// ...at some point should added some additional type checking...
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not found") { namefile = ""; }
- else if (namefile == "not open") { abort = true; }
+ else if (namefile == "not open") { namefile = ""; abort = true; }
else { readNameFile(); m->setNameFile(namefile); }
string temp;
temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, diffs);
+ m->mothurConvert(temp, diffs);
temp = validParameter.validFile(parameters, "percent", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, percent);
+ m->mothurConvert(temp, percent);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}