forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 8656fd0b5b314084c6fd08cf614288aca2bbc763..414c73cd1d2e6740b89d5200a5c7e7c704097ed6 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -49,7 +49,8 @@ private:
        vector<unsigned long long> getFlowFileBreaks();
        int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
        int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+    string reverseOligo(string);
+    
        vector<string> outputNames;
        set<string> filesToRemove;
        
@@ -58,9 +59,7 @@ private:
        bool allFiles;
        int processors;
        int numFPrimers, numRPrimers;
-    int numLinkers, numSpacers;
-
-    int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
        int numFlows;
        float signal, noise;
        bool fasta;
@@ -71,6 +70,8 @@ private:
        map<string, int> barcodes;
        map<string, int> primers;
        vector<string> revPrimer;
+    vector<string> linker;
+    vector<string> spacer;
 
        vector<string> primerNameVector;        //needed here?
        vector<string> barcodeNameVector;       //needed here?
@@ -131,7 +132,7 @@ struct trimFlowData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){ 
        trimFlowData* pDataArray;