Package org.broadinstitute.gatk.utils.pileup

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

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        // create the iterator by state with the fake reads and fake records
        li = makeLTBS(reads,readAttributes);

        while (li.hasNext()) {
            AlignmentContext context = li.next();
            ReadBackedPileup pileup = context.getBasePileup();
            Assert.assertEquals(pileup.depthOfCoverage(), 4);
        }
    }
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        li = makeLTBS(reads,readAttributes);

        boolean foundIndel = false;
        while (li.hasNext()) {
            AlignmentContext context = li.next();
            ReadBackedPileup pileup = context.getBasePileup().getBaseFilteredPileup(10);
            for (PileupElement p : pileup) {
                if (p.isBeforeInsertion()) {
                    foundIndel = true;
                    Assert.assertEquals(p.getLengthOfImmediatelyFollowingIndel(), 2, "Wrong event length");
                    Assert.assertEquals(p.getBasesOfImmediatelyFollowingInsertion(), "CT", "Inserted bases are incorrect");
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        // Traditionally, reads that end with indels bleed into the pileup at the following locus.  Verify that the next pileup contains this read
        // and considers it to be an indel-containing read.
        Assert.assertTrue(li.hasNext(),"Should have found a whole-indel read in the normal base pileup without extended events enabled");
        AlignmentContext alignmentContext = li.next();
        Assert.assertEquals(alignmentContext.getLocation().getStart(), firstLocus, "Base pileup is at incorrect location.");
        ReadBackedPileup basePileup = alignmentContext.getBasePileup();
        Assert.assertEquals(basePileup.getReads().size(),1,"Pileup is of incorrect size");
        Assert.assertSame(basePileup.getReads().get(0), indelOnlyRead, "Read in pileup is incorrect");
    }
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        // create the iterator by state with the fake reads and fake records
        li = makeLTBS(reads, createTestReadProperties());

        while(li.hasNext()) {
            AlignmentContext alignmentContext = li.next();
            ReadBackedPileup p = alignmentContext.getBasePileup();
            Assert.assertTrue(p.getNumberOfElements() == 1);
            // TODO -- fix tests
//            PileupElement pe = p.iterator().next();
//            Assert.assertTrue(pe.isBeforeInsertion());
//            Assert.assertFalse(pe.isAfterInsertion());
//            Assert.assertEquals(pe.getBasesOfImmediatelyFollowingInsertion(), "A");
        }

        GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,secondLocus,10);
        read2.setReadBases(Utils.dupBytes((byte) 'A', 10));
        read2.setBaseQualities(Utils.dupBytes((byte) '@', 10));
        read2.setCigarString("10I");

        reads = Arrays.asList(read2);

        // create the iterator by state with the fake reads and fake records
        li = makeLTBS(reads, createTestReadProperties());

        while(li.hasNext()) {
            AlignmentContext alignmentContext = li.next();
            ReadBackedPileup p = alignmentContext.getBasePileup();
            Assert.assertTrue(p.getNumberOfElements() == 1);
            // TODO -- fix tests
//            PileupElement pe = p.iterator().next();
//            Assert.assertTrue(pe.isBeforeInsertion());
//            Assert.assertFalse(pe.isAfterInsertion());
//            Assert.assertEquals(pe.getBasesOfImmediatelyFollowingInsertion(), "AAAAAAAAAA");
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        Assert.assertEquals(pe.getLengthOfImmediatelyFollowingIndel(), eventSize, "Length of event failed");
        Assert.assertEquals(pe.getBasesOfImmediatelyFollowingInsertion(), eventBases, "Getbases of following event failed");
    }

    private PileupElement getFirstPileupElement(final AlignmentContext context) {
        final ReadBackedPileup p = context.getBasePileup();
        Assert.assertEquals(p.getNumberOfElements(), 1);
        return p.iterator().next();
    }
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        int lastOffset = 0;
        while ( li.hasNext() ) {
            bpVisited++;

            AlignmentContext alignmentContext = li.next();
            ReadBackedPileup p = alignmentContext.getBasePileup();
            Assert.assertEquals(p.getNumberOfElements(), 1);
            PileupElement pe = p.iterator().next();

            Assert.assertEquals(p.getNumberOfDeletions(), pe.isDeletion() ? 1 : 0, "wrong number of deletions in the pileup");
            Assert.assertEquals(p.getNumberOfMappingQualityZeroReads(), 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");
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        final Set<GATKSAMRecord> keptReads = new HashSet<GATKSAMRecord>();
        int bpVisited = 0;
        while ( li.hasNext() ) {
            bpVisited++;
            final AlignmentContext alignmentContext = li.next();
            final ReadBackedPileup p = alignmentContext.getBasePileup();

            AssertWellOrderedPileup(p);

            if ( downsample ) {
                // just not a safe test
                //Assert.assertTrue(p.getNumberOfElements() <= maxDownsampledCoverage * nSamples, "Too many reads at locus after downsampling");
            } else {
                final int minPileupSize = nReadsPerLocus * nSamples;
                Assert.assertTrue(p.getNumberOfElements() >= minPileupSize);
            }

            // the number of reads starting here
            int nReadsStartingHere = 0;
            for ( final GATKSAMRecord read : p.getReads() )
                if ( read.getAlignmentStart() == alignmentContext.getPosition() )
                    nReadsStartingHere++;

            // we can have no more than maxDownsampledCoverage per sample
            final int maxCoveragePerLocus = downsample ? downsampleTo : nReadsPerLocus;
            Assert.assertTrue(nReadsStartingHere <= maxCoveragePerLocus * nSamples);

            seenSoFar.addAll(p.getReads());
            if ( keepReads && grabReadsAfterEachCycle ) {
                final List<GATKSAMRecord> locusReads = li.transferReadsFromAllPreviousPileups();


                if ( downsample ) {
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     */
    @Argument(fullName="continue_after_error",doc="Continue after encountering an error",required=false)
    public boolean CONTINUE_AFTER_AN_ERROR = false;

    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        ReadBackedPileup pileup = context.getBasePileup();
        SAMPileupFeature truePileup = getTruePileup( tracker );

        if ( truePileup == null ) {
            out.printf("No truth pileup data available at %s%n", pileup.getPileupString(ref.getBaseAsChar()));
            if ( ! CONTINUE_AFTER_AN_ERROR ) {
                throw new UserException.BadInput(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
                        context.getLocation(), new String(pileup.getBases())));
            }
        } else {
            String pileupDiff = pileupDiff(pileup, truePileup, true);
            if ( pileupDiff != null ) {
                out.printf("%s vs. %s%n", pileup.getPileupString(ref.getBaseAsChar()), truePileup.getPileupString());
                if ( ! CONTINUE_AFTER_AN_ERROR ) {
                    throw new UserException.BadInput(String.format("The input pileup doesn't match the GATK's internal pileup: %s", pileupDiff));
                }
            }
        }

        return pileup.getNumberOfElements();
    }
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  • org.broadinstitute.gatk.tools.walkers.annotator.MappingQualityZeroBySample
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