else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
+ if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") {
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
outputDir = "";
outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
-
+
+ if ((namefile == "") && (fastafile != "")){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}