*/
#include "command.hpp"
-
+#include "groupmap.h"
/**********************************************************/
struct CommonHeader {
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"; }
void help() { m->mothurOut(getHelpString()); }
private:
- string sffFilename, sfftxtFilename, outputDir, accnosName;
- vector<string> filenames, outputNames, accnosFileNames;
- bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
- int mycount;
+ 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;
+ int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, numNoMatch;
set<string> seqNames;
-
+ map<string, int> barcodes;
+ map<string, int> primers;
+ GroupMap* groupMap;
+ vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
+ vector<vector<int> > numSplitReads;
+ vector<vector<string> > filehandles;
+ vector<vector<string> > filehandlesHeaders;
+
//extract sff file functions
- int extractSffInfo(string, string);
+ int extractSffInfo(string, string, string);
int readCommonHeader(ifstream&, CommonHeader&);
int readHeader(ifstream&, Header&);
- int readSeqData(ifstream&, seqRead&, int, int);
+ bool readSeqData(ifstream&, seqRead&, int, Header&);
int decodeName(string&, string&, string&, string);
+ bool readOligos(string oligosFile);
+ bool readGroup(string oligosFile);
int printCommonHeader(ofstream&, CommonHeader&);
int printHeader(ofstream&, 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);
+ 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);