@jbrowse/core 2.13.1 → 2.15.0

package/PluginManager.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-unsafe-function-type */
 const mobx_state_tree_1 = require("mobx-state-tree");
 const RendererType_1 = __importDefault(require("./pluggableElementTypes/renderers/RendererType"));
 const AdapterType_1 = __importDefault(require("./pluggableElementTypes/AdapterType"));
@@ -105,6 +106,7 @@ class PluginManager {
         this.jbrequire = (lib) => {
             if (typeof lib === 'string') {
                 const pack = this.lib[lib];
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 if (!pack) {
                     throw new TypeError(`No jbrequire re-export defined for package '${lib}'. If this package must be shared between plugins, add it to ReExports.js. If it does not need to be shared, just import it normally.`);
                 }
@@ -113,6 +115,7 @@ class PluginManager {
             if (typeof lib === 'function') {
                 return this.load(lib);
             }
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             if (lib.default) {
                 return this.jbrequire(lib.default);
             }
@@ -170,7 +173,7 @@ class PluginManager {
         // see elementCreationSchedule above for the creation order
         if (this.elementCreationSchedule) {
             this.elementCreationSchedule.run();
-            delete this.elementCreationSchedule;
+            this.elementCreationSchedule = undefined;
         }
         return this;
     }
@@ -181,7 +184,9 @@ class PluginManager {
         if (this.configured) {
             throw new Error('already configured');
         }
-        this.plugins.forEach(plugin => plugin.configure(this));
+        this.plugins.forEach(plugin => {
+            plugin.configure(this);
+        });
         this.configured = true;
         return this;
     }

package/ReExports/modules.js

@@ -178,24 +178,22 @@ const Entries = {
     Typography: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Typography')))),
 };
 const LazyMUICore = Object.fromEntries(Object.entries(Entries).map(([key, ReactComponent]) => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
         react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
     Component.displayName = key;
     return [key, Component];
 }));
 const MaterialPrefixMUI = Object.fromEntries(Object.entries(LazyMUICore).map(([key, value]) => [
-    '@material-ui/core/' + key,
+    `@material-ui/core/${key}`,
     value,
 ]));
 const MuiPrefixMUI = Object.fromEntries(Object.entries(LazyMUICore).map(([key, value]) => [
-    '@mui/material/' + key,
+    `@mui/material/${key}`,
     value,
 ]));
 const Attributes = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./Attributes'))));
 const FeatureDetails = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./FeatureDetails'))));
 const BaseCard = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BaseCard'))));
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 const DataGridEntries = {
     DataGrid: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({ default: module.DataGrid }))),
     GridActionsCellItem: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
@@ -348,21 +346,17 @@ const DataGridEntries = {
     }))),
 };
 const LazyDataGridComponents = Object.fromEntries(Object.entries(DataGridEntries).map(([key, ReactComponent]) => {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
         react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
     Component.displayName = key;
     return [key, Component];
 }));
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 const LazyAttributes = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
     react_1.default.createElement(Attributes, { ...props, ref: ref }))));
 LazyAttributes.displayName = 'Attributes';
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 const LazyFeatureDetails = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
     react_1.default.createElement(FeatureDetails, { ...props, ref: ref }))));
 LazyFeatureDetails.displayName = 'FeatureDetails';
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 const LazyBaseCard = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
     react_1.default.createElement(BaseCard, { ...props, ref: ref }))));
 LazyBaseCard.displayName = 'BaseCard';
@@ -387,7 +381,6 @@ const libs = {
         ...LazyMUICore,
         useTheme: material_1.useTheme,
         alpha: MUIStyles.alpha,
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         makeStyles: (args) => {
             const useStyles = (0, mui_1.makeStyles)()(args);
             return () => useStyles().classes;
@@ -402,7 +395,6 @@ const libs = {
     // material-ui subcomponents, should get rid of these
     '@mui/material/styles': {
         MUIStyles,
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         makeStyles: (args) => {
             const useStyles = (0, mui_1.makeStyles)()(args);
             return () => useStyles().classes;
@@ -410,7 +402,6 @@ const libs = {
     },
     '@material-ui/core/styles': {
         MUIStyles,
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         makeStyles: (args) => {
             const useStyles = (0, mui_1.makeStyles)()(args);
             return () => useStyles().classes;

package/assemblyManager/assembly.d.ts

@@ -4,7 +4,7 @@ import PluginManager from '../PluginManager';
 import { Region, Feature } from '../util';
 import RpcManager from '../rpc/RpcManager';
 type AdapterConf = Record<string, unknown>;
-type RefNameAliases = Record<string, string | undefined>;
+type RefNameAliases = Record<string, string>;
 export interface RefNameMap {
     forwardMap: RefNameAliases;
     reverseMap: RefNameAliases;
@@ -15,29 +15,31 @@ export interface BasicRegion {
     refName: string;
     assemblyName: string;
 }
-export interface Loading {
-    adapterRegionsWithAssembly: Region[];
-    refNameAliases: RefNameAliases;
-    lowerCaseRefNameAliases: RefNameAliases;
-    cytobands: Feature[];
-}
 /**
  * #stateModel Assembly
  */
-export default function assemblyFactory(assemblyConfigType: IAnyType, pm: PluginManager): import("mobx-state-tree").IModelType<{
+export default function assemblyFactory(assemblyConfigType: IAnyType, pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     /**
      * #property
      */
     configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
 }, {
     error: unknown;
-    loaded: boolean;
     loadingP: Promise<void> | undefined;
     volatileRegions: BasicRegion[] | undefined;
     refNameAliases: RefNameAliases | undefined;
-    lowerCaseRefNameAliases: RefNameAliases | undefined;
     cytobands: Feature[] | undefined;
 } & {
+    /**
+     * #getter
+     */
+    readonly lowerCaseRefNameAliases: {
+        [k: string]: string;
+    } | undefined;
+} & {
+    /**
+     * #method
+     */
     getConf(arg: string): any;
 } & {
     /**
@@ -113,7 +115,11 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pm: Plugin
     /**
      * #action
      */
-    setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: Loading): void;
+    setLoaded({ regions, refNameAliases, cytobands, }: {
+        regions: Region[];
+        refNameAliases: RefNameAliases;
+        cytobands: Feature[];
+    }): void;
     /**
      * #action
      */
@@ -125,7 +131,7 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pm: Plugin
     /**
      * #action
      */
-    setRefNameAliases(aliases: RefNameAliases, lcAliases: RefNameAliases): void;
+    setRefNameAliases(aliases: RefNameAliases): void;
     /**
      * #action
      */

package/assemblyManager/assembly.js

@@ -11,6 +11,7 @@ const configuration_1 = require("../configuration");
 const util_1 = require("../util");
 const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
 const dataAdapterCache_1 = require("../data_adapters/dataAdapterCache");
+/* biome-ignore lint/complexity/useRegexLiterals: */
 const refNameRegex = new RegExp('[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*');
 // Based on the UCSC Genome Browser chromosome color palette:
 // https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h
@@ -63,14 +64,12 @@ async function loadRefNameMap(assembly, adapterConfig, options, signal) {
         checkRefName(name);
         return [assembly.getCanonicalRefName(name), name];
     }));
-    // make the reversed map too
-    const reversed = Object.fromEntries(Object.entries(refNameMap).map(([canonicalName, adapterName]) => [
-        adapterName,
-        canonicalName,
-    ]));
     return {
         forwardMap: refNameMap,
-        reverseMap: reversed,
+        reverseMap: Object.fromEntries(Object.entries(refNameMap).map(([canonicalName, adapterName]) => [
+            adapterName,
+            canonicalName,
+        ])),
     };
 }
 // Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
@@ -82,7 +81,7 @@ function checkRefName(refName) {
 /**
  * #stateModel Assembly
  */
-function assemblyFactory(assemblyConfigType, pm) {
+function assemblyFactory(assemblyConfigType, pluginManager) {
     const adapterLoads = new abortable_promise_cache_1.default({
         cache: new QuickLRU_1.default({ maxSize: 1000 }),
         // @ts-expect-error
@@ -100,14 +99,28 @@ function assemblyFactory(assemblyConfigType, pm) {
     })
         .volatile(() => ({
         error: undefined,
-        loaded: false,
         loadingP: undefined,
         volatileRegions: undefined,
         refNameAliases: undefined,
-        lowerCaseRefNameAliases: undefined,
         cytobands: undefined,
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
+        get lowerCaseRefNameAliases() {
+            return self.refNameAliases
+                ? Object.fromEntries(Object.entries(self.refNameAliases).map(([key, val]) => [
+                    key.toLowerCase(),
+                    val,
+                ]))
+                : undefined;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         */
         getConf(arg) {
             return self.configuration ? (0, configuration_1.getConf)(self, arg) : undefined;
         },
@@ -176,7 +189,7 @@ function assemblyFactory(assemblyConfigType, pm) {
         get lowerCaseRefNames() {
             return !self.lowerCaseRefNameAliases
                 ? undefined
-                : Object.keys(self.lowerCaseRefNameAliases || {});
+                : Object.keys(self.lowerCaseRefNameAliases);
         },
         /**
          * #getter
@@ -190,7 +203,6 @@ function assemblyFactory(assemblyConfigType, pm) {
          * #getter
          */
         get rpcManager() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             return (0, mobx_state_tree_1.getParent)(self, 2).rpcManager;
         },
         /**
@@ -228,10 +240,9 @@ function assemblyFactory(assemblyConfigType, pm) {
                 return undefined;
             }
             const idx = self.refNames.indexOf(refName);
-            if (idx === -1) {
-                return undefined;
-            }
-            return self.refNameColors[idx % self.refNameColors.length];
+            return idx === -1
+                ? undefined
+                : self.refNameColors[idx % self.refNameColors.length];
         },
         /**
          * #method
@@ -247,17 +258,15 @@ function assemblyFactory(assemblyConfigType, pm) {
         /**
          * #action
          */
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }) {
-            self.loaded = true;
-            this.setRegions(adapterRegionsWithAssembly);
-            this.setRefNameAliases(refNameAliases, lowerCaseRefNameAliases);
+        setLoaded({ regions, refNameAliases, cytobands, }) {
+            this.setRegions(regions);
+            this.setRefNameAliases(refNameAliases);
             this.setCytobands(cytobands);
         },
         /**
          * #action
          */
         setError(e) {
-            console.error(e);
             self.error = e;
         },
         /**
@@ -269,9 +278,8 @@ function assemblyFactory(assemblyConfigType, pm) {
         /**
          * #action
          */
-        setRefNameAliases(aliases, lcAliases) {
+        setRefNameAliases(aliases) {
             self.refNameAliases = aliases;
-            self.lowerCaseRefNameAliases = lcAliases;
         },
         /**
          * #action
@@ -290,7 +298,7 @@ function assemblyFactory(assemblyConfigType, pm) {
          */
         load() {
             if (!self.loadingP) {
-                self.loadingP = this.loadPre().catch(e => {
+                self.loadingP = this.loadPre().catch((e) => {
                     this.setLoadingP(undefined);
                     this.setError(e);
                 });
@@ -302,38 +310,53 @@ function assemblyFactory(assemblyConfigType, pm) {
          */
         async loadPre() {
             var _a, _b;
+            var _c;
             const conf = self.configuration;
             const refNameAliasesAdapterConf = (_a = conf === null || conf === void 0 ? void 0 : conf.refNameAliases) === null || _a === void 0 ? void 0 : _a.adapter;
             const cytobandAdapterConf = (_b = conf === null || conf === void 0 ? void 0 : conf.cytobands) === null || _b === void 0 ? void 0 : _b.adapter;
             const sequenceAdapterConf = conf === null || conf === void 0 ? void 0 : conf.sequence.adapter;
             const assemblyName = self.name;
-            const regions = await getAssemblyRegions(sequenceAdapterConf, pm);
+            const regions = await getAssemblyRegions({
+                config: sequenceAdapterConf,
+                pluginManager,
+            });
             const adapterRegionsWithAssembly = regions.map(r => {
                 checkRefName(r.refName);
                 return { ...r, assemblyName };
             });
             const refNameAliases = {};
-            const ret = await getRefNameAliases(refNameAliasesAdapterConf, pm);
-            const cytobands = await getCytobands(cytobandAdapterConf, pm);
-            ret.forEach(({ refName, aliases }) => {
-                aliases.forEach(a => {
-                    checkRefName(a);
-                    refNameAliases[a] = refName;
-                });
+            const refNameAliasCollection = await getRefNameAliases({
+                config: refNameAliasesAdapterConf,
+                pluginManager,
             });
+            for (const { refName, aliases, override } of refNameAliasCollection) {
+                for (const alias of aliases) {
+                    checkRefName(alias);
+                    refNameAliases[alias] = refName;
+                }
+                // the override field is supplied by a RefNameAliasAdapter to make
+                // the refName field returned by the adapter to be used as the
+                // primary names for this assembly
+                if (override) {
+                    refNameAliases[refName] = refName;
+                }
+            }
             // add identity to the refNameAliases list
-            adapterRegionsWithAssembly.forEach(region => {
-                refNameAliases[region.refName] = region.refName;
-            });
-            const lowerCaseRefNameAliases = Object.fromEntries(Object.entries(refNameAliases).map(([key, val]) => [
-                key.toLowerCase(),
-                val,
-            ]));
+            for (const region of adapterRegionsWithAssembly) {
+                // this ||= means that if the refNameAliasAdapter already set a
+                // mapping for the primary region to be an alias
+                refNameAliases[_c = region.refName] || (refNameAliases[_c] = region.refName);
+            }
             this.setLoaded({
-                adapterRegionsWithAssembly,
                 refNameAliases,
-                lowerCaseRefNameAliases,
-                cytobands,
+                regions: adapterRegionsWithAssembly.map(r => ({
+                    ...r,
+                    refName: refNameAliases[r.refName] || r.refName,
+                })),
+                cytobands: await getCytobands({
+                    config: cytobandAdapterConf,
+                    pluginManager,
+                }),
             });
         },
     }))
@@ -348,7 +371,7 @@ function assemblyFactory(assemblyConfigType, pm) {
             }
             return adapterLoads.get((0, dataAdapterCache_1.adapterConfigCacheKey)(adapterConf), {
                 adapterConf,
-                self: self,
+                self,
                 options: rest,
             }, 
             // signal intentionally not passed here, fixes issues like #2221.
@@ -360,7 +383,7 @@ function assemblyFactory(assemblyConfigType, pm) {
          * get Map of `canonical-name -> adapter-specific-name`
          */
         async getRefNameMapForAdapter(adapterConf, opts) {
-            if (!(opts === null || opts === void 0 ? void 0 : opts.sessionId)) {
+            if (!opts.sessionId) {
                 throw new Error('sessionId is required');
             }
             const map = await this.getAdapterMapEntry(adapterConf, opts);
@@ -376,22 +399,22 @@ function assemblyFactory(assemblyConfigType, pm) {
         },
     }));
 }
-async function getRefNameAliases(config, pm, signal) {
-    const type = pm.getAdapterType(config.type);
+async function getRefNameAliases({ config, pluginManager, signal, }) {
+    const type = pluginManager.getAdapterType(config.type);
     const CLASS = await type.getAdapterClass();
-    const adapter = new CLASS(config, undefined, pm);
+    const adapter = new CLASS(config, undefined, pluginManager);
     return adapter.getRefNameAliases({ signal });
 }
-async function getCytobands(config, pm) {
-    const type = pm.getAdapterType(config.type);
+async function getCytobands({ config, pluginManager, }) {
+    const type = pluginManager.getAdapterType(config.type);
     const CLASS = await type.getAdapterClass();
-    const adapter = new CLASS(config, undefined, pm);
+    const adapter = new CLASS(config, undefined, pluginManager);
     // @ts-expect-error
     return adapter.getData();
 }
-async function getAssemblyRegions(config, pm, signal) {
-    const type = pm.getAdapterType(config.type);
+async function getAssemblyRegions({ config, pluginManager, signal, }) {
+    const type = pluginManager.getAdapterType(config.type);
     const CLASS = await type.getAdapterClass();
-    const adapter = new CLASS(config, undefined, pm);
+    const adapter = new CLASS(config, undefined, pluginManager);
     return adapter.getRegions({ signal });
 }

package/assemblyManager/assemblyConfigSchema.d.ts

@@ -7,7 +7,8 @@ import PluginManager from '../PluginManager';
 declare function assemblyConfigSchema(pluginManager: PluginManager): import("../configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
-     * aliases are "reference name aliases" e.g. aliases for hg38 might be "GRCh38"
+     * aliases are "reference name aliases" e.g. aliases for hg38 might be
+     * "GRCh38"
      */
     aliases: {
         type: string;
@@ -16,8 +17,9 @@ declare function assemblyConfigSchema(pluginManager: PluginManager): import("../
     };
     /**
      * #slot
-     * sequence refers to a reference sequence track that has an adapter containing,
-     * importantly, a sequence adapter such as IndexedFastaAdapter
+     * sequence refers to a reference sequence track that has an adapter
+     * containing, importantly, a sequence adapter such as
+     * IndexedFastaAdapter
      */
     sequence: import("../configuration").AnyConfigurationSchemaType;
     /**
@@ -31,8 +33,8 @@ declare function assemblyConfigSchema(pluginManager: PluginManager): import("../
     refNameAliases: import("../configuration/configurationSchema").ConfigurationSchemaType<{
         /**
          * #slot refNameAliases.adapter
-         * refNameAliases help resolve e.g. chr1 and 1 as the same entity
-         * the data for refNameAliases are fetched from an adapter, that is
+         * refNameAliases help resolve e.g. chr1 and 1 as the same entity the
+         * data for refNameAliases are fetched from an adapter, that is
          * commonly a tsv like chromAliases.txt from UCSC or similar
          */
         adapter: import("mobx-state-tree").IAnyModelType;
@@ -40,8 +42,8 @@ declare function assemblyConfigSchema(pluginManager: PluginManager): import("../
     cytobands: import("../configuration/configurationSchema").ConfigurationSchemaType<{
         /**
          * #slot cytobands.adapter
-         * cytoband data is fetched from an adapter, and can be displayed by a
-         * view type as ideograms
+         * cytoband data is fetched from an adapter, and can be displayed by
+         * a view type as ideograms
          */
         adapter: import("mobx-state-tree").IAnyModelType;
     }, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/assemblyManager/assemblyConfigSchema.js

@@ -10,7 +10,8 @@ function assemblyConfigSchema(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('BaseAssembly', {
         /**
          * #slot
-         * aliases are "reference name aliases" e.g. aliases for hg38 might be "GRCh38"
+         * aliases are "reference name aliases" e.g. aliases for hg38 might be
+         * "GRCh38"
          */
         aliases: {
             type: 'stringArray',
@@ -19,8 +20,9 @@ function assemblyConfigSchema(pluginManager) {
         },
         /**
          * #slot
-         * sequence refers to a reference sequence track that has an adapter containing,
-         * importantly, a sequence adapter such as IndexedFastaAdapter
+         * sequence refers to a reference sequence track that has an adapter
+         * containing, importantly, a sequence adapter such as
+         * IndexedFastaAdapter
          */
         sequence: pluginManager.getTrackType('ReferenceSequenceTrack')
             .configSchema,
@@ -35,15 +37,14 @@ function assemblyConfigSchema(pluginManager) {
         refNameAliases: (0, configuration_1.ConfigurationSchema)('RefNameAliases', {
             /**
              * #slot refNameAliases.adapter
-             * refNameAliases help resolve e.g. chr1 and 1 as the same entity
-             * the data for refNameAliases are fetched from an adapter, that is
+             * refNameAliases help resolve e.g. chr1 and 1 as the same entity the
+             * data for refNameAliases are fetched from an adapter, that is
              * commonly a tsv like chromAliases.txt from UCSC or similar
              */
             adapter: pluginManager.pluggableConfigSchemaType('adapter'),
         }, {
             preProcessSnapshot: snap => {
                 // allow refNameAliases to be unspecified
-                // @ts-expect-error
                 if (!snap.adapter) {
                     return { adapter: { type: 'RefNameAliasAdapter' } };
                 }
@@ -53,18 +54,16 @@ function assemblyConfigSchema(pluginManager) {
         cytobands: (0, configuration_1.ConfigurationSchema)('Cytoband', {
             /**
              * #slot cytobands.adapter
-             * cytoband data is fetched from an adapter, and can be displayed by a
-             * view type as ideograms
+             * cytoband data is fetched from an adapter, and can be displayed by
+             * a view type as ideograms
              */
             adapter: pluginManager.pluggableConfigSchemaType('adapter'),
         }, {
             preProcessSnapshot: snap => {
                 // allow cytoBand to be unspecified
-                // @ts-expect-error
-                if (!snap.adapter) {
-                    return { adapter: { type: 'CytobandAdapter' } };
-                }
-                return snap;
+                return !snap.adapter
+                    ? { adapter: { type: 'CytobandAdapter' } }
+                    : snap;
             },
         }),
         /**
@@ -78,9 +77,9 @@ function assemblyConfigSchema(pluginManager) {
     }, {
         /**
          * #identifier name
-         * the name acts as a unique identifier in the config, so it cannot be duplicated.
-         * it usually a short human readable "id" like hg38, but you can also optionally
-         * customize the assembly "displayName" config slot
+         * the name acts as a unique identifier in the config, so it cannot be
+         * duplicated. it usually a short human readable "id" like hg38, but you
+         * can also optionally customize the assembly "displayName" config slot
          */
         explicitIdentifier: 'name',
     });