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();
}