@jbrowse/plugin-bed 3.6.5 → 4.0.0

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -1,114 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_2 = require("./util");
-class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.intervalTrees = {};
-    }
-    async loadDataP(opts) {
-        const data = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.openLocation)(this.getConf('bedpeLocation'), this.pluginManager), opts);
-        const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
-        const headerLines = [];
-        let i = 0;
-        for (; i < lines.length && lines[i].startsWith('#'); i++) {
-            headerLines.push(lines[i]);
-        }
-        const header = headerLines.join('\n');
-        const feats1 = {};
-        const feats2 = {};
-        for (; i < lines.length; i++) {
-            const line = lines[i];
-            const cols = line.split('\t');
-            const r1 = cols[0];
-            const r2 = cols[3];
-            if (!feats1[r1]) {
-                feats1[r1] = [];
-            }
-            if (!feats2[r2]) {
-                feats2[r2] = [];
-            }
-            feats1[r1].push(line);
-            feats2[r2].push(line);
-        }
-        const columnNames = this.getConf('columnNames');
-        return {
-            header,
-            feats1,
-            feats2,
-            columnNames,
-        };
-    }
-    async loadData(opts = {}) {
-        if (!this.bedpeFeatures) {
-            this.bedpeFeatures = this.loadDataP(opts).catch((e) => {
-                this.bedpeFeatures = undefined;
-                throw e;
-            });
-        }
-        return this.bedpeFeatures;
-    }
-    async getRefNames(opts = {}) {
-        const { feats1, feats2 } = await this.loadData(opts);
-        return [...new Set([...Object.keys(feats1), ...Object.keys(feats2)])];
-    }
-    async getHeader(opts = {}) {
-        const { header } = await this.loadData(opts);
-        return header;
-    }
-    async getNames() {
-        const { header, columnNames } = await this.loadData();
-        if (columnNames.length) {
-            return columnNames;
-        }
-        const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs.at(-1);
-        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
-            ? defline
-                .slice(1)
-                .split('\t')
-                .map(field => field.trim())
-            : undefined;
-    }
-    async loadFeatureTreeP(refName) {
-        var _a, _b, _c, _d;
-        const { feats1, feats2 } = await this.loadData();
-        const names = await this.getNames();
-        const intervalTree = new interval_tree_1.default();
-        const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
-        const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
-        for (const obj of [...ret1, ...ret2]) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
-        }
-        return intervalTree;
-    }
-    async loadFeatureTree(refName) {
-        if (!this.intervalTrees[refName]) {
-            this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch((e) => {
-                this.intervalTrees[refName] = undefined;
-                throw e;
-            });
-        }
-        return this.intervalTrees[refName];
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { start, end, refName } = query;
-            const intervalTree = await this.loadFeatureTree(refName);
-            for (const f of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
-                observer.next(f);
-            }
-            observer.complete();
-        }, opts.stopToken);
-    }
-}
-BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = BedpeAdapter;

package/dist/BedpeAdapter/configSchema.d.ts

@@ -1,16 +0,0 @@
-declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    bedpeLocation: {
-        type: string;
-        description: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    columnNames: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BedpeAdapter;

package/dist/BedpeAdapter/configSchema.js

@@ -1,33 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
-    bedpeLocation: {
-        type: 'fileLocation',
-        description: 'can be plaintext or gzipped, not indexed so loaded into memory on startup',
-        defaultValue: {
-            uri: '/path/to/my.bedpe.gz',
-            locationType: 'UriLocation',
-        },
-    },
-    columnNames: {
-        type: 'stringArray',
-        description: 'List of column names',
-        defaultValue: [],
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                bedpeLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = BedpeAdapter;

package/dist/BedpeAdapter/index.d.ts

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

package/dist/BedpeAdapter/index.js

@@ -1,49 +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 = BedpeAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BedpeAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'BedpeAdapter',
-        displayName: 'BEDPE adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedpeAdapter'))).then(r => r.default),
-    }));
-}

package/dist/BedpeAdapter/util.d.ts

@@ -1,2 +0,0 @@
-import { SimpleFeature } from '@jbrowse/core/util';
-export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;

package/dist/BedpeAdapter/util.js

@@ -1,55 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.featureData = featureData;
-const util_1 = require("@jbrowse/core/util");
-const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
-function featureData(line, uniqueId, flip, names) {
-    const l = line.split('\t');
-    const ref1 = l[flip ? 3 : 0];
-    const start1 = +l[flip ? 4 : 1];
-    const end1 = +l[flip ? 5 : 2];
-    const ref2 = l[!flip ? 3 : 0];
-    const start2 = +l[!flip ? 4 : 1];
-    const end2 = +l[!flip ? 5 : 2];
-    const name = l[6];
-    const score = +l[7];
-    const strand1 = parseStrand(l[8]);
-    const strand2 = parseStrand(l[9]);
-    const extra = l.slice(10);
-    const rest = names
-        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
-        : {};
-    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
-    return new util_1.SimpleFeature({
-        ...rest,
-        start: start1,
-        end: end1,
-        type: 'paired_feature',
-        refName: ref1,
-        strand: strand1,
-        name,
-        score,
-        uniqueId,
-        mate: {
-            refName: ref2,
-            start: start2,
-            end: end2,
-            strand: strand2,
-        },
-        ...(ALT ? { ALT: [ALT] } : {}),
-    });
-}
-function parseStrand(strand) {
-    if (strand === '+') {
-        return 1;
-    }
-    else if (strand === '-') {
-        return -1;
-    }
-    else if (strand === '.') {
-        return 0;
-    }
-    else {
-        return undefined;
-    }
-}

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,46 +0,0 @@
-import { BigBed } from '@gmod/bbi';
-import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature } from '@jbrowse/core/util';
-import type { Region } from '@jbrowse/core/util/types';
-import type { Observer } from 'rxjs';
-export default class BigBedAdapter extends BaseFeatureDataAdapter {
-    private cachedP?;
-    configurePre(opts?: BaseOptions): Promise<{
-        bigbed: BigBed;
-        header: import("@gmod/bbi/dist/types").BigWigHeaderWithRefNames;
-        parser: BED;
-    }>;
-    configure(opts?: BaseOptions): Promise<{
-        bigbed: BigBed;
-        header: Awaited<ReturnType<BigBed["getHeader"]>>;
-        parser: BED;
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getRefNameAliases(opts?: BaseOptions): Promise<{
-        refName: unknown;
-        aliases: unknown[];
-        override: boolean;
-    }[]>;
-    getData(): Promise<Feature[]>;
-    getHeader(opts?: BaseOptions): Promise<{
-        version: number;
-        fileType: string;
-        autoSql: {};
-        fields: {
-            [k: string]: string;
-        };
-    }>;
-    getMetadata(opts?: BaseOptions): Promise<{
-        [k: string]: string;
-    }>;
-    getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
-        query: Region;
-        opts: BaseOptions;
-        observer: Observer<Feature>;
-        allowRedispatch: boolean;
-        originalQuery?: Region;
-    }): Promise<void>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -1,230 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const bbi_1 = require("@gmod/bbi");
-const bed_1 = __importDefault(require("@gmod/bed"));
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const rxjs_2 = require("rxjs");
-const util_2 = require("../util");
-class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre(opts) {
-        const pm = this.pluginManager;
-        const bigbed = new bbi_1.BigBed({
-            filehandle: (0, io_1.openLocation)(this.getConf('bigBedLocation'), pm),
-        });
-        const header = await bigbed.getHeader(opts);
-        const parser = new bed_1.default({
-            autoSql: header.autoSql,
-        });
-        return {
-            bigbed,
-            header,
-            parser,
-        };
-    }
-    async configure(opts) {
-        if (!this.cachedP) {
-            this.cachedP = this.configurePre(opts).catch((e) => {
-                this.cachedP = undefined;
-                throw e;
-            });
-        }
-        return this.cachedP;
-    }
-    async getRefNames(opts) {
-        const { header } = await this.configure(opts);
-        return Object.keys(header.refsByName);
-    }
-    async getRefNameAliases(opts) {
-        const { header } = await this.configure(opts);
-        const ret = await Promise.all(Object.keys(header.refsByName).map(async (refName) => (await (0, rxjs_2.firstValueFrom)(this.getFeatures({
-            assemblyName: '',
-            refName,
-            start: 0,
-            end: 1,
-        }).pipe((0, rxjs_2.toArray)())))[0]));
-        return ret
-            .map(r => r.toJSON())
-            .map(r => ({
-            refName: r.ucsc,
-            aliases: [r.ncbi, r.refseq, r.genbank],
-            override: true,
-        }));
-    }
-    async getData() {
-        const refNames = await this.getRefNames();
-        const features = [];
-        for (const refName of refNames) {
-            const f = await (0, rxjs_2.firstValueFrom)(this.getFeatures({
-                assemblyName: 'unknown',
-                refName,
-                start: 0,
-                end: Number.MAX_SAFE_INTEGER,
-            }).pipe((0, rxjs_2.toArray)()));
-            features.push(f);
-        }
-        return features.flat();
-    }
-    async getHeader(opts) {
-        const { parser, header } = await this.configure(opts);
-        const { version, fileType } = header;
-        const { fields, ...autoSql } = parser.autoSql;
-        return {
-            version,
-            fileType,
-            autoSql,
-            fields: await this.getMetadata(opts),
-        };
-    }
-    async getMetadata(opts) {
-        const { parser } = await this.configure(opts);
-        const { fields } = parser.autoSql;
-        return Object.fromEntries(fields.map(({ name, comment }) => [name, comment]));
-    }
-    async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        const { statusCallback = () => { } } = opts;
-        const scoreColumn = this.getConf('scoreColumn');
-        const aggregateField = this.getConf('aggregateField');
-        const { parser, bigbed } = await (0, util_1.updateStatus)('Downloading header', statusCallback, () => this.configure(opts));
-        const feats = await (0, util_1.updateStatus)('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
-            basesPerSpan: query.end - query.start,
-        }));
-        await (0, util_1.updateStatus)('Processing features', statusCallback, async () => {
-            var _a;
-            const parentAggregation = {};
-            const parentAggregationFlat = [];
-            if (feats.some(f => f.uniqueId === undefined)) {
-                throw new Error('found uniqueId undefined');
-            }
-            for (const feat of feats) {
-                const splitLine = [
-                    query.refName,
-                    `${feat.start}`,
-                    `${feat.end}`,
-                    ...(((_a = feat.rest) === null || _a === void 0 ? void 0 : _a.split('\t')) || []),
-                ];
-                const data = parser.parseLine(splitLine, {
-                    uniqueId: feat.uniqueId,
-                });
-                const aggr = data[aggregateField];
-                const aggrIsNotNone = aggr && aggr !== 'none';
-                if (aggrIsNotNone && !parentAggregation[aggr]) {
-                    parentAggregation[aggr] = [];
-                }
-                const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
-                const f = (0, util_2.featureData2)({
-                    ...rest,
-                    scoreColumn,
-                    splitLine,
-                    parser,
-                    uniqueId,
-                    start: feat.start,
-                    end: feat.end,
-                    refName: query.refName,
-                });
-                if (aggrIsNotNone) {
-                    parentAggregation[aggr].push(f);
-                    parentAggregationFlat.push(f);
-                }
-                else {
-                    if ((0, util_1.doesIntersect2)(f.start, f.end, originalQuery.start, originalQuery.end)) {
-                        observer.next(new util_1.SimpleFeature({
-                            id: `${this.id}-${uniqueId}`,
-                            data: f,
-                        }));
-                    }
-                }
-            }
-            if (allowRedispatch && parentAggregationFlat.length) {
-                let minStart = Number.POSITIVE_INFINITY;
-                let maxEnd = Number.NEGATIVE_INFINITY;
-                for (const feat of parentAggregationFlat) {
-                    if (feat.start < minStart) {
-                        minStart = feat.start;
-                    }
-                    if (feat.end > maxEnd) {
-                        maxEnd = feat.end;
-                    }
-                }
-                if (maxEnd > query.end || minStart < query.start) {
-                    await this.getFeaturesHelper({
-                        query: {
-                            ...query,
-                            start: minStart - 500000,
-                            end: maxEnd + 500000,
-                        },
-                        opts,
-                        observer,
-                        allowRedispatch: false,
-                        originalQuery: query,
-                    });
-                    return;
-                }
-            }
-            Object.entries(parentAggregation).map(([name, subfeatures]) => {
-                var _a, _b, _c;
-                const s = (0, util_1.min)(subfeatures.map(f => f.start));
-                const e = (0, util_1.max)(subfeatures.map(f => f.end));
-                if ((0, util_1.doesIntersect2)(s, e, originalQuery.start, originalQuery.end)) {
-                    const subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
-                    if (subs.some((a, i) => subs.some((b, j) => i !== j && (0, util_1.doesIntersect2)(a.start, a.end, b.start, b.end)))) {
-                        observer.next(new util_1.SimpleFeature({
-                            id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
-                            data: {
-                                type: 'gene',
-                                subfeatures: subs,
-                                strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
-                                name,
-                                start: s,
-                                end: e,
-                                refName: query.refName,
-                            },
-                        }));
-                    }
-                    else {
-                        for (const sub of subs) {
-                            observer.next(new util_1.SimpleFeature({
-                                id: `${this.id}-${sub.uniqueId}-parent`,
-                                data: {
-                                    type: 'gene',
-                                    subfeatures: [sub],
-                                    strand: ((_c = subs[0]) === null || _c === void 0 ? void 0 : _c.strand) || 1,
-                                    name,
-                                    start: sub.start,
-                                    end: sub.end,
-                                    refName: query.refName,
-                                },
-                            }));
-                        }
-                    }
-                }
-            });
-        });
-        observer.complete();
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            try {
-                await this.getFeaturesHelper({
-                    query: {
-                        ...query,
-                        start: query.start,
-                        end: query.end,
-                    },
-                    opts,
-                    observer,
-                    allowRedispatch: true,
-                });
-            }
-            catch (e) {
-                observer.error(e);
-            }
-        }, opts.stopToken);
-    }
-}
-exports.default = BigBedAdapter;

package/dist/BigBedAdapter/configSchema.d.ts

@@ -1,20 +0,0 @@
-declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    bigBedLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    scoreColumn: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    aggregateField: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BigBedAdapter;

package/dist/BigBedAdapter/configSchema.js

@@ -1,37 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter', {
-    bigBedLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.bb',
-            locationType: 'UriLocation',
-        },
-    },
-    scoreColumn: {
-        type: 'string',
-        description: 'The column to use as a "score" attribute',
-        defaultValue: '',
-    },
-    aggregateField: {
-        type: 'string',
-        description: 'An attribute to aggregate features with',
-        defaultValue: 'geneName2',
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                bigBedLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = BigBedAdapter;

package/dist/BigBedAdapter/index.d.ts

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

package/dist/BigBedAdapter/index.js

@@ -1,49 +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 = BigBedAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BigBedAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'BigBedAdapter',
-        displayName: 'BigBed adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigBedAdapter'))).then(r => r.default),
-    }));
-}

package/dist/GuessAdapter/index.d.ts

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