unsigned short clipAdapterLeft;
unsigned short clipAdapterRight;
string name; //length depends on nameLength
+ string timestamp;
+ string region;
+ string xy;
Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
~Header() { }
public:
SffInfoCommand(string);
+ SffInfoCommand();
~SffInfoCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
vector<string> filenames, outputNames, accnosFileNames;
bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
set<string> seqNames;
+ map<string, vector<string> > outputTypes;
int extractSffInfo(string, string);
int readCommonHeader(ifstream&, CommonHeader&);
int readHeader(ifstream&, Header&);
int readSeqData(ifstream&, seqRead&, int, int);
+ int decodeName(string&, string&, string&, string);
int printCommonHeader(ofstream&, CommonHeader&);
int printHeader(ofstream&, Header&);
- int printSffTxtSeqData(ofstream&, seqRead&);
+ int printSffTxtSeqData(ofstream&, seqRead&, Header&);
int printFlowSeqData(ofstream&, seqRead&, Header&);
int printFastaSeqData(ofstream&, seqRead&, Header&);
int printQualSeqData(ofstream&, seqRead&, Header&);