modified mpi code to save ram by writing out every 10 seqs.

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 7721ef8e9428a9e12b1ad0e930f419389d813fca..040d2dde543b9311762640680d1a8ba874e3fcf5 100644 (file)
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -26,11 +26,24 @@ 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, string);
+       int createProcesses(string, string, string);
+       void appendOutputFiles(string, string); 
+
        bool abort;
-       string method, fastafile, templatefile, consfile, quanfile;
-       bool filter, correction;
-       int processors, midpoint, averageLeft, averageRight, window, iters, increment;
+       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, templateSeqsLength;
+       float divR;
        Chimera* chimera;