Comparing samples visually or in search ("which sample has this sequence") requires pruning or otherwise filtering the GenGraph to get rid of the reference edges (search), and gray them out + dotted lines for edges (visualization). A chromosome_index of PRESERVE_EDIT_SITE_CHROMOSOME_INDEX should be the way to do that. (To confirm)
Comparing samples visually or in search ("which sample has this sequence") requires pruning or otherwise filtering the GenGraph to get rid of the reference edges (search), and gray them out + dotted lines for edges (visualization). A chromosome_index of PRESERVE_EDIT_SITE_CHROMOSOME_INDEX should be the way to do that. (To confirm)