Sneha Ramesh Watharkar (Inactive) added a comment - 01/Dec/17 5:30 PM This issue occurs on graphs when a region is loaded, and then another region that contains genes that overlap with the first region is loaded. The overlapping genes are loaded each time a new region containing them is loaded into view. Annotations, .bed files, are saved correctly when overlapping regions are selected. This issue only exists with graphs. The first difference between the two methods of file saving exists in the exportFile method in the ExportFileAction class. This is the same class that was altered in issue 1090, but the issue existed before those changes were implemented. In exportFile, annotations and graphs follow two different if blocks to save. The annotations if block calls a function 'collectSyms' which then adds the syms and their children, in order, to a rootsym which is a List. The size of this list is in the 60s when working with Arabidopsis Thaliana. The if block for graphs simply adds all of the syms into an array list with an .addAll method. These syms do not have children. Attached is a .py to help determine if a file contains duplicate rows.

Ann Loraine added a comment - 13/Dec/17 2:55 PM We will address this for release 9.0.2. Moving to backlog.