[med-svn] [python-pysam] branch master updated (62d43f6 -> 534713f)
Andreas Tille
tille at debian.org
Wed Dec 13 13:09:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository python-pysam.
from 62d43f6 Changelog for 0.12.0.1+ds-4
adds b6750cc New upstream version 0.12.0.1+ds
new f3bd90a New upstream version 0.13.0+ds
new d06b7e2 Update upstream source from tag 'upstream/0.13.0+ds'
new d5ab2c2 New upstream version
new 9b1e2d6 Refresh patches
new 534713f Bump versioned Build-Depends on libhts-dev, samtools and bcftools to 1.6
The 5 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:
.travis.yml | 2 +
INSTALL | 117 ++-
MANIFEST.in | 5 +
doc/release.rst => NEWS | 19 +
bcftools/consensus.c | 129 +++-
bcftools/consensus.c.pysam.c | 129 +++-
bcftools/csq.c | 133 ++--
bcftools/csq.c.pysam.c | 133 ++--
bcftools/filter.c | 652 +++++++++++-----
bcftools/filter.c.pysam.c | 652 +++++++++++-----
bcftools/kheap.h | 5 +-
bcftools/main.c | 5 +
bcftools/main.c.pysam.c | 5 +
bcftools/mpileup.c | 9 +-
bcftools/mpileup.c.pysam.c | 9 +-
bcftools/vcfcnv.c | 6 +
bcftools/vcfcnv.c.pysam.c | 6 +
bcftools/vcfconvert.c | 5 +-
bcftools/vcfconvert.c.pysam.c | 5 +-
bcftools/vcfindex.c | 7 +
bcftools/vcfindex.c.pysam.c | 7 +
bcftools/vcfisec.c | 14 +-
bcftools/vcfisec.c.pysam.c | 14 +-
bcftools/vcfmerge.c | 14 +-
bcftools/vcfmerge.c.pysam.c | 14 +-
bcftools/vcfnorm.c | 18 +
bcftools/vcfnorm.c.pysam.c | 18 +
bcftools/vcfquery.c | 17 +
bcftools/vcfquery.c.pysam.c | 17 +
bcftools/vcfsort.c | 306 ++++++++
bcftools/vcfsort.c.pysam.c | 308 ++++++++
bcftools/vcfstats.c | 63 +-
bcftools/vcfstats.c.pysam.c | 63 +-
bcftools/version.h | 2 +-
debian/changelog | 7 +
debian/control | 6 +-
...linking-tests-only-when-explicitely-reque.patch | 49 +-
...o-prevent-it-from-being-picked-up-by-nose.patch | 39 -
debian/patches/series | 1 -
debian/patches/xfail.patch | 6 +-
doc/installation.rst | 23 +
doc/release.rst | 11 +
import.py | 2 +
pysam/libcalignedsegment.pyx | 380 ++++++---
pysam/libcalignmentfile.pxd | 4 +-
pysam/libcalignmentfile.pyx | 2 +-
pysam/libctabix.pyx | 99 ++-
pysam/libctabixproxies.pyx | 1 +
pysam/version.py | 8 +-
run_tests_travis.sh | 11 +-
samtools/bam.h | 2 +-
samtools/bam_lpileup.c | 1 +
samtools/bam_lpileup.c.pysam.c | 1 +
samtools/bam_markdup.c | 844 ++++++++++++++++++++
samtools/bam_markdup.c.pysam.c | 846 +++++++++++++++++++++
samtools/bam_mate.c | 50 +-
samtools/bam_mate.c.pysam.c | 50 +-
samtools/bam_plcmd.c | 22 +
samtools/bam_plcmd.c.pysam.c | 22 +
samtools/bam_reheader.c.pysam.c | 2 +-
samtools/bam_sort.c | 494 +++++++++---
samtools/bam_sort.c.pysam.c | 494 +++++++++---
samtools/bamtk.c | 15 +
samtools/bamtk.c.pysam.c | 22 +-
samtools/bedidx.c | 4 -
samtools/bedidx.c.pysam.c | 4 -
samtools/dict.c | 4 +
samtools/dict.c.pysam.c | 4 +
samtools/padding.c | 31 +-
samtools/padding.c.pysam.c | 31 +-
samtools/phase.c | 1 +
samtools/phase.c.pysam.c | 1 +
samtools/sam_view.c | 33 +-
samtools/sam_view.c.pysam.c | 33 +-
samtools/version.h | 2 +-
setup.py | 12 +-
tests/AlignedSegment_test.py | 261 +++++--
tests/AlignmentFile_test.py | 137 +---
tests/TestUtils.py | 10 +-
tests/linking_test.py | 16 +-
tests/samtools_test.py | 16 +-
tests/tabix_test.py | 53 +-
tests/tabixproxies_test.py | 22 +-
83 files changed, 5708 insertions(+), 1389 deletions(-)
copy doc/release.rst => NEWS (96%)
create mode 100644 bcftools/vcfsort.c
create mode 100644 bcftools/vcfsort.c.pysam.c
delete mode 100644 debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
create mode 100644 samtools/bam_markdup.c
create mode 100644 samtools/bam_markdup.c.pysam.c
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