From 5c9b659c02aef41527ee07cd9c2e472a23de977b Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 28 Sep 2011 12:10:47 -0400
Subject: [PATCH] clipping both ends of the reads was modifying the original
 read

This goes against the ReadClipper contract, and was affecting the second part of the read that spans over multiple intervals. Fixed.
---
 .../broadinstitute/sting/utils/clipreads/ReadClipper.java    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

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 83db20238..275f476dc 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -93,8 +93,9 @@ public class ReadClipper {
     public SAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
         if (left == right)
             return new SAMRecord(read.getHeader());
-        this.read = hardClipByReferenceCoordinates(right, -1);
-        return hardClipByReferenceCoordinates(-1, left);
+        SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
+        ReadClipper clipper = new ReadClipper(leftTailRead);
+        return clipper.hardClipByReferenceCoordinatesLeftTail(left);
     }
 
     public SAMRecord hardClipLowQualEnds(byte lowQual) {