From aa39037be8c00a0dfdbe92d4f15951b1cfb81fba Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 19 Dec 2012 11:31:35 -0500
Subject: [PATCH] updating UG integration tests.

---
 ...UnifiedGenotyperGeneralPloidyIntegrationTest.java |  4 ++--
 .../genotyper/UnifiedGenotyperIntegrationTest.java   | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
index f26194e00..cdd31a5ef 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
@@ -70,12 +70,12 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","481452ad7d6378cffb5cd834cc621d55");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","6987b89e04dcb604d3743bb09aa9587d");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","812957e51277aca9925c1a7bb4d9a118");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","d0780f70365ed1b431099fd3b4cec449");
     }
 
     @Test(enabled = true)
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 4f88732b0..a5debff60 100755
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -62,7 +62,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("97df6c2a8d390d43b9bdf56c979d9b09"));
+                Arrays.asList("b41b95aaa2c453c9b75b3b29a9c2718e"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -289,7 +289,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("50329e15e5139be9e3b643f0b3ba8a53"));
+                Arrays.asList("f6f8fbf733f20fbc1dd9ebaf8faefe6c"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -304,7 +304,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("2b85e3bd6bf981afaf7324666740d74b"));
+                Arrays.asList("4438ad0f03bbdd182d9bb59b15af0fa5"));
 
         executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
     }
@@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("a6fd46eff78827060451a62cffd698a7"));
+                 Arrays.asList("27b4ace2ad5a83d8cccb040f97f29183"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }
@@ -345,7 +345,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSampleIndels1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
-                Arrays.asList("69df7a00f800204564ca3726e1871132"));
+                Arrays.asList("d3d518448b01bf0f751824b3d946cd04"));
         List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
@@ -462,7 +462,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testReducedBamINDELs() {
-        testReducedCalling("INDEL", "3c02ee5187933bed44dc416a2e28511f");
+        testReducedCalling("INDEL", "9d5418ddf1b227ae4d463995507f2b1c");
     }