X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=2cbd5d8343f8b96614020d2be5f04250089b73ee;hb=9ada98592a54c82d08f3d46c9b1d8c3e472a922d;hp=b2c0a0561a0f6baf035f83fc4113d3a0f16ef643;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index b2c0a05..2cbd5d8 100644
--- 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