Package htsjdk.samtools

Examples of htsjdk.samtools.CigarElement

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            int length = (cigarBytes[i] - ZERO_BYTE);
            for (++i; isDigit(cigarBytes[i]); ++i) {
                length = (length * 10) + cigarBytes[i] - ZERO_BYTE;
            }
            final CigarOperator operator = CigarOperator.characterToEnum(cigarBytes[i]);
            ret.add(new CigarElement(length, operator));
        }
        return ret;
    }
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    int getNumClippedBasesAtStart(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        final CigarElement first = c.getCigarElement(0);

        int numStartClippedBases = 0;
        if (first.getOperator() == CigarOperator.H) {
            numStartClippedBases = first.getLength();
        }
        byte[] unclippedReadBases = read.getReadBases();
        byte[] unclippedReadQuals = read.getBaseQualities();

        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,
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    int getNumClippedBasesAtEnd(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);

        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
        byte[] unclippedReadBases = read.getReadBases();
        byte[] unclippedReadQuals = read.getBaseQualities();

        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,
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    int getNumClippedBasesAtStart(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        final CigarElement first = c.getCigarElement(0);

        int numStartClippedBases = 0;
        if (first.getOperator() == CigarOperator.H) {
            numStartClippedBases = first.getLength();
        }
        byte[] unclippedReadBases = read.getReadBases();
        byte[] unclippedReadQuals = read.getBaseQualities();

        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,
View Full Code Here
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    int getNumClippedBasesAtEnd(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);

        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
        byte[] unclippedReadBases = read.getReadBases();
        byte[] unclippedReadQuals = read.getBaseQualities();

        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,
View Full Code Here
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    int getNumClippedBasesAtStart(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        final CigarElement first = c.getCigarElement(0);

        int numStartClippedBases = 0;
        if (first.getOperator() == CigarOperator.H) {
            numStartClippedBases = first.getLength();
        }
        byte[] unclippedReadBases = read.getReadBases();
        byte[] unclippedReadQuals = read.getBaseQualities();

        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,
View Full Code Here
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    int getNumClippedBasesAtEnd(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);

        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
        byte[] unclippedReadBases = read.getReadBases();
        byte[] unclippedReadQuals = read.getBaseQualities();

        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,
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        final int originalIndex = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
        final byte[] originalIndel = makeHaplotype(vc, refSeq, originalIndex, indelLength);

        // create a CIGAR string to represent the event
        ArrayList<CigarElement> elements = new ArrayList<CigarElement>();
        elements.add(new CigarElement(originalIndex, CigarOperator.M));
        elements.add(new CigarElement(indelLength, vc.isSimpleDeletion() ? CigarOperator.D : CigarOperator.I));
        elements.add(new CigarElement(refSeq.length - originalIndex, CigarOperator.M));
        Cigar originalCigar = new Cigar(elements);

        // left align the CIGAR
        Cigar newCigar = AlignmentUtils.leftAlignIndel(originalCigar, refSeq, originalIndel, 0, 0, true);
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        path = new Path<>(path, graph.getEdge(v, v2Alt));
        path = new Path<>(path, graph.getEdge(v2Alt, v3));

        // Construct the actual cigar string implied by the test path
        Cigar expectedCigar = new Cigar();
        expectedCigar.add(new CigarElement(preRef.length(), CigarOperator.M));
        if( refBubbleLength > altBubbleLength ) {
            expectedCigar.add(new CigarElement(refBubbleLength - altBubbleLength, CigarOperator.D));
            expectedCigar.add(new CigarElement(altBubbleLength, CigarOperator.M));
        } else if ( refBubbleLength < altBubbleLength ) {
            expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M));
            expectedCigar.add(new CigarElement(altBubbleLength - refBubbleLength,CigarOperator.I));
        } else {
            expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M));
        }
        expectedCigar.add(new CigarElement(postRef.length(), CigarOperator.M));

        final String ref = preRef + v2Ref.getSequenceString() + postRef;
        Assert.assertEquals(path.calculateCigar(ref.getBytes()).toString(), AlignmentUtils.consolidateCigar(expectedCigar).toString(), "Cigar string mismatch");
    }
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            path = new Path<>(path, graph.getEdge(v7,postV));

        // Construct the actual cigar string implied by the test path
        Cigar expectedCigar = new Cigar();
        if( offRefBeginning ) {
            expectedCigar.add(new CigarElement(preAltOption.length(), CigarOperator.I));
        }
        expectedCigar.add(new CigarElement(preRef.length(), CigarOperator.M));
        // first bubble
        if( refBubbleLength > altBubbleLength ) {
            expectedCigar.add(new CigarElement(refBubbleLength - altBubbleLength, CigarOperator.D));
            expectedCigar.add(new CigarElement(altBubbleLength,CigarOperator.M));
        } else if ( refBubbleLength < altBubbleLength ) {
            expectedCigar.add(new CigarElement(refBubbleLength,CigarOperator.M));
            expectedCigar.add(new CigarElement(altBubbleLength - refBubbleLength,CigarOperator.I));
        } else {
            expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M));
        }
        expectedCigar.add(new CigarElement(midRef1.length(), CigarOperator.M));
        // second bubble is ref path
        expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M));
        expectedCigar.add(new CigarElement(midRef2.length(), CigarOperator.M));
        // third bubble
        if( refBubbleLength > altBubbleLength ) {
            expectedCigar.add(new CigarElement(refBubbleLength - altBubbleLength, CigarOperator.D));
            expectedCigar.add(new CigarElement(altBubbleLength,CigarOperator.M));
        } else if ( refBubbleLength < altBubbleLength ) {
            expectedCigar.add(new CigarElement(refBubbleLength,CigarOperator.M));
            expectedCigar.add(new CigarElement(altBubbleLength - refBubbleLength,CigarOperator.I));
        } else {
            expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M));
        }
        expectedCigar.add(new CigarElement(postRef.length(), CigarOperator.M));
        if( offRefEnding ) {
            expectedCigar.add(new CigarElement(postAltOption.length(), CigarOperator.I));
        }

        Assert.assertEquals(path.calculateCigar(ref.getBytes()).toString(),
                AlignmentUtils.consolidateCigar(expectedCigar).toString(),
                "Cigar string mismatch: ref = " + ref + " alt " + new String(path.getBases()));
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Related Classes of htsjdk.samtools.CigarElement

  • bcbio.gatk.tools.walkers.LeftAlignVariants
  • bcbio.variation.annotate.ReadMeanLen
  • bcbio.variation.annotate.ReadMeanPos
  • bcbio.variation.annotate.ReadPosEndDist
  • org.broad.igv.sam.reader.SamUtils
  • org.broadinstitute.gatk.engine.alignment.bwa.java.AlignmentMatchSequence
  • org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtilsUnitTest
  • org.broadinstitute.gatk.engine.filters.NDNCigarReadTransformer
  • org.broadinstitute.gatk.tools.walkers.annotator.ReadPosRankSumTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar
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