├── .gitignore ├── .gitmodules ├── CMakeLists.txt ├── Dockerfile ├── LICENSE ├── NOREC_requirements.txt ├── README.md ├── codewords ├── cw_40_60_hp3.fasta ├── cw_40_60_hp3.json ├── in_vitro_test.fasta └── in_vitro_test.json ├── config.json ├── cpp ├── include │ ├── ACBase.h │ ├── ACDecode.h │ ├── ACEncode.h │ ├── ECDecoding.h │ ├── FastaParser.h │ ├── FreqTable.h │ ├── ProbabilityEval.h │ ├── bitIO.h │ ├── commons.h │ └── debug_log.h ├── single_include │ ├── CRC.h │ ├── argparse.hpp │ ├── nlohmann │ │ └── json.hpp │ └── robin_hood.h └── src │ ├── ACBase.cpp │ ├── ACDecode.cpp │ ├── ACEncode.cpp │ ├── ECDecoding.cpp │ ├── FreqTable.cpp │ ├── ProbabilityEval.cpp │ ├── bitIO.cpp │ ├── commons.cpp │ └── main.cpp ├── data ├── D └── Dorn ├── decode.py ├── docker-compose.yml ├── encode.py ├── error_simulation.py ├── eval.py ├── example_configuration_files ├── 0.5_3366_used_conf.json ├── 0.5_4060_used_conf.json ├── 1.0_3366_used_conf.json ├── 1.0_4060_used_conf.json ├── 1.5_3366_used_conf.json ├── 1.5_4060_config.json ├── 2.0_3366_used_conf.json ├── 2.0_4060_config.json ├── 2.5_3366_used_conf.json ├── 2.5_4060_used_conf.json ├── README.md └── general_configuration_fixed_param_evaluation.json ├── examples ├── Dorn ├── Dorn3_Thu_Feb_24_10_09_28_2022.ini ├── Dorn5_Thu_Feb_24_10_14_38_2022.ini ├── Dorn_Tue_Feb_22_11_57_13_2022.ini ├── dorn.json ├── dorn3.json ├── dorn5.json ├── el.jpg ├── el.jpg_Thu_Feb_24_09_58_39_2022.ini ├── el.json ├── mosla.json ├── mosla.png └── mosla.png_Tue_Feb_22_11_50_32_2022.ini ├── generate_codebook.py ├── readme_images ├── dna_aeon_logo.png └── logo-dna.pdf ├── setup.py └── test ├── CMakeLists.txt ├── test_arithmetic_encoder.cc └── test_base.h /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MW55/DNA-Aeon/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: 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