new_contents: """
  Analyze a fasta file using a four-state HMM.
  """
  
  import numpy as np
  
  import zygohelper
  
  # state 0: homozygous-rich
  # state 1: heterozygous-rich
  # state 2: null-rich
  # state 3: wildcard
  
  # emission 0: ACGT
  # emission 1: MRWSYK
  # emission 2: N
  
  g_letter_to_emission = {
          'A':0, 'C':0, 'G':0, 'T':0,
          'M':1, 'R':1, 'W':1, 'S':1, 'Y':1, 'K':1,
          'N':2}
  
  g_default_trans = np.array([
      [0.7, 0.1, 0.1, 0.1],
      [0.1, 0.7, 0.1, 0.1],
      [0.1, 0.1, 0.7, 0.1],
      [0.1, 0.1, 0.1, 0.7]])
  
  g_default_emiss = np.array([
      [0.8, 0.1, 0.1],
      [0.1, 0.8, 0.1],
      [0.1, 0.1, 0.8],
      [0.4, 0.3, 0.3]])
  
  if __name__ == '__main__':
      zygohelper.run(__doc__,
              g_letter_to_emission, g_default_trans, g_default_emiss)
  
subject: add another model to the sample app