-
- string comboGroupName = "";
- string fastaFileName = "";
- string qualFileName = "";
- string nameFileName = "";
- string countFileName = "";
-
- if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->first];
- }
- else{
- if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->first];
- }
- else{
- comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
- }
- }
-
-
- ofstream temp;
- fastaFileName = rootname + comboGroupName + ".fasta";
- if (uniqueNames.count(fastaFileName) == 0) {
- outputNames.push_back(fastaFileName);
- outputTypes["fasta"].push_back(fastaFileName);
- uniqueNames.insert(fastaFileName);
- }
-
- fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
- m->openOutputFile(fastaFileName, temp); temp.close();
-
- if ((fqualfile != "") || (ffastqfile != "") || (file != "")) {
- qualFileName = rootname + ".qual";
- if (uniqueNames.count(qualFileName) == 0) {
- outputNames.push_back(qualFileName);
- outputTypes["qfile"].push_back(qualFileName);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->first];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->first];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ }
+ }
+
+
+ ofstream temp;
+ fastaFileName = rootname + comboGroupName + ".fasta";
+ if (uniqueNames.count(fastaFileName) == 0) {
+ outputNames.push_back(fastaFileName);
+ outputTypes["fasta"].push_back(fastaFileName);
+ uniqueNames.insert(fastaFileName);
+ }
+
+ fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
+ m->openOutputFile(fastaFileName, temp); temp.close();
+
+ if ((fqualfile != "") || (ffastqfile != "") || (file != "")) {
+ qualFileName = rootname + ".qual";
+ if (uniqueNames.count(qualFileName) == 0) {
+ outputNames.push_back(qualFileName);
+ outputTypes["qfile"].push_back(qualFileName);
+ }
+
+ qualFileNames[itBar->first][itPrimer->first] = qualFileName;
+ m->openOutputFile(qualFileName, temp); temp.close();