From d514c424fd6b44b2db22a8bdfa8e1d56d9348262 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 10 Aug 2010 06:05:40 +0000
Subject: [PATCH] adding tests for BTI in the ROD validation tests

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3997 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/test/org/broadinstitute/sting/BaseTest.java       |  2 --
 .../validation/RodSystemValidationIntegrationTest.java | 10 ++++++++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java
index b6c206522..36bdc8b56 100755
--- a/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/java/test/org/broadinstitute/sting/BaseTest.java
@@ -112,12 +112,10 @@ public abstract class BaseTest {
                 foundString = true;
         }
 
-        @Override
         public void close() {
             // do nothing
         }
 
-        @Override
         public boolean requiresLayout() {
             return false;
         }
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
index e6a7a61f4..379bd6654 100644
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
@@ -41,6 +41,16 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
         executeTest("testComplexVCFPileup", spec);
     }
 
+    @Test
+    public void testBTIWithROD() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
+                " -B eval2,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4" + " -BTI eval"
+                , 1,
+                Arrays.asList("ccfc0389a3c614f7892dbe972543f0ec"));
+        executeTest("testBTIWithROD", spec);
+    }
+
     @Test
     public void testLargeComplexVCFPileup() {
         WalkerTestSpec spec = new WalkerTestSpec(