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Add doc for chromsizes grid overlay#187

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manzt merged 4 commits into
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kerpedji/chromsizes-overlay
Apr 10, 2025
Merged

Add doc for chromsizes grid overlay#187
manzt merged 4 commits into
mainfrom
kerpedji/chromsizes-overlay

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@pkerpedjiev

@pkerpedjiev pkerpedjiev commented Apr 9, 2025

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Description

Add doc for chromsizes grid overlay.

Checklist

  • Clear PR title (used for generating release notes).
    • Prefer using prefixes like fix: or feat: to help organize auto-generated
      notes.
  • Unit tests added or updated.
  • Documentation added or updated.

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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.

@pkerpedjiev

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What do you think of having a designated chromsizes helper from higlass.tilesets that we could export at the top-level API?

I'm on board with this. Added a commit adding it to this PR.

it could also be overloaded to to accept a sequences of chromsizes:

I would do this on an as-needed basis.

@manzt manzt merged commit 2819a7a into main Apr 10, 2025
@manzt manzt deleted the kerpedji/chromsizes-overlay branch April 10, 2025 13:33
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2 participants