Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
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

Conversation

jkgoodrich
Copy link
Contributor

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
Closed
@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
View reviewed changes
Copy link
Contributor

@mike-w-wilson mike-w-wilson left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

jkgoodrich
jkgoodrich commented Jan 19, 2024
View reviewed changes
mike-w-wilson
mike-w-wilson approved these changes Jan 19, 2024
View reviewed changes
Copy link
Contributor

@mike-w-wilson mike-w-wilson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ok one tiny thing on the GT logic now but other than that this looks good!

@jkgoodrich jkgoodrich merged commit c310157 into main Jan 19, 2024
@jkgoodrich jkgoodrich deleted the jg/generalize_stat_compute_at_all_ref_sites branch January 19, 2024 21:39
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@mike-w-wilson mike-w-wilson mike-w-wilson approved these changes

Assignees

@mike-w-wilson mike-w-wilson

@jkgoodrich jkgoodrich

Labels

Changelog: new feature v4.1

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@jkgoodrich @mike-w-wilson