LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
src/GenAIRR/__init__.py
src/GenAIRR/experiment.py
src/GenAIRR/mcp_server.py
src/GenAIRR/ops.py
src/GenAIRR/protocol.py
src/GenAIRR/py.typed
src/GenAIRR/result.py
src/GenAIRR/seed.py
src/GenAIRR/steps.py
src/GenAIRR.egg-info/PKG-INFO
src/GenAIRR.egg-info/SOURCES.txt
src/GenAIRR.egg-info/dependency_links.txt
src/GenAIRR.egg-info/entry_points.txt
src/GenAIRR.egg-info/requires.txt
src/GenAIRR.egg-info/top_level.txt
src/GenAIRR/_native/__init__.py
src/GenAIRR/_native/csrc/CMakeLists.txt
src/GenAIRR/_native/csrc/benchmarks/bench_e2e.c
src/GenAIRR/_native/csrc/data/human_igh_imgt.c
src/GenAIRR/_native/csrc/data/human_igh_imgt.h
src/GenAIRR/_native/csrc/include/genairr/airr.h
src/GenAIRR/_native/csrc/include/genairr/allele.h
src/GenAIRR/_native/csrc/include/genairr/allele_bitmap.h
src/GenAIRR/_native/csrc/include/genairr/aseq.h
src/GenAIRR/_native/csrc/include/genairr/codon.h
src/GenAIRR/_native/csrc/include/genairr/functionality.h
src/GenAIRR/_native/csrc/include/genairr/gdc_format.h
src/GenAIRR/_native/csrc/include/genairr/gdc_io.h
src/GenAIRR/_native/csrc/include/genairr/genairr.h
src/GenAIRR/_native/csrc/include/genairr/genairr_api.h
src/GenAIRR/_native/csrc/include/genairr/nuc.h
src/GenAIRR/_native/csrc/include/genairr/pipeline.h
src/GenAIRR/_native/csrc/include/genairr/rand_util.h
src/GenAIRR/_native/csrc/include/genairr/s5f.h
src/GenAIRR/_native/csrc/include/genairr/sim_config.h
src/GenAIRR/_native/csrc/include/genairr/trace.h
src/GenAIRR/_native/csrc/include/genairr/types.h
src/GenAIRR/_native/csrc/src/allele/allele_pool.c
src/GenAIRR/_native/csrc/src/api/genairr_api.c
src/GenAIRR/_native/csrc/src/core/airr.c
src/GenAIRR/_native/csrc/src/core/allele_bitmap.c
src/GenAIRR/_native/csrc/src/core/aseq.c
src/GenAIRR/_native/csrc/src/core/codon.c
src/GenAIRR/_native/csrc/src/core/functionality.c
src/GenAIRR/_native/csrc/src/corruption/corrupt_3_prime.c
src/GenAIRR/_native/csrc/src/corruption/corrupt_5_prime.c
src/GenAIRR/_native/csrc/src/corruption/insert_indels.c
src/GenAIRR/_native/csrc/src/corruption/insert_ns.c
src/GenAIRR/_native/csrc/src/corruption/long_read_errors.c
src/GenAIRR/_native/csrc/src/corruption/paired_end.c
src/GenAIRR/_native/csrc/src/corruption/pcr_amplification.c
src/GenAIRR/_native/csrc/src/corruption/primer_mask.c
src/GenAIRR/_native/csrc/src/corruption/quality_errors.c
src/GenAIRR/_native/csrc/src/corruption/reverse_complement.c
src/GenAIRR/_native/csrc/src/corruption/simulate_umi.c
src/GenAIRR/_native/csrc/src/corruption/spike_contaminants.c
src/GenAIRR/_native/csrc/src/corruption/trim_to_length.c
src/GenAIRR/_native/csrc/src/io/gdc_read.c
src/GenAIRR/_native/csrc/src/io/gdc_write.c
src/GenAIRR/_native/csrc/src/mutation/s5f.c
src/GenAIRR/_native/csrc/src/mutation/uniform.c
src/GenAIRR/_native/csrc/src/pipeline/pipeline.c
src/GenAIRR/_native/csrc/src/pipeline/sim_config.c
src/GenAIRR/_native/csrc/src/rearrangement/assemble.c
src/GenAIRR/_native/csrc/src/rearrangement/sample.c
src/GenAIRR/_native/csrc/src/rearrangement/trim.c
src/GenAIRR/_native/csrc/src/simulation/d_inversion.c
src/GenAIRR/_native/csrc/src/simulation/receptor_revision.c
src/GenAIRR/_native/csrc/src/simulation/selection_pressure.c
src/GenAIRR/_native/csrc/src/simulation/simulate_csr.c
src/GenAIRR/_native/csrc/src/util/rand_util.c
src/GenAIRR/_native/csrc/src/util/trace.c
src/GenAIRR/_native/csrc/tests/test_airr.c
src/GenAIRR/_native/csrc/tests/test_aseq.c
src/GenAIRR/_native/csrc/tests/test_bitmap.c
src/GenAIRR/_native/csrc/tests/test_codon_rail.c
src/GenAIRR/_native/csrc/tests/test_corrections.c
src/GenAIRR/_native/csrc/tests/test_functionality.c
src/GenAIRR/_native/csrc/tests/test_gdc.c
src/GenAIRR/_native/csrc/tests/test_ops.c
src/GenAIRR/_native/csrc/tests/test_pipeline.c
src/GenAIRR/_native/csrc/tests/test_real_data.c
src/GenAIRR/_native/csrc/tests/test_s5f.c
src/GenAIRR/_native/csrc/tests/test_serialize.c
src/GenAIRR/alleles/__init__.py
src/GenAIRR/alleles/allele.py
src/GenAIRR/data/__init__.py
src/GenAIRR/data/builtin_dataconfigs/ALPACA_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CAT_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CAT_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CAT_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CAT_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CAT_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CAT_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CHICKEN_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CHICKEN_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/COW_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/COW_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/COW_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/COW_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/COW_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/COW_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/COW_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CYNOMOLGUS_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/CYNOMOLGUS_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DOG_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DOG_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DOG_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DOG_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DOG_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DOG_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DOG_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DROMEDARY_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DROMEDARY_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/DROMEDARY_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/FERRET_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/FERRET_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/FERRET_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/FERRET_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/FERRET_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/FERRET_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/FERRET_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GOAT_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GOAT_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GORILLA_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GORILLA_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GORILLA_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GORILLA_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GORILLA_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GORILLA_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/GORILLA_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HORSE_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HORSE_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGH_EXTENDED.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGH_OGRDB.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGK_OGRDB.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_IGL_OGRDB.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/HUMAN_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_C57BL6J_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_C57BL6J_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_C57BL6J_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_C57BL6J_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_C57BL6J_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_C57BL6J_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_C57BL6J_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/MOUSE_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/PIG_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/PIG_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/PIG_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/PIG_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/PIG_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/PLATYPUS_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RABBIT_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RABBIT_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RABBIT_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RABBIT_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RABBIT_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RABBIT_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RABBIT_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RAT_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RAT_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RAT_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RHESUS_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RHESUS_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RHESUS_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RHESUS_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RHESUS_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RHESUS_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/RHESUS_TCRG_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/SALMON_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/SHEEP_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/SHEEP_IGK_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/SHEEP_IGL_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/SHEEP_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/SHEEP_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/SHEEP_TCRD_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/TROUT_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/TROUT_TCRB_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/ZEBRAFISH_IGH_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/ZEBRAFISH_TCRA_IMGT.pkl
src/GenAIRR/data/builtin_dataconfigs/ZEBRAFISH_TCRD_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/gdc_io.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/utilities/AlleleNComparer.py
src/GenAIRR/utilities/__init__.py
src/GenAIRR/utilities/asc_utilities.py
src/GenAIRR/utilities/data_utilities.py
src/GenAIRR/utilities/imgt_regions.py
src/GenAIRR/utilities/mcp_helpers.py
src/GenAIRR/utilities/misc.py
src/GenAIRR/utilities/visualize.py
tests/test_c_backend.py
tests/test_clause_compiler.py
tests/test_experiment_dsl.py
tests/test_experiment_phase_calls.py
tests/test_gdc_format.py
tests/test_god_aligner.py
tests/test_integration_clause_dsl.py
tests/test_ops.py
tests/test_selection_pressure.py