[med-svn] [python-pysam] branch master updated (fca3a7d -> de70961)

[Afif Elghraoui]

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

      from  fca3a7d   releasing package python-pysam version 0.9.1.4+ds-1
       new  dadf905   Imported Upstream version 0.10.0+ds
       new  c125365   Merge tag 'upstream/0.10.0+ds'
       new  47981ea   Update patches
       new  de70961   Bump minimum htslib version

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:
 .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 -
 debian/control                                     |    2 +-
 debian/patches/rpath.patch                         |    8 +-
 debian/patches/series                              |    1 -
 debian/patches/spelling.patch                      |   91 --
 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 +
 56 files changed, 2544 insertions(+), 1391 deletions(-)
 create mode 100644 benchmark/cython_flagstat.py
 create mode 100644 benchmark/python_flagstat.py
 create mode 100755 buildwheels.sh
 delete mode 100644 debian/patches/spelling.patch
 delete mode 100644 pysam/chtslib.pyx
 rename pysam/{calignedsegment.pxd => libcalignedsegment.pxd} (97%)
 rename pysam/{calignedsegment.pyx => libcalignedsegment.pyx} (97%)
 rename pysam/{calignmentfile.pxd => libcalignmentfile.pxd} (83%)
 rename pysam/{calignmentfile.pyx => libcalignmentfile.pyx} (92%)
 rename pysam/{cbcf.pxd => libcbcf.pxd} (72%)
 rename pysam/{cbcf.pyx => libcbcf.pyx} (76%)
 create mode 100644 pysam/libcbgzf.pyx
 rename pysam/{cfaidx.pxd => libcfaidx.pxd} (94%)
 rename pysam/{cfaidx.pyx => libcfaidx.pyx} (97%)
 rename pysam/{chtslib.pxd => libchtslib.pxd} (99%)
 create mode 100644 pysam/libchtslib.pyx
 rename pysam/{csamfile.pxd => libcsamfile.pxd} (93%)
 rename pysam/{csamfile.pyx => libcsamfile.pyx} (92%)
 rename pysam/{ctabix.pxd => libctabix.pxd} (89%)
 rename pysam/{ctabix.pyx => libctabix.pyx} (94%)
 rename pysam/{ctabixproxies.pxd => libctabixproxies.pxd} (100%)
 rename pysam/{ctabixproxies.pyx => libctabixproxies.pyx} (99%)
 rename pysam/{cutils.pxd => libcutils.pxd} (100%)
 rename pysam/{cutils.pyx => libcutils.pyx} (92%)
 rename pysam/{cvcf.pxd => libcvcf.pxd} (100%)
 rename pysam/{cvcf.pyx => libcvcf.pyx} (99%)
 create mode 100644 tests/StreamFiledescriptors_test.py
 delete mode 100644 tests/cython_flagstat.py
 create mode 100644 tests/pysam_data/ex_spliced.sam
 delete mode 100644 tests/python_flagstat.py

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