X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=4e72a960a7bb07d4e94df795bea462519f6d777a;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=0e242afa2f3eab6e53b1d8927c1658aecee97fc6;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 0e242af..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;
@@ -69,8 +69,11 @@ public:
 	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()); }	
 	
@@ -80,7 +83,7 @@ private:
 	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
 	int mycount;
 	set<string> seqNames;
-	
+    
 	//extract sff file functions
 	int extractSffInfo(string, string);
 	int readCommonHeader(ifstream&, CommonHeader&);
@@ -96,7 +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);