int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs;
set<string> seqNames;
map<string, int> barcodes;
- map<string, int> rbarcodes;
map<string, int> primers;
vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
vector<vector<int> > numSplitReads;