From 23359d1c6c797f2374484cfdb3d23722bb1331f2 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 17 Nov 2011 15:32:52 -0500
Subject: [PATCH] Bugfix for pruneVariantContext, which was dropping the ref
 base for padding

---
 .../sting/utils/variantcontext/VariantContextUtils.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index b77f606f5..5d2c86f84 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -302,7 +302,7 @@ public class VariantContextUtils {
         }
 
         return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(),
-                vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.getFilters(), attributes);
+                vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.getFilters(), attributes, vc.getReferenceBaseForIndel());
     }
 
     public enum GenotypeMergeType {