added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 36bccc2b205635c6b1b0df872332534d615e3bb1..7f262bf9019de7e26d611e9d8b6c37c9f47e7cc6 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -658,7 +658,6 @@ int ClassifySeqsCommand::execute(){
                        }
                        
                        outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
-                       outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
                        outputNames.push_back(taxSummary);      outputTypes["taxsummary"].push_back(taxSummary);
                        
                        int start = time(NULL);
@@ -782,7 +781,9 @@ int ClassifySeqsCommand::execute(){
                        }
 #endif
                        
-                       if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); }
+                       if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); 
+                outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
+            }else { m->mothurRemove(newaccnosFile); }
 
                m->mothurOutEndLine();
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -895,12 +896,12 @@ int ClassifySeqsCommand::execute(){
                        #ifdef USE_MPI  
                                }
                        #endif
-
-                       m->mothurOutEndLine();
-                       m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
-                       m->mothurOutEndLine();
                }
+        
+        m->mothurOutEndLine();
+        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+        for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+        m->mothurOutEndLine();
                
                //set taxonomy file as new current taxonomyfile
                string current = "";