Java Genotype.isHomVar方法代码示例

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
public void addFormatGenotype(Genotype gt) {
	if(gt == null){
		this.setText(' ');
	}
	else if(gt.isHomRef()){
		this.setText('.');
		this.setBgColor(Config.get(ConfigKey.feature_background_no_strand));
	}
	else if(gt.isHomVar()){
		this.setText('O');
		this.setBgColor(Config.get(ConfigKey.feature_background_negative_strand));
	}
	else if(gt.isHet()){
		this.setText('E');
		this.setBgColor(Config.get(ConfigKey.feature_background_positive_strand));
	} 
	else {
		this.setText('?');
	}
}
 

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
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
@NotNull
private Collection<EligibilityReport> processVariant(final VariantContext variant, final String patient, final String sample,
        final EligibilityReport.ReportType type) {

    if (variant.isFiltered()) {
        return Collections.emptyList();
    }

    // we will skip when an ALT is not present in the sample
    final Genotype genotype = variant.getGenotype(sample);
    if (genotype == null || !(genotype.isHomVar() || genotype.isHet())) {
        return Collections.emptyList();
    }

    // TODO: do we need to verify specific ALTS have specific SnpEff effects

    final VariantModel model = VariantModel.from(variant);

    final List<String> matchingPrograms = programs.entrySet()
            .stream()
            .filter(program -> program.getValue().vcfProcessor.test(model))
            .map(Map.Entry::getKey)
            .collect(Collectors.toList());

    // TODO: only add matching annotations of variant
    final String alts = variant.getAlternateAlleles().stream().map(Object::toString).collect(Collectors.joining("|"));
    final String effects = String.join("|", model.Annotations.stream().flatMap(a -> a.Effects.stream()).collect(Collectors.toSet()));
    final String genes = String.join("|", model.Annotations.stream().map(a -> a.GeneName).collect(Collectors.toSet()));

    return matchingPrograms.stream()
            .map(p -> ImmutableEligibilityReport.builder()
                    .patient(patient)
                    .source(type)
                    .program(p)
                    .id(variant.getID())
                    .genes(genes)
                    .chrom(variant.getContig())
                    .pos(variant.getStart())
                    .ref(variant.getReference().toString())
                    .alts(alts)
                    .effects(effects)
                    .build())
            .collect(Collectors.toList());
}
 

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
public Map<String, Object> annotate(final VariantDataTracker tracker,
                                    final ChromosomeInformationShare ref,
                                    final Mpileup mpileup,
                                    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 depth = 0;

    for ( final Genotype genotype : genotypes ) {

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

        if (mpileup!= null) {
            Pileup pileup = mpileup.getCurrentPosPileup().get(genotype.getSampleName());
            if ( pileup == null )
                continue;
            depth += pileup.depthOfCoverage(false);

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

            depth += perReadAlleleLikelihoods.getNumberOfStoredElements();
        }
    }

    if ( depth == 0 )
        return null;

    double QD = -10.0 * vc.getLog10PError() / (double)depth;

    Map<String, Object> map = new HashMap<String, Object>();
    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;
}