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Add compute_stats_per_ref_site to generalize computation of aggregate stats at all sites in a reference Table #662

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merged 20 commits into from
Jan 19, 2024
Merged

Add compute_stats_per_ref_site to generalize computation of aggregate stats at all sites in a reference Table #662

merged 20 commits into from
Jan 19, 2024

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jkgoodrich
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Also add a helper function compute_allele_number_per_ref_site to use compute_stats_per_ref_site to compute AN

@jkgoodrich jkgoodrich mentioned this pull request Jan 11, 2024
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@jkgoodrich
Merge branch 'jg/generalize_densify_at_all_ref_sites' of https://gith…
e41547a 
…ub.com/broadinstitute/gnomad_methods into jg/generalize_stat_compute_at_all_ref_sites

# Conflicts:
#	gnomad/utils/sparse_mt.py
@jkgoodrich
Merge branch 'jg/generalize_densify_at_all_ref_sites' of https://gith…
365c448 
…ub.com/broadinstitute/gnomad_methods into jg/generalize_stat_compute_at_all_ref_sites
@jkgoodrich
adj_group -> adj_groups
cf712cc
@jkgoodrich
Merge branch 'jg/generalize_densify_at_all_ref_sites' of https://gith…
e5df5b1 
…ub.com/broadinstitute/gnomad_methods into jg/generalize_stat_compute_at_all_ref_sites

# Conflicts:
#	gnomad/utils/sparse_mt.py
@jkgoodrich
Attempt to rearrange to remove nesting
292ed2d
@jkgoodrich
Fix loggers
15d1829
@jkgoodrich
Add missing hl.eval
40d189b
@jkgoodrich
{} -> set([])
7716d14
@jkgoodrich
switch order in if statement for adj_fields
6923260
@jkgoodrich
remove unneeded pop
8837f38
@jkgoodrich
use select_globals instead of annotate_globals
7d0c4cf
@jkgoodrich
fix adj function in _agg_by_group
bccc7b0
Base automatically changed from jg/generalize_densify_at_all_ref_sites to main January 19, 2024 18:18
@jkgoodrich
Merge branch 'main' of https://github.com/broadinstitute/gnomad_methods…
d842359 
… into jg/generalize_stat_compute_at_all_ref_sites
mike-w-wilson
mike-w-wilson reviewed Jan 19, 2024
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This looks good. Sorry it took awhile, it's dense. I only have one thing with a value error, everything else is small comments or nitpicks with style. I tested this AN against the compute_freq_by_strata on the test VDS.

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mike-w-wilson
mike-w-wilson approved these changes Jan 19, 2024
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Ok one tiny thing on the GT logic now but other than that this looks good!

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@jkgoodrich jkgoodrich merged commit c310157 into main Jan 19, 2024
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@jkgoodrich jkgoodrich deleted the jg/generalize_stat_compute_at_all_ref_sites branch January 19, 2024 21:39
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