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 <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pysam.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
