X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerarealigner.cpp;h=c95a1e7a4fee9efe7c821c5448fc44bf5dbd7a75;hp=abad4807212d3d2681f13bf7fd64a14c6ff8f42d;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=2405cc589aaaf0c44809a48fe98d3b96863dac0b

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index abad480..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++;		}
 				
 			}
 		}