if (temp == "not found") { debug = false; nodebug=true; }
else { debug = m->isTrue(temp); }
m->debug = debug;
+
+ if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
if ((input == "") && (output == "") && (tempdefault == "") && nodebug) {
m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true;