}
oldNameMapFName = validParameter.validFile(parameters, "name", true);
- if (oldNameMapFName == "not open") { abort = true; }
+ if (oldNameMapFName == "not open") { oldNameMapFName = ""; abort = true; }
else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; }
else { m->setNameFile(oldNameMapFName); }
+
+ if (oldNameMapFName == "") {
+ vector<string> files; files.push_back(inFastaName);
+ parser.getNameFile(files);
+ }
+
}
}
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; }