[med-svn] [python-pysam] 03/03: Merge tag 'upstream/0.8.1'
Jorge Soares
jssoares-guest at moszumanska.debian.org
Fri Nov 28 09:30:06 UTC 2014
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jssoares-guest pushed a commit to branch master
in repository python-pysam.
commit 0cdc10d6a94a05940ab7687c6d3851fe6adc5020
Merge: 95bb6c1 5128bf9
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Fri Nov 28 09:29:24 2014 +0000
Merge tag 'upstream/0.8.1'
Upstream version 0.8.1
.gitignore | 77 +
.hgignore | 7 +
.hgtags | 4 +
.travis.yml | 14 +
AUTHORS | 32 +
PKG-INFO | 16 -
benchmark/tabix_bench.py | 76 +
benchmark/windows_small.bed | 100000 ++++++++++++++++++
benchmark/windows_small.bed.gz | Bin 0 -> 459587 bytes
benchmark/windows_small.bed.gz.tbi | Bin 0 -> 34590 bytes
doc/out | 30 -
htslib/INSTALL | 25 +
htslib/LICENSE | 69 +
htslib/Makefile | 337 +
htslib/README | 5 +
htslib/faidx.5 | 147 +
htslib/htslib.mk | 144 +
htslib/htslib.pc.in | 10 +
htslib/htslib_vars.mk | 38 +
htslib/sam.5 | 68 +
htslib/tabix.1 | 155 +
htslib/test/aux#aux.sam | 5 +
htslib/test/aux.fa | 2 +
htslib/test/aux.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 | 143 +
htslib/test/test-vcf-api.c | 235 +
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 | 151 +
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 +
install-CGAT-tools.sh | 281 +
pysam/VCF.py.obsolete | 1087 +
pysam/alternatives.py.obsolete | 82 +
pysam/calignmentfile.c | 48377 ---------
requires.txt | 1 +
samtools/bam.c | 190 +
samtools/bam2bcf.c | 804 +
samtools/bam2bcf_indel.c | 533 +
samtools/bam2depth.c | 199 +
samtools/bam_aux.c | 71 +
samtools/bam_cat.c | 156 +
samtools/bam_color.c | 169 +
samtools/bam_flags.c | 68 +
samtools/bam_import.c | 63 +
samtools/bam_index.c | 110 +
samtools/bam_lpileup.c | 223 +
samtools/bam_mate.c | 347 +
samtools/bam_md.c | 413 +
samtools/bam_plbuf.c | 66 +
samtools/bam_plcmd.c | 881 +
samtools/bam_reheader.c | 81 +
samtools/bam_rmdup.c | 231 +
samtools/bam_rmdupse.c | 184 +
samtools/bam_sort.c | 1181 +
samtools/bam_split.c | 508 +
samtools/bam_stat.c | 111 +
samtools/bam_tview.c | 443 +
samtools/bam_tview_curses.c | 332 +
samtools/bam_tview_html.c | 373 +
samtools/bamshuf.c | 183 +
samtools/bedcov.c | 156 +
samtools/bedidx.c | 258 +
samtools/cut_target.c | 224 +
samtools/errmod.c | 193 +
samtools/faidx.c | 95 +
samtools/kaln.c | 486 +
samtools/misc/ace2sam.c | 249 +
samtools/misc/md5.c | 298 +
samtools/padding.c | 513 +
samtools/phase.c | 722 +
samtools/sam.c | 108 +
samtools/sam_header.c | 834 +
samtools/sam_view.c | 706 +
samtools/sample.c | 132 +
samtools/stats.c | 1538 +
samtools/stats_isize.c | 219 +
samtools/test/merge/test_bam_translate.c | 591 +
samtools/test/merge/test_bam_translate.c.pysam.c | 593 +
samtools/test/merge/test_pretty_header.c | 87 +
samtools/test/merge/test_pretty_header.c.pysam.c | 89 +
samtools/test/merge/test_rtrans_build.c | 118 +
samtools/test/merge/test_rtrans_build.c.pysam.c | 120 +
samtools/test/merge/test_trans_tbl_init.c | 471 +
samtools/test/merge/test_trans_tbl_init.c.pysam.c | 473 +
samtools/test/split/test_count_rg.c | 124 +
samtools/test/split/test_count_rg.c.pysam.c | 126 +
samtools/test/split/test_expand_format_string.c | 124 +
.../test/split/test_expand_format_string.c.pysam.c | 126 +
samtools/test/split/test_filter_header_rg.c | 191 +
.../test/split/test_filter_header_rg.c.pysam.c | 193 +
samtools/test/split/test_parse_args.c | 215 +
samtools/test/split/test_parse_args.c.pysam.c | 217 +
samtools/test/test.c | 53 +
samtools/test/tview/test_get_rg_sample.c | 81 +
samtools/test/tview/test_get_rg_sample.c.pysam.c | 83 +
save/example.py | 79 +
save/pysam_bench.py | 63 +
save/pysam_test2.6.py | 1607 +
save/pysam_test_stdin.py | 10 +
save/pysam_testpp.py | 13 +
save/segfault_tests.py | 37 +
save/vcf_test.py | 123 +
setup.cfg | 6 -
win32/getopt.c | 1261 +
win32/getopt.h | 187 +
win32/stdint.h | 799 +
win32/unistd.h | 26 +
143 files changed, 148165 insertions(+), 48429 deletions(-)
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