X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.h;h=f5493eb7517db72c20048da57080a587ae675f7e;hp=2594815f6b763a303382f9730bce36e84060b713;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 2594815..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"; }
 
@@ -67,7 +69,6 @@ private:
 	
 	string flowFileName, oligoFileName, outputDir;
 
-
 	map<string, int> barcodes;
 	map<string, int> primers;
 	vector<string> revPrimer;
@@ -223,7 +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;