MRG: fix performance regression in manysearch by removing unnecessary downsampling
#464
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ctb
changed the title
manysearchmanysearch
ctb
changed the title
manysearchmanysearch by removing unnecessary downsampling
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@bluegenes ready for review & merge! |
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bump :) |
bluegenes
reviewed
Oct 8, 2024
| // avoid calculating details unless there is overlap | ||
| let overlap = query | ||
| .minhash | ||
| .count_common(against_mh, true) |
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ah, count_common handles downsampling only if needed. Didn't realized downsample_scaled always downsampled, even if not needed!
This was referenced Oct 13, 2024
Merged
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Tackles #463
This PR adjusts
manysearchso that downsampling is only done on sketches when actually needed. Prior to this, thedownsample_max_hash/downsample_scaledcode was running on sketches even when there was no need.This PR also adds
--ignore-abundancetomanysearchwhich optionally turns off potentially expensive abundance estimation (which in practice is not that expensive, apparently; see #463).Fixes #466