[med-svn] [python-pysam] 01/02: Merge tag 'debian/0.9.0+ds-1' into debian/jessie-backports
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 commit to branch debian/jessie-backports
in repository python-pysam.
commit a1a62c58fbb98b1f6c21b9f57debd358f877004b
Merge: 07c538d 09caf28
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Apr 9 15:12:49 2016 -0700
Merge tag 'debian/0.9.0+ds-1' into debian/jessie-backports
python-pysam (0.9.0+ds-1) unstable; urgency=medium
* Add filenamemangle to d/watch and space out content
* Imported Upstream version 0.9.0+ds (Closes: #814765)
* Bump htslib and samtools minimum versions
* Update policy statndards-version to 3.9.7
* Use encrypted protocols for Vcs URLs in d/control
* Use readthedocs page as pysam's homepage
* Update packaging for external htslib link
* Refresh patches
* Delete obsolete patch
.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 ++++++++++
samtools/samtools.h => bcftools/convert.h | 41 +-
bcftools/em.c | 259 +++
bcftools/em.c.pysam.c | 261 +++
bcftools/filter.c | 1788 +++++++++++++++++
bcftools/filter.c.pysam.c | 1790 +++++++++++++++++
bcftools/filter.h | 52 +
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 ++
bcftools/kmin.h | 46 +
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 +
bcftools/pysam.h | 5 +
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/samtools.h => bcftools/version.c | 40 +-
samtools/samtools.h => bcftools/version.c.pysam.c | 42 +-
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 | 14 +
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
tests/cbcf_data/example_vcf40.vcf | 24 +
tests/cbcf_data/example_vcf42.vcf | 24 +
tests/cbcf_data/example_vcf42_only_header.vcf | 19 +
tests/cbcf_data/example_vcf42_withcontigs.vcf | 27 +
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
tests/tabix_data/example_0v23.bed.gz | Bin 0 -> 819 bytes
tests/tabix_data/example_0v23.bed.gz.tbi | Bin 0 -> 244 bytes
tests/tabix_data/example_0v23.vcf.gz | Bin 0 -> 328 bytes
tests/tabix_data/example_0v23.vcf.gz.tbi | Bin 0 -> 155 bytes
tests/tabix_data/example_0v26.bed.gz | Bin 0 -> 819 bytes
tests/tabix_data/example_0v26.bed.gz.tbi | Bin 0 -> 244 bytes
tests/tabix_data/example_0v26.vcf.gz | Bin 0 -> 328 bytes
tests/tabix_data/example_0v26.vcf.gz.tbi | Bin 0 -> 155 bytes
tests/tabix_data/vcf/vcf_v42.vcf | 25 +
tests/tabix_test.py | 636 ++++--
268 files changed, 68933 insertions(+), 7245 deletions(-)
diff --cc debian/changelog
index 067444b,ab05c13..36953f7
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,17 +1,23 @@@
+ python-pysam (0.9.0+ds-1) unstable; urgency=medium
+
+ * Add filenamemangle to d/watch and space out content
+ * Imported Upstream version 0.9.0+ds (Closes: #814765)
+ * Bump htslib and samtools minimum versions
+ * Update policy statndards-version to 3.9.7
+ * Use encrypted protocols for Vcs URLs in d/control
+ * Use readthedocs page as pysam's homepage
+ * Update packaging for external htslib link
+ * Refresh patches
+ * Delete obsolete patch
+
+ -- Afif Elghraoui <afif at debian.org> Wed, 09 Mar 2016 23:43:59 -0800
+
+python-pysam (0.8.4+ds-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <afif at ghraoui.name> Fri, 27 Nov 2015 11:54:21 -0800
+
python-pysam (0.8.4+ds-1) unstable; urgency=medium
* Add version constraints to build-dependencies.
--
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