void LevMarBeadAssistant::FinalComputeAndSetAverageResidual(BeadTracker& my_beads)
{
avg_resid = 0.0;
float beads_counted = 0.0001;
for (int ibd=0; ibd < numLBeads; ibd++){
// if this iteration is a region-wide parameter fit, then only process beads
// in the sampled sub-group
if ( my_beads.isSampled ) {
// regional sampling enabled
if (my_beads.Sampled(ibd) ) {// && my_beads.BeadIncluded(ibd,skip_beads) ) {
avg_resid += residual[ibd];
beads_counted += 1.0f;
}
}
else {
// rolling regional groups enabled
if (ValidBeadGroup (ibd)) {
if (my_beads.BeadIncluded(ibd,skip_beads)) {
avg_resid += residual[ibd];
beads_counted += 1.0f;
}
}
}
}
avg_resid /= beads_counted;
avg_resid_state = res_state;
}
void SearchAmplitude::ProjectionSearchAmplitude (
BeadTracker &my_beads, bool , bool sampledOnly, int flow_block_size, int flow_block_start
) const
{
// should be using a specific region pointer, not the universal one, to match the bead list
// as we may generate more region pointers from more beads
my_scratch->FillShiftedBkg ( *empty_trace, pointer_regions->rp.tshift, *time_c, true, flow_block_size );
my_scratch->ResetXtalkToZero();
// "emphasis" originally set to zero here, boosted up to the calling function to be explicit
int TmpEmphasis[flow_block_size];
for( int fnum = 0 ; fnum < flow_block_size ; ++fnum )
TmpEmphasis[fnum] = 0; // all zero
my_scratch->FillEmphasis ( TmpEmphasis,emphasis_data->EmphasisVectorByHomopolymer,emphasis_data->EmphasisScale, flow_block_size );
pointer_regions->cache_step.ForceLockCalculateNucRiseCoarseStep ( &pointer_regions->rp, *time_c, *my_flow ); // technically the same over the whole region
for ( int ibd=0;ibd < my_beads.numLBeads;ibd++ )
{
// want this for all beads, even if they are polyclonal.
if (!sampledOnly || (sampledOnly && my_beads.Sampled(ibd))) {
my_scratch->FillObserved ( *my_trace,ibd, flow_block_size ); // set scratch space for this bead
ProjectionSearchOneBead ( &my_beads.params_nn[ibd], flow_block_size, flow_block_start );
my_beads.params_nn[ibd].ApplyAmplitudeZeros ( my_flow->dbl_tap_map, flow_block_size ); // force double-taps to zero
}
}
// undo any problems we may have caused for the rest of the code
pointer_regions->cache_step.Unlock();
}
void IdentifyDmult (BeadTracker &my_beads, RegionTracker &my_regions)
{
float mean_dmult = my_beads.CenterDmult();
for (int nnuc=0;nnuc < NUMNUC;nnuc++)
{
my_regions.rp.d[nnuc] *= mean_dmult;
}
}
void IdentifyDmult ( BeadTracker &my_beads, RegionTracker &my_regions, bool skip_beads )
{
float mean_dmult = my_beads.CenterDmult ( skip_beads ); // only active set
for ( int nnuc=0;nnuc < NUMNUC;nnuc++ )
{
my_regions.rp.d[nnuc] *= mean_dmult;
}
}
void IdentifyDmultFromSample ( BeadTracker &my_beads, RegionTracker &my_regions, bool skip_beads, const LevMarBeadAssistant& lm_state )
{
float mean_dmult = my_beads.CenterDmultFromSample ( skip_beads );
for ( int nnuc=0;nnuc < NUMNUC;nnuc++ )
{
my_regions.rp.d[nnuc] *= mean_dmult;
}
}
void IdentifyNucMultiplyRatio (BeadTracker &my_beads, RegionTracker &my_regions)
{
// provide identifiability constraint
float mean_x = 0.0;
for (int nnuc=0; nnuc<NUMNUC; nnuc++)
{
mean_x += my_regions.rp.NucModifyRatio[nnuc];
}
mean_x /=NUMNUC;
for (int nnuc=0; nnuc<NUMNUC; nnuc++)
{
my_regions.rp.NucModifyRatio[nnuc] /=mean_x;
}
my_beads.RescaleRatio (1.0/mean_x);
}
