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A new benchmarking tool #168

Merged
merged 28 commits into from
Apr 27, 2024
Merged

A new benchmarking tool #168

merged 28 commits into from
Apr 27, 2024

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sampsyo
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@sampsyo sampsyo commented Apr 27, 2024

This PR bootstraps a simple benchmarking infrastructure for comparing the performance of three different GFA analysis implementations (odgi, slow-odgi, and fgfa). Not that these results are all that interesting for the moment, but hopefully some of this stuff makes it possible to measure real differences once they exist?

There's a README that describes how to use these things. It can produce hilarious bar graphs like this:
paths-med-2024-04-16-09-29-35 907880

That's comparing odgi paths with fgfa paths on a few GFAs (pre-converted to each tool's native format). In this run, odgi paths takes 3–12 seconds while fgfa paths takes 3–6 milliseconds (because it has no serialization step, and it never even reads the entire file).

@sampsyo sampsyo merged commit a7f542c into main Apr 27, 2024
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@sampsyo sampsyo deleted the bench branch April 27, 2024 00:05
sampsyo added a commit that referenced this pull request Dec 29, 2024
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