groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else if (groups == "all") {
- if (groupfile != "") { Groups = groupMap->namesOfGroups; }
+ if (groupfile != "") { Groups = groupMap->getNamesOfGroups(); }
else { m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; }
}else {
m->splitAtDash(groups, Groups);
accnos = m->isTrue(temp);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "0"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
if (cutoff == 0) { m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
-
}
}