chimeras

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index bac02852744952477c97c0ea7dc284f56ff589bc..3e437ec33c5382b57b2364570a4a4caa094c97ea 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -40,8 +40,8 @@ private:
        void appendOutputFiles(string, string); 
 
        bool abort;
-       string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir;
-       bool filter, correction, svg, printAll;
+       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;
        float divR;
        Chimera* chimera;