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

2012-12-03 15:59:14 -05:00 · 2012-12-03 15:59:14 -05:00 · 67932b357d
parent d5ed184691
commit 67932b357d
1 changed files with 3 additions and 0 deletions
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@ -397,6 +397,9 @@ public class GATKSAMRecord extends BAMRecord {
                else if (op != CigarOperator.HARD_CLIP)
                    break;
            }
+
+            if ( softStart < 1 )
+                softStart = 1;
        }
        return softStart;
    }