[med-svn] [python-pysam] branch debian/jessie-backports updated (07c538d -> 54f17ad)
Afif Elghraoui
afif at moszumanska.debian.org
Sat Apr 9 22:45:51 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch debian/jessie-backports
in repository python-pysam.
from 07c538d python-pysam (0.8.4+ds-1~bpo8+1) jessie-backports; urgency=medium
adds 66a5ff6 Add filenamemangle to d/watch and space out content
adds 364e45a Imported Upstream version 0.9.0+ds
adds 3c3562d Merge tag 'upstream/0.9.0+ds'
adds 4fd4236 Bump htslib and samtools minimum versions
adds c92925d Update policy statndards-version to 3.9.7
adds a2862d5 Use encrypted protocols for Vcs URLs in d/control
adds 7038dab Use readthedocs page as pysam's homepage
adds c2da576 Update packaging for external htslib link due to build system changes
adds dfd66a5 Refresh patches
adds b17b8fa Delete obsolete patch
adds 68d7dfd Prepare new revision
adds bcff0a2 Update patch for external HTSlib
adds d54a163 Update d/rules clean target
adds 905db6e Update python-pysam-test lintian overrides
adds 684ab0b Update d/rules to allow package to build
adds 93b27e8 Clean up d/control
adds 0ad90be Support running tests requiring bcftools
adds 9a1905f Add copyright information for debian/*
adds f183121 Remove trailing whitespace from d/copyright
adds 7410bf3 Update d/copyright
adds 7d7c3d2 Disable setting rpath for compiled modules
adds fbb7868 Remove copyright declaration for nonexistent files
adds b2e7823 Add tabix as build-dependency to run tests
adds 92640fa Document remaining steps to take before upload
adds c47196e Completely fix rpath issue
adds 624c346 Fix some failing tests
adds 13efc4e Update autopkgtest command and dependencies
adds 09caf28 Finalize changelog
new a1a62c5 Merge tag 'debian/0.9.0+ds-1' into debian/jessie-backports
new 54f17ad releasing package python-pysam version 0.9.0+ds-1~bpo8+1
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 16 +
.hgignore | 7 -
.hgtags | 4 -
.travis.yml | 26 +-
INSTALL | 2 +
MANIFEST.in | 10 +
README.rst | 22 +-
THANKS | 4 -
bcftools/HMM.c | 435 ++++
bcftools/HMM.c.pysam.c | 437 +++++
bcftools/HMM.h | 115 ++
bcftools/bcftools.h | 71 +
bcftools/call.h | 126 ++
bcftools/ccall.c | 343 ++++
bcftools/ccall.c.pysam.c | 345 ++++
bcftools/consensus.c | 658 +++++++
bcftools/consensus.c.pysam.c | 660 +++++++
bcftools/convert.c | 1056 ++++++++++
bcftools/convert.c.pysam.c | 1058 ++++++++++
COPYING => bcftools/convert.h | 29 +-
bcftools/em.c | 259 +++
bcftools/em.c.pysam.c | 261 +++
bcftools/filter.c | 1788 +++++++++++++++++
bcftools/filter.c.pysam.c | 1790 +++++++++++++++++
COPYING => bcftools/filter.h | 37 +-
bcftools/gvcf.c | 227 +++
bcftools/gvcf.c.pysam.c | 229 +++
bcftools/gvcf.h | 41 +
bcftools/khash_str2str.h | 89 +
bcftools/kmin.c | 209 ++
bcftools/kmin.c.pysam.c | 211 ++
samtools/kprobaln.h => bcftools/kmin.h | 25 +-
bcftools/main.c | 264 +++
bcftools/main.c.pysam.c | 266 +++
bcftools/mcall.c | 1537 +++++++++++++++
bcftools/mcall.c.pysam.c | 1539 +++++++++++++++
bcftools/ploidy.c | 254 +++
bcftools/ploidy.c.pysam.c | 256 +++
bcftools/ploidy.h | 129 ++
bcftools/prob1.c | 529 +++++
bcftools/prob1.c.pysam.c | 531 +++++
bcftools/prob1.h | 93 +
{samtools => bcftools}/pysam.h | 0
bcftools/rbuf.h | 201 ++
bcftools/tabix.c | 129 ++
bcftools/tabix.c.pysam.c | 131 ++
bcftools/tsv2vcf.c | 121 ++
bcftools/tsv2vcf.c.pysam.c | 123 ++
bcftools/tsv2vcf.h | 85 +
bcftools/vcfannotate.c | 1760 +++++++++++++++++
bcftools/vcfannotate.c.pysam.c | 1762 +++++++++++++++++
bcftools/vcfcall.c | 822 ++++++++
bcftools/vcfcall.c.pysam.c | 824 ++++++++
bcftools/vcfcnv.c | 1386 +++++++++++++
bcftools/vcfcnv.c.pysam.c | 1388 +++++++++++++
bcftools/vcfconcat.c | 662 +++++++
bcftools/vcfconcat.c.pysam.c | 664 +++++++
bcftools/vcfconvert.c | 1448 ++++++++++++++
bcftools/vcfconvert.c.pysam.c | 1450 ++++++++++++++
bcftools/vcffilter.c | 568 ++++++
bcftools/vcffilter.c.pysam.c | 570 ++++++
bcftools/vcfgtcheck.c | 804 ++++++++
bcftools/vcfgtcheck.c.pysam.c | 806 ++++++++
bcftools/vcfindex.c | 240 +++
bcftools/vcfindex.c.pysam.c | 242 +++
bcftools/vcfisec.c | 596 ++++++
bcftools/vcfisec.c.pysam.c | 598 ++++++
bcftools/vcfmerge.c | 2067 +++++++++++++++++++
bcftools/vcfmerge.c.pysam.c | 2069 ++++++++++++++++++++
bcftools/vcfnorm.c | 1810 +++++++++++++++++
bcftools/vcfnorm.c.pysam.c | 1812 +++++++++++++++++
bcftools/vcfplugin.c | 614 ++++++
bcftools/vcfplugin.c.pysam.c | 616 ++++++
bcftools/vcfquery.c | 373 ++++
bcftools/vcfquery.c.pysam.c | 375 ++++
bcftools/vcfroh.c | 794 ++++++++
bcftools/vcfroh.c.pysam.c | 796 ++++++++
bcftools/vcfsom.c | 715 +++++++
bcftools/vcfsom.c.pysam.c | 717 +++++++
bcftools/vcfstats.c | 1590 +++++++++++++++
bcftools/vcfstats.c.pysam.c | 1592 +++++++++++++++
bcftools/vcfview.c | 746 +++++++
bcftools/vcfview.c.pysam.c | 748 +++++++
bcftools/vcmp.c | 132 ++
bcftools/vcmp.c.pysam.c | 134 ++
bcftools/vcmp.h | 62 +
samtools/test/test.h => bcftools/version.c | 40 +-
.../test.c.pysam.c => bcftools/version.c.pysam.c | 48 +-
bcftools/version.h | 1 +
ci/conda-recipe/build.sh | 8 +
ci/conda-recipe/meta.yaml | 29 +
install-CGAT-tools.sh => ci/install-CGAT-tools.sh | 62 +-
cy_build.py | 87 +
debian/TODO | 4 +
debian/changelog | 20 +
debian/control | 59 +-
debian/copyright | 39 +-
debian/patches/adding-include-hts-dirs | 11 -
.../change-htslib-statement-to-link-to-debian | 25 -
...e-htslib-statement-in-setuppy-to-link-to-debian | 12 -
debian/patches/compile-test.patch | 15 +
.../patches/disable-tests-requiring-network.patch | 75 +-
debian/patches/external-htslib.patch | 84 +
debian/patches/ignore-htslib-dir.patch | 27 -
debian/patches/rpath.patch | 32 +
debian/patches/series | 6 +-
debian/python-pysam-tests.lintian-overrides | 3 +
debian/rules | 12 +
debian/tests/control | 24 +-
debian/watch | 5 +-
doc/api.rst | 30 +-
doc/conf.py | 76 +-
doc/faq.rst | 42 +-
doc/index.rst | 29 +-
doc/installation.rst | 65 +
doc/release.rst | 67 +
doc/usage.rst | 196 +-
import.py | 140 ++
pysam/__init__.py | 202 +-
pysam/bcftools.py | 24 +
pysam/calignedsegment.pxd | 7 +-
pysam/calignedsegment.pyx | 527 ++---
pysam/calignmentfile.pyx | 314 +--
pysam/cbcf.pxd | 9 +-
pysam/cbcf.pyx | 1757 +++++++++++++----
pysam/cfaidx.pxd | 1 +
pysam/cfaidx.pyx | 101 +-
pysam/chtslib.pxd | 286 ++-
pysam/csamtools.pxd | 8 -
pysam/csamtools.pyx | 146 --
pysam/ctabix.pxd | 6 +-
pysam/ctabix.pyx | 90 +-
pysam/cutils.pxd | 16 +-
pysam/cutils.pyx | 243 ++-
pysam/cvcf.pyx | 3 +
pysam/htslib_util.h | 1 +
pysam/pysam_util.c | 106 +-
pysam/pysam_util.h | 2 +
pysam/samtools.py | 46 +
pysam/utils.py | 88 +
pysam/version.py | 6 +-
run_tests_travis.sh | 113 ++
samtools/bam.c | 67 +-
samtools/bam.c.pysam.c | 67 +-
samtools/bam.h | 7 +-
samtools/bam2bcf.c | 75 +-
samtools/bam2bcf.c.pysam.c | 75 +-
samtools/bam2bcf.h | 13 +-
samtools/bam2bcf_indel.c | 14 +-
samtools/bam2bcf_indel.c.pysam.c | 14 +-
samtools/bam2depth.c | 142 +-
samtools/bam2depth.c.pysam.c | 142 +-
samtools/bam_addrprg.c | 476 +++++
samtools/bam_addrprg.c.pysam.c | 478 +++++
samtools/bam_aux.c | 18 +-
samtools/bam_aux.c.pysam.c | 18 +-
samtools/bam_cat.c | 432 +++-
samtools/bam_cat.c.pysam.c | 432 +++-
samtools/bam_index.c | 29 +-
samtools/bam_index.c.pysam.c | 29 +-
samtools/bam_mate.c | 58 +-
samtools/bam_mate.c.pysam.c | 58 +-
samtools/bam_md.c | 173 +-
samtools/bam_md.c.pysam.c | 173 +-
samtools/bam_plcmd.c | 232 ++-
samtools/bam_plcmd.c.pysam.c | 232 ++-
samtools/bam_quickcheck.c | 134 ++
samtools/bam_quickcheck.c.pysam.c | 136 ++
samtools/bam_reheader.c | 437 ++++-
samtools/bam_reheader.c.pysam.c | 438 ++++-
samtools/bam_rmdup.c | 94 +-
samtools/bam_rmdup.c.pysam.c | 94 +-
samtools/bam_rmdupse.c | 31 +-
samtools/bam_rmdupse.c.pysam.c | 31 +-
samtools/bam_sort.c | 1472 ++++++++++----
samtools/bam_sort.c.pysam.c | 1472 ++++++++++----
samtools/bam_split.c | 99 +-
samtools/bam_split.c.pysam.c | 99 +-
samtools/bam_stat.c | 66 +-
samtools/bam_stat.c.pysam.c | 66 +-
samtools/bam_tview.c | 88 +-
samtools/bam_tview.c.pysam.c | 88 +-
samtools/bam_tview.h | 6 +-
samtools/bam_tview_curses.c | 112 +-
samtools/bam_tview_curses.c.pysam.c | 112 +-
samtools/bam_tview_html.c | 10 +-
samtools/bam_tview_html.c.pysam.c | 10 +-
samtools/bamshuf.c | 112 +-
samtools/bamshuf.c.pysam.c | 112 +-
samtools/bamtk.c | 227 +++
samtools/bamtk.c.pysam.c | 229 +++
samtools/bedcov.c | 31 +-
samtools/bedcov.c.pysam.c | 31 +-
samtools/cut_target.c | 70 +-
samtools/cut_target.c.pysam.c | 70 +-
samtools/dict.c | 151 ++
samtools/dict.c.pysam.c | 153 ++
samtools/errmod.c | 4 +-
samtools/errmod.c.pysam.c | 4 +-
samtools/misc/md5.c | 298 ---
samtools/misc/md5.c.pysam.c | 300 ---
samtools/misc/md5.h | 57 -
samtools/padding.c | 287 ++-
samtools/padding.c.pysam.c | 287 ++-
samtools/phase.c | 44 +-
samtools/phase.c.pysam.c | 44 +-
samtools/sam.c | 29 +-
samtools/sam.c.pysam.c | 29 +-
samtools/sam.h | 26 +-
samtools/sam_opts.c | 153 ++
samtools/sam_opts.c.pysam.c | 155 ++
samtools/sam_opts.h | 99 +
samtools/sam_view.c | 795 +++++---
samtools/sam_view.c.pysam.c | 795 +++++---
samtools/samtools.h | 12 +-
samtools/stats.c | 1075 +++++-----
samtools/stats.c.pysam.c | 1075 +++++-----
samtools/test/merge/test_bam_translate.c | 35 +-
samtools/test/merge/test_bam_translate.c.pysam.c | 35 +-
samtools/test/merge/test_pretty_header.c | 87 -
samtools/test/merge/test_pretty_header.c.pysam.c | 89 -
samtools/test/merge/test_trans_tbl_init.c | 415 ++--
samtools/test/merge/test_trans_tbl_init.c.pysam.c | 415 ++--
samtools/test/split/test_count_rg.c | 9 +-
samtools/test/split/test_count_rg.c.pysam.c | 9 +-
samtools/test/split/test_expand_format_string.c | 13 +-
.../test/split/test_expand_format_string.c.pysam.c | 13 +-
samtools/test/split/test_filter_header_rg.c | 15 +-
.../test/split/test_filter_header_rg.c.pysam.c | 15 +-
samtools/test/split/test_parse_args.c | 32 +-
samtools/test/split/test_parse_args.c.pysam.c | 32 +-
samtools/version.h | 2 +-
setup.cfg | 6 -
setup.py | 531 ++---
tests/AlignedSegment_test.py | 94 +-
tests/AlignmentFile_test.py | 288 ++-
tests/SamFile_test.py | 81 +-
tests/TestUtils.py | 55 +-
tests/VariantFile_test.py | 418 ++++
tests/cbcf_data/Makefile | 23 +
KNOWN_BUGS => tests/cbcf_data/example_empty.vcf | 0
.../example.vcf40 => cbcf_data/example_vcf40.vcf} | 1 +
.../example.vcf40 => cbcf_data/example_vcf42.vcf} | 3 +-
.../example_vcf42_only_header.vcf} | 8 +-
.../example_vcf42_withcontigs.vcf} | 12 +-
tests/cbcf_data/missing_genotypes.vcf | 6 +
tests/faidx_test.py | 51 +
tests/pysam_data/Makefile | 22 +-
tests/pysam_data/ex1.vcf.gz | Bin 0 -> 16982 bytes
tests/pysam_data/ex1.vcf.gz.tbi | Bin 0 -> 5636 bytes
tests/pysam_data/example_aligned_pairs.sam | 81 +
tests/pysam_data/example_empty_with_header.sam | 1 +
tests/pysam_data/faidx_empty_seq.fq | 40 +
tests/pysam_data/test_mapped_unmapped.sam | 17 +
tests/pysam_data/test_query_position.sam | 9 +
tests/samtools_test.py | 535 +++--
tests/tabix_data/empty.bed.gz | Bin 0 -> 28 bytes
tests/tabix_data/empty.bed.gz.tbi | Bin 0 -> 75 bytes
.../{example.bed.gz => example_0v23.bed.gz} | Bin
tests/tabix_data/example_0v23.bed.gz.tbi | Bin 0 -> 244 bytes
.../{example.vcf.gz => example_0v23.vcf.gz} | Bin
tests/tabix_data/example_0v23.vcf.gz.tbi | Bin 0 -> 155 bytes
.../{example.bed.gz => example_0v26.bed.gz} | Bin
tests/tabix_data/example_0v26.bed.gz.tbi | Bin 0 -> 244 bytes
.../{example.vcf.gz => example_0v26.vcf.gz} | Bin
tests/tabix_data/example_0v26.vcf.gz.tbi | Bin 0 -> 155 bytes
.../tabix_data/{example.vcf40 => vcf/vcf_v42.vcf} | 14 +-
tests/tabix_test.py | 636 ++++--
268 files changed, 68774 insertions(+), 7282 deletions(-)
delete mode 100644 .hgignore
delete mode 100644 .hgtags
delete mode 100644 THANKS
create mode 100644 bcftools/HMM.c
create mode 100644 bcftools/HMM.c.pysam.c
create mode 100644 bcftools/HMM.h
create mode 100644 bcftools/bcftools.h
create mode 100644 bcftools/call.h
create mode 100644 bcftools/ccall.c
create mode 100644 bcftools/ccall.c.pysam.c
create mode 100644 bcftools/consensus.c
create mode 100644 bcftools/consensus.c.pysam.c
create mode 100644 bcftools/convert.c
create mode 100644 bcftools/convert.c.pysam.c
copy COPYING => bcftools/convert.h (58%)
create mode 100644 bcftools/em.c
create mode 100644 bcftools/em.c.pysam.c
create mode 100644 bcftools/filter.c
create mode 100644 bcftools/filter.c.pysam.c
copy COPYING => bcftools/filter.h (51%)
create mode 100644 bcftools/gvcf.c
create mode 100644 bcftools/gvcf.c.pysam.c
create mode 100644 bcftools/gvcf.h
create mode 100644 bcftools/khash_str2str.h
create mode 100644 bcftools/kmin.c
create mode 100644 bcftools/kmin.c.pysam.c
copy samtools/kprobaln.h => bcftools/kmin.h (71%)
create mode 100644 bcftools/main.c
create mode 100644 bcftools/main.c.pysam.c
create mode 100644 bcftools/mcall.c
create mode 100644 bcftools/mcall.c.pysam.c
create mode 100644 bcftools/ploidy.c
create mode 100644 bcftools/ploidy.c.pysam.c
create mode 100644 bcftools/ploidy.h
create mode 100644 bcftools/prob1.c
create mode 100644 bcftools/prob1.c.pysam.c
create mode 100644 bcftools/prob1.h
copy {samtools => bcftools}/pysam.h (100%)
create mode 100644 bcftools/rbuf.h
create mode 100644 bcftools/tabix.c
create mode 100644 bcftools/tabix.c.pysam.c
create mode 100644 bcftools/tsv2vcf.c
create mode 100644 bcftools/tsv2vcf.c.pysam.c
create mode 100644 bcftools/tsv2vcf.h
create mode 100644 bcftools/vcfannotate.c
create mode 100644 bcftools/vcfannotate.c.pysam.c
create mode 100644 bcftools/vcfcall.c
create mode 100644 bcftools/vcfcall.c.pysam.c
create mode 100644 bcftools/vcfcnv.c
create mode 100644 bcftools/vcfcnv.c.pysam.c
create mode 100644 bcftools/vcfconcat.c
create mode 100644 bcftools/vcfconcat.c.pysam.c
create mode 100644 bcftools/vcfconvert.c
create mode 100644 bcftools/vcfconvert.c.pysam.c
create mode 100644 bcftools/vcffilter.c
create mode 100644 bcftools/vcffilter.c.pysam.c
create mode 100644 bcftools/vcfgtcheck.c
create mode 100644 bcftools/vcfgtcheck.c.pysam.c
create mode 100644 bcftools/vcfindex.c
create mode 100644 bcftools/vcfindex.c.pysam.c
create mode 100644 bcftools/vcfisec.c
create mode 100644 bcftools/vcfisec.c.pysam.c
create mode 100644 bcftools/vcfmerge.c
create mode 100644 bcftools/vcfmerge.c.pysam.c
create mode 100644 bcftools/vcfnorm.c
create mode 100644 bcftools/vcfnorm.c.pysam.c
create mode 100644 bcftools/vcfplugin.c
create mode 100644 bcftools/vcfplugin.c.pysam.c
create mode 100644 bcftools/vcfquery.c
create mode 100644 bcftools/vcfquery.c.pysam.c
create mode 100644 bcftools/vcfroh.c
create mode 100644 bcftools/vcfroh.c.pysam.c
create mode 100644 bcftools/vcfsom.c
create mode 100644 bcftools/vcfsom.c.pysam.c
create mode 100644 bcftools/vcfstats.c
create mode 100644 bcftools/vcfstats.c.pysam.c
create mode 100644 bcftools/vcfview.c
create mode 100644 bcftools/vcfview.c.pysam.c
create mode 100644 bcftools/vcmp.c
create mode 100644 bcftools/vcmp.c.pysam.c
create mode 100644 bcftools/vcmp.h
copy samtools/test/test.h => bcftools/version.c (57%)
copy samtools/test/test.c.pysam.c => bcftools/version.c.pysam.c (56%)
create mode 100644 bcftools/version.h
create mode 100644 ci/conda-recipe/build.sh
create mode 100644 ci/conda-recipe/meta.yaml
rename install-CGAT-tools.sh => ci/install-CGAT-tools.sh (84%)
create mode 100644 cy_build.py
create mode 100644 debian/TODO
delete mode 100644 debian/patches/adding-include-hts-dirs
delete mode 100644 debian/patches/change-htslib-statement-to-link-to-debian
delete mode 100644 debian/patches/chenge-htslib-statement-in-setuppy-to-link-to-debian
create mode 100644 debian/patches/compile-test.patch
create mode 100644 debian/patches/external-htslib.patch
delete mode 100644 debian/patches/ignore-htslib-dir.patch
create mode 100644 debian/patches/rpath.patch
create mode 100644 doc/installation.rst
create mode 100644 import.py
create mode 100644 pysam/bcftools.py
delete mode 100644 pysam/csamtools.pxd
delete mode 100644 pysam/csamtools.pyx
create mode 100644 pysam/samtools.py
create mode 100644 pysam/utils.py
create mode 100755 run_tests_travis.sh
create mode 100644 samtools/bam_addrprg.c
create mode 100644 samtools/bam_addrprg.c.pysam.c
create mode 100644 samtools/bam_quickcheck.c
create mode 100644 samtools/bam_quickcheck.c.pysam.c
create mode 100644 samtools/bamtk.c
create mode 100644 samtools/bamtk.c.pysam.c
create mode 100644 samtools/dict.c
create mode 100644 samtools/dict.c.pysam.c
delete mode 100644 samtools/misc/md5.c
delete mode 100644 samtools/misc/md5.c.pysam.c
delete mode 100644 samtools/misc/md5.h
create mode 100644 samtools/sam_opts.c
create mode 100644 samtools/sam_opts.c.pysam.c
create mode 100644 samtools/sam_opts.h
delete mode 100644 samtools/test/merge/test_pretty_header.c
delete mode 100644 samtools/test/merge/test_pretty_header.c.pysam.c
delete mode 100644 setup.cfg
create mode 100644 tests/VariantFile_test.py
create mode 100644 tests/cbcf_data/Makefile
rename KNOWN_BUGS => tests/cbcf_data/example_empty.vcf (100%)
copy tests/{tabix_data/example.vcf40 => cbcf_data/example_vcf40.vcf} (96%)
copy tests/{tabix_data/example.vcf40 => cbcf_data/example_vcf42.vcf} (95%)
copy tests/{tabix_data/example.vcf40 => cbcf_data/example_vcf42_only_header.vcf} (65%)
copy tests/{tabix_data/example.vcf40 => cbcf_data/example_vcf42_withcontigs.vcf} (85%)
create mode 100644 tests/cbcf_data/missing_genotypes.vcf
create mode 100644 tests/pysam_data/ex1.vcf.gz
create mode 100644 tests/pysam_data/ex1.vcf.gz.tbi
create mode 100644 tests/pysam_data/example_aligned_pairs.sam
create mode 100644 tests/pysam_data/example_empty_with_header.sam
create mode 100644 tests/pysam_data/faidx_empty_seq.fq
create mode 100644 tests/pysam_data/test_mapped_unmapped.sam
create mode 100644 tests/pysam_data/test_query_position.sam
create mode 100644 tests/tabix_data/empty.bed.gz
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copy tests/tabix_data/{example.bed.gz => example_0v23.bed.gz} (100%)
create mode 100644 tests/tabix_data/example_0v23.bed.gz.tbi
copy tests/tabix_data/{example.vcf.gz => example_0v23.vcf.gz} (100%)
create mode 100644 tests/tabix_data/example_0v23.vcf.gz.tbi
copy tests/tabix_data/{example.bed.gz => example_0v26.bed.gz} (100%)
create mode 100644 tests/tabix_data/example_0v26.bed.gz.tbi
copy tests/tabix_data/{example.vcf.gz => example_0v26.vcf.gz} (100%)
create mode 100644 tests/tabix_data/example_0v26.vcf.gz.tbi
copy tests/tabix_data/{example.vcf40 => vcf/vcf_v42.vcf} (66%)
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