@jbrowse/cli 2.4.0 → 2.4.1

package/README.md

@@ -173,7 +173,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -228,7 +228,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -259,6 +259,10 @@ OPTIONS
 
   -t, --trackType=trackType             Type of track, by default inferred from track file
 
+  --bed1=bed1                           Used only for mcscan anchors/simpleAnchors types
+
+  --bed2=bed2                           Used only for mcscan anchors/simpleAnchors types
+
   --category=category                   Optional Comma separated string of categories to group tracks
 
   --config=config                       Any extra config settings to add to a track. i.e '{"defaultRendering":
@@ -303,7 +307,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -330,7 +334,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -361,7 +365,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -406,7 +410,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -449,7 +453,7 @@ EXAMPLE
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -487,7 +491,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse text-index`
 
@@ -551,7 +555,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -600,7 +604,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.0/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.1/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.js

@@ -85,12 +85,7 @@ class JBrowseCommand extends command_1.default {
         }
         let locationPath;
         try {
-            if (check) {
-                locationPath = await fs_1.promises.realpath(location);
-            }
-            else {
-                locationPath = location;
-            }
+            locationPath = check ? await fs_1.promises.realpath(location) : location;
         }
         catch (e) {
             // ignore
@@ -128,7 +123,7 @@ class JBrowseCommand extends command_1.default {
                 _d = false;
                 try {
                     const iter = _c;
-                    versions = versions.concat(iter);
+                    versions = [...versions, ...iter];
                 }
                 finally {
                     _d = true;
@@ -158,8 +153,8 @@ class JBrowseCommand extends command_1.default {
                     const nonprereleases = versions
                         .filter(release => release.prerelease === false)
                         .filter(release => release.assets && release.assets.length > 0);
-                    if (nonprereleases.length !== 0) {
-                        // @ts-ignore
+                    if (nonprereleases.length > 0) {
+                        // @ts-expect-error
                         const file = (_d = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))) === null || _d === void 0 ? void 0 : _d.browser_download_url;
                         if (!file) {
                             throw new Error('no jbrowse-web download found');

package/lib/commands/add-assembly.js

@@ -42,24 +42,17 @@ class AddAssembly extends base_1.default {
         }
         switch (type) {
             case 'indexedFasta': {
-                let sequenceLocation = await this.resolveFileLocation(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+                const { skipCheck, force, load, faiLocation } = runFlags;
+                let sequenceLocation = await this.resolveFileLocation(argsSequence, !(skipCheck || force), load === 'inPlace');
                 this.debug(`FASTA location resolved to: ${sequenceLocation}`);
-                let indexLocation = await this.resolveFileLocation(runFlags.faiLocation || `${argsSequence}.fai`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+                let indexLocation = await this.resolveFileLocation(faiLocation || `${argsSequence}.fai`, !(skipCheck || force), load === 'inPlace');
                 this.debug(`FASTA index location resolved to: ${indexLocation}`);
                 if (!name) {
-                    if (sequenceLocation.endsWith('.fasta')) {
-                        name = path_1.default.basename(sequenceLocation, '.fasta');
-                    }
-                    else {
-                        name = path_1.default.basename(sequenceLocation, '.fa');
-                    }
+                    name = path_1.default.basename(sequenceLocation, sequenceLocation.endsWith('.fasta') ? '.fasta' : '.fa');
                     this.debug(`Guessing name: ${name}`);
                 }
-                const loaded = runFlags.load
-                    ? await this.loadData(runFlags.load, [
-                        sequenceLocation,
-                        indexLocation,
-                    ])
+                const loaded = load
+                    ? await this.loadData(load, [sequenceLocation, indexLocation])
                     : false;
                 if (loaded) {
                     sequenceLocation = path_1.default.basename(sequenceLocation);
@@ -87,12 +80,7 @@ class AddAssembly extends base_1.default {
                 let bgzipIndexLocation = await this.resolveFileLocation(runFlags.gziLocation || `${sequenceLocation}.gzi`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
                 this.debug(`bgzip index location resolved to: ${bgzipIndexLocation}`);
                 if (!name) {
-                    if (sequenceLocation.endsWith('.fasta.gz')) {
-                        name = path_1.default.basename(sequenceLocation, '.fasta.gz');
-                    }
-                    else {
-                        name = path_1.default.basename(sequenceLocation, '.fa.gz');
-                    }
+                    name = path_1.default.basename(sequenceLocation, sequenceLocation.endsWith('.fasta.gz') ? '.fasta.gz' : '.fa.gz');
                     this.debug(`Guessing name: ${name}`);
                 }
                 const loaded = runFlags.load

package/lib/commands/add-connection.js

@@ -18,10 +18,11 @@ class AddConnection extends base_1.default {
         const { connectionUrlOrPath: argsPath } = runArgs;
         const { config } = runFlags;
         let { type, name, connectionId, assemblyName } = runFlags;
-        const url = await this.resolveURL(argsPath, !(runFlags.skipCheck || runFlags.force));
+        const { skipCheck, force } = runFlags;
+        const url = await this.resolveURL(argsPath, !(skipCheck || force));
         const configContents = await this.readJsonFile(this.target);
         this.debug(`Using config file ${this.target}`);
-        if (!configContents.assemblies || !configContents.assemblies.length) {
+        if (!configContents.assemblies || configContents.assemblies.length === 0) {
             this.error('No assemblies found. Please add one before adding connections', { exit: 120 });
         }
         else if (configContents.assemblies.length > 1 && !assemblyName) {

package/lib/commands/add-track.d.ts

@@ -35,26 +35,53 @@ export default class AddTrack extends JBrowseCommand {
         overwrite: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
         force: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
         protocol: flags.IOptionFlag<string>;
+        bed1: flags.IOptionFlag<string | undefined>;
+        bed2: flags.IOptionFlag<string | undefined>;
     };
     run(): Promise<void>;
-    guessFileNames(fileName: string, index?: string): {
+    guessFileNames({ location, index, bed1, bed2, }: {
+        location: string;
+        index?: string;
+        bed1?: string;
+        bed2?: string;
+    }): {
+        file: string;
+        bed1: string;
+        bed2: string;
+        index?: undefined;
+        index2?: undefined;
+    } | {
         file: string;
         index: string;
+        bed1?: undefined;
+        bed2?: undefined;
         index2?: undefined;
     } | {
         file: string;
+        index: string;
+        index2: string;
+        bed1?: undefined;
+        bed2?: undefined;
+    } | {
+        file: string;
+        bed1?: undefined;
+        bed2?: undefined;
         index?: undefined;
         index2?: undefined;
     } | {
         file?: undefined;
+        bed1?: undefined;
+        bed2?: undefined;
         index?: undefined;
         index2?: undefined;
-    } | {
-        file: string;
-        index: string;
-        index2: string;
     };
-    guessAdapter(fileName: string, protocol: string, index?: string): {
+    guessAdapter({ location, protocol, index, bed1, bed2, }: {
+        location: string;
+        protocol: string;
+        index?: string;
+        bed1?: string;
+        bed2?: string;
+    }): {
         type: string;
         bamLocation: UriLocation | LocalPathLocation;
         index: {
@@ -80,6 +107,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         cramLocation: UriLocation | LocalPathLocation;
@@ -103,6 +137,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         gffLocation: UriLocation | LocalPathLocation;
@@ -126,6 +167,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         gffGzLocation: UriLocation | LocalPathLocation;
@@ -152,6 +200,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         gtfLocation: UriLocation | LocalPathLocation;
@@ -175,6 +230,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         vcfLocation: UriLocation | LocalPathLocation;
@@ -198,6 +260,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         vcfGzLocation: UriLocation | LocalPathLocation;
@@ -224,6 +293,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         bamLocation?: undefined;
@@ -247,6 +323,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         bedGzLocation: UriLocation | LocalPathLocation;
@@ -273,6 +356,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         bedLocation: UriLocation | LocalPathLocation;
@@ -296,6 +386,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         bigBedLocation: UriLocation | LocalPathLocation;
@@ -319,6 +416,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         bigWigLocation: UriLocation | LocalPathLocation;
@@ -342,6 +446,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         fastaLocation: UriLocation | LocalPathLocation;
@@ -365,6 +476,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         fastaLocation: UriLocation | LocalPathLocation;
@@ -388,6 +506,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         twoBitLocation: UriLocation | LocalPathLocation;
@@ -411,6 +536,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         rootUrlTemplate: UriLocation | LocalPathLocation;
@@ -434,6 +566,13 @@ export default class AddTrack extends JBrowseCommand {
         endpoint?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         endpoint: string;
@@ -457,6 +596,13 @@ export default class AddTrack extends JBrowseCommand {
         rootUrlTemplate?: undefined;
         hicLocation?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         hicLocation: UriLocation | LocalPathLocation;
@@ -480,6 +626,13 @@ export default class AddTrack extends JBrowseCommand {
         rootUrlTemplate?: undefined;
         endpoint?: undefined;
         pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
     } | {
         type: string;
         pafLocation: UriLocation | LocalPathLocation;
@@ -503,6 +656,163 @@ export default class AddTrack extends JBrowseCommand {
         rootUrlTemplate?: undefined;
         endpoint?: undefined;
         hicLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
+    } | {
+        type: string;
+        outLocation: UriLocation | LocalPathLocation;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
+        bedGzLocation?: undefined;
+        bedLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
+    } | {
+        type: string;
+        chainLocation: UriLocation | LocalPathLocation;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
+        bedGzLocation?: undefined;
+        bedLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+        outLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
+    } | {
+        type: string;
+        deltaLocation: UriLocation | LocalPathLocation;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
+        bedGzLocation?: undefined;
+        bedLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
+        bed1Location?: undefined;
+        bed2Location?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
+    } | {
+        type: string;
+        mcscanAnchorsLocation: UriLocation | LocalPathLocation;
+        bed1Location: UriLocation | LocalPathLocation | undefined;
+        bed2Location: UriLocation | LocalPathLocation | undefined;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
+        bedGzLocation?: undefined;
+        bedLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanSimpleAnchorsLocation?: undefined;
+    } | {
+        type: string;
+        mcscanSimpleAnchorsLocation: UriLocation | LocalPathLocation;
+        bed1Location: UriLocation | LocalPathLocation | undefined;
+        bed2Location: UriLocation | LocalPathLocation | undefined;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
+        bedGzLocation?: undefined;
+        bedLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+        outLocation?: undefined;
+        chainLocation?: undefined;
+        deltaLocation?: undefined;
+        mcscanAnchorsLocation?: undefined;
     };
     guessTrackType(adapterType: string): string;
 }