*/
#include "command.hpp"
+#include "groupmap.h"
+#include "oligos.h"
+#include "trimoligos.h"
-
-/**********************************************************/
-struct CommonHeader {
- unsigned int magicNumber;
- string version;
- unsigned long int indexOffset;
- unsigned int indexLength;
- unsigned int numReads;
- unsigned short headerLength;
- unsigned short keyLength;
- unsigned short numFlowsPerRead;
- int flogramFormatCode;
- string flowChars; //length depends on number flow reads
- string keySequence; //length depends on key length
-
- CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
- ~CommonHeader() { }
-};
-/**********************************************************/
-struct Header {
- unsigned short headerLength;
- unsigned short nameLength;
- unsigned int numBases;
- unsigned short clipQualLeft;
- unsigned short clipQualRight;
- 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() { }
-};
-/**********************************************************/
-struct seqRead {
- vector<unsigned short> flowgram;
- vector<unsigned int> flowIndex;
- string bases;
- vector<unsigned int> qualScores;
-
- seqRead() { }
- ~seqRead() { }
-};
/**********************************************************/
class SffInfoCommand : public Command {
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, 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, 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);
+ 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&, TrimOligos*&, TrimOligos*&);
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, 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);