if (m->control_pressed) { return 0; }
if(allFiles){
- //clear out all old group files
map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
map<string, string>::iterator it;
set<string> namesToRemove;
map<string, int> groupToIndex;
vector<string> primerNameVector; //needed here?
vector<string> barcodeNameVector; //needed here?
+ vector<int> groupCounts; //same order as barcodeNameVector
vector<int> processIDS; //processid
vector<linePair*> lines;