Package htsjdk.samtools

Examples of htsjdk.samtools.Cigar

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     *
     * @param cigar the original cigar
     * @return an object with the shifts (see CigarShift class)
     */
    private CigarShift cleanHardClippedCigar(final Cigar cigar) {
        final Cigar cleanCigar = new Cigar();
        int shiftFromStart = 0;
        int shiftFromEnd = 0;
        Stack<CigarElement> cigarStack = new Stack<CigarElement>();
        final Stack<CigarElement> inverseCigarStack = new Stack<CigarElement>();

        for (final CigarElement cigarElement : cigar.getCigarElements())
            cigarStack.push(cigarElement);

        for (int i = 1; i <= 2; i++) {
            int shift = 0;
            int totalHardClip = 0;
            boolean readHasStarted = false;
            boolean addedHardClips = false;

            while (!cigarStack.empty()) {
                CigarElement cigarElement = cigarStack.pop();

                if (!readHasStarted &&
                        cigarElement.getOperator() != CigarOperator.DELETION &&
                        cigarElement.getOperator() != CigarOperator.SKIPPED_REGION &&
                        cigarElement.getOperator() != CigarOperator.HARD_CLIP)
                    readHasStarted = true;

                else if (!readHasStarted && cigarElement.getOperator() == CigarOperator.HARD_CLIP)
                    totalHardClip += cigarElement.getLength();

                else if (!readHasStarted && cigarElement.getOperator() == CigarOperator.DELETION)
                    totalHardClip += cigarElement.getLength();

                else if (!readHasStarted && cigarElement.getOperator() == CigarOperator.SKIPPED_REGION)
                    totalHardClip += cigarElement.getLength();

                if (readHasStarted) {
                    if (i == 1) {
                        if (!addedHardClips) {
                            if (totalHardClip > 0)
                                inverseCigarStack.push(new CigarElement(totalHardClip, CigarOperator.HARD_CLIP));
                            addedHardClips = true;
                        }
                        inverseCigarStack.push(cigarElement);
                    } else {
                        if (!addedHardClips) {
                            if (totalHardClip > 0)
                                cleanCigar.add(new CigarElement(totalHardClip, CigarOperator.HARD_CLIP));
                            addedHardClips = true;
                        }
                        cleanCigar.add(cigarElement);
                    }
                }
            }
            // first pass  (i=1) is from end to start of the cigar elements
            if (i == 1) {
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                                                              boolean isUnmapped,
                                                              int referenceIndex,
                                                              int alignmentEnd,
                                                              int readLength,
                                                              Cigar oldCigar) {
        Cigar newCigar = null;
        if (!isUnmapped) {
            final SAMSequenceRecord refseq = header.getSequence(referenceIndex);
            final int overhang = alignmentEnd - refseq.getSequenceLength();
            if (overhang > 0) {
                // 1-based index of first base in read to clip.
                int clipFrom = readLength - overhang + 1;
                // we have to check if the last element is soft-clipping, so we can subtract that from clipFrom
                final CigarElement cigarElement = oldCigar.getCigarElement(oldCigar.getCigarElements().size()-1);
                if (CigarOperator.SOFT_CLIP == cigarElement.getOperator()) clipFrom -= cigarElement.getLength();
                final List<CigarElement> newCigarElements  = CigarUtil.softClipEndOfRead(clipFrom, oldCigar.getCigarElements());
                newCigar = new Cigar(newCigarElements);
            }
        }
        return newCigar;
    }
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     * @param rec
     */
    public static void createNewCigarsIfMapsOffEndOfReference(final SAMRecord rec) {
        // If the read maps off the end of the alignment, clip it
        if (!rec.getReadUnmappedFlag()) {
            final Cigar readCigar = createNewCigarIfMapsOffEndOfReference(rec.getHeader(),
                    rec.getReadUnmappedFlag(),
                    rec.getReferenceIndex(),
                    rec.getAlignmentEnd(),
                    rec.getReadLength(),
                    rec.getCigar());
            if (null != readCigar) rec.setCigar(readCigar);
        }

        // If the read's mate maps off the end of the alignment, clip it
        if (SAMUtils.hasMateCigar(rec)) {
            Cigar mateCigar = SAMUtils.getMateCigar(rec);
            mateCigar = createNewCigarIfMapsOffEndOfReference(rec.getHeader(),
                    rec.getMateUnmappedFlag(),
                    rec.getMateReferenceIndex(),
                    SAMUtils.getMateAlignmentEnd(rec), // NB: this could be computed without another call to getMateCigar
                    mateCigar.getReadLength(),
                    mateCigar);
            if (null != mateCigar) rec.setAttribute(SAMTag.MC.name(), mateCigar.toString());
        }
    }
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            if (endHardClip   > 0) elements.set(elements.size()-1, new CigarElement(last.getLength(), CigarOperator.S));

            // Set the update structures on the new record
            rec.setReadBases(bases);
            rec.setBaseQualities(quals);
            rec.setCigar(new Cigar(elements));
        }
   }
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        rec.setReadName(unmappedRec.getReadName());
        rec.setReadBases(unmappedRec.getReadBases());
        rec.setBaseQualities(unmappedRec.getBaseQualities());
        rec.setMappingQuality(hitSpec.mapq);
        if (!hitSpec.primary) rec.setNotPrimaryAlignmentFlag(true);
        final Cigar cigar = new Cigar();
        final int readLength = rec.getReadLength();
        if (hitSpec.filtered) {
            // Add two insertions so alignment is filtered.
            cigar.add(new CigarElement(readLength-4, CigarOperator.M));
            cigar.add(new CigarElement(1, CigarOperator.I));
            cigar.add(new CigarElement(1, CigarOperator.M));
            cigar.add(new CigarElement(1, CigarOperator.I));
            cigar.add(new CigarElement(1, CigarOperator.M));
        } else {
            cigar.add(new CigarElement(readLength, CigarOperator.M));
        }
        rec.setCigar(cigar);

        rec.setReferenceName(bigSequenceName);
        rec.setAttribute(SAMTag.HI.name(), hitIndex);
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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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