From 40d305bc7e819d278f2b2e1014b2aad0c50dfc62 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 10 Mar 2010 21:00:41 +0000
Subject: [PATCH] Added test of Nway cleaning for Matt; thanks to Aaron for the
 help.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../indels/IndelRealignerIntegrationTest.java | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index bc5ac2ea9..66c8440be 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -4,6 +4,7 @@ import org.broadinstitute.sting.WalkerTest;
 import org.junit.Test;
 
 import java.util.Arrays;
+import java.io.File;
 
 public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
@@ -14,13 +15,27 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
                 "-T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s",
                  2,
                  Arrays.asList(md5lod5));
-        executeTest("testLod5", spec1);
+        executeTest("test Lod5", spec1);
 
         String[] md5lod200 = {"96edef86cea95f312ee8295b38227eb8", "d4d8ff567b614729ab8c52bd7d6bef48"};
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T IndelRealigner -LOD 200 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023800-10332350 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -snps %s",
                  2,
                  Arrays.asList(md5lod200));
-        executeTest("testLod200", spec2);
+        executeTest("test Lod200", spec2);
+
+        String filename1 = "NA12878.chrom1.SLX.SRP000032.2009_06";
+        String filename2 = "low_coverage_CEU.chr1.10k-11k";
+        WalkerTestSpec spec3 = new WalkerTestSpec(
+                "-T IndelRealigner -nway -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + filename1 + ".bam -I " + validationDataLocation + filename2 + ".bam -L 1:10023900-10024000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O /tmp -snps %s",
+                 1,
+                 Arrays.asList("bd42a4fa66d7ec7a480c2b94313a78d3"));
+        File file1 = new File("/tmp/" + filename1 + ".cleaned.bam");
+        file1.deleteOnExit();
+        spec3.addAuxFile("7e1c5a74e572c3e0fbc14f98021e04b4", file1);
+        File file2 = new File("/tmp/" + filename2 + ".cleaned.bam");
+        file2.deleteOnExit();
+        spec3.addAuxFile("7a796195c3f13a3c84cd7209f3030d85", file2);
+        executeTest("test NWay", spec3);
     }
 }
\ No newline at end of file