added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 3e437ec33c5382b57b2364570a4a4caa094c97ea..56477a11c5249b88ded4acd2c87ac547e8bc9754 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -35,14 +35,14 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        
-       int driver(linePair*, string, string);
-       void createProcesses(string, string);
+       int driver(linePair*, string, string, string);
+       void createProcesses(string, string, string);
        void appendOutputFiles(string, string); 
 
        bool abort;
        string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir, search;
        bool filter, correction, svg, printAll, realign;
-       int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs;
+       int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;