X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerarealigner.cpp;h=c95a1e7a4fee9efe7c821c5448fc44bf5dbd7a75;hp=82c4427fb6a9ae4c635b44d64e13a6254c351aa7;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=ba7b97649aaae1d879a1e4ace513ee8a0a20c433

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 82c4427..c95a1e7 100644
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -93,7 +93,6 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<string> parents) {
 			alignmentLength = query->getAlignLength();	//x
 			int queryUnalignedLength = query->getNumBases();	//y
 			
-			
 			buildTemplateProfile(parents);
 			
 			createAlignMatrix(queryUnalignedLength, alignmentLength);
@@ -127,7 +126,7 @@ void ChimeraReAligner::buildTemplateProfile(vector<string> parents) {
 				else if(seq[j] == 'C')	{	profile[j].C++;		}
 				else if(seq[j] == '-')	{	profile[j].Gap++;	}
 				else if(seq[j] == '.')	{	profile[j].Gap++;	}
-				else					{	profile[j].A++;		}
+//				else					{	profile[j].A++;		}
 				
 			}
 		}
@@ -310,7 +309,7 @@ string ChimeraReAligner::getNewAlignment(string query){
 		for(int i=alignmentLength-1;i>=0;i--){
 			flipSeq += queryAlignment[i];			
 		}
-		
+
 		return flipSeq;
 	}
 	catch(exception& e) {