added paralellization for windows to dist.seqs and summary.seqs

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 8d2a4280c0e0c5a53eedf76192413b5fae19cb83..1b173911c3d79218413e76533da53b7a3ffa3649 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -26,8 +26,8 @@ public:
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Chimera.slayer"; }
-
+       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()); }          
@@ -52,8 +52,8 @@ private:
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 
-       bool abort, realign, trim, trimera;
-       string fastafile, templatefile, outputDir, search, namefile;
+       bool abort, realign, trim, trimera, save;
+       string fastafile, templatefile, outputDir, search, namefile, blastlocation;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;