/*************************************************************************************************
*************************************************************************************************
*
* Start of Main Function
*
*************************************************************************************************
************************************************************************************************/
int main (int argc, char *argv[])
{
init_salute();
#ifdef _DEBUG
atexit (memstatus);
dbgmemInit();
#endif /* _DEBUG */
ofstream null_ostream("/dev/null"); // must stay live for entire scope, or crash when writing
TheSilenceOfTheArmadillos(null_ostream);
TrackProgress my_progress;
DumpStartingStateOfProgram (argc,argv,my_progress);
CommandLineOpts inception_state (argc, argv);
SeqListClass my_keys;
ImageSpecClass my_image_spec;
SlicedPrequel my_prequel_setup;
SetUpOrLoadInitialState(inception_state, my_keys, my_progress, my_image_spec, my_prequel_setup);
// Start logging process parameters & timing now that we have somewhere to log
my_progress.InitFPLog(inception_state);
// Write processParameters.parse file now that processing is about to begin
my_progress.WriteProcessParameters(inception_state);
// Do separator
Region wholeChip(0, 0, my_image_spec.cols, my_image_spec.rows);
IsolatedBeadFind( my_prequel_setup, my_image_spec, wholeChip, inception_state,
inception_state.sys_context.GetResultsFolder(), inception_state.sys_context.analysisLocation, my_keys, my_progress);
exit (EXIT_SUCCESS);
}
/*************************************************************************************************
*************************************************************************************************
*
* Start of Main Function
*
*************************************************************************************************
************************************************************************************************/
int main (int argc, char *argv[])
{
init_salute();
#ifdef _DEBUG
atexit (memstatus);
dbgmemInit();
#endif /* _DEBUG */
ofstream null_ostream("/dev/null"); // must stay live for entire scope, or crash when writing
TheSilenceOfTheArmadillos(null_ostream);
TrackProgress my_progress;
DumpStartingStateOfProgram (argc,argv,my_progress);
CommandLineOpts inception_state (argc, argv);
SeqListClass my_keys;
ImageSpecClass my_image_spec;
SlicedPrequel my_prequel_setup;
InitStackUnwind(inception_state.sys_context.stackDumpFile);
SetUpOrLoadInitialState(inception_state, my_keys, my_progress, my_image_spec, my_prequel_setup);
// Start logging process parameters & timing now that we have somewhere to log
my_progress.InitFPLog(inception_state);
// Write processParameters.parse file now that processing is about to begin
my_progress.WriteProcessParameters(inception_state);
// Do background model
RealImagesToWells ( inception_state, my_keys, my_progress, my_image_spec,
my_prequel_setup);
my_progress.ReportState ("Analysis (wells file only) Complete");
exit (EXIT_SUCCESS);
}
/*************************************************************************************************
*************************************************************************************************
*
* Start of Main Function
*
*************************************************************************************************
************************************************************************************************/
int main (int argc, char *argv[])
{
init_salute();
ofstream null_ostream("/dev/null"); // must stay live for entire scope, or crash when writing
TheSilenceOfTheArmadillos(null_ostream);
TrackProgress my_progress;
DumpStartingStateOfProgram (argc,argv,my_progress);
if(argc < 2)
{
PrintHelp();
}
for(int i = 1; i < argc; ++i)
{
string s = argv[i];
if(s == "-" || s == "--")
{
cerr << "ERROR: command line input \"-\" must be followed by a short option name (a letter) and \"--\" must be followed by a long option name." << endl;
exit ( EXIT_FAILURE );
}
else if(s == "-?" || s == "-h" || s == "--help")
{
PrintHelp();
}
}
ValidateOpts validater;
validater.Validate(argc, argv);
char** argv2 = new char*[argc];
int datind = TrapAndDeprecateOldArgs(argc, argv, argv2);
OptArgs opts;
opts.ParseCmdLine(argc, (const char**)argv2);
for(int k = 0; k < argc ; ++k)
{
delete [] argv2[k];
}
delete [] argv2;
Json::Value json_params;
CommandLineOpts inception_state;
inception_state.SetOpts(opts, json_params);
if(datind < 0) // there is no "--dat-source-directory"
{
inception_state.sys_context.dat_source_directory = argv[argc - 1];
cout << "dat_source_directory = " << inception_state.sys_context.dat_source_directory << endl;
}
inception_state.PostProcessArgs(opts);
SeqListClass my_keys;
ImageSpecClass my_image_spec;
SlicedPrequel my_prequel_setup;
SetUpOrLoadInitialState(inception_state, my_keys, my_progress, my_image_spec, my_prequel_setup);
// Start logging process parameters & timing now that we have somewhere to log
my_progress.InitFPLog(inception_state);
// Write processParameters.parse file now that processing is about to begin
my_progress.WriteProcessParameters(inception_state);
// Do separator
Region wholeChip(0, 0, my_image_spec.cols, my_image_spec.rows);
IsolatedBeadFind( my_prequel_setup, my_image_spec, wholeChip, inception_state,
inception_state.sys_context.GetResultsFolder(), inception_state.sys_context.analysisLocation, my_keys, my_progress);
exit (EXIT_SUCCESS);
}
/*************************************************************************************************
*************************************************************************************************
*
* Start of Main Function
*
*************************************************************************************************
************************************************************************************************/
int main (int argc, char *argv[])
{
init_salute();
#ifdef _DEBUG
atexit (memstatus);
dbgmemInit();
#endif /* _DEBUG */
// Disable armadillo warning messages.
ofstream null_ostream("/dev/null");
arma::set_stream_err1(null_ostream);
arma::set_stream_err2(null_ostream);
TrackProgress my_progress;
DumpStartingStateOfProgram (argc,argv,my_progress);
CommandLineOpts clo (argc, argv);
InitPinnedWellReporterSystem (clo.img_control);
// Directory to which results files will be written
char *experimentName = NULL;
experimentName = strdup (clo.GetExperimentName());
CreateResultsFolder (experimentName);
CreateResultsFolder (clo.sys_context.basecaller_output_directory);
string analysisLocation;
clo.sys_context.SetUpAnalysisLocation (experimentName,analysisLocation);
// Start logging process parameters & timing now that we have somewhere to log to
my_progress.fpLog = clo.InitFPLog();
// create a raw wells file object
// for new analysis, this is a file to be created; for reprocessing, this is the wells file to be read.
// create the new wells file on a local partition.
ClearStaleWellsFile();
clo.sys_context.MakeNewTmpWellsFile (experimentName);
RawWells rawWells (clo.sys_context.wellsFilePath, clo.sys_context.wellsFileName);
int well_rows, well_cols; // dimension of wells file - found out from images if we use them - why is this separate from the rawWells object?
// structure our flows & special key sequences we look for
int numFlows = clo.GetNumFlows();
SeqListClass my_keys;
my_keys.StdInitialize (clo.flow_context.flowOrder,clo.key_context.libKey, clo.key_context.tfKey,my_progress.fpLog); // 8th duplicated flow processing code
//@TODO: these parameters are just for reporting purposes???
// they appear to be ignored everywhere
my_keys.UpdateMinFlows (clo.key_context.minNumKeyFlows);
my_keys.UpdateMaxFlows (clo.key_context.maxNumKeyFlows);
// GENERATE FUNCTIONAL WELLS FILE & BEADFIND FROM IMAGES OR PREVIOUS PROCESS
Region wholeChip;
//Create empty Mask object
ExportSubRegionSpecsToMask (clo.loc_context);
Mask bfmask (1, 1);
Mask *maskPtr = &bfmask;
GetFromImagesToWells (rawWells, maskPtr, clo, experimentName, analysisLocation, numFlows, my_keys,my_progress, wholeChip, well_rows,well_cols);
if (!clo.mod_control.USE_RAWWELLS & clo.mod_control.WELLS_FILE_ONLY)
{
// stop after generating the functional wells file
UpdateBeadFindOutcomes (maskPtr, wholeChip, experimentName, !clo.bfd_control.SINGLEBF, clo.mod_control.USE_RAWWELLS);
my_progress.ReportState ("Analysis (wells file only) Complete");
}
else
{
fprintf (stderr, "\n");
fprintf (stderr, "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\n");
fprintf (stderr, "ERROR: Analysis has reached removed BaseCalling code section\n");
fprintf (stderr, "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\n");
fprintf (stderr, "\n");
exit (EXIT_FAILURE);
/*
// Update progress bar status file: img proc complete/sig proc started
updateProgress (IMAGE_TO_SIGNAL);
// ==============================================
// BASE CALLING
// ==============================================
// no images below this point
// operating from a wells file generated above
GenerateBasesFromWells (clo, rawWells, maskPtr, my_keys.seqList, well_rows, well_cols, experimentName, my_progress);
UpdateBeadFindOutcomes (maskPtr, wholeChip, experimentName, !clo.bfd_control.SINGLEBF, clo.mod_control.USE_RAWWELLS);
my_progress.ReportState ("Analysis Complete");
*/
}
clo.sys_context.CleanupTmpWellsFile (clo.mod_control.USE_RAWWELLS);
free (experimentName);
exit (EXIT_SUCCESS);
}