fixed seq. error align=f issue. added std and ave calcs to mothurout. working on...

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 93adb7bf53b280892715411c66aedcf15b5c0df3..0c6ebe2de76c957f2a3f9c072b9127efb002e5fb 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -28,9 +28,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }
-       string getOutputFileNameTag(string, string);
+       
        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 getOutputPattern(string);   
+       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  21:494.\nhttp://www.mothur.org/wiki/Chimera.slayer"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 
@@ -69,7 +70,7 @@ private:
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
        #endif
 
-       bool abort, realign, trim, trimera, save, hasName, hasCount;
+       bool abort, realign, trim, trimera, save, hasName, hasCount, dups;
        string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;