MRG: fix performance regression in manysearch by removing unnecessary downsampling
#464
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ctb
changed the title
manysearchmanysearch
ctb
changed the title
manysearchmanysearch by removing unnecessary downsampling
|
@bluegenes ready for review & merge! |
|
bump :) |
bluegenes
reviewed
Oct 8, 2024
| // avoid calculating details unless there is overlap | ||
| let overlap = query | ||
| .minhash | ||
| .count_common(against_mh, true) |
There was a problem hiding this comment.
ah, count_common handles downsampling only if needed. Didn't realized downsample_scaled always downsampled, even if not needed!
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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