Examples of AlignmentContext

org.apache.fop.layoutmgr.inline.AlignmentContext
The alignment context is carried within a LayoutContext and as part of the Knuth Inline elements to facilitate proper line building. All measurements are in mpt.
org.broadinstitute.gatk.engine.contexts.AlignmentContext
Useful class for forwarding on locusContext data from this iterator Created by IntelliJ IDEA. User: mdepristo Date: Feb 22, 2009 Time: 3:01:34 PM To change this template use File | Settings | File Templates.

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        // Can't do anything without a genotype here
        if(genotype == null)
            return null;


        int[] retVal = genotype.getAD();
        AlignmentContext context;


        if ( retVal == null && stratifiedContexts != null &&
                (context = stratifiedContexts.get(genotype.getSampleName())) != null){
            // If we get to this point, the getAD() function returned no information
            // about AlleleDepth by Sample - perhaps it wasn't annotated?
            // 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];

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        if ( requestedGenotypeAnnotations.isEmpty() )
            return vc.getGenotypes();


        final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
        for ( final Genotype genotype : vc.getGenotypes() ) {
            AlignmentContext context = null;
            PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = null;
            if (stratifiedContexts != null)
                context = stratifiedContexts.get(genotype.getSampleName());
            if (stratifiedPerReadAlleleLikelihoodMap != null)
                perReadAlleleLikelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext


        // 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");
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext


        // 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);
        }
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        // create the iterator by state with the fake reads and fake records
        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");

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        li = makeLTBS(reads, readAttributes);


        // 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");
    }

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        li = makeLTBS(reads, createTestReadProperties());
        int currentLocus = firstLocus;
        int numAlignmentContextsFound = 0;


        while(li.hasNext()) {
            AlignmentContext alignmentContext = li.next();
            Assert.assertEquals(alignmentContext.getLocation().getStart(),currentLocus,"Current locus returned by alignment context is incorrect");


            if(currentLocus == firstLocus) {
                List<GATKSAMRecord> 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) {
                List<GATKSAMRecord> 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++;

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext


        // 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());

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        int bpVisited = 0;
        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");

View Full Code Here

Examples of org.broadinstitute.gatk.engine.contexts.AlignmentContext

        final Set<GATKSAMRecord> seenSoFar = new HashSet<GATKSAMRecord>();
        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);

View Full Code Here

0 1 2 3 4

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.