[med-svn] [python-pysam] branch upstream updated (3cbc6e0 -> 18e4903)

[Afif Elghraoui]

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afif-guest pushed a change to branch upstream
in repository python-pysam.

      from  3cbc6e0   Imported Upstream version 0.8.3+ds1
       new  18e4903   Imported Upstream version 0.8.4+ds

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
been added to this reference.


Summary of changes:
 README.rst                                  |    5 +-
 benchmark/AlignedSegment_bench.py           |   43 +
 doc/api.rst                                 |   15 +-
 doc/conf.py                                 |   20 +-
 doc/faq.rst                                 |   26 +-
 doc/glossary.rst                            |   34 +-
 doc/release.rst                             |   86 +
 doc/usage.rst                               |   22 +-
 pysam/TabProxies.pxd                        |   94 -
 pysam/__init__.py                           |   64 +-
 pysam/calignedsegment.pxd                   |   94 +
 pysam/calignedsegment.pyx                   | 2277 ++++++++++
 pysam/calignmentfile.pxd                    |   71 +-
 pysam/calignmentfile.pyx                    | 3595 +++++----------
 pysam/cbcf.pxd                              |    2 +-
 pysam/cbcf.pyx                              |  694 ++-
 pysam/cfaidx.pxd                            |   54 +-
 pysam/cfaidx.pyx                            |  470 +-
 pysam/chtslib.pxd                           |   43 +-
 pysam/chtslib.pyx                           |   97 +-
 pysam/csamfile.pxd                          |    4 +-
 pysam/csamfile.pyx                          |    2 +-
 pysam/csamtools.pxd                         |   13 +-
 pysam/csamtools.pyx                         |   63 +-
 pysam/ctabix.pxd                            |   39 +-
 pysam/ctabix.pyx                            |  312 +-
 pysam/ctabixproxies.pxd                     |   59 +
 pysam/{TabProxies.pyx => ctabixproxies.pyx} |  176 +-
 pysam/cutils.pxd                            |   27 +
 pysam/cutils.pyx                            |  214 +
 pysam/cvcf.pxd                              |   40 -
 pysam/cvcf.pyx                              |  152 +-
 pysam/htslib_util.h                         |    3 -
 pysam/pysam_util.c                          |    2 +-
 pysam/tabix_util.c                          |    5 +-
 pysam/version.py                            |    2 +-
 requires.txt => requirements.txt            |    0
 save/pysam_test2.6.py                       |    2 +-
 setup.py                                    |  228 +-
 tests/AlignedSegment_test.py                |  236 +-
 tests/AlignmentFile_test.py                 |  314 +-
 tests/SamFile_test.py                       |   74 +-
 tests/TestUtils.py                          |    6 +-
 tests/faidx_test.py                         |   99 +-
 tests/pysam_data/Makefile                   |    2 +-
 tests/pysam_data/faidx_ex1.fa               | 6540 +++++++++++++++++++++++++++
 tests/pysam_data/{ex1.fq => faidx_ex1.fq}   |    0
 tests/samtools_test.py                      |   93 +-
 tests/tabix_test.py                         |   46 +-
 49 files changed, 12538 insertions(+), 4021 deletions(-)
 create mode 100644 benchmark/AlignedSegment_bench.py
 delete mode 100644 pysam/TabProxies.pxd
 create mode 100644 pysam/calignedsegment.pxd
 create mode 100644 pysam/calignedsegment.pyx
 create mode 100644 pysam/ctabixproxies.pxd
 rename pysam/{TabProxies.pyx => ctabixproxies.pyx} (87%)
 create mode 100644 pysam/cutils.pxd
 create mode 100644 pysam/cutils.pyx
 rename requires.txt => requirements.txt (100%)
 create mode 100644 tests/pysam_data/faidx_ex1.fa
 rename tests/pysam_data/{ex1.fq => faidx_ex1.fq} (100%)

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