/** returns true if the cigar string ends With a clipping operator */ public boolean isRightClipped() { return !isEmpty() && isClippingOperator(getLastCigarElement().getOperator()); }
/** returns true if the cigar string ends With a clipping operator */ public boolean isRightClipped() { return !isEmpty() && isClippingOperator(getLastCigarElement().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); }
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; } }
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; r.setCigar(new Cigar(CigarUtil.clean(list.stream() .map(ce -> ce.getOperator() == CigarOperator.HARD_CLIP
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")) { log.warn(String.format("Read %s is hard clipped. Please run %s to soften hard clips.",
CigarElement lastElement = second.getCigar().getLastCigarElement();