From b93829e505615f88a865130ea2a032746de151ae Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Jun 2011 22:26:06 +0000
Subject: [PATCH] The underlying bam file for this test was busted for many
 reasons preventing Picard folks from making unrelated changes, so I needed to
 fix it.  Updating md5s accordingly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5943 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../indels/IndelRealignerIntegrationTest.java      | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 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 f9de2af55..20edf9b08 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -10,12 +10,12 @@ import java.util.Map;
 
 public class IndelRealignerIntegrationTest extends WalkerTest {
 
-    private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.bam";
+    private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.bam";
     private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals";
     private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
     private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
     private static final String baseCommand = baseCommandPrefix + "-o %s ";
-    private static final String base_md5 = "28c045a821e541820a049595759fe962";
+    private static final String base_md5 = "d7c7acd346ee4c8d34f1e2499ff7c313";
 
     @Test
     public void testDefaults() {
@@ -45,13 +45,13 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
                 1,
-                Arrays.asList("ea91283e0af5432c1d63b052ed3dcfe4"));
+                Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888"));
         executeTest("realigner known indels only from VCF", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseCommand + "-knownsOnly -D " + GATKDataLocation + "dbsnp_129_b36.rod",
                 1,
-                Arrays.asList("3eed07873a474d8d8d4935399c99f793"));
+                Arrays.asList("78850024ac9ff3ba51b6f097c7041c1d"));
         executeTest("realigner known indels only from dbsnp", spec2);
     }
 
@@ -59,7 +59,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testLods() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( "-LOD 60", base_md5 );
-        e.put( "-LOD 1",  "9a59cd8508f72f8935410b6fb2e6e7d3" );
+        e.put( "-LOD 1",  "f158f18198cf48bbb3d4f1b7127928a3" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -84,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseCommand + "--noOriginalAlignmentTags",
                 1,
-                Arrays.asList("4bbd9a0d998bc0483cd9bbbdac8cb9c2"));
+                Arrays.asList("e77e59cc6363cf58f392ce5ea8d7e0b6"));
         executeTest("realigner no output tags", spec);
     }
 
@@ -106,7 +106,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testMaxReadsInMemory() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "--maxReadsInMemory 10000", "87605e2dea24d3e01efaeec5f44e8671" );
+        e.put( "--maxReadsInMemory 10000", "d7c7acd346ee4c8d34f1e2499ff7c313" );
         e.put( "--maxReadsInMemory 40000",  base_md5 );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {