added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index f2d592aab2bd66340de6dcea679ee8a3efda515c..0557c71bda3453068175fe3d405ff87972df80e1 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -207,6 +207,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
                        numFPrimers = 0;
                        numRPrimers = 0;
+            numLinkers = 0;
+            numSpacers = 0;
                }
                
        }
@@ -407,7 +409,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                                success = 0;
                                trashCode += 'l';
                        }
-                       cout << currSeq.getName() << endl << currSeq.getUnaligned() << endl;
+                       
                        int primerIndex = 0;
                        int barcodeIndex = 0;