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Add BedGraphAdapter and BedGraphTabixAdapter #4672

Merged
merged 6 commits into from
Nov 20, 2024
Merged

Add BedGraphAdapter and BedGraphTabixAdapter #4672

merged 6 commits into from
Nov 20, 2024

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cmdcolin
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As a motivating example, this can visualize the values of from the lab project for transition matrices

This is an older PR that I revitalized. I made it not derive from the BedAdapter base class though

A BedGraphTabixAdapter might be valuable as well

@cmdcolin
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note that it is capable of "multi-bedgraph" because there can be more than one score column. i just refer to this as bedgraph

a precedence for having multi-bedgraph is e.g. https://bedtools.readthedocs.io/en/latest/content/tools/unionbedg.html but the concept is just that there are multiple score values per position

in this adapter, it actually creates a separate N features, each with a "source" field indicating which column it came from, for each of N columns

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alternatives to something like this could include: encoding as multiple bigwigs (1 per row) or something sort of exotic like hdf5 (might be worth looking at hdf5 js libraries at some point)

Attempting to load single cell data could be useful with this as well, since it's generally in a matrix format rather than series of bigwigs, but it could also reveal scalability limitations of the current multibigwig approach since you quickly get a lot of rows and columns multiplied together:)

@cmdcolin cmdcolin changed the title Allow loading "multi-bedgraph" files Add BedGraphAdapter and BedGraphTabixAdapter Nov 20, 2024
@cmdcolin cmdcolin merged commit 3872967 into main Nov 20, 2024
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@cmdcolin cmdcolin deleted the bedgraph branch November 20, 2024 15:54
@cmdcolin cmdcolin added the enhancement New feature or request label Nov 21, 2024
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