[med-svn] [cnvkit] 02/03: Updated version 0.9.0 from 'upstream/0.9.0'
Andreas Tille
tille at debian.org
Fri Sep 29 08:22:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cnvkit.
commit c7e50ccba3cb1e11bafd5bffb000e7bfc544f5c7
Merge: 35e4fd0 42bc619
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 29 09:15:12 2017 +0200
Updated version 0.9.0 from 'upstream/0.9.0'
with Debian dir 34a44cf51de7cee128fc093b435a5787b6a89481
.codecov.yml | 2 +
.gitignore | 1 +
.travis.yml | 63 +-
CITATION | 17 +-
README.rst | 46 +-
cnvkit.py | 2 +
cnvlib/__init__.py | 9 +-
cnvlib/_cnarray.py | 600 -
cnvlib/_version.py | 2 +-
cnvlib/access.py | 102 +-
cnvlib/antitarget.py | 156 +-
cnvlib/autobin.py | 185 +
cnvlib/batch.py | 205 +
cnvlib/call.py | 110 +-
cnvlib/cmdutil.py | 90 +
cnvlib/cnary.py | 398 +-
cnvlib/commands.py | 1759 ++-
cnvlib/core.py | 155 +-
cnvlib/coverage.py | 247 +-
cnvlib/descriptives.py | 274 +
cnvlib/diagram.py | 35 +-
cnvlib/export.py | 229 +-
cnvlib/fix.py | 147 +-
cnvlib/gary.py | 490 -
cnvlib/heatmap.py | 119 +
cnvlib/importers.py | 145 +-
cnvlib/jenks.py | 9 +-
cnvlib/metrics.py | 283 +-
cnvlib/ngfrills/__init__.py | 113 -
cnvlib/ngfrills/faidx.py | 34 -
cnvlib/ngfrills/regions.py | 248 -
cnvlib/ngfrills/shared.py | 10 -
cnvlib/parallel.py | 81 +-
cnvlib/params.py | 7 +-
cnvlib/plots.py | 425 +-
cnvlib/rary.py | 176 -
cnvlib/reference.py | 246 +-
cnvlib/reports.py | 60 +-
cnvlib/{ngfrills => }/samutil.py | 62 +-
cnvlib/scatter.py | 533 +
cnvlib/segfilters.py | 153 +
cnvlib/segmentation/__init__.py | 208 +-
cnvlib/segmentation/cbs.py | 4 +-
cnvlib/segmentation/flasso.py | 10 +-
cnvlib/segmentation/haar.py | 134 +-
cnvlib/smoothing.py | 79 +-
cnvlib/target.py | 313 +-
cnvlib/vary.py | 409 +-
devtools/conda-recipe/build.sh | 2 +
devtools/conda-recipe/meta.yaml | 43 +
devtools/travis-ci/install_miniconda.sh | 19 +
doc/baf.rst | 45 +
doc/calling.rst | 36 +-
doc/cnvlib.rst | 141 +-
doc/conf.py | 19 +-
doc/fileformats.rst | 75 +-
doc/germline.rst | 33 +
doc/heterogeneity.rst | 44 +-
doc/importexport.rst | 47 +-
doc/index.rst | 82 +-
doc/nonhybrid.rst | 115 +-
doc/pipeline.rst | 170 +-
doc/plots.rst | 96 +-
doc/quickstart.rst | 50 +-
doc/reports.rst | 70 +-
doc/scripts.rst | 56 +-
doc/sex.rst | 73 +
doc/skgenome.rst | 112 +
doc/tumor.rst | 42 +
doc/workflow.svg | 17 +-
docker/Dockerfile | 24 +-
scripts/cnn_annotate.py | 35 +
scripts/cnn_updater.py | 51 +
scripts/genome2access.py | 46 -
scripts/guess_baits.py | 238 +
scripts/refFlat2bed.py | 168 +-
scripts/reference2targets.py | 43 +-
scripts/skg_convert.py | 35 +
setup.cfg | 2 +
setup.py | 22 +-
skgenome/__init__.py | 2 +
skgenome/chromsort.py | 61 +
skgenome/combiners.py | 67 +
skgenome/gary.py | 615 +
skgenome/intersect.py | 181 +
skgenome/merge.py | 178 +
skgenome/rangelabel.py | 69 +
skgenome/subdivide.py | 62 +
skgenome/subtract.py | 72 +
skgenome/tabio/__init__.py | 267 +
skgenome/tabio/bedio.py | 125 +
skgenome/tabio/genepred.py | 163 +
skgenome/tabio/gff.py | 55 +
skgenome/tabio/picard.py | 90 +
skgenome/tabio/seg.py | 228 +
skgenome/tabio/simplevcf.py | 41 +
skgenome/tabio/tab.py | 33 +
skgenome/tabio/textcoord.py | 30 +
skgenome/tabio/util.py | 14 +
skgenome/tabio/vcfio.py | 305 +
test/.coveragerc | 4 +-
test/Makefile | 33 +-
test/formats/amplicon.cnr | 2868 ++---
test/formats/blank.vcf | 140 +
test/formats/chrM-Y-trunc.hg19.fa | 821 ++
test/formats/dac-my.bed | 3 +
test/formats/example.gff | 8 +
test/formats/my-refflat.bed | 276 +
test/formats/my-targets.bed | 4 +
test/formats/na12878-chrM-Y-trunc.bam | Bin 0 -> 4397336 bytes
test/formats/na12878_na12882_mix.vcf | 4703 ++++++++
test/formats/nosample.vcf | 140 +
test/formats/p2-20_1.cnr | 19090 ++++++++++++++++++++++++++++++
test/formats/p2-20_2.cnr | 19090 ++++++++++++++++++++++++++++++
test/formats/refflat-mini.txt | 100 +
test/formats/tr95t.cns | 251 +-
test/formats/tr95t.segmetrics.cns | 125 +
test/formats/warning.seg | 13 +
test/test_cnvlib.py | 493 +-
test/test_genome.py | 543 +
test/test_io.py | 130 +
test/test_r.py | 39 +-
122 files changed, 55500 insertions(+), 7268 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnvkit.git
More information about the debian-med-commit
mailing list