fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not found") { cout << "fasta is a required parameter for the screen.seqs command." << endl; abort = true; }
else if (fastafile == "not open") { abort = true; }
-
+
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
alignreport = validParameter.validFile(parameters, "alignreport", true);
if (alignreport == "not open") { abort = true; }
- else if (alignreport == "not found") { namefile = ""; }
+ else if (alignreport == "not found") { alignreport = ""; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...