Merge branch 'main' into ea-loglabel-240906

browser/src/GenePage/VariantsInGene.tsx

@@ -246,6 +246,7 @@ query ${operationName}($geneId: String!, $datasetId: DatasetId!, $referenceGenom
           faf99_max
           faf99_max_gen_anc
         }
+	flags
       }
       genome {
         ac
@@ -265,6 +266,7 @@ query ${operationName}($geneId: String!, $datasetId: DatasetId!, $referenceGenom
           ac_hemi
           ac_hom
         }
+	flags
       }
       joint {
         ac

browser/src/RegionPage/VariantsInRegion.tsx

@@ -155,6 +155,7 @@ query ${operationName}($chrom: String!, $start: Int!, $stop: Int!, $datasetId: D
           faf99_max
           faf99_max_gen_anc
         }
+	flags
       }
       genome {
         ac
@@ -174,6 +175,7 @@ query ${operationName}($chrom: String!, $start: Int!, $stop: Int!, $datasetId: D
           ac_hemi
           ac_hom
         }
+	flags
       }
       joint {
         ac

browser/src/VariantList/VariantFlag.tsx

@@ -8,6 +8,17 @@ type Flag = {
   formatTooltip: (input: any) => string
 }
 
+const formatMonoallelicFlag = (variant: any) => {
+  if (variant.exome && variant.exome.flags && variant.exome.flags.includes('monoallelic')) {
+    if (variant.genome && variant.genome.flags && variant.genome.flags.includes('monoallelic')) {
+      return 'All samples are homozygous alternate for the variant in both the exome and genome data'
+    }
+    return 'All samples are homozygous alternate for the variant in the exome data'
+  }
+
+  return 'All samples are homozygous alternate for the variant in the genome data'
+}
+
 export const FLAGS_CONFIG: Record<string, Flag> = {
   lcr: {
     label: 'LCR',
@@ -46,7 +57,7 @@ export const FLAGS_CONFIG: Record<string, Flag> = {
   monoallelic: {
     label: 'Monoallelic',
     level: 'info',
-    formatTooltip: () => 'All samples are homozygous alternate for the variant',
+    formatTooltip: formatMonoallelicFlag,
   },
   // Mitochondrial variants
   common_low_heteroplasmy: {

browser/src/VariantList/variantTableColumns.tsx

@@ -46,6 +46,15 @@ const getConsequenceDescription = (contextType: any) => {
       return ' for consequence in this transcript'
   }
 }
+
+const consolidatedFlags = (row: any) => {
+  const variantFlags = row.flags || []
+  const exomeFlags = row.exome?.flags || []
+  const genomeFlags = row.genome?.flags || []
+  const allFlags = Array.from(new Set([...variantFlags, ...exomeFlags, ...genomeFlags]))
+  return allFlags.sort()
+}
+
 export type VariantTableColumn = {
   key: string
   heading: string
@@ -163,11 +172,16 @@ const variantTableColumns: VariantTableColumn[] = [
     description: 'Flags that may affect annotation and/or confidence',
     grow: 0,
     minWidth: 140,
-    compareFunction: makeNumericCompareFunction((variant: any) => variant.flags.length || null),
-    render: (row: any, key: any) =>
-      row[key]
-        .filter((flag: any) => flag !== 'segdup' && flag !== 'par')
-        .map((flag: any) => <VariantFlag key={flag} type={flag} variant={row} />),
+    compareFunction: makeNumericCompareFunction(
+      (variant: any) => consolidatedFlags(variant).length || null
+    ),
+    render: (row: any) => (
+      <>
+        {consolidatedFlags(row).map((flag: any) => (
+          <VariantFlag key={flag} type={flag} variant={row} />
+        ))}
+      </>
+    ),
   },
 
   {
@@ -208,7 +222,7 @@ const variantTableColumns: VariantTableColumn[] = [
     minWidth: 160,
     compareFunction: makeStringCompareFunction('hgvs'),
     getSearchTerms: (variant: any) => [variant.hgvs],
-    render: (variant: any, key: any, { highlightWords }: any) => (
+    render: (variant: any, _: any, { highlightWords }: any) => (
       <Cell>
         <Highlighter autoEscape searchWords={highlightWords} textToHighlight={variant.hgvs || ''} />
       </Cell>
@@ -225,7 +239,7 @@ const variantTableColumns: VariantTableColumn[] = [
     minWidth: 160,
     compareFunction: makeStringCompareFunction('hgvsc'),
     getSearchTerms: (variant: any) => [variant.hgvsc],
-    render: (variant: any, key: any, { highlightWords }: any) => (
+    render: (variant: any, _: any, { highlightWords }: any) => (
       <Cell>
         <Highlighter
           autoEscape
@@ -246,7 +260,7 @@ const variantTableColumns: VariantTableColumn[] = [
     minWidth: 160,
     compareFunction: makeStringCompareFunction('hgvsp'),
     getSearchTerms: (variant: any) => [variant.hgvsp],
-    render: (variant: any, key: any, { highlightWords }: any) => (
+    render: (variant: any, _: any, { highlightWords }: any) => (
       <Cell>
         <Highlighter
           autoEscape
@@ -315,7 +329,7 @@ const variantTableColumns: VariantTableColumn[] = [
       rsids1[0].localeCompare(rsids2[0])
     ),
     getSearchTerms: (variant: any) => variant.rsids || [],
-    render: (variant: any, key: any, { highlightWords }: any) => (
+    render: (variant: any, _: any, { highlightWords }: any) => (
       <Cell>
         <Highlighter
           autoEscape
@@ -366,7 +380,7 @@ const variantTableColumns: VariantTableColumn[] = [
     grow: 1,
     compareFunction: makeNumericCompareFunction('pos'),
     getSearchTerms: (variant: any) => [variant.variant_id].concat(variant.rsids || []),
-    render: (row: any, key: any, { highlightWords }: any) => (
+    render: (row: any, _: any, { highlightWords }: any) => (
       <Cell>
         <Link target="_blank" to={`/variant/${row.variant_id}`}>
           <Highlighter autoEscape searchWords={highlightWords} textToHighlight={row.variant_id} />
@@ -409,7 +423,7 @@ export const getColumnsForContext = (context: any) => {
       : context.canonical_transcript_id
 
     // @ts-expect-error TS(2339) Property 'hgvs' does not exist on type '{}'.
-    columns.hgvs.render = (variant: any, key: any, { highlightWords }: any) => (
+    columns.hgvs.render = (variant: any, _: any, { highlightWords }: any) => (
       <Cell>
         <Highlighter autoEscape searchWords={highlightWords} textToHighlight={variant.hgvs || ''} />
         {primaryTranscriptId && variant.transcript_id !== primaryTranscriptId && ' †'}

browser/src/VariantPage/VariantPage.tsx

@@ -205,6 +205,7 @@ export type SequencingType = BaseSequencingType & {
   ac_hom: number
   ac_hemi: number
   af?: number
+  flags: string[] | null
 }
 
 export type JointSequencingType = BaseSequencingType & {
@@ -585,6 +586,7 @@ query ${operationName}($variantId: String!, $datasetId: DatasetId!, $referenceGe
           value
         }
       }
+      flags
     }
     genome {
       ac
@@ -664,6 +666,7 @@ query ${operationName}($variantId: String!, $datasetId: DatasetId!, $referenceGe
           value
         }
       }
+      flags
     }
     joint {
       ac

browser/src/__factories__/Variant.ts

@@ -190,9 +190,11 @@ export const variantTableVariantFactory = Factory.define<VariantTableVariant>(
     const {
       exome = {
         filters: [],
+        flags: [],
       },
       genome = {
         filters: [],
+        flags: [],
       },
     } = associations
 
@@ -228,6 +230,7 @@ export const sequencingFactory = Factory.define<SequencingType>(({ params, assoc
     homozygote_count = 0,
     hemizygote_count = 0,
     filters = [],
+    flags = [],
     populations = [],
     local_ancestry_populations = [],
     ac_hemi = 1,
@@ -256,6 +259,7 @@ export const sequencingFactory = Factory.define<SequencingType>(({ params, assoc
     homozygote_count,
     hemizygote_count,
     filters,
+    flags,
     populations,
     local_ancestry_populations,
     age_distribution,

graphql-api/src/graphql/types/variant.graphql

@@ -115,6 +115,7 @@ type VariantSequencingTypeData {
   populations: [VariantPopulation]
   faf95: VariantFilteringAlleleFrequency
   fafmax: Fafmax
+  flags: [String!]
 
   # Deprecated - calculate from AC and AN
   # Preserved for compatibility with existing browser queries
@@ -222,6 +223,7 @@ type VariantDetailsSequencingTypeData {
   faf95: VariantFilteringAlleleFrequency
   faf99: VariantFilteringAlleleFrequency
   filters: [String!]
+  flags: [String!]
   populations: [VariantPopulation]
   local_ancestry_populations: [VariantLocalAncestryPopulation]!
   age_distribution: VariantAgeDistribution

graphql-api/src/queries/mitochondrial-variant-datasets/gnomad-v3-mitochondrial-variant-queries.ts

@@ -33,9 +33,8 @@ const fetchMitochondrialVariantById = async (esClient: any, variantIdOrRsid: any
   const variant = response.body.hits.hits[0]._source.value
 
   // Remove nc_transcript flag due to issues with LOFTEE on mitochondrial variants
-  const flags = getFlagsForContext({ type: 'region' })(variant).filter(
-    (f: any) => f !== 'nc_transcript'
-  )
+  const { variantFlags } = getFlagsForContext({ type: 'region' }, variant)
+  const flags = variantFlags.filter((f: any) => f !== 'nc_transcript')
 
   return {
     ...variant,
@@ -73,12 +72,12 @@ const FIELDS_TO_FETCH = [
 
 const shapeMitochondrialVariantSummary = (context: any) => {
   const getConsequence = getConsequenceForContext(context)
-  const getFlags = getFlagsForContext(context)
 
   return (variant: any) => {
     const transcriptConsequence = getConsequence(variant) || {}
     // Remove nc_transcript flag due to issues with LOFTEE on mitochondrial variants
-    const flags = getFlags(variant).filter((f: any) => f !== 'nc_transcript')
+    const { variantFlags } = getFlagsForContext(context, variant)
+    const flags = variantFlags.filter((f: any) => f !== 'nc_transcript')
 
     return {
       ...omit(variant, 'transcript_consequences', 'locus', 'alleles'), // Omit full transcript consequences list to avoid caching it

graphql-api/src/queries/variant-datasets/exac-variant-queries.ts

@@ -75,7 +75,7 @@ export const fetchVariantById = async (esClient: any, variantIdOrRsid: any) => {
 
   const variant = response.body.hits.hits[0]._source.value
 
-  const flags = getFlagsForContext({ type: 'region' })(variant)
+  const { variantFlags, exomeFlags } = getFlagsForContext({ type: 'region' }, variant)
 
   const lofCurationResults = await fetchLofCurationResultsByVariant(esClient, variant.variant_id)
 
@@ -97,9 +97,10 @@ export const fetchVariantById = async (esClient: any, variantIdOrRsid: any) => {
         },
         site_quality_metrics: variant.exome.quality_metrics.site_quality_metrics,
       },
+      flags: exomeFlags,
     },
     genome: null,
-    flags,
+    flags: variantFlags,
     lof_curations: lofCurationResults,
     transcript_consequences: variant.transcript_consequences || [],
   }
@@ -111,16 +112,15 @@ export const fetchVariantById = async (esClient: any, variantIdOrRsid: any) => {
 
 const shapeVariantSummary = (context: any) => {
   const getConsequence = getConsequenceForContext(context)
-  const getFlags = getFlagsForContext(context)
 
   return (variant: any) => {
     const transcriptConsequence = getConsequence(variant) || {}
-    const flags = getFlags(variant)
+    const { variantFlags } = getFlagsForContext(context, variant)
 
     return {
       ...variant,
       reference_genome: 'GRCh37',
-      flags,
+      flags: variantFlags,
       transcript_consequence: transcriptConsequence,
     }
   }

graphql-api/src/queries/variant-datasets/gnomad-v2-variant-queries.ts

@@ -116,7 +116,7 @@ const fetchVariantById = async (esClient: any, variantIdOrRsid: any, subset: any
     genomeFilters.push('AC0')
   }
 
-  const flags = getFlagsForContext({ type: 'region' })(variant)
+  const { variantFlags, exomeFlags, genomeFlags } = getFlagsForContext({ type: 'region' }, variant)
 
   const lofCurationResults = await fetchLofCurationResultsByVariant(esClient, variant.variant_id)
 
@@ -131,6 +131,7 @@ const fetchVariantById = async (esClient: any, variantIdOrRsid: any, subset: any
           quality_metrics: formatVariantQualityMetrics(variant.exome.quality_metrics),
           age_distribution: variant.exome.age_distribution[exomeSubset],
           filters: exomeFilters,
+          flags: exomeFlags,
         }
       : null,
     genome: variant.genome.freq[genomeSubset].ac_raw
@@ -140,9 +141,10 @@ const fetchVariantById = async (esClient: any, variantIdOrRsid: any, subset: any
           quality_metrics: formatVariantQualityMetrics(variant.genome.quality_metrics),
           age_distribution: variant.genome.age_distribution[genomeSubset],
           filters: genomeFilters,
+          flags: genomeFlags,
         }
       : null,
-    flags,
+    flags: variantFlags,
     lof_curations: lofCurationResults,
     transcript_consequences: variant.transcript_consequences || [],
   }
@@ -154,11 +156,10 @@ const fetchVariantById = async (esClient: any, variantIdOrRsid: any, subset: any
 
 const shapeVariantSummary = (exomeSubset: any, genomeSubset: any, context: any) => {
   const getConsequence = getConsequenceForContext(context)
-  const getFlags = getFlagsForContext(context)
 
   return (variant: any) => {
     const transcriptConsequence = getConsequence(variant) || {}
-    const flags = getFlags(variant)
+    const { variantFlags, exomeFlags, genomeFlags } = getFlagsForContext(context, variant)
 
     const exomeFilters = variant.exome.filters || []
     const genomeFilters = variant.genome.filters || []
@@ -181,6 +182,7 @@ const shapeVariantSummary = (exomeSubset: any, genomeSubset: any, context: any)
               (pop: any) => !(pop.id.includes('_') || pop.id === 'XX' || pop.id === 'XY')
             ),
             filters: exomeFilters,
+            flags: exomeFlags,
           }
         : null,
       genome: variant.genome.freq[genomeSubset].ac_raw
@@ -191,9 +193,10 @@ const shapeVariantSummary = (exomeSubset: any, genomeSubset: any, context: any)
               (pop: any) => !(pop.id.includes('_') || pop.id === 'XX' || pop.id === 'XY')
             ),
             filters: genomeFilters,
+            flags: genomeFlags,
           }
         : null,
-      flags,
+      flags: variantFlags,
       transcript_consequence: transcriptConsequence,
     }
   }
@@ -238,6 +241,8 @@ const fetchVariantsByGene = async (esClient: any, gene: any, subset: any) => {
       `value.genome.freq.${genomeSubset}`,
       'value.exome.filters',
       'value.genome.filters',
+      'value.exome.flags',
+      'value.genome.flags',
       'value.alt',
       'value.caid',
       'value.chrom',