[med-svn] [python-cutadapt] 05/12: Merge tag 'upstream/1.10'

[Andreas Tille]

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

commit 614fb4da73e71e145e69a1707c53c1066f6e8f45
Merge: 01a0b97 250b0dc
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 20 15:26:00 2016 +0200

    Merge tag 'upstream/1.10'
    
    Upstream version 1.10

 CHANGES.rst                  |   22 +
 LICENSE                      |    2 +-
 PKG-INFO                     |    2 +-
 cutadapt/__init__.py         |    2 +-
 cutadapt/__main__.py         |   12 -
 cutadapt/_align.c            | 4016 +++++++++---------------------------------
 cutadapt/_align.pyx          |    1 +
 cutadapt/_align.so           |  Bin 532496 -> 0 bytes
 cutadapt/_qualtrim.c         |  743 ++++++--
 cutadapt/_qualtrim.pyx       |   36 +
 cutadapt/_qualtrim.so        |  Bin 92136 -> 0 bytes
 cutadapt/_seqio.c            | 2320 ++++++++----------------
 cutadapt/_seqio.pyx          |   59 +-
 cutadapt/_seqio.so           |  Bin 397664 -> 0 bytes
 cutadapt/adapters.py         |  264 ++-
 cutadapt/filters.py          |    8 +-
 cutadapt/modifiers.py        |   63 +-
 cutadapt/qualtrim.py         |   31 +-
 cutadapt/report.py           |   35 +-
 cutadapt/scripts/cutadapt.py |  214 +--
 cutadapt/seqio.py            |  413 +++--
 cutadapt/xopen.py            |   10 +-
 doc/colorspace.rst           |   23 +-
 doc/conf.py                  |    2 +-
 doc/guide.rst                |   59 +-
 doc/ideas.rst                |   14 +-
 doc/installation.rst         |   72 +-
 setup.py                     |   57 +-
 tests/cut/linked.fasta       |   10 +
 tests/cut/nextseq.fastq      |    8 +
 tests/cut/small.fasta        |    6 +
 tests/data/linked.fasta      |   10 +
 tests/data/nextseq.fastq     |    8 +
 tests/testadapters.py        |   43 +-
 tests/testpaired.py          |   11 +-
 tests/testqualtrim.py        |   14 +
 tests/tests.py               |   30 +-
 tests/testseqio.py           |   53 +-
 tests/utils.py               |    2 +-
 39 files changed, 3324 insertions(+), 5351 deletions(-)

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