+ 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;
+ }