[med-svn] [python-pysam] branch debian/jessie-backports updated (54f17ad -> 82d5aed)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Aug 22 06:39:09 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 54f17ad releasing package python-pysam version 0.9.0+ds-1~bpo8+1
adds f470810 Imported Upstream version 0.9.1+ds
adds f2ee928 Merge tag 'upstream/0.9.1+ds'
adds b7bb657 Force at least matching versions of the samtools suite
adds 122bb6d Bump Standards-Version to 3.9.8
adds 2443a95 Prepare new revision
adds 9715aba Globally use C.UTF-8 locale
adds d08e2fd Update patch for external htslib
adds 681de8a Refresh patch
adds 9e08301 Drop obsolete patches
adds 298ee9a Fix handling of configuration headers generated at build time
adds 846ad26 Rely more on pybuild for build-time tests
adds 21ea7ea Fix autopkgtests
adds b872a94 releasing package python-pysam version 0.9.1+ds-1
adds 6528922 Imported Upstream version 0.9.1.4+ds
adds 735a6d3 Merge tag 'upstream/0.9.1.4+ds'
adds 6d8e9e3 Drop patch applied upstream
adds 56b6f2f Drop unused lintian overrides
adds cd54fe4 Fix spelling issues (forwarded)
adds fca3a7d releasing package python-pysam version 0.9.1.4+ds-1
new 9743ded Merge tag 'debian/0.9.1.4+ds-1' into debian/jessie-backports
new d55021e Bump minimum dh-python (pybuild) version
new 82d5aed releasing package python-pysam version 0.9.1.4+ds-1~bpo8+1
The 3 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:
INSTALL | 14 +-
MANIFEST.in | 4 +
README.rst | 12 +-
bcftools/bcftools.h | 3 +-
bcftools/consensus.c | 2 +-
bcftools/consensus.c.pysam.c | 48 +--
bcftools/convert.c.pysam.c | 8 +-
bcftools/em.c.pysam.c | 8 +-
bcftools/filter.c.pysam.c | 22 +-
bcftools/khash_str2str.h | 19 +-
bcftools/main.c | 4 +-
bcftools/main.c.pysam.c | 18 +-
bcftools/mcall.c.pysam.c | 20 +-
bcftools/ploidy.c | 30 +-
bcftools/ploidy.c.pysam.c | 30 +-
bcftools/prob1.c.pysam.c | 8 +-
bcftools/pysam.h | 4 +-
bcftools/tabix.c.pysam.c | 34 +-
bcftools/vcfannotate.c | 212 ++++++++--
bcftools/vcfannotate.c.pysam.c | 256 +++++++++---
bcftools/vcfcall.c | 43 +-
bcftools/vcfcall.c.pysam.c | 155 +++++---
bcftools/vcfcnv.c.pysam.c | 84 ++--
bcftools/vcfconcat.c | 139 ++++++-
bcftools/vcfconcat.c.pysam.c | 187 +++++++--
bcftools/vcfconvert.c | 18 +-
bcftools/vcfconvert.c.pysam.c | 196 +++++-----
bcftools/vcffilter.c | 8 +-
bcftools/vcffilter.c.pysam.c | 50 +--
bcftools/vcfgtcheck.c.pysam.c | 52 +--
bcftools/vcfindex.c | 3 +-
bcftools/vcfindex.c.pysam.c | 67 ++--
bcftools/vcfisec.c | 12 +-
bcftools/vcfisec.c.pysam.c | 84 ++--
bcftools/vcfmerge.c | 10 +-
bcftools/vcfmerge.c.pysam.c | 96 ++---
bcftools/vcfnorm.c | 20 +-
bcftools/vcfnorm.c.pysam.c | 76 ++--
bcftools/vcfplugin.c | 41 +-
bcftools/vcfplugin.c.pysam.c | 127 +++---
bcftools/vcfquery.c.pysam.c | 52 +--
bcftools/vcfroh.c | 43 +-
bcftools/vcfroh.c.pysam.c | 107 +++--
bcftools/vcfsom.c.pysam.c | 56 +--
bcftools/vcfstats.c.pysam.c | 242 ++++++------
bcftools/vcfview.c | 8 +-
bcftools/vcfview.c.pysam.c | 102 ++---
bcftools/version.c.pysam.c | 2 +-
bcftools/version.h | 2 +-
cy_build.py | 7 +-
debian/TODO | 4 -
debian/changelog | 32 ++
debian/control | 10 +-
debian/patches/compile-test.patch | 15 -
.../patches/disable-tests-requiring-network.patch | 89 -----
debian/patches/external-htslib.patch | 84 ----
debian/patches/rpath.patch | 2 +-
debian/patches/series | 4 +-
debian/patches/spelling.patch | 91 +++++
debian/python-pysam.lintian-overrides | 2 -
debian/rules | 43 +-
debian/tests/control | 8 +-
doc/faq.rst | 2 +-
doc/glossary.rst | 3 +-
doc/installation.rst | 5 -
doc/release.rst | 20 +
import.py | 82 +++-
pysam/__init__.py | 2 +
pysam/calignedsegment.pyx | 127 +++++-
pysam/calignmentfile.pxd | 1 +
pysam/calignmentfile.pyx | 54 ++-
pysam/cbcf.pyx | 2 +-
pysam/cfaidx.pxd | 12 +-
pysam/cfaidx.pyx | 44 ++-
pysam/chtslib.pxd | 39 +-
pysam/ctabix.pxd | 13 +-
pysam/ctabix.pyx | 27 +-
pysam/ctabixproxies.pyx | 68 +++-
pysam/cutils.pxd | 3 +
pysam/cutils.pyx | 212 ++++------
pysam/cvcf.pyx | 13 +-
pysam/pysam_stream.h | 3 +-
pysam/pysam_util.c | 50 ++-
pysam/pysam_util.h | 19 +-
pysam/tabix_util.c | 2 -
pysam/utils.py | 20 +-
pysam/version.py | 6 +-
run_tests_travis.sh | 76 +++-
samtools/bam.c | 18 +-
samtools/bam.c.pysam.c | 18 +-
samtools/bam.h | 9 +-
samtools/bam2bcf.c | 2 +
samtools/bam2bcf.c.pysam.c | 10 +-
samtools/bam2bcf_indel.c | 2 +
samtools/bam2bcf_indel.c.pysam.c | 22 +-
samtools/bam2depth.c | 2 +
samtools/bam2depth.c.pysam.c | 70 ++--
samtools/bam_addrprg.c | 2 +
samtools/bam_addrprg.c.pysam.c | 42 +-
samtools/bam_aux.c | 2 +
samtools/bam_aux.c.pysam.c | 2 +
samtools/bam_cat.c | 93 +++--
samtools/bam_cat.c.pysam.c | 121 ++++--
samtools/bam_color.c | 2 +
samtools/bam_color.c.pysam.c | 2 +
samtools/bam_flags.c | 2 +
samtools/bam_flags.c.pysam.c | 42 +-
samtools/bam_import.c | 2 +
samtools/bam_import.c.pysam.c | 4 +-
samtools/bam_index.c | 2 +
samtools/bam_index.c.pysam.c | 20 +-
samtools/bam_lpileup.c | 2 +
samtools/bam_lpileup.c.pysam.c | 12 +-
samtools/bam_mate.c | 80 ++--
samtools/bam_mate.c.pysam.c | 88 +++--
samtools/bam_md.c | 64 ++-
samtools/bam_md.c.pysam.c | 84 ++--
samtools/bam_plbuf.c | 2 +
samtools/bam_plbuf.c.pysam.c | 2 +
samtools/bam_plcmd.c | 6 +-
samtools/bam_plcmd.c.pysam.c | 74 ++--
samtools/bam_quickcheck.c | 22 +-
samtools/bam_quickcheck.c.pysam.c | 48 ++-
samtools/bam_reheader.c | 64 ++-
samtools/bam_reheader.c.pysam.c | 95 +++--
samtools/bam_rmdup.c | 109 ++++--
samtools/bam_rmdup.c.pysam.c | 129 ++++--
samtools/bam_rmdupse.c | 64 ++-
samtools/bam_rmdupse.c.pysam.c | 66 +++-
samtools/bam_sort.c | 267 +++++++++----
samtools/bam_sort.c.pysam.c | 329 +++++++++++-----
samtools/bam_split.c | 88 +++--
samtools/bam_split.c.pysam.c | 124 +++---
samtools/bam_stat.c | 2 +
samtools/bam_stat.c.pysam.c | 46 +--
samtools/bam_tview.c | 2 +
samtools/bam_tview.c.pysam.c | 18 +-
samtools/bam_tview_curses.c.pysam.c | 2 +-
samtools/bam_tview_html.c | 2 +
samtools/bam_tview_html.c.pysam.c | 8 +-
samtools/bamshuf.c | 141 +++++--
samtools/bamshuf.c.pysam.c | 163 ++++++--
samtools/bamtk.c | 6 +-
samtools/bamtk.c.pysam.c | 36 +-
samtools/bedcov.c | 2 +
samtools/bedcov.c.pysam.c | 16 +-
samtools/bedidx.c | 2 +
samtools/bedidx.c.pysam.c | 6 +-
samtools/cut_target.c | 2 +
samtools/cut_target.c.pysam.c | 24 +-
samtools/dict.c | 5 +-
samtools/dict.c.pysam.c | 29 +-
samtools/errmod.c | 2 +
samtools/errmod.c.pysam.c | 2 +
samtools/faidx.c | 6 +-
samtools/faidx.c.pysam.c | 20 +-
samtools/kprobaln.c | 2 +
samtools/kprobaln.c.pysam.c | 14 +-
samtools/misc/ace2sam.c | 2 +
samtools/misc/ace2sam.c.pysam.c | 38 +-
samtools/padding.c | 42 +-
samtools/padding.c.pysam.c | 136 ++++---
samtools/phase.c | 89 +++--
samtools/phase.c.pysam.c | 167 +++++---
samtools/pysam.h | 4 +-
samtools/sam.c | 18 +-
samtools/sam.c.pysam.c | 26 +-
samtools/sam_header.c | 2 +
samtools/sam_header.c.pysam.c | 8 +-
samtools/sam_opts.c | 2 +
samtools/sam_opts.c.pysam.c | 4 +-
samtools/sam_view.c | 84 ++--
samtools/sam_view.c.pysam.c | 152 ++++----
samtools/sample.c | 2 +
samtools/sample.c.pysam.c | 2 +
samtools/stats.c | 2 +
samtools/stats.c.pysam.c | 60 +--
samtools/stats_isize.c | 2 +
samtools/stats_isize.c.pysam.c | 4 +-
samtools/test/merge/test_bam_translate.c | 2 +
samtools/test/merge/test_bam_translate.c.pysam.c | 170 ++++----
samtools/test/merge/test_rtrans_build.c | 2 +
samtools/test/merge/test_rtrans_build.c.pysam.c | 26 +-
samtools/test/merge/test_trans_tbl_init.c | 16 +-
samtools/test/merge/test_trans_tbl_init.c.pysam.c | 152 ++++----
samtools/test/split/test_count_rg.c | 2 +
samtools/test/split/test_count_rg.c.pysam.c | 32 +-
samtools/test/split/test_expand_format_string.c | 2 +
.../test/split/test_expand_format_string.c.pysam.c | 32 +-
samtools/test/split/test_filter_header_rg.c | 2 +
.../test/split/test_filter_header_rg.c.pysam.c | 50 +--
samtools/test/split/test_parse_args.c | 2 +
samtools/test/split/test_parse_args.c.pysam.c | 120 +++---
samtools/test/test.c | 2 +
samtools/test/test.c.pysam.c | 16 +-
samtools/test/tview/test_get_rg_sample.c | 2 +
samtools/test/tview/test_get_rg_sample.c.pysam.c | 6 +-
samtools/version.h | 2 +-
setup.py | 192 +++++----
tests/AlignedSegment_test.py | 121 +++++-
tests/AlignmentFile_test.py | 431 +++++++++++++--------
tests/TestUtils.py | 34 +-
tests/VariantFile_test.py | 47 ++-
tests/cbcf_data/example_vcf42.vcf | 6 +-
tests/faidx_test.py | 63 ++-
tests/pysam_data/Makefile | 9 +-
tests/samtools_test.py | 82 +++-
tests/tabix_test.py | 145 ++++---
tests/test_samtools_python.py | 35 ++
209 files changed, 6242 insertions(+), 3409 deletions(-)
delete mode 100644 debian/TODO
delete mode 100644 debian/patches/compile-test.patch
delete mode 100644 debian/patches/disable-tests-requiring-network.patch
delete mode 100644 debian/patches/external-htslib.patch
create mode 100644 debian/patches/spelling.patch
create mode 100644 tests/test_samtools_python.py
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