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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
