minor bug in chimera maligner

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index c6613bfd507c3dd74f00edeaaa452c8e9d39e950..73037c783be84270a28b0dacf1795c51a3668d0e 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -751,14 +751,14 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                if (m->control_pressed) {  return 0;  }
                
                vector<results> Results = maligner.getOutput();
-       
-               if (realign) {
-                       ChimeraReAligner realigner(thisTemplate, match, misMatch);
-                       realigner.reAlign(query, Results);
-               }
 
                if (chimeraFlag == "yes") {
                        
+                       if (realign) {
+                               ChimeraReAligner realigner(thisTemplate, match, misMatch);
+                               realigner.reAlign(query, Results);
+                       }
+                       
                        //get sequence that were given from maligner results
                        vector<SeqDist> seqs;
                        map<string, float> removeDups;