Repository navigation
Cover the counts-based multi-population LD moment API - #278
Merged
Merged
Conversation
…consistency ld_statistics.dz / pi2 accept a per-population counts array and a population- index tuple and dispatch to per-pattern formulas whose three- and four-distinct- population branches (Dz all-different; pi2 iikl / ijkk / shared / all-different) have no in-package caller -- the pipeline uses the fused CUDA kernels -- and were untested, though the module is public. Cross-check each pattern against the fused kernels (compute_all_dz_hap / compute_all_pi2_hap) on the same counts. The fused kernels return the raw single-index term for every pattern and are validated against moments.LD, so agreement pins the counts-API formula. dz agrees for every pattern. pi2 does not: the _pi2_multi iikk branch self-symmetrizes (returns 0.5*(numer1+numer2)) while every other pi2 branch returns a single term, so ld_statistics.pi2 returns a different kind of quantity depending on the index pattern. That case is marked xfail(strict) so the mismatch is pinned and unifying the convention trips the marker.
Member
|
awesome. this one looks good and i'm going to merge. |
This file contains hidden or 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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Closes #275 which needed test coverage rather than dead-code cleanup. This found an inconsistency in the pi2 statistic through this route, and
xfailsa test to pin the behaviour, which is filed as #279