X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=0557c71bda3453068175fe3d405ff87972df80e1;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=c0c569cfd7975ba34e08adaf6fafdba203be9e9b;hpb=755185afe1c287b8c6eddf9eedd293a38fc9f998;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index c0c569c..0557c71 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -207,6 +207,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
 			numFPrimers = 0;
 			numRPrimers = 0;
+            numLinkers = 0;
+            numSpacers = 0;
 		}
 		
 	}
@@ -235,7 +237,7 @@ int TrimFlowsCommand::execute(){
 		}
 		
 		vector<unsigned long long> flowFilePos;
-	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		flowFilePos = getFlowFileBreaks();
 		for (int i = 0; i < (flowFilePos.size()-1); i++) {
 			lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
@@ -387,7 +389,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 		int count = 0;
 		bool moreSeqs = 1;
 		
-		TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
+		TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 		
 		while(moreSeqs) {
 				
@@ -468,7 +470,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 			//report progress
 			if((count) % 10000 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			unsigned long long pos = flowFile.tellg();
 
 			if ((pos == -1) || (pos >= line->end)) { break; }
@@ -542,9 +544,8 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 
 				}
 				else if(type == "REVERSE"){
-					Sequence oligoRC("reverse", oligo);
-					oligoRC.reverseComplement();
-					revPrimer.push_back(oligoRC.getUnaligned());
+					string oligoRC = reverseOligo(oligo);
+					revPrimer.push_back(oligoRC);
 				}
 				else if(type == "BARCODE"){
 					oligosFile >> group;
@@ -633,6 +634,47 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 		exit(1);
 	}
 }
+//********************************************************************/
+string TrimFlowsCommand::reverseOligo(string oligo){
+	try {
+        string reverse = "";
+        
+        for(int i=oligo.length()-1;i>=0;i--){
+            
+            if(oligo[i] == 'A')		{	reverse += 'T';	}
+            else if(oligo[i] == 'T'){	reverse += 'A';	}
+            else if(oligo[i] == 'U'){	reverse += 'A';	}
+            
+            else if(oligo[i] == 'G'){	reverse += 'C';	}
+            else if(oligo[i] == 'C'){	reverse += 'G';	}
+            
+            else if(oligo[i] == 'R'){	reverse += 'Y';	}
+            else if(oligo[i] == 'Y'){	reverse += 'R';	}
+            
+            else if(oligo[i] == 'M'){	reverse += 'K';	}
+            else if(oligo[i] == 'K'){	reverse += 'M';	}
+            
+            else if(oligo[i] == 'W'){	reverse += 'W';	}
+            else if(oligo[i] == 'S'){	reverse += 'S';	}
+            
+            else if(oligo[i] == 'B'){	reverse += 'V';	}
+            else if(oligo[i] == 'V'){	reverse += 'B';	}
+            
+            else if(oligo[i] == 'D'){	reverse += 'H';	}
+            else if(oligo[i] == 'H'){	reverse += 'D';	}
+            
+            else						{	reverse += 'N';	}
+        }
+        
+        
+        return reverse;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
+		exit(1);
+	}
+}
+
 /**************************************************************************************************/
 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 
@@ -715,7 +757,7 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
 		processIDS.clear();
 		int exitCommand = 1;
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		
 		//loop through and create all the processes you want