X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequence.cpp;h=685f0726e6ec5042d32379874e54b83e8a6eff26;hp=aa1f1c7eae3c0b1cb08105a070a172169ecf320e;hb=861f46b74c17adec8c6ad6d89f232ae7485797bf;hpb=6e63c5ff52bd2830b689417df8ba3db831e63a96

diff --git a/sequence.cpp b/sequence.cpp
index aa1f1c7..685f072 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -53,7 +53,7 @@ Sequence::Sequence(ifstream& fastaFile){
 		}
 	}
 
-	if(sequence.find_first_of('-') != string::npos){	//	if there are any gaps in the sequence, assume that it is
+	if((sequence.find_first_of('-') != string::npos) || (sequence.find_first_of('.') != string::npos)) {	//	if there are any gaps in the sequence, assume that it is
 		setAligned(sequence);							//	an alignment file
 	}
 	setUnaligned(sequence);								//	also set the unaligned sequence file