[med-svn] [python-pysam] 02/03: Updated version 0.12.0+ds from 'upstream/0.12.0+ds'
Andreas Tille
tille at debian.org
Tue Aug 29 20:53:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-pysam.
commit c9364b8223776ce4250109133006f33d1b533af4
Merge: 88b270a 05f5851
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 29 22:51:44 2017 +0200
Updated version 0.12.0+ds from 'upstream/0.12.0+ds'
with Debian dir 6aee94dbe15c4663e14bd3849d2a988c9eaf4b2a
.gitignore | 2 +
README.rst | 18 +-
bcftools/HMM.c | 95 +++--
bcftools/HMM.c.pysam.c | 95 +++--
bcftools/HMM.h | 9 +-
bcftools/bam2bcf.c | 35 +-
bcftools/bam2bcf.c.pysam.c | 35 +-
bcftools/bam2bcf_indel.c | 8 +-
bcftools/bam2bcf_indel.c.pysam.c | 8 +-
bcftools/bcftools.h | 6 +
bcftools/consensus.c | 11 +-
bcftools/consensus.c.pysam.c | 11 +-
bcftools/filter.c | 47 ++
bcftools/filter.c.pysam.c | 47 ++
bcftools/main.c | 6 +
bcftools/main.c.pysam.c | 6 +
bcftools/rbuf.h | 66 ++-
bcftools/vcfbuf.c | 442 +++++++++++++++++++
bcftools/vcfbuf.c.pysam.c | 444 +++++++++++++++++++
bcftools/vcfbuf.h | 81 ++++
bcftools/vcfconvert.c | 8 +-
bcftools/vcfconvert.c.pysam.c | 8 +-
bcftools/vcfmerge.c | 32 +-
bcftools/vcfmerge.c.pysam.c | 32 +-
bcftools/vcfnorm.c | 27 +-
bcftools/vcfnorm.c.pysam.c | 27 +-
bcftools/vcfplugin.c | 18 +-
bcftools/vcfplugin.c.pysam.c | 18 +-
bcftools/vcfroh.c | 18 +-
bcftools/vcfroh.c.pysam.c | 18 +-
bcftools/version.h | 2 +-
cy_build.py | 24 +-
doc/conf.py | 5 +-
doc/faq.rst | 14 +
doc/glossary.rst | 45 +-
doc/installation.rst | 41 +-
doc/release.rst | 67 ++-
import.py | 2 +-
.../PysamTestModule_link_pre_489/BuildRead.pyx | 24 ++
.../PysamTestModule_link_pre_489/__init__.py | 3 +
.../link_pre_489/cy_build.py | 24 +-
linker_tests/link_pre_489/setup.py | 28 ++
linker_tests/link_pre_489/tests/test_module.py | 15 +
.../PysamTestModule_link_with_rpath/BuildRead.pyx | 24 ++
.../PysamTestModule_link_with_rpath/__init__.py | 3 +
linker_tests/link_with_rpath/setup.py | 36 ++
linker_tests/link_with_rpath/tests/test_module.py | 15 +
.../BuildRead.pyx | 24 ++
.../PysamTestModule_link_without_rpath/__init__.py | 3 +
linker_tests/link_without_rpath/setup.py | 35 ++
.../link_without_rpath/tests/test_module.py | 15 +
pysam/htslib_util.c | 10 +-
pysam/htslib_util.h | 2 +-
pysam/libcalignedsegment.pxd | 10 +-
pysam/libcalignedsegment.pyx | 62 ++-
pysam/libcalignmentfile.pxd | 6 +-
pysam/libcalignmentfile.pyx | 475 ++++++++++-----------
pysam/libcbcf.pyx | 217 ++++++----
pysam/libcbgzf.pyx | 6 +-
pysam/libcfaidx.pxd | 5 +-
pysam/libcfaidx.pyx | 108 ++++-
pysam/libchtslib.pxd | 20 +-
pysam/libchtslib.pyx | 215 ++++++++--
pysam/libctabix.pyx | 96 +++--
pysam/libctabixproxies.pyx | 22 +-
pysam/libcutils.pyx | 2 +-
pysam/version.py | 8 +-
run_tests_travis.sh | 45 +-
samtools/bam.h | 2 +-
samtools/bam_reheader.c.pysam.c | 12 +-
samtools/bam_sort.c | 237 ++++++++--
samtools/bam_sort.c.pysam.c | 237 ++++++++--
samtools/bam_stat.c.pysam.c | 10 +-
samtools/bamtk.c.pysam.c | 2 +-
samtools/sam_view.c | 342 +++++++++++----
samtools/sam_view.c.pysam.c | 342 +++++++++++----
samtools/stats.c.pysam.c | 9 +-
samtools/version.h | 2 +-
setup.cfg | 8 +
tests/AlignedSegment_test.py | 18 +-
tests/AlignmentFile_test.py | 301 +++++++------
tests/StreamFiledescriptors_test.py | 8 +-
tests/TestUtils.py | 17 +-
tests/VariantFile_test.py | 110 +++--
tests/compile_test.py | 15 +-
tests/faidx_test.py | 90 +++-
tests/linking_test.py | 79 ++++
tests/pysam_data/test_mapped_unmapped.sam | 11 +
tests/samtools_test.py | 244 ++++++-----
tests/tabix_test.py | 129 +++---
tests/tabixproxies_test.py | 40 +-
tests/test_samtools_python.py | 35 +-
92 files changed, 4309 insertions(+), 1427 deletions(-)
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