projects / python-pysam.git / commit
? search:
summary | shortlog | log | commit | commitdiff | tree
(parent: 2632641) | patch
Imported Upstream version 0.8.1
authorJorge Soares <j.s.soares@gmail.com>
Wed, 26 Nov 2014 14:54:20 +0000 (14:54 +0000)
committerJorge Soares <j.s.soares@gmail.com>
Wed, 26 Nov 2014 14:54:20 +0000 (14:54 +0000)
commitb4fcfcb75609ef4756d04eff0d1e95571f65952a
tree22ca5115094dccd8705b0c3743c57b1e884ac616tree | snapshot
parent26326418c967469011181f7b34c8dee705a6e1d8commit | diff
Imported Upstream version 0.8.1
260 files changed:
AUTHORS [deleted file] blob | history
PKG-INFO [new file with mode: 0644] blob
benchmark/tabix_bench.py [deleted file] blob | history
benchmark/windows_small.bed [deleted file] blob | history
benchmark/windows_small.bed.gz [deleted file] blob | history
benchmark/windows_small.bed.gz.tbi [deleted file] blob | history
debian/changelog [deleted file] blob | history
debian/compat [deleted file] blob | history
debian/control [deleted file] blob | history
debian/copyright [deleted file] blob | history
debian/gbp.conf [deleted file] blob | history
debian/patches/do_not_use_distribute_setup.patch [deleted file] blob | history
debian/patches/fix_cleanup_tests.patch [deleted file] blob | history
debian/patches/offline-tests.patch [deleted file] blob | history
debian/patches/series [deleted file] blob | history
debian/patches/use_external_htslib.patch [deleted file] blob | history
debian/python-pysam-tests.README.Debian [deleted file] blob | history
debian/python-pysam-tests.docs [deleted file] blob | history
debian/python-pysam-tests.install [deleted file] blob | history
debian/rules [deleted file] blob | history
debian/source/format [deleted file] blob | history
debian/tests/control [deleted file] blob | history
debian/tests/run-unit-test [deleted file] blob | history
debian/watch [deleted file] blob | history
doc/out [new file with mode: 0644] blob
htslib/INSTALL [deleted file] blob | history
htslib/LICENSE [deleted file] blob | history
htslib/Makefile [deleted file] blob | history
htslib/README [deleted file] blob | history
htslib/faidx.5 [deleted file] blob | history
htslib/htslib.mk [deleted file] blob | history
htslib/htslib.pc.in [deleted file] blob | history
htslib/htslib_vars.mk [deleted file] blob | history
htslib/sam.5 [deleted file] blob | history
htslib/tabix.1 [deleted file] blob | history
htslib/test/aux#aux.sam [deleted file] blob | history
htslib/test/aux.fa [deleted file] blob | history
htslib/test/aux.fa.fai [deleted file] blob | history
htslib/test/c1#bounds.sam [deleted file] blob | history
htslib/test/c1#clip.sam [deleted file] blob | history
htslib/test/c1#pad1.sam [deleted file] blob | history
htslib/test/c1#pad2.sam [deleted file] blob | history
htslib/test/c1#pad3.sam [deleted file] blob | history
htslib/test/c1.fa [deleted file] blob | history
htslib/test/c1.fa.fai [deleted file] blob | history
htslib/test/ce#1.sam [deleted file] blob | history
htslib/test/ce#2.sam [deleted file] blob | history
htslib/test/ce#5.sam [deleted file] blob | history
htslib/test/ce#5b.sam [deleted file] blob | history
htslib/test/ce#large_seq.sam [deleted file] blob | history
htslib/test/ce#tag_depadded.sam [deleted file] blob | history
htslib/test/ce#tag_padded.sam [deleted file] blob | history
htslib/test/ce#unmap.sam [deleted file] blob | history
htslib/test/ce#unmap1.sam [deleted file] blob | history
htslib/test/ce#unmap2.sam [deleted file] blob | history
htslib/test/ce.fa [deleted file] blob | history
htslib/test/ce.fa.fai [deleted file] blob | history
htslib/test/compare_sam.pl [deleted file] blob | history
htslib/test/fieldarith.c [deleted file] blob | history
htslib/test/fieldarith.sam [deleted file] blob | history
htslib/test/hfile.c [deleted file] blob | history
htslib/test/sam.c [deleted file] blob | history
htslib/test/test-vcf-api.c [deleted file] blob | history
htslib/test/test-vcf-api.out [deleted file] blob | history
htslib/test/test-vcf-sweep.c [deleted file] blob | history
htslib/test/test-vcf-sweep.out [deleted file] blob | history
htslib/test/test.pl [deleted file] blob | history
htslib/test/test_view.c [deleted file] blob | history
htslib/test/test_view.pl [deleted file] blob | history
htslib/test/xx#blank.sam [deleted file] blob | history
htslib/test/xx#large_aux.sam [deleted file] blob | history
htslib/test/xx#large_aux2.sam [deleted file] blob | history
htslib/test/xx#minimal.sam [deleted file] blob | history
htslib/test/xx#pair.sam [deleted file] blob | history
htslib/test/xx#rg.sam [deleted file] blob | history
htslib/test/xx#triplet.sam [deleted file] blob | history
htslib/test/xx#unsorted.sam [deleted file] blob | history
htslib/test/xx.fa [deleted file] blob | history
htslib/test/xx.fa.fai [deleted file] blob | history
htslib/vcf.5 [deleted file] blob | history
install-CGAT-tools.sh [deleted file] blob | history
pysam.egg-info/PKG-INFO [new file with mode: 0644] blob
pysam.egg-info/SOURCES.txt [new file with mode: 0644] blob
pysam.egg-info/dependency_links.txt [new file with mode: 0644] blob
pysam.egg-info/not-zip-safe [new file with mode: 0644] blob
pysam.egg-info/top_level.txt [new file with mode: 0644] blob
pysam/TabProxies.c [new file with mode: 0644] blob
pysam/VCF.py.obsolete [deleted file] blob | history
pysam/alternatives.py.obsolete [deleted file] blob | history
pysam/calignmentfile.c [new file with mode: 0644] blob
pysam/cfaidx.c [new file with mode: 0644] blob
pysam/chtslib.c [new file with mode: 0644] blob
pysam/csamfile.c [new file with mode: 0644] blob
pysam/csamtools.c [new file with mode: 0644] blob
pysam/ctabix.c [new file with mode: 0644] blob
pysam/cvcf.c [new file with mode: 0644] blob
requires.txt [deleted file] blob | history
samtools/bam.c [deleted file] blob | history
samtools/bam2bcf.c [deleted file] blob | history
samtools/bam2bcf_indel.c [deleted file] blob | history
samtools/bam2depth.c [deleted file] blob | history
samtools/bam_aux.c [deleted file] blob | history
samtools/bam_cat.c [deleted file] blob | history
samtools/bam_color.c [deleted file] blob | history
samtools/bam_flags.c [deleted file] blob | history
samtools/bam_import.c [deleted file] blob | history
samtools/bam_index.c [deleted file] blob | history
samtools/bam_lpileup.c [deleted file] blob | history
samtools/bam_mate.c [deleted file] blob | history
samtools/bam_md.c [deleted file] blob | history
samtools/bam_plbuf.c [deleted file] blob | history
samtools/bam_plcmd.c [deleted file] blob | history
samtools/bam_reheader.c [deleted file] blob | history
samtools/bam_rmdup.c [deleted file] blob | history
samtools/bam_rmdupse.c [deleted file] blob | history
samtools/bam_sort.c [deleted file] blob | history
samtools/bam_split.c [deleted file] blob | history
samtools/bam_stat.c [deleted file] blob | history
samtools/bam_tview.c [deleted file] blob | history
samtools/bam_tview_curses.c [deleted file] blob | history
samtools/bam_tview_html.c [deleted file] blob | history
samtools/bamshuf.c [deleted file] blob | history
samtools/bedcov.c [deleted file] blob | history
samtools/bedidx.c [deleted file] blob | history
samtools/cut_target.c [deleted file] blob | history
samtools/errmod.c [deleted file] blob | history
samtools/faidx.c [deleted file] blob | history
samtools/kaln.c [deleted file] blob | history
samtools/misc/ace2sam.c [deleted file] blob | history
samtools/misc/md5.c [deleted file] blob | history
samtools/padding.c [deleted file] blob | history
samtools/phase.c [deleted file] blob | history
samtools/sam.c [deleted file] blob | history
samtools/sam_header.c [deleted file] blob | history
samtools/sam_view.c [deleted file] blob | history
samtools/sample.c [deleted file] blob | history
samtools/stats.c [deleted file] blob | history
samtools/stats_isize.c [deleted file] blob | history
samtools/test/merge/test_bam_translate.c [deleted file] blob | history
samtools/test/merge/test_bam_translate.c.pysam.c [deleted file] blob | history
samtools/test/merge/test_pretty_header.c [deleted file] blob | history
samtools/test/merge/test_pretty_header.c.pysam.c [deleted file] blob | history
samtools/test/merge/test_rtrans_build.c [deleted file] blob | history
samtools/test/merge/test_rtrans_build.c.pysam.c [deleted file] blob | history
samtools/test/merge/test_trans_tbl_init.c [deleted file] blob | history
samtools/test/merge/test_trans_tbl_init.c.pysam.c [deleted file] blob | history
samtools/test/split/test_count_rg.c [deleted file] blob | history
samtools/test/split/test_count_rg.c.pysam.c [deleted file] blob | history
samtools/test/split/test_expand_format_string.c [deleted file] blob | history
samtools/test/split/test_expand_format_string.c.pysam.c [deleted file] blob | history
samtools/test/split/test_filter_header_rg.c [deleted file] blob | history
samtools/test/split/test_filter_header_rg.c.pysam.c [deleted file] blob | history
samtools/test/split/test_parse_args.c [deleted file] blob | history
samtools/test/split/test_parse_args.c.pysam.c [deleted file] blob | history
samtools/test/test.c [deleted file] blob | history
samtools/test/tview/test_get_rg_sample.c [deleted file] blob | history
samtools/test/tview/test_get_rg_sample.c.pysam.c [deleted file] blob | history
save/example.py [deleted file] blob | history
save/pysam_bench.py [deleted file] blob | history
save/pysam_test2.6.py [deleted file] blob | history
save/pysam_test_stdin.py [deleted file] blob | history
save/pysam_testpp.py [deleted file] blob | history
save/segfault_tests.py [deleted file] blob | history
save/vcf_test.py [deleted file] blob | history
setup.cfg diff | blob | history
tests/AlignmentFile_test.py [deleted file] blob | history
tests/SamFile_test.py [deleted file] blob | history
tests/TestUtils.py [deleted file] blob | history
tests/_compile_test.pyx [deleted file] blob | history
tests/_compile_test.pyxbld [deleted file] blob | history
tests/_cython_flagstat.pyx [deleted file] blob | history
tests/_cython_flagstat.pyxbld [deleted file] blob | history
tests/compile_test.py [deleted file] blob | history
tests/cython_flagstat.py [deleted file] blob | history
tests/faidx_test.py [deleted file] blob | history
tests/pysam_data/Makefile [deleted file] blob | history
tests/pysam_data/ex1.bed [deleted file] blob | history
tests/pysam_data/ex1.fa [deleted file] blob | history
tests/pysam_data/ex1.fq [deleted file] blob | history
tests/pysam_data/ex1.sam.gz [deleted file] blob | history
tests/pysam_data/ex10.sam [deleted file] blob | history
tests/pysam_data/ex3.sam [deleted file] blob | history
tests/pysam_data/ex4.sam [deleted file] blob | history
tests/pysam_data/ex5.sam [deleted file] blob | history
tests/pysam_data/ex6.sam [deleted file] blob | history
tests/pysam_data/ex7.sam.donottest [deleted file] blob | history
tests/pysam_data/ex8.sam [deleted file] blob | history
tests/pysam_data/ex9_fail.sam [deleted file] blob | history
tests/pysam_data/ex9_nofail.sam [deleted file] blob | history
tests/pysam_data/example_btag.sam [deleted file] blob | history
tests/pysam_data/example_empty_header.sam [deleted file] blob | history
tests/pysam_data/example_unmapped_reads_no_sq.sam [deleted file] blob | history
tests/pysam_data/example_user_header.sam [deleted file] blob | history
tests/pysam_data/issue100.sam [deleted file] blob | history
tests/pysam_data/rg_with_tab.sam [deleted file] blob | history
tests/pysam_data/softclip.sam [deleted file] blob | history
tests/pysam_data/tag_bug.sam [deleted file] blob | history
tests/pysam_data/test.gtf [deleted file] blob | history
tests/pysam_data/test.gtf.gz [deleted file] blob | history
tests/pysam_data/test_unaligned.sam [deleted file] blob | history
tests/python_flagstat.py [deleted file] blob | history
tests/refactoring.pl [deleted file] blob | history
tests/refactoring.txt [deleted file] blob | history
tests/samtools_test.py [deleted file] blob | history
tests/tabix_data/example.bed.gz [deleted file] blob | history
tests/tabix_data/example.bed.gz.tbi [deleted file] blob | history
tests/tabix_data/example.gtf.gz [deleted file] blob | history
tests/tabix_data/example.gtf.gz.tbi [deleted file] blob | history
tests/tabix_data/example.sam.gz [deleted file] blob | history
tests/tabix_data/example.sam.gz.tbi [deleted file] blob | history
tests/tabix_data/example.vcf.gz [deleted file] blob | history
tests/tabix_data/example.vcf.gz.tbi [deleted file] blob | history
tests/tabix_data/example.vcf40 [deleted file] blob | history
tests/tabix_data/example_badcomments.bed.gz [deleted file] blob | history
tests/tabix_data/example_badcomments.bed.gz.tbi [deleted file] blob | history
tests/tabix_data/example_badcomments.gtf.gz [deleted file] blob | history
tests/tabix_data/example_badcomments.gtf.gz.tbi [deleted file] blob | history
tests/tabix_data/example_badcomments.sam.gz [deleted file] blob | history
tests/tabix_data/example_badcomments.sam.gz.tbi [deleted file] blob | history
tests/tabix_data/example_badcomments.vcf.gz [deleted file] blob | history
tests/tabix_data/example_badcomments.vcf.gz.tbi [deleted file] blob | history
tests/tabix_data/example_comments.bed.gz [deleted file] blob | history
tests/tabix_data/example_comments.bed.gz.tbi [deleted file] blob | history
tests/tabix_data/example_comments.gtf.gz [deleted file] blob | history
tests/tabix_data/example_comments.gtf.gz.tbi [deleted file] blob | history
tests/tabix_data/example_comments.sam.gz [deleted file] blob | history
tests/tabix_data/example_comments.sam.gz.tbi [deleted file] blob | history
tests/tabix_data/example_comments.vcf.gz [deleted file] blob | history
tests/tabix_data/example_comments.vcf.gz.tbi [deleted file] blob | history
tests/tabix_data/example_unicode.vcf [deleted file] blob | history
tests/tabix_data/gtf_toofew_fields.gtf.gz [deleted file] blob | history
tests/tabix_data/gtf_toomany_fields.gtf.gz [deleted file] blob | history
tests/tabix_data/gtf_wrong_fields.gtf.gz [deleted file] blob | history
tests/tabix_data/vcf/10.vcf [deleted file] blob | history
tests/tabix_data/vcf/11.vcf [deleted file] blob | history
tests/tabix_data/vcf/12.vcf [deleted file] blob | history
tests/tabix_data/vcf/13.vcf [deleted file] blob | history
tests/tabix_data/vcf/15.vcf [deleted file] blob | history
tests/tabix_data/vcf/16.vcf [deleted file] blob | history
tests/tabix_data/vcf/18.vcf [deleted file] blob | history
tests/tabix_data/vcf/2.vcf [deleted file] blob | history
tests/tabix_data/vcf/20.vcf [deleted file] blob | history
tests/tabix_data/vcf/21.vcf [deleted file] blob | history
tests/tabix_data/vcf/22.vcf [deleted file] blob | history
tests/tabix_data/vcf/23.vcf [deleted file] blob | history
tests/tabix_data/vcf/24.vcf [deleted file] blob | history
tests/tabix_data/vcf/3.vcf [deleted file] blob | history
tests/tabix_data/vcf/4.vcf [deleted file] blob | history
tests/tabix_data/vcf/5.vcf [deleted file] blob | history
tests/tabix_data/vcf/6.vcf [deleted file] blob | history
tests/tabix_data/vcf/7.vcf [deleted file] blob | history
tests/tabix_data/vcf/8.vcf [deleted file] blob | history
tests/tabix_data/vcf/9.vcf [deleted file] blob | history
tests/tabix_data/vcf/README.txt [deleted file] blob | history
tests/tabix_data/vcf/issue85.vcf [deleted file] blob | history
tests/tabix_test.py [deleted file] blob | history
win32/getopt.c [deleted file] blob | history
win32/getopt.h [deleted file] blob | history
win32/stdint.h [deleted file] blob | history
win32/unistd.h [deleted file] blob | history
Unnamed repository; edit this file 'description' to name the repository.