else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (fastafile == "not open") { fastafile = ""; abort = true; }
+ else { m->setFastaFile(fastafile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not found") { namefile = ""; }
else if (namefile == "not open") { abort = true; }
- else { readNameFile(); }
+ else { readNameFile(); m->setNameFile(namefile); }
string temp;
temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found"){ temp = "0"; }