working on current change

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index bcf996b53a1f2cd385fa7bb00a2c2c7c50cf4343..ec043360ad1cd553d782d1d67ab531c9a4610778 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -157,7 +157,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "oligos", true);
                        if (temp == "not found")        {       oligoFileName = "";             }
                        else if(temp == "not open")     {       abort = true;                   } 
-                       else                                            {       oligoFileName = temp;   }
+                       else                                            {       oligoFileName = temp;   m->setOligosFile(oligoFileName); }
                        
                        temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
                        else if(m->isTrue(temp))        {       fasta = 1;      }
@@ -612,7 +612,7 @@ int TrimFlowsCommand::stripBarcode(Sequence& seq, int& group){
                        if (barcodes.size() > 0) {
                                map<string,int>::iterator it=barcodes.begin();
                                
-                               for(it;it!=barcodes.end();it++){
+                               for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
                                        if(it->first.length() > maxLength){
                                                maxLength = it->first.length();
                                        }