X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=67e43aa0d4b7f6a6ff251bc45a8254ca49b8b162;hb=20071b183e619c122bf9f63b4bb42722507c4e4a;hp=1fe60e8954acd14dc1a1e02d37c0d8bd987cc1c0;hpb=8159f34321e2c771638059b59a986caca9f3ab60;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 1fe60e8..67e43aa 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -298,7 +298,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			}
             else{
                 if(reportFileName != ""){
-                    m->mothurOut("we are ignoring the report file if your sequences are not aligned.  we will check that the sequences in your fasta and and qual fileare the same length.");
+                    m->mothurOut("we are ignoring the report file if your sequences are not aligned.  we will check that the sequences in your fasta and and qual file are the same length.");
                     m->mothurOutEndLine();
                 }
             }
@@ -759,7 +759,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
             int numParentSeqs = -1;
             int closestRefIndex = -1;
                         
-            numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned(), outChimeraReport);
+            string querySeq = query.getAligned();
+            if (!aligned) {  querySeq = query.getUnaligned();  }
+            
+            numParentSeqs = chimeraTest.analyzeQuery(query.getName(), querySeq, outChimeraReport);
             
             closestRefIndex = chimeraTest.getClosestRefIndex();