Package htsjdk.samtools

Examples of htsjdk.samtools.CigarElement

509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
            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);
                    }
                }
View Full Code Here
586
587
588
589
590
591
592
593
594
595
596
597
            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;
View Full Code Here
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
    private void replaceHardWithSoftClips(final SAMRecord rec) {
        if (rec.getReadUnmappedFlag()) return;
        if (rec.getCigar().isEmpty()) return;

        List<CigarElement> elements = rec.getCigar().getCigarElements();
        final CigarElement first = elements.get(0);
        final CigarElement last  = elements.size() == 1 ? null : elements.get(elements.size()-1);
        final int startHardClip = first.getOperator() == CigarOperator.H ? first.getLength() : 0;
        final int endHardClip   = (last != null && last.getOperator() == CigarOperator.H) ? last.getLength() : 0;

        if (startHardClip + endHardClip > 0) {
            final int len = rec.getReadBases().length + startHardClip + endHardClip;

            // Fix the basecalls
            final byte[] bases = new byte[len];
            Arrays.fill(bases, (byte) 'N');
            System.arraycopy(rec.getReadBases(), 0, bases, startHardClip, rec.getReadBases().length);

            // Fix the quality scores
            final byte[] quals = new byte[len];
            Arrays.fill(quals, (byte) 2  );
            System.arraycopy(rec.getBaseQualities(), 0, quals, startHardClip, rec.getBaseQualities().length);

            // Fix the cigar!
            elements = new ArrayList<CigarElement>(elements); // make it modifiable
            if (startHardClip > 0) elements.set(0, new CigarElement(first.getLength(), CigarOperator.S));
            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));
View Full Code Here
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
            final int notWrittenToFastq = sam.getReadLength() - (trim + alignment.getReadLength());
            final int beginning = sam.getReadNegativeStrandFlag() ? notWrittenToFastq : trim;
            final int end = sam.getReadNegativeStrandFlag() ? trim : notWrittenToFastq;

            if (!sam.getReadUnmappedFlag()) {
                final CigarElement firstMergedCigarElement = sam.getCigar().getCigarElement(0);
                final CigarElement lastMergedCigarElement = sam.getCigar().getCigarElement(sam.getCigar().getCigarElements().size() - 1);
                final CigarElement firstAlignedCigarElement = alignment.getCigar().getCigarElement(0);
                final CigarElement lastAlignedCigarElement = alignment.getCigar().getCigarElement(alignment.getCigar().getCigarElements().size() - 1);

                if (beginning > 0) {
                    Assert.assertEquals(firstMergedCigarElement.getOperator(), CigarOperator.S, "First element is not a soft clip");
                    Assert.assertEquals(firstMergedCigarElement.getLength(), beginning + ((firstAlignedCigarElement.getOperator() == CigarOperator.S) ? firstAlignedCigarElement.getLength() : 0));
                }
                if (end > 0) {
                    Assert.assertEquals(lastMergedCigarElement.getOperator(), CigarOperator.S, "Last element is not a soft clip");
                    Assert.assertEquals(lastMergedCigarElement.getLength(), end + ((lastAlignedCigarElement.getOperator() == CigarOperator.S) ? lastAlignedCigarElement.getLength() : 0));
                }
            }
        }

    }
View Full Code Here
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
        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);
View Full Code Here
TOP

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
    • Copyright © 2018 www.massapicom. All rights reserved.
    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.