@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js

@@ -1,80 +0,0 @@
-"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/VariantSampleFilters.d.ts

@@ -1,9 +0,0 @@
-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/VariantSampleGrid/VariantSampleFilters.js

@@ -1,10 +0,0 @@
-"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/VariantSampleGrid.d.ts

@@ -1,6 +0,0 @@
-import type { VariantFieldDescriptions } from './types';
-import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-export default function VariantSampleGrid(props: {
-    feature: SimpleFeatureSerialized;
-    descriptions?: VariantFieldDescriptions | null;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js

@@ -1,54 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-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"));
-const getSampleGridRows_1 = require("./getSampleGridRows");
-function VariantSampleGrid(props) {
-    const { feature, descriptions = {} } = props;
-    const [filter, setFilter] = (0, react_1.useState)({});
-    const [columnDisplayMode, setColumnDisplayMode] = (0, react_1.useState)('all');
-    const [showFilters, setShowFilters] = (0, react_1.useState)(false);
-    const samples = (feature.samples || {});
-    const ALT = feature.ALT;
-    const REF = feature.REF;
-    const { rows, error } = (0, getSampleGridRows_1.getSampleGridRows)(samples, REF, ALT, filter);
-    const colKeySet = new Set(['sample', ...Object.keys(rows[0] || {})]);
-    colKeySet.delete('id');
-    const keys = [...colKeySet];
-    const widths = keys.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e])));
-    const columns = keys.map((field, index) => {
-        var _a, _b;
-        return ({
-            field,
-            description: (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.FORMAT) === null || _a === void 0 ? void 0 : _a[field]) === null || _b === void 0 ? void 0 : _b.Description,
-            width: widths[index],
-        });
-    });
-    const s1 = new Set(['sample', 'GT']);
-    const s2 = new Set(['sample', 'GT', 'genotype']);
-    return !rows.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.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(Checkbox2_1.default, { label: "Show filters", checked: showFilters, onChange: event => {
-                                    setShowFilters(event.target.checked);
-                                } }), (0, jsx_runtime_1.jsxs)(material_1.ToggleButtonGroup, { value: columnDisplayMode, exclusive: true, size: "small", onChange: (_, newValue) => {
-                                    if (newValue !== null) {
-                                        setColumnDisplayMode(newValue);
-                                    }
-                                }, children: [(0, jsx_runtime_1.jsx)(material_1.ToggleButton, { value: "all", children: "All" }), (0, jsx_runtime_1.jsx)(material_1.ToggleButton, { value: "gtOnly", children: "GT only" }), (0, jsx_runtime_1.jsx)(material_1.ToggleButton, { value: "genotypeOnly", children: "GT+resolved genotype" })] })] }), 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: columnDisplayMode === 'gtOnly'
-                                ? columns.filter(f => s1.has(f.field))
-                                : columnDisplayMode === 'genotypeOnly'
-                                    ? columns.filter(f => s2.has(f.field))
-                                    : columns, rowHeight: 25, columnHeaderHeight: 35, showToolbar: true }) })] })] }));
-}

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

@@ -1,5 +0,0 @@
-import type { Filters, InfoFields, VariantSampleGridRow } from './types';
-export declare function getSampleGridRows(samples: Record<string, InfoFields>, REF: string, ALT: string[], filter: Filters): {
-    rows: VariantSampleGridRow[];
-    error: unknown;
-};

package/dist/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js

@@ -1,51 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSampleGridRows = getSampleGridRows;
-const util_1 = require("../../VcfFeature/util");
-function getSampleGridRows(samples, REF, ALT, filter) {
-    const preFilteredRows = Object.entries(samples).map(([key, val]) => {
-        var _a;
-        const gt = (_a = val.GT) === null || _a === void 0 ? void 0 : _a[0];
-        return [
-            key,
-            {
-                ...val,
-                ...(gt
-                    ? {
-                        GT: `${gt}`,
-                        genotype: (0, util_1.makeSimpleAltString)(`${gt}`, REF, ALT),
-                    }
-                    : {}),
-            },
-        ];
-    });
-    let error;
-    let rows = [];
-    const filters = Object.keys(filter);
-    try {
-        rows = preFilteredRows
-            .map(([key, val]) => {
-            return {
-                ...Object.fromEntries(Object.entries(val).map(([formatField, formatValue]) => [
-                    formatField,
-                    formatValue,
-                ])),
-                sample: key,
-                id: key,
-            };
-        })
-            .filter(row => filters.length
-            ? filters.every(key => {
-                const currFilter = filter[key];
-                return currFilter
-                    ? new RegExp(currFilter, 'i').exec(row[key])
-                    : true;
-            })
-            : true);
-    }
-    catch (e) {
-        console.error(e);
-        error = e;
-    }
-    return { rows, error };
-}

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

@@ -1 +0,0 @@
-export { default } from './VariantSampleGrid';

package/dist/VariantFeatureWidget/VariantSampleGrid/index.js

@@ -1,8 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var VariantSampleGrid_1 = require("./VariantSampleGrid");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(VariantSampleGrid_1).default; } });

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

@@ -1,21 +0,0 @@
-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/types.js

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

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

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

package/dist/VariantFeatureWidget/VariantSampleGrid/util.js

@@ -1,14 +0,0 @@
-"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/configSchema.d.ts

@@ -1 +0,0 @@
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/VariantFeatureWidget/configSchema.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('VariantFeatureWidget', {});

package/dist/VariantFeatureWidget/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function VariantFeatureWidgetF(pluginManager: PluginManager): void;

package/dist/VariantFeatureWidget/index.js

@@ -1,52 +0,0 @@
-"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 () {
-    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 });
-exports.default = VariantFeatureWidgetF;
-const react_1 = require("react");
-const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-const configSchema_1 = require("./configSchema");
-const stateModelFactory_1 = require("./stateModelFactory");
-function VariantFeatureWidgetF(pluginManager) {
-    pluginManager.addWidgetType(() => new WidgetType_1.default({
-        name: 'VariantFeatureWidget',
-        heading: 'Feature details',
-        configSchema: configSchema_1.configSchema,
-        stateModel: (0, stateModelFactory_1.stateModelFactory)(pluginManager),
-        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantFeatureWidget')))),
-    }));
-}

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -1,104 +0,0 @@
-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">;
-    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<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>>;
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
-        showCoordinatesSetting: string;
-        intronBp: number;
-        upDownBp: number;
-        upperCaseCDS: boolean;
-        charactersPerRow: number;
-        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
-    } & {
-        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-        setUpDownBp(f: number): void;
-        setIntronBp(f: number): void;
-        setUpperCaseCDS(f: boolean): void;
-        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
-    } & {
-        readonly showCoordinates: boolean;
-        readonly showGenomicCoordsOption: boolean;
-        readonly hasCDS: boolean | undefined;
-        readonly hasExon: boolean | undefined;
-        readonly hasExonOrCDS: boolean | undefined;
-    } & {
-        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: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-    clearFeatureData(): void;
-    setFormattedData(feat: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
-    setError(e: unknown): void;
-} & {
-    afterCreate(): void;
-}, {
-    type: "BaseFeatureWidget";
-} & 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<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<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>>;
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
-        showCoordinatesSetting: string;
-        intronBp: number;
-        upDownBp: number;
-        upperCaseCDS: boolean;
-        charactersPerRow: number;
-        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
-    } & {
-        setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
-        setUpDownBp(f: number): void;
-        setIntronBp(f: number): void;
-        setUpperCaseCDS(f: boolean): void;
-        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
-    } & {
-        readonly showCoordinates: boolean;
-        readonly showGenomicCoordsOption: boolean;
-        readonly hasCDS: boolean | undefined;
-        readonly hasExon: boolean | undefined;
-        readonly hasExonOrCDS: boolean | undefined;
-    } & {
-        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;
-    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    trackId: string | undefined;
-    trackType: string | undefined;
-    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>;
-export type VariantFeatureWidgetModel = Instance<VariantFeatureWidgetStateModel>;

package/dist/VariantFeatureWidget/stateModelFactory.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.stateModelFactory = stateModelFactory;
-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', {
-        type: mobx_state_tree_1.types.literal('VariantFeatureWidget'),
-        descriptions: mobx_state_tree_1.types.frozen(),
-    }));
-}

package/dist/VariantFeatureWidget/types.d.ts

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

package/dist/VariantFeatureWidget/types.js

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

package/dist/VariantFeatureWidget/variantFieldDescriptions.d.ts

@@ -1,9 +0,0 @@
-export declare const variantFieldDescriptions: {
-    CHROM: string;
-    POS: string;
-    ID: string;
-    REF: string;
-    ALT: string;
-    QUAL: string;
-    FILTER: string;
-};

package/dist/VariantFeatureWidget/variantFieldDescriptions.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.variantFieldDescriptions = void 0;
-exports.variantFieldDescriptions = {
-    CHROM: 'chromosome: An identifier from the reference genome',
-    POS: 'position: The reference position, with the 1st base having position 1',
-    ID: 'identifier: Semi-colon separated list of unique identifiers where available',
-    REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
-    ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
-    QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
-    FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
-};

package/dist/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts

@@ -1,14 +0,0 @@
-import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { ClusterGenotypeMatrixArgs } from './types';
-export declare class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
-    name: string;
-    execute(args: ClusterGenotypeMatrixArgs, rpcDriverClassName: string): Promise<{
-        clusters: {
-            height: number;
-            indexes: number[];
-        } | undefined;
-        distances: number[][];
-        order: number[];
-        clustersGivenK: number[][][];
-    }>;
-}

package/dist/VariantRPC/MultiVariantClusterGenotypeMatrix.js

@@ -1,30 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.MultiVariantClusterGenotypeMatrix = void 0;
-const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
-const cluster_1 = require("@jbrowse/core/util/cluster");
-const getGenotypeMatrix_1 = require("./getGenotypeMatrix");
-class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'MultiVariantClusterGenotypeMatrix';
-    }
-    async execute(args, rpcDriverClassName) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const matrix = await (0, getGenotypeMatrix_1.getGenotypeMatrix)({
-            pluginManager: this.pluginManager,
-            args: deserializedArgs,
-        });
-        return (0, cluster_1.clusterData)({
-            data: Object.values(matrix),
-            stopToken: deserializedArgs.stopToken,
-            onProgress: progress => {
-                deserializedArgs.statusCallback(progress);
-            },
-        });
-    }
-}
-exports.MultiVariantClusterGenotypeMatrix = MultiVariantClusterGenotypeMatrix;

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -1,6 +0,0 @@
-import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { GetGenotypeMatrixArgs } from './types';
-export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
-    name: string;
-    execute(args: GetGenotypeMatrixArgs, rpcDriverClassName: string): Promise<Record<string, number[]>>;
-}

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -1,21 +0,0 @@
-"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 RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
-const getGenotypeMatrix_1 = require("./getGenotypeMatrix");
-class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'MultiVariantGetGenotypeMatrix';
-    }
-    async execute(args, rpcDriverClassName) {
-        return (0, getGenotypeMatrix_1.getGenotypeMatrix)({
-            pluginManager: this.pluginManager,
-            args: await this.deserializeArguments(args, rpcDriverClassName),
-        });
-    }
-}
-exports.MultiVariantGetGenotypeMatrix = MultiVariantGetGenotypeMatrix;

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,19 +0,0 @@
-import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { GetSimplifiedFeaturesArgs } from './types';
-import type { SampleInfo } from '../shared/types';
-export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
-    name: string;
-    execute(args: GetSimplifiedFeaturesArgs, rpcDriverClassName: string): Promise<{
-        hasPhased: boolean;
-        sampleInfo: Record<string, SampleInfo>;
-        features: {
-            id: string;
-            data: {
-                start: number;
-                end: number;
-                refName: string;
-                name: any;
-            };
-        }[];
-    }>;
-}