@jbrowse/plugin-bed 2.17.0 → 2.18.0

package/dist/BedAdapter/BedAdapter.d.ts

@@ -1,7 +1,8 @@
-import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
+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, Region } from '@jbrowse/core/util';
 export default class BedAdapter extends BaseFeatureDataAdapter {
     protected bedFeatures?: Promise<{
         header: string;
@@ -16,12 +17,21 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
-    private loadData;
+    loadData(opts?: BaseOptions): Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        parser: BED;
+        columnNames: string[];
+        scoreColumn: string;
+        colRef: number;
+        colStart: number;
+        colEnd: number;
+    }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
-    private loadFeatureIntervalTree;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/dist/BedAdapter/BedAdapter.js

@@ -3,13 +3,12 @@ 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 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 util_1 = require("@jbrowse/core/util");
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-// locals
 const util_2 = require("../util");
 class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -20,7 +19,6 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedLocation');
         const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, pm), opts);
-        // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
         }
@@ -99,9 +97,10 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         const names = await this.getNames();
         const intervalTree = new interval_tree_1.default();
-        const ret = lines.map((line, i) => {
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i];
             const uniqueId = `${this.id}-${refName}-${i}`;
-            return new util_1.SimpleFeature((0, util_2.featureData)({
+            const feat = new util_1.SimpleFeature((0, util_2.featureData)({
                 line,
                 colRef,
                 colStart,
@@ -111,9 +110,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 uniqueId,
                 names,
             }));
-        });
-        for (const obj of ret) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            intervalTree.insert([feat.get('start'), feat.get('end')], feat);
         }
         return intervalTree;
     }
@@ -134,7 +131,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 observer.next(f);
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/dist/BedAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bedLocation: {
         type: string;
         defaultValue: {
@@ -9,49 +6,31 @@ declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;
         defaultValue: never[];
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     autoSql: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     colRef: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     colStart: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     colEnd: {
         type: string;
         description: string;

package/dist/BedAdapter/configSchema.js

@@ -1,61 +1,37 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config BedAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
-    /**
-     * #slot
-     */
     bedLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     autoSql: {
         type: 'string',
         description: 'The autoSql definition for the data fields in the file',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     colRef: {
         type: 'number',
         description: 'The column to use as a "refName" attribute',
         defaultValue: 0,
     },
-    /**
-     * #slot
-     */
     colStart: {
         type: 'number',
         description: 'The column to use as a "start" attribute',
         defaultValue: 1,
     },
-    /**
-     * #slot
-     */
     colEnd: {
         type: 'number',
         description: 'The column to use as a "end" attribute',

package/dist/BedAdapter/index.d.ts

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

package/dist/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -0,0 +1,24 @@
+import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
+export default class BedGraphAdapter extends BaseFeatureDataAdapter {
+    protected bedFeatures?: Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        columnNames: string[];
+    }>;
+    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    getNames(): Promise<string[] | undefined>;
+    private loadFeatureIntervalTreeHelper;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    private loadDataP;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
+    loadData(opts?: BaseOptions): Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        columnNames: string[];
+    }>;
+    getFeatures(query: Region, _opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/BedGraphAdapter/BedGraphAdapter.js

@@ -0,0 +1,130 @@
+"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");
+class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.intervalTrees = {};
+    }
+    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 loadFeatureIntervalTreeHelper(refName) {
+        var _a;
+        const { features } = await this.loadData();
+        const lines = features[refName];
+        if (!lines) {
+            return undefined;
+        }
+        const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(3)) || [];
+        const intervalTree = new interval_tree_1.default();
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i];
+            const [refName, s, e, ...rest] = line.split('\t');
+            for (let j = 0; j < rest.length; j++) {
+                const uniqueId = `${this.id}-${refName}-${i}-${j}`;
+                const start = +s;
+                const end = +e;
+                const score = +rest[j];
+                const source = names[j] || `col${j}`;
+                if (score) {
+                    intervalTree.insert([start, end], new util_1.SimpleFeature({
+                        id: uniqueId,
+                        data: {
+                            refName,
+                            start,
+                            end,
+                            score,
+                            source,
+                        },
+                    }));
+                }
+            }
+        }
+        return intervalTree;
+    }
+    async getRefNames(opts = {}) {
+        const { features } = await this.loadData(opts);
+        return Object.keys(features);
+    }
+    async loadDataP(opts = {}) {
+        const pm = this.pluginManager;
+        const bedLoc = this.getConf('bedGraphLocation');
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, pm), opts);
+        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|\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 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 columnNames = this.getConf('columnNames');
+        return {
+            header,
+            features,
+            columnNames,
+        };
+    }
+    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];
+    }
+    async loadData(opts = {}) {
+        if (!this.bedFeatures) {
+            this.bedFeatures = this.loadDataP(opts).catch((e) => {
+                this.bedFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.bedFeatures;
+    }
+    getFeatures(query, _opts = {}) {
+        return (0, rxjs_1.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();
+        });
+    }
+    freeResources() { }
+}
+exports.default = BedGraphAdapter;

package/dist/BedGraphAdapter/configSchema.d.ts

@@ -0,0 +1,15 @@
+declare const BedGraphAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    bedGraphLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    columnNames: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default BedGraphAdapter;

package/dist/BedGraphAdapter/configSchema.js

@@ -0,0 +1,19 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+function x() { }
+const BedGraphAdapter = (0, configuration_1.ConfigurationSchema)('BedGraphAdapter', {
+    bedGraphLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bedgraph',
+            locationType: 'UriLocation',
+        },
+    },
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+exports.default = BedGraphAdapter;

package/dist/BedGraphAdapter/index.d.ts

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

package/dist/BedGraphAdapter/index.js

@@ -0,0 +1,39 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BedGraphAdapterF;
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+function BedGraphAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'BedGraphAdapter',
+        displayName: 'BedGraph adapter',
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedGraphAdapter'))).then(r => r.default),
+    }));
+}

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -0,0 +1,18 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
+export default class BedGraphAdapter extends BaseFeatureDataAdapter {
+    private configured?;
+    private configurePre;
+    protected configure(): Promise<{
+        bedGraph: TabixIndexedFile;
+        header: string;
+        columnNames: string[];
+    }>;
+    getNames(): Promise<string[] | undefined>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(): Promise<string>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -0,0 +1,105 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tabix_1 = require("@gmod/tabix");
+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");
+class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    async configurePre() {
+        const pm = this.pluginManager;
+        const bedGraphGzLocation = this.getConf('bedGraphGzLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const filehandle = (0, io_1.openLocation)(bedGraphGzLocation, pm);
+        const isCSI = indexType === 'CSI';
+        const bedGraph = new tabix_1.TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
+            tbiFilehandle: !isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+        const columnNames = this.getConf('columnNames');
+        const header = await bedGraph.getHeader();
+        return {
+            columnNames,
+            bedGraph,
+            header,
+        };
+    }
+    async configure() {
+        if (!this.configured) {
+            this.configured = this.configurePre().catch((e) => {
+                this.configured = undefined;
+                throw e;
+            });
+        }
+        return this.configured;
+    }
+    async getNames() {
+        const { bedGraph, columnNames } = await this.configure();
+        if (columnNames.length) {
+            return columnNames;
+        }
+        const header = await bedGraph.getHeader();
+        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(f => f.trim())
+            : undefined;
+    }
+    async getRefNames(opts = {}) {
+        const { bedGraph } = await this.configure();
+        return bedGraph.getReferenceSequenceNames(opts);
+    }
+    async getHeader() {
+        const { bedGraph } = await this.configure();
+        return bedGraph.getHeader();
+    }
+    getFeatures(query, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            var _a;
+            const { bedGraph } = await this.configure();
+            const meta = await bedGraph.getMetadata();
+            const { columnNumbers } = meta;
+            const colRef = columnNumbers.ref - 1;
+            const colStart = columnNumbers.start - 1;
+            const colEnd = columnNumbers.end - 1;
+            const same = colStart === colEnd;
+            const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(same ? 2 : 3)) || [];
+            await bedGraph.getLines(query.refName, query.start + (same ? -1 : 0), query.end, {
+                lineCallback: (line, fileOffset) => {
+                    const cols = line.split('\t');
+                    const refName = cols[colRef];
+                    const start = +cols[colStart];
+                    const end = +(same ? start + 1 : cols[colEnd]);
+                    const rest = cols.slice(colEnd + 1);
+                    for (let j = 0; j < rest.length; j++) {
+                        const uniqueId = `${this.id}-${fileOffset}-${j}`;
+                        const score = Math.abs(+rest[j]);
+                        const source = names[j] || `col${j}`;
+                        if (score) {
+                            observer.next(new util_1.SimpleFeature({
+                                id: uniqueId,
+                                data: {
+                                    refName,
+                                    start,
+                                    end,
+                                    score,
+                                    source,
+                                },
+                            }));
+                        }
+                    }
+                },
+                ...opts,
+            });
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}
+exports.default = BedGraphAdapter;

package/dist/BedGraphTabixAdapter/configSchema.d.ts

@@ -0,0 +1,29 @@
+declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    bedGraphGzLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    columnNames: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default BedGraphTabixAdapter;

package/dist/BedGraphTabixAdapter/configSchema.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function x() { }
+const BedGraphTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedGraphTabixAdapter', {
+    bedGraphGzLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bedgraph',
+            locationType: 'UriLocation',
+        },
+    },
+    index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
+        indexType: {
+            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.vcf.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+exports.default = BedGraphTabixAdapter;

package/dist/BedGraphTabixAdapter/index.d.ts

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