//**********************************************************************************************************************
-SharedCommand::SharedCommand(){
+SharedCommand::SharedCommand(string o) : outputDir(o) {
try {
globaldata = GlobalData::getInstance();
//getting output filename
filename = globaldata->inputFileName;
- filename = getRootName(filename);
+ if (outputDir == "") { outputDir += hasPath(filename); }
+
+ filename = outputDir + getRootName(getSimpleName(filename));
filename = filename + "shared";
+
openOutputFile(filename, out);
pickedGroups = false;
}
//set fileroot
- fileroot = getRootName(globaldata->getListFile());
+ fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
//clears file before we start to write to it below
for (int i=0; i<groups.size(); i++) {
//lookup.clear();
string errorOff = "no error";
//errorOff = "";
-
+cout << globaldata->inputFileName << endl;
//read in listfile
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
delete it3->second;
}
+ globaldata->setSharedFile(filename);
return 0;
}
string name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
string group = groupMap->getGroup(name);
- cout << name << endl;
+
if(group == "not found") { outMisMatch << name << endl; }
}
- cout << names << endl;
+
//get last name
string group = groupMap->getGroup(names);
if(group == "not found") { outMisMatch << names << endl; }