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Add get_summary_stats_variant_filter_expr and get_summary_stats_csq_filter_expr to build filtering expressions for summary stats #701

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merged 28 commits into from
May 24, 2024
Merged

Add get_summary_stats_variant_filter_expr and get_summary_stats_csq_filter_expr to build filtering expressions for summary stats #701

merged 28 commits into from
May 24, 2024

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jkgoodrich
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@jkgoodrich jkgoodrich requested review from KoalaQin and matren395 May 9, 2024 19:56
@jkgoodrich jkgoodrich mentioned this pull request May 10, 2024
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matren395 reviewed May 13, 2024
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just pedantry about types and documentation - I'll look in a bit at the filter exprs themselves

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@jkgoodrich @matren395
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Co-authored-by: Daniel Marten <78616802+matren395@users.noreply.github.com>
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matren395 reviewed May 13, 2024
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I think variant_filter_expr looks good to me, putting a pin in csq_filter_expr for now

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last few questions - think I've got a good handle on the PR now !

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KoalaQin requested changes May 16, 2024
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I have two major comments:

  1. where the lof_flags is;
  2. if we could simplify the name of the keys, later the row name.

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jkgoodrich and others added 3 commits May 20, 2024 14:09
@jkgoodrich
remove unused imports
524dd55
@jkgoodrich @KoalaQin
Update gnomad/assessment/summary_stats.py
52ff64f 
Co-authored-by: Qin He <44242118+KoalaQin@users.noreply.github.com>
@jkgoodrich
Fix reviewer's suggestion
652b384
@jkgoodrich jkgoodrich requested review from KoalaQin and matren395 May 20, 2024 20:13
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Small things, you can move the 2 functions here.

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jkgoodrich and others added 3 commits May 24, 2024 09:52
@jkgoodrich @KoalaQin
Update gnomad/assessment/summary_stats.py
192404e 
Co-authored-by: Qin He <44242118+KoalaQin@users.noreply.github.com>
@jkgoodrich
Add generate_filter_combinations and get_summary_stats_filter_group_meta
ecf79f1
@jkgoodrich
Merge remote-tracking branch 'origin/jg/build_filtering_expressions_i…
27a40b0 
…n_sum_stats' into jg/build_filtering_expressions_in_sum_stats
@jkgoodrich jkgoodrich requested a review from KoalaQin May 24, 2024 16:25
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LGTM!

KoalaQin
KoalaQin approved these changes May 24, 2024
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LGTM!

@jkgoodrich jkgoodrich merged commit 0198658 into main May 24, 2024
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@jkgoodrich jkgoodrich deleted the jg/build_filtering_expressions_in_sum_stats branch May 24, 2024 16:56
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@KoalaQin KoalaQin KoalaQin approved these changes

@matren395 matren395 Awaiting requested review from matren395

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