X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.cpp;fp=chimerarealigner.cpp;h=0f2556aff6983107067635fba4015f88c9e9d33a;hb=c5f38b0c83719306fd2e5a7a83e04988b1853f62;hp=1da327819ab446fe62fb965f36b48211d484b97e;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 1da3278..0f2556a 100644
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -24,7 +24,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 			
 			string qAligned = query->getAligned();
 			string newQuery = "";
-			
+	//cout << qAligned.length() << endl;		
 			//sort parents by region start
 			sort(parents.begin(), parents.end(), compareRegionStart);
 
@@ -80,7 +80,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 		
 			//set query to new aligned string
 			query->setAligned(newQuery);
-			
+	//cout << newQuery.length() << endl;		
 			//free memory
 			for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i];  }
 			for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i];  }