From 4099ec262302f035a1362906e4872196e480991e Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Tue, 15 Apr 2025 15:50:55 -0500
Subject: [PATCH] update ToDos

---
 readme.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/readme.md b/readme.md
index d7731d7..ea22fe2 100644
--- a/readme.md
+++ b/readme.md
@@ -634,7 +634,10 @@ a means of exploring some very beautiful math.
 
 ## TODO
 
-* Update CLI option text in this readme to include Zipf distribution options
+* Consider whether a graph database might be a better option than keeping things in memory.
+* Look at fastUtil for more performant maps and arrays. Note that there is an optional jGraphT library to work with fastUtil (see FastutilMapIntVertexGraph, for example).
+* Consider implementing an option to use the jGrapht sparse graph representation for a lower memory cost with very large graphs (tens or hundreds of thousands of distinct sequences).
+* ~~Update CLI option text in this readme to include Zipf distribution options~~
 * ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE
 * ~~Hold graph data in memory until another graph is read-in? ABANDONED UNABANDONED~~ DONE
     * ~~*No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*~~