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Filter gene variant queries to exons consistently #1667

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Filter gene variant queries to exons consistently #1667

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10 changes: 9 additions & 1 deletion graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -394,6 +394,14 @@ const getMultiVariantSourceFields = (
// Gene query
// ================================================================================================

export const getFilteredRegions = (gene: any) => {
const hasCDS = gene.exons.some((exon: any) => exon.feature_type === 'CDS')
const filteredRegions = hasCDS
? gene.exons.filter((exon: any) => exon.feature_type === 'CDS')
: gene.exons.filter((exon: any) => exon.feature_type === 'exon')
return filteredRegions
}

const fetchVariantsByGene = async (esClient: any, gene: any, subset: Subset) => {
const exomeSubset = subset
const genomeSubset = 'all'
Expand All @@ -404,7 +412,7 @@ const fetchVariantsByGene = async (esClient: any, gene: any, subset: Subset) =>
const pageSize = isLargeGene ? 500 : 10000

try {
const filteredRegions = gene.exons.filter((exon: any) => exon.feature_type === 'CDS')
const filteredRegions = getFilteredRegions(gene)
const sortedRegions = filteredRegions.sort((r1: any, r2: any) => r1.xstart - r2.xstart)
const padding = 75
const paddedRegions = sortedRegions.map((r: any) => ({
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