void UpdateMask(Mask& mask, std::vector<RegionalizedData *>& sliced_chip)
{
unsigned int numRegions = sliced_chip.size();
for (unsigned int rgn=0; rgn<numRegions; ++rgn)
{
RegionalizedData& local_patch = *sliced_chip[rgn];
int numWells = local_patch.GetNumLiveBeads();
int rowOffset = local_patch.region->row;
int colOffset = local_patch.region->col;
for (int well=0; well<numWells; ++well)
{
BeadParams& bead = local_patch.GetParams (well);
bead_state& state = *bead.my_state;
// Record clonal reads in mask:
int row = rowOffset + bead.y;
int col = colOffset + bead.x;
if(mask.Match(col, row, MaskLib)){
if(state.bad_read)
mask.Set(col, row, MaskFilteredBadKey);
else if(state.ppf >= mixed_ppf_cutoff())
mask.Set(col, row, MaskFilteredBadResidual);
else if(not state.clonal_read)
mask.Set(col, row, MaskFilteredBadPPF);
}
}
}
}