X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=38e9b6230838424dd136562111f25967f6822099;hb=c27e902ede71ea4d20af65752ef04459c101611b;hp=b9e1c4b3ffbc4951d23204b3b761a74708003edc;hpb=80c3fe03a8fd1635d3ad7918ff00beb973449f50;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index b9e1c4b..38e9b62 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -480,6 +480,18 @@ int Sequence::getAmbigBases(){
 
 //********************************************************************************************************************
 
+void Sequence::removeAmbigBases(){
+	
+	for(int j=0;j<alignmentLength;j++){
+		if(aligned[j] != 'A' && aligned[j] != 'T' && aligned[j] != 'G' && aligned[j] != 'C'){
+			aligned[j] = '-';
+		}
+	}
+	setUnaligned(aligned);
+}
+	
+//********************************************************************************************************************
+
 int Sequence::getLongHomoPolymer(){
 	if(longHomoPolymer == -1){
 		longHomoPolymer = 1;