- for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
- for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
-
- string primerName = primerNameVector[itPrimer->second];
- string barcodeName = barcodeNameVector[itBar->second];
-
- 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();
- }
- }
- }
-
- numFPrimers = primers.size();
- numRPrimers = revPrimer.size();
- numLinkers = linker.size();
- numSpacers = spacer.size();
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getOligos");
- exit(1);
- }
-}
-//********************************************************************/
-string TrimFlowsCommand::reverseOligo(string oligo){
- try {
- string reverse = "";
-
- for(int i=oligo.length()-1;i>=0;i--){
-
- if(oligo[i] == 'A') { reverse += 'T'; }
- else if(oligo[i] == 'T'){ reverse += 'A'; }
- else if(oligo[i] == 'U'){ reverse += 'A'; }
-
- else if(oligo[i] == 'G'){ reverse += 'C'; }
- else if(oligo[i] == 'C'){ reverse += 'G'; }
-
- else if(oligo[i] == 'R'){ reverse += 'Y'; }
- else if(oligo[i] == 'Y'){ reverse += 'R'; }
-
- else if(oligo[i] == 'M'){ reverse += 'K'; }
- else if(oligo[i] == 'K'){ reverse += 'M'; }
-
- else if(oligo[i] == 'W'){ reverse += 'W'; }
- else if(oligo[i] == 'S'){ reverse += 'S'; }
-
- else if(oligo[i] == 'B'){ reverse += 'V'; }
- else if(oligo[i] == 'V'){ reverse += 'B'; }
-
- else if(oligo[i] == 'D'){ reverse += 'H'; }
- else if(oligo[i] == 'H'){ reverse += 'D'; }
+ if (allFiles) {
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ if (pairedOligos) {
+ map<int, oligosPair> barcodes = oligos.getPairedBarcodes();
+ map<int, oligosPair> primers = oligos.getPairedPrimers();
+ for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = oligos.getPrimerName(itPrimer->first);
+ string barcodeName = oligos.getBarcodeName(itBar->first);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
+ string comboGroupName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
+ }
+ else{
+ comboGroupName = barcodeName + "." + primerName;
+ }
+ }
+
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ variables["[tag]"] = comboGroupName;
+ string fileName = getOutputFileName("flow", variables);
+ if (uniqueNames.count(fileName) == 0) {
+ outputNames.push_back(fileName);
+ outputTypes["flow"].push_back(fileName);
+ uniqueNames.insert(fileName);
+ }
+
+ outFlowFileNames[itBar->first][itPrimer->first] = fileName;
+ m->openOutputFile(fileName, temp); temp.close();
+ }
+ }
+ }
+ }else {
+ map<string, int> barcodes = oligos.getBarcodes() ;
+ map<string, int> primers = oligos.getPrimers();
+ for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = oligos.getPrimerName(itPrimer->second);
+ string barcodeName = oligos.getBarcodeName(itBar->second);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
+ string comboGroupName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
+ }
+ else{
+ comboGroupName = barcodeName + "." + primerName;
+ }
+ }
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ variables["[tag]"] = comboGroupName;
+ string fileName = getOutputFileName("flow", variables);
+ if (uniqueNames.count(fileName) == 0) {
+ outputNames.push_back(fileName);
+ outputTypes["flow"].push_back(fileName);
+ uniqueNames.insert(fileName);
+ }
+
+ outFlowFileNames[itBar->second][itPrimer->second] = fileName;
+ m->openOutputFile(fileName, temp); temp.close();
+ }
+ }
+ }
+ }