From 7c386fa428ceca8c7667c7c1181386eec3ada648 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 Nov 2009 00:07:35 +0000
Subject: [PATCH] Another case of reordering of read groups blowing up
 checksums.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2030 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/IntervalCleanerIntegrationTest.java | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
index 5c65581a8..ebb014c37 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
@@ -9,21 +9,21 @@ public class IntervalCleanerIntegrationTest extends WalkerTest {
     @Test
     public void testIntervals() {
 
-        String[] md5lod5 = {"54ba9ef0d90659475f7d694fb97b5f2b", "4aa3637e86822c95af3e2c9b414530c3"};
+        String[] md5lod5 = {"163d2f1b04741986151636d3c7e04c94", "4aa3637e86822c95af3e2c9b414530c3"};
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 "-T IntervalCleaner -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
                  2,
                  Arrays.asList(md5lod5));
         executeTest("testLod5", spec1);
 
-        String[] md5lod200 = {"55097ed556f41c5d527d7381b8e858dd", "e39aa718c9810364ebe30964d878d5ff"};
+        String[] md5lod200 = {"1d89ee2af03df79eb5de494c77767221", "e39aa718c9810364ebe30964d878d5ff"};
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T IntervalCleaner -LOD 200 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
                  2,
                  Arrays.asList(md5lod200));
         executeTest("testLod200", spec2);
 
-        String[] md5cleanedOnly = {"1f844be094cd30c351586ebf0f8ff38c", "4aa3637e86822c95af3e2c9b414530c3"};
+        String[] md5cleanedOnly = {"710f9114ec496c73f1c3782b5cb09757", "4aa3637e86822c95af3e2c9b414530c3"};
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 "-T IntervalCleaner -LOD 5 -cleanedOnly -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
                  2,