[med-svn] [SCM] picard-tools annotated tag, debian/1.75-1, created. debian/1.75-1

[Olivier Sallou]

The annotated tag, debian/1.75-1 has been created
        at  877863bd4a539b79295c912bc17b6e9cd0ffe207 (tag)
   tagging  f864f757d545f571eefb979142f87c62355c9609 (commit)
  replaces  upstream/1.75
 tagged by  Olivier Sallou
        on  Thu Sep 6 09:16:39 2012 +0200

- Shortlog ------------------------------------------------------------
Debian release 1.75-1

Charles Plessy (44):
      get-orig-source target adapted from ‘http://wiki.debian.org/SandroTosi/Svn_get-orig-source’.
      Merge commit 'upstream/1.23'
      New upstream release 1.23.
      Found GPL and “All rights reserved” upstream files.
      Change the path to javac in the second place where it appears as well.
      Making sure that the empty lib directory is present at build time.
      Merge commit 'upstream/1.24'
      New upstream release 1.24.
      Renamed the patch for build.xml so that it does not need to be renamed again at each new upstream release.
      Added a DEP-3 header to the Debian patch.
      Deleted unneeded section field for binary package picard-tools (same as source package).
      Also distribute the explain_sam_flags.py script.
      * Removed the fourth number in Standards-Version (debian/control, see Policy §5.6.11).
      Merge commit 'upstream/1.26'
      * New upstream release; refreshed Debian patch.
      Merge commit 'upstream/1.27'
      * New upstream release.
      * Updated manpage version number after checking on upstream doc that no new program has been added.
      * Uploaded.
      Merge commit 'upstream/1.42'
      Merge commit 'upstream/1.43'
      Merge commit 'upstream/1.44'
      Merge commit 'upstream/1.45'
      Merge commit 'upstream/1.46'
      New upstream releases (no change in licensing or copyright, apart from the year).
      Depend on ${python:Depends} and incremented Standards-Version.
      Documented new commands.
      Corrected and validated with config-edit.
      Uploaded picard-tools_1.46-1_amd64.changes.
      Merge commit 'upstream/1.47'
      Merge commit 'upstream/1.48'
      Merge commit 'upstream/1.49'
      New upstream releases, no new license statement nor copyright holder.
      Merge commit 'upstream/1.50'
      Merge commit 'upstream/1.51'
      Merge commit 'upstream/1.52'
      Merge commit 'upstream/1.53'
      Merge commit 'upstream/1.54'
      Merge commit 'upstream/1.55'
      New upstream releases; no new copyright holder nor license statement.
      Build-depend on libsnappy-java.
      Refreshed patch, use Debian's snappy-java.
      Updated changelog.
      Use default java implementation.

Olivier Sallou (10):
      Used snappy1.0.3 and use latest picard-tools version 1.75
      Merge tag 'upstream/1.75'
      Add osallou as uploader
      update patches to latests version
      fix typo
      fix versioned URL
      Add libjbzip2 as dependency and in classpath
      add patch to use libjbzip2-java
      prepare for upload
      fix change date

Shaun Jackman (10):
      Initial release.
      * debian/links: Change sam-1.22.jar to sam-1.23.jar.
      * build.xml (picard.jar): Add the R scripts.
      Merge commit 'upstream/1.25'
      * debian/changelog: New upstream release.
      * debian/bin/picard-tools: Add java -XX:MaxPermSize=256m to avoid the
      * debian/picard-tools.1: Bump the version number to 1.25.
      * debian/control (Architecture): Change to all, was any.
      Merge commit 'upstream/1.41'
      * New upstream release. Closes: #619201.

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manipulate SAM and BAM files