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Introduce GeneAnnotationIndex as an abstraction of RefGeneIndex #102

Merged
merged 3 commits into from
Jun 23, 2024
Merged

Introduce GeneAnnotationIndex as an abstraction of RefGeneIndex #102

merged 3 commits into from
Jun 23, 2024

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k-kom
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@k-kom k-kom commented Jun 19, 2024 •
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Problem

Current implementation of varity.ref-gene/ref-genes only accepts RefGeneIndex as the index argument.
This behavior gives a client an unnecessary memory pressure when the client runs many varity processes, because varity doesn't give any means to off-load RefGeneIndex from the memory.

Solution

  • introduced GeneAnnotationIndex protocol as title says
  • and varity.ref-gene/ref-genes depends on it instead of RefGeneIndex

@k-kom k-kom self-assigned this Jun 19, 2024
@k-kom k-kom requested a review from federkasten June 19, 2024 10:06
federkasten
federkasten approved these changes Jun 23, 2024
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LGTM 🙆‍♂️ Thanks so much!

@federkasten federkasten merged commit a0971a0 into chrovis:master Jun 23, 2024
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@federkasten federkasten federkasten approved these changes

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@k-kom @federkasten