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Fixed bug where deletions messed up interval clipping 

- Instead of using readLength, the ReadUtil function are used to get a proper read coordinate
 - Added debug info in interval clipping ( with -dl)

  NOTE: method might not be safe for production and checks need to be added to the ClippingOp code
This commit is contained in:
Roger Zurawicki 2011-09-06 14:25:57 -04:00
parent 7d79de91c5
commit 47607a7eff
1 changed files with 4 additions and 0 deletions
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4
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -63,6 +63,10 @@ public class ReadClipper {
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 requires statement/check in the Hardclip function
if ( start > stop )
stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
//System.out.println("Clipping start/stop: " + start + "/" + stop);
this.addOp(new ClippingOp(start, stop));
SAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);