working on chimeras

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 46e2bc88300c7a3e89f8fb985100d6edd50129a1..bac02852744952477c97c0ea7dc284f56ff589bc 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -26,11 +26,23 @@ public:
        
                
 private:
+
+       struct linePair {
+               int start;
+               int numSeqs;
+               linePair(long int i, int j) : start(i), numSeqs(j) {}
+       };
+       vector<int> processIDS;   //processid
+       vector<linePair*> lines;
        
+       int driver(linePair*, string, string);
+       void createProcesses(string, string);
+       void appendOutputFiles(string, string); 
+
        bool abort;
        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;
+       int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs;
        float divR;
        Chimera* chimera;