config.json

{
  "decode": {
    "input": "data/encoded.fasta",
    "NOREC4DNA_config": "data/encoded.ini",
    "length": 0,
    "metric": {
      "fano": {
        "error_probability": 0.05,
        "rate": {
          "high": 7,
          "low": 1
        }
      },
      "penalties": {
        "crc": 0.2,
        "no_hit": 9
      }
    },
    "output": "data/decoded.txt",
    "queue": {
      "reduce": 0.5,
      "runs": 1,
      "size": 200000
    },
    "threshold": {
      "checkpoint": 4,
      "finish": 0,
      "loop": 2
    }
  },
  "encode": {
    "input": "data/D",
    "keep_intermediary": false,
    "min_length": 0,
    "output": "data/encoded.fasta",
    "same_length": true,
    "update_config": true
  },
  "general": {
    "as_fasta": true,
    "codebook": {
      "motifs": "./codewords/cw_40_60_hp3.json",
      "words": "./codewords/cw_40_60_hp3.fasta"
    },
    "sync": 2,
    "threads": 4,
    "zip": {
      "decodable_only": true,
      "most_common_only": true
    }
  },
  "NOREC4DNA": {
    "chunk_size": 14,
    "package_redundancy": 0.4,
    "insert_header":true,
    "header_crc_length": 8,
    "error_detection": "crc"
  }
}