private GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
GATKSAMRecord unclipped = (GATKSAMRecord) read.clone();
Cigar unclippedCigar = new Cigar();
int matchesCount = 0;
for (CigarElement element : read.getCigar().getCigarElements()) {
if (element.getOperator() == CigarOperator.SOFT_CLIP
|| element.getOperator() == CigarOperator.MATCH_OR_MISMATCH)
matchesCount += element.getLength();
else if (matchesCount > 0) {
unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
matchesCount = 0;
unclippedCigar.add(element);
} else unclippedCigar.add(element);
}
if (matchesCount > 0)
unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
unclipped.setCigar(unclippedCigar);
final int newStart =
read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), unclippedCigar);
unclipped.setAlignmentStart(newStart);
if (newStart <= 0) {
// if the start of the unclipped read occurs before the contig,
// we must hard clip away the bases since we cannot represent reads with
// negative or 0 alignment start values in the SAMRecord (e.g., 0 means unaligned)
return hardClip(unclipped, 0, -newStart);
} else {
return unclipped;
}
}
/**
* Checks if a hard clipped cigar left a read starting or ending with deletions or gap (N) and
* cleans it up accordingly.
*
* @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) {
shiftFromEnd = shift;
cigarStack = inverseCigarStack;
}
// second pass (i=2) is from start to end with the end already cleaned
else {
shiftFromStart = shift;
}
}
return new CigarShift(cleanCigar, shiftFromStart, shiftFromEnd);
}
@Requires({"!cigar.isEmpty()"})
private CigarShift hardClipCigar(Cigar cigar, int start, int stop) {
Cigar newCigar = new Cigar();
int index = 0;
int totalHardClipCount = stop - start + 1;
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);
}
/** Given a cigar string, soft clip up to startClipEnd and soft clip starting at endClipBegin */
private Cigar softClip(final Cigar __cigar, final int __startClipEnd, final int __endClipBegin) {
if (__endClipBegin <= __startClipEnd) {
// whole thing should be soft clipped
int cigarLength = 0;
for (CigarElement e : __cigar.getCigarElements()) {
cigarLength += e.getLength();
}
Cigar newCigar = new Cigar();
newCigar.add(new CigarElement(cigarLength, CigarOperator.SOFT_CLIP));
assert newCigar.isValid(null, -1) == null;
return newCigar;
}
int curLength = 0;
Vector<CigarElement> newElements = new Vector<CigarElement>();
for (CigarElement curElem : __cigar.getCigarElements()) {
if (!curElem.getOperator().consumesReadBases()) {
if (curElem.getOperator() == CigarOperator.HARD_CLIP
|| curLength > __startClipEnd && curLength < __endClipBegin) {
newElements.add(new CigarElement(curElem.getLength(), curElem.getOperator()));
}
continue;
}
int s = curLength;
int e = curLength + curElem.getLength();
if (e <= __startClipEnd || s >= __endClipBegin) {
// must turn this entire thing into a clip
newElements.add(new CigarElement(curElem.getLength(), CigarOperator.SOFT_CLIP));
} else if (s >= __startClipEnd && e <= __endClipBegin) {
// same thing
newElements.add(new CigarElement(curElem.getLength(), curElem.getOperator()));
} else {
// we are clipping in the middle of this guy
CigarElement newStart = null;
CigarElement newMid = null;
CigarElement newEnd = null;
int midLength = curElem.getLength();
if (s < __startClipEnd) {
newStart = new CigarElement(__startClipEnd - s, CigarOperator.SOFT_CLIP);
midLength -= newStart.getLength();
}
if (e > __endClipBegin) {
newEnd = new CigarElement(e - __endClipBegin, CigarOperator.SOFT_CLIP);
midLength -= newEnd.getLength();
}
assert midLength >= 0;
if (midLength > 0) {
newMid = new CigarElement(midLength, curElem.getOperator());
}
if (newStart != null) {
newElements.add(newStart);
}
if (newMid != null) {
newElements.add(newMid);
}
if (newEnd != null) {
newElements.add(newEnd);
}
}
curLength += curElem.getLength();
}
Vector<CigarElement> finalNewElements = new Vector<CigarElement>();
CigarElement lastElement = null;
for (CigarElement elem : newElements) {
if (lastElement == null || lastElement.getOperator() != elem.getOperator()) {
if (lastElement != null) {
finalNewElements.add(lastElement);
}
lastElement = elem;
} else {
lastElement =
new CigarElement(lastElement.getLength() + elem.getLength(), lastElement.getOperator());
}
}
if (lastElement != null) {
finalNewElements.add(lastElement);
}
Cigar newCigar = new Cigar(finalNewElements);
assert newCigar.isValid(null, -1) == null;
return newCigar;
}
