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afif-guest pushed a change to branch master
in repository python-pysam.
from ed944ba Removed unused paragraphs.
new 91c30fd Imported Upstream version 0.8.3
new 1bd6bae Merge tag 'upstream/0.8.3'
new 1655f1b Fix debian/watch
new 4d54939 Remove unnecessary test-suite declaration in d/control
new a15c155 Remove nonexistent files from copyright explanations
new 60a7bf9 override dh_auto_clean to remove .pybuild directory after
first build
new d2c6f88 Update package version in d/changelog
new eabcdea Allow building of the package when non-ASCII characters
are in the path
The 8 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 +-
AUTHORS | 10 +-
INSTALL | 2 +-
MANIFEST.in | 2 +-
debian/changelog | 7 +-
debian/control | 1 -
debian/copyright | 2 +-
debian/rules | 6 +-
debian/watch | 2 +-
doc/api.rst | 13 +-
doc/conf.py | 2 +-
doc/developer.rst | 17 +-
doc/faq.rst | 85 +-
doc/index.rst | 2 +-
doc/release.rst | 61 +-
doc/usage.rst | 14 +-
htslib/INSTALL | 88 +-
htslib/Makefile | 93 +-
htslib/NEWS | 50 +
htslib/bgzf.c | 58 +-
htslib/bgzip.c | 2 +-
htslib/config.mk | 72 +
htslib/config.mk.in | 72 +
htslib/configure | 4012 +++++++++++++++++++++
htslib/configure.ac | 93 +
htslib/cram/cram.h | 9 +-
htslib/cram/cram_codecs.c | 230 +-
htslib/cram/cram_codecs.h | 22 +-
htslib/cram/cram_decode.c | 1339 +++++--
htslib/cram/cram_encode.c | 1994 ++++++----
htslib/cram/cram_index.c | 82 +-
htslib/cram/cram_io.c | 1382 ++++---
htslib/cram/cram_io.h | 98 +-
htslib/cram/cram_samtools.c | 5 +-
htslib/cram/cram_stats.c | 123 +-
htslib/cram/cram_structs.h | 329 +-
htslib/cram/os.h | 2 +
htslib/cram/rANS_byte.h | 336 ++
htslib/cram/rANS_static.c | 841 +++++
htslib/cram/rANS_static.h | 44 +
htslib/cram/sam_header.c | 8 +-
htslib/cram/sam_header.h | 8 -
htslib/cram/thread_pool.c | 178 +-
htslib/cram/thread_pool.h | 15 +-
htslib/cram/vlen.c | 2 +-
htslib/faidx.c | 46 +-
htslib/hfile.c | 23 +-
htslib/hfile_internal.h | 3 +-
htslib/hfile_irods.c | 243 ++
htslib/hts.c | 531 ++-
htslib/htsfile.1 | 71 +
htslib/htsfile.c | 168 +
htslib/htslib.mk | 8 +-
htslib/htslib/bgzf.h | 7 +-
htslib/htslib/faidx.h | 2 +-
htslib/htslib/hfile.h | 10 +-
htslib/htslib/hts.h | 146 +-
htslib/htslib/khash.h | 8 +-
htslib/htslib/khash_str2int.h | 9 +
htslib/htslib/kseq.h | 10 +-
htslib/htslib/regidx.h | 147 +
htslib/htslib/sam.h | 2 +-
htslib/htslib/synced_bcf_reader.h | 15 +-
htslib/htslib/vcf.h | 15 +-
htslib/htslib_vars.mk | 1 +
htslib/knetfile.c | 11 +-
htslib/regidx.c | 338 ++
htslib/sam.c | 134 +-
htslib/synced_bcf_reader.c | 88 +-
htslib/tabix.1 | 121 +-
htslib/tabix.c | 268 +-
htslib/tbx.c | 5 +
htslib/test/{aux#aux.sam => auxf#values.sam} | 0
htslib/test/{aux.fa => auxf.fa} | 0
htslib/test/{aux.fa.fai => auxf.fa.fai} | 0
htslib/test/hfile.c | 4 +-
htslib/test/sam.c | 52 +-
htslib/test/test-regidx.c | 116 +
htslib/test/test-vcf-api.c | 57 +-
htslib/test/test_view.c | 92 +-
htslib/vcf.c | 207 +-
htslib/vcfutils.c | 63 +-
htslib/version.h | 2 +-
install-CGAT-tools.sh | 8 +-
pysam/TabProxies.pyx | 142 +-
pysam/__init__.py | 10 +-
pysam/calignmentfile.pxd | 30 +-
pysam/calignmentfile.pyx | 1109 ++++--
pysam/cbcf.pxd | 158 +
pysam/cbcf.pyx | 2419 +++++++++++++
pysam/cfaidx.pxd | 9 +-
pysam/cfaidx.pyx | 39 +-
pysam/chtslib.pxd | 891 ++++-
pysam/chtslib.pyx | 2 +-
pysam/csamtools.pyx | 2 +
pysam/ctabix.pyx | 4 +-
pysam/cvcf.pyx | 2 +-
pysam/htslib_util.c | 18 +
pysam/htslib_util.h | 20 +-
pysam/version.py | 6 +-
requires.txt | 2 +-
samtools/bam.h | 2 +-
samtools/bam2bcf_indel.c | 40 +-
samtools/bam2bcf_indel.c.pysam.c | 40 +-
samtools/bam2depth.c | 16 +-
samtools/bam2depth.c.pysam.c | 16 +-
samtools/bam_mate.c | 3 +-
samtools/bam_mate.c.pysam.c | 3 +-
samtools/bam_md.c | 1 -
samtools/bam_md.c.pysam.c | 1 -
samtools/bam_plcmd.c | 45 +-
samtools/bam_plcmd.c.pysam.c | 45 +-
samtools/bam_sort.c | 61 +-
samtools/bam_sort.c.pysam.c | 61 +-
samtools/bam_stat.c | 40 +-
samtools/bam_stat.c.pysam.c | 40 +-
samtools/errmod.c | 7 +-
samtools/errmod.c.pysam.c | 7 +-
samtools/kaln.c | 486 ---
samtools/kaln.c.pysam.c | 488 ---
samtools/kaln.h | 67 -
samtools/misc/ace2sam.c | 2 +-
samtools/misc/ace2sam.c.pysam.c | 2 +-
samtools/padding.c | 2 +-
samtools/padding.c.pysam.c | 2 +-
samtools/sam.c | 8 +-
samtools/sam.c.pysam.c | 8 +-
samtools/sam.h | 3 +-
samtools/sam_view.c | 27 +-
samtools/sam_view.c.pysam.c | 27 +-
samtools/stats.c | 21 +-
samtools/stats.c.pysam.c | 21 +-
samtools/test/merge/test_rtrans_build.c | 4 +-
samtools/test/merge/test_rtrans_build.c.pysam.c | 4 +-
samtools/test/merge/test_trans_tbl_init.c | 2 +-
samtools/test/merge/test_trans_tbl_init.c.pysam.c | 2 +-
samtools/version.h | 2 +-
setup.py | 169 +-
tests/AlignedSegment_test.py | 447 +++
tests/AlignmentFile_test.py | 1387 +++----
tests/SamFile_test.py | 14 +-
tests/TestUtils.py | 72 +-
tests/cython_flagstat.py | 1 -
tests/pysam_data/Makefile | 13 +-
tests/python_flagstat.py | 2 -
tests/samtools_test.py | 45 +-
tests/tabix_test.py | 7 +-
147 files changed, 18527 insertions(+), 4945 deletions(-)
create mode 100644 htslib/NEWS
create mode 100644 htslib/config.mk
create mode 100644 htslib/config.mk.in
create mode 100755 htslib/configure
create mode 100644 htslib/configure.ac
create mode 100644 htslib/cram/rANS_byte.h
create mode 100644 htslib/cram/rANS_static.c
create mode 100644 htslib/cram/rANS_static.h
create mode 100644 htslib/hfile_irods.c
create mode 100644 htslib/htsfile.1
create mode 100644 htslib/htsfile.c
create mode 100644 htslib/htslib/regidx.h
create mode 100644 htslib/regidx.c
rename htslib/test/{aux#aux.sam => auxf#values.sam} (100%)
rename htslib/test/{aux.fa => auxf.fa} (100%)
rename htslib/test/{aux.fa.fai => auxf.fa.fai} (100%)
create mode 100644 htslib/test/test-regidx.c
create mode 100644 pysam/cbcf.pxd
create mode 100644 pysam/cbcf.pyx
delete mode 100644 samtools/kaln.c
delete mode 100644 samtools/kaln.c.pysam.c
delete mode 100644 samtools/kaln.h
create mode 100644 tests/AlignedSegment_test.py
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