X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.cpp;h=9a25162bd60fcd35b25c18073947f1a8f6502673;hb=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c;hp=0f2556aff6983107067635fba4015f88c9e9d33a;hpb=edd8b9d9392a99e0b1527507de3a4ca8fabfc1c6;p=mothur.git

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 0f2556a..9a25162 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);
 
@@ -56,6 +56,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 			//align each peice to correct parent from results
 			for (int i = 0; i < queryParts.size(); i++) {
 				alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
+				
 				Nast nast(alignment, queryParts[i], parentParts[i]);
 				delete alignment;
 			}
@@ -80,7 +81,7 @@ 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];  }