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Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
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Migrating code to allow beachmat to read HDF5Matrix objects #19

Closed LTLA closed 4 years ago

LTLA commented 5 years ago

This is in response to #15, and at this stage, is intended for discussion rather than being merged.

Specifically, it is unfortunately quite intrusive - it adds C++ code to the HDF5Matrix binary, and a lot of fairly custom code at that. I've aimed to minimize its effects to src/beachmat.

Another problem is that any updates to beachmat's API will also require an update to this package as well (otherwise the entire R session crashes in a flaming heap of segfaults), so we need to make sure our communication lines are clear around that.

LTLA commented 4 years ago

With the refactoring of beachmat to version 3, this is no longer necessary. We rely on block processing to realize HDF5Matrix objects into dense or sparse blocks that can then be directly processed bybeachmat-powered code.