[med-svn] [python-cutadapt] branch upstream updated (e14cd5a -> 250b0dc)

[Andreas Tille]

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

      from  e14cd5a   Imported Upstream version 1.9.1
       new  250b0dc   Imported Upstream version 1.10

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                  |   22 +
 LICENSE                      |    2 +-
 PKG-INFO                     |    2 +-
 cutadapt/__init__.py         |    2 +-
 cutadapt/__main__.py         |   12 -
 cutadapt/_align.c            | 4016 +++++++++---------------------------------
 cutadapt/_align.pyx          |    1 +
 cutadapt/_align.so           |  Bin 532496 -> 0 bytes
 cutadapt/_qualtrim.c         |  743 ++++++--
 cutadapt/_qualtrim.pyx       |   36 +
 cutadapt/_qualtrim.so        |  Bin 92136 -> 0 bytes
 cutadapt/_seqio.c            | 2320 ++++++++----------------
 cutadapt/_seqio.pyx          |   59 +-
 cutadapt/_seqio.so           |  Bin 397664 -> 0 bytes
 cutadapt/adapters.py         |  264 ++-
 cutadapt/filters.py          |    8 +-
 cutadapt/modifiers.py        |   63 +-
 cutadapt/qualtrim.py         |   31 +-
 cutadapt/report.py           |   35 +-
 cutadapt/scripts/cutadapt.py |  214 +--
 cutadapt/seqio.py            |  413 +++--
 cutadapt/xopen.py            |   10 +-
 doc/colorspace.rst           |   23 +-
 doc/conf.py                  |    2 +-
 doc/guide.rst                |   59 +-
 doc/ideas.rst                |   14 +-
 doc/installation.rst         |   72 +-
 setup.py                     |   57 +-
 tests/cut/linked.fasta       |   10 +
 tests/cut/nextseq.fastq      |    8 +
 tests/cut/small.fasta        |    6 +
 tests/data/linked.fasta      |   10 +
 tests/data/nextseq.fastq     |    8 +
 tests/testadapters.py        |   43 +-
 tests/testpaired.py          |   11 +-
 tests/testqualtrim.py        |   14 +
 tests/tests.py               |   30 +-
 tests/testseqio.py           |   53 +-
 tests/utils.py               |    2 +-
 39 files changed, 3324 insertions(+), 5351 deletions(-)
 delete mode 100755 cutadapt/__main__.py
 delete mode 100755 cutadapt/_align.so
 delete mode 100755 cutadapt/_qualtrim.so
 delete mode 100755 cutadapt/_seqio.so
 create mode 100644 tests/cut/linked.fasta
 create mode 100644 tests/cut/nextseq.fastq
 create mode 100644 tests/cut/small.fasta
 create mode 100644 tests/data/linked.fasta
 create mode 100644 tests/data/nextseq.fastq
 create mode 100644 tests/testqualtrim.py

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