[med-svn] [python-pysam] branch upstream updated (b6750cc -> f3bd90a)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

      from  b6750cc   New upstream version 0.12.0.1+ds
       new  f3bd90a   New upstream version 0.13.0+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:
 .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(-)
 copy doc/release.rst => NEWS (96%)
 create mode 100644 bcftools/vcfsort.c
 create mode 100644 bcftools/vcfsort.c.pysam.c
 create mode 100644 samtools/bam_markdup.c
 create mode 100644 samtools/bam_markdup.c.pysam.c

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