minor mods to seq.error

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 6ca0310d109c117cf5205ac0725e79338540676a..35ff7627552d2e2d15fe4e03adcd9c634e8b8b3c 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -26,6 +26,8 @@ public:
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
+       string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          
@@ -44,7 +46,7 @@ private:
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string);
        int divideInHalf(Sequence, string&, string&);
-       string sortFastaFile(string, string);
+       map<string, int> sortFastaFile(string, string);
                
        #ifdef USE_MPI
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);