added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow...

[mothur.git] / sffmultiplecommand.h

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
index ae881aa7fcacb2aab09224d204f301db0531fa35..ecf33b7b87b04890479ef41ce2cc09dd6048e658 100644 (file)
--- a/sffmultiplecommand.h
+++ b/sffmultiplecommand.h
@@ -30,14 +30,26 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
+    
+    struct linePair {
+               int start;
+               int end;
+               linePair(int i, int j) : start(i), end(j) {}
+       };
+
        string filename, outputDir, flowOrder;
        vector<string> outputNames;
-       bool abort, trim;
+       bool abort, trim, large, flip, qtrim, allFiles, keepforward;
        int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
-       int numFlows, numFPrimers, numRPrimers, processors;
-       float signal, noise;
+       int numFlows, numFPrimers, numRPrimers, processors, maxIters, largeSize;
+       float signal, noise, cutoff, sigma, minDelta;
+    int qWindowSize, qWindowStep, keepFirst, removeLast, maxAmbig;
+       double qRollAverage, qThreshold, qWindowAverage, qAverage;
     
     int readFile(vector<string>& sffFiles, vector<string>& oligosFiles);
+    int createProcesses(vector<string> sffFiles, vector<string> oligosFiles);
+    int driver(vector<string> sffFiles, vector<string> oligosFiles, int start, int end);
+
     
 };