LICENSE
README.md
pyproject.toml
bonsai_prp.egg-info/PKG-INFO
bonsai_prp.egg-info/SOURCES.txt
bonsai_prp.egg-info/dependency_links.txt
bonsai_prp.egg-info/entry_points.txt
bonsai_prp.egg-info/requires.txt
bonsai_prp.egg-info/top_level.txt
prp/__init__.py
prp/__version__.py
prp/cli.py
prp/models/__init__.py
prp/models/base.py
prp/models/metadata.py
prp/models/phenotype.py
prp/models/qc.py
prp/models/sample.py
prp/models/species.py
prp/models/tags.py
prp/models/typing.py
prp/parse/__init__.py
prp/parse/mapping.py
prp/parse/metadata.py
prp/parse/qc.py
prp/parse/species.py
prp/parse/typing.py
prp/parse/utils.py
prp/parse/variant.py
prp/parse/phenotype/__init__.py
prp/parse/phenotype/amrfinder.py
prp/parse/phenotype/emmtyper.py
prp/parse/phenotype/mykrobe.py
prp/parse/phenotype/resfinder.py
prp/parse/phenotype/serotypefinder.py
prp/parse/phenotype/shigapass.py
prp/parse/phenotype/tbprofiler.py
prp/parse/phenotype/virulencefinder.py
tests/test_cli.py