X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sffinfocommand.h;h=12f0180db565edf8818455648eadcc19107ec5ab;hp=6e9d87c30d0898e0b6027bb5d3e4a22bfaa388bd;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=df1ea5f2151b9334c471bf4310f78f51bba098be

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 6e9d87c..12f0180 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -11,66 +11,71 @@
  */
 
 #include "command.hpp"
+#include "groupmap.h"
 
-#define SFF_MAGIC   0x2e736666 /* ".sff" */
-#define SFF_VERSION "\0\0\0\1"
-
-/**********************************************************/
-struct CommonHeader {
-	unsigned int magicNumber;
-	char* version;
-	unsigned long int indexOffset;
-	unsigned int indexLength;
-	unsigned int numReads;
-	unsigned short headerLength;
-	unsigned short keyLength;
-	unsigned short numFlowsPerRead;
-	char flogramFormatCode;
-	char* flowChars; //length depends on number flow reads
-	char* keySequence; //length depends on key length
-};
-/**********************************************************/
-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
-};
-/**********************************************************/
-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);
-	int readCommonHeader(ifstream&, CommonHeader*&);
-	int readHeader(ifstream&, Header*&);
-	int readSeqData(ifstream&, seqRead*&, 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;
+	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, string);
+	int readCommonHeader(ifstream&, CommonHeader&);
+	int readHeader(ifstream&, Header&);
+	bool readSeqData(ifstream&, seqRead&, int, Header&);
+	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);
+    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&);
 };
 
 /**********************************************************/