some alterations to chimera.slayer

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 6aa0c0f8ae2c46a32edde8a67276ccb966bc0003..69e905e6bc93e401a242f695577b95019be191c3 100644 (file)
--- 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;
                        }
                }