sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 414c73cd1d2e6740b89d5200a5c7e7c704097ed6..f5493eb7517db72c20048da57080a587ae675f7e 100644 (file)
--- 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"; }
 
@@ -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;