[med-svn] [python-pysam] branch upstream updated (18e4903 -> 364e45a)
Afif Elghraoui
afif at moszumanska.debian.org
Sun Mar 6 07:57:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository python-pysam.
from 18e4903 Imported Upstream version 0.8.4+ds
new 364e45a Imported Upstream version 0.9.0+ds
The 1 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 +
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 ++++--
251 files changed, 68461 insertions(+), 7142 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 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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