CHANGELOG.md
CITATION.cff
INSTALL.md
LICENSE
MANIFEST.in
README.md
RELEASE_NOTICE.md
pyproject.toml
docs/ALGORITHM_REVIEW.md
docs/DEPLOYMENT.md
docs/EXTERNAL_VALIDATION.md
docs/PUBLIC_VALIDATION_PROTOCOL.md
docs/QUICK_VALIDATION.md
docs/RECONCILED_REQUIREMENTS.md
docs/SCIENTIFIC_AUDIT.md
docs/VALIDATION_PLAN.md
examples/README.md
examples/fixtures/example-alleles.json
mutationsieve/__init__.py
mutationsieve/__main__.py
mutationsieve/_spikeforge_policy.py
mutationsieve/_spikeforge_worker.py
mutationsieve/alignment.py
mutationsieve/bamio.py
mutationsieve/batch.py
mutationsieve/benchmark.py
mutationsieve/cli.py
mutationsieve/config.py
mutationsieve/evidence.py
mutationsieve/external_validation.py
mutationsieve/llm.py
mutationsieve/outputs.py
mutationsieve/pipeline.py
mutationsieve/pon.py
mutationsieve/provenance.py
mutationsieve/py.typed
mutationsieve/reference.py
mutationsieve/release.py
mutationsieve/report.py
mutationsieve/representation.py
mutationsieve/rules.py
mutationsieve/simulate.py
mutationsieve/stats.py
mutationsieve/validation.py
mutationsieve/variants.py
mutationsieve.egg-info/PKG-INFO
mutationsieve.egg-info/SOURCES.txt
mutationsieve.egg-info/dependency_links.txt
mutationsieve.egg-info/entry_points.txt
mutationsieve.egg-info/requires.txt
mutationsieve.egg-info/top_level.txt
schemas/config.schema.json
schemas/pon.schema.json
schemas/result.schema.json
scripts/build_release.py
scripts/quick_validate.cmd
scripts/quick_validate.sh
scripts/run_mutationsieve.cmd
scripts/run_mutationsieve.sh
scripts/verify_release.py
tests/test_alignment.py
tests/test_bamio_reference.py
tests/test_batch.py
tests/test_benchmark_validation.py
tests/test_cli.py
tests/test_config_provenance.py
tests/test_evidence_units.py
tests/test_external_validation.py
tests/test_matched_normal_compatibility.py
tests/test_pipeline.py
tests/test_release.py
tests/test_representation.py
tests/test_rules.py
tests/test_simulate_consistency.py
tests/test_variants_stats.py