[med-svn] [python-pysam] branch master updated (81ff5d2 -> dffe5f1)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Thu Jun 25 07:19:46 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch master
in repository python-pysam.
from 81ff5d2 python-pysam (0.8.3-1) unstable; urgency=medium
new 9f99688 Exclude bundled htslib convenience-copy
new 494f56a Provide get-orig-source rule
new 3cbc6e0 Imported Upstream version 0.8.3+ds1
new b2cf913 Merge tag 'upstream/0.8.3+ds1'
new bb5c719 Support building with missing htslib directory
new 5a6adf6 Add dependency on cython for autopkgtests to provide pyximport
new dffe5f1 Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/python-pysam
The 7 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:
debian/changelog | 2 +-
debian/copyright | 1 +
debian/patches/correct-spelling-errors.patch | 11 -
debian/patches/ignore-htslib-dir.patch | 27 +
debian/patches/series | 1 +
debian/rules | 3 +
debian/tests/control | 6 +-
debian/watch | 2 +-
htslib/INSTALL | 79 -
htslib/LICENSE | 69 -
htslib/Makefile | 386 -
htslib/NEWS | 50 -
htslib/README | 5 -
htslib/bgzf.c | 1124 --
htslib/bgzip.c | 284 -
htslib/config.h | 3 -
htslib/config.mk | 72 -
htslib/config.mk.in | 72 -
htslib/configure | 4012 -----
htslib/configure.ac | 93 -
htslib/cram/cram.h | 63 -
htslib/cram/cram_codecs.c | 1846 ---
htslib/cram/cram_codecs.h | 165 -
htslib/cram/cram_decode.c | 2775 ----
htslib/cram/cram_decode.h | 112 -
htslib/cram/cram_encode.c | 3068 ----
htslib/cram/cram_encode.h | 105 -
htslib/cram/cram_index.c | 557 -
htslib/cram/cram_index.h | 98 -
htslib/cram/cram_io.c | 4202 -----
htslib/cram/cram_io.h | 596 -
htslib/cram/cram_samtools.c | 147 -
htslib/cram/cram_samtools.h | 97 -
htslib/cram/cram_stats.c | 450 -
htslib/cram/cram_stats.h | 59 -
htslib/cram/cram_structs.h | 809 -
htslib/cram/files.c | 76 -
htslib/cram/mFILE.c | 634 -
htslib/cram/mFILE.h | 88 -
htslib/cram/md5.c | 295 -
htslib/cram/md5.h | 54 -
htslib/cram/misc.h | 110 -
htslib/cram/open_trace_file.c | 351 -
htslib/cram/open_trace_file.h | 115 -
htslib/cram/os.h | 308 -
htslib/cram/pooled_alloc.c | 170 -
htslib/cram/pooled_alloc.h | 56 -
htslib/cram/rANS_byte.h | 336 -
htslib/cram/rANS_static.c | 841 -
htslib/cram/rANS_static.h | 44 -
htslib/cram/sam_header.c | 1218 --
htslib/cram/sam_header.h | 444 -
htslib/cram/string_alloc.c | 153 -
htslib/cram/string_alloc.h | 69 -
htslib/cram/thread_pool.c | 811 -
htslib/cram/thread_pool.h | 210 -
htslib/cram/vlen.c | 432 -
htslib/cram/vlen.h | 48 -
htslib/cram/zfio.c | 185 -
htslib/cram/zfio.h | 54 -
htslib/faidx.5 | 147 -
htslib/faidx.c | 475 -
htslib/hfile.c | 547 -
htslib/hfile_internal.h | 76 -
htslib/hfile_irods.c | 243 -
htslib/hfile_net.c | 99 -
htslib/hts.c | 1665 --
htslib/htsfile.1 | 71 -
htslib/htsfile.c | 168 -
htslib/htslib.mk | 150 -
htslib/htslib.pc.in | 10 -
htslib/htslib/bgzf.h | 315 -
htslib/htslib/faidx.h | 135 -
htslib/htslib/hfile.h | 212 -
htslib/htslib/hts.h | 456 -
htslib/htslib/hts_defs.h | 47 -
htslib/htslib/kfunc.h | 75 -
htslib/htslib/khash.h | 619 -
htslib/htslib/khash_str2int.h | 133 -
htslib/htslib/klist.h | 121 -
htslib/htslib/knetfile.h | 101 -
htslib/htslib/kseq.h | 253 -
htslib/htslib/ksort.h | 285 -
htslib/htslib/kstring.h | 270 -
htslib/htslib/regidx.h | 147 -
htslib/htslib/sam.h | 426 -
htslib/htslib/synced_bcf_reader.h | 301 -
htslib/htslib/tbx.h | 77 -
htslib/htslib/vcf.h | 883 --
htslib/htslib/vcf_sweep.h | 39 -
htslib/htslib/vcfutils.h | 112 -
htslib/htslib_vars.mk | 39 -
htslib/kfunc.c | 280 -
htslib/knetfile.c | 632 -
htslib/kstring.c | 254 -
htslib/regidx.c | 338 -
htslib/sam.5 | 68 -
htslib/sam.c | 1882 ---
htslib/synced_bcf_reader.c | 1257 --
htslib/tabix.1 | 180 -
htslib/tabix.c | 519 -
htslib/tbx.c | 320 -
htslib/test/auxf#values.sam | 5 -
htslib/test/auxf.fa | 2 -
htslib/test/auxf.fa.fai | 1 -
htslib/test/c1#bounds.sam | 4 -
htslib/test/c1#clip.sam | 8 -
htslib/test/c1#pad1.sam | 10 -
htslib/test/c1#pad2.sam | 14 -
htslib/test/c1#pad3.sam | 14 -
htslib/test/c1.fa | 2 -
htslib/test/c1.fa.fai | 1 -
htslib/test/ce#1.sam | 2 -
htslib/test/ce#2.sam | 3 -
htslib/test/ce#5.sam | 11 -
htslib/test/ce#5b.sam | 12 -
htslib/test/ce#large_seq.sam | 3 -
htslib/test/ce#tag_depadded.sam | 11 -
htslib/test/ce#tag_padded.sam | 11 -
htslib/test/ce#unmap.sam | 6 -
htslib/test/ce#unmap1.sam | 20 -
htslib/test/ce#unmap2.sam | 29 -
htslib/test/ce.fa | 20803 -------------------------
htslib/test/ce.fa.fai | 7 -
htslib/test/compare_sam.pl | 172 -
htslib/test/fieldarith.c | 72 -
htslib/test/fieldarith.sam | 15 -
htslib/test/hfile.c | 204 -
htslib/test/sam.c | 187 -
htslib/test/test-regidx.c | 116 -
htslib/test/test-vcf-api.c | 282 -
htslib/test/test-vcf-api.out | 28 -
htslib/test/test-vcf-sweep.c | 112 -
htslib/test/test-vcf-sweep.out | 4 -
htslib/test/test.pl | 202 -
htslib/test/test_view.c | 239 -
htslib/test/test_view.pl | 71 -
htslib/test/xx#blank.sam | 0
htslib/test/xx#large_aux.sam | 4 -
htslib/test/xx#large_aux2.sam | 11 -
htslib/test/xx#minimal.sam | 10 -
htslib/test/xx#pair.sam | 7 -
htslib/test/xx#rg.sam | 13 -
htslib/test/xx#triplet.sam | 7 -
htslib/test/xx#unsorted.sam | 8 -
htslib/test/xx.fa | 5 -
htslib/test/xx.fa.fai | 2 -
htslib/vcf.5 | 120 -
htslib/vcf.c | 3212 ----
htslib/vcf_sweep.c | 182 -
htslib/vcfutils.c | 675 -
htslib/version.h | 1 -
152 files changed, 38 insertions(+), 69882 deletions(-)
create mode 100644 debian/patches/ignore-htslib-dir.patch
delete mode 100644 htslib/INSTALL
delete mode 100644 htslib/LICENSE
delete mode 100644 htslib/Makefile
delete mode 100644 htslib/NEWS
delete mode 100644 htslib/README
delete mode 100644 htslib/bgzf.c
delete mode 100644 htslib/bgzip.c
delete mode 100644 htslib/config.h
delete mode 100644 htslib/config.mk
delete mode 100644 htslib/config.mk.in
delete mode 100755 htslib/configure
delete mode 100644 htslib/configure.ac
delete mode 100644 htslib/cram/cram.h
delete mode 100644 htslib/cram/cram_codecs.c
delete mode 100644 htslib/cram/cram_codecs.h
delete mode 100644 htslib/cram/cram_decode.c
delete mode 100644 htslib/cram/cram_decode.h
delete mode 100644 htslib/cram/cram_encode.c
delete mode 100644 htslib/cram/cram_encode.h
delete mode 100644 htslib/cram/cram_index.c
delete mode 100644 htslib/cram/cram_index.h
delete mode 100644 htslib/cram/cram_io.c
delete mode 100644 htslib/cram/cram_io.h
delete mode 100644 htslib/cram/cram_samtools.c
delete mode 100644 htslib/cram/cram_samtools.h
delete mode 100644 htslib/cram/cram_stats.c
delete mode 100644 htslib/cram/cram_stats.h
delete mode 100644 htslib/cram/cram_structs.h
delete mode 100644 htslib/cram/files.c
delete mode 100644 htslib/cram/mFILE.c
delete mode 100644 htslib/cram/mFILE.h
delete mode 100644 htslib/cram/md5.c
delete mode 100644 htslib/cram/md5.h
delete mode 100644 htslib/cram/misc.h
delete mode 100644 htslib/cram/open_trace_file.c
delete mode 100644 htslib/cram/open_trace_file.h
delete mode 100644 htslib/cram/os.h
delete mode 100644 htslib/cram/pooled_alloc.c
delete mode 100644 htslib/cram/pooled_alloc.h
delete mode 100644 htslib/cram/rANS_byte.h
delete mode 100644 htslib/cram/rANS_static.c
delete mode 100644 htslib/cram/rANS_static.h
delete mode 100644 htslib/cram/sam_header.c
delete mode 100644 htslib/cram/sam_header.h
delete mode 100644 htslib/cram/string_alloc.c
delete mode 100644 htslib/cram/string_alloc.h
delete mode 100644 htslib/cram/thread_pool.c
delete mode 100644 htslib/cram/thread_pool.h
delete mode 100644 htslib/cram/vlen.c
delete mode 100644 htslib/cram/vlen.h
delete mode 100644 htslib/cram/zfio.c
delete mode 100644 htslib/cram/zfio.h
delete mode 100644 htslib/faidx.5
delete mode 100644 htslib/faidx.c
delete mode 100644 htslib/hfile.c
delete mode 100644 htslib/hfile_internal.h
delete mode 100644 htslib/hfile_irods.c
delete mode 100644 htslib/hfile_net.c
delete mode 100644 htslib/hts.c
delete mode 100644 htslib/htsfile.1
delete mode 100644 htslib/htsfile.c
delete mode 100644 htslib/htslib.mk
delete mode 100644 htslib/htslib.pc.in
delete mode 100644 htslib/htslib/bgzf.h
delete mode 100644 htslib/htslib/faidx.h
delete mode 100644 htslib/htslib/hfile.h
delete mode 100644 htslib/htslib/hts.h
delete mode 100644 htslib/htslib/hts_defs.h
delete mode 100644 htslib/htslib/kfunc.h
delete mode 100644 htslib/htslib/khash.h
delete mode 100644 htslib/htslib/khash_str2int.h
delete mode 100644 htslib/htslib/klist.h
delete mode 100644 htslib/htslib/knetfile.h
delete mode 100644 htslib/htslib/kseq.h
delete mode 100644 htslib/htslib/ksort.h
delete mode 100644 htslib/htslib/kstring.h
delete mode 100644 htslib/htslib/regidx.h
delete mode 100644 htslib/htslib/sam.h
delete mode 100644 htslib/htslib/synced_bcf_reader.h
delete mode 100644 htslib/htslib/tbx.h
delete mode 100644 htslib/htslib/vcf.h
delete mode 100644 htslib/htslib/vcf_sweep.h
delete mode 100644 htslib/htslib/vcfutils.h
delete mode 100644 htslib/htslib_vars.mk
delete mode 100644 htslib/kfunc.c
delete mode 100644 htslib/knetfile.c
delete mode 100644 htslib/kstring.c
delete mode 100644 htslib/regidx.c
delete mode 100644 htslib/sam.5
delete mode 100644 htslib/sam.c
delete mode 100644 htslib/synced_bcf_reader.c
delete mode 100644 htslib/tabix.1
delete mode 100644 htslib/tabix.c
delete mode 100644 htslib/tbx.c
delete mode 100644 htslib/test/auxf#values.sam
delete mode 100644 htslib/test/auxf.fa
delete mode 100644 htslib/test/auxf.fa.fai
delete mode 100644 htslib/test/c1#bounds.sam
delete mode 100644 htslib/test/c1#clip.sam
delete mode 100644 htslib/test/c1#pad1.sam
delete mode 100644 htslib/test/c1#pad2.sam
delete mode 100644 htslib/test/c1#pad3.sam
delete mode 100644 htslib/test/c1.fa
delete mode 100644 htslib/test/c1.fa.fai
delete mode 100644 htslib/test/ce#1.sam
delete mode 100644 htslib/test/ce#2.sam
delete mode 100644 htslib/test/ce#5.sam
delete mode 100644 htslib/test/ce#5b.sam
delete mode 100644 htslib/test/ce#large_seq.sam
delete mode 100644 htslib/test/ce#tag_depadded.sam
delete mode 100644 htslib/test/ce#tag_padded.sam
delete mode 100644 htslib/test/ce#unmap.sam
delete mode 100644 htslib/test/ce#unmap1.sam
delete mode 100644 htslib/test/ce#unmap2.sam
delete mode 100644 htslib/test/ce.fa
delete mode 100644 htslib/test/ce.fa.fai
delete mode 100755 htslib/test/compare_sam.pl
delete mode 100644 htslib/test/fieldarith.c
delete mode 100644 htslib/test/fieldarith.sam
delete mode 100644 htslib/test/hfile.c
delete mode 100644 htslib/test/sam.c
delete mode 100644 htslib/test/test-regidx.c
delete mode 100644 htslib/test/test-vcf-api.c
delete mode 100644 htslib/test/test-vcf-api.out
delete mode 100644 htslib/test/test-vcf-sweep.c
delete mode 100644 htslib/test/test-vcf-sweep.out
delete mode 100755 htslib/test/test.pl
delete mode 100644 htslib/test/test_view.c
delete mode 100755 htslib/test/test_view.pl
delete mode 100644 htslib/test/xx#blank.sam
delete mode 100644 htslib/test/xx#large_aux.sam
delete mode 100644 htslib/test/xx#large_aux2.sam
delete mode 100644 htslib/test/xx#minimal.sam
delete mode 100644 htslib/test/xx#pair.sam
delete mode 100644 htslib/test/xx#rg.sam
delete mode 100644 htslib/test/xx#triplet.sam
delete mode 100644 htslib/test/xx#unsorted.sam
delete mode 100644 htslib/test/xx.fa
delete mode 100644 htslib/test/xx.fa.fai
delete mode 100644 htslib/vcf.5
delete mode 100644 htslib/vcf.c
delete mode 100644 htslib/vcf_sweep.c
delete mode 100644 htslib/vcfutils.c
delete mode 100644 htslib/version.h
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pysam.git
More information about the debian-med-commit
mailing list