT_KEY) ) {
            attrs.put(HaplotypeCaller.HAPLOTYPE_CALLER_PHASING_GT_KEY, "1|1");
        }

        // create AD if it's not there
        if ( !oldGT.hasAD() && VC.isVariant() ) {
            final int[] AD = new int[VC.getNAlleles()];
            AD[0] = depth;
            builder.AD(AD);
        }

        if ( createRefGTs ) {
            final int ploidy = oldGT.getPloidy();
            final List<Allele> refAlleles = Collections.nCopies(ploidy,VC.getReference());

            //keep 0 depth samples as no-call
            if (depth > 0) {
                builder.alleles(refAlleles);
            }

            // also, the PLs are technically no longer usable
            builder.noPL();
        }

        recoveredGs.add(builder.noAttributes().attributes(attrs).make());
    }
    return recoveredGs;
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                    final AnnotatorCompatible walker,
                                    final ReferenceContext ref,
                                    final Map<String, AlignmentContext> stratifiedContexts,
                                    final VariantContext vc,
                                    final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap ) {
    if ( !vc.hasLog10PError() )
        return null;

    final GenotypesContext genotypes = vc.getGenotypes();
    if ( genotypes == null || genotypes.size() == 0 )
        return null;

    int standardDepth = 0;
    int ADrestrictedDepth = 0;

    for ( final Genotype genotype : genotypes ) {

        // we care only about variant calls with likelihoods
        if ( !genotype.isHet() && !genotype.isHomVar() )
            continue;

        // if we have the AD values for this sample, let's make sure that the variant depth is greater than 1!
        // TODO -- If we like how this is working and want to apply it to a situation other than the single sample HC pipeline,
        // TODO --  then we will need to modify the annotateContext() - and related - routines in the VariantAnnotatorEngine
        // TODO --  so that genotype-level annotations are run first (to generate AD on the samples) and then the site-level
        // TODO --  annotations must come afterwards (so that QD can use the AD).
        if ( genotype.hasAD() ) {
            final int[] AD = genotype.getAD();
            final int totalADdepth = (int) MathUtils.sum(AD);
            if ( totalADdepth - AD[0] > 1 )
                ADrestrictedDepth += totalADdepth;
            standardDepth += totalADdepth;
            continue;
        }

        if (stratifiedContexts!= null && !stratifiedContexts.isEmpty()) {
            final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
            if ( context == null )
                continue;
            standardDepth += context.getBasePileup().depthOfCoverage();

        } else if (perReadAlleleLikelihoodMap != null) {
            final PerReadAlleleLikelihoodMap perReadAlleleLikelihoods = perReadAlleleLikelihoodMap.get(genotype.getSampleName());
            if (perReadAlleleLikelihoods == null || perReadAlleleLikelihoods.isEmpty())
                continue;

            standardDepth += perReadAlleleLikelihoods.getNumberOfStoredElements();
        } else if ( genotype.hasDP() ) {
            standardDepth += genotype.getDP();
        }
    }

    // if the AD-restricted depth is a usable value (i.e. not zero), then we should use that one going forward
    if ( ADrestrictedDepth > 0 )
        standardDepth = ADrestrictedDepth;

    if ( standardDepth == 0 )
        return null;

    final double altAlleleLength = GATKVariantContextUtils.getMeanAltAlleleLength(vc);
    // Hack: when refContext == null then we know we are coming from the HaplotypeCaller and do not want to do a
    //  full length-based normalization (because the indel length problem is present only in the UnifiedGenotyper)
    double QD = -10.0 * vc.getLog10PError() / ((double)standardDepth * indelNormalizationFactor(altAlleleLength, ref != null));

    // Hack: see note in the fixTooHighQD method below
    QD = fixTooHighQD(QD);

    final Map<String, Object> map = new HashMap<>();
    map.put(getKeyNames().get(0), String.format("%.2f", QD));
    return map;
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
private List<Genotype> cleanupGenotypeAnnotations(final VariantContext VC, final boolean createRefGTs) {
	final GenotypesContext oldGTs = VC.getGenotypes();
	final List<Genotype> recoveredGs = new ArrayList<>(oldGTs.size());
	for (final Genotype oldGT : oldGTs) {
		final Map<String, Object> attrs = new HashMap<>(oldGT.getExtendedAttributes());

		final GenotypeBuilder builder = new GenotypeBuilder(oldGT);
		int depth = oldGT.hasDP() ? oldGT.getDP() : 0;

		// move the MIN_DP to DP
		if (oldGT.hasExtendedAttribute(GaeaVCFConstants.MIN_DP_FORMAT_KEY)) {
			depth = Integer.parseInt((String) oldGT.getAnyAttribute(GaeaVCFConstants.MIN_DP_FORMAT_KEY));
			builder.DP(depth);
			attrs.remove(GaeaVCFConstants.MIN_DP_FORMAT_KEY);
		}

		// move the GQ to RGQ
		if (createRefGTs && oldGT.hasGQ()) {
			builder.noGQ();
			attrs.put(GaeaVCFConstants.REFERENCE_GENOTYPE_QUALITY, oldGT.getGQ());
		}

		// remove SB
		attrs.remove(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY);

		// update PGT for hom vars
		if (oldGT.isHomVar() && oldGT.hasExtendedAttribute(GaeaVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY)) {
			attrs.put(GaeaVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY, "1|1");
		}

		// create AD if it's not there
		if (!oldGT.hasAD() && VC.isVariant()) {
			final int[] AD = new int[VC.getNAlleles()];
			AD[0] = depth;
			builder.AD(AD);
		}

		if (createRefGTs) {
			final int ploidy = oldGT.getPloidy();
			final List<Allele> refAlleles = Collections.nCopies(ploidy, VC.getReference());

			// keep 0 depth samples and 0 GQ samples as no-call
			if (depth > 0 && oldGT.hasGQ() && oldGT.getGQ() > 0) {
				builder.alleles(refAlleles);
			}

			// also, the PLs are technically no longer usable
			builder.noPL();
		}

		recoveredGs.add(builder.noAttributes().attributes(attrs).make());
	}
	return recoveredGs;
}