- int printCommonHeader(ofstream&, CommonHeader*, bool); //bool is debug mode
- int printHeader(ofstream&, Header*, bool);
- int printSeqData(ofstream&, seqRead*, bool);
-
+ int printCommonHeader(ofstream&, CommonHeader&);
+ int printHeader(ofstream&, Header&);
+ int printSffTxtSeqData(ofstream&, seqRead&, Header&);
+ int printFlowSeqData(ofstream&, seqRead&, Header&);
+ int printFastaSeqData(ofstream&, seqRead&, Header&);
+ int printQualSeqData(ofstream&, seqRead&, Header&);
+ int readAccnosFile(string);
+ int parseSffTxt();
+ bool sanityCheck(Header&, seqRead&);
+
+ //parsesfftxt file functions
+ int parseHeaderLineToInt(ifstream&);
+ vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+ vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+ string parseHeaderLineToString(ifstream&);