Repository navigation
Conversation
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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 #377.
GenotypeDaskArray.copy()currently returns a baredask.array.Array, so the copy loses methods such ascount_alleles. Wrap copied values in the same array class, and copy genotype masks and phasing arrays independently, matching the eager array behavior. The operation stays lazy and retains its chunk layout.Fourteen regressions cover all six Dask wrapper types, genotype vectors/arrays, masks, phasing and later assignments to the original. They all fail before the change. The affected Dask checks pass 178 tests, and full suites pass 895 versus 881 on unchanged master, on Python 3.12/NumPy 1.26 and Python 3.10/NumPy 2.2. Whole-project correctness Flake8 passes.
A simulated cohort is read through the native VCF reader and stored in Zarr. All 24 copy-then-analysis workflows now continue through population slicing, native allele counting and dosage calculation, with masks/phasing preserved and zero tasks executed during copying. All 24 direct-analysis controls remain identical. The replay materializes values and annotations explicitly; the separate existing masked/phased whole-wrapper
compute()ordering issue is outside this fix.The installed Python 3.12 wheel reproduces all 24 analysis records and controls exactly, with imported source and native paths checked.