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eugenefischer
2022-09-25 22:35:52 -05:00
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@@ -347,11 +347,10 @@ roughly as though it had a constant well population equal to the plate's average
* ~~Apache Commons CSV library writes entries a row at a time~~
* _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing.
* ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE
* ~~Custom vertex type with attribute for sequence occupancy?~~ DONE
* 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
* Advantage: would eliminate the need to use maps to associate vertices with sequences, which would make the code easier to understand.
* 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 simulation of read depth, and of read errors. Pre-filter graph for difference in read count to eliminate spurious sequences.