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Looks good to me. Thanks for documenting.
Only nit is that the ClodiusTileset constructor was intentionally not "public" (not under __all__ for hg.tilesets module), hence why it's not exported at the top level like hg.Tileset (which is the recommended way to make custom tilesets). Public in quotes because everything is a convention in Python.
For now, this is great, but I'm wondering if we could maybe have a more opinionated helper (like the other clodius tilesets) for this use case. What do you think of having a designated chromsizes helper from higlass.tilesets that we could export at the top-level API? E.g.,
import higlass as hg
cs_ts = hg.chromsizes('chromSizes_hg19_reordered.tsv')
cool_ts = hg.cooler("my.multires.cool")it could also be overloaded to to accept a sequences of chromsizes:
cs_ts = hg.chromsizes([("a", 10_000), ("b", 50_000)])Let's merge this, and depending on what you think, we could have a separate PR to add such a utility and update the recommended usage.
I'm on board with this. Added a commit adding it to this PR.
I would do this on an as-needed basis. |
Description
Add doc for chromsizes grid overlay.
Checklist
fix:orfeat:to help organize auto-generatednotes.