@jbrowse/plugin-bed 1.7.10 → 2.0.1

package/esm/BedAdapter/BedAdapter.js

@@ -0,0 +1,130 @@
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { featureData } from '../util';
+import IntervalTree from '@flatten-js/interval-tree';
+import { unzip } from '@gmod/bgzf-filehandle';
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export default class BedAdapter extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.intervalTrees = {};
+    }
+    async loadDataP(opts = {}) {
+        const pm = this.pluginManager;
+        const bedLoc = this.getConf('bedLocation');
+        const buf = await openLocation(bedLoc, pm).readFile(opts);
+        const buffer = isGzip(buf) ? await unzip(buf) : buf;
+        // 512MB  max chrome string length is 512MB
+        if (buffer.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const lines = data.split('\n').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 features = {};
+        for (; i < lines.length; i++) {
+            const line = lines[i];
+            const tab = line.indexOf('\t');
+            const refName = line.slice(0, tab);
+            if (!features[refName]) {
+                features[refName] = [];
+            }
+            features[refName].push(line);
+        }
+        const autoSql = this.getConf('autoSql');
+        const parser = new BED({ autoSql });
+        const columnNames = this.getConf('columnNames');
+        const scoreColumn = this.getConf('scoreColumn');
+        const colRef = this.getConf('colRef');
+        const colStart = this.getConf('colStart');
+        const colEnd = this.getConf('colEnd');
+        return {
+            header,
+            features,
+            parser,
+            columnNames,
+            scoreColumn,
+            colRef,
+            colStart,
+            colEnd,
+        };
+    }
+    async loadData(opts = {}) {
+        if (!this.bedFeatures) {
+            this.bedFeatures = this.loadDataP(opts).catch(e => {
+                this.bedFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.bedFeatures;
+    }
+    async getRefNames(opts = {}) {
+        const { features } = await this.loadData(opts);
+        return Object.keys(features);
+    }
+    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').filter(f => !!f);
+        const defline = defs[defs.length - 1];
+        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+            ? defline
+                .slice(1)
+                .split('\t')
+                .map(field => field.trim())
+            : undefined;
+    }
+    async loadFeatureIntervalTreeHelper(refName) {
+        const { colRef, colStart, colEnd, features, parser, scoreColumn } = await this.loadData();
+        const lines = features[refName];
+        if (!lines) {
+            return undefined;
+        }
+        const names = await this.getNames();
+        const intervalTree = new IntervalTree();
+        const ret = lines.map((f, i) => {
+            const uniqueId = `${this.id}-${refName}-${i}`;
+            return featureData(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
+        });
+        for (let i = 0; i < ret.length; i++) {
+            const obj = ret[i];
+            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        }
+        return intervalTree;
+    }
+    async loadFeatureIntervalTree(refName) {
+        if (!this.intervalTrees[refName]) {
+            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(e => {
+                this.intervalTrees[refName] = undefined;
+                throw e;
+            });
+        }
+        return this.intervalTrees[refName];
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { start, end, refName } = query;
+            const intervalTree = await this.loadFeatureIntervalTree(refName);
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => observer.next(f));
+            observer.complete();
+        }, opts.signal);
+    }
+    freeResources() { }
+}
+BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
+//# sourceMappingURL=BedAdapter.js.map

package/esm/BedAdapter/BedAdapter.js.map

@@ -0,0 +1 @@
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package/esm/BedAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/BedAdapter/configSchema.js

@@ -0,0 +1,38 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('BedAdapter', {
+    bedLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+    scoreColumn: {
+        type: 'string',
+        description: 'The column to use as a "score" attribute',
+        defaultValue: '',
+    },
+    autoSql: {
+        type: 'string',
+        description: 'The autoSql definition for the data fields in the file',
+        defaultValue: '',
+    },
+    colRef: {
+        type: 'number',
+        description: 'The column to use as a "refName" attribute',
+        defaultValue: 0,
+    },
+    colStart: {
+        type: 'number',
+        description: 'The column to use as a "start" attribute',
+        defaultValue: 1,
+    },
+    colEnd: {
+        type: 'number',
+        description: 'The column to use as a "end" attribute',
+        defaultValue: 2,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/BedAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4CAA4C;QACzD,YAAY,EAAE,CAAC;KAChB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,CAAC;KAChB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wCAAwC;QACrD,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/BedAdapter/index.d.ts

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

package/esm/BedAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/BedAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BedAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -0,0 +1,19 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import { TabixIndexedFile } from '@gmod/tabix';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class BedTabixAdapter extends BaseFeatureDataAdapter {
+    private parser;
+    protected bed: TabixIndexedFile;
+    protected columnNames: string[];
+    protected scoreColumn: string;
+    static capabilities: string[];
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(opts?: BaseOptions): Promise<any>;
+    getHeader(): Promise<string>;
+    getNames(): Promise<string[] | undefined>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -0,0 +1,69 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { TabixIndexedFile } from '@gmod/tabix';
+import { featureData } from '../util';
+export default class BedTabixAdapter extends BaseFeatureDataAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const bedGzLoc = this.getConf('bedGzLocation');
+        const type = this.getConf(['index', 'indexType']);
+        const loc = this.getConf(['index', 'location']);
+        const autoSql = this.getConf('autoSql');
+        const pm = this.pluginManager;
+        this.bed = new TabixIndexedFile({
+            filehandle: openLocation(bedGzLoc, pm),
+            csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,
+            tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+        this.columnNames = this.getConf('columnNames');
+        this.scoreColumn = this.getConf('scoreColumn');
+        this.parser = new BED({ autoSql });
+    }
+    async getRefNames(opts = {}) {
+        return this.bed.getReferenceSequenceNames(opts);
+    }
+    async getHeader() {
+        return this.bed.getHeader();
+    }
+    async getNames() {
+        if (this.columnNames.length) {
+            return this.columnNames;
+        }
+        const header = await this.bed.getHeader();
+        const defs = header.split('\n').filter(f => !!f);
+        const defline = defs[defs.length - 1];
+        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+            ? defline
+                .slice(1)
+                .split('\t')
+                .map(f => f.trim())
+            : undefined;
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const meta = await this.bed.getMetadata();
+            const { columnNumbers } = meta;
+            const colRef = columnNumbers.ref - 1;
+            const colStart = columnNumbers.start - 1;
+            const colEnd = columnNumbers.end - 1;
+            // colSame handles special case for tabix where a single column is both
+            // the start and end, this is assumed to be covering the base at this
+            // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same
+            const names = await this.getNames();
+            await this.bed.getLines(query.refName, query.start, query.end, {
+                lineCallback: (line, fileOffset) => {
+                    observer.next(featureData(line, colRef, colStart, colEnd, this.scoreColumn, this.parser, `${this.id}-${fileOffset}`, names));
+                },
+                signal: opts.signal,
+            });
+            observer.complete();
+        }, opts.signal);
+    }
+    freeResources() { }
+}
+BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
+//# sourceMappingURL=BedTabixAdapter.js.map

package/esm/BedTabixAdapter/BedTabixAdapter.js.map

@@ -0,0 +1 @@
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package/esm/BedTabixAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/BedTabixAdapter/configSchema.js

@@ -0,0 +1,38 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+export default ConfigurationSchema('BedTabixAdapter', {
+    bedGzLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+    index: ConfigurationSchema('TabixIndex', {
+        indexType: {
+            model: types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.bed.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+    scoreColumn: {
+        type: 'string',
+        description: 'The column to use as a "score" attribute',
+        defaultValue: '',
+    },
+    autoSql: {
+        type: 'string',
+        description: 'The autoSql definition for the data fields in the file',
+        defaultValue: '',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/BedTabixAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/BedTabixAdapter/index.d.ts

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

package/esm/BedTabixAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/BedTabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -0,0 +1,46 @@
+import { BigBed } from '@gmod/bbi';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+interface BEDFeature {
+    chrom: string;
+    chromStart: number;
+    chromEnd: number;
+    [key: string]: any;
+}
+interface Parser {
+    parseLine: (line: string, opts: {
+        uniqueId: string | number;
+    }) => BEDFeature;
+    autoSql: {
+        fields: {
+            name: string;
+            comment: string;
+        }[];
+    };
+}
+export default class BigBedAdapter extends BaseFeatureDataAdapter {
+    private cached?;
+    configurePre(opts?: BaseOptions): Promise<{
+        bigbed: BigBed;
+        header: any;
+        parser: Parser;
+    }>;
+    configure(opts?: BaseOptions): Promise<{
+        bigbed: BigBed;
+        header: any;
+        parser: Parser;
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<{
+        version: any;
+        fileType: any;
+        autoSql: {};
+        fields: {
+            [k: string]: string;
+        };
+    }>;
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -0,0 +1,104 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { BigBed } from '@gmod/bbi';
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { map, mergeAll } from 'rxjs/operators';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { ucscProcessedTranscript } from '../util';
+function isUCSC(f) {
+    return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
+}
+export default class BigBedAdapter extends BaseFeatureDataAdapter {
+    async configurePre(opts) {
+        const bigbed = new BigBed({
+            filehandle: openLocation(readConfObject(this.config, 'bigBedLocation'), this.pluginManager),
+        });
+        const header = await bigbed.getHeader(opts);
+        const parser = new BED({ autoSql: header.autoSql });
+        return { bigbed, header, parser };
+    }
+    async configure(opts) {
+        if (!this.cached) {
+            this.cached = this.configurePre(opts).catch(e => {
+                this.cached = undefined;
+                throw e;
+            });
+        }
+        return this.cached;
+    }
+    async getRefNames(opts) {
+        const { header } = await this.configure(opts);
+        return Object.keys(header.refsByName);
+    }
+    async getHeader(opts) {
+        const { parser, header } = await this.configure(opts);
+        const { version, fileType } = header;
+        const { fields, ...rest } = parser.autoSql;
+        return {
+            version,
+            fileType,
+            autoSql: { ...rest },
+            fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
+        };
+    }
+    getFeatures(region, opts = {}) {
+        const { refName, start, end } = region;
+        const { signal } = opts;
+        return ObservableCreate(async (observer) => {
+            try {
+                const { parser, bigbed } = await this.configure(opts);
+                const ob = await bigbed.getFeatureStream(refName, start, end, {
+                    signal,
+                    basesPerSpan: end - start,
+                });
+                ob.pipe(mergeAll(), map(r => {
+                    const data = parser.parseLine(`${refName}\t${r.start}\t${r.end}\t${r.rest}`, {
+                        uniqueId: r.uniqueId,
+                    });
+                    const { blockCount, blockSizes, blockStarts, chromStarts } = data;
+                    if (blockCount) {
+                        const starts = chromStarts || blockStarts || [];
+                        const sizes = blockSizes;
+                        const blocksOffset = r.start;
+                        data.subfeatures = [];
+                        for (let b = 0; b < blockCount; b += 1) {
+                            const bmin = (starts[b] || 0) + blocksOffset;
+                            const bmax = bmin + (sizes[b] || 0);
+                            data.subfeatures.push({
+                                uniqueId: `${r.uniqueId}-${b}`,
+                                start: bmin,
+                                end: bmax,
+                                type: 'block',
+                            });
+                        }
+                    }
+                    if (r.uniqueId === undefined) {
+                        throw new Error('invalid bbi feature');
+                    }
+                    const { chromStart, chromEnd, chrom, ...rest } = data;
+                    const f = new SimpleFeature({
+                        id: `${this.id}-${r.uniqueId}`,
+                        data: {
+                            ...rest,
+                            start: r.start,
+                            end: r.end,
+                            refName,
+                        },
+                    });
+                    // collection of heuristics for suggesting that this feature
+                    // should be converted to a gene, CNV bigbed has many gene like
+                    // features including thickStart and blockCount but no strand
+                    return isUCSC(f) ? ucscProcessedTranscript(f) : f;
+                })).subscribe(observer);
+            }
+            catch (e) {
+                observer.error(e);
+            }
+        }, opts.signal);
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=BigBedAdapter.js.map

package/esm/BigBedAdapter/BigBedAdapter.js.map

@@ -0,0 +1 @@
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package/esm/BigBedAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/BigBedAdapter/configSchema.js

@@ -0,0 +1,8 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('BigBedAdapter', {
+    bigBedLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/BigBedAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/BigBedAdapter/index.d.ts

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

package/esm/BigBedAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/BigBedAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigBedAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class BedPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,81 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import Plugin from '@jbrowse/core/Plugin';
+import { configSchema as bigBedAdapterConfigSchema } from './BigBedAdapter';
+import { configSchema as bedTabixAdapterConfigSchema } from './BedTabixAdapter';
+import { configSchema as bedAdapterConfigSchema } from './BedAdapter';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
+export default class BedPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'BedPlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'BigBedAdapter',
+            configSchema: bigBedAdapterConfigSchema,
+            getAdapterClass: () => import('./BigBedAdapter/BigBedAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.(bb|bigbed)$/i;
+                const adapterName = 'BigBedAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    bigBedLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'BedTabixAdapter',
+            configSchema: bedTabixAdapterConfigSchema,
+            getAdapterClass: () => import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default),
+        }));
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'BedAdapter',
+            configSchema: bedAdapterConfigSchema,
+            getAdapterClass: () => import('./BedAdapter/BedAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.bed\.b?gz$/i;
+                const adapterName = 'BedTabixAdapter';
+                const fileName = getFileName(file);
+                const indexName = index && getFileName(index);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bedGzLocation: file,
+                        index: {
+                            location: index || makeIndex(file, '.tbi'),
+                            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                        },
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.bed$/i;
+                const adapterName = 'BedAdapter';
+                const fileName = getFileName(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bedLocation: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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