Node script to generate context-sensitive error model

[Ian Holmes]

• Affine gap model with left & right flanking input contexts (one for each base, plus one for empty context i.e. end-of-sequence)
• 3 states, 25 input contexts
  • no insert->delete transition
• The 16 nonempty contexts have the following parameters:
  • 4x4 substitution matrix
  • P(begin deletion), P(continue deletion), 4*P(confirm deletion|state=X)
  • P(begin insertion), P(continue insertion), 4*P(state=X|insertion)
• The empty contexts are equilibrium frequency-weighted averages of the nonempty contexts