Examples with ReadPileup org.broadinstitute.hellbender.utils.pileup.ReadPileup used on opensource projects

Example 1 with ReadPileup

use of org.broadinstitute.hellbender.utils.pileup.ReadPileup in project gatk by broadinstitute.

the class PileupSpark method pileupFunction.

private static Function<LocusWalkerContext, String> pileupFunction(List<FeatureInput<Feature>> metadata, boolean outputInsertLength, boolean showVerbose) {
    return (Function<LocusWalkerContext, String>) context -> {
        AlignmentContext alignmentContext = context.getAlignmentContext();
        ReferenceContext referenceContext = context.getReferenceContext();
        FeatureContext featureContext = context.getFeatureContext();
        final String features = getFeaturesString(featureContext, metadata);
        final ReadPileup basePileup = alignmentContext.getBasePileup();
        final StringBuilder s = new StringBuilder();
        s.append(String.format("%s %s", basePileup.getPileupString((referenceContext.hasBackingDataSource()) ? (char) referenceContext.getBase() : 'N'), features));
        if (outputInsertLength) {
            s.append(" ").append(insertLengthOutput(basePileup));
        }
        if (showVerbose) {
            s.append(" ").append(createVerboseOutput(basePileup));
        }
        s.append("\n");
        return s.toString();
    };
}

Example 2 with ReadPileup

use of org.broadinstitute.hellbender.utils.pileup.ReadPileup in project gatk by broadinstitute.

the class FragmentCollectionUnitTest method createFromMultiSamplePileup.

@Test
public void createFromMultiSamplePileup() throws Exception {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "10M");
    final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, "10M");
    read1.setPosition(new SimpleInterval("22", 200, 210));
    read2.setPosition(new SimpleInterval("22", 208, 218));
    read1.setMatePosition(read2);
    read2.setMatePosition(read1);
    final Locatable loc = new SimpleInterval("22", 208, 208);
    final Map<String, ReadPileup> stratified = new LinkedHashMap<>();
    stratified.put("sample1", new ReadPileup(loc, Arrays.asList(read2), 0));
    stratified.put("sample2", new ReadPileup(loc, Arrays.asList(read1), 9));
    final ReadPileup combined = new ReadPileup(loc, stratified);
    final FragmentCollection<PileupElement> elements = FragmentCollection.create(combined);
    Assert.assertTrue(elements.getSingletonReads().isEmpty());
    Assert.assertEquals(elements.getOverlappingPairs().size(), 1);
}

Example 3 with ReadPileup

use of org.broadinstitute.hellbender.utils.pileup.ReadPileup in project gatk-protected by broadinstitute.

the class CalculateMixingFractions method apply.

@Override
public void apply(final VariantContext vc, final ReadsContext readsContext, final ReferenceContext refContext, final FeatureContext fc) {
    if (!isBiallelicSingletonHetSnp(vc)) {
        return;
    }
    final Optional<String> variantSample = StreamSupport.stream(vc.getGenotypes().spliterator(), false).filter(genotype -> genotype.isHet()).map(genotype -> genotype.getSampleName()).findFirst();
    if (!variantSample.isPresent()) {
        return;
    }
    final List<GATKRead> reads = new ArrayList<>();
    final List<Integer> offsets = new ArrayList<>();
    for (final GATKRead read : readsContext) {
        if (read.failsVendorQualityCheck()) {
            continue;
        }
        final AlignmentStateMachine asm = new AlignmentStateMachine(read);
        while (asm.stepForwardOnGenome() != null && asm.getGenomePosition() < vc.getStart()) {
        }
        if (asm.getGenomePosition() == vc.getStart()) {
            reads.add(read);
            offsets.add(asm.getReadOffset());
        }
    }
    final ReadPileup pileup = new ReadPileup(vc, reads, offsets);
    final byte altBase = vc.getAlternateAllele(0).getBases()[0];
    final long altCount = StreamSupport.stream(pileup.spliterator(), false).filter(pe -> pe.getBase() == altBase).count();
    final long totalCount = pileup.size();
    sampleCounts.get(variantSample.get()).addCounts(altCount, totalCount);
}

Example 4 with ReadPileup

use of org.broadinstitute.hellbender.utils.pileup.ReadPileup in project gatk-protected by broadinstitute.

the class HaplotypeCallerGenotypingEngineUnitTest method testAddMiscellaneousAllele.

@Test(dataProvider = "AddMiscellaneousDataProvider", enabled = false)
public void testAddMiscellaneousAllele(final String readBases, final int readOffset, final String ref, final int refOffset, final String referenceAllele, final String[] alternatives, final double[] likelihoods, final double[] expected) {
    final byte baseQual = (byte) 30;
    final byte[] baseQuals = Utils.dupBytes(baseQual, readBases.length());
    final GATKRead read = ArtificialReadUtils.createArtificialRead(readBases.getBytes(), baseQuals, readBases.length() + "M");
    final Locatable loc = new SimpleInterval("20", refOffset, refOffset);
    final ReadPileup pileup = new ReadPileup(loc, Collections.singletonList(read), readOffset);
    final VariantContextBuilder vcb = new VariantContextBuilder();
    final GenotypeBuilder gb = new GenotypeBuilder();
    final List<String> alleleStrings = new ArrayList<>(1 + alternatives.length);
    alleleStrings.add(referenceAllele);
    alleleStrings.addAll(Arrays.asList(alternatives));
    gb.AD(new int[] { 1 });
    gb.DP(1);
    gb.PL(likelihoods);
    vcb.alleles(alleleStrings);
    vcb.loc("20", refOffset, refOffset + referenceAllele.length() - 1);
    vcb.genotypes(gb.make());
    final VariantContext vc = vcb.make();
    // GenotypingEngine.addMiscellaneousAllele(vc,pileup,ref.getBytes(),0);
    final VariantContext updatedVc = null;
    final GenotypeLikelihoods updatedLikelihoods = updatedVc.getGenotype(0).getLikelihoods();
    Assert.assertEquals(updatedLikelihoods.getAsVector().length, expected.length);
    final double[] updatedLikelihoodsArray = updatedVc.getGenotype(0).getLikelihoods().getAsVector();
    for (int i = 0; i < updatedLikelihoodsArray.length; i++) {
        Assert.assertEquals(updatedLikelihoodsArray[i], expected[i], 0.0001);
    }
    Allele altAllele = null;
    for (final Allele allele : updatedVc.getAlleles()) if (allele.isSymbolic() && allele.getBaseString().equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE_NAME))
        altAllele = allele;
    Assert.assertNotNull(altAllele);
}

Example 5 with ReadPileup

use of org.broadinstitute.hellbender.utils.pileup.ReadPileup in project gatk by broadinstitute.

the class PileupUnitTest method testCreateVerboseOutput.

@Test
public void testCreateVerboseOutput() throws Exception {
    // the header
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    final SimpleInterval loc = new SimpleInterval("1:2");
    // create one read/pileup element with deletion with the following verbose string
    final String read1String = "read1@1@10@20";
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10);
    read1.setMappingQuality(20);
    read1.setCigar("1M1D9M");
    final PileupElement pe1 = new PileupElement(read1, 1, read1.getCigar().getCigarElement(1), 1, 0);
    // create a second one without it with the following verbose string
    final String read2String = "read2@1@50@10";
    final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, "read2", 0, 2, 50);
    read2.setMappingQuality(10);
    read2.setCigar("50M");
    final PileupElement pe2 = PileupElement.createPileupForReadAndOffset(read2, 1);
    // generate the pileups
    final ReadPileup pileup = new ReadPileup(loc, Arrays.asList(pe1, pe2));
    // test one read
    Assert.assertEquals(Pileup.createVerboseOutput(pileup.makeFilteredPileup(p -> p.getRead().getName().equals("read1"))), "1 " + read1String);
    Assert.assertEquals(Pileup.createVerboseOutput(pileup.makeFilteredPileup(p -> p.getRead().getName().equals("read2"))), "0 " + read2String);
    // test two reads
    Assert.assertEquals(Pileup.createVerboseOutput(pileup), "1 " + read1String + "," + read2String);
    // test an empty pileup
    Assert.assertEquals(Pileup.createVerboseOutput(new ReadPileup(loc)), "0 ");
}