From 8fb37f5f7a67d203bd3adb2ac2c00c4fd0e74d0f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 30 Jun 2010 13:56:16 +0000
Subject: [PATCH] For Kiran: warn the user when the actual and vcf ref bases
 differ so that if an exception is generated later, he knows why.  All: should
 we generate the actual exception here? Is there any reason to allow cases
 where the vcf record has a different ref base than the actual reference?  I'd
 vote that we die here.  Thoughts?

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3680 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/VariantContextAdaptors.java              | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index dace443ad..2deb6b8e5 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -214,6 +214,8 @@ public class VariantContextAdaptors {
 //            refAllele = Allele.create(vcf.getReference(), true);
         } else if ( !vcf.isIndel() ) {
             refAllele = Allele.create(ref.getBase(), true);
+            if ( (char)ref.getBase() != vcf.getReference().charAt(0) )
+                System.err.println("\n*** WARN: The VCF reference base (" + vcf.getReference().charAt(0) + ") doesn't match the actual reference base (" + (char)ref.getBase() + "); there is a good chance this will generate an exception!");
         } else if ( vcf.isDeletion() ) {
             int start = vcf.getPosition() - (int)ref.getWindow().getStart() + 1;
             int delLength = 0;