@jbrowse/cli 1.4.3 → 1.5.2

package/lib/commands/create.js

@@ -2,10 +2,10 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
-const unzipper_1 = tslib_1.__importDefault(require("unzipper"));
-const base_1 = tslib_1.__importDefault(require("../base"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+const unzipper_1 = (0, tslib_1.__importDefault)(require("unzipper"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 const fsPromises = fs_1.default.promises;
 class Create extends base_1.default {
     async run() {
@@ -28,7 +28,7 @@ class Create extends base_1.default {
             (branch ? await this.getBranch(branch) : '') ||
             (tag ? await this.getTag(tag) : await this.getLatest());
         this.log(`Fetching ${locationUrl}...`);
-        const response = await node_fetch_1.default(locationUrl);
+        const response = await (0, node_fetch_1.default)(locationUrl);
         if (!response.ok) {
             this.error(`Failed to fetch: ${response.statusText}`, { exit: 100 });
         }
@@ -47,8 +47,8 @@ class Create extends base_1.default {
             this.error(`${userPath} This directory has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files`, { exit: 120 });
         }
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     async catch(error) {
+        // @ts-ignore
         if (error.parse && error.parse.output.flags.listVersions) {
             const versions = (await this.fetchGithubVersions()).map(version => version.tag_name);
             this.log(`All JBrowse versions:\n${versions.join('\n')}`);
@@ -60,11 +60,20 @@ class Create extends base_1.default {
 exports.default = Create;
 Create.description = 'Downloads and installs the latest JBrowse 2 release';
 Create.examples = [
+    '# Download latest release from github, and put in specific path',
     '$ jbrowse create /path/to/new/installation',
+    '',
+    '# Download latest release from github and force overwrite existing contents at path',
     '$ jbrowse create /path/to/new/installation --force',
+    '',
+    '# Download latest release from a specific URL',
     '$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip',
+    '',
+    '# Download a specific tag from github',
     '$ jbrowse create /path/to/new/installation --tag v1.0.0',
-    '$ jbrowse create --listVersions # Lists out all available versions of JBrowse 2',
+    '',
+    '# List available versions',
+    '$ jbrowse create --listVersions',
 ];
 Create.args = [
     {

package/lib/commands/set-default-session.js

@@ -2,9 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const json_parse_better_errors_1 = tslib_1.__importDefault(require("json-parse-better-errors"));
-const base_1 = tslib_1.__importDefault(require("../base"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const json_parse_better_errors_1 = (0, tslib_1.__importDefault)(require("json-parse-better-errors"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 const fsPromises = fs_1.default.promises;
 class SetDefaultSession extends base_1.default {
     async run() {
@@ -86,7 +86,7 @@ class SetDefaultSession extends base_1.default {
             return this.error('Could not read the provided file', { exit: 150 });
         }
         try {
-            const session = json_parse_better_errors_1.default(defaultSessionJson);
+            const session = (0, json_parse_better_errors_1.default)(defaultSessionJson);
             // return top-level "session" if it exists, such as in files created by
             // "File -> Export session"
             return session.session || session;

package/lib/commands/text-index.js

@@ -1,16 +1,20 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const path_1 = tslib_1.__importDefault(require("path"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
 const stream_1 = require("stream");
 const ixixx_1 = require("ixixx");
 const command_1 = require("@oclif/command");
 const gff3Adapter_1 = require("../types/gff3Adapter");
-const gtfAdapter_1 = require("../types/gtfAdapter");
 const vcfAdapter_1 = require("../types/vcfAdapter");
-const base_1 = tslib_1.__importDefault(require("../base"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 const common_1 = require("../types/common");
+const object_fromentries_1 = (0, tslib_1.__importDefault)(require("object.fromentries"));
+if (!Object.fromEntries) {
+    // @ts-ignore
+    object_fromentries_1.default.shim();
+}
 function readConf(confFilePath) {
     return JSON.parse(fs_1.default.readFileSync(confFilePath, 'utf8'));
 }
@@ -43,7 +47,8 @@ class TextIndex extends base_1.default {
             fs_1.default.mkdirSync(trixDir);
         }
         const aggregateAdapters = config.aggregateTextSearchAdapters || [];
-        const asms = (assemblies === null || assemblies === void 0 ? void 0 : assemblies.split(',')) || ((_a = config.assemblies) === null || _a === void 0 ? void 0 : _a.map(a => a.name)) ||
+        const asms = (assemblies === null || assemblies === void 0 ? void 0 : assemblies.split(',')) ||
+            ((_a = config.assemblies) === null || _a === void 0 ? void 0 : _a.map(a => a.name)) ||
             (config.assembly ? [config.assembly.name] : []);
         if (!(asms === null || asms === void 0 ? void 0 : asms.length)) {
             throw new Error('No assemblies found');
@@ -78,12 +83,15 @@ class TextIndex extends base_1.default {
                     textSearchAdapterId: id,
                     ixFilePath: {
                         uri: `trix/${asm}.ix`,
+                        locationType: 'UriLocation',
                     },
                     ixxFilePath: {
                         uri: `trix/${asm}.ixx`,
+                        locationType: 'UriLocation',
                     },
                     metaFilePath: {
                         uri: `trix/${asm}_meta.json`,
+                        locationType: 'UriLocation',
                     },
                     assemblyNames: [asm],
                 };
@@ -142,12 +150,15 @@ class TextIndex extends base_1.default {
                             textSearchAdapterId: id,
                             ixFilePath: {
                                 uri: `trix/${trackId}.ix`,
+                                locationType: 'UriLocation',
                             },
                             ixxFilePath: {
                                 uri: `trix/${trackId}.ixx`,
+                                locationType: 'UriLocation',
                             },
                             metaFilePath: {
                                 uri: `trix/${trackId}_meta.json`,
+                                locationType: 'UriLocation',
                             },
                             assemblyNames: assemblyNames,
                         } }) });
@@ -167,8 +178,8 @@ class TextIndex extends base_1.default {
             fs_1.default.mkdirSync(trixDir);
         }
         const configs = file
-            .map(file => common_1.guessAdapterFromFileName(file))
-            .filter(fileConfig => common_1.supported(fileConfig.adapter.type));
+            .map(file => (0, common_1.guessAdapterFromFileName)(file))
+            .filter(fileConfig => (0, common_1.supported)(fileConfig.adapter.type));
         await this.indexDriver({
             configs,
             outDir: outFlag,
@@ -183,7 +194,7 @@ class TextIndex extends base_1.default {
     async indexDriver({ configs, attributes, outDir, name, quiet, exclude, assemblyNames, }) {
         const readable = stream_1.Readable.from(this.indexFiles(configs, attributes, outDir, quiet, exclude));
         const ixIxxStream = await this.runIxIxx(readable, outDir, name);
-        await common_1.generateMeta({
+        await (0, common_1.generateMeta)({
             configs,
             attributes,
             outDir,
@@ -194,27 +205,25 @@ class TextIndex extends base_1.default {
         return ixIxxStream;
     }
     indexFiles(trackConfigs, attributes, outLocation, quiet, typesToExclude) {
-        return tslib_1.__asyncGenerator(this, arguments, function* indexFiles_1() {
+        return (0, tslib_1.__asyncGenerator)(this, arguments, function* indexFiles_1() {
             for (const config of trackConfigs) {
                 const { adapter, textSearching } = config;
                 const { type } = adapter;
                 const { indexingFeatureTypesToExclude: types = typesToExclude, indexingAttributes: attrs = attributes, } = textSearching || {};
                 if (type === 'Gff3TabixAdapter') {
-                    yield tslib_1.__await(yield* tslib_1.__asyncDelegator(tslib_1.__asyncValues(gff3Adapter_1.indexGff3(config, attrs, outLocation, types, quiet))));
-                }
-                else if (type === 'GtfTabixAdapter') {
-                    yield tslib_1.__await(yield* tslib_1.__asyncDelegator(tslib_1.__asyncValues(gtfAdapter_1.indexGtf(config, attrs, outLocation, types, quiet))));
+                    yield (0, tslib_1.__await)(yield* (0, tslib_1.__asyncDelegator)((0, tslib_1.__asyncValues)((0, gff3Adapter_1.indexGff3)(config, attrs, outLocation, types, quiet))));
                 }
                 else if (type === 'VcfTabixAdapter') {
-                    yield tslib_1.__await(yield* tslib_1.__asyncDelegator(tslib_1.__asyncValues(vcfAdapter_1.indexVcf(config, attrs, outLocation, types, quiet))));
+                    yield (0, tslib_1.__await)(yield* (0, tslib_1.__asyncDelegator)((0, tslib_1.__asyncValues)((0, vcfAdapter_1.indexVcf)(config, attrs, outLocation, types, quiet))));
                 }
+                // gtf unused currently
             }
         });
     }
     runIxIxx(readStream, outLocation, name) {
         const ixFilename = path_1.default.join(outLocation, 'trix', `${name}.ix`);
         const ixxFilename = path_1.default.join(outLocation, 'trix', `${name}.ixx`);
-        return ixixx_1.ixIxxStream(readStream, ixFilename, ixxFilename);
+        return (0, ixixx_1.ixIxxStream)(readStream, ixFilename, ixxFilename);
     }
     async getTrackConfigs(configPath, trackIds, assemblyName) {
         const { tracks } = readConf(configPath);
@@ -230,7 +239,7 @@ class TextIndex extends base_1.default {
             }
             return currentTrack;
         })
-            .filter(track => common_1.supported(track.adapter.type))
+            .filter(track => { var _a; return (0, common_1.supported)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
             .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true);
     }
 }

package/lib/commands/upgrade.d.ts

@@ -3,19 +3,12 @@ import JBrowseCommand from '../base';
 export default class Upgrade extends JBrowseCommand {
     static description: string;
     static examples: string[];
-    static args: ({
+    static args: {
         name: string;
         required: boolean;
         description: string;
         default: string;
-        hidden?: undefined;
-    } | {
-        name: string;
-        required: boolean;
-        description: string;
-        hidden: boolean;
-        default?: undefined;
-    })[];
+    }[];
     static flags: {
         help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
         listVersions: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;

package/lib/commands/upgrade.js

@@ -2,11 +2,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const path_1 = tslib_1.__importDefault(require("path"));
-const node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
-const unzipper_1 = tslib_1.__importDefault(require("unzipper"));
-const base_1 = tslib_1.__importDefault(require("../base"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+const unzipper_1 = (0, tslib_1.__importDefault)(require("unzipper"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 class Upgrade extends base_1.default {
     async run() {
         const { args: runArgs, flags: runFlags } = this.parse(Upgrade);
@@ -30,7 +30,7 @@ class Upgrade extends base_1.default {
             (branch ? await this.getBranch(branch) : '') ||
             (tag ? await this.getTag(tag) : await this.getLatest());
         this.log(`Fetching ${locationUrl}...`);
-        const response = await node_fetch_1.default(locationUrl);
+        const response = await (0, node_fetch_1.default)(locationUrl);
         if (!response.ok) {
             this.error(`Failed to fetch: ${response.statusText}`, { exit: 100 });
         }
@@ -47,11 +47,23 @@ class Upgrade extends base_1.default {
 exports.default = Upgrade;
 Upgrade.description = 'Upgrades JBrowse 2 to latest version';
 Upgrade.examples = [
-    '$ jbrowse upgrade # Upgrades current directory to latest jbrowse release',
+    '# Upgrades current directory to latest jbrowse release',
+    '$ jbrowse upgrade',
+    '',
+    '# Upgrade jbrowse instance at a specific filesystem path',
     '$ jbrowse upgrade /path/to/jbrowse2/installation',
+    '',
+    '# Upgrade to a specific tag',
     '$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0',
-    '$ jbrowse upgrade --listVersions # Lists out all available versions of JBrowse 2',
+    '',
+    '# List versions available on github',
+    '$ jbrowse upgrade --listVersions',
+    '',
+    '# Upgrade from a specific URL',
     '$ jbrowse upgrade --url https://sample.com/jbrowse2.zip',
+    '',
+    '# Get nightly release from main branch',
+    '$ jbrowse upgrade --nightly',
 ];
 Upgrade.args = [
     {
@@ -60,12 +72,6 @@ Upgrade.args = [
         description: `Location where JBrowse 2 is installed`,
         default: '.',
     },
-    {
-        name: 'placeholder',
-        required: false,
-        description: `Placeholder for config file migration scripts`,
-        hidden: true,
-    },
 ];
 Upgrade.flags = {
     help: command_1.flags.help({ char: 'h' }),

package/lib/index.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.run = void 0;
 var command_1 = require("@oclif/command");
 Object.defineProperty(exports, "run", { enumerable: true, get: function () { return command_1.run; } });
 // trigger build

package/lib/types/common.js

@@ -2,9 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.generateMeta = exports.supported = exports.guessAdapterFromFileName = exports.isURL = exports.createRemoteStream = void 0;
 const tslib_1 = require("tslib");
-const fs_1 = tslib_1.__importDefault(require("fs"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
 const follow_redirects_1 = require("follow-redirects");
-const path_1 = tslib_1.__importDefault(require("path"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
 // Method for handing off the parsing of a gff3 file URL.
 // Calls the proper parser depending on if it is gzipped or not.
 // Returns a @gmod/gff stream.
@@ -37,7 +37,7 @@ function guessAdapterFromFileName(filePath) {
             assemblyNames: [],
             adapter: {
                 type: 'VcfTabixAdapter',
-                vcfGzLocation: { uri },
+                vcfGzLocation: { uri, locationType: 'UriLocation' },
             },
         };
     }
@@ -48,7 +48,7 @@ function guessAdapterFromFileName(filePath) {
             assemblyNames: [],
             adapter: {
                 type: 'Gff3TabixAdapter',
-                gffGzLocation: { uri },
+                gffGzLocation: { uri, locationType: 'UriLocation' },
             },
         };
     }
@@ -58,8 +58,8 @@ function guessAdapterFromFileName(filePath) {
             name,
             assemblyNames: [],
             adapter: {
-                type: 'GtfTabixAdapter',
-                gtfGzLocation: { uri },
+                type: 'GtfAdapter',
+                gtfLocation: { uri, locationType: 'UriLocation' },
             },
         };
     }
@@ -69,7 +69,7 @@ function guessAdapterFromFileName(filePath) {
 }
 exports.guessAdapterFromFileName = guessAdapterFromFileName;
 function supported(type) {
-    return ['Gff3TabixAdapter', 'GtfTabixAdapter', 'VcfTabixAdapter'].includes(type);
+    return ['Gff3TabixAdapter', 'VcfTabixAdapter'].includes(type);
 }
 exports.supported = supported;
 /**

package/lib/types/gff3Adapter.js

@@ -5,11 +5,11 @@ const tslib_1 = require("tslib");
 const common_1 = require("../types/common");
 const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
-const readline_1 = tslib_1.__importDefault(require("readline"));
-const path_1 = tslib_1.__importDefault(require("path"));
-const fs_1 = tslib_1.__importDefault(require("fs"));
+const readline_1 = (0, tslib_1.__importDefault)(require("readline"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
 function indexGff3(config, attributes, outLocation, typesToExclude, quiet) {
-    return tslib_1.__asyncGenerator(this, arguments, function* indexGff3_1() {
+    return (0, tslib_1.__asyncGenerator)(this, arguments, function* indexGff3_1() {
         var e_1, _a;
         const { adapter, trackId } = config;
         const { gffGzLocation: { uri }, } = adapter;
@@ -22,8 +22,8 @@ function indexGff3(config, attributes, outLocation, typesToExclude, quiet) {
         let fileDataStream;
         let totalBytes = 0;
         let receivedBytes = 0;
-        if (common_1.isURL(uri)) {
-            fileDataStream = yield tslib_1.__await(common_1.createRemoteStream(uri));
+        if ((0, common_1.isURL)(uri)) {
+            fileDataStream = yield (0, tslib_1.__await)((0, common_1.createRemoteStream)(uri));
             totalBytes = +(fileDataStream.headers['content-length'] || 0);
         }
         else {
@@ -40,11 +40,11 @@ function indexGff3(config, attributes, outLocation, typesToExclude, quiet) {
         });
         const rl = readline_1.default.createInterface({
             input: uri.endsWith('.gz')
-                ? fileDataStream.pipe(zlib_1.createGunzip())
+                ? fileDataStream.pipe((0, zlib_1.createGunzip)())
                 : fileDataStream,
         });
         try {
-            for (var rl_1 = tslib_1.__asyncValues(rl), rl_1_1; rl_1_1 = yield tslib_1.__await(rl_1.next()), !rl_1_1.done;) {
+            for (var rl_1 = (0, tslib_1.__asyncValues)(rl), rl_1_1; rl_1_1 = yield (0, tslib_1.__await)(rl_1.next()), !rl_1_1.done;) {
                 const line = rl_1_1.value;
                 if (line.startsWith('#')) {
                     continue;
@@ -75,7 +75,7 @@ function indexGff3(config, attributes, outLocation, typesToExclude, quiet) {
                             encodeURIComponent(trackId),
                             ...attrs.map(a => encodeURIComponent(a)),
                         ]).replace(/,/g, '|');
-                        yield yield tslib_1.__await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
+                        yield yield (0, tslib_1.__await)(`${record} ${[...new Set(attrs)].join(' ')}\n`);
                     }
                 }
             }
@@ -83,7 +83,7 @@ function indexGff3(config, attributes, outLocation, typesToExclude, quiet) {
         catch (e_1_1) { e_1 = { error: e_1_1 }; }
         finally {
             try {
-                if (rl_1_1 && !rl_1_1.done && (_a = rl_1.return)) yield tslib_1.__await(_a.call(rl_1));
+                if (rl_1_1 && !rl_1_1.done && (_a = rl_1.return)) yield (0, tslib_1.__await)(_a.call(rl_1));
             }
             finally { if (e_1) throw e_1.error; }
         }

package/lib/types/gtfAdapter.js

@@ -5,14 +5,14 @@ const tslib_1 = require("tslib");
 const common_1 = require("../types/common");
 const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
-const readline_1 = tslib_1.__importDefault(require("readline"));
-const path_1 = tslib_1.__importDefault(require("path"));
-const fs_1 = tslib_1.__importDefault(require("fs"));
+const readline_1 = (0, tslib_1.__importDefault)(require("readline"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
 function indexGtf(config, attributes, outLocation, typesToExclude, quiet) {
-    return tslib_1.__asyncGenerator(this, arguments, function* indexGtf_1() {
+    return (0, tslib_1.__asyncGenerator)(this, arguments, function* indexGtf_1() {
         var e_1, _a;
         const { adapter, trackId } = config;
-        const { gtfGzLocation: { uri }, } = adapter;
+        const { gtfLocation: { uri }, } = adapter;
         // progress bar code was aided by blog post at
         // https://webomnizz.com/download-a-file-with-progressbar-using-node-js/
         const progressBar = new cli_progress_1.SingleBar({
@@ -22,8 +22,8 @@ function indexGtf(config, attributes, outLocation, typesToExclude, quiet) {
         let fileDataStream;
         let totalBytes = 0;
         let receivedBytes = 0;
-        if (common_1.isURL(uri)) {
-            fileDataStream = yield tslib_1.__await(common_1.createRemoteStream(uri));
+        if ((0, common_1.isURL)(uri)) {
+            fileDataStream = yield (0, tslib_1.__await)((0, common_1.createRemoteStream)(uri));
             totalBytes = +(fileDataStream.headers['content-length'] || 0);
         }
         else {
@@ -39,13 +39,13 @@ function indexGtf(config, attributes, outLocation, typesToExclude, quiet) {
             progressBar.update(receivedBytes);
         });
         const gzStream = uri.endsWith('.gz')
-            ? fileDataStream.pipe(zlib_1.createGunzip())
+            ? fileDataStream.pipe((0, zlib_1.createGunzip)())
             : fileDataStream;
         const rl = readline_1.default.createInterface({
             input: gzStream,
         });
         try {
-            for (var rl_1 = tslib_1.__asyncValues(rl), rl_1_1; rl_1_1 = yield tslib_1.__await(rl_1.next()), !rl_1_1.done;) {
+            for (var rl_1 = (0, tslib_1.__asyncValues)(rl), rl_1_1; rl_1_1 = yield (0, tslib_1.__await)(rl_1.next()), !rl_1_1.done;) {
                 const line = rl_1_1.value;
                 if (line.startsWith('#')) {
                     continue;
@@ -67,24 +67,16 @@ function indexGtf(config, attributes, outLocation, typesToExclude, quiet) {
                             val.trim().split(',').join(' ').replace(/("|')/g, ''),
                         ];
                     }));
-                    const name = col9Attrs['gene_name'] || '';
-                    const id = col9Attrs['gene_id'] || '';
                     const attrs = attributes
                         .map(attr => col9Attrs[attr])
                         .filter((f) => !!f);
-                    const restAttrs = attributes
-                        .filter(attr => attr !== 'gene_name' && attr !== 'gene_id')
-                        .map(attr => col9Attrs[attr])
-                        .filter((f) => !!f);
-                    if (name || id) {
+                    if (attrs.length) {
                         const record = JSON.stringify([
                             encodeURIComponent(locStr),
                             encodeURIComponent(trackId),
-                            encodeURIComponent(name),
-                            encodeURIComponent(id),
-                            ...restAttrs.map(a => encodeURIComponent(a || '')),
+                            ...attrs.map(a => encodeURIComponent(a || '')),
                         ]).replace(/,/g, '|');
-                        yield yield tslib_1.__await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
+                        yield yield (0, tslib_1.__await)(`${record} ${[...new Set(attrs)].join(' ')}\n`);
                     }
                 }
             }
@@ -92,7 +84,7 @@ function indexGtf(config, attributes, outLocation, typesToExclude, quiet) {
         catch (e_1_1) { e_1 = { error: e_1_1 }; }
         finally {
             try {
-                if (rl_1_1 && !rl_1_1.done && (_a = rl_1.return)) yield tslib_1.__await(_a.call(rl_1));
+                if (rl_1_1 && !rl_1_1.done && (_a = rl_1.return)) yield (0, tslib_1.__await)(_a.call(rl_1));
             }
             finally { if (e_1) throw e_1.error; }
         }

package/lib/types/vcfAdapter.js

@@ -5,11 +5,11 @@ const tslib_1 = require("tslib");
 const common_1 = require("../types/common");
 const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
-const readline_1 = tslib_1.__importDefault(require("readline"));
-const path_1 = tslib_1.__importDefault(require("path"));
-const fs_1 = tslib_1.__importDefault(require("fs"));
+const readline_1 = (0, tslib_1.__importDefault)(require("readline"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
 function indexVcf(config, attributesToIndex, outLocation, typesToExclude, quiet) {
-    return tslib_1.__asyncGenerator(this, arguments, function* indexVcf_1() {
+    return (0, tslib_1.__asyncGenerator)(this, arguments, function* indexVcf_1() {
         var e_1, _a;
         const { adapter, trackId } = config;
         const { vcfGzLocation: { uri }, } = adapter;
@@ -22,8 +22,8 @@ function indexVcf(config, attributesToIndex, outLocation, typesToExclude, quiet)
         let fileDataStream;
         let totalBytes = 0;
         let receivedBytes = 0;
-        if (common_1.isURL(uri)) {
-            fileDataStream = yield tslib_1.__await(common_1.createRemoteStream(uri));
+        if ((0, common_1.isURL)(uri)) {
+            fileDataStream = yield (0, tslib_1.__await)((0, common_1.createRemoteStream)(uri));
             totalBytes = +(fileDataStream.headers['content-length'] || 0);
         }
         else {
@@ -39,17 +39,18 @@ function indexVcf(config, attributesToIndex, outLocation, typesToExclude, quiet)
             progressBar.update(receivedBytes);
         });
         const gzStream = uri.endsWith('.gz')
-            ? fileDataStream.pipe(zlib_1.createGunzip())
+            ? fileDataStream.pipe((0, zlib_1.createGunzip)())
             : fileDataStream;
         const rl = readline_1.default.createInterface({
             input: gzStream,
         });
         try {
-            for (var rl_1 = tslib_1.__asyncValues(rl), rl_1_1; rl_1_1 = yield tslib_1.__await(rl_1.next()), !rl_1_1.done;) {
+            for (var rl_1 = (0, tslib_1.__asyncValues)(rl), rl_1_1; rl_1_1 = yield (0, tslib_1.__await)(rl_1.next()), !rl_1_1.done;) {
                 const line = rl_1_1.value;
                 if (line.startsWith('#')) {
                     continue;
                 }
+                // eslint-disable-next-line @typescript-eslint/no-unused-vars
                 const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
                 // turns gff3 attrs into a map, and converts the arrays into space
                 // separated strings
@@ -80,14 +81,14 @@ function indexVcf(config, attributesToIndex, outLocation, typesToExclude, quiet)
                         encodeURIComponent(id || ''),
                         ...infoAttrs.map(a => encodeURIComponent(a || '')),
                     ]).replace(/,/g, '|');
-                    yield yield tslib_1.__await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
+                    yield yield (0, tslib_1.__await)(`${record} ${[...new Set(attrs)].join(' ')}\n`);
                 }
             }
         }
         catch (e_1_1) { e_1 = { error: e_1_1 }; }
         finally {
             try {
-                if (rl_1_1 && !rl_1_1.done && (_a = rl_1.return)) yield tslib_1.__await(_a.call(rl_1));
+                if (rl_1_1 && !rl_1_1.done && (_a = rl_1.return)) yield (0, tslib_1.__await)(_a.call(rl_1));
             }
             finally { if (e_1) throw e_1.error; }
         }