*/
#include "command.hpp"
+#include "groupmap.h"
+#include "oligos.h"
+#include "trimoligos.h"
-#define SFF_MAGIC 0x2e736666 /* ".sff" */
-#define SFF_VERSION "\0\0\0\1"
-
-/**********************************************************/
-struct CommonHeader {
- uint32_t magicNumber;
- char* version;
- uint64_t indexOffset;
- uint32_t indexLength;
- uint32_t numReads;
- uint16_t headerLength;
- uint16_t keyLength;
- uint16_t numFlowsPerRead;
- uint8_t flogramFormatCode;
- char* flowChars; //length depends on number flow reads
- char* keySequence; //length depends on key length
-
- CommonHeader() { magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
-};
-/**********************************************************/
-struct Header {
- unsigned short headerLength;
- unsigned short nameLength;
- unsigned int numBases;
- unsigned short clipQualLeft;
- unsigned short clipQualRight;
- unsigned short clipAdapterLeft;
- unsigned short clipAdapterRight;
- char* name; //length depends on nameLength
-
- Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
-};
-/**********************************************************/
-struct seqRead {
- vector<unsigned short> flowgram;
- vector<unsigned int> flowIndex;
- char* bases;
- vector<unsigned int> qualScores;
-};
/**********************************************************/
class SffInfoCommand : public Command {
public:
SffInfoCommand(string);
- ~SffInfoCommand();
- int execute();
- void help();
+ SffInfoCommand();
+ ~SffInfoCommand(){}
-private:
- string sffFilename, outputDir;
- vector<string> filenames, outputNames;
- bool abort;
+ vector<string> setParameters();
+ string getCommandName() { return "sffinfo"; }
+ string getCommandCategory() { return "Sequence Processing"; }
- int extractSffInfo(string, string);
- CommonHeader* readCommonHeader(ifstream&);
- Header* readHeader(ifstream&);
- seqRead* readSeqData(ifstream&, int, int);
+ 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, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile, groupfile;
+ vector<string> filenames, outputNames, accnosFileNames, oligosFileNames, groupFileNames;
+ bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos, hasGroup, reorient, pairedOligos;
+ int mycount, split, numBarcodes, numFPrimers, numLinkers, numSpacers, numRPrimers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, numNoMatch;
+ set<string> seqNames;
+ GroupMap* groupMap;
+ vector<vector<int> > numSplitReads;
+ vector<vector<string> > filehandles;
+ vector<vector<string> > filehandlesHeaders;
+ Oligos* oligosObject;
+
+ //extract sff file functions
+ int extractSffInfo(string, string, string);
+ int readCommonHeader(ifstream&, CommonHeader&);
+ int readHeader(ifstream&, Header&);
+ bool readSeqData(ifstream&, seqRead&, int, Header&, TrimOligos*&, TrimOligos*&);
+ int decodeName(string&, string&, string&, string);
+ bool readOligos(string oligosFile);
+ bool readGroup(string oligosFile);
- 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&);
+ int adjustCommonHeader(CommonHeader);
+ int findGroup(Header header, seqRead read, int& barcode, int& primer, TrimOligos*&, TrimOligos*&);
+ int findGroup(Header header, seqRead read, int& barcode, int& primer, string);
+ 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&);
};
/**********************************************************/