[med-svn] [cnvkit] branch upstream updated (370ea2e -> 42bc619)
Andreas Tille
tille at debian.org
Fri Sep 29 08:23:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository cnvkit.
from 370ea2e Imported Upstream version 0.7.11
new 42bc619 New upstream version 0.9.0
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:
.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(-)
create mode 100644 .codecov.yml
delete mode 100644 cnvlib/_cnarray.py
mode change 100755 => 100644 cnvlib/access.py
create mode 100644 cnvlib/autobin.py
create mode 100644 cnvlib/batch.py
create mode 100644 cnvlib/cmdutil.py
create mode 100644 cnvlib/descriptives.py
delete mode 100644 cnvlib/gary.py
create mode 100644 cnvlib/heatmap.py
delete mode 100644 cnvlib/ngfrills/__init__.py
delete mode 100644 cnvlib/ngfrills/faidx.py
delete mode 100644 cnvlib/ngfrills/regions.py
delete mode 100644 cnvlib/ngfrills/shared.py
delete mode 100644 cnvlib/rary.py
rename cnvlib/{ngfrills => }/samutil.py (50%)
create mode 100644 cnvlib/scatter.py
create mode 100644 cnvlib/segfilters.py
create mode 100644 devtools/conda-recipe/build.sh
create mode 100644 devtools/conda-recipe/meta.yaml
create mode 100755 devtools/travis-ci/install_miniconda.sh
create mode 100644 doc/baf.rst
create mode 100644 doc/germline.rst
create mode 100644 doc/sex.rst
create mode 100644 doc/skgenome.rst
create mode 100644 doc/tumor.rst
create mode 100755 scripts/cnn_annotate.py
create mode 100755 scripts/cnn_updater.py
delete mode 100755 scripts/genome2access.py
create mode 100755 scripts/guess_baits.py
create mode 100755 scripts/skg_convert.py
create mode 100644 setup.cfg
create mode 100644 skgenome/__init__.py
create mode 100644 skgenome/chromsort.py
create mode 100644 skgenome/combiners.py
create mode 100644 skgenome/gary.py
create mode 100644 skgenome/intersect.py
create mode 100644 skgenome/merge.py
create mode 100644 skgenome/rangelabel.py
create mode 100644 skgenome/subdivide.py
create mode 100644 skgenome/subtract.py
create mode 100644 skgenome/tabio/__init__.py
create mode 100644 skgenome/tabio/bedio.py
create mode 100644 skgenome/tabio/genepred.py
create mode 100644 skgenome/tabio/gff.py
create mode 100644 skgenome/tabio/picard.py
create mode 100644 skgenome/tabio/seg.py
create mode 100644 skgenome/tabio/simplevcf.py
create mode 100644 skgenome/tabio/tab.py
create mode 100644 skgenome/tabio/textcoord.py
create mode 100644 skgenome/tabio/util.py
create mode 100644 skgenome/tabio/vcfio.py
create mode 100644 test/formats/blank.vcf
create mode 100644 test/formats/chrM-Y-trunc.hg19.fa
create mode 100644 test/formats/dac-my.bed
create mode 100644 test/formats/example.gff
create mode 100644 test/formats/my-refflat.bed
create mode 100644 test/formats/my-targets.bed
create mode 100644 test/formats/na12878-chrM-Y-trunc.bam
create mode 100644 test/formats/na12878_na12882_mix.vcf
create mode 100644 test/formats/nosample.vcf
create mode 100644 test/formats/p2-20_1.cnr
create mode 100644 test/formats/p2-20_2.cnr
create mode 100644 test/formats/refflat-mini.txt
create mode 100644 test/formats/tr95t.segmetrics.cns
create mode 100644 test/formats/warning.seg
create mode 100755 test/test_genome.py
create mode 100755 test/test_io.py
mode change 100644 => 100755 test/test_r.py
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