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update TODO

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eugenefischer
2022-09-27 22:20:57 -05:00
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@@ -342,24 +342,25 @@ roughly as though it had a constant well population equal to the plate's average
* ~~Add controllable heap-type parameter?~~
* Parameter implemented. Fibonacci heap the current default.
* ~~Implement sample plates with random numbers of T cells per well.~~ DONE
* Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not.
* Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not due to nature of probability calculations.
* preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
* See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows.
* ~~See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows.~~
* ~~Problem is variable number of cells in a well~~
* ~~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.
* 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
* ~~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.~~ DONE
* Pre-filtering based on comparing (read depth) * (occupancy) to (read count) for each sequence works extremely well
* ~~Add read depth simulation options to CLI~~ DONE
* Update matching metadata output options in CLI
* Update graphml output to reflect current Vertex class attributes
* Update performance data in this readme
* Re-implement CDR1 matching method
* Refactor simulator code to collect all needed data in a single scan of the plate
* Currently it scans once for the vertices and then again for the edge weights. This made simulating read depth awkward, and incompatible with caching of plate files.
* This would be a fairly major rewrite of the simulator code, but could make things faster, and would definitely make them cleaner.