Examples with AlignmentContext org.broadinstitute.hellbender.engine.AlignmentContext used on opensource projects

Example 21 with AlignmentContext

use of org.broadinstitute.hellbender.engine.AlignmentContext in project gatk by broadinstitute.

the class LocusIteratorByStateUnitTest method testLIBS_NotHoldingTooManyReads.

@Test(enabled = true, dataProvider = "LIBS_NotHoldingTooManyReads")
public void testLIBS_NotHoldingTooManyReads(final int nReadsPerLocus, final int downsampleTo, final int payloadInBytes) {
    logger.warn(String.format("testLIBS_NotHoldingTooManyReads %d %d %d", nReadsPerLocus, downsampleTo, payloadInBytes));
    final int readLength = 10;
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 100000);
    final int nSamples = 1;
    final List<String> samples = new ArrayList<>(nSamples);
    for (int i = 0; i < nSamples; i++) {
        final SAMReadGroupRecord rg = new SAMReadGroupRecord("rg" + i);
        final String sample = "sample" + i;
        samples.add(sample);
        rg.setSample(sample);
        rg.setPlatform(NGSPlatform.ILLUMINA.getDefaultPlatform());
        header.addReadGroup(rg);
    }
    final boolean downsample = downsampleTo != -1;
    final DownsamplingMethod downsampler = downsample ? new DownsamplingMethod(DownsampleType.BY_SAMPLE, downsampleTo, null) : new DownsamplingMethod(DownsampleType.NONE, null, null);
    final WeakReadTrackingIterator iterator = new WeakReadTrackingIterator(nReadsPerLocus, readLength, payloadInBytes, header);
    final LocusIteratorByState li;
    li = new LocusIteratorByState(iterator, downsampler, false, samples, header, true);
    while (li.hasNext()) {
        final AlignmentContext next = li.next();
        Assert.assertTrue(next.getBasePileup().size() <= downsampleTo, "Too many elements in pileup " + next);
    // TODO -- assert that there are <= X reads in memory after GC for some X
    }
}

Example 22 with AlignmentContext

use of org.broadinstitute.hellbender.engine.AlignmentContext in project gatk by broadinstitute.

the class LocusIteratorByStateUnitTest method testWholeIndelRead.

/**
     * Test to make sure that reads supporting only an indel (example cigar string: 76I) do
     * not negatively influence the ordering of the pileup.
     */
@Test
public void testWholeIndelRead() {
    final int firstLocus = 44367788, secondLocus = firstLocus + 1;
    final GATKRead leadingRead = ArtificialReadUtils.createArtificialRead(header, "leading", 0, firstLocus, 76);
    leadingRead.setBases(Utils.dupBytes((byte) 'A', 76));
    leadingRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
    leadingRead.setCigar("1M75I");
    final GATKRead indelOnlyRead = ArtificialReadUtils.createArtificialRead(header, "indelOnly", 0, secondLocus, 76);
    indelOnlyRead.setBases(Utils.dupBytes((byte) 'A', 76));
    indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
    indelOnlyRead.setCigar("76I");
    final GATKRead fullMatchAfterIndel = ArtificialReadUtils.createArtificialRead(header, "fullMatch", 0, secondLocus, 76);
    fullMatchAfterIndel.setBases(Utils.dupBytes((byte) 'A', 76));
    fullMatchAfterIndel.setBaseQualities(Utils.dupBytes((byte) '@', 76));
    fullMatchAfterIndel.setCigar("75I1M");
    final List<GATKRead> reads = Arrays.asList(leadingRead, indelOnlyRead, fullMatchAfterIndel);
    // create the iterator by state with the fake reads and fake records
    final LocusIteratorByState li;
    li = makeLIBS(reads, null, false, header);
    int currentLocus = firstLocus;
    int numAlignmentContextsFound = 0;
    while (li.hasNext()) {
        final AlignmentContext alignmentContext = li.next();
        Assert.assertEquals(alignmentContext.getLocation().getStart(), currentLocus, "Current locus returned by alignment context is incorrect");
        if (currentLocus == firstLocus) {
            final List<GATKRead> readsAtLocus = alignmentContext.getBasePileup().getReads();
            Assert.assertEquals(readsAtLocus.size(), 1, "Wrong number of reads at locus " + currentLocus);
            Assert.assertSame(readsAtLocus.get(0), leadingRead, "leadingRead absent from pileup at locus " + currentLocus);
        } else if (currentLocus == secondLocus) {
            final List<GATKRead> readsAtLocus = alignmentContext.getBasePileup().getReads();
            Assert.assertEquals(readsAtLocus.size(), 1, "Wrong number of reads at locus " + currentLocus);
            Assert.assertSame(readsAtLocus.get(0), fullMatchAfterIndel, "fullMatchAfterIndel absent from pileup at locus " + currentLocus);
        }
        currentLocus++;
        numAlignmentContextsFound++;
    }
    Assert.assertEquals(numAlignmentContextsFound, 2, "Found incorrect number of alignment contexts");
}

Example 23 with AlignmentContext

use of org.broadinstitute.hellbender.engine.AlignmentContext in project gatk by broadinstitute.

the class LocusIteratorByStateUnitTest method testXandEQOperators.

@Test
public void testXandEQOperators() {
    final byte[] bases1 = { 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A' };
    final byte[] bases2 = { 'A', 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'A', 'C' };
    final GATKRead r1 = ArtificialReadUtils.createArtificialRead(header, "r1", 0, 1, 10);
    r1.setBases(bases1);
    r1.setBaseQualities(new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20 });
    r1.setCigar("10M");
    final GATKRead r2 = ArtificialReadUtils.createArtificialRead(header, "r2", 0, 1, 10);
    r2.setBases(bases2);
    r2.setBaseQualities(new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20 });
    r2.setCigar("3=1X5=1X");
    final GATKRead r3 = ArtificialReadUtils.createArtificialRead(header, "r3", 0, 1, 10);
    r3.setBases(bases2);
    r3.setBaseQualities(new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20 });
    r3.setCigar("3=1X5M1X");
    final GATKRead r4 = ArtificialReadUtils.createArtificialRead(header, "r4", 0, 1, 10);
    r4.setBases(bases2);
    r4.setBaseQualities(new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20 });
    r4.setCigar("10M");
    final List<GATKRead> reads = Arrays.asList(r1, r2, r3, r4);
    // create the iterator by state with the fake reads and fake records
    final LocusIteratorByState li;
    li = makeLIBS(reads, header);
    while (li.hasNext()) {
        final AlignmentContext context = li.next();
        final ReadPileup pileup = context.getBasePileup();
        Assert.assertEquals(pileup.size(), 4);
    }
}

Example 24 with AlignmentContext

use of org.broadinstitute.hellbender.engine.AlignmentContext in project gatk by broadinstitute.

the class IntervalAlignmentContextIteratorUnitTest method testSimple.

@Test
public void testSimple() {
    // Note: IGV was used to determine coverage in the input bam file. (chr20:9,999,875-9,999,945)
    //   Make sure that viewing is *not* downsampled and *includes* dupe reads
    // Totally uncovered
    final SimpleInterval record_20_9999600_9999600 = new SimpleInterval("20:9999600-9999600");
    // Partially covered
    final SimpleInterval record_20_9999900_9999910 = new SimpleInterval("20:9999900-9999910");
    // Totally covered
    final SimpleInterval record_20_9999910_9999913 = new SimpleInterval("20:9999910-9999913");
    final List<SimpleInterval> locusIntervals = new ArrayList<>(3);
    locusIntervals.add(record_20_9999600_9999600);
    locusIntervals.add(record_20_9999900_9999910);
    locusIntervals.add(record_20_9999910_9999913);
    final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(locusIntervals, BAM_FILE_NAME);
    Assert.assertEquals(allAlignmentContexts.size(), 16);
    Assert.assertTrue(allAlignmentContexts.stream().allMatch(ac -> ac != null));
    // No reads in the first three alignment contexts
    Assert.assertEquals(allAlignmentContexts.get(0).getBasePileup().getReads().size(), 0);
    Assert.assertEquals(allAlignmentContexts.get(1).getBasePileup().getReads().size(), 0);
    Assert.assertEquals(allAlignmentContexts.get(2).getBasePileup().getReads().size(), 0);
    // Make sure that at least one locus-interval has at least one read
    Assert.assertTrue(allAlignmentContexts.stream().anyMatch(ac -> ac.getBasePileup().getReads().size() > 0));
    Assert.assertTrue(allAlignmentContexts.stream().anyMatch(ac -> ac.getBasePileup().getReads().size() == 0));
    Assert.assertEquals(allAlignmentContexts.get(3).getBasePileup().getReads().size(), 2);
    Assert.assertEquals(allAlignmentContexts.get(4).getBasePileup().getReads().size(), 4);
    Assert.assertEquals(allAlignmentContexts.get(13).getBasePileup().getReads().size(), 17);
}

Example 25 with AlignmentContext

use of org.broadinstitute.hellbender.engine.AlignmentContext in project gatk by broadinstitute.

the class IntervalAlignmentContextIteratorUnitTest method testPileupToNextPileup.

@Test
public void testPileupToNextPileup() {
    // Test reading the end of one pileup then no coverage then beginning of one pileup in one interval
    //  IGV: chr20:10,098,446-10,098,587
    final SimpleInterval record_20_10098490_10098560 = new SimpleInterval("20:10098490-10098560");
    final List<SimpleInterval> locusIntervals = new ArrayList<>(1);
    locusIntervals.add(record_20_10098490_10098560);
    final List<AlignmentContext> allAlignmentContexts = getAlignmentContexts(locusIntervals, BAM_FILE_NAME);
    Assert.assertEquals(allAlignmentContexts.size(), 71);
    Assert.assertTrue(allAlignmentContexts.stream().allMatch(ac -> ac.getBasePileup().getReads().size() < 2));
    Assert.assertTrue(IntStream.range(0, 6).allMatch(i -> allAlignmentContexts.get(i).size() == 1));
    Assert.assertTrue(IntStream.range(6, 62).allMatch(i -> allAlignmentContexts.get(i).size() == 0));
    Assert.assertTrue(IntStream.range(62, 71).allMatch(i -> allAlignmentContexts.get(i).size() == 1));
    Assert.assertTrue(allAlignmentContexts.stream().allMatch(ac -> ac != null));
}