.dockerignore
.gitignore
Dockerfile-slim
LICENSE
README.md
coverage-badge.svg
coverage.xml
docker-compose-slim.yml
environment.yml
requirements.txt
requirements_dev.txt
setup.py
.github/workflows/ci.yml
annotation/genes.txt
decoil/__init__.py
decoil/command.py
decoil/main.py
decoil/utils.py
decoil.egg-info/PKG-INFO
decoil.egg-info/SOURCES.txt
decoil.egg-info/dependency_links.txt
decoil.egg-info/entry_points.txt
decoil.egg-info/not-zip-safe
decoil.egg-info/requires.txt
decoil.egg-info/top_level.txt
decoil/cli/Snakefile
decoil/cli/__init__.py
decoil/cli/decoil-full.json
decoil/cli/params-decoil-full.json
decoil/cli/reconstruct-only-params.json
decoil/cli/reconstruct-only.json
decoil/cli/reconstruct-plot.json
decoil/cli/sv-only-params.json
decoil/cli/sv-only.json
decoil/cli/sv-reconstruct-params.json
decoil/cli/sv-reconstruct.json
decoil/cli/envs/cov.yaml
decoil/cli/envs/sv.yaml
decoil/cli/rules/decoil.smk
decoil/cli/rules/sv.smk
decoil/encode/__init__.py
decoil/encode/encode.py
decoil/encode/graph.py
decoil/encode/operations.py
decoil/output/__init__.py
decoil/output/metrics.py
decoil/output/parse.py
decoil/search/__init__.py
decoil/search/cycles.py
decoil/search/quantify.py
decoil/search/search.py
decoil/validate/__init__.py
decoil/validate/compare.py
docs/README_dev.md
docs/decoil_pipeline_modes.md
docs/decoil_reconstruct.md
docs/example.md
tests/__init__.py
tests/bugs.txt
tests/data/test3.txt
tests/encode/__init__.py
tests/encode/test_cleaning.py
tests/encode/test_cycles.py
tests/encode/test_graph.py
tests/encode/test_input.py
tests/examples/COLO829.nanomonsv.result.vcf
tests/examples/ecdna1/cutesv.vcf
tests/examples/ecdna1/sniffles1.vcf
tests/examples/ecdna1/sniffles2.vcf
tests/examples/vcfs/sim1010_sniffles1.vcf
tests/examples/vcfs/sim1010_sniffles2.vcf
tests/search/__init__.py
tests/search/test_DFS.py
tests/search/test_cycles.py