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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-09-24 09:26:45 -04:00
parent 8d9e136bba 1803bd6ae2
commit bb11951255
2 changed files with 33 additions and 28 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
View File

@ -59,7 +59,7 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
*/ */
public FilePointer next() { public FilePointer next() {
FilePointer current = wrappedIterator.next(); FilePointer current = wrappedIterator.next();
while(wrappedIterator.hasNext() && current.minus(wrappedIterator.peek()) == 0) while(wrappedIterator.hasNext() && current.isRegionUnmapped == wrappedIterator.peek().isRegionUnmapped && current.minus(wrappedIterator.peek()) == 0)
current = current.combine(parser,wrappedIterator.next()); current = current.combine(parser,wrappedIterator.next());
return current; return current;
} }

59
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
View File

@ -398,7 +398,9 @@ public class ClippingOp {
for (int i = 1; i <= 2; i++) { for (int i = 1; i <= 2; i++) {
int shift = 0; int shift = 0;
int totalHardClip = 0;
boolean readHasStarted = false; boolean readHasStarted = false;
boolean addedHardClips = false;
while(!cigarStack.empty()) { while(!cigarStack.empty()) {
CigarElement cigarElement = cigarStack.pop(); CigarElement cigarElement = cigarStack.pop();
@ -408,14 +410,33 @@ public class ClippingOp {
cigarElement.getOperator() != CigarOperator.DELETION && cigarElement.getOperator() != CigarOperator.DELETION &&
cigarElement.getOperator() != CigarOperator.HARD_CLIP) cigarElement.getOperator() != CigarOperator.HARD_CLIP)
readHasStarted = true; readHasStarted = true;
else if ( !readHasStarted && cigarElement.getOperator() == CigarOperator.HARD_CLIP)
totalHardClip += cigarElement.getLength();
else if ( !readHasStarted && cigarElement.getOperator() == CigarOperator.INSERTION) else if ( !readHasStarted && cigarElement.getOperator() == CigarOperator.INSERTION)
shift += cigarElement.getLength(); shift += cigarElement.getLength();
if (readHasStarted || cigarElement.getOperator() == CigarOperator.HARD_CLIP) { else if ( !readHasStarted && cigarElement.getOperator() == CigarOperator.DELETION)
if (i==1) 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); inverseCigarStack.push(cigarElement);
else }
else {
if (!addedHardClips) {
if (totalHardClip > 0)
cleanCigar.add(new CigarElement(totalHardClip, CigarOperator.HARD_CLIP));
addedHardClips = true;
}
cleanCigar.add(cigarElement); cleanCigar.add(cigarElement);
}
} }
} }
// first pass (i=1) is from end to start of the cigar elements // first pass (i=1) is from end to start of the cigar elements
@ -434,7 +455,6 @@ public class ClippingOp {
private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) { private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) {
int newShift = 0; int newShift = 0;
int oldShift = 0; int oldShift = 0;
int deletionShift = 0;
for (CigarElement cigarElement : newCigar.getCigarElements()) { for (CigarElement cigarElement : newCigar.getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP) if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
@ -449,34 +469,19 @@ public class ClippingOp {
else else
break; break;
} }
return newShift - oldShift;
int basesClipped = 0;
for (CigarElement cigarElement : oldCigar.getCigarElements()) {
if (basesClipped > newShift) // are we beyond the clipped region?
break;
else if (cigarElement.getOperator() == CigarOperator.DELETION) // if this is a deletion, we have to adjust the starting shift
deletionShift += cigarElement.getLength();
else
basesClipped += cigarElement.getLength();
}
return newShift - oldShift + deletionShift;
} }
private int calculateHardClippingAlignmentShift(CigarElement cigarElement, int clippedLength) { private int calculateHardClippingAlignmentShift(CigarElement cigarElement, int clippedLength) {
if (cigarElement.getOperator() == CigarOperator.INSERTION) { // Insertions should be discounted from the total hard clip count
int cigarElementLength = cigarElement.getLength(); if (cigarElement.getOperator() == CigarOperator.INSERTION)
if (clippedLength >= cigarElementLength) return -clippedLength;
return -cigarElement.getLength();
else
return -clippedLength;
}
// if (cigarElement.getOperator() == CigarOperator.DELETION) // Deletions should be added to the total hard clip count
// return cigarElement.getLength(); else if (cigarElement.getOperator() == CigarOperator.DELETION)
return cigarElement.getLength();
// There is no shift if we are not clipping an indel
return 0; return 0;
} }