LICENSE.md
README.md
setup.py
ligo/__init__.py
ligo.egg-info/PKG-INFO
ligo.egg-info/SOURCES.txt
ligo.egg-info/dependency_links.txt
ligo.egg-info/entry_points.txt
ligo.egg-info/requires.txt
ligo.egg-info/top_level.txt
ligo/IO/__init__.py
ligo/IO/dataset_export/AIRRExporter.py
ligo/IO/dataset_export/DataExporter.py
ligo/IO/dataset_export/ImmuneMLExporter.py
ligo/IO/dataset_export/__init__.py
ligo/IO/dataset_import/AIRRImport.py
ligo/IO/dataset_import/DataImport.py
ligo/IO/dataset_import/DatasetImportParams.py
ligo/IO/dataset_import/GenericImport.py
ligo/IO/dataset_import/IGoRImport.py
ligo/IO/dataset_import/IReceptorImport.py
ligo/IO/dataset_import/ImmuneMLImport.py
ligo/IO/dataset_import/ImmunoSEQRearrangementImport.py
ligo/IO/dataset_import/ImmunoSEQSampleImport.py
ligo/IO/dataset_import/MiXCRImport.py
ligo/IO/dataset_import/OLGAImport.py
ligo/IO/dataset_import/SingleLineReceptorImport.py
ligo/IO/dataset_import/TenxGenomicsImport.py
ligo/IO/dataset_import/VDJdbImport.py
ligo/IO/dataset_import/__init__.py
ligo/IO/dataset_import/conversion/imgt_adaptive_conversion.csv
ligo/app/LigoApp.py
ligo/app/__init__.py
ligo/config/default_params/datasets/airr_params.yaml
ligo/config/default_params/datasets/generic_params.yaml
ligo/config/default_params/datasets/i_receptor_params.yaml
ligo/config/default_params/datasets/igor_params.yaml
ligo/config/default_params/datasets/immuno_seq_rearrangement_params.yaml
ligo/config/default_params/datasets/immuno_seq_sample_params.yaml
ligo/config/default_params/datasets/mixcr_params.yaml
ligo/config/default_params/datasets/olga_params.yaml
ligo/config/default_params/datasets/random_receptor_dataset_params.yaml
ligo/config/default_params/datasets/random_repertoire_dataset_params.yaml
ligo/config/default_params/datasets/random_sequence_dataset_params.yaml
ligo/config/default_params/datasets/tenx_genomics_params.yaml
ligo/config/default_params/datasets/vdjdb_params.yaml
ligo/config/default_params/instructions/feasibility_summary_params.yaml
ligo/config/default_params/instructions/ligo_sim_params.yaml
ligo/config/default_params/simulation/ligo_sim_config_item_params.yaml
ligo/config/default_params/simulation/ligo_sim_config_params.yaml
ligo/data_model/DatasetItem.py
ligo/data_model/__init__.py
ligo/data_model/cell/Cell.py
ligo/data_model/cell/CellList.py
ligo/data_model/cell/__init__.py
ligo/data_model/dataset/Dataset.py
ligo/data_model/dataset/ElementDataset.py
ligo/data_model/dataset/ReceptorDataset.py
ligo/data_model/dataset/RepertoireDataset.py
ligo/data_model/dataset/SequenceDataset.py
ligo/data_model/dataset/__init__.py
ligo/data_model/encoded_data/EncodedData.py
ligo/data_model/encoded_data/__init__.py
ligo/data_model/receptor/BCKReceptor.py
ligo/data_model/receptor/BCReceptor.py
ligo/data_model/receptor/ChainPair.py
ligo/data_model/receptor/ElementGenerator.py
ligo/data_model/receptor/Receptor.py
ligo/data_model/receptor/ReceptorBuilder.py
ligo/data_model/receptor/RegionType.py
ligo/data_model/receptor/TCABReceptor.py
ligo/data_model/receptor/TCGDReceptor.py
ligo/data_model/receptor/__init__.py
ligo/data_model/receptor/receptor_sequence/Chain.py
ligo/data_model/receptor/receptor_sequence/ReceptorSequence.py
ligo/data_model/receptor/receptor_sequence/SequenceAnnotation.py
ligo/data_model/receptor/receptor_sequence/SequenceFrameType.py
ligo/data_model/receptor/receptor_sequence/SequenceMetadata.py
ligo/data_model/receptor/receptor_sequence/__init__.py
ligo/data_model/repertoire/Repertoire.py
ligo/data_model/repertoire/__init__.py
ligo/dsl/DefaultParamsLoader.py
ligo/dsl/InstructionParser.py
ligo/dsl/LigoParser.py
ligo/dsl/ObjectParser.py
ligo/dsl/OutputParser.py
ligo/dsl/Parser.py
ligo/dsl/Util.py
ligo/dsl/__init__.py
ligo/dsl/definition_parsers/DefinitionParser.py
ligo/dsl/definition_parsers/DefinitionParserOutput.py
ligo/dsl/definition_parsers/MotifParser.py
ligo/dsl/definition_parsers/SignalParser.py
ligo/dsl/definition_parsers/SimulationParser.py
ligo/dsl/definition_parsers/__init__.py
ligo/dsl/import_parsers/ImportParser.py
ligo/dsl/import_parsers/__init__.py
ligo/dsl/instruction_parsers/FeasibilitySummaryParser.py
ligo/dsl/instruction_parsers/LigoSimParser.py
ligo/dsl/instruction_parsers/__init__.py
ligo/dsl/semantic_model/MLResult.py
ligo/dsl/semantic_model/SemanticModel.py
ligo/dsl/semantic_model/__init__.py
ligo/dsl/symbol_table/SymbolTable.py
ligo/dsl/symbol_table/SymbolTableEntry.py
ligo/dsl/symbol_table/SymbolType.py
ligo/dsl/symbol_table/__init__.py
ligo/environment/Constants.py
ligo/environment/EnvironmentSettings.py
ligo/environment/SequenceType.py
ligo/environment/__init__.py
ligo/presentation/InstructionPresentation.py
ligo/presentation/PresentationFactory.py
ligo/presentation/PresentationFormat.py
ligo/presentation/TemplateParser.py
ligo/presentation/__init__.py
ligo/presentation/html/FeasibilitySummaryHTMLBuilder.py
ligo/presentation/html/HTMLBuilder.py
ligo/presentation/html/LIgOSimulationHTMLBuilder.py
ligo/presentation/html/Util.py
ligo/presentation/html/__init__.py
ligo/presentation/html/templates/DatasetExport.html
ligo/presentation/html/templates/FeasibilitySummary.html
ligo/presentation/html/templates/Simulation.html
ligo/presentation/html/templates/index.html
ligo/presentation/html/templates/css/custom.css
ligo/simulation/LigoSimState.py
ligo/simulation/SimConfig.py
ligo/simulation/SimConfigItem.py
ligo/simulation/__init__.py
ligo/simulation/dataset_generation/RandomDatasetGenerator.py
ligo/simulation/dataset_generation/__init__.py
ligo/simulation/generative_models/BackgroundSequences.py
ligo/simulation/generative_models/ExperimentalImport.py
ligo/simulation/generative_models/GenerativeModel.py
ligo/simulation/generative_models/InternalOlgaModel.py
ligo/simulation/generative_models/OLGA.py
ligo/simulation/generative_models/__init__.py
ligo/simulation/implants/ImplantAnnotation.py
ligo/simulation/implants/LigoPWM.py
ligo/simulation/implants/Motif.py
ligo/simulation/implants/MotifInstance.py
ligo/simulation/implants/SeedMotif.py
ligo/simulation/implants/Signal.py
ligo/simulation/implants/__init__.py
ligo/simulation/simulation_strategy/ImplantingStrategy.py
ligo/simulation/simulation_strategy/RejectionSamplingStrategy.py
ligo/simulation/simulation_strategy/SimulationStrategy.py
ligo/simulation/simulation_strategy/__init__.py
ligo/simulation/util/__init__.py
ligo/simulation/util/bnp_util.py
ligo/simulation/util/igor_helper.py
ligo/simulation/util/util.py
ligo/util/AdaptiveImportHelper.py
ligo/util/DistanceMetrics.py
ligo/util/DocEnumHelper.py
ligo/util/ExporterHelper.py
ligo/util/FilenameHandler.py
ligo/util/ImportHelper.py
ligo/util/Logger.py
ligo/util/NameBuilder.py
ligo/util/NumpyHelper.py
ligo/util/ParameterValidator.py
ligo/util/PathBuilder.py
ligo/util/PositionHelper.py
ligo/util/ReadsType.py
ligo/util/ReflectionHandler.py
ligo/util/RepertoireBuilder.py
ligo/util/Reports.py
ligo/util/StringHelper.py
ligo/util/__init__.py
ligo/workflows/__init__.py
ligo/workflows/instructions/Instruction.py
ligo/workflows/instructions/__init__.py
ligo/workflows/instructions/ligo_sim_feasibility/FeasibilitySummaryInstruction.py
ligo/workflows/instructions/ligo_sim_feasibility/__init__.py
ligo/workflows/instructions/ligo_sim_feasibility/feasibility_reports.py
ligo/workflows/instructions/ligo_simulation/LigoSimInstruction.py
ligo/workflows/instructions/ligo_simulation/__init__.py
ligo/workflows/instructions/ligo_simulation/runtime_reports.py
scripts/DocumentatonFormat.py
scripts/__init__.py
scripts/specification_util.py
scripts/specs_docs_generation.py