[med-svn] [python-pysam] 02/04: Merge tag 'upstream/0.10.0+ds'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-pysam.

commit c1253658bf2fad7b7ecb5074e98b3191bd949566
Merge: fca3a7d dadf905
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Jan 23 19:10:24 2017 -0800

    Merge tag 'upstream/0.10.0+ds'
    
    Upstream version 0.10.0+ds

 .travis.yml                                        |    4 +-
 bcftools/vcfisec.c                                 |    2 +-
 bcftools/vcfisec.c.pysam.c                         |    2 +-
 benchmark/cython_flagstat.py                       |   23 +
 benchmark/python_flagstat.py                       |   23 +
 buildwheels.sh                                     |   69 +
 cy_build.py                                        |    2 -
 doc/api.rst                                        |    2 +-
 doc/release.rst                                    |   29 +
 doc/usage.rst                                      |   14 +-
 pysam/__init__.py                                  |   77 +-
 pysam/chtslib.pyx                                  |   19 -
 ...{calignedsegment.pxd => libcalignedsegment.pxd} |    4 +-
 ...{calignedsegment.pyx => libcalignedsegment.pyx} |   88 +-
 .../{calignmentfile.pxd => libcalignmentfile.pxd}  |   40 +-
 .../{calignmentfile.pyx => libcalignmentfile.pyx}  |  343 ++---
 pysam/{cbcf.pxd => libcbcf.pxd}                    |   33 +-
 pysam/{cbcf.pyx => libcbcf.pyx}                    | 1505 +++++++++++---------
 pysam/libcbgzf.pyx                                 |  209 +++
 pysam/{cfaidx.pxd => libcfaidx.pxd}                |    4 +-
 pysam/{cfaidx.pyx => libcfaidx.pyx}                |   13 +-
 pysam/{chtslib.pxd => libchtslib.pxd}              |   18 +
 pysam/libchtslib.pyx                               |  265 ++++
 pysam/{csamfile.pxd => libcsamfile.pxd}            |    4 +-
 pysam/{csamfile.pyx => libcsamfile.pyx}            |    2 +-
 pysam/{ctabix.pxd => libctabix.pxd}                |   28 +-
 pysam/{ctabix.pyx => libctabix.pyx}                |   94 +-
 pysam/{ctabixproxies.pxd => libctabixproxies.pxd}  |    0
 pysam/{ctabixproxies.pyx => libctabixproxies.pyx}  |    4 +-
 pysam/{cutils.pxd => libcutils.pxd}                |    0
 pysam/{cutils.pyx => libcutils.pyx}                |   44 +-
 pysam/{cvcf.pxd => libcvcf.pxd}                    |    0
 pysam/{cvcf.pyx => libcvcf.pyx}                    |   12 +-
 pysam/utils.py                                     |    2 +-
 pysam/version.py                                   |    6 +-
 requirements.txt                                   |    2 +-
 run_tests_travis.sh                                |   82 +-
 samtools/sam_view.c.pysam.c                        |    4 +-
 setup.py                                           |   76 +-
 tests/AlignedSegment_test.py                       |   39 +-
 tests/AlignmentFile_test.py                        |  130 +-
 tests/SamFile_test.py                              |   12 +-
 tests/StreamFiledescriptors_test.py                |   82 ++
 tests/VariantFile_test.py                          |   80 +-
 tests/_compile_test.pyx                            |    4 +-
 tests/_cython_flagstat.pyx                         |    6 +-
 tests/cython_flagstat.py                           |   11 -
 tests/pysam_data/Makefile                          |    8 +-
 tests/pysam_data/ex3.sam                           |    4 +-
 tests/pysam_data/ex_spliced.sam                    |  297 ++++
 tests/python_flagstat.py                           |   11 -
 tests/samtools_test.py                             |    1 +
 52 files changed, 2539 insertions(+), 1294 deletions(-)

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