added debug statements to trim.seqs

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index abfaa4b8a088713278a9384c08909f9eaaad70d2..4e72a960a7bb07d4e94df795bea462519f6d777a 100644 (file)
--- 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;
@@ -69,9 +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()); }  
        
@@ -81,7 +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&);
@@ -97,7 +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);