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update ToDos

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eugenefischer
2025-04-15 15:50:55 -05:00
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@@ -634,7 +634,10 @@ a means of exploring some very beautiful math.
## TODO ## 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 * ~~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 * ~~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.*~~ * ~~*No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.*~~