[med-svn] [trimmomatic] branch debian/jessie-backports updated (f38fd9b -> 8414619)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch debian/jessie-backports
in repository trimmomatic.

      from  f38fd9b   Backport to Jessie
      adds  57c6e09   Introduced EDAM annotation
      adds  9465f4d   Added publication for trimmomatic
      adds  266d514   Added notion of log to EDAM for trimmomatic
      adds  4b8a42f   Trimmomatic shall find adapters by name
      adds  b061ccf   Use bibtex syntax
      adds  63c32f4   Merge branch 'master' of git+ssh://anonscm.debian.org/git/debian-med/trimmomatic
      adds  fdac137   Corrected patch for trimmomatic
      adds  f101d8a   Code for alternative adapter location works
      adds  b6477f2   DEP3 header
      adds  03750e0   Introduced .gitignore
      adds  e7c8ce9   Use xz compression in watch file
      adds  c39d405   Imported Upstream version 0.36+dfsg
      adds  db493e2   Merge tag 'upstream/0.36+dfsg'
      adds  cd2a4c5   cme fix dpkg-control
      adds  e660e1c   Adapt patches
      adds  e3cc663   Upload to unstable
       new  724cc04   Merge tag 'debian/0.36+dfsg-1' into debian/jessie-backports
       new  8414619   Rebuild for jessie-backports

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitignore                                         |  9 ++++
 build.xml                                          |  4 +-
 debian/README.source                               | 17 ++++++
 debian/changelog                                   | 19 +++++++
 debian/control                                     |  6 +--
 debian/patches/buildxmlJbzip2.patch                |  2 +-
 debian/patches/remove_jar_version.path             |  2 +-
 .../patches/search_in_usr_share_trimmomatic.patch  | 28 ++++++++++
 debian/patches/series                              |  1 +
 debian/rules                                       |  3 --
 debian/upstream/edam                               | 16 ++++++
 debian/upstream/metadata                           | 12 +++++
 debian/watch                                       |  2 +-
 src/org/usadellab/trimmomatic/Trimmomatic.java     | 33 ++++++++++--
 src/org/usadellab/trimmomatic/TrimmomaticPE.java   | 11 +++-
 src/org/usadellab/trimmomatic/TrimmomaticSE.java   |  9 +++-
 .../trimmomatic/trim/HeadCropTrimmer.java          | 26 +++++++--
 .../trimmomatic/trim/TailCropTrimmer.java          | 61 ++++++++++++++++++++++
 .../usadellab/trimmomatic/trim/TrimmerFactory.java |  3 ++
 .../trimmomatic/util/ConcatGZIPInputStream.java    | 51 ++----------------
 20 files changed, 245 insertions(+), 70 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 debian/README.source
 create mode 100644 debian/patches/search_in_usr_share_trimmomatic.patch
 create mode 100644 debian/upstream/edam
 create mode 100644 debian/upstream/metadata
 create mode 100644 src/org/usadellab/trimmomatic/trim/TailCropTrimmer.java

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