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Fixed alignment start for hard clipping insertions

This commit is contained in:
Mauricio Carneiro 2011-09-22 13:28:25 -04:00
parent d3cc25454c
commit 4e9020c9f7
1 changed files with 25 additions and 13 deletions
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38
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
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@ -432,25 +432,37 @@ public class ClippingOp {
} }
private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) { private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCigar) {
int shift = 0; int newShift = 0;
int oldShift = 0;
int deletionShift = 0;
// Rewind to previous start (by counting everything that was already clipped in this read)
for (CigarElement cigarElement : oldCigar.getCigarElements()) {
if (!cigarElement.getOperator().consumesReferenceBases())
shift -= cigarElement.getLength();
else
break;
}
// Advance to new start (by counting everything new that has been clipped )
for (CigarElement cigarElement : newCigar.getCigarElements()) { for (CigarElement cigarElement : newCigar.getCigarElements()) {
if (!cigarElement.getOperator().consumesReferenceBases()) if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP)
shift += cigarElement.getLength(); newShift += cigarElement.getLength();
else else
break; break;
} }
return shift; for (CigarElement cigarElement : oldCigar.getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP || cigarElement.getOperator() == CigarOperator.SOFT_CLIP )
oldShift += Math.min(cigarElement.getLength(), newShift - oldShift);
else
break;
}
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 if (cigarElement.getOperator() != CigarOperator.INSERTION) // if it's not an insertion or deletion, than it counts as hard clipped base.
basesClipped += cigarElement.getLength();
}
return newShift - oldShift + deletionShift;
} }
private int calculateHardClippingAlignmentShift(CigarElement cigarElement, int clippedLength) { private int calculateHardClippingAlignmentShift(CigarElement cigarElement, int clippedLength) {