feat(csv): emit the whole gnomAD record in the gnomad namespace - #836
Merged
bencap merged 1 commit intoAug 12, 2026
Merged
Conversation
Coverage Report for CI Build 31625618558Warning No base build found for commit Coverage: 89.285%Details
Uncovered ChangesNo uncovered changes found. Coverage RegressionsRequires a base build to compare against. How to fix this → Coverage Stats
💛 - Coveralls |
bencap
force-pushed
the
feature/bencap/gnomad-af-support
branch
2 times, most recently
from
August 11, 2026 16:27
0014240 to
9194bfd
Compare
The namespace carried gnomad_af alone, which is not enough to act on a frequency: linking out to the gnomAD variant page needs the variant id, and judging whether a frequency is well sampled needs AC/AN and FAF95 (ACMG BA1/BS1). - Extend the gnomad namespace spec to seven columns: gnomad_af, gnomad_ac, gnomad_an, gnomad_faf95_max, gnomad_faf95_max_ancestry, gnomad_id and gnomad_version. - Widen the namespace label to "gnomAD population frequency", which no longer describes a single column. The label is served to the CSV column picker. - Document the new columns in the public data dump README, since the dump requests this namespace and its output gains them too. Covers the columns at the row-building layer rather than re-testing the shared NA coercion: variant_to_csv_row routes every namespace through _value_or_na, which test_is_output_null already specifies exhaustively.
bencap
force-pushed
the
feature/bencap/gnomad-af-support
branch
from
August 12, 2026 18:02
9194bfd to
aead12c
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The namespace carried gnomad_af alone, which is not enough to act on a frequency: linking out to the gnomAD variant page needs the variant id, and judging whether a frequency is well sampled needs AC/AN and FAF95 (ACMG BA1/BS1).