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

Example 6 with PileupElement

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

the class LocusIteratorByStateUnitTest method testLIBS.

@Test(enabled = true, dataProvider = "MyLIBSTest")
public void testLIBS(final LIBSTest params) {
    // create the iterator by state with the fake reads and fake records
    final GATKRead read = params.makeRead();
    final LocusIteratorByState li;
    li = makeLIBS(Arrays.asList(read), null, false, header);
    final LIBS_position tester = new LIBS_position(read);
    int bpVisited = 0;
    int lastOffset = 0;
    while (li.hasNext()) {
        bpVisited++;
        final AlignmentContext alignmentContext = li.next();
        final ReadPileup p = alignmentContext.getBasePileup();
        Assert.assertEquals(p.size(), 1);
        final PileupElement pe = p.iterator().next();
        Assert.assertEquals(p.getNumberOfElements(el -> el.isDeletion()), pe.isDeletion() ? 1 : 0, "wrong number of deletions in the pileup");
        Assert.assertEquals(p.getNumberOfElements(el -> el.getRead().getMappingQuality() == 0), pe.getRead().getMappingQuality() == 0 ? 1 : 0, "wront number of mapq reads in the pileup");
        tester.stepForwardOnGenome();
        if (!hasNeighboringPaddedOps(params.getElements(), pe.getCurrentCigarOffset())) {
            Assert.assertEquals(pe.isBeforeDeletionStart(), tester.isBeforeDeletionStart, "before deletion start failure");
            Assert.assertEquals(pe.isAfterDeletionEnd(), tester.isAfterDeletionEnd, "after deletion end failure");
        }
        Assert.assertEquals(pe.isBeforeInsertion(), tester.isBeforeInsertion, "before insertion failure");
        Assert.assertEquals(pe.isAfterInsertion(), tester.isAfterInsertion, "after insertion failure");
        Assert.assertEquals(pe.isNextToSoftClip(), tester.isNextToSoftClip, "next to soft clip failure");
        Assert.assertTrue(pe.getOffset() >= lastOffset, "Somehow read offsets are decreasing: lastOffset " + lastOffset + " current " + pe.getOffset());
        Assert.assertEquals(pe.getOffset(), tester.getCurrentReadOffset(), "Read offsets are wrong at " + bpVisited);
        Assert.assertEquals(pe.getCurrentCigarElement(), read.getCigar().getCigarElement(tester.currentOperatorIndex), "CigarElement index failure");
        Assert.assertEquals(pe.getOffsetInCurrentCigar(), tester.getCurrentPositionOnOperatorBase0(), "CigarElement index failure");
        Assert.assertEquals(read.getCigar().getCigarElement(pe.getCurrentCigarOffset()), pe.getCurrentCigarElement(), "Current cigar element isn't what we'd get from the read itself");
        Assert.assertTrue(pe.getOffsetInCurrentCigar() >= 0, "Offset into current cigar too small");
        Assert.assertTrue(pe.getOffsetInCurrentCigar() < pe.getCurrentCigarElement().getLength(), "Offset into current cigar too big");
        Assert.assertEquals(pe.getOffset(), tester.getCurrentReadOffset(), "Read offset failure");
        lastOffset = pe.getOffset();
    }
    final int expectedBpToVisit = read.getEnd() - read.getStart() + 1;
    Assert.assertEquals(bpVisited, expectedBpToVisit, "Didn't visit the expected number of bp");
}

Example 7 with PileupElement

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

the class LocusIteratorByStateUnitTest method AssertWellOrderedPileup.

private void AssertWellOrderedPileup(final ReadPileup pileup) {
    if (!pileup.isEmpty()) {
        final int leftMostPos = -1;
        for (final PileupElement pe : pileup) {
            Assert.assertTrue(pileup.getLocation().getContig().equals(pe.getRead().getContig()), "ReadPileup contains an element " + pe + " that's on a different contig than the pileup itself");
            Assert.assertTrue(pe.getRead().getStart() >= leftMostPos, "ReadPileup contains an element " + pe + " whose read's alignment start " + pe.getRead().getStart() + " occurs before the leftmost position we've seen previously " + leftMostPos);
        }
    }
}

Example 8 with PileupElement

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

the class LocusIteratorByStateUnitTest method testWholeIndelReadRepresentedTest.

/**
     * Test to make sure that reads supporting only an indel (example cigar string: 76I) are represented properly
     */
@Test
public void testWholeIndelReadRepresentedTest() {
    final int firstLocus = 44367788, secondLocus = firstLocus + 1;
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, secondLocus, 1);
    read1.setBases(Utils.dupBytes((byte) 'A', 1));
    read1.setBaseQualities(Utils.dupBytes((byte) '@', 1));
    read1.setCigar("1I");
    List<GATKRead> reads = Arrays.asList(read1);
    // create the iterator by state with the fake reads and fake records
    LocusIteratorByState li;
    li = makeLIBS(reads, null, false, header);
    while (li.hasNext()) {
        final AlignmentContext alignmentContext = li.next();
        final ReadPileup p = alignmentContext.getBasePileup();
        Assert.assertTrue(p.size() == 1);
        PileupElement pe = p.iterator().next();
        Assert.assertTrue(pe.isBeforeInsertion());
        Assert.assertFalse(pe.isAfterInsertion());
        Assert.assertEquals(pe.getBasesOfImmediatelyFollowingInsertion(), "A");
    }
    final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, "read2", 0, secondLocus, 10);
    read2.setBases(Utils.dupBytes((byte) 'A', 10));
    read2.setBaseQualities(Utils.dupBytes((byte) '@', 10));
    read2.setCigar("10I");
    reads = Arrays.asList(read2);
    // create the iterator by state with the fake reads and fake records
    li = makeLIBS(reads, null, false, header);
    while (li.hasNext()) {
        final AlignmentContext alignmentContext = li.next();
        final ReadPileup p = alignmentContext.getBasePileup();
        Assert.assertTrue(p.size() == 1);
        PileupElement pe = p.iterator().next();
        Assert.assertTrue(pe.isBeforeInsertion());
        Assert.assertFalse(pe.isAfterInsertion());
        Assert.assertEquals(pe.getBasesOfImmediatelyFollowingInsertion(), "AAAAAAAAAA");
    }
}

Example 9 with PileupElement

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

the class ReferenceConfidenceModel method calcNIndelInformativeReads.

/**
     * Calculate the number of indel informative reads at pileup
     *
     * @param pileup a pileup
     * @param pileupOffsetIntoRef the position of the pileup in the reference
     * @param ref the ref bases
     * @param maxIndelSize maximum indel size to consider in the informativeness calculation
     * @return an integer >= 0
     */
@VisibleForTesting
int calcNIndelInformativeReads(final ReadPileup pileup, final int pileupOffsetIntoRef, final byte[] ref, final int maxIndelSize) {
    int nInformative = 0;
    for (final PileupElement p : pileup) {
        final GATKRead read = p.getRead();
        final int offset = p.getOffset();
        // doesn't count as evidence
        if (p.isBeforeDeletionStart() || p.isBeforeInsertion() || p.isDeletion()) {
            continue;
        }
        // todo -- this code really should handle CIGARs directly instead of relying on the above tests
        if (isReadInformativeAboutIndelsOfSize(read, offset, ref, pileupOffsetIntoRef, maxIndelSize)) {
            nInformative++;
            if (nInformative > MAX_N_INDEL_INFORMATIVE_READS) {
                return MAX_N_INDEL_INFORMATIVE_READS;
            }
        }
    }
    return nInformative;
}

Example 10 with PileupElement

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

the class ASEReadCounter method calculateLineForSite.

private String calculateLineForSite(final ReadPileup pileup, final String siteID, final char refAllele, final char altAllele) {
    int rawDepth = 0, lowBaseQDepth = 0, lowMAPQDepth = 0, refCount = 0, altCount = 0, totalNonFilteredCount = 0, otherBasesCount = 0, improperPairsCount = 0;
    for (final PileupElement base : pileup) {
        rawDepth++;
        if (base.getRead().isPaired() && (base.getRead().mateIsUnmapped() || !base.getRead().isProperlyPaired())) {
            improperPairsCount++;
            continue;
        }
        if (base.getMappingQual() < minMappingQuality) {
            lowMAPQDepth++;
            continue;
        }
        if (base.getQual() < minBaseQuality) {
            lowBaseQDepth++;
            continue;
        }
        if (base.getBase() == refAllele) {
            refCount++;
        } else if (base.getBase() == altAllele) {
            altCount++;
        } else {
            otherBasesCount++;
            continue;
        }
        totalNonFilteredCount++;
    }
    if (totalNonFilteredCount < minDepthOfNonFilteredBases) {
        return null;
    }
    final StringBuilder line = new StringBuilder();
    line.append(pileup.getLocation().getContig()).append(separator);
    line.append(pileup.getLocation().getStart()).append(separator);
    line.append(siteID).append(separator);
    line.append(refAllele).append(separator);
    line.append(altAllele).append(separator);
    line.append(refCount).append(separator);
    line.append(altCount).append(separator);
    line.append(totalNonFilteredCount).append(separator);
    line.append(lowMAPQDepth).append(separator);
    line.append(lowBaseQDepth).append(separator);
    line.append(rawDepth).append(separator);
    line.append(otherBasesCount).append(separator);
    line.append(improperPairsCount);
    return line.toString();
}