X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=69e905e6bc93e401a242f695577b95019be191c3;hb=0d4b21e5ccc56276b0c18d17d8e75d94ce1df4e7;hp=6aa0c0f8ae2c46a32edde8a67276ccb966bc0003;hpb=1e4552ceb0f67f70a147d1cdca7244b62ac115ab;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index 6aa0c0f..69e905e 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -233,6 +233,9 @@ string Sequence::getSequenceString(ifstream& fastaFile) {
 			else if(isprint(letter)){
 				letter = toupper(letter);
 				if(letter == 'U'){letter = 'T';}
+				if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G'  && letter != 'C'){
+					letter = 'N';
+				}
 				sequence += letter;
 			}
 		}