X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sffinfocommand.h;h=5ec6e72239d0772548ce10f584ebccb435230d25;hp=d98edbd3e04f0213a24ed51471d09aab1b74d46a;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hpb=3b137af694d322b7162e97275c070c41b42597a3

diff --git a/sffinfocommand.h b/sffinfocommand.h
index d98edbd..5ec6e72 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -17,7 +17,7 @@
 struct CommonHeader {
 	unsigned int magicNumber;
 	string version;
-	unsigned long int indexOffset;
+	unsigned long long indexOffset;
 	unsigned int indexLength;
 	unsigned int numReads;
 	unsigned short headerLength;
@@ -64,27 +64,39 @@ class SffInfoCommand : public Command {
 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, sfftxtFilename, 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;
-	
+    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);
+	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&);
@@ -94,7 +106,11 @@ private:
 	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);