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.*~~