X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.h;h=414c73cd1d2e6740b89d5200a5c7e7c704097ed6;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=0dc1cd977c9b106b4986e2cb839939cae7541db2;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 0dc1cd9..414c73c 100644
--- 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;
 	
@@ -58,7 +59,7 @@ private:
 	bool allFiles;
 	int processors;
 	int numFPrimers, numRPrimers;
-	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;
@@ -66,10 +67,11 @@ private:
 	
 	string flowFileName, oligoFileName, outputDir;
 
-
 	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?
@@ -130,7 +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;