map<string, string> nameMap;
map<string, string>::iterator itNames;
- if (oldNameMapFName != "") { m->readNames(oldNameMapFName, nameMap); }
+ if (oldNameMapFName != "") {
+ m->readNames(oldNameMapFName, nameMap);
+ if (oldNameMapFName == outNameFile){ outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique.names"; }
+ }
if (m->control_pressed) { return 0; }