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Render fafs of 0 as '-' character on variant pages #1646

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merged 2 commits into from
Oct 30, 2024

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rileyhgrant
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Previously, our variant pipeline took the faf array, took the relevant genetic ancestry group's filtered AFs from this array, filtered out all the entries of this smaller list where the faf was 0, then took the max of this array to render as the "Grpmax filtering AF (95% confidence)".

With v4, the step that filtered out entries from this reduced array with a faf of 0 was mistakenly dropped. This led to the fafmax for a given variant being possible to be 0, where it was previously not able to be. In these cases, the methods team calls the fafmax for these variants as missing, rather than 0.

This PR does two small things

  • Re-adds the filter to remove fafmax array entries with a faf of 0
  • Changes the frontend to display '-', rather than 0, when the fafmax for a variant is 0

This achieves both a quick fix that does not require a variant reload, and fixes the problem more systematically when the v4 variants pipeline is next rerun.

@rileyhgrant rileyhgrant self-assigned this Oct 29, 2024
@rileyhgrant rileyhgrant marked this pull request as ready for review October 29, 2024 21:03
@rileyhgrant rileyhgrant merged commit 477a90c into main Oct 30, 2024
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@rileyhgrant rileyhgrant deleted the fix-variant-0-fafmax branch October 30, 2024 20:26
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