From c103623cf69b272706da0b3748c3be6a2425c4fb Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Mon, 28 Jan 2013 19:04:39 -0500
Subject: [PATCH] bug fix in my new function at SampleUtils.java

---
 .../java/src/org/broadinstitute/sting/utils/SampleUtils.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index 6a430588b..6e4904585 100644
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -143,8 +143,11 @@ public class SampleUtils {
         for ( Map.Entry<String, VCFHeader> val : VCF_Headers.entrySet() ) {
             VCFHeader header = val.getValue();
             for ( String sample : header.getGenotypeSamples() ) {
-                if (samples.add(sample))
+                if (samples.contains(sample)){
+
                     return false;
+                }
+                samples.add(sample);
             }
         }