[med-svn] [python-pysam] branch upstream updated (547982f -> 91878cb)
Jorge Soares
jssoares-guest at moszumanska.debian.org
Wed Nov 26 11:06:56 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a change to branch upstream
in repository python-pysam.
from 547982f Imported Upstream version 0.8.0
adds 54ce4d5 Cleanup changelog from never released versions; move git repository and source package from pysam to python-pysam
adds e4da676 Initial release to Debian
adds 2f5aef8 Test needs samtools
adds 9a92b04 Enhance copyright according to ftpmaster
adds dafe61e Apply patch by Piotr Ożarowski <piotr at debian.org> to properly run test on all architectures
adds 96b3205 Upload to unstable
adds 67f266d Tests should not be world writable
adds d998823 Do not provide a code copy of the test script in README.Debian but rather provide the script for execution; create temp dir using mktemp; upload to unstable
adds a35d9c2 Fix autopkgtest
adds f003020 Upload to unstable
adds 65394cf Remove duplicated (useless) cd
adds c31faae Add make to autopkgtest dependencies
adds 56c7e56 Moved to GitHub.
adds 8466bd3 Watch the Python Package Index since there are no relevant tags on GitHub.
adds e630e81 Add a git-buildpackage configuration file to mark its usage.
adds c26522e Merge tag 'upstream/0.7.6'
adds 782c755 Merge tag 'upstream/0.7.7'
adds dc0b7bd New upstream release; no new copyright nor license notice.
adds b796897 Add back files that were accidentally deleted when merging upstream release.
adds 3dd0f19 Refresh patches.
adds 3cd5ab8 Correct an error in the upstream test suite.
adds 69348e4 Build-depend samtools (>= 0.1.19).
adds c6c96d7 python-pysam (0.7.7-1) unstable; urgency=medium
adds c9e8ef0 Requires Python 2.7 or higher.
adds 0b21c50 Merge tag 'upstream/0.8.0'
adds f618553 New upstream version
adds 9a87711 Try linking against htslib; ATTENTION: Testsuite fails with ImportError: /usr/lib/python2.7/dist-packages/pysam/csamfile.x86_64-linux-gnu.so: undefined symbol: sam_itr_queryi This needs to be tracked down
adds 342f3f1 Reenable check to ask for help on Debian Python list
adds bca3445 Try to explicitly set HTSLIB_LIBRARY_DIR as recommended in https://github.com/pysam-developers/pysam/issues/34 but failed anyway
adds 867b474 In case we try to build with Git checkout which does not contain Cython generated files check for these files before trying to move them
adds 3d2e27b starting to implement python 3 support
new 91878cb Imported Upstream version 0.8.1
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:
INSTALL | 4 +-
PKG-INFO | 4 +-
README.rst | 4 +-
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 -
179 files changed, 51413 insertions(+), 98356 deletions(-)
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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