//check for required parameters
qualfile = validParameter.validFile(parameters, "qfile", true);
- if (qualfile == "not open") { abort = true; }
+ if (qualfile == "not open") { qualfile = ""; abort = true; }
else if (qualfile == "not found") {
qualfile = m->getQualFile();
if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- m->mothurConvert(temp, processors);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(qualfile);
+ parser.getNameFile(files);
+ }
}
}
catch(exception& e) {