added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 865a84d378d0429a77e833aa5b1db7eca097a83f..46e2bc88300c7a3e89f8fb985100d6edd50129a1 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -28,8 +28,8 @@ public:
 private:
        
        bool abort;
-       string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile;
-       bool filter, correction, svg;
+       string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir;
+       bool filter, correction, svg, printAll;
        int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity;
        float divR;
        Chimera* chimera;