Complex traits#11
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Feb 1, 2026
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- Refactors complex traits dataset using latest UKBB finemapping data
Co-Authored-By: Claude Opus 4.5 <[email protected]>
Drop null pip variants at download, inner join methods, and average pips when they agree within 5%. Co-Authored-By: Claude Opus 4.5 <[email protected]>
Average PIPs when both methods agree, use single method when only one available, exclude when they disagree by >5%. Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Add download_all_finemapping target rule for batch downloads - Add aggregate_traits rule to combine all trait-level results - Compute max PIP across traits and list high-PIP traits - Label positives (PIP > 0.9) and negatives (PIP < 0.01, no nulls) Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Add build_dataset() function to traitgym.intervals for shared logic - Refactor mendelian_traits_dataset_all and complex_traits_dataset_all rules - Add complex_traits_annotate and complex_traits_full_consequence_counts rules - Add check_ref_alt function to traitgym.variants - Mark slow tests with @pytest.mark.slow (skipped by default) - Fix CHROMS test to expect lexicographic ordering Co-Authored-By: Claude Opus 4.5 <[email protected]>
Drop ~34 high-PIP variants with very low MAF not present in LD score file during annotation. Add null validation for all matching features in match_features() to catch similar issues early. Co-Authored-By: Claude Opus 4.5 <[email protected]>
Co-Authored-By: Claude Opus 4.5 <[email protected]>
Change pull-requests permission back to read to pass workflow validation in the Claude Code Review action. Co-Authored-By: Claude Opus 4.5 <[email protected]>
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No issues found. Checked for bugs and CLAUDE.md compliance. |
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