From 02d5e3025e3672f945c3a6f9701b3ab0a2a25a69 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 9 Nov 2011 15:34:19 -0500
Subject: [PATCH] Added integration test for intervals from bed file

---
 .../utils/interval/IntervalIntegrationTest.java    | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
index 75bdc3142..3fb330853 100644
--- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
@@ -162,6 +162,20 @@ public class IntervalIntegrationTest extends WalkerTest {
         executeTest("testMixedIntervalMerging", spec);
     }
 
+    @Test(enabled = true)
+    public void testBed() {
+        String md5 = "cf4278314ef8e4b996e1b798d8eb92cf";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.bed",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testBed", spec);
+    }
+
     @Test(enabled = true)
     public void testComplexVCF() {
         String md5 = "166d77ac1b46a1ec38aa35ab7e628ab5";