[med-svn] [trimmomatic] branch master updated (03750e0 -> e3cc663)

[Andreas Tille]

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tille pushed a change to branch master
in repository trimmomatic.

      from  03750e0   Introduced .gitignore
       new  e7c8ce9   Use xz compression in watch file
       new  c39d405   Imported Upstream version 0.36+dfsg
       new  db493e2   Merge tag 'upstream/0.36+dfsg'
       new  cd2a4c5   cme fix dpkg-control
       new  e660e1c   Adapt patches
       new  e3cc663   Upload to unstable

The 6 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
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Summary of changes:
 build.xml                                          |  4 +-
 debian/changelog                                   |  9 +++-
 debian/control                                     |  6 +--
 debian/patches/buildxmlJbzip2.patch                |  2 +-
 debian/patches/remove_jar_version.path             |  2 +-
 .../patches/search_in_usr_share_trimmomatic.patch  |  4 +-
 debian/rules                                       |  3 --
 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 ++----------------
 15 files changed, 152 insertions(+), 74 deletions(-)
 create mode 100644 src/org/usadellab/trimmomatic/trim/TailCropTrimmer.java

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