@jbrowse/cli 2.5.0 → 2.6.2

package/README.md

@@ -173,7 +173,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -189,46 +189,45 @@ ARGUMENTS
                        For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/
 
 OPTIONS
-  -a, --assemblyName=assemblyName  Assembly name of the connection If none, will default to the assembly in your config
-                                   file
+  -a, --assemblyNames=assemblyNames  For UCSC, optional: Comma separated list of assembly name(s) to filter from this
+                                     connection. For JBrowse: a single assembly name
 
-  -c, --config=config              Any extra config settings to add to connection in JSON object format, such as
-                                   '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'
+  -c, --config=config                Any extra config settings to add to connection in JSON object format, such as
+                                     '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'
 
-  -f, --force                      Equivalent to `--skipCheck --overwrite`
+  -f, --force                        Equivalent to `--skipCheck --overwrite`
 
-  -h, --help                       show CLI help
+  -h, --help                         show CLI help
 
-  -n, --name=name                  Name of the connection. Defaults to connectionId if not provided
+  -n, --name=name                    Name of the connection. Defaults to connectionId if not provided
 
-  -t, --type=type                  type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom
+  -t, --type=type                    type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom
 
-  --connectionId=connectionId      Id for the connection that must be unique to JBrowse.  Defaults to
-                                   'connectionType-assemblyName-currentTime'
+  --connectionId=connectionId        Id for the connection that must be unique to JBrowse.  Defaults to
+                                     'connectionType-assemblyName-currentTime'
 
-  --out=out                        synonym for target
+  --out=out                          synonym for target
 
-  --overwrite                      Overwrites any existing connections if same connection id
+  --overwrite                        Overwrites any existing connections if same connection id
 
-  --skipCheck                      Don't check whether or not the data directory URL exists or if you are in a JBrowse
-                                   directory
+  --skipCheck                        Don't check whether or not the data directory URL exists or if you are in a JBrowse
+                                     directory
 
-  --target=target                  path to config file in JB2 installation directory to write out to.
+  --target=target                    path to config file in JB2 installation directory to write out to.
 
 EXAMPLES
-  $ jbrowse add-connection http://mysite.com/jbrowse/data/
-  $ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection
-  $ jbrowse add-connection http://mysite.com/path/to/hub.txt --assemblyName hg19
-  $ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName
-  hg19
+  $ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19
+  $ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38
+  $ jbrowse add-connection http://mysite.com/path/to/hub.txt
+  $ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection
   $ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config
-  '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' --assemblyName hg19
+  '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19
   $ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target
   /path/to/jb2/installation/config.json
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -307,7 +306,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -334,7 +333,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -365,7 +364,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -410,7 +409,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -453,7 +452,7 @@ EXAMPLE
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -491,7 +490,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse text-index`
 
@@ -555,7 +554,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -604,7 +603,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.5.0/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.2/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.js

@@ -118,16 +118,11 @@ class JBrowseCommand extends command_1.default {
         var _a, e_1, _b, _c;
         let versions = [];
         try {
-            for (var _d = true, _e = __asyncValues(this.fetchVersions()), _f; _f = await _e.next(), _a = _f.done, !_a;) {
+            for (var _d = true, _e = __asyncValues(this.fetchVersions()), _f; _f = await _e.next(), _a = _f.done, !_a; _d = true) {
                 _c = _f.value;
                 _d = false;
-                try {
-                    const iter = _c;
-                    versions = [...versions, ...iter];
-                }
-                finally {
-                    _d = true;
-                }
+                const iter = _c;
+                versions = [...versions, ...iter];
             }
         }
         catch (e_1_1) { e_1 = { error: e_1_1 }; }
@@ -143,27 +138,22 @@ class JBrowseCommand extends command_1.default {
         var _a, e_2, _b, _c;
         var _d;
         try {
-            for (var _e = true, _f = __asyncValues(this.fetchVersions()), _g; _g = await _f.next(), _a = _g.done, !_a;) {
+            for (var _e = true, _f = __asyncValues(this.fetchVersions()), _g; _g = await _f.next(), _a = _g.done, !_a; _e = true) {
                 _c = _g.value;
                 _e = false;
-                try {
-                    const versions = _c;
-                    // if a release was just uploaded, or an erroneous build was made
-                    // then it might have no build asset
-                    const nonprereleases = versions
-                        .filter(release => release.prerelease === false)
-                        .filter(release => release.assets && release.assets.length > 0);
-                    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');
-                        }
-                        return file;
+                const versions = _c;
+                // if a release was just uploaded, or an erroneous build was made
+                // then it might have no build asset
+                const nonprereleases = versions
+                    .filter(release => release.prerelease === false)
+                    .filter(release => release.assets && release.assets.length > 0);
+                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');
                     }
-                }
-                finally {
-                    _e = true;
+                    return file;
                 }
             }
         }

package/lib/commands/add-connection.js

@@ -4,98 +4,54 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const command_1 = require("@oclif/command");
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
+// locals
+const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const base_1 = __importDefault(require("../base"));
 class AddConnection extends base_1.default {
     async run() {
+        var _a, _b;
         const { args: runArgs, flags: runFlags } = this.parse(AddConnection);
         const output = runFlags.target || runFlags.out || '.';
         const isDir = fs_1.default.lstatSync(output).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
-        const { connectionUrlOrPath: argsPath } = runArgs;
-        const { config } = runFlags;
-        let { type, name, connectionId, assemblyName } = runFlags;
+        const { connectionUrlOrPath } = runArgs;
+        const { assemblyNames, type, name, config, connectionId } = runFlags;
         const { skipCheck, force } = runFlags;
-        const url = await this.resolveURL(argsPath, !(skipCheck || force));
+        const url = await this.resolveURL(connectionUrlOrPath, !(skipCheck || force));
         const configContents = await this.readJsonFile(this.target);
         this.debug(`Using config file ${this.target}`);
-        if (!configContents.assemblies || configContents.assemblies.length === 0) {
+        if (!((_a = configContents.assemblies) === null || _a === void 0 ? void 0 : _a.length)) {
             this.error('No assemblies found. Please add one before adding connections', { exit: 120 });
         }
-        else if (configContents.assemblies.length > 1 && !assemblyName) {
-            this.error('Too many assemblies, cannot default to one. Please specify the assembly with the --assemblyNames flag');
-        }
-        if (assemblyName) {
-            configContents.assemblies.findIndex(assemblies => assemblies.name === assemblyName) === -1
-                ? this.error(`Assembly name provided does not match any in config. Valid assembly names are ${configContents.assemblies.map(assembly => assembly.name)}`, { exit: 130 })
-                : this.debug(`Assembly name(s) is :${assemblyName}`);
-        }
-        else {
-            assemblyName = configContents.assemblies[0].name;
-            this.log(`Inferred default assembly name ${assemblyName}`);
-        }
-        if (type) {
-            this.debug(`Type is ${type}`);
-        }
-        else {
-            type = this.determineConnectionType(url, config);
-        }
-        if (connectionId) {
-            this.debug(`Connection id is ${connectionId}`);
-        }
-        else {
-            connectionId = `${type}-${assemblyName}-${Date.now()}`;
-        }
-        if (name) {
-            this.debug(`Name is: ${name}`);
-        }
-        else {
-            name = connectionId;
-        }
-        let configObj = {};
-        if (config) {
-            try {
-                configObj = (0, json_parse_better_errors_1.default)(config);
-            }
-            catch (error) {
-                this.error('Could not parse provided JSON object');
-            }
-        }
-        const connectionConfig = Object.assign({ type,
-            connectionId, name: name || connectionId, assemblyName }, configObj);
-        switch (type) {
-            case 'UCSCTrackHubConnection': {
-                connectionConfig.hubTxtLocation = {
+        const configType = type || this.determineConnectionType(url);
+        const id = connectionId ||
+            [configType, assemblyNames, +Date.now()].filter(f => !!f).join('-');
+        const connectionConfig = Object.assign(Object.assign(Object.assign(Object.assign({ type: configType, name: name || id }, (configType === 'UCSCTrackHubConnection'
+            ? {
+                hubTxtLocation: {
                     uri: url,
                     locationType: 'UriLocation',
-                };
-                break;
+                },
             }
-            case 'JBrowse1Connection': {
-                connectionConfig.dataDirLocation = {
+            : {})), (configType === 'JBrowse1Connection'
+            ? {
+                dataDirLocation: {
                     uri: url,
                     locationType: 'UriLocation',
-                };
-                break;
-            }
-            default: {
-                if (!config || !this.isValidJSON(config)) {
-                    this.error('When type is not UCSCTrackHubConnection or JBrowse1Connection, config object must be provided.\nPlease enter a config object using --config', { exit: 140 });
-                }
-                break;
+                },
             }
-        }
+            : {})), { connectionId: id, assemblyNames: assemblyNames || type === 'JBrowse1Connection'
+                ? [(_b = configContents.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name]
+                : undefined }), (config ? (0, json_parse_better_errors_1.default)(config) : {}));
         if (!configContents.connections) {
             configContents.connections = [];
         }
-        const idx = configContents.connections.findIndex(configConnection => configConnection.connectionId === connectionId);
+        const idx = configContents.connections.findIndex(c => c.connectionId === connectionId);
         if (idx !== -1) {
-            this.debug(`Found existing connectionId ${connectionId} in configuration`);
             if (runFlags.force || runFlags.overwrite) {
-                this.debug(`Overwriting connection ${connectionId} in configuration`);
                 configContents.connections[idx] = connectionConfig;
             }
             else {
@@ -137,17 +93,14 @@ class AddConnection extends base_1.default {
             exit: 180,
         });
     }
-    determineConnectionType(url, config) {
+    determineConnectionType(url) {
         if (path_1.default.basename(url) === 'hub.txt') {
             return 'UCSCTrackHubConnection';
         }
         if (url.includes('jbrowse/data')) {
             return 'JBrowse1Connection';
         }
-        if (config && this.isValidJSON(config)) {
-            return 'custom';
-        }
-        return this.error(`Unable to determine a specific connection from URL given.\nPlease specify a type with --type.\nIf you want a custom type, please provide the config object with --config`);
+        return 'custom';
     }
     isValidJSON(str) {
         try {
@@ -161,11 +114,11 @@ class AddConnection extends base_1.default {
 }
 AddConnection.description = 'Add a connection to a JBrowse 2 configuration';
 AddConnection.examples = [
-    '$ jbrowse add-connection http://mysite.com/jbrowse/data/',
-    '$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection',
-    '$ jbrowse add-connection http://mysite.com/path/to/hub.txt --assemblyName hg19',
-    '$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName hg19',
-    `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' --assemblyName hg19`,
+    '$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19',
+    '$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38',
+    '$ jbrowse add-connection http://mysite.com/path/to/hub.txt',
+    '$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection',
+    `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19`,
     '$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json',
 ];
 AddConnection.args = [
@@ -180,9 +133,9 @@ AddConnection.flags = {
         char: 't',
         description: 'type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom',
     }),
-    assemblyName: command_1.flags.string({
+    assemblyNames: command_1.flags.string({
         char: 'a',
-        description: 'Assembly name of the connection If none, will default to the assembly in your config file',
+        description: 'For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name',
     }),
     config: command_1.flags.string({
         char: 'c',

package/lib/commands/create.js

@@ -6,8 +6,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const command_1 = require("@oclif/command");
 const fs_1 = __importDefault(require("fs"));
 const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
-const unzipper_1 = __importDefault(require("unzipper"));
 const base_1 = __importDefault(require("../base"));
+const decompress_1 = __importDefault(require("decompress"));
 const fsPromises = fs_1.default.promises;
 class Create extends base_1.default {
     async run() {
@@ -40,7 +40,7 @@ class Create extends base_1.default {
             type !== 'application/octet-stream') {
             this.error('The URL provided does not seem to be a JBrowse installation URL');
         }
-        await response.body.pipe(unzipper_1.default.Extract({ path: argsPath })).promise();
+        await (0, decompress_1.default)(Buffer.from(await response.arrayBuffer()), argsPath);
         this.log(`Unpacked ${locationUrl} at ${argsPath}`);
     }
     async checkPath(userPath) {
@@ -50,8 +50,9 @@ class Create extends base_1.default {
         }
     }
     async catch(error) {
+        var _a;
         // @ts-expect-error
-        if (error.parse && error.parse.output.flags.listVersions) {
+        if ((_a = error.parse) === null || _a === void 0 ? void 0 : _a.output.flags.listVersions) {
             const versions = (await this.fetchGithubVersions()).map(version => version.tag_name);
             this.log(`All JBrowse versions:\n${versions.join('\n')}`);
             this.exit();

package/lib/commands/upgrade.js

@@ -7,8 +7,8 @@ const command_1 = require("@oclif/command");
 const rimraf_1 = require("rimraf");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
+const decompress_1 = __importDefault(require("decompress"));
 const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
-const unzipper_1 = __importDefault(require("unzipper"));
 const base_1 = __importDefault(require("../base"));
 class Upgrade extends base_1.default {
     async run() {
@@ -49,7 +49,7 @@ class Upgrade extends base_1.default {
                 .filter(f => f.includes('worker.js'))
                 .forEach(f => fs_1.default.unlinkSync(path_1.default.join(argsPath, f)));
         }
-        await response.body.pipe(unzipper_1.default.Extract({ path: argsPath })).promise();
+        await (0, decompress_1.default)(Buffer.from(await response.arrayBuffer()), argsPath);
         this.log(`Unpacked ${locationUrl} at ${argsPath}`);
     }
 }

package/lib/fetchWithProxy.js

@@ -4,9 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const node_fetch_1 = __importDefault(require("node-fetch"));
-const proxy_agent_1 = __importDefault(require("proxy-agent"));
+const proxy_agent_1 = require("proxy-agent");
+// The correct proxy `Agent` implementation to use will be determined
+// via the `http_proxy` / `https_proxy` / `no_proxy` / etc. env vars
 function fetchWithProxy(url, options = {}) {
-    const agent = new proxy_agent_1.default();
+    const agent = new proxy_agent_1.ProxyAgent();
     return (0, node_fetch_1.default)(url, Object.assign({ agent }, options));
 }
 exports.default = fetchWithProxy;

package/lib/types/gff3Adapter.js

@@ -50,46 +50,44 @@ function indexGff3({ config, attributesToIndex, inLocation, outLocation, typesTo
             input: inLocation.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
         });
         try {
-            for (var _d = true, rl_1 = __asyncValues(rl), rl_1_1; rl_1_1 = yield __await(rl_1.next()), _a = rl_1_1.done, !_a;) {
+            for (var _d = true, rl_1 = __asyncValues(rl), rl_1_1; rl_1_1 = yield __await(rl_1.next()), _a = rl_1_1.done, !_a; _d = true) {
                 _c = rl_1_1.value;
                 _d = false;
-                try {
-                    const line = _c;
-                    if (line.startsWith('#')) {
-                        continue;
-                    }
-                    else if (line.startsWith('>')) {
-                        break;
-                    }
-                    const [seq_id, , type, start, end, , , , col9] = line.split('\t');
-                    const locStr = `${seq_id}:${start}..${end}`;
-                    if (!typesToExclude.includes(type)) {
-                        // turns gff3 attrs into a map, and converts the arrays into space
-                        // separated strings
-                        const col9attrs = Object.fromEntries(col9
-                            .split(';')
-                            .map(f => f.trim())
-                            .filter(f => !!f)
-                            .map(f => f.split('='))
-                            .map(([key, val]) => [
-                            key.trim(),
-                            decodeURIComponent(val).trim().split(',').join(' '),
-                        ]));
-                        const attrs = attributesToIndex
-                            .map(attr => col9attrs[attr])
-                            .filter((f) => !!f);
-                        if (attrs.length) {
-                            const record = JSON.stringify([
-                                encodeURIComponent(locStr),
-                                encodeURIComponent(trackId),
-                                ...attrs.map(a => encodeURIComponent(a)),
-                            ]).replace(/,/g, '|');
-                            yield yield __await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
-                        }
-                    }
+                const line = _c;
+                if (!line.trim()) {
+                    continue;
                 }
-                finally {
-                    _d = true;
+                else if (line.startsWith('#')) {
+                    continue;
+                }
+                else if (line.startsWith('>')) {
+                    break;
+                }
+                const [seq_id, , type, start, end, , , , col9] = line.split('\t');
+                const locStr = `${seq_id}:${start}..${end}`;
+                if (!typesToExclude.includes(type)) {
+                    // turns gff3 attrs into a map, and converts the arrays into space
+                    // separated strings
+                    const col9attrs = Object.fromEntries(col9
+                        .split(';')
+                        .map(f => f.trim())
+                        .filter(f => !!f)
+                        .map(f => f.split('='))
+                        .map(([key, val]) => [
+                        key.trim(),
+                        decodeURIComponent(val).trim().split(',').join(' '),
+                    ]));
+                    const attrs = attributesToIndex
+                        .map(attr => col9attrs[attr])
+                        .filter((f) => !!f);
+                    if (attrs.length) {
+                        const record = JSON.stringify([
+                            encodeURIComponent(locStr),
+                            encodeURIComponent(trackId),
+                            ...attrs.map(a => encodeURIComponent(a)),
+                        ]).replaceAll(',', '|');
+                        yield yield __await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
+                    }
                 }
             }
         }

package/lib/types/vcfAdapter.js

@@ -53,50 +53,45 @@ function indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }
             input: gzStream,
         });
         try {
-            for (var _d = true, rl_1 = __asyncValues(rl), rl_1_1; rl_1_1 = yield __await(rl_1.next()), _a = rl_1_1.done, !_a;) {
+            for (var _d = true, rl_1 = __asyncValues(rl), rl_1_1; rl_1_1 = yield __await(rl_1.next()), _a = rl_1_1.done, !_a; _d = true) {
                 _c = rl_1_1.value;
                 _d = false;
-                try {
-                    const line = _c;
-                    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
-                    const fields = Object.fromEntries(info
-                        .split(';')
-                        .map(f => f.trim())
-                        .filter(f => !!f)
-                        .map(f => f.split('='))
-                        .map(([key, val]) => [
-                        key.trim(),
-                        val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
-                    ]));
-                    const end = fields.END;
-                    const locStr = `${ref}:${pos}..${end || +pos + 1}`;
-                    if (id === '.') {
-                        continue;
-                    }
-                    const infoAttrs = attributesToIndex
-                        .map(attr => fields[attr])
-                        .filter((f) => !!f);
-                    const ids = id.split(',');
-                    for (let i = 0; i < ids.length; i++) {
-                        const id = ids[i];
-                        const attrs = [id];
-                        const record = JSON.stringify([
-                            encodeURIComponent(locStr),
-                            encodeURIComponent(trackId),
-                            encodeURIComponent(id || ''),
-                            ...infoAttrs.map(a => encodeURIComponent(a || '')),
-                        ]).replace(/,/g, '|');
-                        yield yield __await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
-                    }
+                const line = _c;
+                if (line.startsWith('#')) {
+                    continue;
                 }
-                finally {
-                    _d = true;
+                // eslint-disable-next-line @typescript-eslint/no-unused-vars
+                const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
+                // turns gff3 attrs into a map, and converts the arrays into space
+                // separated strings
+                const fields = Object.fromEntries(info
+                    .split(';')
+                    .map(f => f.trim())
+                    .filter(f => !!f)
+                    .map(f => f.split('='))
+                    .map(([key, val]) => [
+                    key.trim(),
+                    val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
+                ]));
+                const end = fields.END;
+                const locStr = `${ref}:${pos}..${end || +pos + 1}`;
+                if (id === '.') {
+                    continue;
+                }
+                const infoAttrs = attributesToIndex
+                    .map(attr => fields[attr])
+                    .filter((f) => !!f);
+                const ids = id.split(',');
+                for (let i = 0; i < ids.length; i++) {
+                    const id = ids[i];
+                    const attrs = [id];
+                    const record = JSON.stringify([
+                        encodeURIComponent(locStr),
+                        encodeURIComponent(trackId),
+                        encodeURIComponent(id || ''),
+                        ...infoAttrs.map(a => encodeURIComponent(a || '')),
+                    ]).replaceAll(',', '|');
+                    yield yield __await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
                 }
             }
         }