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Fixed hard clipping soft clipped bases after hard clips 

if soft clipped bases were after a hard clipped section of the read, the hard clip was clipping the left soft clip tail as if it were a right tail. Mayhem.
This commit is contained in:
Mauricio Carneiro 2011-09-22 15:46:55 -04:00
parent 1acf7945c5
commit 39b54211d0
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -145,7 +145,7 @@ public class ReadClipper {
cutLeft = readIndex + cigarElement.getLength() - 1; cutLeft = readIndex + cigarElement.getLength() - 1;
} }
} }
else else if (cigarElement.getOperator() != CigarOperator.HARD_CLIP)
rightTail = true; rightTail = true;
if (cigarElement.getOperator().consumesReadBases()) if (cigarElement.getOperator().consumesReadBases())