From 07b134a124fbd1b9612d49075b00895c5a8b7ec8 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 16 Oct 2009 15:22:10 +0000
Subject: [PATCH] Added some integration tests for multiple samples

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1861 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../UnifiedGenotyperIntegrationTest.java      | 22 ++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 9df3ae16b..28dd717fe 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -34,6 +34,27 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //    return true;
     //}
 
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // testing multi-sample calling
+    //
+    // --------------------------------------------------------------------------------------------------------------
+    @Test
+    public void testMultiSamplePilot1() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm EM_POINT_ESTIMATE -lod 5", 1,
+                Arrays.asList("3c806bb0649a889c242a430f1d5bb7f9"));
+        executeTest("testMultiSamplePilot1", spec);
+    }
+
+    @Test
+    public void testMultiSamplePilot2() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -lod 5", 1,
+                Arrays.asList("d41d8cd98f00b204e9800998ecf8427e"));
+        executeTest("testMultiSamplePilot2", spec);
+    }
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing calls with SLX, 454, and SOLID data
@@ -187,5 +208,4 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 Arrays.asList("915abf82a04fcd1842f6865501bae67c"));
         executeTest("empirical1MbTestBinaryGeli", spec);
     }
-
 }