htsjdk.variant.variantcontext.VariantContextUtils Java Examples

public VariantContext ensureAnnotations(final VariantContext vc, final VariantContext vcsub) {
    final int originalAlleleCount = vc.getHetCount() + 2 * vc.getHomVarCount();
    final int newAlleleCount = vcsub.getHetCount() + 2 * vcsub.getHomVarCount();
    final boolean isSingleton = originalAlleleCount == newAlleleCount && newAlleleCount == 1;
    final boolean hasChrCountAnnotations = vcsub.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) &&
            vcsub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) &&
            vcsub.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY);

    if ( ! isSingleton && hasChrCountAnnotations ) {
        // nothing to update
        return vcsub;
    } else {
        // have to do the work
        VariantContextBuilder builder = new VariantContextBuilder(vcsub);

        if ( isSingleton )
            builder.attribute(VariantEval.IS_SINGLETON_KEY, true);

        if ( ! hasChrCountAnnotations )
            VariantContextUtils.calculateChromosomeCounts(builder, true);

        return builder.make();
    }
}
 

/** Determine whether a given variant context represents a segment.
 *
 * Dev note: this is done by examining the length and the alt allele of the segment.
 *
 * @param vc Never {@code null}
 * @param minSizeForSegment Minimum size for a segment to be valid.
 * @return Boolean whether the given variant context could represent a copy number segment.
 */
public static boolean isSegmentVariantContext(final VariantContext vc, final int minSizeForSegment) {
    Utils.nonNull(vc);
    final List<String> ACCEPTABLE_ALT_ALLELES = Stream.concat(
            Stream.of(SimpleSVType.SupportedType.values())
                    .map(s -> SimpleSVType.createBracketedSymbAlleleString(s.toString())),
            Stream.of(AnnotatedIntervalToSegmentVariantContextConverter.COPY_NEUTRAL_ALLELE.getDisplayString(), Allele.UNSPECIFIED_ALTERNATE_ALLELE_STRING)
    ).collect(Collectors.toList());

    boolean acceptableAlternateAllele = false;
    for (final Allele a: vc.getAlternateAlleles()) {
        final String representation = a.getDisplayString();
        if (ACCEPTABLE_ALT_ALLELES.contains(representation)) {
            acceptableAlternateAllele = true;
        }
    }

    return acceptableAlternateAllele && (VariantContextUtils.getSize(vc) > minSizeForSegment);
}
 

@Override
public void apply(final VariantContext variant,
                  final ReadsContext readsContext,
                  final ReferenceContext referenceContext,
                  final FeatureContext featureContext) {
    final Collection<VariantContext> vcs = featureContext.getValues(getDrivingVariantsFeatureInput());

    final Collection<VariantContext> otherVCs = featureContext.getValues(supportVariants);

    final int missing = supportVariants.size() - otherVCs.size();

    for ( final VariantContext vc : vcs ) {
        final VariantContext vc_familyPriors;
        final VariantContext vc_bothPriors;

        //do family priors first (if applicable)
        final VariantContextBuilder builder = new VariantContextBuilder(vc);
        //only compute family priors for biallelelic sites
        if (!skipFamilyPriors && vc.isBiallelic()){
            final GenotypesContext gc = famUtils.calculatePosteriorGLs(vc);
            builder.genotypes(gc);
        }
        VariantContextUtils.calculateChromosomeCounts(builder, false);
        vc_familyPriors = builder.make();

        if (!skipPopulationPriors) {
            vc_bothPriors = PosteriorProbabilitiesUtils.calculatePosteriorProbs(vc_familyPriors, otherVCs, missing * numRefIfMissing, globalPrior, !ignoreInputSamples, defaultToAC, useACoff);
        } else {
            final VariantContextBuilder builder2 = new VariantContextBuilder(vc_familyPriors);
            VariantContextUtils.calculateChromosomeCounts(builder, false);
            vc_bothPriors = builder2.make();
        }
        vcfWriter.add(vc_bothPriors);
    }
}
 

@Override
public void apply(final VariantContext variant,
                  final ReadsContext readsContext,
                  final ReferenceContext referenceContext,
                  final FeatureContext featureContext) {

    final Collection<VariantContext> otherVCs = featureContext.getValues(supportVariants);

    //If no resource contains a matching variant, then add numRefIfMissing as a pseudocount to the priors
    List<VariantContext> resourcesWithMatchingStarts = otherVCs.stream()
            .filter(vc -> variant.getStart() == vc.getStart()).collect(Collectors.toList());

    //do family priors first (if applicable)
    final VariantContextBuilder builder = new VariantContextBuilder(variant);
    //only compute family priors for biallelelic sites
    if (!skipFamilyPriors && variant.isBiallelic()){
        final GenotypesContext gc = famUtils.calculatePosteriorGLs(variant);
        builder.genotypes(gc);
    }
    VariantContextUtils.calculateChromosomeCounts(builder, false);
    final VariantContext vc_familyPriors = builder.make();

    final VariantContext vc_bothPriors;
    if (!skipPopulationPriors) {
        vc_bothPriors = PosteriorProbabilitiesUtils.calculatePosteriorProbs(vc_familyPriors, resourcesWithMatchingStarts,
                resourcesWithMatchingStarts.isEmpty() ? numRefIfMissing : 0, options);
    } else {
        vc_bothPriors = vc_familyPriors;
    }
    vcfWriter.add(vc_bothPriors);
}
 

@Override
public Map<String, Object> annotate(final ReferenceContext ref,
                                    final VariantContext vc,
                                    AlleleLikelihoods<GATKRead, Allele> likelihoods) {
    Utils.nonNull(vc);
    if ( ! vc.hasGenotypes() ) {
        return Collections.emptyMap();
    }

    return VariantContextUtils.calculateChromosomeCounts(vc, new LinkedHashMap<>(), true, Collections.emptySet());
}
 

public List<Object> getRelevantStates(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
    ArrayList<Object> relevantStates = new ArrayList<Object>();
    relevantStates.add("none");

    for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) {
        if (eval != null && VariantContextUtils.match(eval, jexlExpression)) {
            relevantStates.add(jexlExpression.name);
        }
    }

    return relevantStates;
}
 

private VariantContext makeVariantContext(Build37ExtendedIlluminaManifestRecord record, final InfiniumGTCRecord gtcRecord,
                                          final InfiniumEGTFile egtFile, final ProgressLogger progressLogger) {
    // If the record is not flagged as errant in the manifest we include it in the VCF
    Allele A = record.getAlleleA();
    Allele B = record.getAlleleB();
    Allele ref = record.getRefAllele();

    final String chr = record.getB37Chr();
    final Integer position = record.getB37Pos();
    final Integer endPosition = position + ref.length() - 1;
    Integer egtIndex = egtFile.rsNameToIndex.get(record.getName());
    if (egtIndex == null) {
        throw new PicardException("Found no record in cluster file for manifest entry '" + record.getName() + "'");
    }

    progressLogger.record(chr, position);

    // Create list of unique alleles
    final List<Allele> assayAlleles = new ArrayList<>();
    assayAlleles.add(ref);

    if (A.equals(B)) {
        throw new PicardException("Found same allele (" + A.getDisplayString() + ") for A and B ");
    }

    if (!ref.equals(A, true)) {
        assayAlleles.add(A);
    }

    if (!ref.equals(B, true)) {
        assayAlleles.add(B);
    }

    final String sampleName = FilenameUtils.removeExtension(INPUT.getName());
    final Genotype genotype = getGenotype(sampleName, gtcRecord, record, A, B);

    final VariantContextBuilder builder = new VariantContextBuilder();

    builder.source(record.getName());
    builder.chr(chr);
    builder.start(position);
    builder.stop(endPosition);
    builder.alleles(assayAlleles);
    builder.log10PError(VariantContext.NO_LOG10_PERROR);
    builder.id(record.getName());
    builder.genotypes(genotype);

    VariantContextUtils.calculateChromosomeCounts(builder, false);

    //custom info fields
    builder.attribute(InfiniumVcfFields.ALLELE_A, record.getAlleleA());
    builder.attribute(InfiniumVcfFields.ALLELE_B, record.getAlleleB());
    builder.attribute(InfiniumVcfFields.ILLUMINA_STRAND, record.getIlmnStrand());
    builder.attribute(InfiniumVcfFields.PROBE_A, record.getAlleleAProbeSeq());
    builder.attribute(InfiniumVcfFields.PROBE_B, record.getAlleleBProbeSeq());
    builder.attribute(InfiniumVcfFields.BEADSET_ID, record.getBeadSetId());
    builder.attribute(InfiniumVcfFields.ILLUMINA_CHR, record.getChr());
    builder.attribute(InfiniumVcfFields.ILLUMINA_POS, record.getPosition());
    builder.attribute(InfiniumVcfFields.ILLUMINA_BUILD, record.getGenomeBuild());
    builder.attribute(InfiniumVcfFields.SOURCE, record.getSource().replace(' ', '_'));
    builder.attribute(InfiniumVcfFields.GC_SCORE, formatFloatForVcf(egtFile.totalScore[egtIndex]));

    for (InfiniumVcfFields.GENOTYPE_VALUES gtValue : InfiniumVcfFields.GENOTYPE_VALUES.values()) {
        final int ordinalValue = gtValue.ordinal();
        builder.attribute(InfiniumVcfFields.N[ordinalValue], egtFile.n[egtIndex][ordinalValue]);
        builder.attribute(InfiniumVcfFields.DEV_R[ordinalValue], formatFloatForVcf(egtFile.devR[egtIndex][ordinalValue]));
        builder.attribute(InfiniumVcfFields.MEAN_R[ordinalValue], formatFloatForVcf(egtFile.meanR[egtIndex][ordinalValue]));
        builder.attribute(InfiniumVcfFields.DEV_THETA[ordinalValue], formatFloatForVcf(egtFile.devTheta[egtIndex][ordinalValue]));
        builder.attribute(InfiniumVcfFields.MEAN_THETA[ordinalValue], formatFloatForVcf(egtFile.meanTheta[egtIndex][ordinalValue]));

        final EuclideanValues genotypeEuclideanValues = polarToEuclidean(egtFile.meanR[egtIndex][ordinalValue], egtFile.devR[egtIndex][ordinalValue],
                egtFile.meanTheta[egtIndex][ordinalValue], egtFile.devTheta[egtIndex][ordinalValue]);
        builder.attribute(InfiniumVcfFields.DEV_X[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.devX));
        builder.attribute(InfiniumVcfFields.MEAN_X[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.meanX));
        builder.attribute(InfiniumVcfFields.DEV_Y[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.devY));
        builder.attribute(InfiniumVcfFields.MEAN_Y[ordinalValue], formatFloatForVcf(genotypeEuclideanValues.meanY));
    }


    final String rsid = record.getRsId();
    if (StringUtils.isNotEmpty(rsid)) {
        builder.attribute(InfiniumVcfFields.RS_ID, rsid);
    }
    if (egtFile.totalScore[egtIndex] == 0.0) {
        builder.filter(InfiniumVcfFields.ZEROED_OUT_ASSAY);
        if (genotype.isCalled()) {
            if (DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS) {
                throw new PicardException("Found a call (genotype: " + genotype + ") on a zeroed out Assay!!");
            } else {
                log.warn("Found a call (genotype: " + genotype + ") on a zeroed out Assay. " +
                        "This could occur if you called genotypes on a different cluster file than used here.");
            }
        }
    }
    if (record.isDupe()) {
        builder.filter(InfiniumVcfFields.DUPE);
    }
    return builder.make();
}
 

/**
 * Writes out the VariantContext objects in the order presented to the supplied output file
 * in VCF format.
 */
private void writeVcf(final CloseableIterator<VariantContext> variants,
                      final File output,
                      final SAMSequenceDictionary dict,
                      final VCFHeader vcfHeader, ZCallPedFile zCallPedFile) {

    try(VariantContextWriter writer = new VariantContextWriterBuilder()
            .setOutputFile(output)
            .setReferenceDictionary(dict)
            .setOptions(VariantContextWriterBuilder.DEFAULT_OPTIONS)
            .build()) {
        writer.writeHeader(vcfHeader);
        while (variants.hasNext()) {
            final VariantContext context = variants.next();

            final VariantContextBuilder builder = new VariantContextBuilder(context);
            if (zCallThresholds.containsKey(context.getID())) {
                final String[] zThresh = zCallThresholds.get(context.getID());
                builder.attribute(InfiniumVcfFields.ZTHRESH_X, zThresh[0]);
                builder.attribute(InfiniumVcfFields.ZTHRESH_Y, zThresh[1]);
            }
            final Genotype originalGenotype = context.getGenotype(0);
            final Map<String, Object> newAttributes = originalGenotype.getExtendedAttributes();
            final VCFEncoder vcfEncoder = new VCFEncoder(vcfHeader, false, false);
            final Map<Allele, String> alleleMap = vcfEncoder.buildAlleleStrings(context);

            final String zCallAlleles = zCallPedFile.getAlleles(context.getID());
            if (zCallAlleles == null) {
                throw new PicardException("No zCall alleles found for snp " + context.getID());
            }
            final List<Allele> zCallPedFileAlleles = buildNewAllelesFromZCall(zCallAlleles, context.getAttributes());
            newAttributes.put(InfiniumVcfFields.GTA, alleleMap.get(originalGenotype.getAllele(0)) + UNPHASED + alleleMap.get(originalGenotype.getAllele(1)));
            newAttributes.put(InfiniumVcfFields.GTZ, alleleMap.get(zCallPedFileAlleles.get(0)) + UNPHASED + alleleMap.get(zCallPedFileAlleles.get(1)));

            final Genotype newGenotype = GenotypeBuilder.create(originalGenotype.getSampleName(), zCallPedFileAlleles,
                    newAttributes);
            builder.genotypes(newGenotype);
            logger.record("0", 0);
            // AC, AF, and AN are recalculated here
            VariantContextUtils.calculateChromosomeCounts(builder, false);
            final VariantContext newContext = builder.make();
            writer.add(newContext);
        }
    }
}
 

/**
 * Merges multiple VariantContexts all for the same locus into a single hybrid.
 *
 * @param variantContexts           list of VCs
 * @return new VariantContext       representing the merge of variantContexts
 */
public static VariantContext merge(final List<VariantContext> variantContexts) {
    if ( variantContexts == null || variantContexts.isEmpty() )
        return null;

    // establish the baseline info from the first VC
    final VariantContext first = variantContexts.get(0);
    final String name = first.getSource();

    final Set<String> filters = new HashSet<>();

    int depth = 0;
    double log10PError = CommonInfo.NO_LOG10_PERROR;
    boolean anyVCHadFiltersApplied = false;
    GenotypesContext genotypes = GenotypesContext.create();

    // Go through all the VCs, verify that the loci and ID and other attributes agree.
    final Map<String, Object> firstAttributes = first.getAttributes();
    for (final VariantContext vc : variantContexts ) {
        if ((vc.getStart() != first.getStart()) || (!vc.getContig().equals(first.getContig()))) {
            throw new PicardException("Mismatch in loci among input VCFs");
        }
        if (!vc.getID().equals(first.getID())) {
            throw new PicardException("Mismatch in ID field among input VCFs");
        }
        if (!vc.getReference().equals(first.getReference())) {
            throw new PicardException("Mismatch in REF allele among input VCFs");
        }
        checkThatAllelesMatch(vc, first);

        genotypes.addAll(vc.getGenotypes());

        // We always take the QUAL of the first VC with a non-MISSING qual for the combined value
        if ( log10PError == CommonInfo.NO_LOG10_PERROR )
            log10PError =  vc.getLog10PError();

        filters.addAll(vc.getFilters());
        anyVCHadFiltersApplied |= vc.filtersWereApplied();

        // add attributes
        // special case DP (add it up)
        if (vc.hasAttribute(VCFConstants.DEPTH_KEY))
            depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);

        // Go through all attributes - if any differ (other than AC, AF, or AN) that's an error.  (recalc AC, AF, and AN later)
        for (final Map.Entry<String, Object> p : vc.getAttributes().entrySet()) {
            final String key = p.getKey();
            if ((!key.equals("AC")) && (!key.equals("AF")) && (!key.equals("AN")) && (!key.equals("devX_AB")) && (!key.equals("devY_AB"))) {
                final Object value = p.getValue();
                final Object extantValue = firstAttributes.get(key);
                if (extantValue == null) {
                    // attribute in one VCF but not another.  Die!
                    throw new PicardException("Attribute '" + key + "' not found in all VCFs");
                }
                else if (!extantValue.equals(value)) {
                    // Attribute disagrees in value between one VCF Die! (if not AC, AF, nor AN, skipped above)
                    throw new PicardException("Values for attribute '" + key + "' disagrees among input VCFs");
                }
            }
        }
    }

    if (depth > 0)
        firstAttributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));

    final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(first.getID());
    builder.loc(first.getContig(), first.getStart(), first.getEnd());
    builder.alleles(first.getAlleles());
    builder.genotypes(genotypes);

    builder.attributes(new TreeMap<>(firstAttributes));
    // AC, AF, and AN are recalculated here
    VariantContextUtils.calculateChromosomeCounts(builder, false);

    builder.log10PError(log10PError);
    if ( anyVCHadFiltersApplied ) {
        builder.filters(filters.isEmpty() ? filters : new TreeSet<>(filters));
    }

    return builder.make();
}
 

/**
 * Set up the VCF writer, the sample expressions and regexs, filters inputs, and the JEXL matcher
 *
 */
@Override
public void onTraversalStart() {
    final Map<String, VCFHeader> vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());

    // Initialize VCF header lines
    final Set<VCFHeaderLine> headerLines = createVCFHeaderLineList(vcfHeaders);

    for (int i = 0; i < selectExpressions.size(); i++) {
        // It's not necessary that the user supply select names for the JEXL expressions, since those
        // expressions will only be needed for omitting records.  Make up the select names here.
        selectNames.add(String.format("select-%d", i));
    }

    jexls = VariantContextUtils.initializeMatchExps(selectNames, selectExpressions);

    // Prepare the sample names and types to be used by the corresponding filters
    samples = createSampleNameInclusionList(vcfHeaders);
    selectedTypes = createSampleTypeInclusionList();

    // Look at the parameters to decide which analysis to perform
    discordanceOnly = discordanceTrack != null;
    if (discordanceOnly) {
        logger.info("Selecting only variants discordant with the track: " + discordanceTrack.getName());
    }

    concordanceOnly = concordanceTrack != null;
    if (concordanceOnly) {
        logger.info("Selecting only variants concordant with the track: " + concordanceTrack.getName());
    }

    if (mendelianViolations) {
        sampleDB = initializeSampleDB();
        mv = new MendelianViolation(mendelianViolationQualThreshold, false, true);
    }

    selectRandomFraction = fractionRandom > 0;
    if (selectRandomFraction) {
        logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track");
    }

    //TODO: this should be refactored/consolidated as part of
    // https://github.com/broadinstitute/gatk/issues/121 and
    // https://github.com/broadinstitute/gatk/issues/1116
    Set<VCFHeaderLine> actualLines = null;
    SAMSequenceDictionary sequenceDictionary = null;
    if (hasReference()) {
        Path refPath = referenceArguments.getReferencePath();
        sequenceDictionary= this.getReferenceDictionary();
        actualLines = VcfUtils.updateHeaderContigLines(headerLines, refPath, sequenceDictionary, suppressReferencePath);
    }
    else {
        sequenceDictionary = getHeaderForVariants().getSequenceDictionary();
        if (null != sequenceDictionary) {
            actualLines = VcfUtils.updateHeaderContigLines(headerLines, null, sequenceDictionary, suppressReferencePath);
        }
        else {
            actualLines = headerLines;
        }
    }
    if (!infoAnnotationsToDrop.isEmpty()) {
        for (final String infoField : infoAnnotationsToDrop) {
            logger.info(String.format("Will drop info annotation: %s",infoField));
        }
    }
    if (!genotypeAnnotationsToDrop.isEmpty()) {
        for (final String genotypeAnnotation : genotypeAnnotationsToDrop) {
            logger.info(String.format("Will drop genotype annotation: %s",genotypeAnnotation));
        }
    }

    final Path outPath = vcfOutput.toPath();
    vcfWriter = createVCFWriter(outPath);
    vcfWriter.writeHeader(new VCFHeader(actualLines, samples));
}
 

private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC, final Set<String> selectedSampleNames) {
    if (fullyDecode) {
        return; // TODO -- annotations are broken with fully decoded data
    }

    if (keepOriginalChrCounts) {
        final int[] indexOfOriginalAlleleForNewAllele;
        final List<Allele> newAlleles = builder.getAlleles();
        final int numOriginalAlleles = originalVC.getNAlleles();

        // if the alleles already match up, we can just copy the previous list of counts
        if (numOriginalAlleles == newAlleles.size()) {
            indexOfOriginalAlleleForNewAllele = null;
        }
        // otherwise we need to parse them and select out the correct ones
        else {
            indexOfOriginalAlleleForNewAllele = new int[newAlleles.size() - 1];
            Arrays.fill(indexOfOriginalAlleleForNewAllele, -1);

            // note that we don't care about the reference allele at position 0
            for (int newI = 1; newI < newAlleles.size(); newI++) {
                final Allele newAlt = newAlleles.get(newI);
                for (int oldI = 0; oldI < numOriginalAlleles - 1; oldI++) {
                    if (newAlt.equals(originalVC.getAlternateAllele(oldI), false)) {
                        indexOfOriginalAlleleForNewAllele[newI - 1] = oldI;
                        break;
                    }
                }
            }
        }

        if (originalVC.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AC_KEY,
                    getReorderedAttributes(originalVC.getAttribute(VCFConstants.ALLELE_COUNT_KEY), indexOfOriginalAlleleForNewAllele));
        }
        if (originalVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AF_KEY,
                    getReorderedAttributes(originalVC.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY), indexOfOriginalAlleleForNewAllele));
        }
        if (originalVC.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY)) {
            builder.attribute(GATKVCFConstants.ORIGINAL_AN_KEY, originalVC.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
        }
    }

    VariantContextUtils.calculateChromosomeCounts(builder, false);

    if (keepOriginalDepth && originalVC.hasAttribute(VCFConstants.DEPTH_KEY)) {
        builder.attribute(GATKVCFConstants.ORIGINAL_DP_KEY, originalVC.getAttribute(VCFConstants.DEPTH_KEY));
    }

    boolean sawDP = false;
    int depth = 0;
    for (final String sample : selectedSampleNames ) {
        final Genotype g = originalVC.getGenotype(sample);
        if (!g.isFiltered()) {
            if (g.hasDP()) {
                depth += g.getDP();
                sawDP = true;
            }
        }
    }

    if (sawDP) {
        builder.attribute(VCFConstants.DEPTH_KEY, depth);
    }
}