string temp = validParameter.validFile(parameters, "nseqs", false);
if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
- else { convert(temp, nseqs); }
+ else { m->mothurConvert(temp, nseqs); }
temp = validParameter.validFile(parameters, "bygroup", false); if (temp == "not found") { temp = "f"; }
byGroup = m->isTrue(temp);
if (groupfile != "") {
groupMap = new GroupMap(groupfile); groupMap->readMap();
SharedUtil util;
- util.setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> namesGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, namesGroups);
m->openOutputFile(outputGroupFileName, outGroup);
}
//**********************************************************************************************************************
int RemoveRareCommand::processShared(){
try {
- m->Groups = Groups;
+ m->setGroups(Groups);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }