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Add partial subcommand #422

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Add partial subcommand #422

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@jakobnissen jakobnissen commented Mar 12, 2025 •
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The partial subcommand allows a user to run single, individual parts of the Vamb pipelines. There is no plan to allow specific subsets (e.g. run composition, then abundance).
For now, the planned parts are:

  • Compute composition
  • Compute abundance
  • Run training + encoding with VAE
  • Run training + encoding with VAEVAE
  • Run clustering

TODO

  • Documentation
  • CLI tests

Implements #414

@jakobnissen jakobnissen linked an issue Mar 12, 2025 that may be closed by this pull request
Feature request: Ability to run BAM parsing, fitting and clustering independently #414
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@jakobnissen jakobnissen added this to the Version 5.1 milestone Mar 12, 2025
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Feature request: Ability to run BAM parsing, fitting and clustering independently

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