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Dm 38 subset reads for single read plotting#23

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OberonDixon merged 6 commits intomainfrom
DM-38-Subset-reads-for-single-read-plotting
Mar 12, 2025
Merged

Dm 38 subset reads for single read plotting#23
OberonDixon merged 6 commits intomainfrom
DM-38-Subset-reads-for-single-read-plotting

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@thekugelmeister
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Description

  • Added a single source of randomness to utils.py, for use in the future. All future random effects should reference utils.rng, an instance of numpy.random.Generator`.
  • Added read subset functionality to the read loaders in load_processed.py
  • Percolated read subset functionality up to plot_read_browser

Known issues, to bring up during review:

  • There is not currently a way to set the random seed for deterministic results.
  • The interface for specifying random selection is clunky. Is it overkill? Any better ideas?
  • KNOWN BUG: Requesting the plotting of a specific number of reads in plot_read_browser will not always result in plotting the same number of reads.
    • This is because of the preexisting read duplication bug, documented elsewhere.
    • I deemed this to be out of scope of this simple PR. Do you disagree?
  • Consistent with the other existing sources of randomness, there is no test infrastructure to verify this functionality.

@OberonDixon
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I agree that the subset specification interface is a bit clunky but it seems workable for now, and easier to design better once we implement other subsampling in other parts of the package

@OberonDixon OberonDixon merged commit 6be060d into main Mar 12, 2025
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2 participants