- m->readNames(oldNameMapFName, nameMap);
- if (oldNameMapFName == outNameFile){
- variables["[tag]"] = "unique";
- outNameFile = getOutputFileName("name", variables); }
+ m->readNames(oldNameMapFName, nameMap);
+ if (oldNameMapFName == outNameFile){
+ //prepare filenames and open files
+ map<string, string> mvariables;
+ mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+ mvariables["[tag]"] = "unique";
+ outNameFile = getOutputFileName("name", mvariables);
+ }