From 708731037390f175e53951ddb97cf2897e89fa25 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 22 Nov 2011 10:16:36 -0500
Subject: [PATCH] Embarassing bug fixed

---
 .../sting/utils/variantcontext/VariantContextUtils.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 05e768ea7..0d3f7fae7 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -965,7 +965,7 @@ public class VariantContextUtils {
     private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) {
         for ( Genotype g : oneVC.getGenotypes() ) {
             String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples);
-            if ( mergedGenotypes.containsSample(name) ) {
+            if ( ! mergedGenotypes.containsSample(name) ) {
                 // only add if the name is new
                 Genotype newG = g;