From 67932b357d4a845efe439ad49f35b08695e3edb4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 3 Dec 2012 15:59:14 -0500
Subject: [PATCH] Bug fix for RR: don't let the softclip start position be less
 than 1

---
 .../src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java  | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 9fdb48b34..6c7a162f8 100755
--- 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;
     }