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

This commit is contained in:
Mark DePristo 2011-09-07 13:13:17 -04:00
parent 430da23446 6857d0324e
commit 3bcbfa6e06
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) if (start < 0 || stop > read.getReadLength() - 1)
throw new ReviewedStingException("Trying to clip before the start or after the end of a read"); 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); //System.out.println("Clipping start/stop: " + start + "/" + stop);
this.addOp(new ClippingOp(start, stop)); this.addOp(new ClippingOp(start, stop));
SAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES); SAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);