countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
- else { ct.readTable(countfile); m->setCountTableFile(countfile); }
+ else { ct.readTable(countfile, true); m->setCountTableFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }