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Optimized local #50

Merged
merged 4 commits into from
Dec 25, 2023
Merged

Optimized local #50

merged 4 commits into from
Dec 25, 2023

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OndrejSladky
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@OndrejSladky OndrejSladky commented Dec 25, 2023 •
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Changes:

  • Local:
    • Read k-mers as integers
    • Store only a single k-mer from RC pair
    • Compute RCs efficiently using bit-tricks

Improvements (for spneumo and k=13):

  • Local: 26% Memory; 56% Runtime
  • Global 100% Memory; 86% Runtime

@OndrejSladky OndrejSladky changed the title [WIP] Optimized local Optimized local Dec 25, 2023
@OndrejSladky OndrejSladky merged commit 0cf7aa2 into main Dec 25, 2023
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@OndrejSladky OndrejSladky deleted the local-optimized branch December 25, 2023 17:24
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