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Switch bedToBigBed to bigTools written in rust #89

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khoroshevskyi opened this issue Jan 16, 2025 · 2 comments
Open

Switch bedToBigBed to bigTools written in rust #89

khoroshevskyi opened this issue Jan 16, 2025 · 2 comments
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It will be great improvement to run bedToBigBed in rust using python bindings.

For this we would use bigToold package, and implementation would be written in gtars
@khoroshevskyi khoroshevskyi added the enhancement New feature or request label Jan 16, 2025
@nsheff nsheff mentioned this issue Jan 24, 2025
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nsheff commented Jan 24, 2025

Alex says it's working in principle.

Will suggest putting this in bigtools today

@khoroshevskyi khoroshevskyi changed the title Migrate bedToBigBed to bigTools written in rust Switch bedToBigBed to bigTools written in rust Jan 25, 2025
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khoroshevskyi commented Jan 25, 2025 •
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Some benchmarks:

  • CLI Rust bedtobigbed: 0.437 seconds
  • Geniml Regionset using bigtools bindings: 16.17 seconds
  • My implementation in Rust (Python bindings not implemented yet): 0.492 seconds

@khoroshevskyi khoroshevskyi self-assigned this Feb 21, 2025
@khoroshevskyi khoroshevskyi mentioned this issue Feb 21, 2025
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