changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 0e242afa2f3eab6e53b1d8927c1658aecee97fc6..837435b3a6ca4c4c7f2e7e7579141b8fbece342b 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;
@@ -70,7 +70,9 @@ public:
        string getCommandName()                 { return "sffinfo";                                     }
        string getCommandCategory()             { return "Sequence Processing";         }
        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 +82,7 @@ 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 +98,8 @@ 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);