@jbrowse/plugin-variants 2.4.2 → 2.6.1

package/esm/VariantFeatureWidget/index.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -14,10 +14,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
 }, {
+    error: unknown;
+} & {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
     setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, {

package/esm/VariantTrack/configSchema.d.ts

@@ -1,3 +1,75 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchema;

package/esm/VcfAdapter/VcfAdapter.js

@@ -25,7 +25,7 @@ const readVcf = (f) => {
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-export default class VcfAdapter extends BaseFeatureDataAdapter {
+class VcfAdapter extends BaseFeatureDataAdapter {
     async getHeader() {
         const { header } = await this.setup();
         return header;
@@ -98,4 +98,5 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
+export default VcfAdapter;
 //# sourceMappingURL=VcfAdapter.js.map

package/esm/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAxFjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;eADxC,UAAU"}

package/esm/VcfAdapter/configSchema.d.ts

@@ -1,2 +1,13 @@
-declare const VcfAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    vcfLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;

package/esm/VcfTabixAdapter/configSchema.d.ts

@@ -1,2 +1,33 @@
-declare const VcfTabixAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    vcfGzLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfTabixAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.4.2",
+  "version": "2.6.1",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
     "@gmod/tabix": "^1.5.6",
     "@gmod/vcf": "^5.0.9",
     "@mui/icons-material": "^5.0.2",
-    "@mui/x-data-grid": "^5.0.1",
+    "@mui/x-data-grid": "^6.0.1",
     "generic-filehandle": "^3.0.0"
   },
   "peerDependencies": {
@@ -64,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
 }

package/src/VariantFeatureWidget/AnnotGrid.tsx

@@ -1,28 +1,51 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import React from 'react'
-import { DataGrid } from '@mui/x-data-grid'
+import React, { useState } from 'react'
+import {
+  DataGrid,
+  GridColDef,
+  GridToolbar,
+  GridValidRowModel,
+} from '@mui/x-data-grid'
+import { Checkbox, FormControlLabel, Typography } from '@mui/material'
+import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar'
+import { measureGridWidth } from '@jbrowse/core/util'
 
 export default function VariantAnnotPanel({
   rows,
   columns,
 }: {
-  rows: any
-  columns: any[]
+  rows: GridValidRowModel[]
+  columns: GridColDef[]
 }) {
-  const rowHeight = 25
-  const hideFooter = rows.length < 100
-  const headerHeight = 80
+  const { ref, scrollLeft } = useResizeBar()
+  const [checked, setChecked] = useState(false)
+  const [widths, setWidths] = useState(
+    columns.map(e => measureGridWidth(rows.map(r => r[e.field]))),
+  )
+
   return rows.length ? (
-    <div
-      style={{
-        height:
-          Math.min(rows.length, 100) * rowHeight +
-          headerHeight +
-          (hideFooter ? 0 : 50),
-        width: '100%',
-      }}
-    >
-      <DataGrid rowHeight={rowHeight} rows={rows} columns={columns} />
+    <div ref={ref}>
+      <FormControlLabel
+        control={
+          <Checkbox
+            checked={checked}
+            onChange={event => setChecked(event.target.checked)}
+          />
+        }
+        label={<Typography variant="body2">Show options</Typography>}
+      />
+      <div ref={ref}>
+        <ResizeBar
+          widths={widths}
+          setWidths={setWidths}
+          scrollLeft={scrollLeft}
+        />
+        <DataGrid
+          rowHeight={25}
+          rows={rows}
+          columns={columns.map((c, i) => ({ ...c, width: widths[i] }))}
+          slots={{ toolbar: checked ? GridToolbar : null }}
+        />
+      </div>
     </div>
   ) : null
 }

package/src/VariantFeatureWidget/BreakendOptionDialog.tsx

@@ -20,7 +20,7 @@ const useStyles = makeStyles()({
   },
 })
 
-function BreakendOptionDialog({
+export default observer(function BreakendOptionDialog({
   model,
   handleClose,
   feature,
@@ -43,7 +43,7 @@ function BreakendOptionDialog({
           control={
             <Checkbox
               checked={copyTracks}
-              onChange={() => setCopyTracks(val => !val)}
+              onChange={event => setCopyTracks(event.target.checked)}
             />
           }
           label="Copy tracks into the new view"
@@ -54,7 +54,7 @@ function BreakendOptionDialog({
           control={
             <Checkbox
               checked={mirrorTracks}
-              onChange={() => setMirrorTracks(val => !val)}
+              onChange={event => setMirrorTracks(event.target.checked)}
             />
           }
           label="Mirror tracks vertically in vertically stacked view"
@@ -114,5 +114,4 @@ function BreakendOptionDialog({
       </DialogActions>
     </Dialog>
   )
-}
-export default observer(BreakendOptionDialog)
+})

package/src/VariantFeatureWidget/VariantAnnotationTable.tsx

@@ -0,0 +1,27 @@
+import React from 'react'
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
+import AnnotGrid from './AnnotGrid'
+
+export default function VariantAnnotationTable({
+  data,
+  fields,
+  title,
+}: {
+  data: string[]
+  fields: string[]
+  title: string
+}) {
+  return data.length ? (
+    <BaseCard title={title}>
+      <AnnotGrid
+        rows={
+          data.map((elt, id) => ({
+            id,
+            ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
+          })) || []
+        }
+        columns={fields.map(c => ({ field: c }))}
+      />
+    </BaseCard>
+  ) : null
+}

package/src/VariantFeatureWidget/VariantFeatureWidget.tsx

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import React from 'react'
 import { observer } from 'mobx-react'
 import { Divider, Paper } from '@mui/material'
@@ -7,25 +6,31 @@ import { parseBreakend } from '@gmod/vcf'
 
 // locals
 import VariantSampleGrid from './VariantSampleGrid'
-import VariantCsqPanel from './VariantCsqPanel'
-import VariantAnnPanel from './VariantAnnPanel'
 import BreakendPanel from './BreakendPanel'
+import VariantAnnotationTable from './VariantAnnotationTable'
+import { SimpleFeatureSerialized } from '@jbrowse/core/util'
 
-function VariantFeatureDetails(props: any) {
+const basicDescriptions = {
+  CHROM: 'chromosome: An identifier from the reference genome',
+  POS: 'position: The reference position, with the 1st base having position 1',
+  ID: 'identifier: Semi-colon separated list of unique identifiers where available',
+  REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
+  ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
+  QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
+  FILTER:
+    'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
+}
+
+function VariantFeatureDetails(props: {
+  model: {
+    featureData: SimpleFeatureSerialized
+    descriptions: Record<string, string>
+  }
+}) {
   const { model } = props
   const { featureData, descriptions } = model
   const feat = JSON.parse(JSON.stringify(featureData))
   const { samples, ...rest } = feat
-  const basicDescriptions = {
-    CHROM: 'chromosome: An identifier from the reference genome',
-    POS: 'position: The reference position, with the 1st base having position 1',
-    ID: 'identifier: Semi-colon separated list of unique identifiers where available',
-    REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
-    ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
-    QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
-    FILTER:
-      'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
-  }
 
   return (
     <Paper data-testid="variant-side-drawer">
@@ -35,9 +40,9 @@ function VariantFeatureDetails(props: any) {
         {...props}
       />
       <Divider />
-      <VariantCsqPanel feature={rest} descriptions={descriptions} />
+      <CsqPanel feature={rest} descriptions={descriptions} />
       <Divider />
-      <VariantAnnPanel feature={rest} descriptions={descriptions} />
+      <AnnPanel feature={rest} descriptions={descriptions} />
       <Divider />
       {feat.type === 'breakend' ? (
         <BreakendPanel
@@ -64,4 +69,44 @@ function VariantFeatureDetails(props: any) {
   )
 }
 
+function AnnPanel({
+  descriptions,
+  feature,
+}: {
+  descriptions: { INFO?: { ANN?: { Description?: string } } }
+  feature: { INFO?: { ANN?: string[] } }
+}) {
+  const annDesc = descriptions?.INFO?.ANN?.Description
+  const annFields =
+    annDesc?.match(/.*Functional annotations:'(.*)'$/)?.[1].split('|') || []
+  const ann = feature.INFO?.ANN || []
+  return (
+    <VariantAnnotationTable
+      fields={annFields}
+      data={ann}
+      title="Variant ANN field"
+    />
+  )
+}
+
+function CsqPanel({
+  descriptions,
+  feature,
+}: {
+  descriptions: { INFO?: { CSQ?: { Description?: string } } }
+  feature: { INFO?: { CSQ?: string[] } }
+}) {
+  const csqDescription = descriptions?.INFO?.CSQ?.Description
+  const csqFields =
+    csqDescription?.match(/.*Format: (.*)/)?.[1].split('|') || []
+  const csq = feature.INFO?.CSQ || []
+  return (
+    <VariantAnnotationTable
+      fields={csqFields}
+      data={csq}
+      title="Variant CSQ field"
+    />
+  )
+}
+
 export default observer(VariantFeatureDetails)

package/src/VariantFeatureWidget/VariantSampleGrid.tsx

@@ -7,7 +7,7 @@ import {
   Typography,
 } from '@mui/material'
 
-import { DataGrid } from '@mui/x-data-grid'
+import { DataGrid, GridToolbar } from '@mui/x-data-grid'
 import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
 import { measureGridWidth, SimpleFeatureSerialized } from '@jbrowse/core/util'
 import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar'
@@ -30,46 +30,31 @@ function SampleFilters({
   filter: Filters
   setFilter: (arg: Filters) => void
 }) {
-  const [showFilters, setShowFilters] = useState(false)
   return (
     <>
-      <FormControlLabel
-        control={
-          <Checkbox
-            checked={showFilters}
-            onChange={() => setShowFilters(f => !f)}
-          />
-        }
-        label="Show sample filters"
-      />
-      {showFilters ? (
-        <>
-          <Typography>
-            These filters can use a plain text search or regex style query, e.g.
-            in the genotype field, entering 1 will query for all genotypes that
-            include the first alternate allele e.g. 0|1 or 1|1, entering
-            [1-9]\d* will find any non-zero allele e.g. 0|2 or 2/33
-          </Typography>
-          {columns.map(({ field }) => (
-            <TextField
-              key={`filter-${field}`}
-              placeholder={`Filter ${field}`}
-              value={filter[field] || ''}
-              onChange={event =>
-                setFilter({ ...filter, [field]: event.target.value })
-              }
-            />
-          ))}
-        </>
-      ) : null}
+      <Typography>
+        These filters can use a plain text search or regex style query, e.g. in
+        the genotype field, entering 1 will query for all genotypes that include
+        the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\d* will find
+        any non-zero allele e.g. 0|2 or 2/33
+      </Typography>
+      {columns.map(({ field }) => (
+        <TextField
+          key={`filter-${field}`}
+          placeholder={`Filter ${field}`}
+          value={filter[field] || ''}
+          onChange={event =>
+            setFilter({ ...filter, [field]: event.target.value })
+          }
+        />
+      ))}
     </>
   )
 }
 
 export default function VariantSamples(props: {
   feature: SimpleFeatureSerialized
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  descriptions: any
+  descriptions: { FORMAT?: { [key: string]: { Description?: string } } }
 }) {
   const { feature, descriptions = {} } = props
   const { ref, scrollLeft } = useResizeBar()
@@ -98,9 +83,10 @@ export default function VariantSamples(props: {
       .filter(row =>
         filters.length
           ? filters.every(key => {
-              const val = row[key]
               const currFilter = filter[key]
-              return currFilter ? val.match(new RegExp(currFilter, 'i')) : true
+              return currFilter
+                ? row[key].match(new RegExp(currFilter, 'i'))
+                : true
             })
           : true,
       )
@@ -109,7 +95,7 @@ export default function VariantSamples(props: {
   }
 
   const keys = ['sample', ...Object.keys(preFilteredRows[0]?.[1] || {})]
-
+  const [checked, setChecked] = useState(false)
   const [widths, setWidths] = useState(
     keys.map(e => measureGridWidth(rows.map(r => r[e]))),
   )
@@ -119,28 +105,46 @@ export default function VariantSamples(props: {
     width: widths[index],
   }))
 
-  // disableSelectionOnClick helps avoid
+  // disableRowSelectionOnClick helps avoid
   // https://github.com/mui-org/material-ui-x/issues/1197
   return !preFilteredRows.length ? null : (
     <BaseCard {...props} title="Samples">
       {error ? <Typography color="error">{`${error}`}</Typography> : null}
-      <SampleFilters setFilter={setFilter} columns={columns} filter={filter} />
+      <FormControlLabel
+        control={
+          <Checkbox
+            checked={checked}
+            onChange={event => setChecked(event.target.checked)}
+          />
+        }
+        label={<Typography variant="body2">Show options</Typography>}
+      />
+      {checked ? (
+        <SampleFilters
+          setFilter={setFilter}
+          columns={columns}
+          filter={filter}
+        />
+      ) : null}
       <div ref={ref}>
         <ResizeBar
           widths={widths}
           setWidths={setWidths}
           scrollLeft={scrollLeft}
         />
-        <div ref={ref} style={{ height: 600, width: '100%', overflow: 'auto' }}>
-          <DataGrid
-            rows={rows}
-            columns={columns}
-            disableSelectionOnClick
-            rowHeight={25}
-            headerHeight={35}
-            disableColumnMenu
-          />
-        </div>
+        <DataGrid
+          rows={rows}
+          hideFooter={rows.length < 100}
+          columns={columns}
+          disableRowSelectionOnClick
+          rowHeight={25}
+          columnHeaderHeight={35}
+          disableColumnMenu
+          slots={{ toolbar: checked ? GridToolbar : null }}
+          slotProps={{
+            toolbar: { printOptions: { disableToolbarButton: true } },
+          }}
+        />
       </div>
     </BaseCard>
   )

package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap

@@ -188,7 +188,7 @@ exports[`renders with just the required model elements 1`] = `
                 </div>
               </div>
               <div
-                class="css-1upvn7b-container2"
+                class="css-1lttu3w-container"
               >
                 <button
                   class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
@@ -224,7 +224,6 @@ exports[`renders with just the required model elements 1`] = `
                     />
                   </button>
                 </div>
-                <br />
               </div>
             </div>
           </div>

package/dist/VariantFeatureWidget/VariantAnnPanel.d.ts

@@ -1,5 +0,0 @@
-/// <reference types="react" />
-export default function VariantAnnPanel({ feature, descriptions, }: {
-    feature: any;
-    descriptions: any;
-}): JSX.Element | null;

package/dist/VariantFeatureWidget/VariantAnnPanel.js

@@ -1,25 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/no-explicit-any */
-const react_1 = __importDefault(require("react"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
-function VariantAnnPanel({ feature, descriptions, }) {
-    var _a, _b, _c, _d;
-    const annFields = (((_d = (_c = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description) === null || _c === void 0 ? void 0 : _c.match(/.*Functional annotations:'(.*)'$/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
-    const ann = (feature.INFO.ANN || []);
-    const rows = ann.map((elt, id) => ({
-        id,
-        ...Object.fromEntries(elt.split('|').map((e, i) => [annFields[i], e])),
-    })) || [];
-    const columns = annFields.map(c => ({
-        field: c,
-    }));
-    return ann.length ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "ANN table" },
-        react_1.default.createElement(AnnotGrid_1.default, { rows: rows, columns: columns }))) : null;
-}
-exports.default = VariantAnnPanel;
-//# sourceMappingURL=VariantAnnPanel.js.map

package/dist/VariantFeatureWidget/VariantAnnPanel.js.map

@@ -1 +0,0 @@
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package/dist/VariantFeatureWidget/VariantCsqPanel.d.ts

@@ -1,5 +0,0 @@
-/// <reference types="react" />
-export default function VariantCsqPanel({ feature, descriptions, }: {
-    feature: any;
-    descriptions: any;
-}): JSX.Element | null;