@jbrowse/plugin-variants 2.16.1 → 2.18.0

package/dist/StructuralVariantChordRenderer/ReactComponent.js

@@ -28,7 +28,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
-// locals
 const Chord_1 = __importDefault(require("./Chord"));
 const StructuralVariantChordsReactComponent = (0, mobx_react_1.observer)(function ({ features, config, blockDefinitions, radius, bezierRadius, displayModel, onChordClick, }) {
     const { selectedFeatureId } = displayModel || {};

package/dist/StructuralVariantChordRenderer/configSchema.d.ts

@@ -1,25 +1,16 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     strokeColor: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     strokeColorSelected: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     strokeColorHover: {
         type: string;
         description: string;

package/dist/StructuralVariantChordRenderer/configSchema.js

@@ -1,32 +1,20 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config StructuralVariantChordRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('StructuralVariantChordRenderer', {
-    /**
-     * #slot
-     */
     strokeColor: {
         type: 'color',
         description: 'the line color of each arc',
         defaultValue: 'rgba(255,133,0,0.32)',
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     strokeColorSelected: {
         type: 'color',
         description: 'the line color of an arc that has been selected',
         defaultValue: 'black',
         contextVariable: ['feature'],
     },
-    /**
-     * #slot
-     */
     strokeColorHover: {
         type: 'color',
         description: 'the line color of an arc that is being hovered over with the mouse',

package/dist/StructuralVariantChordRenderer/index.d.ts

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

package/dist/StructuralVariantChordRenderer/index.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = StructuralVariantChordRendererF;
 const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
 const ReactComponent_1 = __importDefault(require("./ReactComponent"));
+const configSchema_1 = __importDefault(require("./configSchema"));
 function StructuralVariantChordRendererF(pluginManager) {
     pluginManager.addRendererType(() => new CircularChordRendererType_1.default({
         name: 'StructuralVariantChordRenderer',

package/dist/Tooltip.d.ts

@@ -0,0 +1,19 @@
+import React from 'react';
+import type { Feature } from '@jbrowse/core/util';
+type Coord = [number, number];
+export type TooltipContentsComponent = React.ForwardRefExoticComponent<{
+    feature: Feature;
+    model: any;
+} & React.RefAttributes<HTMLDivElement>>;
+declare const Tooltip: ({ model, height, clientMouseCoord, offsetMouseCoord, clientRect, TooltipContents, useClientY, }: {
+    model: {
+        featureUnderMouse?: Feature;
+    };
+    useClientY?: boolean;
+    height: number;
+    clientMouseCoord: Coord;
+    offsetMouseCoord: Coord;
+    clientRect?: DOMRect;
+    TooltipContents: TooltipContentsComponent;
+}) => React.JSX.Element | null;
+export default Tooltip;

package/dist/Tooltip.js

@@ -0,0 +1,58 @@
+"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 });
+const react_1 = __importStar(require("react"));
+const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()({
+    hoverVertical: {
+        background: '#333',
+        border: 'none',
+        width: 1,
+        height: '100%',
+        cursor: 'default',
+        position: 'absolute',
+        pointerEvents: 'none',
+    },
+});
+const Tooltip = (0, mobx_react_1.observer)(function Tooltip({ model, height, clientMouseCoord, offsetMouseCoord, clientRect, TooltipContents, useClientY, }) {
+    const { featureUnderMouse } = model;
+    const { classes } = useStyles();
+    const x = clientMouseCoord[0] + 5;
+    const y = useClientY ? clientMouseCoord[1] : (clientRect === null || clientRect === void 0 ? void 0 : clientRect.top) || 0;
+    return featureUnderMouse ? (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(react_1.Suspense, { fallback: null },
+            react_1.default.createElement(BaseTooltip_1.default, { clientPoint: { x, y } },
+                react_1.default.createElement(TooltipContents, { model: model, feature: featureUnderMouse }))),
+        react_1.default.createElement("div", { className: classes.hoverVertical, style: {
+                left: offsetMouseCoord[0],
+                height: height,
+            } }))) : null;
+});
+exports.default = Tooltip;

package/dist/VariantFeatureWidget/AnnotGrid.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { GridColDef, GridValidRowModel } from '@mui/x-data-grid';
+import type { GridColDef, GridValidRowModel } from '@mui/x-data-grid';
 export default function VariantAnnotPanel({ rows, columns, }: {
     rows: GridValidRowModel[];
     columns: GridColDef[];

package/dist/VariantFeatureWidget/AnnotGrid.js

@@ -25,9 +25,9 @@ var __importStar = (this && this.__importStar) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = VariantAnnotPanel;
 const react_1 = __importStar(require("react"));
-const x_data_grid_1 = require("@mui/x-data-grid");
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const x_data_grid_1 = require("@mui/x-data-grid");
 function VariantAnnotPanel({ 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])));

package/dist/VariantFeatureWidget/BreakendMultiLevelOptionDialog.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
-// re-exported for react lazy
 var sv_core_1 = require("@jbrowse/sv-core");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendMultiLevelOptionDialog; } });

package/dist/VariantFeatureWidget/BreakendSingleLevelOptionDialog.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
-// re-exported for react lazy
 var sv_core_1 = require("@jbrowse/sv-core");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendSingleLevelOptionDialog; } });

package/dist/VariantFeatureWidget/LaunchBreakendPanel.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { VariantFeatureWidgetModel } from './stateModelFactory';
+import type { VariantFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function BreakendPanel(props: {
     locStrings: string[];
     model: VariantFeatureWidgetModel;

package/dist/VariantFeatureWidget/LaunchBreakendPanel.js

@@ -28,19 +28,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = BreakendPanel;
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const util_1 = require("@jbrowse/core/util");
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-// lazies
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
 const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
 function LocStringList({ locStrings, model, }) {
     const session = (0, util_1.getSession)(model);
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.Typography, null, "Navigate to breakend endpoint in linear view:"),
-        react_1.default.createElement("ul", null, locStrings.map((locString, index) => (
-        /* biome-ignore lint/suspicious/noArrayIndexKey: */
-        react_1.default.createElement("li", { key: `${locString}-${index}` },
+        react_1.default.createElement("ul", null, locStrings.map((locString, index) => (react_1.default.createElement("li", { key: `${locString}-${index}` },
             locString,
             ' ',
             react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
@@ -61,9 +58,11 @@ function LocStringList({ locStrings, model, }) {
                     }
                 } }, "(LGV)")))))));
 }
-function LaunchBreakpointSplitViewPanel({ locStrings, model, feature, viewType, }) {
+function LaunchBreakpointSplitViewPanel({ locStrings, model, feature, }) {
+    var _a, _b;
     const session = (0, util_1.getSession)(model);
     const simpleFeature = new util_1.SimpleFeature(feature);
+    const assemblyName = (_b = (_a = model.view) === null || _a === void 0 ? void 0 : _a.displayedRegions[0]) === null || _b === void 0 ? void 0 : _b.assemblyName;
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.Typography, null, "Launch split view"),
         react_1.default.createElement("ul", null, locStrings.map(locString => (react_1.default.createElement("li", { key: JSON.stringify(locString) },
@@ -75,12 +74,11 @@ function LaunchBreakpointSplitViewPanel({ locStrings, model, feature, viewType,
                         BreakendMultiLevelOptionDialog,
                         {
                             handleClose,
-                            model,
+                            session,
                             feature: simpleFeature,
-                            // @ts-expect-error
-                            viewType,
+                            stableViewId: `${model.id}_${assemblyName}_breakpointsplitview_multilevel`,
                             view: model.view,
-                            assemblyName: model.view.displayedRegions[0].assemblyName,
+                            assemblyName,
                         },
                     ]);
                 } }, "(top/bottom)"),
@@ -91,12 +89,11 @@ function LaunchBreakpointSplitViewPanel({ locStrings, model, feature, viewType,
                         BreakendSingleLevelOptionDialog,
                         {
                             handleClose,
-                            model,
+                            session,
                             feature: simpleFeature,
-                            // @ts-expect-error
-                            viewType,
+                            stableViewId: `${model.id}_${assemblyName}_breakpointsplitview_singlelevel`,
                             view: model.view,
-                            assemblyName: model.view.displayedRegions[0].assemblyName,
+                            assemblyName,
                         },
                     ]);
                 } }, "(single row)")))))));
@@ -105,14 +102,13 @@ function BreakendPanel(props) {
     const { model, locStrings, feature } = props;
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.getEnv)(session);
-    let viewType;
+    let hasBreakpointSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakpointSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
     return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Breakends" },
         react_1.default.createElement(LocStringList, { model: model, locStrings: locStrings }),
-        viewType ? (react_1.default.createElement(LaunchBreakpointSplitViewPanel, { viewType: viewType, model: model, locStrings: locStrings, feature: feature })) : null));
+        hasBreakpointSplitView ? (react_1.default.createElement(LaunchBreakpointSplitViewPanel, { model: model, locStrings: locStrings, feature: feature })) : null));
 }

package/dist/VariantFeatureWidget/VariantAnnotationTable.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = VariantAnnotationTable;
 const react_1 = __importDefault(require("react"));
-const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
 function VariantAnnotationTable({ data, fields, title, }) {
     return data.length ? (react_1.default.createElement(BaseCard_1.default, { title: title },
         react_1.default.createElement(AnnotGrid_1.default, { rows: data.map((elt, id) => ({

package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts

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

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -27,15 +27,13 @@ var __importDefault = (this && this.__importDefault) || function (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 vcf_1 = require("@gmod/vcf");
-// locals
-const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
+const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const VariantAnnotationTable_1 = __importDefault(require("./VariantAnnotationTable"));
+const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
 const variantFieldDescriptions_1 = require("./variantFieldDescriptions");
-// lazies
 const LaunchBreakendPanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LaunchBreakendPanel'))));
 function AnnPanel({ descriptions, feature, }) {
     var _a, _b, _c, _d, _e;

package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function VariantSamples(props: {
     feature: SimpleFeatureSerialized;
     descriptions?: {

package/dist/VariantFeatureWidget/VariantSampleGrid.js

@@ -28,10 +28,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = VariantSamples;
 const react_1 = __importStar(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"),
@@ -48,9 +48,6 @@ 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 +80,18 @@ 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,
+        react_1.default.createElement("div", { style: { display: 'flex', flexDirection: 'column' } },
+            react_1.default.createElement(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

@@ -29,8 +29,8 @@ 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">;
@@ -93,8 +93,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

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/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 +1,67 @@
+"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");
+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, mafFilter, 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 = [];
+        for (const feat of feats) {
+            let c = 0;
+            let c2 = 0;
+            const samp = feat.get('genotypes');
+            if (feat.get('end') - feat.get('start') <= 10) {
+                for (const { name } of sources) {
+                    const s = samp[name];
+                    genotypeFactor.add(s);
+                    if (s === '0|0' || s === './.') {
+                        c2++;
+                    }
+                    else if (s === '1|0' || s === '0|1') {
+                        c++;
+                    }
+                    else if (s === '1|1') {
+                        c++;
+                        c2++;
+                    }
+                    else {
+                        c++;
+                    }
+                }
+                if (c / sources.length > mafFilter &&
+                    c2 / sources.length < 1 - mafFilter) {
+                    mafs.push(feat);
+                }
+            }
+        }
+        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 +1,21 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+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<{
+        id: string;
+        data: {
+            start: number;
+            end: number;
+            refName: string;
+        };
+    }[]>;
+}

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -0,0 +1,63 @@
+"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");
+class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetSimplifiedFeatures';
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { mafFilter, sources, 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 genotypeFactor = new Set();
+        const mafs = [];
+        for (const feat of feats) {
+            let c = 0;
+            let c2 = 0;
+            const samp = feat.get('genotypes');
+            if (feat.get('end') - feat.get('start') <= 10) {
+                for (const { name } of sources) {
+                    const s = samp[name];
+                    genotypeFactor.add(s);
+                    if (s === '0|0' || s === './.') {
+                        c2++;
+                    }
+                    else if (s === '1|0' || s === '0|1') {
+                        c++;
+                    }
+                    else if (s === '1|1') {
+                        c++;
+                        c2++;
+                    }
+                    else {
+                        c++;
+                    }
+                }
+                if (c / sources.length > mafFilter &&
+                    c2 / sources.length < 1 - mafFilter) {
+                    mafs.push(feat);
+                }
+            }
+        }
+        return mafs.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>;
+}