From 1b214c0de510df08fbf49689f9ccd818bbb81206 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 14 Oct 2009 02:48:44 +0000
Subject: [PATCH] Fixed logic: throw exception if contigs are NOT equal

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1827 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
index 3f38a53c0..98b89a0ec 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
@@ -203,7 +203,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
                 }
                 this.referenceBase = refBase;
             } else {
-                if (contig.equals(this.contig))
+                if (!contig.equals(this.contig))
                     throw new IllegalArgumentException("The contig name has to be the same at a single locus");
                 if (position != this.position)
                     throw new IllegalArgumentException("The position has to be the same at a single locus");