// ...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 { m->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group", true);
m->setProcessors(temp);
m->mothurConvert(temp, processors);
-
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
//append output files
for(int i=0;i<processIDS.size();i++){
- newFName = m->getFullPathName(".\\" + newFName);
- newNName = m->getFullPathName(".\\" + newNName);
- cout << newFName << endl;
+ //newFName = m->getFullPathName(".\\" + newFName);
+ //newNName = m->getFullPathName(".\\" + newNName);
+
m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));