fixed bug with phylo.diversity. not calculating as intended.

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 90c8383f2a8a6fb23467d6b662879dfde5fd8f49..9cdf1b26619a170b7f7d67cc9edc60d89d66559a 100644 (file)
--- 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; }
                        } 
                }
        }