[med-svn] [python-pysam] branch master updated (96af80c -> 7d7c3d2)
Afif Elghraoui
afif at moszumanska.debian.org
Sun Mar 6 07:57:37 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository python-pysam.
from 96af80c python-pysam (0.8.4+ds-1) unstable; urgency=medium
new 66a5ff6 Add filenamemangle to d/watch and space out content
new 364e45a Imported Upstream version 0.9.0+ds
new 3c3562d Merge tag 'upstream/0.9.0+ds'
new 4fd4236 Bump htslib and samtools minimum versions
new c92925d Update policy statndards-version to 3.9.7
new a2862d5 Use encrypted protocols for Vcs URLs in d/control
new 7038dab Use readthedocs page as pysam's homepage
new c2da576 Update packaging for external htslib link due to build system changes
new dfd66a5 Refresh patches
new b17b8fa Delete obsolete patch
new 68d7dfd Prepare new revision
new bcff0a2 Update patch for external HTSlib
new d54a163 Update d/rules clean target
new 905db6e Update python-pysam-test lintian overrides
new 684ab0b Update d/rules to allow package to build
new 93b27e8 Clean up d/control
new 0ad90be Support running tests requiring bcftools
new 9a1905f Add copyright information for debian/*
new f183121 Remove trailing whitespace from d/copyright
new 7410bf3 Update d/copyright
new 7d7c3d2 Disable setting rpath for compiled modules
The 21 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/changelog | 14 +
debian/control | 58 +-
debian/copyright | 35 +-
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 -
.../patches/disable-tests-requiring-network.patch | 22 +-
debian/patches/external-htslib.patch | 84 +
debian/patches/ignore-htslib-dir.patch | 27 -
debian/patches/rpath.patch | 22 +
debian/patches/series | 5 +-
debian/python-pysam-tests.lintian-overrides | 3 +
debian/rules | 12 +
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 ++++--
265 files changed, 68663 insertions(+), 7275 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
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/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
create mode 100644 tests/tabix_data/empty.bed.gz.tbi
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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