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feat: add optional suppression of allele collection - #545

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jsstevenson merged 1 commit into
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vcf-collection-memory
Apr 14, 2025
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jsstevenson merged 1 commit into
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vcf-collection-memory

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@jsstevenson

@jsstevenson jsstevenson commented Apr 11, 2025 •

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  • VCF annotator should not collect alleles if no output is requested by user. This has major implications for memory usage, apparently.
  • Provide this in a relatively OOP-friendly way without producing a breaking change

At the next major version, there is a cleaner way to do this and it should be implemented at that point

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jsstevenson marked this pull request as ready for review April 11, 2025 20:20
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jsstevenson requested review from a team as code owners April 11, 2025 20:20
@quinnwai

quinnwai commented Apr 12, 2025 •

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Thanks for the PR! This should help address my OOM use case on Terra. For general context:

  • Ran vrs-annotator workflow on Terra w/ 16GB memory allocated
  • Workflow terminated unexpectedly for file input ~4GB at consistently around the 2 hour mark

original slack thread here

I think I should be able to do testing on this by targeting "ga4gh.vrs[extras]@git+https://github.com/ga4gh/vrs-python.git@vcf-collection-memory", will let you know if I can successfully complete VRS annotation of my VCF

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At the next major version, there is a cleaner way to do this and it should be implemented at that point

Could you make an issue for this?

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jsstevenson merged commit 70ec42f into main Apr 14, 2025
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jsstevenson deleted the vcf-collection-memory branch April 14, 2025 16:47
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Yeah wrote up some brain dump here #546

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3 participants