Incorporate exome/genome flags into frontend

broadinstitute · Sep 5, 2024 · 2293dff · 2293dff
1 parent fefd197
commit 2293dff
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Showing 5 changed files with 43 additions and 12 deletions.
diff --git a/browser/src/GenePage/VariantsInGene.tsx b/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

diff --git a/browser/src/RegionPage/VariantsInRegion.tsx b/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

diff --git a/browser/src/VariantList/VariantFlag.tsx b/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: {

diff --git a/browser/src/VariantList/variantTableColumns.tsx b/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 && ' †'}

diff --git a/browser/src/VariantPage/VariantPage.tsx b/browser/src/VariantPage/VariantPage.tsx
@@ -586,6 +586,7 @@ query ${operationName}($variantId: String!, $datasetId: DatasetId!, $referenceGe
           value
         }
       }
+      flags
     }
     genome {
       ac
@@ -665,6 +666,7 @@ query ${operationName}($variantId: String!, $datasetId: DatasetId!, $referenceGe
           value
         }
       }
+      flags
     }
     joint {
       ac