Package org.broadinstitute.gatk.utils.pileup

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

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        final List<GATKSAMRecord> pair = ArtificialSAMUtils.createPair(header, "readpair", 100, 1, 50, true, true);
        final GATKSAMRecord left = pair.get(0);
        final GATKSAMRecord right = pair.get(1);
        final List<GATKSAMRecord> reads = Arrays.asList(right, left); // OUT OF ORDER!
        final List<Integer> offsets = Arrays.asList(0, 50);
        final ReadBackedPileup pileup = new ReadBackedPileupImpl(null, reads, offsets);
        FragmentUtils.create(pileup); // should throw exception
    }
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                        reads.add(right);
                        offsets.add(pos - right.getAlignmentStart());
                    }

                    boolean shouldBeFragment = posCoveredByLeft && posCoveredByRight;
                    ReadBackedPileup pileup = new ReadBackedPileupImpl(null, reads, offsets);
                    TestState testState = new TestState(shouldBeFragment ? 0 : 1, shouldBeFragment ? 1 : 0, pileup, null);
                    statesForPileup.add(testState);
                }

                TestState testState = left.getAlignmentEnd() >= right.getAlignmentStart() ? new TestState(0, 1, null, pair) : new TestState(2, 0, null, pair);
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     */
    @Test()
    public void testWithAPileup() {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("1", 10);
        final ReadBackedPileup pileup = ArtificialSAMUtils.createReadBackedPileup(header, myLocation, 10, 400, 10);
        Assert.assertFalse(pileup.isEmpty());
        // TODO -- add some tests here using pileup
    }
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            read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
            reads.add(read);
        }

        // create a pileup with all reads having offset 0
        final ReadBackedPileup pileup = new ReadBackedPileupImpl(myLocation, reads, 0);
        // TODO -- add some tests here using pileup

        // this code ensures that the pileup example is correct.  Can be deleted
        Assert.assertEquals(pileup.getNumberOfElements(), pileupSize);
        int nA = 0, nC = 0;
        for ( final PileupElement p : pileup ) {
            if ( p.getBase() == 'A' ) nA++;
            if ( p.getBase() == 'C' ) nC++;
        }
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        final HashMap<Byte, Integer> alleleCounts = new HashMap<>();
        for ( final Allele allele : vc.getAlleles() )
            alleleCounts.put(allele.getBases()[0], 0);

        final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
        for ( final PileupElement p : pileup ) {
            if ( alleleCounts.containsKey(p.getBase()) )
                alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+1);
        }
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                         final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
        if ( g == null || !g.isCalled() || stratifiedContext == null )
            return;

        int mq0 = 0;
        final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
        for (PileupElement p : pileup ) {
            if ( p.getMappingQual() == 0 )
                mq0++;
        }
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            // In that case, let's try to build it up using the algorithm that
            // was here in v 3.1-1 and earlier
            // Also, b/c of the assignment check in the if statement above,
            // we know we have a valid AlignmentContext for this sample!

            final ReadBackedPileup pileup = context.getBasePileup();
            final String bases = new String(pileup.getBases());
            List<Allele> alleles = vc.getAlleles();
            final int n_allele = alleles.size();
            retVal = new int[n_allele];

            // Calculate the depth for each allele, under the assumption that
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     * @return a SimpleCall, which stores the genotype we're calling and the LOD score
     */
    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        if (ref.getBase() == 'N' || ref.getBase() == 'n') return null; // we don't deal with the N ref base case

        ReadBackedPileup pileup = context.getBasePileup().getPileupWithoutMappingQualityZeroReads();
        double likelihoods[] = getReferencePolarizedPriors(ref.getBase(),
                HUMAN_SNP_HETEROZYGOSITY,
                0.01);
        // get the bases and qualities from the pileup
        byte bases[] = pileup.getBases();
        byte quals[] = pileup.getQuals();

        // for each genotype, determine it's likelihood value
        for (GENOTYPE genotype : GENOTYPE.values())
            for (int index = 0; index < bases.length; index++) {
                // our epsilon is the de-Phred scored base quality
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    @Override
    public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        final String rods = getReferenceOrderedData( tracker );

        ReadBackedPileup basePileup = context.getBasePileup();

        final StringBuilder s = new StringBuilder();
        s.append(String.format("%s %s", basePileup.getPileupString((char)ref.getBase()), rods));
        if ( outputInsertLength )
            s.append(" ").append(insertLengthOutput(basePileup));
        if ( SHOW_VERBOSE )
            s.append(" ").append(createVerboseOutput(basePileup));
        s.append("\n");
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        // create the iterator by state with the fake reads and fake records
        li = makeLTBS(reads,createTestReadProperties(DownsamplingMethod.NONE, true));

        Assert.assertTrue(li.hasNext());
        AlignmentContext context = li.next();
        ReadBackedPileup pileup = context.getBasePileup();
        Assert.assertEquals(pileup.depthOfCoverage(), 2, "Should see only 2 reads in pileup, even with unmapped and all I reads");

        final List<GATKSAMRecord> rawReads = li.transferReadsFromAllPreviousPileups();
        Assert.assertEquals(rawReads, reads, "Input and transferred read lists should be the same, and include the unmapped and all I reads");
    }
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Related Classes of org.broadinstitute.gatk.utils.pileup.ReadBackedPileup

  • bcbio.gatk.tools.walkers.annotator.RankSumTest
  • bcbio.variation.annotate.AlleleBalanceConfidenceInterval
  • bcbio.variation.annotate.MostProbableGenotype
  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalance
  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalanceBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.DepthPerAlleleBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.HaplotypeScore
  • org.broadinstitute.gatk.tools.walkers.annotator.MappingQualityZero
  • org.broadinstitute.gatk.tools.walkers.annotator.MappingQualityZeroBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest
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