v 19.3

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 07a4c0816020ee0c9678f81dbdafe108c0f0f92d..fd2f4f535dfa3ca7b4be2c99b2e323a2d4d0b49c 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -24,6 +24,7 @@ public:
        string getCommandName()                 { return "consensus.seqs";              }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -37,12 +38,13 @@ 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