[med-svn] [python-pysam] branch upstream updated (91c30fd -> 3cbc6e0)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Thu Jun 25 07:44:27 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch upstream
in repository python-pysam.
from 91c30fd Imported Upstream version 0.8.3
adds 3cbc6e0 Imported Upstream version 0.8.3+ds1
No new revisions were added by this update.
Summary of changes:
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 -
144 files changed, 69867 deletions(-)
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