Package htsjdk.samtools

Examples of htsjdk.samtools.Cigar

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     * @param textCigar CIGAR in String form ala SAM text file.  "*" means empty CIGAR.
     * @throws RuntimeException if textCigar is invalid at the most basic level.
     */
    static Cigar decodeCigar(final String textCigar) {
        if (SAMRecord.NO_ALIGNMENT_CIGAR.equals(textCigar)) {
            return new Cigar();
        }
        final Cigar ret = new Cigar();
        final byte[] cigarBytes = StringUtil.stringToBytes(textCigar);
        for (int i = 0; i < cigarBytes.length; ++i) {
            if (!isDigit(cigarBytes[i])) {
                throw new IllegalArgumentException("Malformed CIGAR string: " + textCigar);
            }
            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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    public int getReferenceLength(String cigarString) {
               // Use htsjdk class for now
        TextCigarCodec codec = new TextCigarCodec();
        Cigar cigar = codec.decode(cigarString);
        return cigar.getReferenceLength();
    }
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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();
        }
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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();
        }
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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();
        }
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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();
        }
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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();
        }
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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();
        }
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        // 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);

        // update if necessary and write
        if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) {
            int difference = originalIndex - newCigar.getCigarElement(0).getLength();
            VariantContext newVC = new VariantContextBuilder(vc).start(vc.getStart()-difference).stop(vc.getEnd()-difference).make();
            //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference));

            final int indelIndex = originalIndex-difference;
            final byte[] newBases = new byte[indelLength + 1];
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    @Test(enabled = true)
    public void testLeftAlignCigarSequentiallyAdjacentID() {
        final String ref = "GTCTCTCTCTCTCTCTCTATATATATATATATATTT";
        final String hap = "GTCTCTCTCTCTCTCTCTCTCTATATATATATATTT";
        final Cigar originalCigar = TextCigarCodec.getSingleton().decode("18M4I12M4D2M");

        final Cigar result = CigarUtils.leftAlignCigarSequentially(originalCigar, ref.getBytes(), hap.getBytes(), 0, 0);
        logger.warn("Result is " + result);
        Assert.assertEquals(originalCigar.getReferenceLength(), result.getReferenceLength(), "Reference lengths are different");
    }
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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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