Support for parallel query for coordinates mappings

jorainer / ensembldb

This is the ensembldb development repository.

https://jorainer.github.io/ensembldb

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Support for parallel query for coordinates mappings #149

Closed Tim-Yu closed 10 months ago

Tim-Yu commented 11 months ago

Hi,

I am recently doing some fun projects using HPC and noticed that the coordinates mapping tools do not support parallel queries due to the limitation of SQLite. Therefore I made some modifications to the transcriptToGenome function, enabling users to use pre loaded exons for running parallel jobs.

I thought it might be helpful for the others interested in parallel queries. If you also found this interesting, I may update other functions and create a PR?

Best wishes,

Tim

jorainer commented 11 months ago

Hey Tim,

that looks great, yes, please, go ahead and make a PR.

Maybe some questions beforehand: is there a particular reason to use a CompressedGRangesList instead of a standard GRAngesList? Also, for the PR, please also add unit tests for your new code.

Thanks!