[med-svn] [python-cutadapt] 02/04: Merge tag 'upstream/1.9.1'

[Olivier Sallou]

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commit 30860eef487c0daa0d3201556d11882c23f8ff3a
Merge: 3c22863 e14cd5a
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Thu Dec 10 13:55:53 2015 +0100

    Merge tag 'upstream/1.9.1'
    
    Upstream version 1.9.1

 CHANGES.rst                         |   39 +-
 PKG-INFO                            |    2 +-
 cutadapt/__init__.py                |    2 +-
 cutadapt/_align.c                   | 8367 ++++++++++++++++++++++++++++-------
 cutadapt/_align.pyx                 |  282 +-
 cutadapt/_align.so                  |  Bin 385272 -> 532496 bytes
 cutadapt/_qualtrim.c                | 1598 ++++---
 cutadapt/_qualtrim.so               |  Bin 118544 -> 92136 bytes
 cutadapt/_seqio.c                   | 3452 ++++++++-------
 cutadapt/_seqio.pyx                 |   65 +-
 cutadapt/_seqio.so                  |  Bin 427936 -> 397664 bytes
 cutadapt/adapters.py                |  162 +-
 cutadapt/align.py                   |    8 +-
 cutadapt/filters.py                 |  230 +-
 cutadapt/modifiers.py               |  153 +-
 cutadapt/report.py                  |   64 +-
 cutadapt/scripts/cutadapt.py        |  581 +--
 cutadapt/seqio.py                   |  413 +-
 doc/guide.rst                       |  349 +-
 doc/ideas.rst                       |   47 +-
 tests/cut/illumina.info.txt         |  200 +-
 tests/cut/illumina5.info.txt        |   16 +-
 tests/cut/interleaved.fastq         |   16 +
 tests/cut/no_indels.fasta           |   18 +
 tests/cut/paired-filterboth.1.fastq |   16 +
 tests/cut/paired-filterboth.2.fastq |   16 +
 tests/cut/paired-too-short.1.fastq  |    4 +
 tests/cut/paired-too-short.2.fastq  |    4 +
 tests/cut/suffix.fastq              |   60 +-
 tests/data/interleaved.fastq        |   32 +
 tests/data/no_indels.fasta          |   20 +
 tests/data/simple.fasta~            |    6 -
 tests/testadapters.py               |   32 +-
 tests/testalign.py                  |   46 +-
 tests/testfilters.py                |   11 +-
 tests/testpaired.py                 |  105 +-
 tests/tests.py                      |   15 +-
 tests/testseqio.py                  |  450 +-
 38 files changed, 11689 insertions(+), 5192 deletions(-)

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