debian/control

@@ -14,6 +14,7 @@ Build-Depends: default-jdk (>= 2:1.9~),
                maven-repo-helper,
                libguava-java (>= 15.0),
                libcommons-lang3-java,
+               libcommons-math3-java, 
                libbarclay-java,
                libgkl-java,
                libgatk-native-bindings-java,
@@ -92,6 +93,7 @@ Depends: ${misc:Depends},
          libbarclay-java,
          libgkl-java,
          libcommons-lang3-java,
+         libcommons-math3-java,
          libgatk-native-bindings-java
 # avoid ${java:Depends} that contains openjdk-8-jdk-headless
 # due to tools.jar in classpath

debian/patches/10-build.xml.patch

@@ -4,7 +4,7 @@ Forwarded: not-needed
 Last-Updated: 2016-07-07
 --- a/build.gradle
 +++ b/build.gradle
-@@ -12,13 +12,7 @@ plugins {
+@@ -12,13 +12,7 @@
      id "java"
      id 'maven'
      id 'signing'
@@ -18,7 +18,7 @@ Last-Updated: 2016-07-07
  }
  
  mainClassName = "picard.cmdline.PicardCommandLine"
-@@ -31,6 +25,7 @@ repositories {
+@@ -31,6 +25,7 @@
      }
  }
  
@@ -26,7 +26,7 @@ Last-Updated: 2016-07-07
  jacocoTestReport {
      dependsOn test
      group = "Reporting"
-@@ -46,6 +41,7 @@ jacocoTestReport {
+@@ -46,21 +41,22 @@
  jacoco {
      toolVersion = "0.7.5.201505241946"
  }
@@ -34,7 +34,31 @@ Last-Updated: 2016-07-07
  
  final requiredJavaVersion = "8"
  final buildPrerequisitesMessage = "See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard"
-@@ -73,7 +69,7 @@ final googleNio = 'org.broadinstitute:go
+ // Ensure that we have the right JDK version, a clone of the git repository
+ def ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage) {
+     // Make sure we can get a ToolProvider class loader. If not we may have just a JRE, or a JDK from the future.
+-    if (ToolProvider.getSystemToolClassLoader() == null) {
+-        throw new GradleException(
+-                "The ClassLoader obtained from the Java ToolProvider is null. "
+-                + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
+-    }
+-    if (!file(".git").isDirectory()) {
+-        throw new GradleException("The Picard Github repository must be cloned using \"git clone\" to run the build. "
+-                + "$buildPrerequisitesMessage")
+-    }
++    //if (ToolProvider.getSystemToolClassLoader() == null) {
++    //    throw new GradleException(
++    //            "The ClassLoader obtained from the Java ToolProvider is null. "
++    //            + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
++    //}
++    //if (!file(".git").isDirectory()) {
++    //    throw new GradleException("The Picard Github repository must be cloned using \"git clone\" to run the build. "
++    //            + "$buildPrerequisitesMessage")
++    //}
+ }
+ ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage)
+ 
+@@ -73,7 +69,7 @@
  // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,
  // test execution, and gatkDoc generation, but we don't want them as part of the runtime
  // classpath and we don't want to redistribute them in the uber jar.
@@ -43,7 +67,7 @@ Last-Updated: 2016-07-07
  
  configurations {
      cloudConfiguration {
-@@ -95,8 +91,8 @@ dependencies {
+@@ -95,8 +91,8 @@
      compileOnly googleNio
  
      // javadoc utilities; compile/test only to prevent redistribution of sdk jars
@@ -54,7 +78,7 @@ Last-Updated: 2016-07-07
  
      testCompile 'org.testng:testng:6.9.10'
      testCompile 'org.apache.commons:commons-lang3:3.6'
-@@ -112,9 +108,18 @@ configurations.all {
+@@ -112,9 +108,18 @@
  sourceCompatibility = 1.8
  targetCompatibility = 1.8
  
@@ -75,7 +99,7 @@ Last-Updated: 2016-07-07
  
  logger.info("build for version:" + version)
  group = 'com.github.broadinstitute'
-@@ -166,6 +171,8 @@ jar {
+@@ -166,6 +171,8 @@
  tasks.withType(Javadoc) {
      // do this for all javadoc tasks, including gatkDoc
      options.addStringOption('Xdoclint:none')
@@ -84,7 +108,7 @@ Last-Updated: 2016-07-07
  }
  
  javadoc {
-@@ -192,7 +199,8 @@ task picardDoc(type: Javadoc, dependsOn:
+@@ -192,7 +199,8 @@
  
      // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
      // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
@@ -94,7 +118,7 @@ Last-Updated: 2016-07-07
      options.docletpath = classpath.asType(List)
      options.doclet = "picard.util.help.PicardHelpDoclet"
  
-@@ -279,6 +287,8 @@ tasks.withType(Test) {
+@@ -279,6 +287,8 @@
          }
      }
  
@@ -103,7 +127,7 @@ Last-Updated: 2016-07-07
      // set heap size for the test JVM(s)
      minHeapSize = "1G"
      maxHeapSize = "2G"
-@@ -415,6 +425,7 @@ task copyPicardDoc(dependsOn: 'picardDoc
+@@ -415,6 +425,7 @@
      into "$htmlDir/picarddoc"
  }
  
@@ -111,7 +135,7 @@ Last-Updated: 2016-07-07
  task updateGhPages(dependsOn: ['copyJavadoc', 'copyPicardDoc']){
    outputs.dir htmlDir
  }
-@@ -430,3 +441,4 @@ githubPages {
+@@ -430,3 +441,4 @@
      into 'newdocs'
    }
  }

debian/patches/40-tests-fix-testng.patch

 Author: Olivier Sallou
-Last-Update: 2017-11-01 08:42:38
-Description: Fix testng version
-
+Last-Update: 2018-09-18 08:42:38
+Description: Fix testng version and disable some tests.
+ testng below or equal to 6.9.13.4 does not correctly map
+ long and Integers. This leads to test issues when provider [0,9] values
+ and methods expects a long (testng sends an Integer).
+ This patch disable some tests around this
 --- a/build.gradle
 +++ b/build.gradle
-@@ -74,9 +74,6 @@ final googleNio = 'org.broadinstitute:go
+@@ -74,9 +74,6 @@
  configurations {
      cloudConfiguration {
          extendsFrom runtime
@@ -14,7 +17,7 @@ Description: Fix testng version
      }
  }
  
-@@ -88,14 +85,13 @@ dependencies {
+@@ -88,14 +85,13 @@
      compile 'org.apache.commons:commons-math3:3.5'
      compile 'com.github.samtools:htsjdk:' + htsjdkVersion
      compile 'org.broadinstitute:barclay:2.0.0'
@@ -31,7 +34,7 @@ Description: Fix testng version
  }
  
  configurations.all {
-@@ -234,6 +230,7 @@ shadowJar {
+@@ -234,6 +230,7 @@
  }
  */
  
@@ -39,7 +42,7 @@ Description: Fix testng version
  task cloudJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar)  {
      configurations = [project.configurations.cloudConfiguration]
      from project.sourceSets.main.output
-@@ -258,6 +255,7 @@ task barclayShadowJar(type: com.github.j
+@@ -258,6 +255,7 @@
      }
      archiveName 'picardBarclay.jar'
  }
@@ -47,7 +50,7 @@ Description: Fix testng version
  
  // Run the tests using the legacy parser only. Assumes that test code is written using
  // legacy command line parser syntax.
-@@ -268,6 +266,8 @@ task legacyTest(type: Test)
+@@ -268,6 +266,8 @@
  task barclayTest(type: Test) {
      systemProperty 'picard.convertCommandLine', 'true'
      systemProperty 'picard.useLegacyParser', 'false'
@@ -56,7 +59,7 @@ Description: Fix testng version
  }
  
  // Run tests using both the legacy and barclay command line parsers.
-@@ -279,6 +279,9 @@ tasks.withType(Test) {
+@@ -279,6 +279,9 @@
      outputs.upToDateWhen { false } // tests will always rerun
      description = "Runs the unit tests"
  
@@ -68,7 +71,7 @@ Description: Fix testng version
              excludeGroups "slow", "broken"
 --- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
 +++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
-@@ -41,51 +41,6 @@ public class CollectHsMetricsTest extend
+@@ -41,51 +41,6 @@
          };
      }
  
@@ -120,7 +123,7 @@ Description: Fix testng version
  
      @Test
      public void testCoverageHistogram() throws IOException {
-@@ -106,7 +61,7 @@ public class CollectHsMetricsTest extend
+@@ -106,7 +61,7 @@
          final boolean clipOverlappingReads = true;
          final int sampleSize = 10;
  
@@ -131,7 +134,7 @@ Description: Fix testng version
          final String[] args = new String[] {
 --- a/src/test/java/picard/analysis/artifacts/TransitionTest.java
 +++ b/src/test/java/picard/analysis/artifacts/TransitionTest.java
-@@ -34,13 +34,4 @@ public class TransitionTest {
+@@ -34,13 +34,4 @@
          return new Object[][] {{Character.MIN_VALUE}, {Transition.Base.A.base - 1}, {'Z'}, {Character.MAX_VALUE}};
      }
  
@@ -147,7 +150,7 @@ Description: Fix testng version
  }
 --- a/src/test/java/picard/util/IntervalListToolsTest.java
 +++ b/src/test/java/picard/util/IntervalListToolsTest.java
-@@ -80,12 +80,6 @@ public class IntervalListToolsTest exten
+@@ -80,12 +80,6 @@
          };
      }
  
@@ -160,3 +163,18 @@ Description: Fix testng version
  
      @DataProvider
      public Object[][] actionAndTotalBasesWithInvertData() {
+--- a/src/test/java/picard/analysis/TheoreticalSensitivityTest.java
++++ b/src/test/java/picard/analysis/TheoreticalSensitivityTest.java
+@@ -351,10 +351,11 @@
+         };
+     }
+ 
++     /*
+     @Test(dataProvider = "callingThresholdDataProvider")
+     public void testCallingThreshold(final int totalDepth, final int altDepth, final double sumOfAltQualities, final double alleleFraction, final double logOddsThreshold, final boolean expectedCall) {
+         Assert.assertEquals(TheoreticalSensitivity.isCalled(totalDepth, altDepth, sumOfAltQualities, alleleFraction, logOddsThreshold), expectedCall);
+-    }
++    } */
+ 
+     @DataProvider(name = "sumOfGaussiansDataProvider")
+     public Object[][] sumOfGaussians() {