From e952296c10a3afa0413c923b2cde35b28f69e226 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 11 Jan 2013 15:01:27 -0500
Subject: [PATCH] Adding HC GGA integration test to cover duplicated input
 alleles.

---
 .../walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 9116afb96..a31494d1f 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -95,7 +95,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
-        HCTestComplexGGA(CEUTRIO_BAM, "-L 20:133041-133161",
+        HCTestComplexGGA(CEUTRIO_BAM, "-L 20:133041-133161 -L 20:300207-300337",
                 "bbbbd25b22a551cae5d70ea30d7feed1");
     }