X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.h;h=f5493eb7517db72c20048da57080a587ae675f7e;hp=f4faacb899a8fd547a14d2bd2224b07882356cdf;hb=615301e57c25e241356a9c2380648d117709458d;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec

diff --git a/trimflowscommand.h b/trimflowscommand.h
index f4faacb..f5493eb 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,7 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "trim.flows";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
 	string getDescription()		{ return "trim.flows"; }
 
@@ -49,7 +51,8 @@ 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;
 	
@@ -66,7 +69,6 @@ private:
 	
 	string flowFileName, oligoFileName, outputDir;
 
-
 	map<string, int> barcodes;
 	map<string, int> primers;
 	vector<string> revPrimer;
@@ -222,7 +224,7 @@ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
 				
 				flowData.printFlows(trimFlowFile);
 				
-				if(pDataArray->fasta)	{	currSeq.printSequence(fastaFile);	}
+				if(pDataArray->fasta)	{	currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile);	}
 				
 				if(pDataArray->allFiles){
 					ofstream output;