[med-svn] [python-pysam] 02/02: Merge tag 'upstream/0.8.1'
Jorge Soares
jssoares-guest at moszumanska.debian.org
Wed Nov 26 11:06:55 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a commit to branch master
in repository python-pysam.
commit 14f241c4e1fc7c002f3e6d5253263968c81bd006
Merge: 3d2e27b 91878cb
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Wed Nov 26 11:06:35 2014 +0000
Merge tag 'upstream/0.8.1'
Upstream version 0.8.1
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 +-
htslib/htslib/hts_defs.h => samtools/samtools.h | 30 +-
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 +
htslib/htslib/hts_defs.h => samtools/test/test.h | 32 +-
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, 51391 insertions(+), 100606 deletions(-)
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