void PhaseEstimator::NormalizeBasecallerRead(DPTreephaser& treephaser, BasecallerRead& read, int start_flow, int end_flow)
{
switch (norm_method_) {
case 0:
treephaser.Normalize(read, start_flow, end_flow);
break;
case 1:
treephaser.WindowedNormalize(read, (end_flow / windowSize_), windowSize_);
break;
case 2:
treephaser.PIDNormalize(read, start_flow, end_flow);
break;
case 3: // Variable per-read normalization based on the number of negative valued zero-mers
if (read.penalty_residual.at(0) > maxfrac_negative_flows_)
treephaser.WindowedNormalize(read, (end_flow / windowSize_), windowSize_);
else
treephaser.Normalize(read, start_flow, end_flow);
break;
case 4: // "off" do not do anything
break;
default:
cerr << "PhaseEstimator: Unknown normalization method " << norm_method_ << endl;
exit(EXIT_FAILURE);
}
};
float PhaseEstimator::EvaluateParameters(vector<BasecallerRead *>& useful_reads, DPTreephaser& treephaser, const float *parameters, const bool usePIDNorm)
{
float try_cf = parameters[0];
float try_ie = parameters[1];
float try_dr = parameters[2];
if (try_cf < 0 or try_ie < 0 or try_dr < 0 or try_cf > 0.04 or try_ie > 0.04 or try_dr > 0.01)
return 1e10;
treephaser.SetModelParameters(try_cf, try_ie, try_dr);
float metric = 0;
for (vector<BasecallerRead *>::iterator read = useful_reads.begin(); read != useful_reads.end(); ++read) {
treephaser.Simulate(**read, 120);
float normalizer = (usePIDNorm ? treephaser.PIDNormalize(**read, 8, 100) : treephaser.Normalize(**read, 20, 100));
for (unsigned int flow = 20; flow < 100 and flow < (*read)->raw_measurements.size(); flow++) {
if ((*read)->raw_measurements[flow] > 1.2)
continue;
float delta = (*read)->raw_measurements[flow] - (*read)->prediction[flow] * normalizer;
metric += delta * delta;
}
}
return isnan(metric) ? 1e10 : metric;
}
