}
string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
//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); }