[med-svn] [python-pysam] 05/10: Merge tag 'upstream/0.8.4+ds'

[Afif Elghraoui]

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commit b8581f9391086bc43ab30131fb040c593406569d
Merge: bb7aa1f 18e4903
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Nov 11 18:46:08 2015 -0800

    Merge tag 'upstream/0.8.4+ds'
    
    Upstream version 0.8.4+ds

 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(-)

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