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/bonsai.py
prp/cli/__init__.py
prp/cli/annotate.py
prp/cli/base.py
prp/cli/parse.py
prp/cli/upload.py
prp/cli/utils.py
prp/cli/validate.py
prp/migration/__init__.py
prp/migration/config.py
prp/migration/convert.py
prp/models/__init__.py
prp/models/base.py
prp/models/config.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/amrfinder.py
prp/parse/emmtyper.py
prp/parse/igv.py
prp/parse/kraken.py
prp/parse/mapping.py
prp/parse/metadata.py
prp/parse/mykrobe.py
prp/parse/qc.py
prp/parse/resfinder.py
prp/parse/sample.py
prp/parse/sccmec.py
prp/parse/serotypefinder.py
prp/parse/shigapass.py
prp/parse/spatyper.py
prp/parse/tbprofiler.py
prp/parse/typing.py
prp/parse/utils.py
prp/parse/variant.py
prp/parse/virulencefinder.py
tests/test_cli.py
tests/test_migration.py