InputData* input;
FastaMap* fasta;
GroupMap* groupMap;
- string filename, fastafile, listfile, namesfile, groupfile, line, label;
+ string filename, fastafile, listfile, namesfile, groupfile, label;
ofstream out;
ifstream in, inNames;
bool groupError;
bool abort, allLines;
- set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix