string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile;
vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;
- int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs;
+ int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, numNoMatch;
set<string> seqNames;
map<string, int> barcodes;
map<string, int> primers;
vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
vector<vector<int> > numSplitReads;
- vector<vector<string> > filehandles, filehandlesHeaders;
+ vector<vector<map<string, ofstream*> > > filehandles;
+ vector<vector<map<string, ofstream*> > > filehandlesHeaders;
//extract sff file functions
int extractSffInfo(string, string, string);
int readCommonHeader(ifstream&, CommonHeader&);
- //int readHeader(ifstream&, Header&);
- int readSeqData(ifstream&, seqRead&, int, Header&);
+ int readHeader(ifstream&, Header&);
+ bool readSeqData(ifstream&, seqRead&, int, Header&);
int decodeName(string&, string&, string&, string);
bool readOligos(string oligosFile);