//-------------------------------------------------------------------------
// New improved normalization strategy
void DPTreephaser::NormalizeAndSolve3(BasecallerRead& well, int max_flows)
{
int window_size = windowSize_;
int solve_flows = 0;
for (int num_steps = 1; solve_flows < max_flows; ++num_steps) {
solve_flows = min((num_steps+1) * window_size, max_flows);
Solve(well, solve_flows);
WindowedNormalize(well, num_steps, window_size);
}
Solve(well, max_flows);
}
// Sliding window adaptive normalization
void DPTreephaser::NormalizeAndSolve5(BasecallerRead& well, int max_flows)
{
int window_size = 50;
int solve_flows = 0;
for (int num_steps = 1; solve_flows < max_flows; ++num_steps) {
solve_flows = min((num_steps+1) * window_size, max_flows);
int restart_flows = max(solve_flows-100, 0);
Solve(well, solve_flows, restart_flows);
WindowedNormalize(well, num_steps, window_size);
}
Solve(well, max_flows);
}
// Sliding window adaptive normalization and joint solving of sequence
void TreephaserLite::NormalizeAndSolve(BasecallerRead& well, int max_flows, bool sliding_window)
{
int window_size = windowSize_;
int solve_flows = 0;
for (int num_steps = 1; solve_flows < max_flows; ++num_steps) {
solve_flows = min((num_steps+1) * window_size, max_flows);
int restart_flows = 0;
if(sliding_window)
restart_flows = max(solve_flows-100, 0);
Solve(well, solve_flows, restart_flows);
WindowedNormalize(well, num_steps, window_size);
}
Solve(well, max_flows);
}
// Sliding window adaptive normalization
void DPTreephaser::NormalizeAndSolve5(BasecallerRead& well, int max_flows)
{
int window_size = windowSize_;
int solve_flows = 0;
for (int num_steps = 1; solve_flows < max_flows; ++num_steps) {
solve_flows = min((num_steps+1) * window_size, max_flows);
int restart_flows = max(solve_flows-100, 0);
Solve(well, solve_flows, restart_flows);
WindowedNormalize(well, num_steps, window_size);
}
if(pm_model_available_) pm_model_enabled_ = true;
Solve(well, max_flows);
pm_model_enabled_ = false;
}
//-------------------------------------------------------------------------
// New improved normalization strategy
void DPTreephaser::NormalizeAndSolve_Adaptive(BasecallerRead& read, int max_flows)
{
int window_size = windowSize_;
int solve_flows = 0;
// Disable recalibration during normalization stage if requested
if (skip_recal_during_normalization_)
recalibrate_predictions_ = false;
for (int num_steps = 1; solve_flows < max_flows; ++num_steps) {
solve_flows = min((num_steps+1) * window_size, max_flows);
Solve(read, solve_flows);
WindowedNormalize(read, num_steps, window_size);
}
// And turn it back on (if available) for the final solving part
EnableRecalibration();
Solve(read, max_flows);
}
