X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=5a5d445cb8624386e90d4c714c1f460f1be0d509;hb=2cfb747aa8f63bde9c1114001e6d2e81ccd26178;hp=a103626f7dd9fbed1074f7132175651360bfe464;hpb=196c22d0f93ba48e8ec54ab76608b6e3ba5e68cc;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a103626..5a5d445 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1533,7 +1533,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 					// get rest of line in case there is a primer name
 					while (!inOligos.eof())	{	
 						char c = inOligos.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;  }
 					} 
@@ -1648,7 +1648,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
         if (hasPairedBarcodes || hasPrimer) {
             pairedOligos = true;
             if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true;  m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine();  return 0; }
-        }
+        }else if (reorient) { m->mothurOut("[Warning]: cannot use checkorient without paired barcodes or primers, ignoring.\n"); m->mothurOutEndLine(); reorient = false; }
         
 		if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){	allFiles = 0;	}