[med-svn] [python-cutadapt] branch upstream updated (89cb1e6 -> 9b0e316)

[Olivier Sallou]

This is an automated email from the git hooks/post-receive script.

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

      from  89cb1e6   New upstream version 1.12
      adds  9b0e316   New upstream version 1.13

No new revisions were added by this update.

Summary of changes:
 CHANGES.rst                                        |   21 +
 LICENSE                                            |    2 +-
 PKG-INFO                                           |    2 +-
 cutadapt.egg-info/PKG-INFO                         |    2 +-
 cutadapt.egg-info/SOURCES.txt                      |    5 +
 cutadapt.egg-info/requires.txt                     |    2 +-
 cutadapt/__init__.py                               |    1 +
 cutadapt/_align.c                                  | 1255 +++++++++---
 cutadapt/_align.pyx                                |    4 +-
 cutadapt/_qualtrim.c                               | 1038 +++++-----
 cutadapt/_seqio.c                                  | 1998 +++++++++++++-------
 cutadapt/_seqio.pyx                                |   12 +-
 cutadapt/_version.py                               |    4 +-
 cutadapt/adapters.py                               |  440 +++--
 cutadapt/filters.py                                |   10 +-
 cutadapt/modifiers.py                              |   65 +-
 cutadapt/qualtrim.py                               |   32 +-
 cutadapt/report.py                                 |  157 +-
 cutadapt/scripts/cutadapt.py                       |  215 ++-
 cutadapt/seqio.py                                  |   26 +-
 doc/conf.py                                        |    4 +-
 doc/guide.rst                                      |  123 +-
 doc/installation.rst                               |    3 +-
 setup.py                                           |   26 +-
 .../linked.fasta => cut/linked-anchored.fasta}     |   14 +-
 .../{linked.fasta => linked-not-anchored.fasta}    |   14 +-
 tests/cut/linked.fasta                             |   12 +-
 tests/data/block1.fastq.bz2                        |  Bin 0 -> 87 bytes
 tests/data/block2.fastq.bz2                        |  Bin 0 -> 206 bytes
 tests/data/linked.fasta                            |   12 +-
 tests/data/multiblock.fastq.bz2                    |  Bin 0 -> 293 bytes
 tests/testadapters.py                              |   26 +-
 tests/testcolorspace.py                            |   26 +-
 tests/testpaired.py                                |  134 +-
 tests/tests.py                                     |  194 +-
 tests/testtrim.py                                  |    5 +-
 tests/utils.py                                     |   19 +-
 37 files changed, 3706 insertions(+), 2197 deletions(-)
 copy tests/{data/linked.fasta => cut/linked-anchored.fasta} (62%)
 copy tests/cut/{linked.fasta => linked-not-anchored.fasta} (64%)
 create mode 100644 tests/data/block1.fastq.bz2
 create mode 100644 tests/data/block2.fastq.bz2
 create mode 100644 tests/data/multiblock.fastq.bz2

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