[med-svn] [python-pysam] 01/03: Merge tag 'debian/0.9.1.4+ds-1' into debian/jessie-backports
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 commit to branch debian/jessie-backports
in repository python-pysam.
commit 9743ded939f40ba925746d6159fab51488841dd3
Merge: 54f17ad fca3a7d
Author: Afif Elghraoui <afif at debian.org>
Date: Sat Jul 30 13:55:27 2016 -0700
Merge tag 'debian/0.9.1.4+ds-1' into debian/jessie-backports
tagging package python-pysam version debian/0.9.1.4+ds-1
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 | 24 ++
debian/control | 8 +-
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, 6233 insertions(+), 3408 deletions(-)
diff --cc debian/changelog
index 2336e69,fa17f36..640f03a
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,27 +1,33 @@@
+ python-pysam (0.9.1.4+ds-1) unstable; urgency=medium
+
+ * Imported Upstream version 0.9.1.4+ds
+ * Drop patch applied upstream
+ * Drop unused lintian overrides
+ * Fix spelling issues
+
+ -- Afif Elghraoui <afif at debian.org> Sat, 23 Jul 2016 18:47:31 -0700
+
+ python-pysam (0.9.1+ds-1) unstable; urgency=medium
+
+ * Imported Upstream version 0.9.1+ds
+ * Force at least matching versions of the samtools suite
+ * Bump Standards-Version to 3.9.8
+ * Globally use C.UTF-8 locale
+ * Update patch for external htslib
+ * Refresh patch
+ * Drop obsolete patches
+ * Fix handling of configuration headers generated at build time
+ * Rely more on pybuild for build-time tests and respect exit code
+ * Fix autopkgtests
+
+ -- Afif Elghraoui <afif at debian.org> Sun, 19 Jun 2016 18:43:53 -0700
+
+python-pysam (0.9.0+ds-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <afif at debian.org> Sat, 09 Apr 2016 15:13:31 -0700
+
python-pysam (0.9.0+ds-1) unstable; urgency=medium
* Add filenamemangle to d/watch and space out content
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