LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
src/GenAIRR/__init__.py
src/GenAIRR/seed.py
src/GenAIRR.egg-info/PKG-INFO
src/GenAIRR.egg-info/SOURCES.txt
src/GenAIRR.egg-info/dependency_links.txt
src/GenAIRR.egg-info/requires.txt
src/GenAIRR.egg-info/top_level.txt
src/GenAIRR/TCR/__init__.py
src/GenAIRR/TCR/sequence/__init__.py
src/GenAIRR/TCR/sequence/heavy_chain.py
src/GenAIRR/TCR/sequence/np_region.py
src/GenAIRR/TCR/simulation/__init__.py
src/GenAIRR/TCR/simulation/heavy_chain_sequence_augmentor.py
src/GenAIRR/TCR/simulation/sequence_augmentor_base.py
src/GenAIRR/alleles/__init__.py
src/GenAIRR/alleles/allele.py
src/GenAIRR/container/SimulationContainer.py
src/GenAIRR/container/__init__.py
src/GenAIRR/data/__init__.py
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGH_EXTENDED.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGH_OGRDB.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGK_OGRDB.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGL_OGRDB.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/__init__.py
src/GenAIRR/data/mutation_model_parameters/HH_S5F_60_META.pkl
src/GenAIRR/data/mutation_model_parameters/HH_S5F_META.pkl
src/GenAIRR/data/mutation_model_parameters/HH_S5F_Opposite_META.pkl
src/GenAIRR/data/mutation_model_parameters/HKL_S5F_META.pkl
src/GenAIRR/data/mutation_model_parameters/__init__.py
src/GenAIRR/dataconfig/__init__.py
src/GenAIRR/dataconfig/config_info.py
src/GenAIRR/dataconfig/data_config.py
src/GenAIRR/dataconfig/enums.py
src/GenAIRR/dataconfig/make/__init__.py
src/GenAIRR/dataconfig/make/base_dataconfig_builder.py
src/GenAIRR/dataconfig/make/custom.py
src/GenAIRR/dataconfig/make/random.py
src/GenAIRR/dataconfig/make/auxiliary_builders/__init__.py
src/GenAIRR/dataconfig/make/auxiliary_builders/correction_map_builder.py
src/GenAIRR/dataconfig/make/auxiliary_builders/np_markov_chain_builder.py
src/GenAIRR/dataconfig/make/auxiliary_builders/trimming_proportion_builder.py
src/GenAIRR/mutation/__init__.py
src/GenAIRR/mutation/config.py
src/GenAIRR/mutation/context.py
src/GenAIRR/mutation/mutation_model.py
src/GenAIRR/mutation/result.py
src/GenAIRR/mutation/s5f.py
src/GenAIRR/mutation/s5f_with_substitutions.py
src/GenAIRR/mutation/uniform.py
src/GenAIRR/mutation/components/__init__.py
src/GenAIRR/mutation/components/anchor_checker.py
src/GenAIRR/mutation/components/stop_codon_checker.py
src/GenAIRR/pipeline/AugmentationPipeline.py
src/GenAIRR/pipeline/__init__.py
src/GenAIRR/pipeline/plot_parameters.py
src/GenAIRR/sequence/__init__.py
src/GenAIRR/sequence/heavy_chain.py
src/GenAIRR/sequence/light_chain.py
src/GenAIRR/sequence/np_region.py
src/GenAIRR/sequence/sequence.py
src/GenAIRR/simulation/__init__.py
src/GenAIRR/simulation/heavy_chain_sequence_augmentor.py
src/GenAIRR/simulation/light_chain_sequence_augmentor.py
src/GenAIRR/simulation/sequence_augmentor_base.py
src/GenAIRR/steps/CorrectForDTrims.py
src/GenAIRR/steps/CorrectForVEndCut.py
src/GenAIRR/steps/CorruptSequenceBeginning.py
src/GenAIRR/steps/DistillMutationRate.py
src/GenAIRR/steps/EnforceSequenceLength.py
src/GenAIRR/steps/FilterTCRDJAmbiguities.py
src/GenAIRR/steps/FixDPositionAfterTrimmingIndexAmbiguity.py
src/GenAIRR/steps/FixJPositionAfterTrimmingIndexAmbiguity.py
src/GenAIRR/steps/FixVPositionAfterTrimmingIndexAmbiguity.py
src/GenAIRR/steps/InsertIndels.py
src/GenAIRR/steps/InsertNs.py
src/GenAIRR/steps/ShortDValidation.py
src/GenAIRR/steps/SimulateSequence.py
src/GenAIRR/steps/StepBase.py
src/GenAIRR/steps/__init__.py
src/GenAIRR/unbiased/__init__.py
src/GenAIRR/unbiased/unbiased_dataset.py
src/GenAIRR/utilities/AlleleNComparer.py
src/GenAIRR/utilities/__init__.py
src/GenAIRR/utilities/asc_utilities.py
src/GenAIRR/utilities/data_utilities.py
src/GenAIRR/utilities/derive_similarity_maps.py
src/GenAIRR/utilities/file_utilities.py
src/GenAIRR/utilities/misc.py
src/GenAIRR/utilities/report.py
src/GenAIRR/validation/__init__.py
src/GenAIRR/validation/base.py
src/GenAIRR/validation/result.py
src/GenAIRR/validation/validator.py
src/GenAIRR/validation/rules/__init__.py
src/GenAIRR/validation/rules/conserved_anchor.py
src/GenAIRR/validation/rules/conserved_cysteine.py
src/GenAIRR/validation/rules/frame_alignment.py
src/GenAIRR/validation/rules/junction_translatable.py
src/GenAIRR/validation/rules/stop_codon.py