X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nast.cpp;fp=nast.cpp;h=9cdf1b26619a170b7f7d67cc9edc60d89d66559a;hb=515c3398ea27e2105f616fc5662b2a7ceb486aa0;hp=90c8383f2a8a6fb23467d6b662879dfde5fd8f49;hpb=0b99c6b6ea875e13febda76903fd4d9cda7add7d;p=mothur.git

diff --git a/nast.cpp b/nast.cpp
index 90c8383..9cdf1b2 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -187,7 +187,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 						}
 					}
 					i -= insertLength;
-	//if (i < 0) { cout << " we have a negative i = " << i << endl; }
 
 				}
 				else{
@@ -208,6 +207,9 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 				}
 			
 //				i -= insertLength;
+				
+				//if i is negative, we want to remove the extra gaps to the right
+				if (i < 0) { cout << "i is negative" << endl; }
 			} 
 		}
 	}