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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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Customized import of alevin bootstrap counts #32

Closed k3yavi closed 4 years ago

k3yavi commented 4 years ago

Hi @mikelove ,

I think it'd great to have a new parameter in the alevinArgs which can be tweaked for importing the mean and the variance bootstrap estimate matrix. Currently, if alevin is run with numCellBootstraps , tximeta will always import the mean and the variance of the matrices, along with the MLE estimates. I think it's great to load all the matrices most of the time, however, it'd be valuable to have a flag which can control this behavior for the cases where we need quick testing !

btw did I say tximeta is super fast !! :D

mikelove commented 4 years ago

This should be covered by alevingArgs=list(dropMeanVar=TRUE) in tximport v1.17.2.

Also while I was poking around, I remembered I have the notice that:

pre-v0.14.0 Alevin import will be deprecated in October 2020

Does that sound ok? It's a lot of extra code, unit tests, and testing data that is no longer used.