X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;fp=trimseqscommand.cpp;h=5a5d445cb8624386e90d4c714c1f460f1be0d509;hb=b740fb182372143e152143c6cc5b9ac8591f09b7;hp=2c88bef2d036e798a0e84a85d0af1120c3fdd6df;hpb=b0997605981902442138b9309e9c43d95c3ba10a;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 2c88bef..5a5d445 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -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;	}