string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
ofstream out;
ifstream in, inNames, inRow;
- bool abort, allLines, groupError, large;
+ bool abort, allLines, groupError, large, weighted;
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
+ map<string, string> nameFileMap;
vector<string> outputNames, Groups;
map<string, string> outputNameFiles;
float cutoff;
map<string, vector<string> > outputTypes;
void readNamesFile();
+ void readNamesFile(bool);
int process(ListVector*);
SeqMap getMap(int);
string findRep(vector<string>); // returns the name of the "representative" sequence of given bin or subset of a bin, for groups