Change log for picard-tools package in Ubuntu

picard-tools (3.1.1+dfsg-1) unstable; urgency=medium

  * New upstream version 3.1.1+dfsg
  * Refreshing patches
  * Enabling the test with BarclayParser again
  * Patching out more code portions using google-nio

 -- Pierre Gruet <email address hidden>  Sat, 16 Dec 2023 22:38:31 +0100

Available diffs

• diff from 3.0.0+dfsg-1 to 3.1.1+dfsg-1 (42.5 KiB)

picard-tools (3.0.0+dfsg-1) unstable; urgency=medium

  * New upstream version 3.0.0+dfsg
  * Refreshing patches
  * Raising Standards version to 4.6.2 (no change)
  * Removing unnecessary versioned B-D
  * Adding nashorn to d/maven.ignoreRules
  * Running the build-time tests from a directory with no '+' in its path
  * Omitting the long-failing jar invocation in the tests

 -- Pierre Gruet <email address hidden>  Tue, 04 Jul 2023 15:23:35 +0200

Available diffs

• diff from 2.27.5+dfsg-2 to 3.0.0+dfsg-1 (43.0 KiB)

picard-tools (2.27.5+dfsg-2) unstable; urgency=medium

  * Stopping exporting ANT_HOME and JAVA_HOME in d/rules, this caused FTBFS
    on buildds since OpenJDK17 became the default JDK

 -- Pierre Gruet <email address hidden>  Sun, 06 Nov 2022 17:21:06 +0100

Available diffs

• diff from 2.27.2+dfsg-2 to 2.27.5+dfsg-2 (131.3 KiB)
• diff from 2.27.5+dfsg-1 to 2.27.5+dfsg-2 (563 bytes)

picard-tools (2.27.5+dfsg-1) unstable; urgency=medium

  * New upstream version 2.27.5+dfsg
  * Refreshing patches
  * Adding a versioned B-D on libhtsjdk-java because of a change in its ABI
  * Building against openjdk-17 (Closes: #1011156):
    - Skipping tests which cannot run because of old Gradle not providing
      --add-opens
    - Stopping shipping BamToBfq because of a byte change in BamToBfqTest when
      switching to OpenJDK17
  * Marking the 60- patch as Forwarded: not-needed

 -- Pierre Gruet <email address hidden>  Fri, 04 Nov 2022 11:09:56 +0100

picard-tools (2.27.2+dfsg-2) unstable; urgency=medium

  * Using maven_repo_helper to provide Maven artifacts

 -- Pierre Gruet <email address hidden>  Thu, 07 Jul 2022 16:28:40 +0200

Available diffs

• diff from 2.27.2+dfsg-1 to 2.27.2+dfsg-2 (1.3 KiB)

picard-tools (2.27.2+dfsg-1) unstable; urgency=medium

  * New upstream version 2.27.2+dfsg
  * Refreshing patches
  * Raising Standards version to 4.6.1 (no change)
  * Switching from XmX4G to XmX2G in d/rules to enhance build on i386
  * Omitting the build of classes concerned by the removal of the
    com.sun.javadoc package in OpenJDK 17 (Closes: #1013577)

 -- Pierre Gruet <email address hidden>  Sun, 26 Jun 2022 21:40:39 +0200

Available diffs

• diff from 2.27.1+dfsg-1 to 2.27.2+dfsg-1 (6.8 KiB)

picard-tools (2.27.1+dfsg-1) unstable; urgency=medium

  * New upstream version 2.27.1+dfsg
  * Refreshing patches
  * Refreshing d/copyright

 -- Pierre Gruet <email address hidden>  Sun, 24 Apr 2022 07:11:18 +0200

Available diffs

• diff from 2.26.10+dfsg-1 to 2.27.1+dfsg-1 (59.6 KiB)

picard-tools (2.26.10+dfsg-1) unstable; urgency=medium

  * New upstream version 2.26.10+dfsg
  * Refreshing patches

 -- Pierre Gruet <email address hidden>  Fri, 18 Feb 2022 14:27:22 +0100

Available diffs

• diff from 2.26.6+dfsg-2 to 2.26.10+dfsg-1 (2.0 KiB)

picard-tools (2.26.6+dfsg-2) unstable; urgency=medium

  * Removing now useless versioned dependencies
  * Deleting the main class name in the jar invocation by PicardCommandLine

 -- Pierre Gruet <email address hidden>  Sat, 04 Dec 2021 10:21:59 +0100

Available diffs

• diff from 2.24.1+dfsg-1 to 2.26.6+dfsg-2 (441.2 KiB)
• diff from 2.26.6+dfsg-1 to 2.26.6+dfsg-2 (982 bytes)

picard-tools (2.26.6+dfsg-1) unstable; urgency=medium

  [ Pierre Gruet ]
  * New upstream version 2.26.6+dfsg
  * Information in d/README.source is outdated, removing the file
  * Raising Standards version to 4.6.0 (no change)
  * Refreshing d/copyright
  * Refreshing patches
  * Setting properly the classpath in the .manifest file, no jar list
    in PicardCommandLine (Closes: #989961)
  * Updating the list of dependencies
  * Correcting a type error in a test concerning Illumina data provider
  * Adding a Lintian override for the embedded javascript
  * Adding a dependency of the doc package in libjs-jquery (Closes: #989328)
  * Adding myself as uploader

  [ Andreas Tille ]
  * Fix typo in d/u/metadata

 -- Pierre Gruet <email address hidden>  Thu, 02 Dec 2021 21:00:23 +0100

picard-tools (2.24.1+dfsg-1) unstable; urgency=medium

  [ Andreas Tille ]
  * New upstream version
  * Do not delete "*.bai" files after testing

  [ Pierre Gruet ]
  * Correcting the data provider for test testActionsWithDontMergeAbutting

 -- Andreas Tille <email address hidden>  Thu, 28 Jan 2021 07:47:42 +0100

Available diffs

• diff from 2.23.8+dfsg-3 to 2.24.1+dfsg-1 (23.8 KiB)

picard-tools (2.23.8+dfsg-3) unstable; urgency=medium

  * Team upload.
  * Oops, should have been Architecture: all everywhere

 -- Michael R. Crusoe <email address hidden>  Wed, 18 Nov 2020 12:19:16 +0100

Available diffs

• diff from 2.23.7+dfsg-1 to 2.23.8+dfsg-3 (2.9 KiB)

picard-tools (2.23.7+dfsg-1) unstable; urgency=medium

  * Team upload.
  * Mark libpicard-java-doc as Multi-Arch: foreign. Thanks multiarch hinter!
  * blhc: ignore false positives with gradle + *ScriptTransformer

 -- Michael R. Crusoe <email address hidden>  Wed, 14 Oct 2020 11:59:07 +0200

Available diffs

• diff from 2.22.8+dfsg-1 to 2.23.7+dfsg-1 (111.6 KiB)

picard-tools (2.22.8+dfsg-1) unstable; urgency=medium

  * New upstream release 
  * Source only upload
    Closes: #961865

 -- Olivier Sallou <email address hidden>  Fri, 29 May 2020 08:25:43 +0000

Available diffs

• diff from 2.18.25+dfsg-3 to 2.22.8+dfsg-1 (1.9 MiB)

picard-tools (2.18.25+dfsg-3) unstable; urgency=medium

  * Remove libguava-java-doc dependency (Closes: #961700).
  * debian/patches/60-tests-exclude-network.patch remove test needing
    network hostname resolution

 -- Olivier Sallou <email address hidden>  Fri, 29 May 2020 07:11:48 +0000

Available diffs

• diff from 2.18.25+dfsg-2 to 2.18.25+dfsg-3 (1.2 KiB)

picard-tools (2.18.25+dfsg-2) unstable; urgency=medium

  * Architecture amd64 (for libpicard-java and picard-tools)
    Closes: #921185
  * Remove trailing whitespace in debian/changelog

 -- Andreas Tille <email address hidden>  Sun, 03 Feb 2019 08:53:09 +0100

Available diffs

• diff from 2.8.1+dfsg-3 to 2.18.25+dfsg-2 (1.7 MiB)
• diff from 2.18.25+dfsg-1 to 2.18.25+dfsg-2 (636 bytes)

picard-tools (2.18.25+dfsg-1) unstable; urgency=medium

  * New upstream release 

 -- Olivier Sallou <email address hidden>  Fri, 25 Jan 2019 10:46:36 +0000

Available diffs

• diff from 2.18.23+dfsg-2 to 2.18.25+dfsg-1 (101.1 KiB)

picard-tools (2.18.23+dfsg-2) unstable; urgency=medium

  * Fix Class-Path in manifest file for dependencies  (Closes: #919559).

 -- Olivier Sallou <email address hidden>  Thu, 17 Jan 2019 15:54:27 +0000

Available diffs

• diff from 2.18.23+dfsg-1 to 2.18.23+dfsg-2 (2.1 KiB)

picard-tools (2.18.23+dfsg-1) unstable; urgency=medium

  * New upstream version
  * debhelper 12
  * Standards-Version: 4.3.0

 -- Andreas Tille <email address hidden>  Fri, 11 Jan 2019 22:52:33 +0100

Available diffs

• diff from 2.18.17+dfsg-1 to 2.18.23+dfsg-1 (20.6 KiB)

picard-tools (2.18.17+dfsg-1) unstable; urgency=medium

  [ Emmanuel Bourg ]
  * Fixed the build failure with Java 11
    Closes: #915898, #880258

  [ Andreas Tille ]
  * New upstream version
  * Secure URI in copyright format
  * Remove trailing whitespace in debian/changelog
  * Remove trailing whitespace in debian/control
  * Remove trailing whitespace in debian/rules
  * Add ALIGNMENT_STATUS=All to command line
    Closes: #905645

 -- Andreas Tille <email address hidden>  Wed, 12 Dec 2018 09:06:37 +0100

Available diffs

• diff from 2.18.14+dfsg-1 to 2.18.17+dfsg-1 (59.9 KiB)

picard-tools (2.18.14+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.2.1
  * Fix link
    Closes: #905706
  * Versioned Build-Depends: libhtsjdk-java (>= 2.16.1~)
  * d/rules: Respect DEB_BUILD_OPTIONS in override_dh_auto_test
  * Simplified d/copyright by not mentioning every single file

 -- Andreas Tille <email address hidden>  Wed, 19 Sep 2018 09:20:48 +0200

Available diffs

• diff from 2.18.2+dfsg-1 to 2.18.14+dfsg-1 (214.5 KiB)

picard-tools (2.18.2+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Backports-friendly debhelper 11
  * Bump versioned Build-Depends on libhtsjdk-java and default-jdk

  [O. Sallou]
  * Java 9/10 fixes
  * Remove Google NIO support (not packaged in Debian)
  * Enable unit tests after jcommander fix

 -- Andreas Tille <email address hidden>  Tue, 17 Apr 2018 22:45:38 +0200

Available diffs

• diff from 2.8.1+dfsg-4 to 2.18.2+dfsg-1 (1.4 MiB)

picard-tools (2.8.1+dfsg-4) unstable; urgency=medium

  * Team upload.
  * Fixed the build failure with Java 9 (Closes: #894329)
  * Standards-Version updated to 4.1.4
  * Switch to debhelper level 11
  * Use salsa.debian.org Vcs-* URLs

 -- Emmanuel Bourg <email address hidden>  Fri, 06 Apr 2018 17:36:09 +0200

picard-tools (2.8.1+dfsg-3) unstable; urgency=medium

  * debian/upstream/metadata: RRID -> SciCrunch
  [ Olivier Sallou ]
  * d/patches/40-tests-fix-testng.patch: fix testng reference
  * d/rules: disable unit tests due to gradle 3.2+testng issue
    (will be fixed by gradle 3.4), lower #880258 severity

 -- Steffen Moeller <email address hidden>  Sun, 22 Oct 2017 18:38:46 +0200

Available diffs

• diff from 2.8.1+dfsg-2 to 2.8.1+dfsg-3 (1.3 KiB)

picard-tools (2.8.1+dfsg-2) unstable; urgency=medium

  * Team upload.
  * Add simple autopkgtest test-suite
    Closes: #848334
  * Add README.test

 -- Nadiya Sitdykova <email address hidden>  Fri, 31 Mar 2017 01:15:20 -0400

Available diffs

• diff from 2.8.1+dfsg-1 to 2.8.1+dfsg-2 (1.4 KiB)

picard-tools (2.8.1+dfsg-1) unstable; urgency=medium

  [ Vincent Danjean ]
  * Ensure versioned B-D and Depends are in sync

  [ Andreas Tille ]
  * New upstream version

 -- Andreas Tille <email address hidden>  Tue, 10 Jan 2017 11:20:45 +0100

Available diffs

• diff from 2.1.1+dfsg-1 to 2.8.1+dfsg-1 (1.6 MiB)
• diff from 2.8.0+dfsg-2 to 2.8.1+dfsg-1 (48.1 KiB)

picard-tools (2.8.0+dfsg-2) unstable; urgency=medium

  * Fix versioned Depends
    Closes: #848831

 -- Andreas Tille <email address hidden>  Tue, 20 Dec 2016 08:52:21 +0100

Available diffs

• diff from 2.8.0+dfsg-1 to 2.8.0+dfsg-2 (495 bytes)

picard-tools (2.8.0+dfsg-1) unstable; urgency=medium

  [ Andreas Tille ]
  * New upstream version
  * debhelper 10
  * d/watch: version=4
  * Ensure that major version of htsjdk is 2.8

  [ Vincent Danjean ]
  * Really force C locale for tests
  * Fix parameter type for one test
  * cleanup generated test files 

 -- Andreas Tille <email address hidden>  Sun, 18 Dec 2016 19:29:34 +0100

Available diffs

• diff from 2.7.1+dfsg-2 to 2.8.0+dfsg-1 (224.0 KiB)

picard-tools (2.7.1+dfsg-2) unstable; urgency=medium

  * Rebuild with htsjdk 2.7
  * Ensure for build and runtime that major versions of picard-tools
    and htsjdk are the same.

 -- Vincent Danjean <email address hidden>  Sun, 27 Nov 2016 21:01:25 +0100

Available diffs

• diff from 2.7.1+dfsg-1 to 2.7.1+dfsg-2 (647 bytes)

picard-tools (2.7.1+dfsg-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <email address hidden>  Thu, 27 Oct 2016 17:10:08 +0200

Available diffs

• diff from 2.5.0-gradle+dfsg-1 to 2.7.1+dfsg-1 (100.6 KiB)

picard-tools (2.5.0-gradle+dfsg-1) unstable; urgency=medium

  * New upstream release
  * Switch to gradle build system

 -- Vincent Danjean <email address hidden>  Thu, 07 Jul 2016 10:21:33 +0200

Available diffs

• diff from 2.1.1+dfsg-1 to 2.5.0-gradle+dfsg-1 (1.3 MiB)

picard-tools (2.1.1+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Adapt debian/watch to use xz compression
  * Remove Shaun Jackman and add myself as Uploader
  * cme fix dpkg-control
 
  [ Steffen Moeller and Jon Ison ]
  * Added EDAM annotation to debian/upstream/edam

 -- Andreas Tille <email address hidden>  Tue, 05 Apr 2016 09:59:27 +0200

Available diffs

• diff from 1.113-2 to 2.1.1+dfsg-1 (5.8 MiB)

picard-tools (1.138+dfsg.1-1) unstable; urgency=medium

  * New release from new upstream location (github). Closes: #798051
  * Full reorganization of the packaging

 -- Vincent Danjean <email address hidden>  Tue, 08 Sep 2015 11:15:42 +0200

picard-tools (1.113-2) unstable; urgency=medium

  * Team upload.
  * Replaced the dependency on libsnappy1.0.3-java with libsnappy-java.
  * Standards-Version updated to 3.9.6 (no changes)

 -- Emmanuel Bourg <email address hidden>  Wed, 02 Sep 2015 13:10:32 +0200

Available diffs

• diff from 1.113-1 to 1.113-2 (1.2 KiB)

picard-tools (1.113-1) unstable; urgency=medium


  * New upstream release 1.113

 -- Olivier Sallou <email address hidden>  Fri, 06 Jun 2014 23:27:25 +0200

Available diffs

• diff from 1.110-1 to 1.113-1 (403.9 KiB)

picard-tools (1.110-1) unstable; urgency=medium


  * Imported Upstream version 1.110. 
  * Normalised debian/control with config-model-edit. 
  * Refreshed patch ‘use_libjbzip2-java’.

 -- Charles Plessy <email address hidden>  Sun, 06 Apr 2014 10:56:12 +0900

Available diffs

• diff from 1.105-1 to 1.110-1 (206.0 KiB)

picard-tools (1.105-1) unstable; urgency=low


  * New upstream release 1.105 
  * Conforms with Policy 3.9.5.

 -- Olivier Sallou <email address hidden>  Tue, 24 Dec 2013 11:16:18 +0100

Available diffs

• diff from 1.100-1 to 1.105-1 (97.1 KiB)

picard-tools (1.100-1) unstable; urgency=low


  [Charles Plessy]
  * Imported Upstream version 1.100
  * Compress the source archive with XZ.
  * Mark the use of git-buildpackage and pristine-tar with a gbp.conf file.
  [Olivier Sallou]
  * d/rules: fix build for release

 -- Charles Plessy <email address hidden>  Sun, 20 Oct 2013 10:38:11 +0900

Available diffs

• diff from 1.95-1 to 1.100-1 (773.0 KiB)

picard-tools (1.95-1) unstable; urgency=low


  * New upstream release
  * Fix man page with missing tools from previous releases
  * Fix picard-tools binary to manage missing tools from previous
    releases
  * Fix management of JAVA_OPTIONS if not set at all. 

 -- Olivier Sallou <email address hidden>  Thu, 25 Jul 2013 13:36:02 +0200

Available diffs

• diff from 1.90-3 to 1.95-1 (43.4 KiB)

picard-tools (1.90-3) unstable; urgency=low


  * Add possibility to specify JAVA options (Closes: #705681),
    with JAVA_OPTIONS env variable.

 -- Olivier Sallou <email address hidden>  Tue, 09 Jul 2013 09:20:07 +0200

Available diffs

• diff from 1.90-2 to 1.90-3 (1.3 KiB)

picard-tools (1.90-2) unstable; urgency=low


  * Load in unstable, all deps are available.

 -- Olivier Sallou <email address hidden>  Sun, 02 Jun 2013 10:57:05 +0200

Available diffs

• diff from 1.46-1ubuntu1 (in Ubuntu) to 1.90-2 (1.9 MiB)

picard-tools (1.46-1ubuntu1) quantal; urgency=low

  * Transition package to use default java implementation:
    - d/control: BD on default-jdk, switch runtime dependency to
      default-jre | java6-runtime.
    - d/rules: Specify source/target = 1.5 to ensure that backwards
      compatible bytecode is built.
 -- James Page <email address hidden>   Tue, 07 Aug 2012 15:09:19 +0100

Available diffs

• diff from 1.46-1build1 to 1.46-1ubuntu1 (1.1 KiB)

picard-tools (1.46-1build1) precise; urgency=low

  * No-change rebuild against current pkgbinarymangler to fix broken
    md5sums. (see LP #875466)
 -- Martin Pitt <email address hidden>   Wed, 29 Feb 2012 09:17:36 +0100

Available diffs

• diff from 1.46-1 to 1.46-1build1 (372 bytes)

picard-tools (1.46-1) unstable; urgency=low

  * New upstream release.
  * Depend on ${python:Depends} (debian/changelog).
  * Incremented Standards-Version to reflect conformance with Policy 3.9.2
    (debian/changelog, no changes needed).
  * Corrected and validated debian/copyright machine-readable format.
 -- Ubuntu Archive Auto-Sync <email address hidden>   Sat,  04 Jun 2011 06:13:26 +0000

Available diffs

• diff from 1.41-1 to 1.46-1 (189.1 KiB)

picard-tools (1.41-1) unstable; urgency=low

  * New upstream release. Closes: #619201.
  * Add five commands to bin/picard-tools and picard-tools.1.
 -- Ubuntu Archive Auto-Sync <email address hidden>   Sat,  30 Apr 2011 13:31:20 +0000

Available diffs

• diff from 1.27-1 to 1.41-1 (131.7 KiB)

picard-tools (1.27-1) unstable; urgency=low

  * New upstream release.
  * Incremented Standards-Version to reflect conformance with Policy 3.9.1
    (debian/changelog, no changes needed).