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broadinstitute / gnomad_methods Public

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Add coverage entry agg function#790

Merged

ch-kr merged 23 commits intomainbroadinstitute/gnomad_methods:mainfrom

kc/coverage_agg_funcbroadinstitute/gnomad_methods:kc/coverage_agg_funcCopy head branch name to clipboard

Jul 18, 2025

Conversation Commits23 (23)Checks Files changed

Merged

Add coverage entry agg function#790
ch-kr merged 23 commits intomainfrom
kc/coverage_agg_func

Commits

Commits on Jul 15, 2025

create get_coverage_agg_func
ch-kr
committed
add dp_field arg to compute_coverage_stats and add periods to docstring
ch-kr
committed

Commits on Jul 16, 2025

move dp_field per copilot suggestion
ch-kr
committed
Update gnomad/utils/sparse_mt.py

ch-kr
and
Copilot
authored
Add tests for get_coverage_agg_func
mike-w-wilson
committed

Commits on Jul 17, 2025

Remove print statements for debugging in test_sparse_mt
mike-w-wilson
committed
Switch to hail's NaN and remove hardocded expected value -- update tests to use transofrmed DP, not raw, as it will be used in prod
mike-w-wilson
committed
Remove pytest import and sample_ht as it wasn't being accessed
mike-w-wilson
committed
Remove unneeded tests and misleading test names
mike-w-wilson
committed
Update tests/utils/test_sparse_mt.py

mike-w-wilson
and
Copilot
authored
Update tests/utils/test_sparse_mt.py

mike-w-wilson
and
Copilot
authored

Commits on Jul 18, 2025

Remove unneeded sparse_mt test
mike-w-wilson
committed
asked cursor to add periods to comments
ch-kr
committed
asked cursor to rename functions _ if they weren't being used
ch-kr
committed
asked cursor to remove irrelevant comment
ch-kr
committed
asked cursor to rename function and remove unncessary max_cov_bin=50 call
ch-kr
committed
unused transform_func > _
ch-kr
committed
asked cursor to remove redundant custom field name tests
ch-kr
committed
asked cursor to update test_transform_and_aggregation_integration
ch-kr
committed
improve median approx test documentation
ch-kr
committed
ask cursor to fix its comment 'accept actual behavior'
ch-kr
committed
ask cursor to fix vague > 0 assert
ch-kr
committed
add link to hail docs
ch-kr
committed

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