diff --git a/readme.md b/readme.md index 73ab977..6ee5bea 100644 --- a/readme.md +++ b/readme.md @@ -351,6 +351,8 @@ roughly as though it had a constant well population equal to the plate's average * Advantage: would eliminate the need to use maps to associate vertices with sequences, which would make the code easier to understand. * ~~Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.~~ * ~~Re-implement command line arguments, to enable scripting and statistical simulation studies~~ DONE +* ~~Implement custom Vertex class to simplify code and make it easier to implement different MWM algorithms~~ DONE + * This also seems to be faster when using the same algorithm than the version with lots of maps, which is a nice bonus! * Re-implement CDR1 matching method * Implement Duan and Su's maximum weight matching algorithm * Add controllable algorithm-type parameter? @@ -361,7 +363,7 @@ roughly as though it had a constant well population equal to the plate's average * Implement Vose's alias method for arbitrary statistical distributions of cells * Should probably refactor to use apache commons rng for this * Use commons JCS for caching -* Enable post-filtering instead of pre-filtering. Pre-filtering of things like singleton sequences or saturating-occupancy sequences reduces graph size, but could conceivably reduce pairing accuracy by throwing away data. While these sequences have very little signal, it would be interesting to compare unfiltered results to filtered results. This would require a much, much faster MWM algorithm, though, to handle the much larger graphs. Possible one of the linear-time approximation algorithms. +* Parameterize pre-filtering. Currently, sequences present in all wells are filtered out before constructing the graph, which massively reduces graph size. But, ideally, no pre-filtering would be necessary. ## CITATIONS