@jbrowse/plugin-variants 3.2.0 → 3.4.0

package/esm/MultiVariantBaseRenderer.d.ts

@@ -22,7 +22,7 @@ export default abstract class MultiVariantBaseRenderer extends FeatureRendererTy
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -30,15 +30,15 @@ export default abstract class MultiVariantBaseRenderer extends FeatureRendererTy
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<string, Feature>;
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
     abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;

package/esm/SplitVcfTabixAdapter/SplitVcfTabixAdapter.d.ts

@@ -15,5 +15,4 @@ export default class SplitVcfTabixAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }

package/esm/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js

@@ -83,5 +83,4 @@ export default class SplitVcfTabixAdapter extends BaseFeatureDataAdapter {
                 .filter(f => s.has(f.name));
         }
     }
-    freeResources() { }
 }

package/esm/SplitVcfTabixAdapter/configSchema.js

@@ -17,9 +17,11 @@ const SplitVcfTabixAdapter = ConfigurationSchema('SplitVcfTabixAdapter', {
         type: 'fileLocation',
         defaultValue: {
             uri: '/path/to/samples.tsv',
-            description: 'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+            description: 'tsv with header like "name\tpopulation\tetc" where the first column is required, and corresponds to the sample names in the VCF files',
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+});
 export default SplitVcfTabixAdapter;

package/esm/VariantFeatureWidget/AltFormatter.d.ts

@@ -0,0 +1,4 @@
+export default function AltFormatter({ value, ref, }: {
+    value: string;
+    ref: string;
+}): string | import("react/jsx-runtime").JSX.Element;

package/esm/VariantFeatureWidget/AltFormatter.js

@@ -0,0 +1,10 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import { getMinimalDesc } from '../VcfFeature/util';
+export default function AltFormatter({ value, ref, }) {
+    const [show, setShow] = useState(false);
+    const alt = getMinimalDesc(ref, value);
+    return alt !== value ? (_jsxs("div", { children: [_jsx("button", { onClick: () => {
+                    setShow(!show);
+                }, children: show ? 'Show simplified ALT' : 'Show raw ALT' }), ' ', show ? value : getMinimalDesc(ref, value)] })) : (value);
+}

package/esm/VariantFeatureWidget/Checkbox2.js

@@ -1,12 +1,5 @@
 import { jsx as _jsx } from "react/jsx-runtime";
-import { Checkbox, FormControlLabel } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()({
-    block: {
-        display: 'block',
-    },
-});
+import { Checkbox, FormControlLabel, Typography } from '@mui/material';
 export default function Checkbox2({ checked, disabled, label, onChange, }) {
-    const { classes } = useStyles();
-    return (_jsx(FormControlLabel, { disabled: disabled, className: classes.block, control: _jsx(Checkbox, { checked: checked, onChange: onChange }), label: label }));
+    return (_jsx(FormControlLabel, { disabled: disabled, control: _jsx(Checkbox, { checked: checked, onChange: onChange }), label: _jsx(Typography, { variant: "body2", children: label }) }));
 }

package/esm/VariantFeatureWidget/Formatter.d.ts

@@ -0,0 +1,3 @@
+export default function Formatter({ value }: {
+    value: unknown;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/VariantFeatureWidget/Formatter.js

@@ -0,0 +1,17 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import copy from 'copy-to-clipboard';
+export default function Formatter({ value }) {
+    const [show, setShow] = useState(false);
+    const [copied, setCopied] = useState(false);
+    const display = String(value);
+    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: () => {
+                    copy(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                }, children: copied ? 'Copied to clipboard' : 'Copy' }), _jsx("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                }, children: show ? 'Show less' : 'Show more' }), _jsx("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : (_jsx("div", { children: display }));
+}

package/esm/VariantFeatureWidget/{VariantConsequenceDataGridWrapper.js → VariantConsequence/VariantConsequenceDataGridWrapper.js}

@@ -2,16 +2,14 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import { measureGridWidth } from '@jbrowse/core/util';
 import { Checkbox, FormControlLabel, Typography } from '@mui/material';
-import { DataGrid, GridToolbar } from '@mui/x-data-grid';
+import { DataGrid } from '@mui/x-data-grid';
 export default function VariantConsequenceDataGridWrapper({ rows, columns, }) {
     const [checked, setChecked] = useState(false);
     const widths = columns.map(e => measureGridWidth(rows.map(r => r[e.field])));
-    return rows.length ? (_jsxs("div", { children: [_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: checked, onChange: event => {
+    return rows.length ? (_jsxs("div", { children: [_jsx(FormControlLabel, { label: _jsx(Typography, { variant: "body2", children: "Show options" }), control: _jsx(Checkbox, { checked: checked, onChange: event => {
                         setChecked(event.target.checked);
-                    } }), label: _jsx(Typography, { variant: "body2", children: "Show options" }) }), _jsx(DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({
+                    } }) }), _jsx(DataGrid, { rowHeight: 25, hideFooter: rows.length < 100, rows: rows, showToolbar: checked, columns: columns.map((c, i) => ({
                     ...c,
                     width: widths[i],
-                })), slots: {
-                    toolbar: checked ? GridToolbar : null,
-                } })] })) : null;
+                })) })] })) : null;
 }

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -4,10 +4,12 @@ import { parseBreakend } from '@gmod/vcf';
 import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
+import AltFormatter from './AltFormatter';
+import Formatter from './Formatter';
 import VariantSampleGrid from './VariantSampleGrid/VariantSampleGrid';
 import { variantFieldDescriptions } from './variantFieldDescriptions';
 const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel/LaunchBreakendPanel'));
-const VariantConsequenceDataGrid = lazy(() => import('./VariantConsequenceDataGrid'));
+const VariantConsequenceDataGrid = lazy(() => import('./VariantConsequence/VariantConsequenceDataGrid'));
 function AnnPanel({ descriptions, feature, }) {
     var _a, _b, _c, _d, _e;
     const annDesc = (_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;
@@ -42,14 +44,22 @@ function LaunchBreakendWidgetArea({ model, }) {
             },
         }, model: model, locStrings: [`${feat.refName}:${feat.end}`] })) : null;
 }
-const VariantFeatureWidget = observer(function (props) {
-    const { model } = props;
-    const { featureData, descriptions } = model;
-    const feat = JSON.parse(JSON.stringify(featureData));
-    const { samples, ALT, ...rest } = feat;
+const FeatDefined = observer(function (props) {
+    const { feat, model } = props;
+    const { descriptions } = model;
+    const { samples, ...rest } = feat;
+    const { REF } = rest;
     return (_jsxs(Paper, { "data-testid": "variant-side-drawer", children: [_jsx(FeatureDetails, { feature: rest, descriptions: {
                     ...variantFieldDescriptions,
                     ...descriptions,
+                }, formatter: (value, key) => {
+                    return key === 'ALT' ? (_jsx(AltFormatter, { value: `${value}`, ref: REF })) : (_jsx(Formatter, { value: value }));
                 }, ...props }), _jsxs(Suspense, { fallback: null, children: [_jsx(CsqPanel, { feature: rest, descriptions: descriptions }), _jsx(AnnPanel, { feature: rest, descriptions: descriptions }), _jsx(LaunchBreakendWidgetArea, { model: model })] }), _jsx(VariantSampleGrid, { feature: feat, ...props, descriptions: descriptions })] }));
 });
+const VariantFeatureWidget = observer(function (props) {
+    const { model } = props;
+    const { featureData } = model;
+    const feat = structuredClone(featureData);
+    return feat ? (_jsx(FeatDefined, { feat: feat, ...props })) : (_jsx("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
+});
 export default VariantFeatureWidget;

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.d.ts

@@ -0,0 +1,4 @@
+import type { VariantSampleGridRow } from './types';
+export default function VariantGenotypeFrequencyTable({ rows, }: {
+    rows: VariantSampleGridRow[];
+}): import("react/jsx-runtime").JSX.Element;

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js

@@ -0,0 +1,74 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
+import { measureGridWidth } from '@jbrowse/core/util';
+import { Checkbox, FormControlLabel, Typography } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+function toP(n) {
+    return n.toPrecision(3);
+}
+export default function VariantGenotypeFrequencyTable({ rows, }) {
+    const [useCounts, setUseCounts] = useState(false);
+    const summary = {};
+    if (!useCounts) {
+        for (const row of rows) {
+            const gt = row.GT;
+            if (!summary[gt]) {
+                summary[gt] = {
+                    count: 0,
+                    GT: row.GT,
+                    genotype: row.genotype,
+                };
+            }
+            summary[gt].count++;
+        }
+    }
+    else {
+        for (const row of rows) {
+            const alleleCounts = {};
+            const alleles = row.GT.split(/[/|]/);
+            for (const allele of alleles) {
+                alleleCounts[allele] = (alleleCounts[allele] || 0) + 1;
+            }
+            const key = Object.entries(alleleCounts)
+                .map(([key, val]) => `${key}:${val}`)
+                .join(';');
+            if (!summary[key]) {
+                summary[key] = {
+                    count: 0,
+                    GT: key,
+                    genotype: row.genotype,
+                };
+            }
+            summary[key].count++;
+        }
+    }
+    const gridRows = Object.entries(summary).map(([key, val]) => ({
+        id: key,
+        ...val,
+        count: `${val.count} / ${rows.length}`,
+        frequency: `${toP((val.count / rows.length) * 100)}%`,
+    }));
+    const keys = gridRows[0] ? Object.keys(gridRows[0]) : [];
+    const widths = keys.map(e => measureGridWidth(gridRows.map(r => `${r[e]}`)));
+    return (_jsxs("div", { children: [_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: useCounts }), label: _jsx(Typography, { variant: "body2", children: "Use allele counts instead of exact GT" }), onChange: (_, checked) => {
+                    setUseCounts(checked);
+                } }), _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: gridRows, hideFooter: true, rowHeight: 25, columnHeaderHeight: 35, columns: [
+                        {
+                            field: 'GT',
+                            width: widths[0],
+                        },
+                        {
+                            field: 'count',
+                            width: widths[1],
+                        },
+                        {
+                            field: 'frequency',
+                            width: widths[2],
+                        },
+                        {
+                            field: 'genotype',
+                            width: widths[3],
+                        },
+                    ] }) })] }));
+}

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.d.ts

@@ -1,12 +1,6 @@
+import type { VariantFieldDescriptions } from './types';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-interface FormatRecord {
-    Description?: string;
-}
-interface Descriptions {
-    FORMAT?: Record<string, FormatRecord>;
-}
-export default function VariantSamples(props: {
+export default function VariantSampleGrid(props: {
     feature: SimpleFeatureSerialized;
-    descriptions?: Descriptions | null;
+    descriptions?: VariantFieldDescriptions | null;
 }): import("react/jsx-runtime").JSX.Element | null;
-export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js

@@ -1,26 +1,50 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { useState } from 'react';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
+import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary';
 import { measureGridWidth } from '@jbrowse/core/util';
-import { Checkbox, FormControlLabel, Typography } from '@mui/material';
-import { DataGrid, GridToolbar } from '@mui/x-data-grid';
+import { Typography } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+import Checkbox2 from '../Checkbox2';
+import VariantGenotypeFrequencyTable from './VariantGenotypeFrequencyTable';
 import SampleFilters from './VariantSampleFilters';
-export default function VariantSamples(props) {
+import { areSetsEqual } from './util';
+import { makeSimpleAltString } from '../../VcfFeature/util';
+export default function VariantSampleGrid(props) {
     var _a;
     const { feature, descriptions = {} } = props;
     const [filter, setFilter] = useState({});
+    const [showOnlyGenotypeColumns, setShowOnlyGenotypeColumns] = useState(true);
+    const [showFilters, setShowFilters] = useState(false);
     const samples = (feature.samples || {});
-    const preFilteredRows = Object.entries(samples);
+    const ALT = feature.ALT;
+    const REF = feature.REF;
+    const preFilteredRows = Object.entries(samples).map(([key, val]) => {
+        var _a, _b;
+        return [
+            key,
+            {
+                ...val,
+                GT: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
+                genotype: makeSimpleAltString(`${(_b = val.GT) === null || _b === void 0 ? void 0 : _b[0]}`, REF, ALT),
+            },
+        ];
+    });
     let error;
     let rows = [];
     const filters = Object.keys(filter);
     try {
         rows = preFilteredRows
-            .map(row => {
+            .map(([key, val]) => {
             return {
-                ...Object.fromEntries(Object.entries(row[1]).map(e => [e[0], `${e[1]}`])),
-                sample: row[0],
-                id: row[0],
+                ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
+                    formatField,
+                    formatValue,
+                ])),
+                sample: key,
+                id: key,
             };
         })
             .filter(row => filters.length
@@ -33,9 +57,9 @@ export default function VariantSamples(props) {
             : true);
     }
     catch (e) {
+        console.error(e);
         error = e;
     }
-    const [checked, setChecked] = useState(false);
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
     const widths = keys.map(e => measureGridWidth(rows.map(r => r[e])));
     const columns = keys.map((field, index) => {
@@ -46,16 +70,13 @@ export default function VariantSamples(props) {
             width: widths[index],
         });
     });
-    return !preFilteredRows.length ? null : (_jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: checked, onChange: event => {
-                        setChecked(event.target.checked);
-                    } }), label: _jsx(Typography, { variant: "body2", children: "Show options" }) }), checked ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx("div", { style: {
-                    display: 'flex',
-                    flexDirection: 'column',
-                }, children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? GridToolbar : null }, slotProps: {
-                        toolbar: {
-                            printOptions: {
-                                disableToolbarButton: true,
-                            },
-                        },
-                    } }) })] }));
+    const s1 = new Set(['sample', 'GT', 'genotype']);
+    const s2 = new Set(keys);
+    return !preFilteredRows.length ? null : (_jsxs(_Fragment, { children: [_jsx(BaseCard, { ...props, title: "Genotype frequencies", children: _jsx(ErrorBoundary, { FallbackComponent: ErrorMessage, children: _jsx(VariantGenotypeFrequencyTable, { rows: rows }) }) }), _jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsx(Checkbox2, { label: "Show filters", checked: showFilters, onChange: event => {
+                            setShowFilters(event.target.checked);
+                        } }), areSetsEqual(s1, s2) ? null : (_jsx(Checkbox2, { label: "Show only genotype columns", checked: showOnlyGenotypeColumns, onChange: event => {
+                            setShowOnlyGenotypeColumns(event.target.checked);
+                        } })), showFilters ? (_jsx(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null, _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: showOnlyGenotypeColumns
+                                ? columns.filter(f => s1.has(f.field))
+                                : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
 }

package/esm/VariantFeatureWidget/VariantSampleGrid/types.d.ts

@@ -0,0 +1,21 @@
+export interface FrequencyTableEntry {
+    count: number;
+    GT: string;
+    genotype: string | undefined;
+}
+export type FrequencyTable = Record<string, FrequencyTableEntry>;
+export interface VariantSampleGridRow {
+    sample: string;
+    id: string;
+    GT: string;
+    [key: string]: string;
+}
+export type InfoFields = Record<string, unknown[]>;
+export type Filters = Record<string, string>;
+interface FormatRecord {
+    Description?: string;
+}
+export interface VariantFieldDescriptions {
+    FORMAT?: Record<string, FormatRecord>;
+}
+export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/util.d.ts

@@ -0,0 +1 @@
+export declare function areSetsEqual<T>(set1: Set<T>, set2: Set<T>): boolean;

package/esm/VariantFeatureWidget/VariantSampleGrid/util.js

@@ -0,0 +1,11 @@
+export function areSetsEqual(set1, set2) {
+    if (set1.size !== set2.size) {
+        return false;
+    }
+    for (const item of set1) {
+        if (!set2.has(item)) {
+            return false;
+        }
+    }
+    return true;
+}

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -3,9 +3,9 @@ import type { Instance } from 'mobx-state-tree';
 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">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -35,15 +35,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
 }, {
     error: unknown;
 } & {
-    setFeatureData(featureData: Record<string, unknown>): void;
+    setFeatureData(featureData: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     clearFeatureData(): void;
-    setFormattedData(feat: Record<string, unknown>): void;
+    setFormattedData(feat: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
@@ -53,9 +54,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -85,6 +86,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: "BaseFeatureWidget";
     id: string;
@@ -95,6 +97,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     maxDepth: number | undefined;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     formattedFields: any;
+    descriptions: Record<string, unknown> | undefined;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts

@@ -1,21 +1,8 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { Source } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-interface Args {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    statusCallback: (arg: string) => void;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    sources: Source[];
-    minorAlleleFrequencyFilter: number;
-}
+import type { ClusterGenotypeMatrixArgs } from './types';
 export declare class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: Args, rpcDriverClassName: string): Promise<{
+    execute(args: ClusterGenotypeMatrixArgs, rpcDriverClassName: string): Promise<{
         clusters: {
             height: number;
             indexes: number[];
@@ -25,4 +12,3 @@ export declare class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWith
         clustersGivenK: number[][][];
     }>;
 }
-export {};

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.js

@@ -1,5 +1,5 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { clusterData } from './cluster';
+import { clusterData } from '@jbrowse/core/util/cluster';
 import { getGenotypeMatrix } from './getGenotypeMatrix';
 export class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     constructor() {
@@ -14,13 +14,10 @@ export class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersA
         });
         return clusterData({
             data: Object.values(matrix),
-            onProgress: a => {
-                deserializedArgs.statusCallback(`${toP(a * 100)}%`);
-            },
             stopToken: deserializedArgs.stopToken,
+            onProgress: progress => {
+                deserializedArgs.statusCallback(progress);
+            },
         });
     }
 }
-function toP(n) {
-    return Number.parseFloat(n.toPrecision(3));
-}

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -1,19 +1,6 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { Source } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-interface Args {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    sources: Source[];
-    minorAlleleFrequencyFilter: number;
-}
+import type { GetGenotypeMatrixArgs } from './types';
 export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: Args, rpcDriverClassName: string): Promise<Record<string, number[]>>;
+    execute(args: GetGenotypeMatrixArgs, rpcDriverClassName: string): Promise<Record<string, number[]>>;
 }
-export {};

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,19 +1,9 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { GetSimplifiedFeaturesArgs } from './types';
 import type { SampleInfo } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-interface Args {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    minorAlleleFrequencyFilter: number;
-}
 export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: Args, rpcDriverClassName: string): Promise<{
+    execute(args: GetSimplifiedFeaturesArgs, rpcDriverClassName: string): Promise<{
         hasPhased: boolean;
         sampleInfo: Record<string, SampleInfo>;
         features: {
@@ -22,8 +12,8 @@ export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWith
                 start: number;
                 end: number;
                 refName: string;
+                name: any;
             };
         }[];
     }>;
 }
-export {};

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -1,5 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
@@ -8,17 +9,21 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         this.name = 'MultiVariantGetSimplifiedFeatures';
     }
     async execute(args, rpcDriverClassName) {
-        var _a, _b;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId } = deserializedArgs;
+        const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
-        const feats = await firstValueFrom(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe(toArray()));
-        const features = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
+        const features = getFeaturesThatPassMinorAlleleFrequencyFilter({
+            minorAlleleFrequencyFilter,
+            lengthCutoffFilter,
+            stopToken,
+            features: await firstValueFrom(dataAdapter
+                .getFeaturesInMultipleRegions(regions, deserializedArgs)
+                .pipe(toArray())),
+        });
         const sampleInfo = {};
         let hasPhased = false;
-        for (const { feature } of features) {
+        forEachWithStopTokenCheck(features, stopToken, ({ feature }) => {
+            var _a, _b;
             const samp = feature.get('genotypes');
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
@@ -28,7 +33,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
                 };
             }
-        }
+        });
         return {
             hasPhased,
             sampleInfo,
@@ -38,6 +43,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     start: feature.get('start'),
                     end: feature.get('end'),
                     refName: feature.get('refName'),
+                    name: feature.get('name'),
                 },
             })),
         };