//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
//get user cutoff and precision or use defaults
string temp;
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
- convert(temp, precision);
+ m->mothurConvert(temp, precision);
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
sim = m->isTrue(temp);
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;
}