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lawremi / rtracklayer

R interface to genome annotation files and the UCSC genome browser
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Changes to rtracklayer for upcoming BiocIO package #25

Open dvantwisk opened 4 years ago

dvantwisk commented 4 years ago

Hi @lawremi I've completed a package named BiocIO https://github.com/Bioconductor/BiocIO. The purpose of this package is to migrate high level IO functionality from rtracklayer. This most notably includes the BiocFile class (was RTLFile) and the import and export generics.

I've created a branch of rtracklayer that modifies the package accordingly https://github.com/dvantwisk/rtracklayer. Methods and classes that were migrated to BiocIO have been deprecated.

I ask that you review these changes and give us any recommendations before we proceed with finalizing the changes.

Thank you!

lawremi commented 4 years ago

Sounds interesting. I would have been happy to participate in this effort earlier. Please submit a pull request and we can iterate through that.

dvantwisk commented 4 years ago

Done. https://github.com/lawremi/rtracklayer/pull/26