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tille pushed a change to branch upstream
in repository python-pysam.
from 1520aab Imported Upstream version 0.11.2.2+ds
new 05f5851 New upstream version 0.12.0+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:
.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(-)
create mode 100644 bcftools/vcfbuf.c
create mode 100644 bcftools/vcfbuf.c.pysam.c
create mode 100644 bcftools/vcfbuf.h
create mode 100644
linker_tests/link_pre_489/PysamTestModule_link_pre_489/BuildRead.pyx
create mode 100644
linker_tests/link_pre_489/PysamTestModule_link_pre_489/__init__.py
copy cy_build.py => linker_tests/link_pre_489/cy_build.py (73%)
create mode 100644 linker_tests/link_pre_489/setup.py
create mode 100644 linker_tests/link_pre_489/tests/test_module.py
create mode 100644
linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/BuildRead.pyx
create mode 100644
linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/__init__.py
create mode 100644 linker_tests/link_with_rpath/setup.py
create mode 100644 linker_tests/link_with_rpath/tests/test_module.py
create mode 100644
linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/BuildRead.pyx
create mode 100644
linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/__init__.py
create mode 100644 linker_tests/link_without_rpath/setup.py
create mode 100644 linker_tests/link_without_rpath/tests/test_module.py
create mode 100644 setup.cfg
create mode 100644 tests/linking_test.py
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