//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
/*//valid paramters for this command
m->openOutputFile(newGroupFile, outGroups);
for (int i = 0; i < matrix->getNumSeqs(); i++) {
- if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
Names temp = matrix->getRowInfo(i);
outGroups << temp.seqName << '\t' << temp.groupName << endl;
groupMap = new GroupMap(groupfile);
groupMap->readMap();
- if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
globaldata->gGroupmap = groupMap;
}