void help();
private:
- string sffFilename, outputDir;
- vector<string> filenames, outputNames;
- bool abort;
+ string sffFilename, outputDir, accnosName;
+ vector<string> filenames, outputNames, accnosFileNames;
+ bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
+ set<string> seqNames;
int extractSffInfo(string, string);
int readCommonHeader(ifstream&, CommonHeader&);
int printCommonHeader(ofstream&, CommonHeader&);
int printHeader(ofstream&, Header&);
- int printSeqData(ofstream&, seqRead&);
+ int printSffTxtSeqData(ofstream&, seqRead&, Header&);
+ int printFlowSeqData(ofstream&, seqRead&, Header&);
+ int printFastaSeqData(ofstream&, seqRead&, Header&);
+ int printQualSeqData(ofstream&, seqRead&, Header&);
+ int readAccnosFile(string);
};