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);
}
};
int HypothesisEvaluator::EvaluateOneHypothesis(DPTreephaser &working_treephaser, BasecallerRead ¤t_hypothesis, int applyNormalization) {
int last_incorporating_flow = LastIncorporatingFlow(current_hypothesis);
// Simulate sequence
working_treephaser.Simulate(current_hypothesis, nFlows);
// Adaptively normalize each hypothesis
if (applyNormalization>0) {
int window_size= 50;
int steps = last_incorporating_flow / window_size;
working_treephaser.WindowedNormalize(current_hypothesis, steps, window_size);
}
// Solver simulates beginning of the read and then fills in the remaining clipped bases
working_treephaser.Solve(current_hypothesis, nFlows, last_incorporating_flow);
/*cout << "Solved sequence of length: " << hypothesesReadsVector[r].sequence.size() << " ;nFlows = " << nFlows << endl;
cout << "Total read: ";
for (int i=0; i<hypothesesReadsVector[r].sequence.size(); i++)
cout << hypothesesReadsVector[r].sequence[i];
cout << endl;*/
return(last_incorporating_flow);
}
