- if (qFileName != "") { outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile); outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
- string groupFile = "";
- if (groupfile == "") { groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups"; }
- else{
- groupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "trim.groups";
- outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- if(allFiles){
- for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {
- groupToIndex[groupMap->namesOfGroups[i]] = i;
- groupVector.push_back(groupMap->namesOfGroups[i]);
- fastaFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupMap->namesOfGroups[i] + ".fasta"));
-
- //we append later, so we want to clear file
- ofstream outRemove;
- m->openOutputFile(fastaFileNames[i], outRemove);
- outRemove.close();
- if(qFileName != ""){
- qualFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupMap->namesOfGroups[i] + ".qual"));
- ofstream outRemove2;
- m->openOutputFile(qualFileNames[i], outRemove2);
- outRemove2.close();
- }
- }
- }
- comboStarts = fastaFileNames.size()-1;
+ if (qFileName != "") {
+ outputNames.push_back(trimQualFile);
+ outputNames.push_back(scrapQualFile);
+ outputTypes["qual"].push_back(trimQualFile);
+ outputTypes["qual"].push_back(scrapQualFile);