From ac3620839c1dd72c728f604e3b0fc49178bbac9b Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Jun 2011 17:06:32 +0000
Subject: [PATCH] Very basic intergration tests for ReducedReads, to allow safe
 optimization of the code

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5970 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../ReduceReadsIntegrationTest.java           | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100755 java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java

diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java
new file mode 100755
index 000000000..05aa20716
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java
@@ -0,0 +1,36 @@
+package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class ReduceReadsIntegrationTest extends WalkerTest {
+    final static String REF = b37KGReference;
+    final String BAM = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
+    final String L = "20:10,100,000-10,200,000";
+
+    private void RRTest(String args, String md5) {
+        String base = String.format("-T ReduceReads -R %s -I %s -L %s", REF, BAM, L) + " -o %s";
+        WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
+        executeTest("testReduceReads1: args=" + args, spec);
+    }
+
+    @Test()
+    public void testReduceReadsBase() {
+        RRTest("", "6c34409f19ba2e5b21f3bfe6847dadda");
+    }
+
+    @Test()
+    public void testReduceReads50MaxReads() {
+        RRTest(" -mravs 50", "3a896ac6e2ea0fc0a3fb4348d31313b6");
+    }
+
+    @Test()
+    public void testReduceReadsMinBasesForConsensus10000() {
+        RRTest(" -mbrc 10000", "d8edbc04fd47cd1d64f2ce08459f7dae");
+    }
+
+}
+