X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=4e72a960a7bb07d4e94df795bea462519f6d777a;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=903a589cd777b89b7e508e48d1173d550210f864;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 903a589..4e72a96 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -69,6 +69,7 @@ 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"; }
@@ -82,7 +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&);
@@ -98,7 +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);