├── .flake8 ├── .github └── workflows │ └── master-test-build-upload.yml ├── .gitignore ├── .mypy.ini ├── .pre-commit-config.yaml ├── .pylintrc ├── CHANGELOG.md ├── Cargo.toml ├── Dockerfile ├── LICENSE.txt ├── README.md ├── notebooks ├── data_processing │ ├── anarci_database_preparation.ipynb │ ├── custom_database.ipynb │ ├── deduplicate_aa_genes.ipynb │ ├── dict_merge.py │ ├── ngs_sample_filter_species.ipynb │ └── therapeutics_preprocess_and_filter_species.py ├── final_benchmark │ ├── aa_gene_assignment_therapeutics.ipynb │ ├── final_benchmark_ngs_validation_flags.ipynb │ ├── nt_gene_assignment_ngs.ipynb │ ├── time_measurments.ipynb │ └── utils.py ├── prefiltering_grid_search │ ├── prefiltering_c_genes_grid_search.ipynb │ ├── prefiltering_d_genes_grid_search.ipynb │ ├── prefiltering_j_genes_grid_search.ipynb │ ├── prefiltering_v_genes_grid_search.ipynb │ └── utils.py ├── segments_regression │ ├── aa_regresion_therapeutics.ipynb │ └── nt_regresion_ngs.ipynb ├── utils.py └── validation_flags │ ├── aa_pipeline_validation_analysis.ipynb │ ├── aa_pipeline_validation_analysis_human.ipynb │ ├── aa_pipeline_validation_analysis_mouse.ipynb │ ├── nt_pipeline_validation_analysis.ipynb │ ├── nt_pipeline_validation_analysis_human.ipynb │ ├── nt_pipeline_validation_analysis_mouse.ipynb │ └── regression_test_validation_analysis.ipynb ├── poetry.lock ├── pyproject.toml ├── riot_na ├── __init__.py ├── airr │ ├── __init__.py │ ├── airr_builder.py │ ├── airr_builder_aa.py │ └── airr_validator.py ├── alignment │ ├── aa_gene_alignments.py │ ├── alignment_metrics.py │ ├── alignment_utils.py │ ├── gene_aligner.py │ ├── nt_gene_alignments.py │ ├── segment_gene_aligner.py │ └── skbio_alignment.py ├── api │ ├── __init__.py │ ├── api_mp.py │ ├── riot_numbering.py │ └── utils.py ├── cli.py ├── common │ ├── __init__.py │ ├── airr_csv_writer.py │ ├── assert_never.py │ ├── debug_utils.py │ ├── gene_match_utils.py │ ├── io.py │ ├── multi_species_prefiltering.py │ ├── multi_species_segment_prefiltering.py │ └── serialization_utils.py ├── config.py ├── data │ ├── __init__.py │ ├── constants.py │ ├── model.py │ ├── scheme_definitions.py │ ├── scheme_mapping_facade.py │ └── scheme_regions.py ├── databases │ ├── gene_db │ │ ├── aa_genes │ │ │ ├── c_genes │ │ │ │ ├── alpaca │ │ │ │ │ └── igh.fasta │ │ │ │ └── human │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ ├── j_genes │ │ │ │ ├── alpaca │ │ │ │ │ └── igh.fasta │ │ │ │ ├── human │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ │ └── mouse │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ └── v_genes │ │ │ │ ├── all_species.fasta │ │ │ │ ├── alpaca.fasta │ │ │ │ ├── human.fasta │ │ │ │ └── mouse.fasta │ │ ├── aa_genes_deduplicated │ │ │ ├── c_genes │ │ │ │ ├── alpaca │ │ │ │ │ └── igh.fasta │ │ │ │ └── human │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ ├── j_genes │ │ │ │ ├── alpaca │ │ │ │ │ └── igh.fasta │ │ │ │ ├── human │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ │ └── mouse │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ └── v_genes │ │ │ │ ├── all_species.fasta │ │ │ │ ├── alpaca.fasta │ │ │ │ ├── human.fasta │ │ │ │ └── mouse.fasta │ │ ├── aa_genes_first_allele │ │ │ ├── j_genes │ │ │ │ ├── human │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ │ └── mouse │ │ │ │ │ ├── igh.fasta │ │ │ │ │ ├── igk.fasta │ │ │ │ │ └── igl.fasta │ │ │ └── v_genes │ │ │ │ ├── human.fasta │ │ │ │ └── mouse.fasta │ │ ├── c_genes │ │ │ ├── alpaca │ │ │ │ └── igh.fasta │ │ │ └── human │ │ │ │ ├── igh.fasta │ │ │ │ ├── igk.fasta │ │ │ │ └── igl.fasta │ │ ├── d_genes │ │ │ ├── alpaca │ │ │ │ └── igh.fasta │ │ │ ├── human │ │ │ │ └── igh.fasta │ │ │ └── mouse │ │ │ │ └── igh.fasta │ │ ├── j_genes │ │ │ ├── alpaca │ │ │ │ └── igh.fasta │ │ │ ├── human │ │ │ │ ├── igh.fasta │ │ │ │ ├── igk.fasta │ │ │ │ └── igl.fasta │ │ │ └── mouse │ │ │ │ ├── igh.fasta │ │ │ │ ├── igk.fasta │ │ │ │ └── igl.fasta │ │ └── v_genes │ │ │ ├── all_species.fasta │ │ │ ├── alpaca.fasta │ │ │ ├── human.fasta │ │ │ └── mouse.fasta │ └── scheme_mappings │ │ ├── alpaca │ │ ├── chothia │ │ │ └── scheme_mapping.csv │ │ ├── imgt │ │ │ └── scheme_mapping.csv │ │ ├── kabat │ │ │ └── scheme_mapping.csv │ │ └── martin │ │ │ └── scheme_mapping.csv │ │ ├── human │ │ ├── chothia │ │ │ └── scheme_mapping.csv │ │ ├── imgt │ │ │ └── scheme_mapping.csv │ │ ├── kabat │ │ │ └── scheme_mapping.csv │ │ └── martin │ │ │ └── scheme_mapping.csv │ │ └── mouse │ │ ├── chothia │ │ └── scheme_mapping.csv │ │ ├── imgt │ │ └── scheme_mapping.csv │ │ ├── kabat │ │ └── scheme_mapping.csv │ │ └── martin │ │ └── scheme_mapping.csv ├── riot_na.pyi └── schemes │ ├── __init__.py │ ├── collapse_alignment.py │ ├── region_offsets.py │ ├── scheme_alignment.py │ └── smooth_alignment.py ├── riot_prefiltering ├── lib.rs ├── model.rs 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