From 2aa28abe0a4948e3308248f5ec57b24d1a6d90b2 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 30 Oct 2012 14:27:10 -0400
Subject: [PATCH] Fixing md5s to reflect the new HapMap file

---
 .../varianteval/VariantEvalIntegrationTest.java      |  2 +-
 .../VariantRecalibrationWalkersIntegrationTest.java  | 12 ++++++------
 .../variantutils/SelectVariantsIntegrationTest.java  |  4 ++--
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index c92d6d4cf..7a3a20bdd 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -354,7 +354,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testCompOverlap() {
         String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + variantEvalTestDataRoot + "pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + variantEvalTestDataRoot + "pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("59ad39e03678011b5f62492fa83ede04"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d0d9208060e69e157dac3bf01bdd83b0"));
         executeTestParallel("testCompOverlap",spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index aec087f2c..0c4924229 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -26,9 +26,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
-            "f360ce3eb2b0b887301be917a9843e2b",  // tranches
-            "287fea5ea066bf3fdd71f5ce9b58eab3",  // recal file
-            "afa297c743437551cc2bd36ddd6d6d75"); // cut VCF
+            "4d08c8eee61dd1bdea8c5765f34e41f0",  // tranches
+            "ce396fe4045e020b61471f6737dff36e",  // recal file
+            "4f59bd61be900b25c6ecedaa68b9c8de"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -75,9 +75,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
-            "a8ce3cd3dccafdf7d580bcce7d660a9a",  // tranches
-            "74c10fc15f9739a938b7138909fbde04",  // recal file
-            "c30d163871a37f2bbf8ee7f761e870b4"); // cut VCF
+            "6a1eef4d02857dbb117a15420b5c0ce9",  // tranches
+            "238366af66b05b6d21749e799c25353d",  // recal file
+            "3928d6bc5007becf52312ade70f14c42"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")
     public Object[][] createVRBCFTest() {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index f29ac8cad..a1d673b56 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -20,7 +20,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " -disc " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("d88bdae45ae0e74e8d8fd196627e612c")
+                Arrays.asList("954415f84996d27b07d00855e96d33a2")
         );
         spec.disableShadowBCF();
 
@@ -49,7 +49,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " -disc " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("c0b937edb6a8b6392d477511d4f1ebcf")
+                Arrays.asList("ca1b5226eaeaffb78d4abd9d2ee10c43")
         );
         spec.disableShadowBCF();