From 5b983fe12f84f3194e6407d726dc7770a945c172 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Fri, 6 May 2011 17:47:04 +0000
Subject: [PATCH] more chimera.slayer stuff

---
 chimerarealigner.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

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++;		}
 				
 			}
 		}
-- 
2.39.2