Import python-pysam_0.12.0.1+ds.orig.tar.gz
authorAfif Elghraoui <afif@debian.org>
Sun, 1 Oct 2017 16:30:30 +0000 (17:30 +0100)
committerAfif Elghraoui <afif@debian.org>
Sun, 1 Oct 2017 16:30:30 +0000 (17:30 +0100)
commitdc3c56e2c44636117c06781fae6e626a221c7c65
treef6fc35b217881f3dc0e2d200034f85856fbb6e16
Import python-pysam_0.12.0.1+ds.orig.tar.gz

[dgit import orig python-pysam_0.12.0.1+ds.orig.tar.gz]
460 files changed:
.gitignore [new file with mode: 0644]
.travis.yml [new file with mode: 0644]
AUTHORS [new file with mode: 0644]
COPYING [new file with mode: 0644]
INSTALL [new file with mode: 0644]
MANIFEST.in [new file with mode: 0644]
README.rst [new file with mode: 0644]
bcftools/HMM.c [new file with mode: 0644]
bcftools/HMM.c.pysam.c [new file with mode: 0644]
bcftools/HMM.h [new file with mode: 0644]
bcftools/bam2bcf.c [new file with mode: 0644]
bcftools/bam2bcf.c.pysam.c [new file with mode: 0644]
bcftools/bam2bcf.h [new file with mode: 0644]
bcftools/bam2bcf_indel.c [new file with mode: 0644]
bcftools/bam2bcf_indel.c.pysam.c [new file with mode: 0644]
bcftools/bam_sample.c [new file with mode: 0644]
bcftools/bam_sample.c.pysam.c [new file with mode: 0644]
bcftools/bam_sample.h [new file with mode: 0644]
bcftools/bcftools.h [new file with mode: 0644]
bcftools/bin.c [new file with mode: 0644]
bcftools/bin.c.pysam.c [new file with mode: 0644]
bcftools/bin.h [new file with mode: 0644]
bcftools/call.h [new file with mode: 0644]
bcftools/ccall.c [new file with mode: 0644]
bcftools/ccall.c.pysam.c [new file with mode: 0644]
bcftools/config.h [new file with mode: 0644]
bcftools/consensus.c [new file with mode: 0644]
bcftools/consensus.c.pysam.c [new file with mode: 0644]
bcftools/convert.c [new file with mode: 0644]
bcftools/convert.c.pysam.c [new file with mode: 0644]
bcftools/convert.h [new file with mode: 0644]
bcftools/csq.c [new file with mode: 0644]
bcftools/csq.c.pysam.c [new file with mode: 0644]
bcftools/em.c [new file with mode: 0644]
bcftools/em.c.pysam.c [new file with mode: 0644]
bcftools/filter.c [new file with mode: 0644]
bcftools/filter.c.pysam.c [new file with mode: 0644]
bcftools/filter.h [new file with mode: 0644]
bcftools/gvcf.c [new file with mode: 0644]
bcftools/gvcf.c.pysam.c [new file with mode: 0644]
bcftools/gvcf.h [new file with mode: 0644]
bcftools/hclust.c [new file with mode: 0644]
bcftools/hclust.c.pysam.c [new file with mode: 0644]
bcftools/hclust.h [new file with mode: 0644]
bcftools/khash_str2str.h [new file with mode: 0644]
bcftools/kheap.h [new file with mode: 0644]
bcftools/kmin.c [new file with mode: 0644]
bcftools/kmin.c.pysam.c [new file with mode: 0644]
bcftools/kmin.h [new file with mode: 0644]
bcftools/main.c [new file with mode: 0644]
bcftools/main.c.pysam.c [new file with mode: 0644]
bcftools/mcall.c [new file with mode: 0644]
bcftools/mcall.c.pysam.c [new file with mode: 0644]
bcftools/mpileup.c [new file with mode: 0644]
bcftools/mpileup.c.pysam.c [new file with mode: 0644]
bcftools/mw.h [new file with mode: 0644]
bcftools/ploidy.c [new file with mode: 0644]
bcftools/ploidy.c.pysam.c [new file with mode: 0644]
bcftools/ploidy.h [new file with mode: 0644]
bcftools/prob1.c [new file with mode: 0644]
bcftools/prob1.c.pysam.c [new file with mode: 0644]
bcftools/prob1.h [new file with mode: 0644]
bcftools/pysam.h [new file with mode: 0644]
bcftools/rbuf.h [new file with mode: 0644]
bcftools/regidx.c [new file with mode: 0644]
bcftools/regidx.c.pysam.c [new file with mode: 0644]
bcftools/regidx.h [new file with mode: 0644]
bcftools/smpl_ilist.c [new file with mode: 0644]
bcftools/smpl_ilist.c.pysam.c [new file with mode: 0644]
bcftools/smpl_ilist.h [new file with mode: 0644]
bcftools/tabix.c [new file with mode: 0644]
bcftools/tabix.c.pysam.c [new file with mode: 0644]
bcftools/tsv2vcf.c [new file with mode: 0644]
bcftools/tsv2vcf.c.pysam.c [new file with mode: 0644]
bcftools/tsv2vcf.h [new file with mode: 0644]
bcftools/vcfannotate.c [new file with mode: 0644]
bcftools/vcfannotate.c.pysam.c [new file with mode: 0644]
bcftools/vcfbuf.c [new file with mode: 0644]
bcftools/vcfbuf.c.pysam.c [new file with mode: 0644]
bcftools/vcfbuf.h [new file with mode: 0644]
bcftools/vcfcall.c [new file with mode: 0644]
bcftools/vcfcall.c.pysam.c [new file with mode: 0644]
bcftools/vcfcnv.c [new file with mode: 0644]
bcftools/vcfcnv.c.pysam.c [new file with mode: 0644]
bcftools/vcfconcat.c [new file with mode: 0644]
bcftools/vcfconcat.c.pysam.c [new file with mode: 0644]
bcftools/vcfconvert.c [new file with mode: 0644]
bcftools/vcfconvert.c.pysam.c [new file with mode: 0644]
bcftools/vcffilter.c [new file with mode: 0644]
bcftools/vcffilter.c.pysam.c [new file with mode: 0644]
bcftools/vcfgtcheck.c [new file with mode: 0644]
bcftools/vcfgtcheck.c.pysam.c [new file with mode: 0644]
bcftools/vcfindex.c [new file with mode: 0644]
bcftools/vcfindex.c.pysam.c [new file with mode: 0644]
bcftools/vcfisec.c [new file with mode: 0644]
bcftools/vcfisec.c.pysam.c [new file with mode: 0644]
bcftools/vcfmerge.c [new file with mode: 0644]
bcftools/vcfmerge.c.pysam.c [new file with mode: 0644]
bcftools/vcfnorm.c [new file with mode: 0644]
bcftools/vcfnorm.c.pysam.c [new file with mode: 0644]
bcftools/vcfplugin.c [new file with mode: 0644]
bcftools/vcfplugin.c.pysam.c [new file with mode: 0644]
bcftools/vcfquery.c [new file with mode: 0644]
bcftools/vcfquery.c.pysam.c [new file with mode: 0644]
bcftools/vcfroh.c [new file with mode: 0644]
bcftools/vcfroh.c.pysam.c [new file with mode: 0644]
bcftools/vcfsom.c [new file with mode: 0644]
bcftools/vcfsom.c.pysam.c [new file with mode: 0644]
bcftools/vcfstats.c [new file with mode: 0644]
bcftools/vcfstats.c.pysam.c [new file with mode: 0644]
bcftools/vcfview.c [new file with mode: 0644]
bcftools/vcfview.c.pysam.c [new file with mode: 0644]
bcftools/vcmp.c [new file with mode: 0644]
bcftools/vcmp.c.pysam.c [new file with mode: 0644]
bcftools/vcmp.h [new file with mode: 0644]
bcftools/version.c [new file with mode: 0644]
bcftools/version.c.pysam.c [new file with mode: 0644]
bcftools/version.h [new file with mode: 0644]
benchmark/AlignedSegment_bench.py [new file with mode: 0644]
benchmark/cython_flagstat.py [new file with mode: 0644]
benchmark/python_flagstat.py [new file with mode: 0644]
benchmark/tabix_bench.py [new file with mode: 0644]
benchmark/windows_small.bed [new file with mode: 0644]
benchmark/windows_small.bed.gz [new file with mode: 0644]
benchmark/windows_small.bed.gz.tbi [new file with mode: 0644]
buildwheels.sh [new file with mode: 0755]
ci/conda-recipe/build.sh [new file with mode: 0644]
ci/conda-recipe/meta.yaml [new file with mode: 0644]
ci/install-CGAT-tools.sh [new file with mode: 0755]
cy_build.py [new file with mode: 0644]
doc/Makefile [new file with mode: 0644]
doc/api.rst [new file with mode: 0644]
doc/conf.py [new file with mode: 0644]
doc/developer.rst [new file with mode: 0644]
doc/faq.rst [new file with mode: 0644]
doc/glossary.rst [new file with mode: 0644]
doc/index.rst [new file with mode: 0644]
doc/installation.rst [new file with mode: 0644]
doc/make.bat [new file with mode: 0644]
doc/release.rst [new file with mode: 0644]
doc/usage.rst [new file with mode: 0644]
import.py [new file with mode: 0644]
linker_tests/link_pre_489/PysamTestModule_link_pre_489/BuildRead.pyx [new file with mode: 0644]
linker_tests/link_pre_489/PysamTestModule_link_pre_489/__init__.py [new file with mode: 0644]
linker_tests/link_pre_489/cy_build.py [new file with mode: 0644]
linker_tests/link_pre_489/setup.py [new file with mode: 0644]
linker_tests/link_pre_489/tests/test_module.py [new file with mode: 0644]
linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/BuildRead.pyx [new file with mode: 0644]
linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/__init__.py [new file with mode: 0644]
linker_tests/link_with_rpath/setup.py [new file with mode: 0644]
linker_tests/link_with_rpath/tests/test_module.py [new file with mode: 0644]
linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/BuildRead.pyx [new file with mode: 0644]
linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/__init__.py [new file with mode: 0644]
linker_tests/link_without_rpath/setup.py [new file with mode: 0644]
linker_tests/link_without_rpath/tests/test_module.py [new file with mode: 0644]
pysam.py [new file with mode: 0644]
pysam/Pileup.py [new file with mode: 0644]
pysam/VCF.py.obsolete [new file with mode: 0644]
pysam/__init__.py [new file with mode: 0644]
pysam/alternatives.py.obsolete [new file with mode: 0644]
pysam/bcftools.py [new file with mode: 0644]
pysam/cbcftools_util.h [new file with mode: 0644]
pysam/csamtools_util.h [new file with mode: 0644]
pysam/htslib_util.c [new file with mode: 0644]
pysam/htslib_util.h [new file with mode: 0644]
pysam/include/__init__.py [new file with mode: 0644]
pysam/libcalignedsegment.pxd [new file with mode: 0644]
pysam/libcalignedsegment.pyx [new file with mode: 0644]
pysam/libcalignmentfile.pxd [new file with mode: 0644]
pysam/libcalignmentfile.pyx [new file with mode: 0644]
pysam/libcbcf.pxd [new file with mode: 0644]
pysam/libcbcf.pyx [new file with mode: 0644]
pysam/libcbcftools.pxd [new file with mode: 0644]
pysam/libcbcftools.pyx [new file with mode: 0644]
pysam/libcbgzf.pyx [new file with mode: 0644]
pysam/libcfaidx.pxd [new file with mode: 0644]
pysam/libcfaidx.pyx [new file with mode: 0644]
pysam/libchtslib.pxd [new file with mode: 0644]
pysam/libchtslib.pyx [new file with mode: 0644]
pysam/libcsamfile.pxd [new file with mode: 0644]
pysam/libcsamfile.pyx [new file with mode: 0644]
pysam/libcsamtools.pxd [new file with mode: 0644]
pysam/libcsamtools.pyx [new file with mode: 0644]
pysam/libctabix.pxd [new file with mode: 0644]
pysam/libctabix.pyx [new file with mode: 0644]
pysam/libctabixproxies.pxd [new file with mode: 0644]
pysam/libctabixproxies.pyx [new file with mode: 0644]
pysam/libcutils.pxd [new file with mode: 0644]
pysam/libcutils.pyx [new file with mode: 0644]
pysam/libcvcf.pxd [new file with mode: 0644]
pysam/libcvcf.pyx [new file with mode: 0644]
pysam/namedtuple.py [new file with mode: 0644]
pysam/pysam_stream.h [new file with mode: 0644]
pysam/pysam_util.c [new file with mode: 0644]
pysam/pysam_util.h [new file with mode: 0644]
pysam/samfile_util.c [new file with mode: 0644]
pysam/samfile_util.h [new file with mode: 0644]
pysam/samtools.py [new file with mode: 0644]
pysam/tabix_util.c [new file with mode: 0644]
pysam/tabix_util.h [new file with mode: 0644]
pysam/utils.py [new file with mode: 0644]
pysam/version.py [new file with mode: 0644]
requirements.txt [new file with mode: 0644]
run_tests_travis.sh [new file with mode: 0755]
samtools/bam.c [new file with mode: 0644]
samtools/bam.c.pysam.c [new file with mode: 0644]
samtools/bam.h [new file with mode: 0644]
samtools/bam2bcf.c [new file with mode: 0644]
samtools/bam2bcf.c.pysam.c [new file with mode: 0644]
samtools/bam2bcf.h [new file with mode: 0644]
samtools/bam2bcf_indel.c [new file with mode: 0644]
samtools/bam2bcf_indel.c.pysam.c [new file with mode: 0644]
samtools/bam2depth.c [new file with mode: 0644]
samtools/bam2depth.c.pysam.c [new file with mode: 0644]
samtools/bam_addrprg.c [new file with mode: 0644]
samtools/bam_addrprg.c.pysam.c [new file with mode: 0644]
samtools/bam_aux.c [new file with mode: 0644]
samtools/bam_aux.c.pysam.c [new file with mode: 0644]
samtools/bam_cat.c [new file with mode: 0644]
samtools/bam_cat.c.pysam.c [new file with mode: 0644]
samtools/bam_color.c [new file with mode: 0644]
samtools/bam_color.c.pysam.c [new file with mode: 0644]
samtools/bam_endian.h [new file with mode: 0644]
samtools/bam_flags.c [new file with mode: 0644]
samtools/bam_flags.c.pysam.c [new file with mode: 0644]
samtools/bam_import.c [new file with mode: 0644]
samtools/bam_import.c.pysam.c [new file with mode: 0644]
samtools/bam_index.c [new file with mode: 0644]
samtools/bam_index.c.pysam.c [new file with mode: 0644]
samtools/bam_lpileup.c [new file with mode: 0644]
samtools/bam_lpileup.c.pysam.c [new file with mode: 0644]
samtools/bam_lpileup.h [new file with mode: 0644]
samtools/bam_mate.c [new file with mode: 0644]
samtools/bam_mate.c.pysam.c [new file with mode: 0644]
samtools/bam_md.c [new file with mode: 0644]
samtools/bam_md.c.pysam.c [new file with mode: 0644]
samtools/bam_plbuf.c [new file with mode: 0644]
samtools/bam_plbuf.c.pysam.c [new file with mode: 0644]
samtools/bam_plbuf.h [new file with mode: 0644]
samtools/bam_plcmd.c [new file with mode: 0644]
samtools/bam_plcmd.c.pysam.c [new file with mode: 0644]
samtools/bam_quickcheck.c [new file with mode: 0644]
samtools/bam_quickcheck.c.pysam.c [new file with mode: 0644]
samtools/bam_reheader.c [new file with mode: 0644]
samtools/bam_reheader.c.pysam.c [new file with mode: 0644]
samtools/bam_rmdup.c [new file with mode: 0644]
samtools/bam_rmdup.c.pysam.c [new file with mode: 0644]
samtools/bam_rmdupse.c [new file with mode: 0644]
samtools/bam_rmdupse.c.pysam.c [new file with mode: 0644]
samtools/bam_sort.c [new file with mode: 0644]
samtools/bam_sort.c.pysam.c [new file with mode: 0644]
samtools/bam_split.c [new file with mode: 0644]
samtools/bam_split.c.pysam.c [new file with mode: 0644]
samtools/bam_stat.c [new file with mode: 0644]
samtools/bam_stat.c.pysam.c [new file with mode: 0644]
samtools/bamshuf.c [new file with mode: 0644]
samtools/bamshuf.c.pysam.c [new file with mode: 0644]
samtools/bamtk.c [new file with mode: 0644]
samtools/bamtk.c.pysam.c [new file with mode: 0644]
samtools/bedcov.c [new file with mode: 0644]
samtools/bedcov.c.pysam.c [new file with mode: 0644]
samtools/bedidx.c [new file with mode: 0644]
samtools/bedidx.c.pysam.c [new file with mode: 0644]
samtools/cut_target.c [new file with mode: 0644]
samtools/cut_target.c.pysam.c [new file with mode: 0644]
samtools/dict.c [new file with mode: 0644]
samtools/dict.c.pysam.c [new file with mode: 0644]
samtools/faidx.c [new file with mode: 0644]
samtools/faidx.c.pysam.c [new file with mode: 0644]
samtools/misc/ace2sam.c [new file with mode: 0644]
samtools/misc/ace2sam.c.pysam.c [new file with mode: 0644]
samtools/padding.c [new file with mode: 0644]
samtools/padding.c.pysam.c [new file with mode: 0644]
samtools/phase.c [new file with mode: 0644]
samtools/phase.c.pysam.c [new file with mode: 0644]
samtools/pysam.h [new file with mode: 0644]
samtools/sam.c [new file with mode: 0644]
samtools/sam.c.pysam.c [new file with mode: 0644]
samtools/sam.h [new file with mode: 0644]
samtools/sam_header.c [new file with mode: 0644]
samtools/sam_header.c.pysam.c [new file with mode: 0644]
samtools/sam_header.h [new file with mode: 0644]
samtools/sam_opts.c [new file with mode: 0644]
samtools/sam_opts.c.pysam.c [new file with mode: 0644]
samtools/sam_opts.h [new file with mode: 0644]
samtools/sam_utils.c [new file with mode: 0644]
samtools/sam_utils.c.pysam.c [new file with mode: 0644]
samtools/sam_view.c [new file with mode: 0644]
samtools/sam_view.c.pysam.c [new file with mode: 0644]
samtools/sample.c [new file with mode: 0644]
samtools/sample.c.pysam.c [new file with mode: 0644]
samtools/sample.h [new file with mode: 0644]
samtools/samtools.h [new file with mode: 0644]
samtools/stats.c [new file with mode: 0644]
samtools/stats.c.pysam.c [new file with mode: 0644]
samtools/stats_isize.c [new file with mode: 0644]
samtools/stats_isize.c.pysam.c [new file with mode: 0644]
samtools/stats_isize.h [new file with mode: 0644]
samtools/test/merge/test_bam_translate.c [new file with mode: 0644]
samtools/test/merge/test_bam_translate.c.pysam.c [new file with mode: 0644]
samtools/test/merge/test_rtrans_build.c [new file with mode: 0644]
samtools/test/merge/test_rtrans_build.c.pysam.c [new file with mode: 0644]
samtools/test/merge/test_trans_tbl_init.c [new file with mode: 0644]
samtools/test/merge/test_trans_tbl_init.c.pysam.c [new file with mode: 0644]
samtools/test/split/test_count_rg.c [new file with mode: 0644]
samtools/test/split/test_count_rg.c.pysam.c [new file with mode: 0644]
samtools/test/split/test_expand_format_string.c [new file with mode: 0644]
samtools/test/split/test_expand_format_string.c.pysam.c [new file with mode: 0644]
samtools/test/split/test_filter_header_rg.c [new file with mode: 0644]
samtools/test/split/test_filter_header_rg.c.pysam.c [new file with mode: 0644]
samtools/test/split/test_parse_args.c [new file with mode: 0644]
samtools/test/split/test_parse_args.c.pysam.c [new file with mode: 0644]
samtools/test/test.c [new file with mode: 0644]
samtools/test/test.c.pysam.c [new file with mode: 0644]
samtools/test/test.h [new file with mode: 0644]
samtools/test/tview/test_get_rg_sample.c [new file with mode: 0644]
samtools/test/tview/test_get_rg_sample.c.pysam.c [new file with mode: 0644]
samtools/version.h [new file with mode: 0644]
samtools/win32/xcurses.h [new file with mode: 0644]
samtools/win32/zconf.h [new file with mode: 0644]
samtools/win32/zlib.h [new file with mode: 0644]
save/example.py [new file with mode: 0644]
save/pysam_bench.py [new file with mode: 0644]
save/pysam_test2.6.py [new file with mode: 0755]
save/pysam_test_stdin.py [new file with mode: 0644]
save/pysam_testpp.py [new file with mode: 0644]
save/segfault_tests.py [new file with mode: 0755]
save/vcf_test.py [new file with mode: 0644]
setup.cfg [new file with mode: 0644]
setup.py [new file with mode: 0644]
tests/00README.txt [new file with mode: 0644]
tests/AlignedSegment_test.py [new file with mode: 0644]
tests/AlignmentFile_test.py [new file with mode: 0644]
tests/StreamFiledescriptors_test.py [new file with mode: 0644]
tests/TestUtils.py [new file with mode: 0644]
tests/VariantFile_test.py [new file with mode: 0644]
tests/_compile_test.pyx [new file with mode: 0644]
tests/_compile_test.pyxbld [new file with mode: 0644]
tests/_cython_flagstat.pyx [new file with mode: 0644]
tests/_cython_flagstat.pyxbld [new file with mode: 0644]
tests/cbcf_data/Makefile [new file with mode: 0644]
tests/cbcf_data/example_empty.vcf [new file with mode: 0644]
tests/cbcf_data/example_vcf40.vcf [new file with mode: 0644]
tests/cbcf_data/example_vcf42.vcf [new file with mode: 0644]
tests/cbcf_data/example_vcf42_only_header.vcf [new file with mode: 0644]
tests/cbcf_data/example_vcf42_withcontigs.vcf [new file with mode: 0644]
tests/cbcf_data/missing_genotypes.vcf [new file with mode: 0644]
tests/compile_test.py [new file with mode: 0644]
tests/faidx_test.py [new file with mode: 0644]
tests/linking_test.py [new file with mode: 0644]
tests/pysam_data/Makefile [new file with mode: 0644]
tests/pysam_data/ex1.bed [new file with mode: 0644]
tests/pysam_data/ex1.fa [new file with mode: 0644]
tests/pysam_data/ex1.sam.gz [new file with mode: 0644]
tests/pysam_data/ex1.vcf.gz [new file with mode: 0644]
tests/pysam_data/ex1.vcf.gz.tbi [new file with mode: 0644]
tests/pysam_data/ex10.sam [new file with mode: 0644]
tests/pysam_data/ex3.sam [new file with mode: 0644]
tests/pysam_data/ex4.sam [new file with mode: 0644]
tests/pysam_data/ex5.sam [new file with mode: 0644]
tests/pysam_data/ex6.sam [new file with mode: 0644]
tests/pysam_data/ex7.sam.donottest [new file with mode: 0644]
tests/pysam_data/ex8.sam [new file with mode: 0644]
tests/pysam_data/ex9_fail.sam [new file with mode: 0644]
tests/pysam_data/ex9_nofail.sam [new file with mode: 0644]
tests/pysam_data/ex_spliced.sam [new file with mode: 0644]
tests/pysam_data/example_aligned_pairs.sam [new file with mode: 0644]
tests/pysam_data/example_btag.sam [new file with mode: 0644]
tests/pysam_data/example_empty_header.sam [new file with mode: 0644]
tests/pysam_data/example_empty_with_header.sam [new file with mode: 0644]
tests/pysam_data/example_unmapped_reads_no_sq.sam [new file with mode: 0644]
tests/pysam_data/example_user_header.sam [new file with mode: 0644]
tests/pysam_data/faidx_empty_seq.fq [new file with mode: 0644]
tests/pysam_data/faidx_ex1.fa [new file with mode: 0644]
tests/pysam_data/faidx_ex1.fq [new file with mode: 0644]
tests/pysam_data/issue100.sam [new file with mode: 0644]
tests/pysam_data/rg_with_tab.sam [new file with mode: 0644]
tests/pysam_data/softclip.sam [new file with mode: 0644]
tests/pysam_data/tag_bug.sam [new file with mode: 0644]
tests/pysam_data/test.gtf [new file with mode: 0644]
tests/pysam_data/test.gtf.gz [new file with mode: 0644]
tests/pysam_data/test_mapped_unmapped.sam [new file with mode: 0644]
tests/pysam_data/test_query_position.sam [new file with mode: 0644]
tests/pysam_data/test_unaligned.sam [new file with mode: 0644]
tests/refactoring.pl [new file with mode: 0644]
tests/refactoring.txt [new file with mode: 0644]
tests/samtools_test.py [new file with mode: 0644]
tests/tabix_data/empty.bed.gz [new file with mode: 0644]
tests/tabix_data/empty.bed.gz.tbi [new file with mode: 0644]
tests/tabix_data/example.bed.gz [new file with mode: 0644]
tests/tabix_data/example.bed.gz.tbi [new file with mode: 0644]
tests/tabix_data/example.gff2.gz [new file with mode: 0644]
tests/tabix_data/example.gff2.gz.tbi [new file with mode: 0644]
tests/tabix_data/example.gff3.gz [new file with mode: 0644]
tests/tabix_data/example.gff3.gz.tbi [new file with mode: 0644]
tests/tabix_data/example.gtf.gz [new file with mode: 0644]
tests/tabix_data/example.gtf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example.sam.gz [new file with mode: 0644]
tests/tabix_data/example.sam.gz.tbi [new file with mode: 0644]
tests/tabix_data/example.vcf.gz [new file with mode: 0644]
tests/tabix_data/example.vcf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example.vcf40 [new file with mode: 0644]
tests/tabix_data/example_0v23.bed.gz [new file with mode: 0644]
tests/tabix_data/example_0v23.bed.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_0v23.vcf.gz [new file with mode: 0644]
tests/tabix_data/example_0v23.vcf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_0v26.bed.gz [new file with mode: 0644]
tests/tabix_data/example_0v26.bed.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_0v26.vcf.gz [new file with mode: 0644]
tests/tabix_data/example_0v26.vcf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_badcomments.bed.gz [new file with mode: 0644]
tests/tabix_data/example_badcomments.bed.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_badcomments.gtf.gz [new file with mode: 0644]
tests/tabix_data/example_badcomments.gtf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_badcomments.sam.gz [new file with mode: 0644]
tests/tabix_data/example_badcomments.sam.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_badcomments.vcf.gz [new file with mode: 0644]
tests/tabix_data/example_badcomments.vcf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_comments.bed.gz [new file with mode: 0644]
tests/tabix_data/example_comments.bed.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_comments.gtf.gz [new file with mode: 0644]
tests/tabix_data/example_comments.gtf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_comments.sam.gz [new file with mode: 0644]
tests/tabix_data/example_comments.sam.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_comments.vcf.gz [new file with mode: 0644]
tests/tabix_data/example_comments.vcf.gz.tbi [new file with mode: 0644]
tests/tabix_data/example_unicode.vcf [new file with mode: 0644]
tests/tabix_data/gtf_toofew_fields.gtf.gz [new file with mode: 0644]
tests/tabix_data/gtf_toomany_fields.gtf.gz [new file with mode: 0644]
tests/tabix_data/gtf_wrong_fields.gtf.gz [new file with mode: 0644]
tests/tabix_data/vcf/10.vcf [new file with mode: 0644]
tests/tabix_data/vcf/11.vcf [new file with mode: 0644]
tests/tabix_data/vcf/12.vcf [new file with mode: 0644]
tests/tabix_data/vcf/13.vcf [new file with mode: 0644]
tests/tabix_data/vcf/15.vcf [new file with mode: 0644]
tests/tabix_data/vcf/16.vcf [new file with mode: 0644]
tests/tabix_data/vcf/18.vcf [new file with mode: 0644]
tests/tabix_data/vcf/2.vcf [new file with mode: 0644]
tests/tabix_data/vcf/20.vcf [new file with mode: 0644]
tests/tabix_data/vcf/21.vcf [new file with mode: 0644]
tests/tabix_data/vcf/22.vcf [new file with mode: 0644]
tests/tabix_data/vcf/23.vcf [new file with mode: 0644]
tests/tabix_data/vcf/24.vcf [new file with mode: 0644]
tests/tabix_data/vcf/3.vcf [new file with mode: 0644]
tests/tabix_data/vcf/4.vcf [new file with mode: 0644]
tests/tabix_data/vcf/5.vcf [new file with mode: 0644]
tests/tabix_data/vcf/6.vcf [new file with mode: 0644]
tests/tabix_data/vcf/7.vcf [new file with mode: 0644]
tests/tabix_data/vcf/8.vcf [new file with mode: 0644]
tests/tabix_data/vcf/9.vcf [new file with mode: 0644]
tests/tabix_data/vcf/README.txt [new file with mode: 0644]
tests/tabix_data/vcf/issue85.vcf [new file with mode: 0644]
tests/tabix_data/vcf/vcf_v42.vcf [new file with mode: 0644]
tests/tabix_test.py [new file with mode: 0644]
tests/tabixproxies_test.py [new file with mode: 0644]
tests/test_samtools_python.py [new file with mode: 0644]
win32/getopt.c [new file with mode: 0644]
win32/getopt.h [new file with mode: 0644]
win32/stdint.h [new file with mode: 0644]
win32/unistd.h [new file with mode: 0644]