From 7ecb96ba54980d303fa066b4c29dae1e5a5be5b9 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Fri, 27 May 2011 18:19:15 +0000
Subject: [PATCH] finished consensus.seqs cutoff change

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

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 323dd45..9d817a2 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -536,7 +536,6 @@ char ConsensusSeqsCommand::getBase(vector<int> counts, int size){  //A,T,G,C,Gap
 			if (counts[i] < zeroCutoff) { counts[i] = 0; }
 		}
 		
-		
 		//any
 		if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'n'; }
 		//any no gap
@@ -600,7 +599,7 @@ char ConsensusSeqsCommand::getBase(vector<int> counts, int size){  //A,T,G,C,Gap
 		//only gap
 		else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = '-'; }
 		//cutoff removed all counts
-		else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  m->mothurOut("cutoff ...."); m->mothurOutEndLine(); }
+		else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'N'; }
 		else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
 		
 		return conBase;
-- 
2.39.2