[med-svn] [python-cutadapt] 02/08: Update upstream source from tag 'upstream/1.15'

[Andreas Tille]

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

commit 54002011f1f52aba4b0a89f8274fff587d7e549c
Merge: e2c0774 500335b
Author: Andreas Tille <tille at debian.org>
Date:   Sat Feb 10 13:14:32 2018 +0100

    Update upstream source from tag 'upstream/1.15'
    
    Update to upstream version '1.15'
    with Debian dir 0f74a7e7d2ec83b009ae3e99c62f9459406b303a

 CHANGES.rst                                        |   35 +-
 MANIFEST.in                                        |   14 +-
 PKG-INFO                                           |    2 +-
 cutadapt.egg-info/entry_points.txt                 |    3 -
 cutadapt.egg-info/requires.txt                     |    1 -
 cutadapt/scripts/__init__.py                       |    0
 doc/conf.py                                        |    6 +-
 doc/develop.rst                                    |  124 +
 doc/guide.rst                                      |  289 +-
 doc/ideas.rst                                      |   16 +-
 doc/index.rst                                      |    1 +
 doc/installation.rst                               |   69 +-
 doc/recipes.rst                                    |   86 +
 setup.cfg                                          |    4 +-
 setup.py                                           |   45 +-
 .../cutadapt.egg-info}/PKG-INFO                    |    2 +-
 .../cutadapt.egg-info}/SOURCES.txt                 |   81 +-
 .../cutadapt.egg-info}/dependency_links.txt        |    0
 src/cutadapt.egg-info/entry_points.txt             |    3 +
 src/cutadapt.egg-info/requires.txt                 |    1 +
 .../cutadapt.egg-info}/top_level.txt               |    0
 {cutadapt => src/cutadapt}/__init__.py             |    0
 .../cutadapt.py => src/cutadapt/__main__.py        |  674 +--
 {cutadapt => src/cutadapt}/_align.c                | 1580 ++---
 {cutadapt => src/cutadapt}/_align.pyx              |    5 +
 {cutadapt => src/cutadapt}/_qualtrim.c             |  266 +-
 {cutadapt => src/cutadapt}/_qualtrim.pyx           |    0
 {cutadapt => src/cutadapt}/_seqio.c                | 6265 ++++++++++++++------
 {cutadapt => src/cutadapt}/_seqio.pyx              |   98 +
 {cutadapt => src/cutadapt}/_version.py             |    4 +-
 {cutadapt => src/cutadapt}/adapters.py             |  165 +-
 {cutadapt => src/cutadapt}/align.py                |    0
 {cutadapt => src/cutadapt}/colorspace.py           |    0
 {cutadapt => src/cutadapt}/compat.py               |    0
 {cutadapt => src/cutadapt}/filters.py              |  183 +-
 {cutadapt => src/cutadapt}/modifiers.py            |   61 +-
 src/cutadapt/pipeline.py                           |  651 ++
 {cutadapt => src/cutadapt}/qualtrim.py             |    0
 {cutadapt => src/cutadapt}/report.py               |  254 +-
 {cutadapt => src/cutadapt}/seqio.py                |  226 +-
 tests/cut/demultiplexed.first.1.fastq              |    4 +
 tests/cut/demultiplexed.first.2.fastq              |    4 +
 tests/cut/demultiplexed.second.1.fastq             |    4 +
 tests/cut/demultiplexed.second.2.fastq             |    4 +
 tests/cut/demultiplexed.unknown.1.fastq            |    8 +
 tests/cut/demultiplexed.unknown.2.fastq            |    8 +
 ...d-not-anchored.fasta => linked-discard-g.fasta} |    6 -
 tests/cut/linked-discard.fasta                     |    6 +
 tests/cut/linked-not-anchored.fasta                |    4 +-
 tests/data/block1.fastq.bz2                        |  Bin 87 -> 0 bytes
 tests/data/block2.fastq.bz2                        |  Bin 206 -> 0 bytes
 tests/{testadapters.py => test_adapters.py}        |   76 +-
 tests/{testalign.py => test_align.py}              |    0
 tests/{testcolorspace.py => test_colorspace.py}    |    4 +-
 tests/{tests.py => test_commandline.py}            |   52 +-
 tests/{testfilters.py => test_filters.py}          |    9 +-
 tests/{testmodifiers.py => test_modifiers.py}      |    0
 tests/{testpaired.py => test_paired.py}            |  257 +-
 tests/{testqualtrim.py => test_qualtrim.py}        |    1 +
 tests/{testseqio.py => test_seqio.py}              |   81 +-
 tests/test_trim.py                                 |   57 +
 tests/testtrim.py                                  |   28 -
 tests/utils.py                                     |   28 +-
 63 files changed, 7696 insertions(+), 4159 deletions(-)

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