[med-svn] [python-pysam] branch master updated (3d2e27b -> 14f241c)
Jorge Soares
jssoares-guest at moszumanska.debian.org
Wed Nov 26 11:06:52 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a change to branch master
in repository python-pysam.
from 3d2e27b starting to implement python 3 support
new 91878cb Imported Upstream version 0.8.1
new 14f241c Merge tag 'upstream/0.8.1'
The 2 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:
INSTALL | 4 +-
PKG-INFO | 4 +-
README.rst | 4 +-
debian/changelog | 57 -
debian/compat | 1 -
debian/control | 77 -
debian/copyright | 109 -
debian/gbp.conf | 5 -
debian/patches/do_not_use_distribute_setup.patch | 17 -
debian/patches/fix_cleanup_tests.patch | 19 -
debian/patches/offline-tests.patch | 1824 -
debian/patches/series | 4 -
debian/patches/use_external_htslib.patch | 23 -
debian/python-pysam-tests.README.Debian | 12 -
debian/python-pysam-tests.docs | 1 -
debian/python-pysam-tests.install | 1 -
debian/rules | 49 -
debian/source/format | 1 -
debian/tests/control | 3 -
debian/tests/run-unit-test | 14 -
debian/watch | 3 -
doc/api.rst | 166 +-
doc/conf.py | 14 +
doc/developer.rst | 40 +-
doc/faq.rst | 47 +-
doc/glossary.rst | 18 +-
doc/index.rst | 42 +-
doc/out | 30 +
doc/release.rst | 208 +-
doc/usage.rst | 308 +-
htslib/__init__.py | 0
htslib/bgzf.c | 975 +-
htslib/bgzip.c | 291 +-
htslib/cram/cram_decode.c | 2 +-
htslib/cram/cram_index.c | 2 +
htslib/cram/cram_io.c | 4 +-
htslib/cram/cram_io.h | 2 +-
htslib/cram/open_trace_file.c | 179 +-
htslib/faidx.c | 552 +-
htslib/hfile.c | 2 +-
htslib/hfile_internal.h | 2 +-
htslib/hfile_net.c | 2 +-
htslib/hts.c | 1874 +-
htslib/htslib/__init__.py | 0
htslib/htslib/bgzf.h | 415 +-
htslib/htslib/faidx.h | 139 +-
htslib/htslib/hfile.h | 2 +-
htslib/htslib/hts.h | 173 +-
htslib/htslib/hts_defs.h | 2 +-
htslib/htslib/kfunc.h | 30 +-
htslib/htslib/khash_str2int.h | 40 +-
htslib/htslib/knetfile.h | 26 +
htslib/htslib/kstdint.h | 64 -
htslib/htslib/kstring.h | 2 +-
htslib/htslib/sam.h | 243 +-
htslib/htslib/synced_bcf_reader.h | 95 +-
htslib/htslib/tbx.h | 67 +-
htslib/htslib/vcf.h | 489 +-
htslib/htslib/vcf_sweep.h | 28 +-
htslib/htslib/vcfutils.h | 60 +-
htslib/kfunc.c | 26 +
htslib/knetfile.c | 17 +-
htslib/kstring.c | 25 +
htslib/sam.c | 2352 +-
htslib/synced_bcf_reader.c | 130 +-
htslib/tabix.c | 61 +-
htslib/tbx.c | 411 +-
htslib/vcf.c | 1370 +-
htslib/vcf_sweep.c | 24 +
htslib/vcfutils.c | 174 +-
htslib/version.h | 2 +-
pysam.egg-info/PKG-INFO | 4 +-
pysam.egg-info/SOURCES.txt | 57 +-
pysam.egg-info/requires.txt | 1 -
pysam.py | 2 +-
pysam/TabProxies.c | 5037 ++-
pysam/TabProxies.pxd | 33 +-
pysam/TabProxies.pyx | 369 +-
pysam/__init__.py | 26 +-
pysam/{csamfile.c => calignmentfile.c} | 33519 +++++++++-------
pysam/{csamfile.pxd => calignmentfile.pxd} | 36 +-
pysam/{csamfile.pyx => calignmentfile.pyx} | 2301 +-
pysam/cfaidx.c | 1344 +-
pysam/cfaidx.pxd | 11 +-
pysam/cfaidx.pyx | 53 +-
pysam/chtslib.c | 2 +-
pysam/chtslib.pxd | 29 +-
pysam/csamfile.c | 44112 +--------------------
pysam/csamfile.pxd | 187 +-
pysam/csamfile.pyx | 3441 +-
pysam/csamtools.c | 2 +-
pysam/ctabix.c | 5593 +--
pysam/ctabix.pxd | 26 +-
pysam/ctabix.pyx | 473 +-
pysam/cvcf.c | 7693 ++--
pysam/cvcf.pyx | 79 +-
pysam/htslib_util.h | 61 +-
pysam/pysam_util.c | 26 +-
pysam/samfile_util.c | 2 +
pysam/samfile_util.h | 1 -
pysam/version.py | 8 +-
samtools/__init__.py | 0
samtools/bam.c.pysam.c | 590 +-
samtools/bam.h | 1019 +-
samtools/bam2bcf.c.pysam.c | 1069 +-
samtools/bam2bcf.h | 137 +-
samtools/bam2bcf_indel.c.pysam.c | 907 +-
samtools/bam2depth.c.pysam.c | 238 +-
samtools/bam_aux.c.pysam.c | 254 +-
samtools/bam_cat.c.pysam.c | 341 +-
samtools/bam_color.c.pysam.c | 226 +-
samtools/bam_endian.h | 54 +-
samtools/bam_flags.c.pysam.c | 70 +
samtools/bam_import.c.pysam.c | 528 +-
samtools/bam_index.c.pysam.c | 802 +-
samtools/bam_lpileup.c.pysam.c | 313 +-
samtools/bam_lpileup.h | 57 +
samtools/bam_mate.c.pysam.c | 423 +-
samtools/bam_md.c.pysam.c | 712 +-
samtools/bam_pileup.c.pysam.c | 439 -
samtools/bam_plbuf.c.pysam.c | 68 +
htslib/htslib/hts_defs.h => samtools/bam_plbuf.h | 50 +-
samtools/bam_plcmd.c.pysam.c | 1223 +-
samtools/bam_reheader.c.pysam.c | 117 +-
samtools/bam_rmdup.c.pysam.c | 329 +-
samtools/bam_rmdupse.c.pysam.c | 259 +-
samtools/bam_sort.c.pysam.c | 1554 +-
samtools/bam_split.c.pysam.c | 510 +
samtools/bam_stat.c.pysam.c | 162 +-
samtools/bam_tview.c.pysam.c | 683 +-
samtools/bam_tview.h | 70 +-
samtools/bam_tview_curses.c.pysam.c | 423 +-
samtools/bam_tview_html.c.pysam.c | 496 +-
samtools/bamshuf.c.pysam.c | 254 +-
samtools/bcftools/__init__.py | 0
samtools/bcftools/bcf.c.pysam.c | 398 -
samtools/bcftools/bcf.h | 197 -
samtools/bcftools/bcf2qcall.c.pysam.c | 93 -
samtools/bcftools/bcfutils.c.pysam.c | 506 -
samtools/bcftools/call1.c.pysam.c | 635 -
samtools/bcftools/em.c.pysam.c | 312 -
samtools/bcftools/fet.c.pysam.c | 114 -
samtools/bcftools/index.c.pysam.c | 338 -
samtools/bcftools/kfunc.c.pysam.c | 164 -
samtools/bcftools/kmin.c.pysam.c | 211 -
samtools/bcftools/kmin.h | 46 -
samtools/bcftools/mut.c.pysam.c | 129 -
samtools/bcftools/prob1.c.pysam.c | 990 -
samtools/bcftools/prob1.h | 49 -
samtools/bcftools/vcf.c.pysam.c | 251 -
samtools/bedcov.c.pysam.c | 241 +-
samtools/bedidx.c.pysam.c | 328 +-
samtools/bgzf.c.pysam.c | 696 -
samtools/bgzf.h | 207 -
samtools/cut_target.c.pysam.c | 351 +-
samtools/errmod.c.pysam.c | 277 +-
samtools/errmod.h | 39 +-
samtools/faidx.c.pysam.c | 486 +-
samtools/faidx.h | 103 -
samtools/kaln.c.pysam.c | 2 +-
samtools/kaln.h | 2 +-
samtools/khash.h | 528 -
samtools/klist.h | 96 -
samtools/knetfile.c.pysam.c | 634 -
samtools/knetfile.h | 75 -
samtools/kprobaln.c | 6 +-
samtools/kprobaln.c.pysam.c | 6 +-
samtools/kprobaln.h | 2 +-
samtools/kseq.h | 235 -
samtools/ksort.h | 285 -
samtools/kstring.c.pysam.c | 214 -
samtools/kstring.h | 169 -
samtools/misc/ace2sam.c.pysam.c | 388 +-
samtools/misc/md5.c.pysam.c | 4 +-
samtools/padding.c.pysam.c | 866 +-
samtools/phase.c.pysam.c | 1217 +-
samtools/razf.c.pysam.c | 855 -
samtools/razf.h | 134 -
samtools/sam.c.pysam.c | 246 +-
samtools/sam.h | 147 +-
samtools/sam_header.c.pysam.c | 156 +-
samtools/sam_header.h | 52 +-
samtools/sam_view.c.pysam.c | 1037 +-
samtools/sample.c.pysam.c | 173 +-
samtools/sample.h | 32 +-
COPYING => samtools/samtools.h | 26 +-
samtools/stats.c.pysam.c | 1540 +
samtools/stats_isize.c.pysam.c | 221 +
samtools/stats_isize.h | 83 +
samtools/test/test.c.pysam.c | 55 +
COPYING => samtools/test/test.h | 28 +-
samtools/version.h | 1 +
samtools/win32/__init__.py | 0
setup.py | 156 +-
tests/example.gtf.gz.tbi | Bin 260 -> 0 bytes
tests/pysam_test.py | 1885 -
tests/tabix_test.py | 908 -
197 files changed, 51413 insertions(+), 100576 deletions(-)
delete mode 100644 debian/changelog
delete mode 100644 debian/compat
delete mode 100644 debian/control
delete mode 100644 debian/copyright
delete mode 100644 debian/gbp.conf
delete mode 100644 debian/patches/do_not_use_distribute_setup.patch
delete mode 100644 debian/patches/fix_cleanup_tests.patch
delete mode 100644 debian/patches/offline-tests.patch
delete mode 100644 debian/patches/series
delete mode 100644 debian/patches/use_external_htslib.patch
delete mode 100644 debian/python-pysam-tests.README.Debian
delete mode 100644 debian/python-pysam-tests.docs
delete mode 100644 debian/python-pysam-tests.install
delete mode 100755 debian/rules
delete mode 100644 debian/source/format
delete mode 100644 debian/tests/control
delete mode 100644 debian/tests/run-unit-test
delete mode 100644 debian/watch
create mode 100644 doc/out
delete mode 100644 htslib/__init__.py
delete mode 100644 htslib/htslib/__init__.py
delete mode 100644 htslib/htslib/kstdint.h
delete mode 100644 pysam.egg-info/requires.txt
copy pysam/{csamfile.c => calignmentfile.c} (60%)
copy pysam/{csamfile.pxd => calignmentfile.pxd} (86%)
copy pysam/{csamfile.pyx => calignmentfile.pyx} (70%)
delete mode 100644 samtools/__init__.py
create mode 100644 samtools/bam_flags.c.pysam.c
create mode 100644 samtools/bam_lpileup.h
delete mode 100644 samtools/bam_pileup.c.pysam.c
create mode 100644 samtools/bam_plbuf.c.pysam.c
copy htslib/htslib/hts_defs.h => samtools/bam_plbuf.h (52%)
create mode 100644 samtools/bam_split.c.pysam.c
delete mode 100644 samtools/bcftools/__init__.py
delete mode 100644 samtools/bcftools/bcf.c.pysam.c
delete mode 100644 samtools/bcftools/bcf.h
delete mode 100644 samtools/bcftools/bcf2qcall.c.pysam.c
delete mode 100644 samtools/bcftools/bcfutils.c.pysam.c
delete mode 100644 samtools/bcftools/call1.c.pysam.c
delete mode 100644 samtools/bcftools/em.c.pysam.c
delete mode 100644 samtools/bcftools/fet.c.pysam.c
delete mode 100644 samtools/bcftools/index.c.pysam.c
delete mode 100644 samtools/bcftools/kfunc.c.pysam.c
delete mode 100644 samtools/bcftools/kmin.c.pysam.c
delete mode 100644 samtools/bcftools/kmin.h
delete mode 100644 samtools/bcftools/mut.c.pysam.c
delete mode 100644 samtools/bcftools/prob1.c.pysam.c
delete mode 100644 samtools/bcftools/prob1.h
delete mode 100644 samtools/bcftools/vcf.c.pysam.c
delete mode 100644 samtools/bgzf.c.pysam.c
delete mode 100644 samtools/bgzf.h
delete mode 100644 samtools/faidx.h
delete mode 100644 samtools/khash.h
delete mode 100644 samtools/klist.h
delete mode 100644 samtools/knetfile.c.pysam.c
delete mode 100644 samtools/knetfile.h
delete mode 100644 samtools/kseq.h
delete mode 100644 samtools/ksort.h
delete mode 100644 samtools/kstring.c.pysam.c
delete mode 100644 samtools/kstring.h
delete mode 100644 samtools/razf.c.pysam.c
delete mode 100644 samtools/razf.h
copy COPYING => samtools/samtools.h (62%)
create mode 100644 samtools/stats.c.pysam.c
create mode 100644 samtools/stats_isize.c.pysam.c
create mode 100644 samtools/stats_isize.h
create mode 100644 samtools/test/test.c.pysam.c
copy COPYING => samtools/test/test.h (61%)
create mode 100644 samtools/version.h
delete mode 100644 samtools/win32/__init__.py
delete mode 100644 tests/example.gtf.gz.tbi
delete mode 100644 tests/pysam_test.py
delete mode 100644 tests/tabix_test.py
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