}
}
/************************************************************/
-int CountTable::readTable(string file, bool readGroups) {
+int CountTable::readTable(string file, bool readGroups, bool mothurRunning) {
try {
filename = file;
ifstream in;
in >> name; m->gobble(in); in >> thisTotal; m->gobble(in);
if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(thisTotal) + "\n"); }
- if (thisTotal == 0) { error=true; m->mothurOut("[ERROR]: Your count table contains a sequence named " + name + " with a total=0. Please correct."); m->mothurOutEndLine();
+ if ((thisTotal == 0) && !mothurRunning) { error=true; m->mothurOut("[ERROR]: Your count table contains a sequence named " + name + " with a total=0. Please correct."); m->mothurOutEndLine();
}
//if group info, then read it