helpString += "Example unifrac.unweighted(groups=A-B-C, iters=500).\n";
helpString += "The default value for groups is all the groups in your groupfile, and iters is 1000.\n";
helpString += "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
return helpString;
}
catch(exception& e) {
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"groups","iters","distance","random","root", "processors","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
}
m->runParse = true;
+ m->Groups.clear();
+ m->namesOfGroups.clear();
+ m->Treenames.clear();
+ m->names.clear();
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->setTreeFile(treefile);
+
if (groupfile != "") {
//read in group map info.
tmap = new TreeMap(groupfile);