[med-svn] [python-pysam] 02/03: Merge tag 'upstream/0.8.1'
Jorge Soares
jssoares-guest at moszumanska.debian.org
Wed Nov 26 14:56:03 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 5713a6cdb04b1d054b8926d7f7c5c38cf265e3e0
Merge: 2632641 b4fcfcb
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Wed Nov 26 14:54:23 2014 +0000
Merge tag 'upstream/0.8.1'
Upstream version 0.8.1
AUTHORS | 32 -
PKG-INFO | 16 +
benchmark/tabix_bench.py | 76 -
benchmark/windows_small.bed | 100000 ------------------
benchmark/windows_small.bed.gz | Bin 459587 -> 0 bytes
benchmark/windows_small.bed.gz.tbi | Bin 34590 -> 0 bytes
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/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.egg-info/PKG-INFO | 16 +
pysam.egg-info/SOURCES.txt | 204 +
pysam.egg-info/dependency_links.txt | 1 +
pysam.egg-info/not-zip-safe | 1 +
pysam.egg-info/top_level.txt | 1 +
pysam/TabProxies.c | 14076 +++
pysam/VCF.py.obsolete | 1087 -
pysam/alternatives.py.obsolete | 82 -
pysam/calignmentfile.c | 48377 +++++++++
pysam/cfaidx.c | 8717 ++
pysam/chtslib.c | 3162 +
pysam/csamfile.c | 2876 +
pysam/csamtools.c | 6962 ++
pysam/ctabix.c | 15462 +++
pysam/cvcf.c | 30127 ++++++
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 +
tests/AlignmentFile_test.py | 2057 -
tests/SamFile_test.py | 1927 -
tests/TestUtils.py | 52 -
tests/_compile_test.pyx | 29 -
tests/_compile_test.pyxbld | 8 -
tests/_cython_flagstat.pyx | 18 -
tests/_cython_flagstat.pyxbld | 8 -
tests/compile_test.py | 46 -
tests/cython_flagstat.py | 12 -
tests/faidx_test.py | 87 -
tests/pysam_data/Makefile | 63 -
tests/pysam_data/ex1.bed | 2 -
tests/pysam_data/ex1.fa | 56 -
tests/pysam_data/ex1.fq | 13080 ---
tests/pysam_data/ex1.sam.gz | Bin 113194 -> 0 bytes
tests/pysam_data/ex10.sam | 16 -
tests/pysam_data/ex3.sam | 13 -
tests/pysam_data/ex4.sam | 9 -
tests/pysam_data/ex5.sam | 5 -
tests/pysam_data/ex6.sam | 5 -
tests/pysam_data/ex7.sam.donottest | 2 -
tests/pysam_data/ex8.sam | 3 -
tests/pysam_data/ex9_fail.sam | 1022 -
tests/pysam_data/ex9_nofail.sam | 1021 -
tests/pysam_data/example_btag.sam | 6 -
tests/pysam_data/example_empty_header.sam | 321 -
tests/pysam_data/example_unmapped_reads_no_sq.sam | 3 -
tests/pysam_data/example_user_header.sam | 8 -
tests/pysam_data/issue100.sam | 27 -
tests/pysam_data/rg_with_tab.sam | 3273 -
tests/pysam_data/softclip.sam | 6 -
tests/pysam_data/tag_bug.sam | 16 -
tests/pysam_data/test.gtf | 10 -
tests/pysam_data/test.gtf.gz | Bin 311 -> 0 bytes
tests/pysam_data/test_unaligned.sam | 6 -
tests/python_flagstat.py | 13 -
tests/refactoring.pl | 60 -
tests/refactoring.txt | 198 -
tests/samtools_test.py | 383 -
tests/tabix_data/example.bed.gz | Bin 819 -> 0 bytes
tests/tabix_data/example.bed.gz.tbi | Bin 192 -> 0 bytes
tests/tabix_data/example.gtf.gz | Bin 3778 -> 0 bytes
tests/tabix_data/example.gtf.gz.tbi | Bin 196 -> 0 bytes
tests/tabix_data/example.sam.gz | Bin 398 -> 0 bytes
tests/tabix_data/example.sam.gz.tbi | Bin 128 -> 0 bytes
tests/tabix_data/example.vcf.gz | Bin 328 -> 0 bytes
tests/tabix_data/example.vcf.gz.tbi | Bin 182 -> 0 bytes
tests/tabix_data/example.vcf40 | 23 -
tests/tabix_data/example_badcomments.bed.gz | Bin 879 -> 0 bytes
tests/tabix_data/example_badcomments.bed.gz.tbi | Bin 194 -> 0 bytes
tests/tabix_data/example_badcomments.gtf.gz | Bin 3825 -> 0 bytes
tests/tabix_data/example_badcomments.gtf.gz.tbi | Bin 198 -> 0 bytes
tests/tabix_data/example_badcomments.sam.gz | Bin 398 -> 0 bytes
tests/tabix_data/example_badcomments.sam.gz.tbi | Bin 128 -> 0 bytes
tests/tabix_data/example_badcomments.vcf.gz | Bin 753 -> 0 bytes
tests/tabix_data/example_badcomments.vcf.gz.tbi | Bin 186 -> 0 bytes
tests/tabix_data/example_comments.bed.gz | Bin 849 -> 0 bytes
tests/tabix_data/example_comments.bed.gz.tbi | Bin 194 -> 0 bytes
tests/tabix_data/example_comments.gtf.gz | Bin 3792 -> 0 bytes
tests/tabix_data/example_comments.gtf.gz.tbi | Bin 198 -> 0 bytes
tests/tabix_data/example_comments.sam.gz | Bin 398 -> 0 bytes
tests/tabix_data/example_comments.sam.gz.tbi | Bin 128 -> 0 bytes
tests/tabix_data/example_comments.vcf.gz | Bin 753 -> 0 bytes
tests/tabix_data/example_comments.vcf.gz.tbi | Bin 186 -> 0 bytes
tests/tabix_data/example_unicode.vcf | 23 -
tests/tabix_data/gtf_toofew_fields.gtf.gz | Bin 400 -> 0 bytes
tests/tabix_data/gtf_toomany_fields.gtf.gz | Bin 400 -> 0 bytes
tests/tabix_data/gtf_wrong_fields.gtf.gz | Bin 400 -> 0 bytes
tests/tabix_data/vcf/10.vcf | 84 -
tests/tabix_data/vcf/11.vcf | 216 -
tests/tabix_data/vcf/12.vcf | 1000 -
tests/tabix_data/vcf/13.vcf | 220 -
tests/tabix_data/vcf/15.vcf | 317 -
tests/tabix_data/vcf/16.vcf | 369 -
tests/tabix_data/vcf/18.vcf | 1000 -
tests/tabix_data/vcf/2.vcf | 334 -
tests/tabix_data/vcf/20.vcf | 307 -
tests/tabix_data/vcf/21.vcf | 310 -
tests/tabix_data/vcf/22.vcf | 1000 -
tests/tabix_data/vcf/23.vcf | 419 -
tests/tabix_data/vcf/24.vcf | 724 -
tests/tabix_data/vcf/3.vcf | 1000 -
tests/tabix_data/vcf/4.vcf | 318 -
tests/tabix_data/vcf/5.vcf | 1000 -
tests/tabix_data/vcf/6.vcf | 278 -
tests/tabix_data/vcf/7.vcf | 317 -
tests/tabix_data/vcf/8.vcf | 84 -
tests/tabix_data/vcf/9.vcf | 1000 -
tests/tabix_data/vcf/README.txt | 11 -
tests/tabix_data/vcf/issue85.vcf | 26 -
tests/tabix_test.py | 1020 -
win32/getopt.c | 1261 -
win32/getopt.h | 187 -
win32/stdint.h | 799 -
win32/unistd.h | 26 -
260 files changed, 130034 insertions(+), 185554 deletions(-)
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