[med-svn] [python-cutadapt] branch master updated (771b508 -> 1b9a5b7)

[Olivier Sallou]

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

      from  771b508   Upload to unstable
       new  9b0e316   New upstream version 1.13
       new  d736ab7   Merge tag 'upstream/1.13'
       new  4b624ad   new release 1.13
       new  1b9a5b7   update patch for release 1.13

The 4 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
been added to this reference.


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 +-
 debian/changelog                                   |    6 +
 debian/patches/0003_fixtest.patch                  |   18 +-
 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 +-
 39 files changed, 3721 insertions(+), 2206 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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