fixed some bugs

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index e616b744b2ec04d52639eca24cef8fb2af65e783..1989365a5a2a653d54c6b4258f65deaceac079c6 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -179,6 +179,7 @@ int TrimSeqsCommand::execute(){
                                if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
                                else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
                                if(!success)                    {       trashCode += 'q';                                                               }
+                               qFile.close();
                        }
                        if(barcodes.size() != 0){
                                success = stripBarcode(currSeq, group);
@@ -308,6 +309,8 @@ void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
                }
        }
        
+       inOligos.close();
+       
        numFPrimers = forPrimer.size();
        numRPrimers = revPrimer.size();
 }