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readmodelformat.md

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Read model format

Illumina model

{
  'model_class': 'illumina',       # This tells Mitty which model class to use
  'model_description': 'My model', # This will be printed in the one page figure describing the model. Good for record keeping
  'bq_mat': None,                  # numpy.array with shape (2, L, 94) storing BQ distribution
  'cum_bq_mat': None,              # numpy.array with shape (2, L, 94) storing normalized cumulative BQ distribution
  'tlen': None,                    # numpy.array with shape (tmax,) giving distribution of template lengthts
  'cum_tlen': None,                # numpy.array with shape (tmax,) storing normalized cumulative distribution of template lengthts
  'mean_rlen': L,                  # These are all L, the length of the read 
  'max_rlen': L, 
  'min_rlen': L, 
}

Where:

L = length of the read tmax = the maximum template length we allow

To gain an intuition of what these parameters mean please see the read model description figures, study the synthetic model generator code (mitty/simulation/sequencing/syntheticsequencer.py) and the Illumina read model code (mitty/simulation/illumina.py).