@jbrowse/plugin-data-management 2.3.1 → 2.3.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/ucsc-trackhub/model.js +11 -17
- package/dist/ucsc-trackhub/model.js.map +1 -1
- package/dist/ucsc-trackhub/ucscTrackHub.d.ts +23 -5
- package/dist/ucsc-trackhub/ucscTrackHub.js +90 -143
- package/dist/ucsc-trackhub/ucscTrackHub.js.map +1 -1
- package/esm/ucsc-trackhub/model.js +11 -17
- package/esm/ucsc-trackhub/model.js.map +1 -1
- package/esm/ucsc-trackhub/ucscTrackHub.d.ts +23 -5
- package/esm/ucsc-trackhub/ucscTrackHub.js +87 -143
- package/esm/ucsc-trackhub/ucscTrackHub.js.map +1 -1
- package/package.json +2 -2
- package/src/ucsc-trackhub/model.ts +15 -26
- package/src/ucsc-trackhub/ucscTrackHub.ts +326 -0
- package/src/ucsc-trackhub/ucscTrackHub.js +0 -442
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@@ -49,32 +49,26 @@ function UCSCTrackHubConnection(pluginManager) {
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if (!conf) {
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throw new Error(`Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`);
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}
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const
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if (!
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const db = genome.get('trackDb');
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if (!db) {
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throw new Error('genomesFile not found on hub');
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}
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const
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const base = new URL(genomeFile, hubUri);
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const trackDbLoc = hubUri
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? {
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uri: new URL(
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uri: new URL(db, base).href,
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locationType: 'UriLocation',
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}
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: {
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localPath:
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localPath: db,
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locationType: 'LocalPathLocation',
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};
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-
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-
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await (0, ucscTrackHub_1.fetchTrackDbFile)(trackDbFileLocation),
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genomeName,
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conf,
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]);
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const trackDb = await (0, ucscTrackHub_1.fetchTrackDbFile)(trackDbLoc);
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trackDbData.push([trackDbLoc, trackDb, genomeName, conf]);
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}
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for (const [
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const
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'adapter',
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]);
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self.addTrackConfs((0, ucscTrackHub_1.generateTracks)(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter));
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for (const [trackDbLoc, trackDbFile, genomeName, conf,] of trackDbData) {
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const seqAdapter = (0, configuration_1.readConfObject)(conf, ['sequence', 'adapter']);
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self.addTrackConfs((0, ucscTrackHub_1.generateTracks)(trackDbFile, trackDbLoc, genomeName, seqAdapter));
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}
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}
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catch (e) {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.ts"],"names":[],"mappings":";;;;;AACA,uEAAuF;AACvF,+DAIoC;AACpC,6CAA+C;AAC/C,qDAAuC;AAEvC,SAAS;AACT,kEAAyC;AACzC,iDAKuB;AAEvB,SAAwB,sBAAsB,CAAC,aAA4B;IACzE,OAAO,uBAAK;SACT,OAAO,CACN,wBAAwB,EACxB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,wBAAwB,CAAC;KAC9C,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,OAAO;YACX,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI;gBACF,MAAM,cAAc,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,MAAM,CAAC,CAAA;gBAC5C,MAAM,eAAe,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;gBACvD,MAAM,OAAO,GAAG,MAAM,IAAA,2BAAY,EAAC,eAAe,CAAC,CAAA;gBACnD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;gBAC7C,IAAI,CAAC,UAAU,EAAE;oBACf,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;iBAChD;gBAED,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAA;gBACpE,MAAM,mBAAmB,GAAG,MAAM;oBAChC,CAAC,CAAC;wBACE,GAAG,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,IAAI;wBACrC,YAAY,EAAE,
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{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.ts"],"names":[],"mappings":";;;;;AACA,uEAAuF;AACvF,+DAIoC;AACpC,6CAA+C;AAC/C,qDAAuC;AAEvC,SAAS;AACT,kEAAyC;AACzC,iDAKuB;AAEvB,SAAwB,sBAAsB,CAAC,aAA4B;IACzE,OAAO,uBAAK;SACT,OAAO,CACN,wBAAwB,EACxB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,wBAAwB,CAAC;KAC9C,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,OAAO;YACX,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI;gBACF,MAAM,cAAc,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,MAAM,CAAC,CAAA;gBAC5C,MAAM,eAAe,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;gBACvD,MAAM,OAAO,GAAG,MAAM,IAAA,2BAAY,EAAC,eAAe,CAAC,CAAA;gBACnD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;gBAC7C,IAAI,CAAC,UAAU,EAAE;oBACf,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;iBAChD;gBAED,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAA;gBACpE,MAAM,mBAAmB,GAAG,MAAM;oBAChC,CAAC,CAAC;wBACE,GAAG,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,IAAI;wBACrC,YAAY,EAAE,aAAsB;qBACrC;oBACH,CAAC,CAAC;wBACE,SAAS,EAAE,UAAU;wBACrB,YAAY,EAAE,mBAA4B;qBAC3C,CAAA;gBACL,MAAM,WAAW,GAAG,MAAM,IAAA,+BAAgB,EAAC,mBAAmB,CAAC,CAAA;gBAC/D,MAAM,WAAW,GAAG,EAAE,CAAA;gBACtB,KAAK,MAAM,CAAC,UAAU,EAAE,MAAM,CAAC,IAAI,WAAW,EAAE;oBAC9C,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,eAAe,CAAC,CAAA;oBACpD,IACE,aAAa,CAAC,MAAM,GAAG,CAAC;wBACxB,CAAC,aAAa,CAAC,QAAQ,CAAC,UAAU,CAAC,EACnC;wBACA,SAAQ;qBACT;oBACD,MAAM,IAAI,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAClC,CAAC,CAAC,EAAE,CAAC,IAAA,8BAAc,EAAC,CAAC,EAAE,MAAM,CAAC,KAAK,UAAU,CAC9C,CAAA;oBACD,IAAI,CAAC,IAAI,EAAE;wBACT,MAAM,IAAI,KAAK,CACb,6BAA6B,UAAU,2CAA2C,cAAc,GAAG,CACpG,CAAA;qBACF;oBACD,MAAM,EAAE,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;oBAChC,IAAI,CAAC,EAAE,EAAE;wBACP,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;qBAChD;oBACD,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAA;oBACxC,MAAM,UAAU,GAAG,MAAM;wBACvB,CAAC,CAAC;4BACE,GAAG,EAAE,IAAI,GAAG,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,IAAI;4BAC3B,YAAY,EAAE,aAAsB;yBACrC;wBACH,CAAC,CAAC;4BACE,SAAS,EAAE,EAAE;4BACb,YAAY,EAAE,mBAA4B;yBAC3C,CAAA;oBACL,MAAM,OAAO,GAAG,MAAM,IAAA,+BAAgB,EAAC,UAAU,CAAC,CAAA;oBAClD,WAAW,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,OAAO,EAAE,UAAU,EAAE,IAAI,CAAU,CAAC,CAAA;iBACnE;gBACD,KAAK,MAAM,CACT,UAAU,EACV,WAAW,EACX,UAAU,EACV,IAAI,EACL,IAAI,WAAW,EAAE;oBAChB,MAAM,UAAU,GAAG,IAAA,8BAAc,EAAC,IAAI,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC,CAAA;oBAChE,IAAI,CAAC,aAAa,CAChB,IAAA,6BAAc,EAAC,WAAW,EAAE,UAAU,EAAE,UAAU,EAAE,UAAU,CAAC,CAChE,CAAA;iBACF;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,MAAM,CACZ,yDAAyD,IAAI,CAAC,aAAa,CAAC,IAAI,6FAA6F,CAAC,GAAG,EACjL,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;aAC5C;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAxFD,yCAwFC"}
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@@ -1,6 +1,24 @@
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export function generateTracks(trackDb: any, trackDbFileLocation: any, assemblyName: any, sequenceAdapter: any): any[];
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import { TrackDbFile } from '@gmod/ucsc-hub';
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import { FileLocation } from '@jbrowse/core/util';
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import ucscAssemblies from './ucscAssemblies';
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export { ucscAssemblies };
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export declare function fetchHubFile(hubLocation: FileLocation): Promise<import("@gmod/ucsc-hub").HubFile>;
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export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<import("@gmod/ucsc-hub").GenomesFile>;
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export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
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export declare function makeLoc(first: string, base: {
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uri: string;
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}): {
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uri: string;
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locationType: string;
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};
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export declare function makeLocAlt(first: string, alt: string, base: {
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uri: string;
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}): {
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uri: string;
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locationType: string;
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};
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export declare function makeLoc2(first: string, alt?: string): {
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uri: string | undefined;
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locationType: string;
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};
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export declare function generateTracks(trackDb: TrackDbFile, trackDbLoc: FileLocation, assemblyName: string, sequenceAdapter: any): any;
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@@ -26,15 +26,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.generateTracks = exports.fetchTrackDbFile = exports.fetchGenomesFile = exports.fetchHubFile = exports.ucscAssemblies = void 0;
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exports.generateTracks = exports.makeLoc2 = exports.makeLocAlt = exports.makeLoc = exports.fetchTrackDbFile = exports.fetchGenomesFile = exports.fetchHubFile = exports.ucscAssemblies = void 0;
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const util_1 = require("@jbrowse/core/util");
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const io_1 = require("@jbrowse/core/util/io");
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const tracks_1 = require("@jbrowse/core/util/tracks");
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const ucscAssemblies_1 = __importDefault(require("./ucscAssemblies"));
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exports.ucscAssemblies = ucscAssemblies_1.default;
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async function fetchHubFile(
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async function fetchHubFile(hubLocation) {
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try {
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const hubFileText = await (0, io_1.openLocation)(
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const hubFileText = await (0, io_1.openLocation)(hubLocation).readFile('utf8');
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const { HubFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
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return new HubFile(hubFileText);
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}
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}
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}
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exports.fetchHubFile = fetchHubFile;
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async function fetchGenomesFile(
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const genomesFileText = await (0, io_1.openLocation)(
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async function fetchGenomesFile(genomesLoc) {
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const genomesFileText = await (0, io_1.openLocation)(genomesLoc).readFile('utf8');
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const { GenomesFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
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return new GenomesFile(genomesFileText);
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}
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exports.fetchGenomesFile = fetchGenomesFile;
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async function fetchTrackDbFile(
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const text = await (0, io_1.openLocation)(
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async function fetchTrackDbFile(trackDbLoc) {
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const text = await (0, io_1.openLocation)(trackDbLoc).readFile('utf8');
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const { TrackDbFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
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return new TrackDbFile(text);
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}
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exports.fetchTrackDbFile = fetchTrackDbFile;
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function
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function makeLoc(first, base) {
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return {
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uri: new URL(first, base.uri).href,
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locationType: 'UriLocation',
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};
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}
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exports.makeLoc = makeLoc;
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function makeLocAlt(first, alt, base) {
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return first ? makeLoc(first, base) : makeLoc(alt, base);
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}
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exports.makeLocAlt = makeLocAlt;
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function makeLoc2(first, alt) {
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return first
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? {
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uri: first,
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locationType: 'LocalPath',
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}
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: {
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uri: alt,
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locationType: 'UriLocation',
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};
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}
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exports.makeLoc2 = makeLoc2;
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function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapter) {
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const tracks = [];
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trackDb.forEach((track, trackName) => {
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var _a;
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const trackKeys = Array.from(track.keys());
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const parentTrackKeys = [
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'superTrack',
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const parentTracks = [];
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let currentTrackName = trackName;
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do {
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currentTrackName = trackDb.get(currentTrackName).get('parent');
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currentTrackName = ((_a = trackDb.get(currentTrackName)) === null || _a === void 0 ? void 0 : _a.get('parent')) || '';
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if (currentTrackName) {
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;
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[currentTrackName] = currentTrackName.split(' ');
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}
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} while (currentTrackName);
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parentTracks.reverse();
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const categories = parentTracks
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res
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tracks.push(
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const categories = parentTracks
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.map(p => p === null || p === void 0 ? void 0 : p.get('shortLabel'))
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.filter((f) => !!f);
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const res = makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter);
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tracks.push({
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...res,
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trackId: `ucsc-trackhub-${(0, util_1.objectHash)(res)}`,
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assemblyNames: [assemblyName],
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});
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});
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return tracks;
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}
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exports.generateTracks = generateTracks;
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function makeTrackConfig(track, categories,
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function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter) {
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var _a;
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let trackType = track.get('type');
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const name = track.get('shortLabel') || '';
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const bigDataUrl = track.get('bigDataUrl') || '';
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const bigDataIdx = track.get('bigDataIndex') || '';
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const isUri = (0, util_1.isUriLocation)(trackDbLoc);
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if (!trackType) {
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trackType = trackDb.get(track.get('parent')).get('type');
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trackType = (_a = trackDb.get(track.get('parent') || '')) === null || _a === void 0 ? void 0 : _a.get('type');
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}
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let baseTrackType = trackType.split(' ')[0];
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if (baseTrackType === 'bam' &&
|
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track.get('bigDataUrl').toLowerCase().endsWith('cram')) {
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let baseTrackType = (trackType === null || trackType === void 0 ? void 0 : trackType.split(' ')[0]) || '';
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if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
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uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
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};
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else {
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bigDataLocation = {
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locationType: 'LocalPathLocation',
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};
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}
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let bigDataIndexLocation;
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const bigDataLocation = isUri
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? makeLoc(bigDataUrl, trackDbLoc)
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: makeLoc2(bigDataUrl);
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switch (baseTrackType) {
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case 'bam':
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if (trackDbFileLocation.uri) {
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? {
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.href,
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locationType: 'UriLocation',
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}
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: {
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uri: new URL(`${track.get('bigDataUrl')}.bai`, trackDbFileLocation.uri).href,
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? {
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: {
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localPath: `${track.get('bigDataUrl')}.bai`,
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}
|
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return {
|
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type: 'AlignmentsTrack',
|
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name: track.get('shortLabel'),
|
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@@ -146,22 +144,16 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
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144
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type: 'BamAdapter',
|
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bamLocation: bigDataLocation,
|
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146
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index: {
|
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location:
|
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location: isUri
|
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? makeLocAlt(bigDataIdx, bigDataUrl + '.bai', trackDbLoc)
|
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: makeLoc2(bigDataIdx, bigDataUrl + '.bai'),
|
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150
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},
|
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151
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},
|
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152
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};
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case 'bed':
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return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
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case 'bed5FloatScore':
|
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return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
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|
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return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
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|
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return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
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153
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case 'bigBarChart':
|
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154
|
return {
|
|
163
155
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type: 'FeatureTrack',
|
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|
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name
|
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name,
|
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157
|
description: track.get('longLabel'),
|
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166
158
|
category: categories,
|
|
167
159
|
adapter: {
|
|
@@ -175,7 +167,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
175
167
|
case 'bigBed':
|
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176
168
|
return {
|
|
177
169
|
type: 'FeatureTrack',
|
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|
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name
|
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|
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name,
|
|
179
171
|
description: track.get('longLabel'),
|
|
180
172
|
category: categories,
|
|
181
173
|
adapter: {
|
|
@@ -186,7 +178,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
186
178
|
case 'bigGenePred':
|
|
187
179
|
return {
|
|
188
180
|
type: 'FeatureTrack',
|
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|
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name
|
|
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|
+
name,
|
|
190
182
|
description: track.get('longLabel'),
|
|
191
183
|
category: categories,
|
|
192
184
|
adapter: {
|
|
@@ -197,7 +189,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
197
189
|
case 'bigChain':
|
|
198
190
|
return {
|
|
199
191
|
type: 'FeatureTrack',
|
|
200
|
-
name
|
|
192
|
+
name,
|
|
201
193
|
description: track.get('longLabel'),
|
|
202
194
|
category: categories,
|
|
203
195
|
adapter: {
|
|
@@ -211,7 +203,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
211
203
|
case 'bigInteract':
|
|
212
204
|
return {
|
|
213
205
|
type: 'FeatureTrack',
|
|
214
|
-
name
|
|
206
|
+
name,
|
|
215
207
|
description: track.get('longLabel'),
|
|
216
208
|
category: categories,
|
|
217
209
|
adapter: {
|
|
@@ -225,7 +217,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
225
217
|
case 'bigMaf':
|
|
226
218
|
return {
|
|
227
219
|
type: 'FeatureTrack',
|
|
228
|
-
name
|
|
220
|
+
name,
|
|
229
221
|
description: track.get('longLabel'),
|
|
230
222
|
category: categories,
|
|
231
223
|
adapter: {
|
|
@@ -239,7 +231,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
239
231
|
case 'bigPsl':
|
|
240
232
|
return {
|
|
241
233
|
type: 'FeatureTrack',
|
|
242
|
-
name
|
|
234
|
+
name,
|
|
243
235
|
description: track.get('longLabel'),
|
|
244
236
|
category: categories,
|
|
245
237
|
adapter: {
|
|
@@ -253,7 +245,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
253
245
|
case 'bigWig':
|
|
254
246
|
return {
|
|
255
247
|
type: 'QuantitativeTrack',
|
|
256
|
-
name
|
|
248
|
+
name,
|
|
257
249
|
description: track.get('longLabel'),
|
|
258
250
|
category: categories,
|
|
259
251
|
adapter: {
|
|
@@ -261,56 +253,25 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
261
253
|
bigWigLocation: bigDataLocation,
|
|
262
254
|
},
|
|
263
255
|
};
|
|
264
|
-
case 'broadPeak':
|
|
265
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
|
266
|
-
case 'coloredExon':
|
|
267
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
|
268
256
|
case 'cram':
|
|
269
|
-
if (trackDbFileLocation.uri) {
|
|
270
|
-
bigDataIndexLocation = track.get('bigDataIndex')
|
|
271
|
-
? {
|
|
272
|
-
uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
|
|
273
|
-
.href,
|
|
274
|
-
locationType: 'UriLocation',
|
|
275
|
-
}
|
|
276
|
-
: {
|
|
277
|
-
uri: new URL(`${track.get('bigDataUrl')}.crai`, trackDbFileLocation.uri).href,
|
|
278
|
-
locationType: 'UriLocation',
|
|
279
|
-
};
|
|
280
|
-
}
|
|
281
|
-
else {
|
|
282
|
-
bigDataIndexLocation = track.get('bigDataIndex')
|
|
283
|
-
? {
|
|
284
|
-
localPath: track.get('bigDataIndex'),
|
|
285
|
-
locationType: 'LocalPathLocation',
|
|
286
|
-
}
|
|
287
|
-
: {
|
|
288
|
-
localPath: `${track.get('bigDataUrl')}.crai`,
|
|
289
|
-
locationType: 'LocalPathLocation',
|
|
290
|
-
};
|
|
291
|
-
}
|
|
292
257
|
return {
|
|
293
258
|
type: 'AlignmentsTrack',
|
|
294
|
-
name
|
|
259
|
+
name,
|
|
295
260
|
description: track.get('longLabel'),
|
|
296
261
|
category: categories,
|
|
297
262
|
adapter: {
|
|
298
263
|
type: 'CramAdapter',
|
|
299
264
|
cramLocation: bigDataLocation,
|
|
300
|
-
craiLocation:
|
|
265
|
+
craiLocation: isUri
|
|
266
|
+
? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
|
|
267
|
+
: makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
|
|
301
268
|
sequenceAdapter,
|
|
302
269
|
},
|
|
303
270
|
};
|
|
304
|
-
case 'gvf':
|
|
305
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
|
306
|
-
case 'ld2':
|
|
307
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
|
308
|
-
case 'narrowPeak':
|
|
309
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
|
310
271
|
case 'bigNarrowPeak':
|
|
311
272
|
return {
|
|
312
273
|
type: 'FeatureTrack',
|
|
313
|
-
name
|
|
274
|
+
name,
|
|
314
275
|
description: track.get('longLabel'),
|
|
315
276
|
category: categories,
|
|
316
277
|
adapter: {
|
|
@@ -319,52 +280,27 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
319
280
|
},
|
|
320
281
|
};
|
|
321
282
|
case 'peptideMapping':
|
|
322
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(
|
|
283
|
+
return (0, tracks_1.generateUnsupportedTrackConf)(name, baseTrackType, categories);
|
|
323
284
|
case 'vcfTabix':
|
|
324
|
-
if (trackDbFileLocation.uri) {
|
|
325
|
-
bigDataIndexLocation = track.get('bigDataIndex')
|
|
326
|
-
? {
|
|
327
|
-
uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
|
|
328
|
-
.href,
|
|
329
|
-
locationType: 'UriLocation',
|
|
330
|
-
}
|
|
331
|
-
: {
|
|
332
|
-
uri: new URL(`${track.get('bigDataUrl')}.tbi`, trackDbFileLocation.uri).href,
|
|
333
|
-
locationType: 'UriLocation',
|
|
334
|
-
};
|
|
335
|
-
}
|
|
336
|
-
else {
|
|
337
|
-
bigDataIndexLocation = track.get('bigDataIndex')
|
|
338
|
-
? {
|
|
339
|
-
localPath: track.get('bigDataIndex'),
|
|
340
|
-
locationType: 'LocalPathLocation',
|
|
341
|
-
}
|
|
342
|
-
: {
|
|
343
|
-
localPath: `${track.get('bigDataUrl')}.tbi`,
|
|
344
|
-
locationType: 'LocalPathLocation',
|
|
345
|
-
};
|
|
346
|
-
}
|
|
347
285
|
return {
|
|
348
286
|
type: 'VariantTrack',
|
|
349
|
-
name
|
|
287
|
+
name,
|
|
350
288
|
description: track.get('longLabel'),
|
|
351
289
|
category: categories,
|
|
352
290
|
adapter: {
|
|
353
291
|
type: 'VcfTabixAdapter',
|
|
354
292
|
vcfGzLocation: bigDataLocation,
|
|
355
293
|
index: {
|
|
356
|
-
location:
|
|
294
|
+
location: isUri
|
|
295
|
+
? makeLocAlt(bigDataIdx, bigDataUrl + '.tbi', trackDbLoc)
|
|
296
|
+
: makeLoc2(bigDataIdx, bigDataUrl + '.tbi'),
|
|
357
297
|
},
|
|
358
298
|
},
|
|
359
299
|
};
|
|
360
|
-
case 'wig':
|
|
361
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
|
362
|
-
case 'wigMaf':
|
|
363
|
-
return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
|
|
364
300
|
case 'hic':
|
|
365
301
|
return {
|
|
366
302
|
type: 'HicTrack',
|
|
367
|
-
name
|
|
303
|
+
name,
|
|
368
304
|
description: track.get('longLabel'),
|
|
369
305
|
category: categories,
|
|
370
306
|
adapter: {
|
|
@@ -372,10 +308,21 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
|
|
|
372
308
|
hicLocation: bigDataLocation,
|
|
373
309
|
},
|
|
374
310
|
};
|
|
375
|
-
|
|
376
|
-
|
|
311
|
+
// unsupported types
|
|
312
|
+
// case 'gvf':
|
|
313
|
+
// case 'ld2':
|
|
314
|
+
// case 'narrowPeak':
|
|
315
|
+
// case 'wig':
|
|
316
|
+
// case 'wigMaf':
|
|
317
|
+
// case 'halSnake':
|
|
318
|
+
// case 'bed':
|
|
319
|
+
// case 'bed5FloatScore':
|
|
320
|
+
// case 'bedGraph':
|
|
321
|
+
// case 'bedRnaElements':
|
|
322
|
+
// case 'broadPeak':
|
|
323
|
+
// case 'coloredExon':
|
|
377
324
|
default:
|
|
378
|
-
return (0, tracks_1.generateUnknownTrackConf)(
|
|
325
|
+
return (0, tracks_1.generateUnknownTrackConf)(name, baseTrackType, categories);
|
|
379
326
|
}
|
|
380
327
|
}
|
|
381
328
|
//# sourceMappingURL=ucscTrackHub.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ucscTrackHub.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscTrackHub.
|
|
1
|
+
{"version":3,"file":"ucscTrackHub.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscTrackHub.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAEA,6CAA4E;AAC5E,8CAAoD;AACpD,sDAGkC;AAClC,sEAA6C;AAEpC,yBAFF,wBAAc,CAEE;AAEhB,KAAK,UAAU,YAAY,CAAC,WAAyB;IAC1D,IAAI;QACF,MAAM,WAAW,GAAG,MAAM,IAAA,iBAAY,EAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,EAAE,OAAO,EAAE,GAAG,wDAAa,gBAAgB,GAAC,CAAA;QAClD,OAAO,IAAI,OAAO,CAAC,WAAW,CAAC,CAAA;KAChC;IAAC,OAAO,KAAK,EAAE;QACd,MAAM,IAAI,KAAK,CAAC,yCAAyC,KAAK,GAAG,CAAC,CAAA;KACnE;AACH,CAAC;AARD,oCAQC;AAEM,KAAK,UAAU,gBAAgB,CAAC,UAAwB;IAC7D,MAAM,eAAe,GAAG,MAAM,IAAA,iBAAY,EAAC,UAAU,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACvE,MAAM,EAAE,WAAW,EAAE,GAAG,wDAAa,gBAAgB,GAAC,CAAA;IACtD,OAAO,IAAI,WAAW,CAAC,eAAe,CAAC,CAAA;AACzC,CAAC;AAJD,4CAIC;AAEM,KAAK,UAAU,gBAAgB,CAAC,UAAwB;IAC7D,MAAM,IAAI,GAAG,MAAM,IAAA,iBAAY,EAAC,UAAU,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5D,MAAM,EAAE,WAAW,EAAE,GAAG,wDAAa,gBAAgB,GAAC,CAAA;IACtD,OAAO,IAAI,WAAW,CAAC,IAAI,CAAC,CAAA;AAC9B,CAAC;AAJD,4CAIC;AAED,SAAgB,OAAO,CAAC,KAAa,EAAE,IAAqB;IAC1D,OAAO;QACL,GAAG,EAAE,IAAI,GAAG,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI;QAClC,YAAY,EAAE,aAAa;KAC5B,CAAA;AACH,CAAC;AALD,0BAKC;AAED,SAAgB,UAAU,CAAC,KAAa,EAAE,GAAW,EAAE,IAAqB;IAC1E,OAAO,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;AAC1D,CAAC;AAFD,gCAEC;AAED,SAAgB,QAAQ,CAAC,KAAa,EAAE,GAAY;IAClD,OAAO,KAAK;QACV,CAAC,CAAC;YACE,GAAG,EAAE,KAAK;YACV,YAAY,EAAE,WAAW;SAC1B;QACH,CAAC,CAAC;YACE,GAAG,EAAE,GAAG;YACR,YAAY,EAAE,aAAa;SAC5B,CAAA;AACP,CAAC;AAVD,4BAUC;AAED,SAAgB,cAAc,CAC5B,OAAoB,EACpB,UAAwB,EACxB,YAAoB,EACpB,eAAoB;IAEpB,MAAM,MAAM,GAAQ,EAAE,CAAA;IAEtB,OAAO,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,SAAS,EAAE,EAAE;;QACnC,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAa,CAAA;QACtD,MAAM,eAAe,GAAG;YACtB,YAAY;YACZ,gBAAgB;YAChB,WAAW;YACX,MAAM;SACP,CAAA;QACD,IAAI,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE;YACxD,OAAM;SACP;QACD,MAAM,YAAY,GAAG,EAAE,CAAA;QACvB,IAAI,gBAAgB,GAAG,SAAS,CAAA;QAChC,GAAG;YACD,gBAAgB,GAAG,CAAA,MAAA,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,0CAAE,GAAG,CAAC,QAAQ,CAAC,KAAI,EAAE,CAAA;YACrE,IAAI,gBAAgB,EAAE;gBACpB,CAAC;gBAAA,CAAC,gBAAgB,CAAC,GAAG,gBAAgB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBACjD,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAC,CAAA;aACjD;SACF,QAAQ,gBAAgB,EAAC;QAC1B,YAAY,CAAC,OAAO,EAAE,CAAA;QACtB,MAAM,UAAU,GAAG,YAAY;aAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,GAAG,CAAC,YAAY,CAAC,CAAC;aAC9B,MAAM,CAAC,CAAC,CAAC,EAAe,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAClC,MAAM,GAAG,GAAG,eAAe,CACzB,KAAK,EACL,UAAU,EACV,UAAU,EACV,OAAO,EACP,eAAe,CAChB,CAAA;QACD,MAAM,CAAC,IAAI,CAAC;YACV,GAAG,GAAG;YACN,OAAO,EAAE,iBAAiB,IAAA,iBAAU,EAAC,GAAG,CAAC,EAAE;YAC3C,aAAa,EAAE,CAAC,YAAY,CAAC;SAC9B,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,OAAO,MAAM,CAAA;AACf,CAAC;AA/CD,wCA+CC;AAED,SAAS,eAAe,CACtB,KAAe,EACf,UAAoB,EACpB,UAAwB,EACxB,OAAoB,EACpB,eAAoB;;IAEpB,IAAI,SAAS,GAAG,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,CAAA;IAC1C,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,CAAA;IAChD,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,cAAc,CAAC,IAAI,EAAE,CAAA;IAClD,MAAM,KAAK,GAAG,IAAA,oBAAa,EAAC,UAAU,CAAC,CAAA;IACvC,IAAI,CAAC,SAAS,EAAE;QACd,SAAS,GAAG,MAAA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,0CAAE,GAAG,CAAC,MAAM,CAAC,CAAA;KAChE;IACD,IAAI,aAAa,GAAG,CAAA,SAAS,aAAT,SAAS,uBAAT,SAAS,CAAE,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,KAAI,EAAE,CAAA;IAClD,IAAI,aAAa,KAAK,KAAK,IAAI,UAAU,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;QACxE,aAAa,GAAG,MAAM,CAAA;KACvB;IACD,MAAM,eAAe,GAAG,KAAK;QAC3B,CAAC,CAAC,OAAO,CAAC,UAAU,EAAE,UAAU,CAAC;QACjC,CAAC,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAA;IAExB,QAAQ,aAAa,EAAE;QACrB,KAAK,KAAK;YACR,OAAO;gBACL,IAAI,EAAE,iBAAiB;gBACvB,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC;gBAC7B,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,YAAY;oBAClB,WAAW,EAAE,eAAe;oBAC5B,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK;4BACb,CAAC,CAAC,UAAU,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,EAAE,UAAU,CAAC;4BACzD,CAAC,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,CAAC;qBAC9C;iBACF;aACF,CAAA;QAEH,KAAK,aAAa;YAChB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,EAAE;oBACR,IAAI,EAAE,oBAAoB;iBAC3B;aACF,CAAA;QACH,KAAK,QAAQ;YACX,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QACH,KAAK,aAAa;YAChB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QACH,KAAK,UAAU;YACb,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,E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|
|
@@ -44,32 +44,26 @@ export default function UCSCTrackHubConnection(pluginManager) {
|
|
|
44
44
|
if (!conf) {
|
|
45
45
|
throw new Error(`Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`);
|
|
46
46
|
}
|
|
47
|
-
const
|
|
48
|
-
if (!
|
|
47
|
+
const db = genome.get('trackDb');
|
|
48
|
+
if (!db) {
|
|
49
49
|
throw new Error('genomesFile not found on hub');
|
|
50
50
|
}
|
|
51
|
-
const
|
|
51
|
+
const base = new URL(genomeFile, hubUri);
|
|
52
|
+
const trackDbLoc = hubUri
|
|
52
53
|
? {
|
|
53
|
-
uri: new URL(
|
|
54
|
+
uri: new URL(db, base).href,
|
|
54
55
|
locationType: 'UriLocation',
|
|
55
56
|
}
|
|
56
57
|
: {
|
|
57
|
-
localPath:
|
|
58
|
+
localPath: db,
|
|
58
59
|
locationType: 'LocalPathLocation',
|
|
59
60
|
};
|
|
60
|
-
|
|
61
|
-
|
|
62
|
-
await fetchTrackDbFile(trackDbFileLocation),
|
|
63
|
-
genomeName,
|
|
64
|
-
conf,
|
|
65
|
-
]);
|
|
61
|
+
const trackDb = await fetchTrackDbFile(trackDbLoc);
|
|
62
|
+
trackDbData.push([trackDbLoc, trackDb, genomeName, conf]);
|
|
66
63
|
}
|
|
67
|
-
for (const [
|
|
68
|
-
const
|
|
69
|
-
|
|
70
|
-
'adapter',
|
|
71
|
-
]);
|
|
72
|
-
self.addTrackConfs(generateTracks(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter));
|
|
64
|
+
for (const [trackDbLoc, trackDbFile, genomeName, conf,] of trackDbData) {
|
|
65
|
+
const seqAdapter = readConfObject(conf, ['sequence', 'adapter']);
|
|
66
|
+
self.addTrackConfs(generateTracks(trackDbFile, trackDbLoc, genomeName, seqAdapter));
|
|
73
67
|
}
|
|
74
68
|
}
|
|
75
69
|
catch (e) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,0BAA0B,EAAE,MAAM,4CAA4C,CAAA;AACvF,OAAO,EACL,sBAAsB,EACtB,cAAc,EACd,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EACL,gBAAgB,EAChB,YAAY,EACZ,gBAAgB,EAChB,cAAc,GACf,MAAM,gBAAgB,CAAA;AAEvB,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAAC,aAA4B;IACzE,OAAO,KAAK;SACT,OAAO,CACN,wBAAwB,EACxB,0BAA0B,CAAC,aAAa,CAAC,EACzC,KAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,wBAAwB,CAAC;KAC9C,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,OAAO;YACX,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI;gBACF,MAAM,cAAc,GAAG,OAAO,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;gBAC5C,MAAM,eAAe,GAAG,OAAO,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;gBACvD,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,eAAe,CAAC,CAAA;gBACnD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;gBAC7C,IAAI,CAAC,UAAU,EAAE;oBACf,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;iBAChD;gBAED,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAA;gBACpE,MAAM,mBAAmB,GAAG,MAAM;oBAChC,CAAC,CAAC;wBACE,GAAG,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,IAAI;wBACrC,YAAY,EAAE,
|
|
1
|
+
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@@ -1,6 +1,24 @@
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export function generateTracks(trackDb: any, trackDbFileLocation: any, assemblyName: any, sequenceAdapter: any): any[];
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import { TrackDbFile } from '@gmod/ucsc-hub';
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import { FileLocation } from '@jbrowse/core/util';
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import ucscAssemblies from './ucscAssemblies';
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4
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export { ucscAssemblies };
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-
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export declare function fetchHubFile(hubLocation: FileLocation): Promise<import("@gmod/ucsc-hub").HubFile>;
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+
export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<import("@gmod/ucsc-hub").GenomesFile>;
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export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
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8
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export declare function makeLoc(first: string, base: {
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uri: string;
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}): {
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uri: string;
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locationType: string;
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};
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export declare function makeLocAlt(first: string, alt: string, base: {
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uri: string;
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16
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}): {
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uri: string;
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locationType: string;
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};
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export declare function makeLoc2(first: string, alt?: string): {
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uri: string | undefined;
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locationType: string;
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};
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24
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export declare function generateTracks(trackDb: TrackDbFile, trackDbLoc: FileLocation, assemblyName: string, sequenceAdapter: any): any;
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