Package htsjdk.samtools

Examples of htsjdk.samtools.Cigar

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            while (bestHaplotypes.hasNext()) {
                final KBestHaplotype kBestHaplotype = bestHaplotypes.next();
                final Haplotype h = kBestHaplotype.haplotype();
                if( !returnHaplotypes.contains(h) ) {
                    final Cigar cigar = CigarUtils.calculateCigar(refHaplotype.getBases(),h.getBases());

                    if ( cigar == null ) {
                        failedCigars++; // couldn't produce a meaningful alignment of haplotype to reference, fail quietly
                        continue;
                    } else if( cigar.isEmpty() ) {
                        throw new IllegalStateException("Smith-Waterman alignment failure. Cigar = " + cigar + " with reference length " + cigar.getReferenceLength() +
                                " but expecting reference length of " + refHaplotype.getCigar().getReferenceLength());
                    } else if ( pathIsTooDivergentFromReference(cigar) || cigar.getReferenceLength() < MIN_HAPLOTYPE_REFERENCE_LENGTH ) {
                        // N cigar elements means that a bubble was too divergent from the reference so skip over this path
                        continue;
                    } else if( cigar.getReferenceLength() != refHaplotype.getCigar().getReferenceLength() ) { // SW failure
                        throw new IllegalStateException("Smith-Waterman alignment failure. Cigar = " + cigar + " with reference length "
                                + cigar.getReferenceLength() + " but expecting reference length of " + refHaplotype.getCigar().getReferenceLength()
                                + " ref = " + refHaplotype + " path " + new String(h.getBases()));
                    }

                    h.setCigar(cigar);
                    h.setAlignmentStartHapwrtRef(activeRegionStart);
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    }

    private int getNumClippedBasesAtStart(final 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();
        }
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    }

    private int getNumClippedBasesAtEnd(final GATKSAMRecord 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();
        }
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                it.previous();
                it.set(new CigarElement(thisElement.getLength() + nextLength, thisElement.getOperator()));
            } else
                it.previous();
       }
       return new Cigar(cigarElements);
    }
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        final SeqGraph graph = new SeqGraph(11);
        final SeqVertex v = new SeqVertex(hap);
        graph.addVertex(v);
        final Path<SeqVertex,BaseEdge> path = new Path<SeqVertex,BaseEdge>(v, graph);
        final Cigar cigar = path.calculateCigar(ref.getBytes());
        Assert.assertNull(cigar, "Should have failed gracefully");
    }
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        Path<SeqVertex,BaseEdge> path = new Path<>(v, graph);
        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(v6Alt, v7));
        if( offRefEnding )
            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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        graph.addEdges(new BaseEdge(false, 1), top, alt, bot);

        // Construct the test path
        Path<SeqVertex,BaseEdge> path = Path.makePath(Arrays.asList(top, alt, bot), graph);

        Cigar expected = new Cigar();
        expected.add(new CigarElement(padSize, CigarOperator.M));
        if ( ! prefix.equals("") ) expected.add(new CigarElement(prefix.length(), CigarOperator.M));
        for ( final CigarElement elt : TextCigarCodec.getSingleton().decode(midCigar).getCigarElements() ) expected.add(elt);
        if ( ! end.equals("") ) expected.add(new CigarElement(end.length(), CigarOperator.M));
        expected.add(new CigarElement(padSize, CigarOperator.M));
        expected = AlignmentUtils.consolidateCigar(expected);

        final String refString = top.getSequenceString() + ref.getSequenceString() + bot.getSequenceString();
        final Cigar pathCigar = path.calculateCigar(refString.getBytes());

        logger.warn("diffs: " + ref + " vs. " + alt + " cigar " + midCigar);
        logger.warn("Path " + path + " with cigar " + pathCigar);
        logger.warn("Expected cigar " + expected);
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        for ( final int indelSize1 : Arrays.asList(1, 2, 3, 4) ) {
            for ( final int indelOp1 : Arrays.asList(1, -1) ) {
                for ( final int indelSize2 : Arrays.asList(1, 2, 3, 4) ) {
                    for ( final int indelOp2 : Arrays.asList(1, -1) ) {

                        Cigar expectedCigar = new Cigar();
                        expectedCigar.add(new CigarElement(refString.length(), CigarOperator.M));
                        expectedCigar.add(new CigarElement(indelSize1, (indelOp1 > 0 ? CigarOperator.I : CigarOperator.D)));
                        expectedCigar.add(new CigarElement((indelOp1 < 0 ? refIndel1 - indelSize1 : refIndel1), CigarOperator.M));
                        expectedCigar.add(new CigarElement(refString.length(), CigarOperator.M));
                        expectedCigar.add(new CigarElement(indelSize2 * 2, (indelOp2 > 0 ? CigarOperator.I : CigarOperator.D)));
                        expectedCigar.add(new CigarElement((indelOp2 < 0 ? (refIndel2 - indelSize2) * 2 : refIndel2 * 2), CigarOperator.M));
                        expectedCigar.add(new CigarElement(refString.length(), CigarOperator.M));

                        Cigar givenCigar = new Cigar();
                        givenCigar.add(new CigarElement(refString.length() + refIndel1/2, CigarOperator.M));
                        givenCigar.add(new CigarElement(indelSize1, (indelOp1 > 0 ? CigarOperator.I : CigarOperator.D)));
                        givenCigar.add(new CigarElement((indelOp1 < 0 ? (refIndel1/2 - indelSize1) : refIndel1/2) + refString.length() + refIndel2/2 * 2, CigarOperator.M));
                        givenCigar.add(new CigarElement(indelSize2 * 2, (indelOp2 > 0 ? CigarOperator.I : CigarOperator.D)));
                        givenCigar.add(new CigarElement((indelOp2 < 0 ? (refIndel2/2 - indelSize2) * 2 : refIndel2/2 * 2) + refString.length(), CigarOperator.M));

                        String theRef = preRefString + refString + Utils.dupString(indelString1, refIndel1) + refString + Utils.dupString(indelString2, refIndel2) + refString + postRefString;
                        String theRead = refString + Utils.dupString(indelString1, refIndel1 + indelOp1 * indelSize1) + refString + Utils.dupString(indelString2, refIndel2 + indelOp2 * indelSize2) + refString;

                        Cigar calculatedCigar = CigarUtils.leftAlignCigarSequentially(AlignmentUtils.consolidateCigar(givenCigar), theRef.getBytes(), theRead.getBytes(), preRefString.length(), 0);
                        Assert.assertEquals(AlignmentUtils.consolidateCigar(calculatedCigar).toString(), AlignmentUtils.consolidateCigar(expectedCigar).toString(), "Cigar strings do not match!");
                    }
                }
            }
        }
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        }

        // move existing indels (for 1 indel reads only) to leftmost position within identical sequence
        int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read);
        if ( numBlocks == 2 ) {
            Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true);
            newCigar = IndelRealigner.reclipCigar(newCigar, read);
            read.setCigar(newCigar);
        }

        emit(read);
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Related Classes of htsjdk.samtools.Cigar

  • bcbio.gatk.tools.walkers.LeftAlignVariants
  • bcbio.variation.annotate.ReadMeanLen
  • bcbio.variation.annotate.ReadMeanPos
  • bcbio.variation.annotate.ReadPosEndDist
  • org.broad.igv.ga4gh.Ga4ghAlignment
  • org.broad.igv.sam.reader.SamUtils
  • org.broadinstitute.gatk.engine.alignment.bwa.java.AlignmentMatchSequence
  • org.broadinstitute.gatk.engine.datasources.reads.TheoreticalMinimaBenchmark
  • org.broadinstitute.gatk.engine.filters.BadCigarFilter
  • org.broadinstitute.gatk.engine.filters.MalformedReadFilterUnitTest
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