MANIFEST.in
README.md
environment.yml
pyproject.toml
requirements.txt
setup.py
docs/dev.md
eccomparator/__init__.py
eccomparator/configs.py
eccomparator/main.py
eccomparator/metrics/__init__.py
eccomparator/metrics/amplicon_similarity.py
eccomparator/metrics/breakpoints.py
eccomparator/metrics/compare.py
eccomparator/metrics/distances.py
eccomparator/metrics/features.py
eccomparator/utils/__init__.py
eccomparator/utils/aggregate.py
eccomparator/utils/cycles_to_bed_modified.py
eccomparator/utils/generate_pairs.py
eccomparator/utils/perturb.py
eccomparator/utils/report.py
eccomparator/utils/threadsviz.py
eccomparator/utils/utils.py
eccomparator/utils/viz.py
eccomparator/utils/template/__init__.py
eccomparator/utils/template/results.html
examples/ecdna1/output/breakpoints_matched.txt
examples/ecdna1/output/breakpoints_profile_s1.txt
examples/ecdna1/output/breakpoints_profile_s2.txt
examples/ecdna1/output/coverage_breakpoints_profile.pdf
examples/ecdna1/output/coverage_breakpoints_profile.png
examples/ecdna1/output/coverage_profile.pdf
examples/ecdna1/output/coverage_profile.png
examples/ecdna1/output/coverage_profile_s1.txt
examples/ecdna1/output/coverage_profile_s2.txt
examples/ecdna1/output/e1_coverage_profile.txt
examples/ecdna1/output/e2_coverage_profile.txt
examples/ecdna1/output/metrics.json
examples/ecdna1/output/original_structures.png
examples/ecdna1/output/report.html
examples/ecdna1/output/report.pdf
examples/ecdna1/output/s1_input_filtered.bed
examples/ecdna1/output/s2_input_filtered.bed
examples/ecdna1/output/total_cost.png
examples/ecdna1/output/total_cost_bar.png
examples/ecdna1/output/total_cost_table.png
tests/test_cli_examples.py