From 490e5e1b0f4a7b6fa3dfbc18eb771ceac742dd72 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 3 Oct 2010 05:40:37 +0000
Subject: [PATCH] Better error when bad ref bases are provided

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4414 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/contexts/variantcontext/VariantContextUtils.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index c77e99bab..9c983d128 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -449,7 +449,7 @@ public class VariantContextUtils {
             if ( ref == null || ref.length() < myRef.length() )
                 ref = myRef;
             else if ( ref.length() == myRef.length() && ! ref.equals(myRef) )
-                throw new ReviewedStingException("BUG: equal length references with difference bases: "+ ref + " " + myRef);
+                throw new UserException.BadInput(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef));
         }
 
         return ref;