[med-svn] [python-cutadapt] branch upstream updated (c2e8d99 -> e14cd5a)

[Olivier Sallou]

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osallou pushed a change to branch upstream
in repository python-cutadapt.

      from  c2e8d99   Imported Upstream version 1.8.3
       new  e14cd5a   Imported Upstream version 1.9.1

The 1 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:
 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/{paired.2.fastq => interleaved.fastq}    |   12 +-
 tests/cut/no_indels.fasta                          |   18 +
 ...-separate.1.fastq => paired-filterboth.1.fastq} |    0
 ...aired.m14.2.fastq => paired-filterboth.2.fastq} |    8 +-
 tests/cut/paired-too-short.1.fastq                 |    4 +
 tests/cut/paired-too-short.2.fastq                 |    4 +
 tests/cut/suffix.fastq                             |   60 +-
 tests/data/{paired.1.fastq => interleaved.fastq}   |   16 +
 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, 11639 insertions(+), 5198 deletions(-)
 copy tests/cut/{paired.2.fastq => interleaved.fastq} (51%)
 create mode 100644 tests/cut/no_indels.fasta
 copy tests/cut/{paired-separate.1.fastq => paired-filterboth.1.fastq} (100%)
 copy tests/cut/{paired.m14.2.fastq => paired-filterboth.2.fastq} (65%)
 create mode 100644 tests/cut/paired-too-short.1.fastq
 create mode 100644 tests/cut/paired-too-short.2.fastq
 copy tests/data/{paired.1.fastq => interleaved.fastq} (50%)
 create mode 100644 tests/data/no_indels.fasta
 delete mode 100644 tests/data/simple.fasta~

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