From a52e3c7e15a1bca6221df4d881642cfce590f84d Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 12 Dec 2012 13:09:39 -0500
Subject: [PATCH] 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.
---
 .../src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java  | 3 ---
 1 file changed, 3 deletions(-)

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 6c7a162f8..9fdb48b34 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -397,9 +397,6 @@ public class GATKSAMRecord extends BAMRecord {
                 else if (op != CigarOperator.HARD_CLIP)
                     break;
             }
-
-            if ( softStart < 1 )
-                softStart = 1;
         }
         return softStart;
     }