[med-svn] [python-pysam] branch upstream updated (364e45a -> f470810)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Jun 20 01:53:30 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 364e45a Imported Upstream version 0.9.0+ds
new f470810 Imported Upstream version 0.9.1+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:
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 +-
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 ++
194 files changed, 5846 insertions(+), 3093 deletions(-)
create mode 100644 tests/test_samtools_python.py
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