X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makecontigscommand.cpp;h=f888fbe4928a9526d34e9b8f25200fb32a329f6f;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=c8f20f10eed04c59df0aa27c136029e43713579e;hpb=67ea6ccd74dbd64828d31b952808255f206364ff;p=mothur.git

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index c8f20f1..f888fbe 100644
--- 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;  }
 					}