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v4 frequency script #376

Merged
merged 66 commits into from
Sep 8, 2023
Merged

v4 frequency script #376

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6fd410a
Fresh start
mike-w-wilson Jun 2, 2023
26df8ea
Clean main
mike-w-wilson Jun 28, 2023
e378797
Add split functionality and clean up main with smaller functions
mike-w-wilson Jul 12, 2023
f9ec345
popmax -> grpmax
mike-w-wilson Jul 12, 2023
9c5df1d
high ab fix
mike-w-wilson Jul 17, 2023
ea9da7a
Merge all histograms
mike-w-wilson Jul 19, 2023
c40bc51
Update use of test datasets
mike-w-wilson Jul 19, 2023
7107b71
add test and adjustment to freq resource
mike-w-wilson Jul 19, 2023
36e2d63
Change param name in get_freq
mike-w-wilson Jul 19, 2023
0f6377e
Sort order fix in freq_dict
mike-w-wilson Jul 20, 2023
fbb7d47
Add final schema describe
mike-w-wilson Jul 20, 2023
b998298
Add proper freq dict creation
mike-w-wilson Jul 20, 2023
78c2f14
Missing fields and notes
mike-w-wilson Jul 20, 2023
1c3288c
Remove test directory in freq resource
mike-w-wilson Jul 20, 2023
6906bc9
Generalize frequency annotation function
jkgoodrich Aug 1, 2023
9ce780d
Small changes to histogram creation
jkgoodrich Aug 1, 2023
3b26e32
Changes needed during testing
jkgoodrich Aug 1, 2023
10787b2
Remove TODOs that I added to PR comments
jkgoodrich Aug 1, 2023
0b3a531
Need to add globals to freq mt
jkgoodrich Aug 1, 2023
79ba8b3
Remaining suggested changes to `run_freq_and_dense_annotations`
jkgoodrich Aug 2, 2023
c29f50b
add eval for freq_meta global annotation
jkgoodrich Aug 2, 2023
2c6467f
Remove/change comments and TODOs, add possible option for adj before …
jkgoodrich Aug 4, 2023
9a61cc0
Small fix for _het_ad
jkgoodrich Aug 4, 2023
25cdd44
Add TODO
jkgoodrich Aug 4, 2023
c6ca7cc
Merge pull request #385 from broadinstitute/jg/annotate_freq_suggestion
jkgoodrich Aug 4, 2023
d709885
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Aug 4, 2023
ef74548
Suggections for freq correction
jkgoodrich Aug 7, 2023
ce4807d
Modifications to improve memory use
jkgoodrich Aug 14, 2023
2b3e98d
Add a few TODOs
jkgoodrich Aug 14, 2023
e06ec52
Apply suggestions from code review
jkgoodrich Aug 16, 2023
33aed23
Update gnomad_qc/v4/annotations/generate_freq.py
mike-w-wilson Aug 16, 2023
a486584
Ran black to fix my git suggestion formatting
mike-w-wilson Aug 16, 2023
b4a04af
Merge pull request #389 from broadinstitute/jg/suggestions_for_freq_c…
jkgoodrich Aug 16, 2023
611c767
Add merge freq_meta_sample_count
mike-w-wilson Aug 17, 2023
d8ed2b6
Add log copy as final step
mike-w-wilson Aug 22, 2023
d1d97a9
Add non_ukb_downsamplings to freq and globals
mike-w-wilson Aug 24, 2023
99cb9d5
lists -> dicts, nest downsamplings in globals
mike-w-wilson Aug 25, 2023
c6592fe
Use subset key
mike-w-wilson Aug 25, 2023
bf3bb9b
Keep all subset freq groups
mike-w-wilson Aug 29, 2023
35cd326
Add subset age hists
mike-w-wilson Aug 29, 2023
84c75ff
Revert "Keep all subset freq groups"
mike-w-wilson Aug 29, 2023
5f376c2
Add in non_ukb subset freqs
mike-w-wilson Aug 29, 2023
76bce57
Add grpmax and faf
mike-w-wilson Aug 30, 2023
0ebf517
Add suggestions to UKB downsampling PR
jkgoodrich Sep 5, 2023
1cbea60
high_ab_hets -> high_ab_hets_by_group
jkgoodrich Sep 5, 2023
dea9c52
rearrange functions for easier review
jkgoodrich Sep 5, 2023
a4d4390
rearrange functions for easier review 2
jkgoodrich Sep 5, 2023
fd25bde
rearrange functions for easier review 3
jkgoodrich Sep 5, 2023
5aaaa97
Apply suggestions from code review
jkgoodrich Sep 6, 2023
4142cd5
Update gnomad_qc/v4/annotations/generate_freq.py
jkgoodrich Sep 6, 2023
08e6640
Merge pull request #414 from broadinstitute/jg/ukb_downsampling_sugge…
jkgoodrich Sep 6, 2023
508a618
Black post github suggestion commits
mike-w-wilson Sep 6, 2023
b1879ee
Drop ukb_sample from strata, artifact of past attempt
mike-w-wilson Sep 6, 2023
ed78b35
Move set y to NA to end after freq dict
mike-w-wilson Sep 6, 2023
df1474b
update resource so temp files are in v4
mike-w-wilson Sep 6, 2023
44be3c8
Update gnomad_qc/v4/annotations/generate_freq.py
mike-w-wilson Sep 7, 2023
c7e6911
Merge pull request #407 from broadinstitute/mw/ukb_downsamplings_v4_freq
jkgoodrich Sep 7, 2023
c3ac21e
Flatten faf
mike-w-wilson Sep 7, 2023
2e6444e
Drop age_hists
mike-w-wilson Sep 7, 2023
98a66af
Add grpmax meta and index dict
mike-w-wilson Sep 7, 2023
22ec834
Drop age_hist_index_dict global
mike-w-wilson Sep 7, 2023
dac6ea1
Apply suggestions from code review
mike-w-wilson Sep 7, 2023
8942dd8
Drop 27k allele site
mike-w-wilson Sep 7, 2023
c1c0e11
make grpmax struct, drop globals
mike-w-wilson Sep 7, 2023
7115eab
drop new line
mike-w-wilson Sep 7, 2023
b7e19cb
Add cuKING to ignore-paths
mike-w-wilson Sep 8, 2023
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