fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 0de118f62016d1497f07461033f7696319b5a7a9..d201ccb5f1baa2c628f217c7c763523e832d70eb 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -43,12 +43,13 @@ private:
        
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string);
+       int divideInHalf(Sequence, 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;
+       bool abort, realign, trim, trimera;
        string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;