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

This commit is contained in:
Eric Banks 2012-12-03 15:59:14 -05:00
parent d5ed184691
commit 67932b357d
1 changed files with 3 additions and 0 deletions
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3
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -397,6 +397,9 @@ 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;
} }