finished consensus.seqs cutoff change

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 323dd45a5690cd047742b16b9bdb9f9c08972a5a..9d817a212cc2ad2ee3a330b982d96cffe251bdce 100644 (file)
--- 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;