/** returns true if the cigar string starts With a clipping operator */ public boolean isLeftClipped() { return !isEmpty() && isClippingOperator(getFirstCigarElement().getOperator()); }
/** returns true if the cigar string starts With a clipping operator */ public boolean isLeftClipped() { return !isEmpty() && isClippingOperator(getFirstCigarElement().getOperator()); }
@Test(dataProvider = "firstLastData") public void testGetFirstOrLastCigarElement(final String textCigar, final CigarElement first, final CigarElement last) { final Cigar cigar = TextCigarCodec.decode(textCigar); Assert.assertEquals(cigar.getFirstCigarElement(), first); Assert.assertEquals(cigar.getLastCigarElement(), last); }
Cigar cigar = TextCigarCodec.decode(sgResult.cigar); CigarElement first = cigar.getFirstCigarElement(); CigarElement last = cigar.getLastCigarElement();
/** * Gets the read offset of the final aligned base. * * @param r * @return zero based offset of the final aligned read base based on fastq * sequencing base order */ public static final int getLastAlignedBaseReadOffset(SAMRecord r) { Cigar c = r.getCigar(); if (c == null || c.getCigarElements().size() == 0) return -1; int length = c.getReadLength(); if (c.getFirstCigarElement().getOperator() == CigarOperator.HARD_CLIP) { length += c.getFirstCigarElement().getLength(); } if (c.getLastCigarElement().getOperator() == CigarOperator.HARD_CLIP) { length += c.getLastCigarElement().getLength(); } if (r.getReadNegativeStrandFlag()) { return length - getStartClipLength(c.getCigarElements()) - 1; } else { return length - getEndClipLength(c.getCigarElements()) - 1; } }
return; List<CigarElement> list = new ArrayList<>(r.getCigar().getCigarElements()); int startlength = r.getCigar().getFirstCigarElement().getOperator() == CigarOperator.HARD_CLIP ? r.getCigar().getFirstCigarElement().getLength() : 0; int endlength = r.getCigar().getLastCigarElement().getOperator() == CigarOperator.HARD_CLIP ? r.getCigar().getLastCigarElement().getLength() : 0;
List<ChimericAlignment> aln = ChimericAlignment.getChimericAlignments(record); if (aln.isEmpty()) return Collections.emptyList(); if (record.getCigar().getFirstCigarElement().getOperator() == CigarOperator.HARD_CLIP || record.getCigar().getLastCigarElement().getOperator() == CigarOperator.HARD_CLIP) { if (!MessageThrottler.Current.shouldSupress(log, "hard clipped bases")) {
CigarElement firstElement = first.getCigar().getFirstCigarElement(); CigarElement lastElement = second.getCigar().getLastCigarElement();