From 3c5eac8c171770f145dbd2b5099294fbef8b6a40 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Mon, 27 Jun 2016 19:43:06 -0400
Subject: [PATCH] Move htsjdk and picard to version 2.5.0

---
 .../java/org/broadinstitute/gatk/engine/CommandLineGATK.java  | 3 +--
 .../gatk/engine/arguments/IntervalIntegrationTest.java        | 2 +-
 public/gatk-root/pom.xml                                      | 4 ++--
 .../tools/walkers/CNV/SymbolicAllelesIntegrationTest.java     | 2 +-
 .../main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java | 4 ++--
 5 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
index 83aab7006..58dc9edc3 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
@@ -178,8 +178,7 @@ public class CommandLineGATK extends CommandLineExecutable {
                     System.getProperty("os.name") + " " + System.getProperty("os.version") +
                     " " + System.getProperty("os.arch"));
             header.add( System.getProperty("java.vm.name") +
-                    " " + System.getProperty("java.runtime.version") +
-                    " " + (DeflaterFactory.usingIntelDeflater()? "IntelDeflater": "JdkDeflater"));
+                    " " + System.getProperty("java.runtime.version"));
         }
         catch (Exception e) { /* Unpossible! */ }
 
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
index 6ba25ec8e..954cbc0a6 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
@@ -89,7 +89,7 @@ public class IntervalIntegrationTest extends WalkerTest {
         File baseOutputFile = createTempFile("testMultipleIntervalInclusionOnCRAM", ".cram");
         spec.setOutputFileLocation(baseOutputFile);
         spec.addAuxFile("", createTempFileFromBase(baseOutputFile.getAbsolutePath()));  // Bypass MD5 check since the CRAM header stores the file name
-        spec.addAuxFile("4bd9185ce1c7d2e97e8c131b77f76aef", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
+        spec.addAuxFile("019bc0dfad029bb86854a0dc6b149983", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
 
         executeTest("testMultipleIntervalInclusionOnCRAM", spec);
     }
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index c0b63cafa..d4daad80e 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>2.4.1</htsjdk.version>
-        <picard.version>2.4.1</picard.version>
+        <htsjdk.version>2.5.0</htsjdk.version>
+        <picard.version>2.5.0</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
index f1746cb6d..c63a6e8ea 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
@@ -57,7 +57,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
                 1,
-                Arrays.asList("c8b294089832bb1a2c450b550318a471"));
+                Arrays.asList("3f97ed3243fad7f953f4859af92d227f"));
         executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
     }
 }
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
index f16178d26..d413f6f79 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
@@ -503,7 +503,7 @@ public class MannWhitneyU {
      * @return P-value based on histogram with u calculated for every possible permutation of group tag.
      */
     public double permutationTest(final double[] series1, final double[] series2, final double testStatU) {
-        final Histogram<Double> histo = new Histogram<Double>();
+        final Histogram<Double> histo = new Histogram<>();
         final int n1 = series1.length;
         final int n2 = series2.length;
 
@@ -555,7 +555,7 @@ public class MannWhitneyU {
          */
         double sumOfAllSmallerBins = histo.get(testStatU).getValue() / 2.0;
 
-        for (final Histogram<Double>.Bin bin : histo.values()) {
+        for (final Histogram.Bin<Double> bin : histo.values()) {
             if (bin.getId() < testStatU) sumOfAllSmallerBins += bin.getValue();
         }