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Fixed hard clipped cigar and alignment start 

* Hard clipped Cigar now includes all insertions that were hard clipped and not the deletions.
* The alignment start is now recalculated according to the new hard clipped cigar representation
This commit is contained in:
Mauricio Carneiro 2011-09-22 14:51:14 -04:00
parent 4e9020c9f7
commit 1acf7945c5
2 changed files with 12 additions and 12 deletions
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6
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
View File

@ -458,7 +458,7 @@ public class ClippingOp {
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.
else
basesClipped += cigarElement.getLength();
}
@ -474,8 +474,8 @@ public class ClippingOp {
return -clippedLength;
}
if (cigarElement.getOperator() == CigarOperator.DELETION)
return cigarElement.getLength();
// if (cigarElement.getOperator() == CigarOperator.DELETION)
// return cigarElement.getLength();
return 0;
}

18
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
View File

@ -71,21 +71,21 @@ public class ReadClipper {
private SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
int stop = (refStop < 0) ? read.getReadLength() - 1: ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
if (start < 0 || stop > read.getReadLength() - 1 + numDeletions(read))
if (start < 0 || stop > read.getReadLength() - 1)
throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
// TODO add check in the Hardclip function
if ( start > stop )
stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
if ( start > stop ) {
// stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
throw new ReviewedStingException("START > STOP -- this should never happen -- call Mauricio!");
}
//This tries to fix the bug where the deletion is counted a read base and as a result, the hardCLipper runs into
//an endless loop when hard clipping the cigar string because the read coordinates are not covered by the read
stop -= numDeletions(read);
if ( start > stop )
start -= numDeletions(read);
// stop -= numDeletions(read);
// if ( start > stop )
// start -= numDeletions(read);
//System.out.println("Clipping start/stop: " + start + "/" + stop);