void IsolatedSignalProcessing (
SlicedPrequel &my_prequel_setup,
ImageSpecClass &my_image_spec,
Region &wholeChip,
OptArgs &opts,
CommandLineOpts &inception_state,
string &analysisLocation,
SeqListClass &my_keys,
TrackProgress &my_progress,
ComplexMask *complex_mask,
BkgFitterTracker *bkg_fitter_tracker)
{
//@TODO: split function here as we immediately pick up the files
ComplexMask from_beadfind_mask; //Todo: check if we can move this one level up so it is at the same level as the read in from the archive.
if(!(inception_state.bkg_control.signal_chunks.restart_from.empty()))
{
from_beadfind_mask = *complex_mask;
}
else
{
// starting execution fresh
from_beadfind_mask.InitMask();
my_prequel_setup.LoadBeadFindForSignalProcessing ( true );
Json::Value json1;
vector<int> region_list;
RetrieveParameterVectorInt(opts, json1, '-', "region-list", "", region_list);
if(!region_list.empty())
{
my_prequel_setup.RestrictRegions(region_list);
}
if ( inception_state.bfd_control.beadMaskFile != NULL )
{
fprintf ( stdout, "overriding beadfind mask with %s\n", inception_state.bfd_control.beadMaskFile );
from_beadfind_mask.my_mask->LoadMaskAndAbortOnFailure ( inception_state.bfd_control.beadMaskFile );
}
else
{
from_beadfind_mask.my_mask->LoadMaskAndAbortOnFailure ( my_prequel_setup.bfMaskFile.c_str() );
}
from_beadfind_mask.InitPinnedInFlow ( inception_state.flow_context.GetNumFlows() );
}
/********************************************************************
*
* Background Modelling Process
*
*******************************************************************/
// set up the directory for a new temporary wells file
// clear out previous ones (can be bad with re-entrant processing!)
ClearStaleWellsFile();
inception_state.sys_context.MakeNewTmpWellsFile ( inception_state.sys_context.GetResultsFolder() );
// feenableexcept(FE_DIVBYZERO | FE_INVALID); // | FE_OVERFLOW);
// we might use some other model here
if ( true )
{
DoThreadedSignalProcessing ( opts, inception_state, from_beadfind_mask, ChipIdDecoder::GetChipType(), my_image_spec,
my_prequel_setup,my_keys, inception_state.mod_control.passTau, bkg_fitter_tracker);
} // end BKG_MODL
// whatever model we run, copy the signals to permanent location
inception_state.sys_context.CopyTmpWellFileToPermanent ( inception_state.sys_context.GetResultsFolder() );
inception_state.sys_context.CleanupTmpWellsFile (); // remove local file(!) how will this work with re-entrant processing????
// mask file may be updated by model processing
// analysis.bfmask.bin is what BaseCaller expects
string analysisMaskFile = analysisLocation + "analysis.bfmask.bin";
string analysisStatFile = analysisLocation + "analysis.bfmask.stats";
from_beadfind_mask.my_mask->UpdateBeadFindOutcomes ( wholeChip, analysisMaskFile.c_str(), !inception_state.bfd_control.SINGLEBF, 0, analysisStatFile.c_str() );
my_progress.ReportState ( "Raw flowgrams complete" );
}
