ofstream out;
ifstream in, inNames, inRow;
bool abort, allLines, groupError, large;
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
ofstream out;
ifstream in, inNames, inRow;
bool abort, allLines, groupError, large;
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix