From 0e04e952455cfe5cb4c5a7ba5c87a4ff6da5d8df Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Feb 2011 16:15:42 +0000
Subject: [PATCH] Bug fix: when extracting reference sequence for the event
 from the reference genome, the tool was treating Deletions and MNPs of length
 N in exactly the same way: ref_bases[current_pos+1,...,current_pos+N]. This
 is correct for Deletions but not for MNPs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5258 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/ValidateVariants.java   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 3fca6088b..19932ca2b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -120,10 +120,14 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
                 return;
             }
 
+            // deletions are associated with the (position of) the last (preceding) non-deleted base;
+            // hence to get actually deleted bases we need offset = 1
+            int offset = 1 ;
+            if ( vc.getType() == VariantContext.Type.MNP ) offset = 0; // if it's an MNP, the reported position IS the first modified base
             byte[] refBytes = ref.getBases();
             byte[] trueRef = new byte[reportedRefAllele.length()];
             for (int i = 0; i < reportedRefAllele.length(); i++)
-                trueRef[i] = refBytes[i+1];
+                trueRef[i] = refBytes[i+offset];
             observedRefAllele = Allele.create(trueRef, true);
         }
         // SNPs, etc.