LICENSE
README.md
pyproject.toml
src/accusnv/__init__.py
src/accusnv/cli.py
src/accusnv/log.py
src/accusnv.egg-info/PKG-INFO
src/accusnv.egg-info/SOURCES.txt
src/accusnv.egg-info/dependency_links.txt
src/accusnv.egg-info/entry_points.txt
src/accusnv.egg-info/requires.txt
src/accusnv.egg-info/top_level.txt
src/accusnv/accusnv/__init__.py
src/accusnv/accusnv/accusnv.py
src/accusnv/accusnv/cnn_pred.py
src/accusnv/downstream/__init__.py
src/accusnv/downstream/annotate.py
src/accusnv/downstream/dnds.py
src/accusnv/downstream/generate_dashboard.py
src/accusnv/downstream/snv.py
src/accusnv/downstream/tree_building.py
src/accusnv/models/checkpoint_best_3conv.pt
src/accusnv/models/train.py
src/accusnv/preprocessing/__init__.py
src/accusnv/preprocessing/build_candidate_mutation_table.py
src/accusnv/preprocessing/pileup2diversity.py
src/accusnv/preprocessing/upstream_rejects.py
src/accusnv/preprocessing/utils.py
src/accusnv/preprocessing/variants2positions.py
src/accusnv/preprocessing/vcf2quals_snakemake.py
src/accusnv/templates/config.yaml
src/accusnv/templates/dashboard.html
src/accusnv/templates/peartree.bundle.min.js
src/accusnv/templates/pipeline.yaml
src/accusnv/workflow/Snakefile
src/accusnv/workflow/resources.py
tests/test_annotation_alignment.py
tests/test_input_validation.py
tests/test_path_handling.py
tests/test_pileup_reference_base.py
tests/test_sample_name_handling.py