Exemple #1
0
std::string BaseQuality::average_base_qualities(std::vector<const std::string*> qualities){
  assert(qualities.size() > 0);

  // Check that all base quality strings are of the same length
  for (unsigned int i = 0; i < qualities.size(); i++){
    if (qualities[i]->size() != qualities[0]->size())
      printErrorAndDie("All base quality strings must be of the same length when averaging probabilities");
  }

  // Average raw error probabilities for each base and convert
  // to the closest quality score
  std::string avg_qualities('N', qualities[0]->size());
  std::vector<double> log_probs(qualities.size());
  for (unsigned int i = 0; i < qualities[0]->size(); i++){
    for (unsigned int j = 0; j < qualities.size(); j++)
      log_probs[j] = log_prob_error(qualities[j]->at(i));
    double log_mean_prob = log_sum_exp(log_probs) - log(qualities.size());
    avg_qualities[i]     = closest_char(log_mean_prob);
  }
  return avg_qualities;
}
void rl_act_perm::act_sample( void ) {
  //  printf( "perm sample %d dim\n", dim );

  log_probs = params;
  grad = 1;

  for ( int i=0; i<dim; i++ ) {
    ll_to_prob( log_probs, probs );
    //    probs.Print();
    int a = sample( probs, &rng_state );

    vals[i] = a;

    // computation of grad = grad + -1*probs
    Add( -1, probs, grad );

    log_probs(a) = MFMIN;
  }

  //  printf( "Gradient: " ); grad.Print();
}