helpString += "Example unifrac.weighted(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.weighted command output two files: .weighted and .wsummary 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) {
}
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);