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Bring in prefetch#33

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jeromekelleher merged 2 commits into
sgkit-dev:mainfrom
jeromekelleher:bring-in-prefect
May 19, 2026
Merged

Bring in prefetch#33
jeromekelleher merged 2 commits into
sgkit-dev:mainfrom
jeromekelleher:bring-in-prefect

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@jeromekelleher
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After sgkit-dev/vcztools#408 we should have a decent perf uptick by reducing stalls in the hot path.

@jeromekelleher
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I did an analysis on this and it's a decent win for BGEN, and a very slight regression for plink.

format chunk size wall-time effect per-advance stall
PLINK 4 KB 25 MB +3 % 80 ms → 9 ms
PLINK 128 KB 25 MB +4 % unchanged (~200 ms)
PLINK qctool 25 MB +9 to +29 % already ~10 µs
BGEN 4 KB 300 MB -14 % 500 ms → 25 ms
BGEN 128 KB 300 MB -18 % 500 ms → 20 ms
BGEN 1 MB 300 MB -22 % 600 ms → 500 ms
BGEN qctool 300 MB -2 to -10 % shaves ~20 %

@jeromekelleher jeromekelleher merged commit 4921f8b into sgkit-dev:main May 19, 2026
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@jeromekelleher jeromekelleher deleted the bring-in-prefect branch May 19, 2026 12:45
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