@jbrowse/plugin-variants 3.2.0 → 3.4.0

package/dist/VariantFeatureWidget/Formatter.d.ts

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

package/dist/VariantFeatureWidget/Formatter.js

@@ -0,0 +1,23 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = Formatter;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+function Formatter({ value }) {
+    const [show, setShow] = (0, react_1.useState)(false);
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const display = String(value);
+    return display.length > 100 ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
+                    (0, copy_to_clipboard_1.default)(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                }, children: copied ? 'Copied to clipboard' : 'Copy' }), (0, jsx_runtime_1.jsx)("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                }, children: show ? 'Show less' : 'Show more' }), (0, jsx_runtime_1.jsx)("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : ((0, jsx_runtime_1.jsx)("div", { children: display }));
+}

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

@@ -9,12 +9,10 @@ const x_data_grid_1 = require("@mui/x-data-grid");
 function VariantConsequenceDataGridWrapper({ rows, columns, }) {
     const [checked, setChecked] = (0, react_1.useState)(false);
     const widths = columns.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e.field])));
-    return rows.length ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: checked, onChange: event => {
+    return rows.length ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { label: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body2", children: "Show options" }), control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: checked, onChange: event => {
                         setChecked(event.target.checked);
-                    } }), label: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body2", children: "Show options" }) }), (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({
+                    } }) }), (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rowHeight: 25, hideFooter: rows.length < 100, rows: rows, showToolbar: checked, columns: columns.map((c, i) => ({
                     ...c,
                     width: widths[i],
-                })), slots: {
-                    toolbar: checked ? x_data_grid_1.GridToolbar : null,
-                } })] })) : null;
+                })) })] })) : null;
 }

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -42,10 +42,12 @@ const vcf_1 = require("@gmod/vcf");
 const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
+const AltFormatter_1 = __importDefault(require("./AltFormatter"));
+const Formatter_1 = __importDefault(require("./Formatter"));
 const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid/VariantSampleGrid"));
 const variantFieldDescriptions_1 = require("./variantFieldDescriptions");
 const LaunchBreakendPanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LaunchBreakendPanel/LaunchBreakendPanel'))));
-const VariantConsequenceDataGrid = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantConsequenceDataGrid'))));
+const VariantConsequenceDataGrid = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./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;
@@ -80,14 +82,22 @@ function LaunchBreakendWidgetArea({ model, }) {
             },
         }, model: model, locStrings: [`${feat.refName}:${feat.end}`] })) : null;
 }
-const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { featureData, descriptions } = model;
-    const feat = JSON.parse(JSON.stringify(featureData));
-    const { samples, ALT, ...rest } = feat;
+const FeatDefined = (0, mobx_react_1.observer)(function (props) {
+    const { feat, model } = props;
+    const { descriptions } = model;
+    const { samples, ...rest } = feat;
+    const { REF } = rest;
     return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { "data-testid": "variant-side-drawer", children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { feature: rest, descriptions: {
                     ...variantFieldDescriptions_1.variantFieldDescriptions,
                     ...descriptions,
+                }, formatter: (value, key) => {
+                    return key === 'ALT' ? ((0, jsx_runtime_1.jsx)(AltFormatter_1.default, { value: `${value}`, ref: REF })) : ((0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value }));
                 }, ...props }), (0, jsx_runtime_1.jsxs)(react_1.Suspense, { fallback: null, children: [(0, jsx_runtime_1.jsx)(CsqPanel, { feature: rest, descriptions: descriptions }), (0, jsx_runtime_1.jsx)(AnnPanel, { feature: rest, descriptions: descriptions }), (0, jsx_runtime_1.jsx)(LaunchBreakendWidgetArea, { model: model })] }), (0, jsx_runtime_1.jsx)(VariantSampleGrid_1.default, { feature: feat, ...props, descriptions: descriptions })] }));
 });
+const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
+    const { model } = props;
+    const { featureData } = model;
+    const feat = structuredClone(featureData);
+    return feat ? ((0, jsx_runtime_1.jsx)(FeatDefined, { feat: feat, ...props })) : ((0, jsx_runtime_1.jsx)("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
+});
 exports.default = VariantFeatureWidget;

package/dist/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/dist/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js

@@ -0,0 +1,80 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantGenotypeFrequencyTable;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const DataGridFlexContainer_1 = __importDefault(require("@jbrowse/core/ui/DataGridFlexContainer"));
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const x_data_grid_1 = require("@mui/x-data-grid");
+function toP(n) {
+    return n.toPrecision(3);
+}
+function VariantGenotypeFrequencyTable({ rows, }) {
+    const [useCounts, setUseCounts] = (0, react_1.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 => (0, util_1.measureGridWidth)(gridRows.map(r => `${r[e]}`)));
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useCounts }), label: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body2", children: "Use allele counts instead of exact GT" }), onChange: (_, checked) => {
+                    setUseCounts(checked);
+                } }), (0, jsx_runtime_1.jsx)(DataGridFlexContainer_1.default, { children: (0, jsx_runtime_1.jsx)(x_data_grid_1.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/dist/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/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js

@@ -3,30 +3,54 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = VariantSamples;
+exports.default = VariantSampleGrid;
 const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const ui_1 = require("@jbrowse/core/ui");
+const DataGridFlexContainer_1 = __importDefault(require("@jbrowse/core/ui/DataGridFlexContainer"));
+const ErrorBoundary_1 = require("@jbrowse/core/ui/ErrorBoundary");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
+const Checkbox2_1 = __importDefault(require("../Checkbox2"));
+const VariantGenotypeFrequencyTable_1 = __importDefault(require("./VariantGenotypeFrequencyTable"));
 const VariantSampleFilters_1 = __importDefault(require("./VariantSampleFilters"));
-function VariantSamples(props) {
+const util_2 = require("./util");
+const util_3 = require("../../VcfFeature/util");
+function VariantSampleGrid(props) {
     var _a;
     const { feature, descriptions = {} } = props;
     const [filter, setFilter] = (0, react_1.useState)({});
+    const [showOnlyGenotypeColumns, setShowOnlyGenotypeColumns] = (0, react_1.useState)(true);
+    const [showFilters, setShowFilters] = (0, react_1.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: `${(_a = val.GT) === null || _a === void 0 ? void 0 : _a[0]}`,
+                genotype: (0, util_3.makeSimpleAltString)(`${(_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], `${e[1]}`])),
-                sample: row[0],
-                id: row[0],
+                ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
+                    formatField,
+                    formatValue,
+                ])),
+                sample: key,
+                id: key,
             };
         })
             .filter(row => filters.length
@@ -39,9 +63,9 @@ function VariantSamples(props) {
             : true);
     }
     catch (e) {
+        console.error(e);
         error = e;
     }
-    const [checked, setChecked] = (0, react_1.useState)(false);
     const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
     const widths = keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e])));
     const columns = keys.map((field, index) => {
@@ -52,16 +76,13 @@ function VariantSamples(props) {
             width: widths[index],
         });
     });
-    return !preFilteredRows.length ? null : ((0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Samples", children: [error ? (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` }) : null, (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: checked, onChange: event => {
-                        setChecked(event.target.checked);
-                    } }), label: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body2", children: "Show options" }) }), checked ? ((0, jsx_runtime_1.jsx)(VariantSampleFilters_1.default, { setFilter: setFilter, columns: columns, filter: filter })) : null, (0, jsx_runtime_1.jsx)("div", { style: {
-                    display: 'flex',
-                    flexDirection: 'column',
-                }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null }, slotProps: {
-                        toolbar: {
-                            printOptions: {
-                                disableToolbarButton: true,
-                            },
-                        },
-                    } }) })] }));
+    const s1 = new Set(['sample', 'GT', 'genotype']);
+    const s2 = new Set(keys);
+    return !preFilteredRows.length ? null : ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(BaseCard_1.default, { ...props, title: "Genotype frequencies", children: (0, jsx_runtime_1.jsx)(ErrorBoundary_1.ErrorBoundary, { FallbackComponent: ui_1.ErrorMessage, children: (0, jsx_runtime_1.jsx)(VariantGenotypeFrequencyTable_1.default, { rows: rows }) }) }), (0, jsx_runtime_1.jsxs)(BaseCard_1.default, { ...props, title: "Samples", children: [error ? (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` }) : null, (0, jsx_runtime_1.jsx)(Checkbox2_1.default, { label: "Show filters", checked: showFilters, onChange: event => {
+                            setShowFilters(event.target.checked);
+                        } }), (0, util_2.areSetsEqual)(s1, s2) ? null : ((0, jsx_runtime_1.jsx)(Checkbox2_1.default, { label: "Show only genotype columns", checked: showOnlyGenotypeColumns, onChange: event => {
+                            setShowOnlyGenotypeColumns(event.target.checked);
+                        } })), showFilters ? ((0, jsx_runtime_1.jsx)(VariantSampleFilters_1.default, { setFilter: setFilter, columns: columns, filter: filter })) : null, (0, jsx_runtime_1.jsx)(DataGridFlexContainer_1.default, { children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: showOnlyGenotypeColumns
+                                ? columns.filter(f => s1.has(f.field))
+                                : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
 }

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

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

package/dist/VariantFeatureWidget/VariantSampleGrid/util.js

@@ -0,0 +1,14 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.areSetsEqual = areSetsEqual;
+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/dist/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/dist/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/dist/VariantRPC/MultiVariantClusterGenotypeMatrix.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultiVariantClusterGenotypeMatrix = void 0;
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
-const cluster_1 = require("./cluster");
+const cluster_1 = require("@jbrowse/core/util/cluster");
 const getGenotypeMatrix_1 = require("./getGenotypeMatrix");
 class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     constructor() {
@@ -20,14 +20,11 @@ class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenam
         });
         return (0, cluster_1.clusterData)({
             data: Object.values(matrix),
-            onProgress: a => {
-                deserializedArgs.statusCallback(`${toP(a * 100)}%`);
-            },
             stopToken: deserializedArgs.stopToken,
+            onProgress: progress => {
+                deserializedArgs.statusCallback(progress);
+            },
         });
     }
 }
 exports.MultiVariantClusterGenotypeMatrix = MultiVariantClusterGenotypeMatrix;
-function toP(n) {
-    return Number.parseFloat(n.toPrecision(3));
-}

package/dist/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/dist/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/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultiVariantGetSimplifiedFeatures = void 0;
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+const util_1 = require("@jbrowse/core/util");
 const rxjs_1 = require("rxjs");
 const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
 class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
@@ -14,17 +15,21 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
         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 (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig);
-        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe((0, rxjs_1.toArray)()));
-        const features = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+        const features = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
+            minorAlleleFrequencyFilter,
+            lengthCutoffFilter,
+            stopToken,
+            features: await (0, rxjs_1.firstValueFrom)(dataAdapter
+                .getFeaturesInMultipleRegions(regions, deserializedArgs)
+                .pipe((0, rxjs_1.toArray)())),
+        });
         const sampleInfo = {};
         let hasPhased = false;
-        for (const { feature } of features) {
+        (0, util_1.forEachWithStopTokenCheck)(features, stopToken, ({ feature }) => {
+            var _a, _b;
             const samp = feature.get('genotypes');
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
@@ -34,7 +39,7 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
                     isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
                 };
             }
-        }
+        });
         return {
             hasPhased,
             sampleInfo,
@@ -44,6 +49,7 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
                     start: feature.get('start'),
                     end: feature.get('end'),
                     refName: feature.get('refName'),
+                    name: feature.get('name'),
                 },
             })),
         };

package/dist/VariantRPC/getGenotypeMatrix.js

@@ -2,29 +2,42 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getGenotypeMatrix = getGenotypeMatrix;
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const util_1 = require("@jbrowse/core/util");
 const rxjs_1 = require("rxjs");
 const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
 async function getGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, } = args;
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
     const adapter = await (0, dataAdapterCache_1.getAdapter)(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
-    const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe((0, rxjs_1.toArray)()));
     const genotypeFactor = new Set();
-    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+        stopToken,
+        features: await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe((0, rxjs_1.toArray)())),
+    });
     for (const { alleleCounts } of mafs) {
-        for (const alt of alleleCounts.keys()) {
+        for (const alt of Object.keys(alleleCounts)) {
             genotypeFactor.add(alt);
         }
     }
     const rows = {};
-    for (const { feature } of mafs) {
+    const cacheSplit = {};
+    (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ feature }) => {
         const genotypes = feature.get('genotypes');
         for (const { name } of sources) {
             if (!rows[name]) {
                 rows[name] = [];
             }
             const val = genotypes[name];
-            const alleles = val.split(/[/|]/);
+            let alleles;
+            if (cacheSplit[val]) {
+                alleles = cacheSplit[val];
+            }
+            else {
+                alleles = val.split(/[/|]/);
+                cacheSplit[val] = alleles;
+            }
             let genotypeStatus = 0;
             let nonRefCount = 0;
             let uncalledCount = 0;
@@ -50,6 +63,6 @@ async function getGenotypeMatrix({ pluginManager, args, }) {
             }
             rows[name].push(genotypeStatus);
         }
-    }
+    });
     return rows;
 }