[med-svn] [python-pysam] branch master updated (09caf28 -> b872a94)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Jun 20 01:53:27 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 09caf28 Finalize changelog
new f470810 Imported Upstream version 0.9.1+ds
new f2ee928 Merge tag 'upstream/0.9.1+ds'
new b7bb657 Force at least matching versions of the samtools suite
new 122bb6d Bump Standards-Version to 3.9.8
new 2443a95 Prepare new revision
new 9715aba Globally use C.UTF-8 locale
new d08e2fd Update patch for external htslib
new 681de8a Refresh patch
new 9e08301 Drop obsolete patches
new 298ee9a Fix handling of configuration headers generated at build time
new 846ad26 Rely more on pybuild for build-time tests
new 21ea7ea Fix autopkgtests
new b872a94 releasing package python-pysam version 0.9.1+ds-1
The 13 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 | 2 +-
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 +-
debian/TODO | 4 -
debian/changelog | 15 +
debian/control | 8 +-
debian/patches/compile-test.patch | 15 -
.../patches/disable-tests-requiring-network.patch | 89 -----
debian/patches/external-htslib.patch | 28 +-
debian/patches/rpath.patch | 2 +-
debian/patches/series | 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 | 41 ++-
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 | 30 +-
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 | 27 +-
tests/AlignedSegment_test.py | 121 ++++++-
tests/AlignmentFile_test.py | 362 +++++++++++----------
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 ++
204 files changed, 5918 insertions(+), 3235 deletions(-)
delete mode 100644 debian/TODO
delete mode 100644 debian/patches/compile-test.patch
delete mode 100644 debian/patches/disable-tests-requiring-network.patch
create mode 100644 tests/test_samtools_python.py
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