- if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->second];
- variables["[tag]"] = comboGroupName;
- fileName = getOutputFileName("flow", variables);
- }
- else{
- if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->second];
- }
- else{
- comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
- }
- variables["[tag]"] = comboGroupName;
- fileName = getOutputFileName("flow", variables);
- }
-
- outFlowFileNames[itBar->second][itPrimer->second] = fileName;
-
- ofstream temp;
- m->openOutputFile(fileName, temp);
- temp.close();
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fileName = "";
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
+ }
+
+ outFlowFileNames[itBar->second][itPrimer->second] = fileName;
+
+ ofstream temp;
+ m->openOutputFile(fileName, temp);
+ temp.close();
+ }