[med-svn] [python-pysam] 02/05: Update upstream source from tag 'upstream/0.13.0+ds'

[Andreas Tille]

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

commit d06b7e2782c4cd69b6fa0927ddd3c6469cf201e9
Merge: 62d43f6 f3bd90a
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 13 12:59:32 2017 +0100

    Update upstream source from tag 'upstream/0.13.0+ds'
    
    Update to upstream version '0.13.0+ds'
    with Debian dir c63bbb266a669569051da8554f9d7f56d23526b6

 .travis.yml                     |   2 +
 INSTALL                         | 117 ++++--
 MANIFEST.in                     |   5 +
 doc/release.rst => NEWS         |  19 +
 bcftools/consensus.c            | 129 ++++--
 bcftools/consensus.c.pysam.c    | 129 ++++--
 bcftools/csq.c                  | 133 ++++---
 bcftools/csq.c.pysam.c          | 133 ++++---
 bcftools/filter.c               | 652 ++++++++++++++++++++++---------
 bcftools/filter.c.pysam.c       | 652 ++++++++++++++++++++++---------
 bcftools/kheap.h                |   5 +-
 bcftools/main.c                 |   5 +
 bcftools/main.c.pysam.c         |   5 +
 bcftools/mpileup.c              |   9 +-
 bcftools/mpileup.c.pysam.c      |   9 +-
 bcftools/vcfcnv.c               |   6 +
 bcftools/vcfcnv.c.pysam.c       |   6 +
 bcftools/vcfconvert.c           |   5 +-
 bcftools/vcfconvert.c.pysam.c   |   5 +-
 bcftools/vcfindex.c             |   7 +
 bcftools/vcfindex.c.pysam.c     |   7 +
 bcftools/vcfisec.c              |  14 +-
 bcftools/vcfisec.c.pysam.c      |  14 +-
 bcftools/vcfmerge.c             |  14 +-
 bcftools/vcfmerge.c.pysam.c     |  14 +-
 bcftools/vcfnorm.c              |  18 +
 bcftools/vcfnorm.c.pysam.c      |  18 +
 bcftools/vcfquery.c             |  17 +
 bcftools/vcfquery.c.pysam.c     |  17 +
 bcftools/vcfsort.c              | 306 +++++++++++++++
 bcftools/vcfsort.c.pysam.c      | 308 +++++++++++++++
 bcftools/vcfstats.c             |  63 ++-
 bcftools/vcfstats.c.pysam.c     |  63 ++-
 bcftools/version.h              |   2 +-
 doc/installation.rst            |  23 ++
 doc/release.rst                 |  11 +
 import.py                       |   2 +
 pysam/libcalignedsegment.pyx    | 380 ++++++++++++------
 pysam/libcalignmentfile.pxd     |   4 +-
 pysam/libcalignmentfile.pyx     |   2 +-
 pysam/libctabix.pyx             |  99 +++--
 pysam/libctabixproxies.pyx      |   1 +
 pysam/version.py                |   8 +-
 run_tests_travis.sh             |  11 +-
 samtools/bam.h                  |   2 +-
 samtools/bam_lpileup.c          |   1 +
 samtools/bam_lpileup.c.pysam.c  |   1 +
 samtools/bam_markdup.c          | 844 +++++++++++++++++++++++++++++++++++++++
 samtools/bam_markdup.c.pysam.c  | 846 ++++++++++++++++++++++++++++++++++++++++
 samtools/bam_mate.c             |  50 ++-
 samtools/bam_mate.c.pysam.c     |  50 ++-
 samtools/bam_plcmd.c            |  22 ++
 samtools/bam_plcmd.c.pysam.c    |  22 ++
 samtools/bam_reheader.c.pysam.c |   2 +-
 samtools/bam_sort.c             | 494 +++++++++++++++++------
 samtools/bam_sort.c.pysam.c     | 494 +++++++++++++++++------
 samtools/bamtk.c                |  15 +
 samtools/bamtk.c.pysam.c        |  22 +-
 samtools/bedidx.c               |   4 -
 samtools/bedidx.c.pysam.c       |   4 -
 samtools/dict.c                 |   4 +
 samtools/dict.c.pysam.c         |   4 +
 samtools/padding.c              |  31 +-
 samtools/padding.c.pysam.c      |  31 +-
 samtools/phase.c                |   1 +
 samtools/phase.c.pysam.c        |   1 +
 samtools/sam_view.c             |  33 +-
 samtools/sam_view.c.pysam.c     |  33 +-
 samtools/version.h              |   2 +-
 setup.py                        |  12 +-
 tests/AlignedSegment_test.py    | 261 +++++++++++--
 tests/AlignmentFile_test.py     | 137 +------
 tests/TestUtils.py              |  10 +-
 tests/linking_test.py           |  16 +-
 tests/samtools_test.py          |  16 +-
 tests/tabix_test.py             |  53 ++-
 tests/tabixproxies_test.py      |  22 +-
 77 files changed, 5692 insertions(+), 1297 deletions(-)

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