@jbrowse/plugin-data-management 3.0.1 → 3.0.2
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/UCSCTrackHub/doConnect.js +10 -1
- package/dist/UCSCTrackHub/ucscTrackHub.d.ts +7 -21
- package/dist/UCSCTrackHub/ucscTrackHub.js +6 -8
- package/esm/UCSCTrackHub/doConnect.js +11 -2
- package/esm/UCSCTrackHub/ucscTrackHub.d.ts +7 -21
- package/esm/UCSCTrackHub/ucscTrackHub.js +6 -8
- package/package.json +5 -5
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@@ -10,6 +10,7 @@ const ucscTrackHub_1 = require("./ucscTrackHub");
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const util_2 = require("./util");
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async function doConnect(self) {
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var _a;
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const { pluginManager } = (0, util_1.getEnv)(self);
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const session = (0, util_1.getSession)(self);
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const notLoadedAssemblies = [];
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try {
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@@ -21,14 +22,16 @@ async function doConnect(self) {
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const hub = new ucsc_hub_1.SingleFileHub(hubFileText);
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const { genome, tracks } = hub;
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const genomeName = genome.name;
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const shortLabel = genome.data.description;
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const asm = assemblyManager.get(genomeName);
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if (!asm) {
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session.addSessionAssembly({
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name: genomeName,
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displayName: shortLabel,
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sequence: {
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type: 'ReferenceSequenceTrack',
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metadata: {
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-
...genome,
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...genome.data,
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...(genome.data.htmlPath
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? {
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htmlPath: `<a href="${(0, util_2.resolve)(genome.data.htmlPath, hubUri)}">${genome.data.htmlPath}</a>`,
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@@ -58,6 +61,12 @@ async function doConnect(self) {
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baseUrl: hubUri,
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});
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self.addTrackConfs(tracksNew);
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pluginManager.evaluateExtensionPoint('LaunchView-LinearGenomeView', {
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session,
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assembly: genomeName,
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tracklist: true,
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loc: genome.data.defaultPos,
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});
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}
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else {
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const hubFile = new ucsc_hub_1.HubFile(hubFileText);
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@@ -14,9 +14,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
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description: string;
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category: string[] | undefined;
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metadata: {
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-
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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} | {
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trackId: string;
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@@ -45,9 +43,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
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hicLocation?: undefined;
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};
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metadata: {
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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} | {
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hicLocation?: undefined;
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};
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metadata: {
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-
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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} | {
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@@ -102,9 +96,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
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hicLocation?: undefined;
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};
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metadata: {
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-
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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} | {
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@@ -129,9 +121,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
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hicLocation?: undefined;
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};
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metadata: {
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-
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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} | {
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@@ -161,9 +151,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
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hicLocation?: undefined;
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};
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metadata: {
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-
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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} | {
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@@ -188,9 +176,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
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vcfGzLocation?: undefined;
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};
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metadata: {
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-
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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})[];
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@@ -35,14 +35,12 @@ function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, ba
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parentTracks.reverse();
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return {
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metadata: {
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: {}),
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},
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...track.data,
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...(track.data.html
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? {
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html: `<a href="${(0, util_2.resolve)(track.data.html, baseUrl)}">${track.data.html}</a>`,
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}
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: {}),
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},
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category: [
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track.data.group,
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@@ -1,12 +1,13 @@
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import { HubFile, SingleFileHub } from '@gmod/ucsc-hub';
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import { getConf } from '@jbrowse/core/configuration';
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import { getSession } from '@jbrowse/core/util';
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import { getEnv, getSession } from '@jbrowse/core/util';
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import { openLocation } from '@jbrowse/core/util/io';
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import { nanoid } from '@jbrowse/core/util/nanoid';
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import { generateTracks } from './ucscTrackHub';
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import { fetchGenomesFile, fetchTrackDbFile, resolve } from './util';
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export async function doConnect(self) {
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var _a;
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const { pluginManager } = getEnv(self);
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const session = getSession(self);
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const notLoadedAssemblies = [];
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try {
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@@ -18,14 +19,16 @@ export async function doConnect(self) {
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const hub = new SingleFileHub(hubFileText);
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const { genome, tracks } = hub;
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const genomeName = genome.name;
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const shortLabel = genome.data.description;
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const asm = assemblyManager.get(genomeName);
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if (!asm) {
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session.addSessionAssembly({
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name: genomeName,
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displayName: shortLabel,
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sequence: {
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type: 'ReferenceSequenceTrack',
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metadata: {
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-
...genome,
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...genome.data,
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...(genome.data.htmlPath
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? {
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htmlPath: `<a href="${resolve(genome.data.htmlPath, hubUri)}">${genome.data.htmlPath}</a>`,
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@@ -55,6 +58,12 @@ export async function doConnect(self) {
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baseUrl: hubUri,
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});
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self.addTrackConfs(tracksNew);
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pluginManager.evaluateExtensionPoint('LaunchView-LinearGenomeView', {
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session,
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assembly: genomeName,
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tracklist: true,
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loc: genome.data.defaultPos,
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});
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}
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else {
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const hubFile = new HubFile(hubFileText);
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description: string;
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category: string[] | undefined;
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metadata: {
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html?: string | undefined;
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html?: string | undefined;
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};
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} | {
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trackId: string;
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hicLocation?: undefined;
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};
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metadata: {
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html?: string | undefined;
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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} | {
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hicLocation?: undefined;
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};
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metadata: {
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};
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category: (string | undefined)[];
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} | {
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hicLocation?: undefined;
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};
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metadata: {
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};
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} | {
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hicLocation?: undefined;
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};
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metadata: {
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};
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category: (string | undefined)[];
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} | {
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hicLocation?: undefined;
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};
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metadata: {
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};
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html?: string | undefined;
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};
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category: (string | undefined)[];
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} | {
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vcfGzLocation?: undefined;
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};
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metadata: {
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};
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})[];
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parentTracks.reverse();
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return {
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metadata: {
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: {}),
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...track.data,
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...(track.data.html
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? {
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html: `<a href="${resolve(track.data.html, baseUrl)}">${track.data.html}</a>`,
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}
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: {}),
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},
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category: [
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track.data.group,
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package/package.json
CHANGED
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{
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"name": "@jbrowse/plugin-data-management",
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"version": "3.0.
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"version": "3.0.2",
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"description": "JBrowse 2 linear genome view",
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"keywords": [
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"jbrowse",
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},
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"dependencies": {
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"@gmod/ucsc-hub": "^1.0.0",
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"@jbrowse/core": "^3.0.
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"@jbrowse/plugin-config": "^3.0.
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"@jbrowse/product-core": "^3.0.
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"@jbrowse/core": "^3.0.2",
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"@jbrowse/plugin-config": "^3.0.2",
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"@jbrowse/product-core": "^3.0.2",
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"@mui/icons-material": "^6.0.0",
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"@mui/material": "^6.0.0",
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"@mui/x-data-grid": "^7.0.0",
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"distModule": "esm/index.js",
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"srcModule": "src/index.ts",
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"module": "esm/index.js",
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"gitHead": "
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"gitHead": "c01a35edcb2612e94661af8793f09c95c0b13c75"
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}
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