From b6c3ed0295395cc07dda28a02c05a619ae1983d8 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 6 Sep 2013 09:30:01 -0400
Subject: [PATCH] Added REVERT SOFTCLIPPED bases to ClipReads

---
 .../sting/gatk/walkers/readutils/ClipReads.java               | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
index 879022299..dfc36954b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
@@ -305,7 +305,7 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
      */
     public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
         if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
-            if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES )
+            if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES || clippingRepresentation == ClippingRepresentation.REVERT_SOFTCLIPPED_BASES )
                 read = ReadClipper.revertSoftClippedBases(read);
             ReadClipperWithData clipper = new ReadClipperWithData(read, sequencesToClip);
 
@@ -600,4 +600,4 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
     }
 
 
-}
\ No newline at end of file
+}