HISTORY.md
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
versioneer.py
clearCNV/__init__.py
clearCNV/__main__.py
clearCNV/_version.py
clearCNV/cnv_arithmetics.py
clearCNV/cnv_calling.py
clearCNV/matchscores.py
clearCNV/misc.py
clearCNV/util.py
clearCNV/visualize_scores.py
clearCNV/workflow_cnv_calling.py
clearCNV/workflow_reassignment.py
clearCNV.egg-info/PKG-INFO
clearCNV.egg-info/SOURCES.txt
clearCNV.egg-info/dependency_links.txt
clearCNV.egg-info/entry_points.txt
clearCNV.egg-info/not-zip-safe
clearCNV.egg-info/requires.txt
clearCNV.egg-info/top_level.txt
clearCNV/viz_reassignment/__init__.py
clearCNV/viz_reassignment/app.py
clearCNV/viz_reassignment/cache.py
clearCNV/viz_reassignment/callbacks.py
clearCNV/viz_reassignment/settings.py
clearCNV/viz_reassignment/store.py
clearCNV/viz_reassignment/ui.py
clearCNV/viz_reassignment/ui_plots.py
clearCNV/viz_reassignment/assets/bootstrap.min.css
clearCNV/viz_reassignment/assets/clear-cnv.css
clearCNV/viz_reassignment/assets/fontawesome/css/all.min.css
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-brands-400.eot
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-brands-400.svg
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-brands-400.ttf
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-brands-400.woff
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-brands-400.woff2
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-regular-400.eot
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-regular-400.svg
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-regular-400.ttf
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-regular-400.woff
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-regular-400.woff2
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-solid-900.eot
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-solid-900.svg
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-solid-900.ttf
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-solid-900.woff
clearCNV/viz_reassignment/assets/fontawesome/webfonts/fa-solid-900.woff2
clearCNV/workflow/Snakefile_cnv_calling
clearCNV/workflow/Snakefile_reassignment
clearCNV/workflow/bih_cluster.json
clearCNV/workflow/config_cnv_calling.yml
clearCNV/workflow/config_reassignment.yml
requirements/base.txt
requirements/test.txt
requirements/test_black.txt
tests/__init__.py
tests/test_misc.py
tests/testdata/GC_annotations.bed
tests/testdata/allbams.txt
tests/testdata/allmerged.bed
tests/testdata/annotations.bed
tests/testdata/annotations2.bed
tests/testdata/bamfiles.txt
tests/testdata/bedfile.bed
tests/testdata/bedfile_alt.bed
tests/testdata/cov.tsv
tests/testdata/cov_reassignment.tsv
tests/testdata/coverages.tsv
tests/testdata/mappability.bed
tests/testdata/mappability.eq.1.bed
tests/testdata/matchscores.tsv
tests/testdata/merged.bed
tests/testdata/meta.tsv
tests/testdata/panel1.bed
tests/testdata/panel2.bed
tests/testdata/reassignment_p1_bamfiles.txt
tests/testdata/reassignment_p2_bamfiles.txt
tests/testdata/reassignment_union.bed
tests/testdata/reference.fa
tests/testdata/reference.fa.fai
tests/testdata/sample01.rtbed
tests/testdata/sample02.rtbed
tests/testdata/sample03.rtbed
tests/testdata/small.bam
tests/testdata/small.bam.bai
tests/testdata/small.rtbed
tests/testdata/targets.bed
tests/testdata/test_merge_bed_input.bed
tests/testdata/test_merge_bed_output.bed
tests/testdata/test_merge_beds_input_0.bed
tests/testdata/test_merge_beds_input_1.bed
tests/testdata/test_merge_beds_output.bed
tests/testdata/test_reassign_meta.tsv
tests/testdata/test_reassign_panel0.bed
tests/testdata/test_reassign_panel1.bed
tests/testdata/test_reassign_small_0.bam
tests/testdata/test_reassign_small_0.bam.bai
tests/testdata/test_reassign_small_1.bam
tests/testdata/test_reassign_small_1.bam.bai
tests/testdata/test_reassignment_coverages.tsv
tests/testdata/test_reassignment_p1_bamfiles.txt
tests/testdata/test_reassignment_p2_bamfiles.txt
tests/testdata/test_reassignment_ref.fa
tests/testdata/test_reassignment_ref.fa.fai
tests/testdata/test_reassignment_union.bed
tests/testdata/covs/test_reassign_small_0.rtbed
tests/testdata/covs/test_reassign_small_1.rtbed