X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.cpp;h=a1e787bab8cd24ebb352593055e7d2fc10b406de;hb=957d67f7d8bbadfd2930de061e89fd9b149270fd;hp=d877f4b93f33d8123ff6a1a9f7f839dc680fcf61;hpb=8da8321bc4d705f6c156248d6229c60a0204f750;p=mothur.git

diff --git a/sequence.cpp b/sequence.cpp
index d877f4b..a1e787b 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -603,7 +603,7 @@ int Sequence::getLongHomoPolymer(){
 int Sequence::getStartPos(){
 	if(startPos == -1){
 		for(int j = 0; j < alignmentLength; j++) {
-			if(aligned[j] != '.'){
+			if((aligned[j] != '.')&&(aligned[j] != '-')){
 				startPos = j + 1;
 				break;
 			}
@@ -668,7 +668,7 @@ int Sequence::filterFromPos(int end){
 int Sequence::getEndPos(){
 	if(endPos == -1){
 		for(int j=alignmentLength-1;j>=0;j--){
-			if(aligned[j] != '.'){
+			if((aligned[j] != '.')&&(aligned[j] != '-')){
 				endPos = j + 1;
 				break;
 			}