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feat(csv): emit the whole gnomAD record in the gnomad namespace - #836

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bencap merged 1 commit into
feature/bencap/variant-level-csv-downloadfrom
feature/bencap/gnomad-af-support
Aug 12, 2026
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feat(csv): emit the whole gnomAD record in the gnomad namespace#836
bencap merged 1 commit into
feature/bencap/variant-level-csv-downloadfrom
feature/bencap/gnomad-af-support

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@bencap

@bencap bencap commented Aug 10, 2026

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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.

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coveralls commented Aug 10, 2026

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Coverage Report for CI Build 31625618558

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No base build found for commit 7843dce on feature/bencap/variant-level-csv-download.
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Coverage: 89.285%

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  • Patch coverage: No coverable lines changed in this PR.

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Coverage Stats

Coverage Status
Relevant Lines: 15035
Covered Lines: 13424
Line Coverage: 89.29%
Coverage Strength: 0.89 hits per line

💛 - Coveralls

@bencap bencap linked an issue Aug 10, 2026 that may be closed by this pull request
@bencap
bencap force-pushed the feature/bencap/gnomad-af-support branch 2 times, most recently from 0014240 to 9194bfd Compare August 11, 2026 16:27
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
bencap force-pushed the feature/bencap/gnomad-af-support branch from 9194bfd to aead12c Compare August 12, 2026 18:02
@bencap
bencap merged commit 7fcf9a9 into release-2026.2.7.1 Aug 12, 2026
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gnomAD minor allele frequency display

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