[med-svn] [Git][med-team/picard-tools][master] 4 commits: New upstream version 2.26.10+dfsg

Pierre Gruet (@pgt) gitlab at salsa.debian.org
Fri Feb 18 14:52:43 GMT 2022 


Pierre Gruet pushed to branch master at Debian Med / picard-tools


Commits:
f3290b0a by Pierre Gruet at 2022-02-18T14:22:54+01:00
New upstream version 2.26.10+dfsg
- - - - -
b4d532c5 by Pierre Gruet at 2022-02-18T14:23:58+01:00
Update upstream source from tag 'upstream/2.26.10+dfsg'

Update to upstream version '2.26.10+dfsg'
with Debian dir d2579c986967dda034407a56c2020f1e7e113d33
- - - - -
77e21d2b by Pierre Gruet at 2022-02-18T14:27:18+01:00
Refreshing patches

- - - - -
7968c757 by Pierre Gruet at 2022-02-18T15:52:18+01:00
Upload to unstable

- - - - -


6 changed files:

- build.gradle
- debian/changelog
- debian/patches/10-build.xml.patch
- debian/patches/20-shadowjar.patch
- debian/patches/40-tests-fix-testng.patch
- src/main/java/picard/vcf/GatherVcfs.java


Changes:

=====================================
build.gradle
=====================================
@@ -91,7 +91,9 @@ dependencies {
     compile 'org.apache.commons:commons-collections4:4.3'
     compile 'commons-lang:commons-lang:2.6'
     compile 'com.github.samtools:htsjdk:' + htsjdkVersion
-    compile 'org.broadinstitute:barclay:3.0.0'
+    compile 'org.broadinstitute:barclay:4.0.2'
+    compile 'org.apache.logging.log4j:log4j-api:2.17.1'
+    compile 'org.apache.logging.log4j:log4j-core:2.17.1'
     compileOnly(googleNio) {
         transitive = false
     }


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+picard-tools (2.26.10+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 2.26.10+dfsg
+  * Refreshing patches
+
+ -- Pierre Gruet <pgt at debian.org>  Fri, 18 Feb 2022 14:27:22 +0100
+
 picard-tools (2.26.6+dfsg-2) unstable; urgency=medium
 
   * Removing now useless versioned dependencies


=====================================
debian/patches/10-build.xml.patch
=====================================
@@ -43,7 +43,7 @@ Last-Updated: 2016-07-07
      compile 'org.apache.commons:commons-math3:3.5'
      compile 'org.apache.commons:commons-collections4:4.3'
      compile 'commons-lang:commons-lang:2.6'
-@@ -97,8 +91,8 @@
+@@ -99,8 +93,8 @@
      }
  
      // javadoc utilities; compile/test only to prevent redistribution of sdk jars
@@ -54,7 +54,7 @@ Last-Updated: 2016-07-07
  
      testCompile 'org.testng:testng:6.14.3'
      testCompile 'org.apache.commons:commons-lang3:3.6'
-@@ -114,9 +108,18 @@
+@@ -116,9 +110,18 @@
  sourceCompatibility = 1.8
  targetCompatibility = 1.8
  
@@ -75,7 +75,7 @@ Last-Updated: 2016-07-07
  
  logger.info("build for version:" + version)
  group = 'com.github.broadinstitute'
-@@ -150,6 +153,7 @@
+@@ -152,6 +155,7 @@
  tasks.withType(Javadoc) {
      // do this for all javadoc tasks, including gatkDoc
      options.addStringOption('Xdoclint:none')
@@ -83,7 +83,7 @@ Last-Updated: 2016-07-07
  }
  
  javadoc {
-@@ -178,7 +182,7 @@
+@@ -180,7 +184,7 @@
      // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
      // The compileClasspath is required in order for the picarDoc doclet process to resolve the googleNio
      // classes, which are compile-time only.
@@ -92,7 +92,7 @@ Last-Updated: 2016-07-07
      options.docletpath = classpath.asType(List)
      options.doclet = "picard.util.help.PicardHelpDoclet"
  
-@@ -239,6 +243,8 @@
+@@ -241,6 +245,8 @@
          }
      }
  
@@ -101,7 +101,7 @@ Last-Updated: 2016-07-07
      // set heap size for the test JVM(s)
      minHeapSize = "1G"
      maxHeapSize = "2G"
-@@ -277,30 +283,18 @@
+@@ -279,30 +285,18 @@
      }
  }
  
@@ -134,7 +134,7 @@ Last-Updated: 2016-07-07
  }
  
  /**
-@@ -384,20 +378,3 @@
+@@ -386,20 +380,3 @@
      from 'build/docs/picarddoc'
      into "$htmlDir/picarddoc"
  }


=====================================
debian/patches/20-shadowjar.patch
=====================================
@@ -3,7 +3,7 @@ Author: Sascha Steinbiss <satta at debian.org>
 Forwarded: not-needed
 --- a/build.gradle
 +++ b/build.gradle
-@@ -126,7 +126,7 @@
+@@ -128,7 +128,7 @@
  
  defaultTasks 'all'
  
@@ -12,7 +12,7 @@ Forwarded: not-needed
  
  // Source file names for the picard command line properties file. We select and include only one of
  // these two files in each jar, renamed to "picardCmdLine.properties", depending on which parser we
-@@ -196,6 +196,7 @@
+@@ -198,6 +198,7 @@
      options.addStringOption("verbose")
  }
  
@@ -20,7 +20,7 @@ Forwarded: not-needed
  task currentJar(type: Copy){
      from shadowJar
      into file("$buildDir/libs")
-@@ -205,8 +206,7 @@
+@@ -207,8 +208,7 @@
  shadowJar {
      finalizedBy currentJar
  }


=====================================
debian/patches/40-tests-fix-testng.patch
=====================================
@@ -18,10 +18,10 @@ Forwarded: not-needed
      }
  }
  
-@@ -86,16 +83,13 @@
-     compile 'commons-lang:commons-lang:2.6'
-     compile 'com.github.samtools:htsjdk:' + htsjdkVersion
-     compile 'org.broadinstitute:barclay:3.0.0'
+@@ -88,16 +85,13 @@
+     compile 'org.broadinstitute:barclay:4.0.2'
+     compile 'org.apache.logging.log4j:log4j-api:2.17.1'
+     compile 'org.apache.logging.log4j:log4j-core:2.17.1'
 -    compileOnly(googleNio) {
 -        transitive = false
 -    }
@@ -37,7 +37,7 @@ Forwarded: not-needed
  }
  
  configurations.all {
-@@ -208,6 +202,7 @@
+@@ -210,6 +204,7 @@
  }
  */
  
@@ -45,7 +45,7 @@ Forwarded: not-needed
  task cloudJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar)  {
      configurations = [project.configurations.cloudConfiguration]
      from project.sourceSets.main.output
-@@ -230,11 +225,15 @@
+@@ -232,11 +227,15 @@
  test {
      dependsOn barclayTest
  }


=====================================
src/main/java/picard/vcf/GatherVcfs.java
=====================================
@@ -31,7 +31,7 @@ import java.util.stream.Collectors;
 
 /**
  * Simple little class that combines multiple VCFs that have exactly the same set of samples
- * and totally discrete sets of loci.
+ * and nonoverlapping sets of loci.
  *
  * @author Tim Fennell
  */



View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/3500e8887eff09c0d49270c951f6a6cdae52798e...7968c7574f7597095f3ab4c7c19ce5e782ad9597

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/3500e8887eff09c0d49270c951f6a6cdae52798e...7968c7574f7597095f3ab4c7c19ce5e782ad9597
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220218/898ea7f4/attachment-0001.htm>

More information about the debian-med-commit mailing list