run_config.yml

run_config:
  input: "data"
  output: "results"
  HMM:
    references:
      - 'EM11'
      - 'EM60'
    replicates:
      - 'P1'
      - 'P2'
      - 'P3'
    timesteps:
      - 'D1'
      - 'D2'
      - 'D4'
      - 'D6'
      - 'D8'
      - 'D10'

alignments:
  length_threshold: 5000

HMM_parameters:
  cores: 20
  initial_probability:
    A: "0.5"
    B: "0.5"
  transition_probability:
    A:
      A: "0.99996"
      B: "0.00004"
    B:
      A: "0.00004"
      B: "0.99996"
  emission_probability:
    A:
      0: "0.972"
      1: "0.027"
      2: "0.001"
    B:
      0: "0.972"
      1: "0.001"
      2: "0.027"

optimization_recombination_parameter:
  flag: true
  timesteps: #timestep data to use for optimization
    - 'D10'
  values: '0.00001,0.00002,0.00003,0.00004,0.00005,0.00006,0.00008,0.0001' #comma separated values
  subsample: 1000

plots:
  coverage_threshold: 0