changing command name classify.shared to classifyrf.shared

[mothur.git] / makecontigscommand.cpp

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index c8f20f10eed04c59df0aa27c136029e43713579e..f888fbe4928a9526d34e9b8f25200fb32a329f6f 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -1541,6 +1541,7 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
             }
             m->gobble(in);
             
+            if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", forward = " + forward + ", reverse = " + reverse + ".\n"); }
             
             //check to make sure both are able to be opened
             ifstream in2;
@@ -1676,17 +1677,21 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                     }
                     //roligo = reverseOligo(roligo);
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: reading - " + roligo + ".\n"); }
+                    
                     group = "";
                     
                                        // get rest of line in case there is a primer name
                                        while (!in.eof())       {       
                                                char c = in.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
                     
                     oligosPair newPrimer(foligo, roligo);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
                                        
                                        //check for repeat barcodes
                     string tempPair = foligo+roligo;
@@ -1713,7 +1718,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                     group = "";
                     while (!in.eof())  {       
                                                char c = in.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        }