From 30665c7dbc883a58e57d73badc7a545d30e6f515 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Sun, 29 May 2016 09:32:39 -0400
Subject: [PATCH] Move Move htsjdk and picard to version 2.4.1

---
 .../VariantRecalibrationWalkersIntegrationTest.java           | 2 +-
 public/gatk-root/pom.xml                                      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 1e4d0681a..7c716fef4 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -196,7 +196,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
             "3ad7f55fb3b072f373cbce0b32b66df4",  // tranches
-            "48c21792897bdbb9adcc64886d03c5d1",  // recal file
+            "051a3b8c15988ee4cd86ae918bec896b",  // recal file
             "93a6e7ab6cbd6ae24a5b2a6f0fd29d92"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index c10fa86ec..c443d6f21 100644
--- a/public/gatk-root/pom.xml
+++ b/public/gatk-root/pom.xml
@@ -44,8 +44,8 @@
         <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
 
         <!-- Version numbers for picard and htsjdk -->
-        <htsjdk.version>2.3.0</htsjdk.version>
-        <picard.version>2.3.0</picard.version>
+        <htsjdk.version>2.4.1</htsjdk.version>
+        <picard.version>2.4.1</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->