int alignmentShift = 0; // caused by hard clipping deletions
// hard clip the beginning of the cigar string
if (start == 0) {
Iterator<CigarElement> cigarElementIterator = cigar.getCigarElements().iterator();
CigarElement cigarElement = cigarElementIterator.next();
// Skip all leading hard clips
while (cigarElement.getOperator() == CigarOperator.HARD_CLIP) {
totalHardClipCount += cigarElement.getLength();
if (cigarElementIterator.hasNext())
cigarElement = cigarElementIterator.next();
else
throw new ReviewedGATKException("Read is entirely hardclipped, shouldn't be trying to clip it's cigar string");
}
// keep clipping until we hit stop
while (index <= stop) {
int shift = 0;
if (cigarElement.getOperator().consumesReadBases())
shift = cigarElement.getLength();
// we're still clipping or just finished perfectly
if (index + shift == stop + 1) {
alignmentShift += calculateHardClippingAlignmentShift(cigarElement, cigarElement.getLength());
newCigar.add(new CigarElement(totalHardClipCount + alignmentShift, CigarOperator.HARD_CLIP));
}
// element goes beyond what we need to clip
else if (index + shift > stop + 1) {
int elementLengthAfterChopping = cigarElement.getLength() - (stop - index + 1);
alignmentShift += calculateHardClippingAlignmentShift(cigarElement, stop - index + 1);
newCigar.add(new CigarElement(totalHardClipCount + alignmentShift, CigarOperator.HARD_CLIP));
newCigar.add(new CigarElement(elementLengthAfterChopping, cigarElement.getOperator()));
}
index += shift;
alignmentShift += calculateHardClippingAlignmentShift(cigarElement, shift);
if (index <= stop && cigarElementIterator.hasNext())
cigarElement = cigarElementIterator.next();
else
break;
}
// add the remaining cigar elements
while (cigarElementIterator.hasNext()) {
cigarElement = cigarElementIterator.next();
newCigar.add(new CigarElement(cigarElement.getLength(), cigarElement.getOperator()));
}
}
// hard clip the end of the cigar string
else {
Iterator<CigarElement> cigarElementIterator = cigar.getCigarElements().iterator();
CigarElement cigarElement = cigarElementIterator.next();
// Keep marching on until we find the start
while (index < start) {
int shift = 0;
if (cigarElement.getOperator().consumesReadBases())
shift = cigarElement.getLength();
// we haven't gotten to the start yet, keep everything as is.
if (index + shift < start)
newCigar.add(new CigarElement(cigarElement.getLength(), cigarElement.getOperator()));
// element goes beyond our clip starting position
else {
int elementLengthAfterChopping = start - index;
alignmentShift += calculateHardClippingAlignmentShift(cigarElement, cigarElement.getLength() - (start - index));
// if this last element is a HARD CLIP operator, just merge it with our hard clip operator to be added later
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP)
totalHardClipCount += elementLengthAfterChopping;
// otherwise, maintain what's left of this last operator
else
newCigar.add(new CigarElement(elementLengthAfterChopping, cigarElement.getOperator()));
}
index += shift;
if (index < start && cigarElementIterator.hasNext())
cigarElement = cigarElementIterator.next();
else
break;
}
// check if we are hard clipping indels
while (cigarElementIterator.hasNext()) {
cigarElement = cigarElementIterator.next();
alignmentShift += calculateHardClippingAlignmentShift(cigarElement, cigarElement.getLength());
// if the read had a HardClip operator in the end, combine it with the Hard Clip we are adding
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP)
totalHardClipCount += cigarElement.getLength();
}
newCigar.add(new CigarElement(totalHardClipCount + alignmentShift, CigarOperator.HARD_CLIP));
}
return cleanHardClippedCigar(newCigar);
}