From 333e5de812884e9a2109cf69e438025474f305ce Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 18 Nov 2011 16:49:59 -0500
Subject: [PATCH] returning read instead of GATKSAMRecord

Do not create new GATKSAMRecord when read has been fully clipped, because it is essentially the same as returning the currently fully clipped read.
---
 .../org/broadinstitute/sting/utils/clipreads/ReadClipper.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
index e4806838d..8c1061494 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -121,7 +121,7 @@ public class ReadClipper {
 
     public GATKSAMRecord hardClipSoftClippedBases () {
         if (read.isEmpty())
-            return new GATKSAMRecord(read.getHeader());
+            return read;
 
         int readIndex = 0;
         int cutLeft = -1;            // first position to hard clip (inclusive)