From b88cfd2939df1f57f109ba380e686a638560f993 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Oct 2010 03:07:40 +0000
Subject: [PATCH] Updated MD5s of VCFs, since the approximate command line
 arguments injected into the VCF headers now have a little more order to them
 thanks to changes in the ParsingEngine.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4538 348d0f76-0448-11de-a6fe-93d51630548a
---
 ...MergeSegregatingPolymorphismsIntegrationTest.java |  6 +++---
 .../phasing/ReadBackedPhasingIntegrationTest.java    | 12 ++++++------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsIntegrationTest.java
index 68b209715..62b859eaf 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsIntegrationTest.java
@@ -22,7 +22,7 @@ public class MergeSegregatingPolymorphismsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("38d88fc6c1880e76ce402cfc60669726"));
+                Arrays.asList("f0e9796bc9866201aed0e97d76ed4a84"));
         executeTest("Merge MNP het sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -32,7 +32,7 @@ public class MergeSegregatingPolymorphismsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("e14a2f062391b6c3f8b36b1b4eed628b"));
+                Arrays.asList("ab2b05dc6e7e4464e8f9e08d1d02f8ae"));
         executeTest("Merge MNP het sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -42,7 +42,7 @@ public class MergeSegregatingPolymorphismsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("fdb4ad8ced0cb461deaff1555258008e"));
+                Arrays.asList("d446a0076f9d3d13c128bc8402b087a4"));
         executeTest("Merge MNP het sites within genomic distance of 100 [TEST THREE]", spec);
     }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index b816b31a7..2d0caaff0 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -25,7 +25,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("973f82098ec931c49a8fdac186702792"));
+                Arrays.asList("2612b279cf651fba2b50c35373311642"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -35,7 +35,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:1232503-1332503",
                 1,
-                Arrays.asList("2342c346c4a586f6d18a432c04a451a9"));
+                Arrays.asList("29bcc72f64088b39df20c0d1bfc9f5f7"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -45,7 +45,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("57e35f44652903493f6ff3fef6b9b9ed"));
+                Arrays.asList("381eeedba5977edabec1a285b77df4a1"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -55,7 +55,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("1520496b65bc4b4b348cacef9660b2d0"));
+                Arrays.asList("513447f80b71a836bc99f569abeaa5d7"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -65,7 +65,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
                         + " -L chr20:332341-482503",
                 1,
-                Arrays.asList("202760f43e3a2852195688b562c360fd"));
+                Arrays.asList("e10e370b0f2823cfc7efdac590abf93b"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -75,7 +75,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:652810-681757",
                 1,
-                Arrays.asList("353c260c81f287bc6c2734f69cb63d39"));
+                Arrays.asList("adb46e988b27e13907d197bd058468bf"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }