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Revert "Bug fix for RR: don't let the softclip start position be less than 1" 

this introduced a bug in reduce reads by de-activating it's hard clipping of the out of bounds soft-clips (specially in the MT).
DEV-322 #resolve #time 4m

This reverts commit 42acfd9d0bccfc0411944c342a5b889f5feae736.
This commit is contained in:
Mauricio Carneiro 2012-12-12 13:09:39 -05:00
parent 216f92276c
commit a52e3c7e15
1 changed files with 0 additions and 3 deletions
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3
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -397,9 +397,6 @@ public class GATKSAMRecord extends BAMRecord {
else if (op != CigarOperator.HARD_CLIP) else if (op != CigarOperator.HARD_CLIP)
break; break;
} }
if ( softStart < 1 )
softStart = 1;
} }
return softStart; return softStart;
} }