bool BaseCallerParameters::InitializeFilesFromOptArgs(OptArgs& opts)
{
bc_files.input_directory = opts.GetFirstString ('i', "input-dir", ".");
bc_files.output_directory = opts.GetFirstString ('o', "output-dir", ".");
bc_files.unfiltered_untrimmed_directory = bc_files.output_directory + "/unfiltered.untrimmed";
bc_files.unfiltered_trimmed_directory = bc_files.output_directory + "/unfiltered.trimmed";
CreateResultsFolder ((char*)bc_files.output_directory.c_str());
CreateResultsFolder ((char*)bc_files.unfiltered_untrimmed_directory.c_str());
CreateResultsFolder ((char*)bc_files.unfiltered_trimmed_directory.c_str());
ValidateAndCanonicalizePath(bc_files.input_directory);
ValidateAndCanonicalizePath(bc_files.output_directory);
ValidateAndCanonicalizePath(bc_files.unfiltered_untrimmed_directory);
ValidateAndCanonicalizePath(bc_files.unfiltered_trimmed_directory);
bc_files.filename_wells = opts.GetFirstString ('-', "wells", bc_files.input_directory + "/1.wells");
bc_files.filename_mask = opts.GetFirstString ('-', "mask", bc_files.input_directory + "/analysis.bfmask.bin");
ValidateAndCanonicalizePath(bc_files.filename_wells);
ValidateAndCanonicalizePath(bc_files.filename_mask, bc_files.input_directory + "/bfmask.bin");
bc_files.filename_filter_mask = bc_files.output_directory + "/bfmask.bin";
bc_files.filename_json = bc_files.output_directory + "/BaseCaller.json";
bc_files.filename_phase = bc_files.output_directory + "/PhaseEstimates.json";
printf("\n");
printf("Input files summary:\n");
printf(" --input-dir %s\n", bc_files.input_directory.c_str());
printf(" --wells %s\n", bc_files.filename_wells.c_str());
printf(" --mask %s\n", bc_files.filename_mask.c_str());
printf("\n");
printf("Output directories summary:\n");
printf(" --output-dir %s\n", bc_files.output_directory.c_str());
printf(" unf.untr %s\n", bc_files.unfiltered_untrimmed_directory.c_str());
printf(" unf.tr %s\n", bc_files.unfiltered_trimmed_directory.c_str());
printf("\n");
bc_files.lib_datasets_file = opts.GetFirstString ('-', "datasets", "");
bc_files.calibration_panel_file = opts.GetFirstString ('-', "calibration-panel", "");
if (not bc_files.lib_datasets_file.empty())
ValidateAndCanonicalizePath(bc_files.lib_datasets_file);
if (not bc_files.calibration_panel_file.empty())
ValidateAndCanonicalizePath(bc_files.calibration_panel_file);
bc_files.options_set = true;
return true;
};
/*************************************************************************************************
*************************************************************************************************
*
* 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);
}