From 5af986e0c17ffba7545465c447ec8ed97c7b53da Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 29 Jul 2010 18:49:22 +0000
Subject: [PATCH] Add an integration test for Beagle (one for
 ProduceBeagleInput and one for BeagleOutputToVCFWalker)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3897 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/BeagleIntegrationTest.java   | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100755 java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java

diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
new file mode 100755
index 000000000..ab2f70cb4
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+ 
+public class BeagleIntegrationTest extends WalkerTest {
+
+    private static final String beagleValidationDataLocation = validationDataLocation + "/Beagle/";
+    @Test
+    public void testBeagleOutput() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T BeagleOutputToVCF -R " + oneKGLocation + "reference/human_g1k_v37.fasta " +
+                        "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
+                        "-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " +
+                        "-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " +
+                        "-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " +
+                        "-output %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0"));
+        executeTest("test BeagleOutputToVCF", spec);
+    }
+   
+    @Test
+    public void testBeagleInput() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T ProduceBeagleInput -R " + oneKGLocation + "reference/human_g1k_v37.fasta " +
+                        "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
+                         "-beagle %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e"));
+        executeTest("test BeagleInput", spec);
+    }
+
+}
\ No newline at end of file