@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/dist/VariantFeatureWidget/VariantConsequenceDataGrid.js

@@ -0,0 +1,15 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantConsequenceDataGrid;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const VariantConsequenceDataGridWrapper_1 = __importDefault(require("./VariantConsequenceDataGridWrapper"));
+function VariantConsequenceDataGrid({ data, fields, title, }) {
+    return data.length ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: title, children: (0, jsx_runtime_1.jsx)(VariantConsequenceDataGridWrapper_1.default, { rows: data.map((elt, id) => ({
+                id,
+                ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
+            })), columns: fields.map(c => ({ field: c })) }) })) : null;
+}

package/dist/VariantFeatureWidget/VariantConsequenceDataGridWrapper.d.ts

@@ -0,0 +1,5 @@
+import type { GridColDef, GridValidRowModel } from '@mui/x-data-grid';
+export default function VariantConsequenceDataGridWrapper({ rows, columns, }: {
+    rows: GridValidRowModel[];
+    columns: GridColDef[];
+}): import("react/jsx-runtime").JSX.Element | null;

package/dist/VariantFeatureWidget/VariantConsequenceDataGridWrapper.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantConsequenceDataGridWrapper;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+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 => {
+                        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) => ({
+                    ...c,
+                    width: widths[i],
+                })), slots: {
+                    toolbar: checked ? x_data_grid_1.GridToolbar : null,
+                } })] })) : null;
+}

package/dist/VariantFeatureWidget/VariantConsequencePanel.d.ts

@@ -0,0 +1,5 @@
+export default function VariantConsequencePanel({ data, fields, title, }: {
+    data: string[];
+    fields: string[];
+    title: string;
+}): import("react/jsx-runtime").JSX.Element | null;

package/dist/VariantFeatureWidget/VariantConsequencePanel.js

@@ -0,0 +1,15 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantConsequencePanel;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const VariantConsequenceDataGridWrapper_1 = __importDefault(require("./VariantConsequenceDataGridWrapper"));
+function VariantConsequencePanel({ data, fields, title, }) {
+    return data.length ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: title, children: (0, jsx_runtime_1.jsx)(VariantConsequenceDataGridWrapper_1.default, { rows: data.map((elt, id) => ({
+                id,
+                ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
+            })), columns: fields.map(c => ({ field: c })) }) })) : null;
+}

package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { VariantFeatureWidgetModel } from './stateModelFactory';
+import type { VariantFeatureWidgetModel } from './stateModelFactory';
 declare const VariantFeatureWidget: (props: {
     model: VariantFeatureWidgetModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default VariantFeatureWidget;

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -15,70 +15,79 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
-const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const vcf_1 = require("@gmod/vcf");
-// locals
+const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
-const VariantAnnotationTable_1 = __importDefault(require("./VariantAnnotationTable"));
 const variantFieldDescriptions_1 = require("./variantFieldDescriptions");
-// lazies
 const LaunchBreakendPanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LaunchBreakendPanel'))));
+const VariantConsequenceDataGrid = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./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;
     const annFields = ((_d = (_c = annDesc === null || annDesc === void 0 ? void 0 : annDesc.match(/.*Functional annotations:'(.*)'$/)) === null || _c === void 0 ? void 0 : _c[1]) === null || _d === void 0 ? void 0 : _d.split('|')) || [];
     const ann = ((_e = feature.INFO) === null || _e === void 0 ? void 0 : _e.ANN) || [];
-    return (react_1.default.createElement(VariantAnnotationTable_1.default, { fields: annFields, data: ann, title: "Variant ANN field" }));
+    return ((0, jsx_runtime_1.jsx)(VariantConsequenceDataGrid, { fields: annFields, data: ann, title: "Variant ANN field" }));
 }
 function CsqPanel({ descriptions, feature, }) {
     var _a, _b, _c, _d, _e;
     const csqDescription = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description;
     const csqFields = ((_d = (_c = csqDescription === null || csqDescription === void 0 ? void 0 : csqDescription.match(/.*Format: (.*)/)) === null || _c === void 0 ? void 0 : _c[1]) === null || _d === void 0 ? void 0 : _d.split('|')) || [];
     const csq = ((_e = feature.INFO) === null || _e === void 0 ? void 0 : _e.CSQ) || [];
-    return (react_1.default.createElement(VariantAnnotationTable_1.default, { fields: csqFields, data: csq, title: "Variant CSQ field" }));
+    return ((0, jsx_runtime_1.jsx)(VariantConsequenceDataGrid, { fields: csqFields, data: csq, title: "Variant CSQ field" }));
+}
+function LaunchBreakendWidgetArea({ model, }) {
+    const { featureData } = model;
+    const feat = JSON.parse(JSON.stringify(featureData));
+    const { type = '' } = feat;
+    return type === 'breakend' ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : type === 'translocation' ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : type === 'paired_feature' ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.mate.refName}:${feat.mate.start}`] })) : type.includes('inversion') ||
+        type.includes('deletion') ||
+        type.includes('duplication') ||
+        type.includes('cnv') ||
+        type.includes('sv') ? ((0, jsx_runtime_1.jsx)(LaunchBreakendPanel, { feature: {
+            uniqueId: 'random',
+            refName: feat.refName,
+            start: feat.start,
+            end: feat.start + 1,
+            mate: {
+                refName: feat.refName,
+                start: feat.end,
+                end: feat.end + 1,
+            },
+        }, model: model, locStrings: [`${feat.refName}:${feat.end}`] })) : null;
 }
 const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { featureData, descriptions } = model;
     const feat = JSON.parse(JSON.stringify(featureData));
-    const { samples, ALT, type = '', ...rest } = feat;
-    return (react_1.default.createElement(material_1.Paper, { "data-testid": "variant-side-drawer" },
-        react_1.default.createElement(FeatureDetails_1.default, { feature: rest, descriptions: { ...variantFieldDescriptions_1.variantFieldDescriptions, ...descriptions }, ...props }),
-        react_1.default.createElement(CsqPanel, { feature: rest, descriptions: descriptions }),
-        react_1.default.createElement(AnnPanel, { feature: rest, descriptions: descriptions }),
-        react_1.default.createElement(react_1.Suspense, { fallback: null },
-            type === 'breakend' ? (react_1.default.createElement(LaunchBreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
-            type === 'translocation' ? (react_1.default.createElement(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
-            type === 'paired_feature' ? (react_1.default.createElement(LaunchBreakendPanel, { feature: feat, model: model, locStrings: [`${feat.mate.refName}:${feat.mate.start}`] })) : null,
-            type.includes('inversion') ||
-                type.includes('deletion') ||
-                type.includes('duplication') ||
-                type.includes('cnv') ||
-                type.includes('sv') ? (react_1.default.createElement(LaunchBreakendPanel, { feature: {
-                    uniqueId: 'random',
-                    refName: feat.refName,
-                    start: feat.start,
-                    end: feat.start + 1,
-                    mate: {
-                        refName: feat.refName,
-                        start: feat.end,
-                        end: feat.end + 1,
-                    },
-                }, model: model, locStrings: [`${feat.refName}:${feat.end}`] })) : null),
-        react_1.default.createElement(VariantSampleGrid_1.default, { feature: feat, ...props, descriptions: descriptions })));
+    const { samples, ALT, ...rest } = feat;
+    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,
+                }, ...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 })] }));
 });
 exports.default = VariantFeatureWidget;

package/dist/VariantFeatureWidget/VariantSampleFilters.d.ts

@@ -0,0 +1,9 @@
+type Filters = Record<string, string>;
+export default function SampleFilters({ columns, filter, setFilter, }: {
+    columns: {
+        field: string;
+    }[];
+    filter: Filters;
+    setFilter: (arg: Filters) => void;
+}): import("react/jsx-runtime").JSX.Element;
+export {};

package/dist/VariantFeatureWidget/VariantSampleFilters.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SampleFilters;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const material_1 = require("@mui/material");
+function SampleFilters({ columns, filter, setFilter, }) {
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "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" }), columns.map(({ field }) => ((0, jsx_runtime_1.jsx)(material_1.TextField, { placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => {
+                    setFilter({ ...filter, [field]: event.target.value });
+                } }, `filter-${field}`)))] }));
+}

package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -1,10 +1,12 @@
-import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+interface FormatRecord {
+    Description?: string;
+}
+interface Descriptions {
+    FORMAT?: Record<string, FormatRecord>;
+}
 export default function VariantSamples(props: {
     feature: SimpleFeatureSerialized;
-    descriptions?: {
-        FORMAT?: Record<string, {
-            Description?: string;
-        }>;
-    } | null;
-}): React.JSX.Element | null;
+    descriptions?: Descriptions | null;
+}): import("react/jsx-runtime").JSX.Element | null;
+export {};

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -1,44 +1,16 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = VariantSamples;
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
-const util_1 = require("@jbrowse/core/util");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-function SampleFilters({ columns, filter, setFilter, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Typography, null, "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"),
-        columns.map(({ field }) => (react_1.default.createElement(material_1.TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => {
-                setFilter({ ...filter, [field]: event.target.value });
-            } })))));
-}
+const VariantSampleFilters_1 = __importDefault(require("./VariantSampleFilters"));
 function VariantSamples(props) {
     var _a;
     const { feature, descriptions = {} } = props;
@@ -48,9 +20,6 @@ function VariantSamples(props) {
     let error;
     let rows = [];
     const filters = Object.keys(filter);
-    // catch some error thrown from regex
-    // note: maps all values into a string, if this is not done rows are not
-    // sortable by the data-grid
     try {
         rows = preFilteredRows
             .map(row => {
@@ -83,19 +52,16 @@ function VariantSamples(props) {
             width: widths[index],
         });
     });
-    // disableRowSelectionOnClick helps avoid
-    // https://github.com/mui-org/material-ui-x/issues/1197
-    return !preFilteredRows.length ? null : (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Samples" },
-        error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
-        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => {
-                    setChecked(event.target.checked);
-                } }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
-        checked ? (react_1.default.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null,
-        react_1.default.createElement(x_data_grid_1.DataGrid, { autoHeight: true, 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,
-                    },
-                },
-            } })));
+    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,
+                            },
+                        },
+                    } }) })] }));
 }

package/dist/VariantFeatureWidget/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function VariantFeatureWidgetF(pluginManager: PluginManager): void;

package/dist/VariantFeatureWidget/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -29,8 +39,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = VariantFeatureWidgetF;
 const react_1 = require("react");
 const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-const stateModelFactory_1 = require("./stateModelFactory");
 const configSchema_1 = require("./configSchema");
+const stateModelFactory_1 = require("./stateModelFactory");
 function VariantFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType_1.default({
         name: 'VariantFeatureWidget',

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { Instance } from 'mobx-state-tree';
+import type PluginManager from '@jbrowse/core/PluginManager';
+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">;

package/dist/VariantFeatureWidget/stateModelFactory.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = stateModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function stateModelFactory(pluginManager) {
     const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
     return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('VariantFeatureWidget', {

package/dist/VariantFeatureWidget/types.d.ts

@@ -0,0 +1,16 @@
+export interface Descriptions {
+    INFO?: {
+        ANN?: {
+            Description?: string;
+        };
+        CSQ?: {
+            Description?: string;
+        };
+    };
+}
+export interface ReducedFeature {
+    INFO?: {
+        ANN?: string[];
+        CSQ?: string[];
+    };
+}

package/dist/VariantFeatureWidget/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -0,0 +1,17 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<Record<string, {
+        name: string;
+        genotypes: number[];
+    }>>;
+}

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -0,0 +1,50 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MultiVariantGetGenotypeMatrix = void 0;
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+const rxjs_1 = require("rxjs");
+const util_1 = require("../util");
+class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetGenotypeMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, } = deserializedArgs;
+        const adapter = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
+        const dataAdapter = adapter.dataAdapter;
+        const region = regions[0];
+        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeatures(region, deserializedArgs).pipe((0, rxjs_1.toArray)()));
+        const genotypeFactor = new Set();
+        const mafs = (0, util_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+        for (const feat of feats) {
+            const samp = feat.get('genotypes');
+            for (const { name } of sources) {
+                const s = samp[name];
+                genotypeFactor.add(s);
+            }
+        }
+        const genotypeFactorMap = Object.fromEntries([...genotypeFactor].map((type, idx) => [type, idx]));
+        const rows = {};
+        for (const feat of mafs) {
+            const samp = feat.get('genotypes');
+            for (const { name } of sources) {
+                if (!rows[name]) {
+                    rows[name] = {
+                        name,
+                        genotypes: [],
+                    };
+                }
+                rows[name].genotypes.push(genotypeFactorMap[samp[name]]);
+            }
+        }
+        return rows;
+    }
+}
+exports.MultiVariantGetGenotypeMatrix = MultiVariantGetGenotypeMatrix;

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -0,0 +1,26 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { SampleInfo } from '../types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<{
+        hasPhased: boolean;
+        sampleInfo: Record<string, SampleInfo>;
+        features: {
+            id: string;
+            data: {
+                start: number;
+                end: number;
+                refName: string;
+            };
+        }[];
+    }>;
+}

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -0,0 +1,53 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+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 rxjs_1 = require("rxjs");
+const util_1 = require("../util");
+class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetSimplifiedFeatures';
+    }
+    async execute(args, rpcDriverClassName) {
+        var _a, _b;
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
+        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe((0, rxjs_1.toArray)()));
+        const features = (0, util_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+        const sampleInfo = {};
+        let hasPhased = false;
+        for (const f of features) {
+            const samp = f.get('genotypes');
+            for (const [key, val] of Object.entries(samp)) {
+                const isPhased = val.includes('|');
+                hasPhased || (hasPhased = isPhased);
+                sampleInfo[key] = {
+                    maxPloidy: Math.max(((_a = sampleInfo[key]) === null || _a === void 0 ? void 0 : _a.maxPloidy) || 0, val.split('|').length),
+                    isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
+                };
+            }
+        }
+        return {
+            hasPhased,
+            sampleInfo,
+            features: features.map(f => ({
+                id: f.id(),
+                data: {
+                    start: f.get('start'),
+                    end: f.get('end'),
+                    refName: f.get('refName'),
+                },
+            })),
+        };
+    }
+}
+exports.MultiVariantGetSimplifiedFeatures = MultiVariantGetSimplifiedFeatures;

package/dist/VariantRPC/MultiVariantGetSources.d.ts

@@ -0,0 +1,14 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MultiVariantGetSources extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<any>;
+}

package/dist/VariantRPC/MultiVariantGetSources.js

@@ -0,0 +1,22 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MultiVariantGetSources = void 0;
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+class MultiVariantGetSources extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetSources';
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
+        return dataAdapter.getSources(regions, deserializedArgs);
+    }
+}
+exports.MultiVariantGetSources = MultiVariantGetSources;

package/dist/VariantTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function VariantTrackF(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;
@@ -77,4 +77,3 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
-export default configSchema;