bug/leaks - Githubissues

gks-anvil / vrs_anvil_toolkit

Extract clinical variant interpretations from VCF using GA4GH VRS IDs

MIT License

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bug/leaks #49

Closed bwalsh closed 8 months ago

bwalsh commented 8 months ago

This PR addresses memory leaks observed on terra vm running python 3.10. It is based on feature/metakb

adds informational logging
degrades translator to a non threaded model

Results:

memory is stable
observed performance, no cache, no SEQREPO_FD_CACHE_MAXSIZE:
- mac running 3.12 : 1800 vcf lines / sec
- terra running 3.10: 800 vcf lines / sec

Next steps:

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