@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/dist/{ucsc-trackhub → UCSCTrackHub}/doConnect.js

@@ -2,14 +2,12 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.doConnect = doConnect;
 const ucsc_hub_1 = require("@gmod/ucsc-hub");
-const ucscTrackHub_1 = require("./ucscTrackHub");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const nanoid_1 = require("@jbrowse/core/util/nanoid");
-function resolve(uri, baseUri) {
-    return new URL(uri, baseUri).href;
-}
+const ucscTrackHub_1 = require("./ucscTrackHub");
+const util_2 = require("./util");
 async function doConnect(self) {
     var _a;
     const session = (0, util_1.getSession)(self);
@@ -17,8 +15,7 @@ async function doConnect(self) {
     try {
         const hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
         const hubFileText = await (0, io_1.openLocation)(hubFileLocation).readFile('utf8');
-        // @ts-expect-error
-        const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
+        const hubUri = (0, util_2.resolve)(hubFileLocation.uri, hubFileLocation.baseUri);
         const { assemblyManager } = session;
         if (hubFileText.includes('useOneFile on')) {
             const hub = new ucsc_hub_1.SingleFileHub(hubFileText);
@@ -26,19 +23,26 @@ async function doConnect(self) {
             const genomeName = genome.name;
             const asm = assemblyManager.get(genomeName);
             if (!asm) {
-                // @ts-expect-error
                 session.addSessionAssembly({
                     name: genomeName,
                     sequence: {
                         type: 'ReferenceSequenceTrack',
+                        metadata: {
+                            ...genome,
+                            ...(genome.data.htmlPath
+                                ? {
+                                    htmlPath: `<a href="${(0, util_2.resolve)(genome.data.htmlPath, hubUri)}">${genome.data.htmlPath}</a>`,
+                                }
+                                : {}),
+                        },
                         trackId: `${genomeName}-${(0, nanoid_1.nanoid)()}`,
                         adapter: {
                             type: 'TwoBitAdapter',
                             twoBitLocation: {
-                                uri: resolve(genome.data.twoBitPath, hubUri),
+                                uri: (0, util_2.resolve)(genome.data.twoBitPath, hubUri),
                             },
                             chromSizesLocation: {
-                                uri: resolve(genome.data.chromSizes, hubUri),
+                                uri: (0, util_2.resolve)(genome.data.chromSizes, hubUri),
                             },
                         },
                     },
@@ -51,6 +55,7 @@ async function doConnect(self) {
                 trackDbLoc: hubFileLocation,
                 assemblyName: genomeName,
                 sequenceAdapter,
+                baseUrl: hubUri,
             });
             self.addTrackConfs(tracksNew);
         }
@@ -60,18 +65,17 @@ async function doConnect(self) {
             if (!genomeFile) {
                 throw new Error('genomesFile not found on hub');
             }
-            // @ts-expect-error
-            const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
+            const hubUri = (0, util_2.resolve)(hubFileLocation.uri, hubFileLocation.baseUri);
             const genomesFileLocation = hubUri
                 ? {
-                    uri: resolve(genomeFile, hubUri),
+                    uri: (0, util_2.resolve)(genomeFile, hubUri),
                     locationType: 'UriLocation',
                 }
                 : {
                     localPath: genomeFile,
                     locationType: 'LocalPathLocation',
                 };
-            const genomesFile = await (0, ucscTrackHub_1.fetchGenomesFile)(genomesFileLocation);
+            const genomesFile = await (0, util_2.fetchGenomesFile)(genomesFileLocation);
             const map = {};
             for (const [genomeName, genome] of Object.entries(genomesFile.data)) {
                 const assemblyNames = (0, configuration_1.getConf)(self, 'assemblyNames');
@@ -83,7 +87,6 @@ async function doConnect(self) {
                     notLoadedAssemblies.push(genomeName);
                     continue;
                 }
-                // @ts-expect-error
                 const db = genome.data.trackDb;
                 if (!db) {
                     throw new Error('genomesFile not found on hub');
@@ -98,13 +101,14 @@ async function doConnect(self) {
                         localPath: db,
                         locationType: 'LocalPathLocation',
                     };
-                const trackDb = await (0, ucscTrackHub_1.fetchTrackDbFile)(loc);
+                const trackDb = await (0, util_2.fetchTrackDbFile)(loc);
                 const sequenceAdapter = (0, configuration_1.getConf)(asm, ['sequence', 'adapter']);
                 const tracks = (0, ucscTrackHub_1.generateTracks)({
                     trackDb,
                     trackDbLoc: loc,
                     assemblyName: genomeName,
                     sequenceAdapter,
+                    baseUrl: hubUri,
                 });
                 self.addTrackConfs(tracks);
                 map[genomeName] = tracks.length;

package/dist/{ucsc-trackhub → UCSCTrackHub}/index.d.ts

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

package/dist/{ucsc-trackhub → UCSCTrackHub}/index.js

@@ -5,15 +5,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = UCSCTrackHubConnectionF;
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const model_1 = __importDefault(require("./model"));
 const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
 function UCSCTrackHubConnectionF(pluginManager) {
-    pluginManager.addConnectionType(() => new pluggableElementTypes_1.ConnectionType({
-        name: 'UCSCTrackHubConnection',
-        configSchema: configSchema_1.default,
-        stateModel: (0, model_1.default)(pluginManager),
-        displayName: 'UCSC Track Hub',
-        description: 'A track or assembly hub in the Track Hub format',
-        url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
-    }));
+    pluginManager.addConnectionType(() => {
+        return new pluggableElementTypes_1.ConnectionType({
+            name: 'UCSCTrackHubConnection',
+            configSchema: configSchema_1.default,
+            stateModel: (0, model_1.default)(pluginManager),
+            displayName: 'UCSC Track Hub',
+            description: 'A track or assembly hub in the Track Hub format',
+            url: 'https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
+        });
+    });
 }

package/dist/{ucsc-trackhub → UCSCTrackHub}/model.d.ts

@@ -1,8 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel UCSCTrackHubConnection
- * extends BaseConnectionModel
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
@@ -19,9 +15,6 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
-    /**
-     * #property
-     */
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         hubTxtLocation: {
             type: string;
@@ -48,9 +41,6 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
             description: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
 }, {
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
@@ -81,8 +71,5 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
     setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {
-    /**
-     * #action
-     */
     connect(): Promise<void>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/{ucsc-trackhub → UCSCTrackHub}/model.js

@@ -15,46 +15,41 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 = UCSCTrackHubConnection;
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configuration_1 = require("@jbrowse/core/configuration");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const configSchema_1 = __importDefault(require("./configSchema"));
-/**
- * #stateModel UCSCTrackHubConnection
- * extends BaseConnectionModel
- */
 function UCSCTrackHubConnection(pluginManager) {
     return mobx_state_tree_1.types
         .compose('UCSCTrackHubConnection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('UCSCTrackHubConnection'),
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         async connect() {
             const { doConnect } = await Promise.resolve().then(() => __importStar(require('./doConnect')));
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             doConnect(self);
         },
     }));

package/dist/{ucsc-trackhub → UCSCTrackHub}/ucscAssemblies.js

@@ -1,7 +1,4 @@
 "use strict";
-// These are the assemblies for which there is a sequence file located at
-// http://hgdownload.soe.ucsc.edu/goldenPath/${assemblyName}/bigZips/${assemblyName}.2bit
-// This list was generated by `getUcscAssemblies.js`
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = `ailMel1
 allMis1

package/dist/{ucsc-trackhub → UCSCTrackHub}/ucscTrackHub.d.ts

@@ -1,29 +1,11 @@
-import { FileLocation } from '@jbrowse/core/util';
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
-export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
-export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
-export declare function makeLoc(first: string, base: {
-    uri: string;
-    baseUri?: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLocAlt(first: string, alt: string, base: {
-    uri: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLoc2(first: string, alt?: string): {
-    uri: string | undefined;
-    locationType: string;
-};
-export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }: {
+import type { TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
+export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }: {
     trackDb: TrackDbFile;
     trackDbLoc: FileLocation;
     assemblyName: string;
     sequenceAdapter: any;
+    baseUrl: string;
 }): ({
     trackId: string;
     assemblyNames: string[];
@@ -31,13 +13,17 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     name: string;
     description: string;
     category: string[] | undefined;
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
-    name: string | undefined;
+    name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         bamLocation: {
@@ -53,18 +39,23 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         cramLocation: {
@@ -78,21 +69,26 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         sequenceAdapter: any;
         bamLocation?: undefined;
         index?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
-        bigBedLocation: {
+        bigWigLocation: {
             uri: string | undefined;
             locationType: string;
         };
@@ -101,20 +97,25 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
-        bigWigLocation: {
+        bigBedLocation: {
             uri: string | undefined;
             locationType: string;
         };
@@ -123,17 +124,22 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         vcfGzLocation: {
@@ -150,17 +156,22 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         hicLocation: {
@@ -172,9 +183,15 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 })[];
 export { default as ucscAssemblies } from './ucscAssemblies';

package/dist/UCSCTrackHub/ucscTrackHub.js

@@ -0,0 +1,170 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ucscAssemblies = void 0;
+exports.generateTracks = generateTracks;
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const util_2 = require("./util");
+function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }) {
+    const parentTrackKeys = new Set([
+        'superTrack',
+        'compositeTrack',
+        'container',
+        'view',
+    ]);
+    return Object.entries(trackDb.data)
+        .map(([trackName, track]) => {
+        var _a;
+        const { data } = track;
+        if (Object.keys(data).some(key => parentTrackKeys.has(key))) {
+            return undefined;
+        }
+        else {
+            const parentTracks = [];
+            let currentTrackName = trackName;
+            do {
+                currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
+                if (currentTrackName) {
+                    currentTrackName = currentTrackName.split(' ')[0];
+                    parentTracks.push(trackDb.data[currentTrackName]);
+                }
+            } while (currentTrackName);
+            parentTracks.reverse();
+            return {
+                metadata: {
+                    ucscConfig: {
+                        ...track.data,
+                        ...(track.data.html
+                            ? {
+                                html: `<a href="${(0, util_2.resolve)(track.data.html, baseUrl)}">${track.data.html}</a>`,
+                            }
+                            : {}),
+                    },
+                },
+                category: [
+                    track.data.group,
+                    ...parentTracks
+                        .map(p => p === null || p === void 0 ? void 0 : p.data.group)
+                        .filter((f) => !!f),
+                ].filter(f => !!f),
+                ...makeTrackConfig({
+                    track,
+                    trackDbLoc,
+                    trackDb,
+                    sequenceAdapter,
+                }),
+            };
+        }
+    })
+        .filter(util_1.notEmpty)
+        .map(r => ({
+        ...r,
+        trackId: `ucsc-trackhub-${(0, util_1.objectHash)(r)}`,
+        assemblyNames: [assemblyName],
+    }));
+}
+function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
+    var _a;
+    const { data } = track;
+    const parent = data.parent || '';
+    const bigDataUrl = data.bigDataUrl || '';
+    const bigDataIdx = data.bigDataIndex || '';
+    const trackType = data.type || ((_a = trackDb.data[parent]) === null || _a === void 0 ? void 0 : _a.data.type) || '';
+    const name = (data.shortLabel || '') + (bigDataUrl.includes('xeno') ? ' (xeno)' : '');
+    const isUri = (0, util_1.isUriLocation)(trackDbLoc);
+    let baseTrackType = trackType.split(' ')[0] || '';
+    if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
+        baseTrackType = 'cram';
+    }
+    const bigDataLocation = isUri
+        ? (0, util_2.makeLoc)(bigDataUrl, trackDbLoc)
+        : (0, util_2.makeLoc2)(bigDataUrl);
+    if (baseTrackType === 'bam') {
+        return {
+            type: 'AlignmentsTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BamAdapter',
+                bamLocation: bigDataLocation,
+                index: {
+                    location: isUri
+                        ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
+                        : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.bai`),
+                },
+            },
+        };
+    }
+    else if (baseTrackType === 'cram') {
+        return {
+            type: 'AlignmentsTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'CramAdapter',
+                cramLocation: bigDataLocation,
+                craiLocation: isUri
+                    ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
+                    : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.crai`),
+                sequenceAdapter,
+            },
+        };
+    }
+    else if (baseTrackType === 'bigWig') {
+        return {
+            type: 'QuantitativeTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BigWigAdapter',
+                bigWigLocation: bigDataLocation,
+            },
+        };
+    }
+    else if (baseTrackType.startsWith('big')) {
+        return {
+            type: 'FeatureTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BigBedAdapter',
+                bigBedLocation: bigDataLocation,
+            },
+        };
+    }
+    else if (baseTrackType === 'vcfTabix') {
+        return {
+            type: 'VariantTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'VcfTabixAdapter',
+                vcfGzLocation: bigDataLocation,
+                index: {
+                    location: isUri
+                        ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
+                        : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.tbi`),
+                },
+            },
+        };
+    }
+    else if (baseTrackType === 'hic') {
+        return {
+            type: 'HicTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'HicAdapter',
+                hicLocation: bigDataLocation,
+            },
+        };
+    }
+    else {
+        return (0, tracks_1.generateUnknownTrackConf)(name, baseTrackType);
+    }
+}
+var ucscAssemblies_1 = require("./ucscAssemblies");
+Object.defineProperty(exports, "ucscAssemblies", { enumerable: true, get: function () { return __importDefault(ucscAssemblies_1).default; } });

package/dist/UCSCTrackHub/util.d.ts

@@ -0,0 +1,22 @@
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
+export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
+export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
+export declare function makeLoc(first: string, base: {
+    uri: string;
+    baseUri?: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLocAlt(first: string, alt: string, base: {
+    uri: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLoc2(first: string, alt?: string): {
+    uri: string | undefined;
+    locationType: string;
+};
+export declare function resolve(uri: string, baseUri: string): string;