From e5c580414113668e5540659784c3b96296137da8 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Tue, 1 Mar 2016 14:05:51 -0500
Subject: [PATCH] Modify MD5s to correct RankSum annotations

---
 .../walkers/annotator/VariantAnnotatorIntegrationTest.java      | 2 +-
 .../haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 16ff38e8a..f37188e73 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -424,7 +424,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testStrandAlleleCountsBySample() {
-        final String MD5 = "93e424f866f03ac23f9ddac94401e348";
+        final String MD5 = "dca6c2b416076ca89769a322cae65bb8";
         final WalkerTestSpec spec = new WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering " +
                 String.format("-R %s -I %s ", REF, CEUTRIO_BAM) +
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index 2e8b57cce..f377a4d69 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -347,7 +347,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testHaplotypeCallerMultiAllelicNonRef() {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A StrandAlleleCountsBySample",
                 b37KGReference, privateTestDir + "multiallelic-nonref.bam", "2:47641259-47641859", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("ba2df96afbf5fe2a59270b6e65c3fb4e"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("2bd863f0b54b9c9a5014097cd3d3f61a"));
         spec.disableShadowBCF();
         executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec);
     }