[med-svn] [python-cutadapt] 02/06: Merge tag 'upstream/1.12'

[Kevin Murray]

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

daube-guest pushed a commit to branch master
in repository python-cutadapt.

commit 0ba091747b8b721baa32b2be0642988ec8009f15
Merge: a148fa4 89cb1e6
Author: Kevin Murray <kdmfoss at gmail.com>
Date:   Fri Dec 2 13:56:23 2016 +1100

    Merge tag 'upstream/1.12'
    
    Upstream version 1.12

 CHANGES.rst                        |  11 +++
 PKG-INFO                           |  45 ++++++++-
 README.rst                         |   2 +-
 bin/_preamble.py                   |  21 -----
 bin/cutadapt                       |  10 --
 cutadapt.egg-info/PKG-INFO         |  45 ++++++++-
 cutadapt.egg-info/SOURCES.txt      |   8 +-
 cutadapt.egg-info/entry_points.txt |   3 +
 cutadapt.egg-info/requires.txt     |   1 +
 cutadapt/_align.c                  |  36 +++++---
 cutadapt/_seqio.c                  |   2 +-
 cutadapt/_seqio.pyx                |   2 +-
 cutadapt/_version.py               |   4 +-
 cutadapt/adapters.py               |  12 +--
 cutadapt/filters.py                |   2 +-
 cutadapt/modifiers.py              |   9 ++
 cutadapt/scripts/cutadapt.py       | 115 ++++++++++++-----------
 cutadapt/seqio.py                  |   4 +-
 cutadapt/xopen.py                  | 182 -------------------------------------
 doc/colorspace.rst                 |  26 +++++-
 doc/guide.rst                      | 157 +++++++++++++++++++++-----------
 doc/recipes.rst                    |  48 +++++++---
 setup.py                           |   7 +-
 tests/cut/shortened.fastq          |  12 +++
 tests/cut/small-no-trim.fasta      |   6 ++
 tests/testmodifiers.py             |  19 +++-
 tests/tests.py                     |   8 ++
 tests/testxopen.py                 | 101 --------------------
 28 files changed, 422 insertions(+), 476 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cutadapt.git