Skip to content
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

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

Merged
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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
28 commits
Select commit Hold shift + click to select a range
bcc7f50
Add summary stats filtering expression functions
jkgoodrich May 9, 2024
5233d9c
Add `low_conf_regions_expr` function to return `filter_low_conf_regio…
jkgoodrich May 9, 2024
67a0323
Add a simple function to annotate a HT/MT with another HT
jkgoodrich May 9, 2024
0a995c2
Changes needed while testing
jkgoodrich May 9, 2024
7dcb9e3
Remove unused imports
jkgoodrich May 9, 2024
5071ffa
Small name change
jkgoodrich May 9, 2024
e6aa0d9
remove "HC" from name
jkgoodrich May 9, 2024
aa070c2
remove "lof_HC" from combo
jkgoodrich May 9, 2024
76fa6d3
A little more clean-up
jkgoodrich May 10, 2024
7a97045
fix issues introduced in last commit
jkgoodrich May 10, 2024
5ceac97
forgot "lof_csq_" in combos
jkgoodrich May 10, 2024
bc04ca5
use variant_qc_pass
jkgoodrich May 10, 2024
0e7e297
Apply suggestions from code review
jkgoodrich May 13, 2024
1320b20
Apply suggestions from code review
jkgoodrich May 13, 2024
6b60480
Remove `collapse_filters` and `lof_flag_set` to simplify PR for curre…
jkgoodrich May 20, 2024
9195c5b
Update docstrings
jkgoodrich May 20, 2024
cdd6b11
Merge branch 'jg/build_filtering_expressions_in_sum_stats' of https:/…
jkgoodrich May 20, 2024
595f97a
Update gnomad/assessment/summary_stats.py
jkgoodrich May 20, 2024
524dd55
remove unused imports
jkgoodrich May 20, 2024
52ff64f
Update gnomad/assessment/summary_stats.py
jkgoodrich May 20, 2024
652b384
Fix reviewer's suggestion
jkgoodrich May 20, 2024
f432b59
Fix reviewer's suggestion
jkgoodrich May 20, 2024
c314780
check for existence of key instead of value
jkgoodrich May 20, 2024
228adc7
Remove lof combinations from summary stats filter expressions and upd…
jkgoodrich May 22, 2024
f88a502
Fix docstring
jkgoodrich May 22, 2024
192404e
Update gnomad/assessment/summary_stats.py
jkgoodrich May 24, 2024
ecf79f1
Add generate_filter_combinations and get_summary_stats_filter_group_meta
jkgoodrich May 24, 2024
27a40b0
Merge remote-tracking branch 'origin/jg/build_filtering_expressions_i…
jkgoodrich May 24, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Loading
Loading