modified chimera.slayer template=self

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 02ebe722a522d763c309bab0ea2215f0ceac6f85..6ca0310d109c117cf5205ac0725e79338540676a 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -14,7 +14,6 @@
 #include "command.hpp"
 #include "chimera.h"
 
-
 /***********************************************************/
 
 class ChimeraSlayerCommand : public Command {
@@ -45,13 +44,14 @@ private:
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string);
        int divideInHalf(Sequence, string&, string&);
+       string sortFastaFile(string, string);
                
        #ifdef USE_MPI
        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, includeAbunds;
+       string fastafile, templatefile, outputDir, search, namefile;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;