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Fixed extra reads showing up in Variable Sites 

Reads that were not hard clipped for the variable site no longer show up in output file
Walker now uses unclippedStart of Read to determine position in the sliding Window
This commit is contained in:
Roger Zurawicki 2011-08-23 11:26:00 -04:00
parent 9597d6edad
commit ac36271457
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -54,7 +54,7 @@ public class ReadClipper {
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
System.out.println("Clipping start/stop: " + start + "/" + stop);
//System.out.println("Clipping start/stop: " + start + "/" + stop);
this.addOp(new ClippingOp(start, stop));
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}