From 1e06d2bf68de55807154e2053471ca8bbc1333d5 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 18 Jun 2010 20:35:27 +0000
Subject: [PATCH] Initial HLA Caller integration tests.  Kind of painful, but
 will improve with code refactoring. This baby is now officially ours.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3593 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../HLAcaller/HLACallerIntegrationTest.java   | 61 +++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100755 java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java

diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java
new file mode 100755
index 000000000..f71c1a841
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java
@@ -0,0 +1,61 @@
+/*
+ * 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.HLAcaller;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+public class HLACallerIntegrationTest extends WalkerTest {
+
+    private static final String intervals = validationDataLocation + "HLA_EXONS.intervals";
+
+
+    @Test
+    public void testFindClosestHLA() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FindClosestHLA -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -PolymorphicSites " + validationDataLocation + "HLA_POLYMORPHIC_SITES.txt -o %s", 1,
+                Arrays.asList("a49b6f54a4585d1dd958c55a5523427d"));
+        executeTest("test FindClosestHLA", spec);
+    }
+
+    @Test
+    public void testCalculateBaseLikelihoods() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T CalculateBaseLikelihoods -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 0 -o %s", 1,
+                Arrays.asList("3272e3db32a3370b728457cd9a071339"));
+        executeTest("test CalculateBaseLikelihoods", spec);
+    }
+
+    @Test
+    public void testHLACaller() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T HLACaller -noVerbose -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 5 -HLAfrequencies " + validationDataLocation + "HLA_FREQUENCIES.txt -bl " + validationDataLocation + "HLA_HISEQ.baselikelihoods -o %s", 1,
+                Arrays.asList("f9931b378bde213e71fca6ecaa24b48b"));
+        executeTest("test HLACaller", spec);
+    }
+}
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