From 6aedede7f31506324a7c3f60223c22f7e7d8fb09 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 16 Jul 2010 15:50:25 +0000
Subject: [PATCH] Added Type.MNP to allowed variant context types; this does
 not break the tests (yet)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3808 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
index 9a561dab0..ba3ee05df 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
@@ -58,7 +58,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
     private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
 
     // Don't allow mixed types for now
-    private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL);
+    private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP,
+            VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL, VariantContext.Type.MNP);
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )