CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
docs/api.md
docs/cached.md
docs/consumer-guide.md
docs/expression-semantics.md
docs/fragments.md
docs/index.md
docs/properties.md
docs/pvacseq.md
docs/quickstart.md
docs/ranking.md
docs/self_proteome.md
tests/__init__.py
tests/common.py
tests/data.py
tests/test_absent_vs_empty_audit.py
tests/test_allele_class.py
tests/test_allele_free_kinds.py
tests/test_allele_set.py
tests/test_amino_acids.py
tests/test_args_outputs.py
tests/test_best_allele.py
tests/test_cache_allele_nulls.py
tests/test_cache_key_allele_set.py
tests/test_cached_predictor.py
tests/test_canonical_methods.py
tests/test_cli_cached_predictor.py
tests/test_cli_coverage.py
tests/test_cli_protein_changes.py
tests/test_cli_ranking.py
tests/test_cli_script.py
tests/test_combine_predictor_results.py
tests/test_consumer_workflows.py
tests/test_contains_mutant_residues.py
tests/test_context_forwarding.py
tests/test_coverage_gaps.py
tests/test_cross_sample_evidence.py
tests/test_dataframe.py
tests/test_default_versions.py
tests/test_deploy_script.py
tests/test_direct_input_regressions.py
tests/test_dsl_extensions.py
tests/test_dsl_polish.py
tests/test_dsl_roundtrip.py
tests/test_edge_case_fixtures.py
tests/test_effect_expression_filters.py
tests/test_empty_and_collision_guards.py
tests/test_end_to_end.py
tests/test_epitopes_from_commandline_args.py
tests/test_evidence.py
tests/test_expression_integration.py
tests/test_expression_loader.py
tests/test_fragment_evidence.py
tests/test_fragment_paths.py
tests/test_frameshift_fragments.py
tests/test_from_predictions.py
tests/test_group_keys.py
tests/test_inputs.py
tests/test_integration.py
tests/test_io.py
tests/test_io_lens.py
tests/test_io_pvacseq.py
tests/test_isovar_run.py
tests/test_kind_mhc_dependence.py
tests/test_kind_support.py
tests/test_lazy_imports.py
tests/test_lens_binding_override.py
tests/test_lens_multi_version.py
tests/test_lens_versions.py
tests/test_load_cufflinks_fpkm.py
tests/test_load_stringtie_gtf_fpkm.py
tests/test_mutant_epitope_predictions_class1.py
tests/test_mutant_epitope_predictions_class2.py
tests/test_named_allele_projection.py
tests/test_padding.py
tests/test_peptide_mutation_interval.py
tests/test_peptide_property_node.py
tests/test_peptide_view.py
tests/test_per_peptide_alleles.py
tests/test_predict_from_fragments.py
tests/test_predict_from_variants_refactor.py
tests/test_prediction_columns.py
tests/test_predictor_internals.py
tests/test_protein_fragment.py
tests/test_public_helpers.py
tests/test_ranking.py
tests/test_result.py
tests/test_rna_evidence_units.py
tests/test_rna_helpers.py
tests/test_scoped_filters.py
tests/test_self_nearest_population.py
tests/test_self_proteome.py
tests/test_sequence_helpers.py
tests/test_shared_context.py
tests/test_shared_expression_vocabulary.py
tests/test_sort_ordering.py
tests/test_sources.py
tests/test_sources_optional.py
tests/test_symmetric_evidence.py
tests/test_twin_conformance.py
tests/test_validation_and_edge_cases.py
tests/test_variant_expression_filters.py
tests/test_wide.py
tests/data/BLOSUM62.ncbi
topiary/__init__.py
topiary/amino_acids.py
topiary/cached.py
topiary/evidence.py
topiary/filters.py
topiary/inputs.py
topiary/io.py
topiary/io_isovar.py
topiary/io_lens.py
topiary/io_protein_fragment.py
topiary/io_pvacseq.py
topiary/optional_dependencies.py
topiary/prediction_columns.py
topiary/predictor.py
topiary/properties.py
topiary/protein_fragment.py
topiary/result.py
topiary/self_proteome.py
topiary/sequence_helpers.py
topiary/sources.py
topiary/wide.py
topiary.egg-info/PKG-INFO
topiary.egg-info/SOURCES.txt
topiary.egg-info/dependency_links.txt
topiary.egg-info/entry_points.txt
topiary.egg-info/requires.txt
topiary.egg-info/top_level.txt
topiary/cli/__init__.py
topiary/cli/args.py
topiary/cli/cached_predictor.py
topiary/cli/errors.py
topiary/cli/filtering.py
topiary/cli/outputs.py
topiary/cli/protein_changes.py
topiary/cli/rna.py
topiary/cli/script.py
topiary/cli/sequence.py
topiary/ranking/__init__.py
topiary/ranking/apply.py
topiary/ranking/nodes.py
topiary/ranking/parser.py
topiary/rna/__init__.py
topiary/rna/common.py
topiary/rna/cufflinks.py
topiary/rna/expression_loader.py
topiary/rna/gtf.py