gnomad_methods
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broadinstitute
Hail helper functions for the gnomAD project and Translational Genomics Group
Just making this more flexible for the future, there's a warning a few lines above that gnomad_gks() is currently only implemented for gnomAD v4
Add v4.1 to releases once release HTs are created and synced
Working on v4.0, we created the gnomad_methods function `split_vds_by_strata` which splits a vds based on a n expression. The desired behavior was to split a vds and maintain all alleles...
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. Release notes Sourced from jinja2's releases. 3.1.4 This is the Jinja 3.1.4 security release, which fixes security issues and bugs but does not otherwise...
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot] avatar"){kind=avatar}
Bumps [idna](https://github.com/kjd/idna) from 3.4 to 3.7. Release notes Sourced from idna's releases. v3.7 What's Changed Fix issue where specially crafted inputs to encode() could take exceptionally long amount of time...
Bumps [requests](https://github.com/psf/requests) from 2.31.0 to 2.32.0. Release notes Sourced from requests's releases. v2.32.0 2.32.0 (2024-05-20) 🐍 PYCON US 2024 EDITION 🐍 Security Fixed an issue where setting verify=False on the...
Also adds: - `filter_to_most_severe_consequences`, which is used by `get_most_severe_csq_from_multiple_csq_lists` - Adds `loftee_labels` and `no_lof_flags` parameters to `filter_vep_transcript_csqs_expr` for filtering by loftee labels and flags. Depends on #713 [updates_to_get_most_severe_consequence_for_summary.html.zip](https://github.com/user-attachments/files/15976998/updates_to_get_most_severe_consequence_for_summary.html.zip) testing to...
Bumps the pip group in /docs with 2 updates: [certifi](https://github.com/certifi/python-certifi) and [urllib3](https://github.com/urllib3/urllib3). Updates `certifi` from 2023.7.22 to 2024.7.4 Commits bd81538 2024.07.04 (#295) 06a2cbf Bump peter-evans/create-pull-request from 6.0.5 to 6.1.0 (#294)...
Bumps the pip group with 1 update in the /docs directory: [urllib3](https://github.com/urllib3/urllib3). Updates `urllib3` from 2.0.7 to 2.2.2 Release notes Sourced from urllib3's releases. 2.2.2 🚀 urllib3 is fundraising for...
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Hail helper functions for the gnomAD project and Translational Genomics Group