Package org.broadinstitute.gatk.utils.pileup

Examples of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup

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        final ArrayList<Double> refQuals = new ArrayList<Double>();
        final ArrayList<Double> altQuals = new ArrayList<Double>();

        for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
            PerReadAlleleLikelihoodMap indelLikelihoodMap = null;
            ReadBackedPileup pileup = null;


            if (stratifiedContexts != null) { // the old UG SNP-only path through the annotations
                final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
                if ( context != null )
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            final PerReadAlleleLikelihoodMap indelLikelihoodMap = stratifiedLikelihoodMap.get(sample);
            final AlignmentContext context = stratifiedContexts.get(sample);
            if ( context == null || indelLikelihoodMap == null )
                continue;

            ReadBackedPileup pileup = context.getBasePileup();
            if (pileup == null)
                 continue;

            for (final PileupElement p: pileup) {
                if ( p.getRead().getMappingQuality() < 20)
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            final PerReadAlleleLikelihoodMap indelLikelihoodMap = stratifiedLikelihoodMap.get(sample);
            final AlignmentContext context = stratifiedContexts.get(sample);
            if ( context == null || indelLikelihoodMap == null )
                continue;

            ReadBackedPileup pileup = context.getBasePileup();
            if (pileup == null)
                 continue;

            for (final PileupElement p: pileup) {
                if ( p.getRead().getMappingQuality() < 20)
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        final int contextWingSize = Math.min((ref.getWindow().size() - 1) / 2, MIN_CONTEXT_WING_SIZE);
        final int contextSize = contextWingSize * 2 + 1;

        final int locus = ref.getLocus().getStart() + (ref.getLocus().getStop() - ref.getLocus().getStart()) / 2;

        final ReadBackedPileup pileup = context.getBasePileup();

        // Compute all haplotypes consistent with the current read pileup
        final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus, vc);

        final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage();
        if (haplotypes != null) {
            for (final Genotype genotype : vc.getGenotypes()) {
                final AlignmentContext thisContext = stratifiedContexts.get(genotype.getSampleName());
                if (thisContext != null) {
                    final ReadBackedPileup thisPileup = thisContext.getBasePileup();
                    scoreRA.add(scoreReadsAgainstHaplotypes(haplotypes, thisPileup, contextSize, locus)); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
                }
            }
        }

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        final HashMap<Byte, Integer> alleleCounts = new HashMap<>();
        for ( final Allele allele : vc.getAlleles() )
            alleleCounts.put(allele.getBases()[0], 0);

        final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
        for ( final PileupElement p : pileup ) {
            if ( alleleCounts.containsKey(p.getBase()) )
                alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+1);
        }
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            return null;

        int mq0 = 0;
        for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
            final AlignmentContext context = sample.getValue();
            final ReadBackedPileup pileup = context.getBasePileup();
            for (PileupElement p : pileup ) {
                if ( p.getMappingQual() == 0 )
                    mq0++;
            }
        }
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        public VariantAndReads(VariantContext variant, AlignmentContext alignment) {
            this.variant = variant;
            this.sampleReadBases = new HashMap<String, ReadBasesAtPosition>();

            if (alignment != null) {
                ReadBackedPileup pileup = alignment.getBasePileup();
                if (pileup != null) {
                    // filter the read-base pileup based on min base and mapping qualities:
                    pileup = pileup.getBaseAndMappingFilteredPileup(MIN_BASE_QUALITY_SCORE, MIN_MAPPING_QUALITY_SCORE);
                    if (pileup != null) {
                        for (final String sample : pileup.getSamples()) {
                            ReadBackedPileup samplePileup = pileup.getPileupForSample(sample);
                            ReadBasesAtPosition readBases = new ReadBasesAtPosition();
                            for (PileupElement p : samplePileup) {
                                if (!p.isDeletion()) // IGNORE deletions for now
                                    readBases.putReadBase(p);
                            }
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        final byte[] quals = Utils.dupBytes(qual, readBases.length());

        for ( int i = 0; i < readBases.getBytes().length; i++ ) {
            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(readBases.getBytes(), quals, readBases.length() + "M");
            final GenomeLoc loc = new UnvalidatingGenomeLoc("20", 0, i, i);
            final ReadBackedPileup pileup = new ReadBackedPileupImpl(loc, Collections.singletonList(read), i);
            final int actual = model.calcNIndelInformativeReads(pileup, i, ref.getBytes(), maxIndelSize);
            Assert.assertEquals(actual, (int)expected.get(i), "failed at position " + i);
        }
    }
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            // no error models
            return add(pileup, (ErrorModel)null);
        }
        for (String laneID : perLaneErrorModels.keySet() ) {
            // get pileup for this lane
            ReadBackedPileup perLanePileup;
            if (ignoreLaneInformation)
                perLanePileup = pileup;
            else
                perLanePileup = pileup.getPileupForLane(laneID);

            if (perLanePileup == null || perLanePileup.isEmpty())
                continue;

            ErrorModel errorModel = perLaneErrorModels.get(laneID);
            n += add(perLanePileup, errorModel);
            if (ignoreLaneInformation)
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            if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                // no likelihoods have been computed for this sample at this site
                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
            }
            final ReadBackedPileup pileup = context.getBasePileup();
            if (pileup != null) {
                final GenotypeBuilder b = new GenotypeBuilder(sample.getKey());
                final double[] genotypeLikelihoods = pairModel.computeDiploidReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap.get(sample.getKey()), UAC.getSampleContamination().get(sample.getKey()));
                b.PL(genotypeLikelihoods);
                b.alleles(noCall);
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Related Classes of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup

  • bcbio.gatk.tools.walkers.annotator.RankSumTest
  • bcbio.variation.annotate.AlleleBalanceConfidenceInterval
  • bcbio.variation.annotate.MostProbableGenotype
  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalance
  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalanceBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.DepthPerAlleleBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.HaplotypeScore
  • org.broadinstitute.gatk.tools.walkers.annotator.MappingQualityZero
  • org.broadinstitute.gatk.tools.walkers.annotator.MappingQualityZeroBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest
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