- int extractSffInfo(string, string);
- CommonHeader* readCommonHeader(ifstream&);
- Header* readHeader(ifstream&);
- seqRead* readSeqData(ifstream&, int, int);
+private:
+ 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;
+ 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;
+
+ //extract sff file functions
+ int extractSffInfo(string, string, string);
+ int readCommonHeader(ifstream&, CommonHeader&);
+ //int readHeader(ifstream&, Header&);
+ int readSeqData(ifstream&, seqRead&, int, Header&);
+ int decodeName(string&, string&, string&, string);
+ bool readOligos(string oligosFile);