From 39b54211d079dc2c70a2a9b4a38b9e08880b24df Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 22 Sep 2011 15:46:55 -0400
Subject: [PATCH] Fixed hard clipping soft clipped bases after hard clips

if soft clipped bases were after a hard clipped section of the read, the hard clip was clipping the left soft clip tail as if it were a right tail. Mayhem.
---
 .../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 e2ecbe46b..d0e7f8371 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -145,7 +145,7 @@ public class ReadClipper {
                     cutLeft = readIndex + cigarElement.getLength() - 1;
                 }
             }
-            else
+            else if (cigarElement.getOperator() != CigarOperator.HARD_CLIP)
                 rightTail = true;
 
             if (cigarElement.getOperator().consumesReadBases())