[med-svn] [python-cutadapt] branch master updated (3c22863 -> 191316c)

[Olivier Sallou]

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

      from  3c22863   add upstream metadata
       new  e14cd5a   Imported Upstream version 1.9.1
       new  30860ee   Merge tag 'upstream/1.9.1'
       new  d816ca1   new upstream release 1.9.1
       new  191316c   upload release 1.9.1

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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 +-
 debian/changelog                                   |    6 +
 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 +-
 39 files changed, 11645 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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