Examples with GATKRead org.broadinstitute.hellbender.utils.read.GATKRead used on opensource projects

Example 56 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class RMSMappingQualityUnitTest method testEmptyLikelihoods.

@Test
public void testEmptyLikelihoods() throws Exception {
    final List<GATKRead> reads = Collections.emptyList();
    final Map<String, List<GATKRead>> readsBySample = ImmutableMap.of("sample1", reads);
    final org.broadinstitute.hellbender.utils.genotyper.SampleList sampleList = new IndexedSampleList(Arrays.asList("sample1"));
    final AlleleList<Allele> alleleList = new IndexedAlleleList<>(Arrays.asList(Allele.create("A")));
    final ReadLikelihoods<Allele> likelihoods = new ReadLikelihoods<>(sampleList, alleleList, readsBySample);
    final VariantContext vc = makeVC();
    final ReferenceContext referenceContext = null;
    final Map<String, Object> annotate = new RMSMappingQuality().annotate(referenceContext, vc, likelihoods);
    Assert.assertTrue(annotate.isEmpty());
}

Example 57 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead 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 58 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class FragmentUtilsUnitTest method makeOverlappingRead.

private GATKRead makeOverlappingRead(final String leftFlank, final int leftQual, final String overlapBases, final byte[] overlapQuals, final String rightFlank, final int rightQual, final int alignmentStart) {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    header.addReadGroup(new SAMReadGroupRecord("RG1"));
    final String bases = leftFlank + overlapBases + rightFlank;
    final int readLength = bases.length();
    final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, alignmentStart, readLength);
    final byte[] leftQuals = Utils.dupBytes((byte) leftQual, leftFlank.length());
    final byte[] rightQuals = Utils.dupBytes((byte) rightQual, rightFlank.length());
    final byte[] quals = Utils.concat(leftQuals, overlapQuals, rightQuals);
    read.setCigar(readLength + "M");
    read.setBases(bases.getBytes());
    read.setBaseQualities(quals);
    read.setReadGroup("RG1");
    read.setMappingQuality(60);
    return read;
}

Example 59 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class FractionalDownsamplerUnitTest method testSignalNoMoreReadsBefore.

@Test
public void testSignalNoMoreReadsBefore() throws Exception {
    FractionalDownsampler rd = new FractionalDownsampler(0.1);
    final GATKRead r1 = ArtificialReadUtils.createArtificialRead("100M");
    final GATKRead r2 = ArtificialReadUtils.createArtificialRead("101M");
    rd.submit(r1);
    //no op
    rd.signalNoMoreReadsBefore(r2);
    rd.submit(r2);
}

Example 60 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class PassThroughDownsamplerUnitTest method testConsumeFinalizedItems.

@Test
public void testConsumeFinalizedItems() throws Exception {
    final PassThroughDownsampler ptd = new PassThroughDownsampler();
    for (int i = 0; i < 10; i++) {
        final GATKRead read = ArtificialReadUtils.createArtificialRead("100M");
        ptd.submit(read);
    }
    Assert.assertEquals(ptd.size(), 10);
    ptd.signalEndOfInput();
    ptd.signalNoMoreReadsBefore(ptd.peekFinalized());
    Assert.assertEquals(ptd.size(), 10);
    final List<GATKRead> finalizedItems = ptd.consumeFinalizedItems();
    Assert.assertEquals(finalizedItems.size(), 10);
    Assert.assertEquals(ptd.size(), 0);
}