added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 226b4c959bf25f9c0629a556755641809401baa4..6542b708ccf016f52c5864c7581489a8898c6bcd 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -25,6 +25,8 @@ public:
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
+       string getDescription()         { return "create a consensus sequence for each OTU or for a fasta file"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -38,12 +40,13 @@ private:
        map<string, string> fastaMap;
        map<string, string> nameMap;
        map<string, string> nameFileMap;
+       int cutoff;
        
        int readFasta();
        int readNames();
        int processList(ListVector*&);
        string getConsSeq(string, ofstream&, string&, int);
-       char getBase(vector<int>);
+       char getBase(vector<int>, int);
 };
 
 #endif