struct CommonHeader {
unsigned int magicNumber;
string version;
- unsigned long int indexOffset;
+ unsigned long long indexOffset;
unsigned int indexLength;
unsigned int numReads;
unsigned short headerLength;
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();
+ ~SffInfoCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "sffinfo"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
+ string getDescription() { return "extract sequences reads from a .sff file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- string sffFilename, outputDir, accnosName;
- vector<string> filenames, outputNames, accnosFileNames;
- bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
+ 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, vector<string> > outputTypes;
-
- int extractSffInfo(string, string);
+ 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, int);
+ //int readHeader(ifstream&, Header&);
+ int readSeqData(ifstream&, seqRead&, int, Header&);
int decodeName(string&, string&, string&, string);
+ bool readOligos(string oligosFile);
int printCommonHeader(ofstream&, CommonHeader&);
int printHeader(ofstream&, Header&);
int printFastaSeqData(ofstream&, seqRead&, Header&);
int printQualSeqData(ofstream&, seqRead&, Header&);
int readAccnosFile(string);
-
+ int parseSffTxt();
+ bool sanityCheck(Header&, seqRead&);
+ int adjustCommonHeader(CommonHeader);
+ int findGroup(Header header, seqRead read, int& barcode, int& primer);
+ string reverseOligo(string oligo);
+
+ //parsesfftxt file functions
+ int parseHeaderLineToInt(ifstream&);
+ vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+ vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+ string parseHeaderLineToString(ifstream&);
};
/**********************************************************/