chimeracode

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index b2c0a0561a0f6baf035f83fc4113d3a0f16ef643..2cbd5d8343f8b96614020d2be5f04250089b73ee 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -64,9 +64,9 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                vector<results> Results = maligner->getOutput();
 
                //realign query to parents to improve slayers detection rate
-               //ChimeraReAligner realigner(templateSeqs, match, misMatch);
-               //realigner.reAlign(query, Results);
-                       
+               ChimeraReAligner realigner(templateSeqs, match, misMatch);
+               realigner.reAlign(query, Results);
+cout << query->getName() << '\n' << query->getAligned() << endl;
                        //if (chimeraFlag == "yes") {
                        
                //get sequence that were given from maligner results