X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=4e72a960a7bb07d4e94df795bea462519f6d777a;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=0fdf6fce6647269d476945031255bb585e78ba83;hpb=01b7dae5525a480d31a1de5bc273692726da8570;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 0fdf6fc..4e72a96 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;
@@ -64,13 +64,18 @@ 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 getOutputFileNameTag(string, string);
+	string getHelpString();	
+	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;
@@ -78,8 +83,7 @@ private:
 	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
 	int mycount;
 	set<string> seqNames;
-	map<string, vector<string> > outputTypes;
-	
+    
 	//extract sff file functions
 	int extractSffInfo(string, string);
 	int readCommonHeader(ifstream&, CommonHeader&);
@@ -95,7 +99,8 @@ private:
 	int printQualSeqData(ofstream&, seqRead&, Header&);
 	int readAccnosFile(string);
 	int parseSffTxt();
-	
+	bool sanityCheck(Header&, seqRead&);
+    
 	//parsesfftxt file functions
 	int parseHeaderLineToInt(ifstream&);
 	vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);