@jbrowse/cli 3.5.1 → 3.6.0

package/lib/commands/admin-server.js

@@ -1,153 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const crypto_1 = __importDefault(require("crypto"));
-const fs_1 = __importDefault(require("fs"));
-const os_1 = __importDefault(require("os"));
-const path_1 = __importDefault(require("path"));
-const core_1 = require("@oclif/core");
-const boxen_1 = __importDefault(require("boxen"));
-const chalk_1 = __importDefault(require("chalk"));
-const cors_1 = __importDefault(require("cors"));
-const express_1 = __importDefault(require("express"));
-const base_1 = __importDefault(require("../base"));
-function isValidPort(port) {
-    return port > 0 && port < 65535;
-}
-// generate a string of random alphanumeric characters to serve as admin key
-function generateKey() {
-    return crypto_1.default.randomBytes(5).toString('hex');
-}
-class AdminServer extends base_1.default {
-    async run() {
-        const { flags: runFlags } = await this.parse(AdminServer);
-        const { root, bodySizeLimit } = runFlags;
-        const output = root || '.';
-        const isDir = fs_1.default.lstatSync(output).isDirectory();
-        const outFile = isDir ? `${output}/config.json` : output;
-        const baseDir = path_1.default.dirname(outFile);
-        if (fs_1.default.existsSync(outFile)) {
-            this.debug(`Found existing config file ${outFile}`);
-        }
-        else {
-            this.debug(`Creating config file ${outFile}`);
-            await this.writeJsonFile(outFile, {
-                assemblies: [],
-                configuration: {},
-                connections: [],
-                defaultSession: {
-                    name: 'New Session',
-                },
-                tracks: [],
-            });
-        }
-        // start server with admin key in URL query string
-        let port = 9090;
-        if (runFlags.port) {
-            if (!isValidPort(Number.parseInt(runFlags.port, 10))) {
-                this.error(`${runFlags.port} is not a valid port`);
-            }
-            else {
-                port = Number.parseInt(runFlags.port, 10);
-            }
-        }
-        const app = (0, express_1.default)();
-        app.use(express_1.default.static(baseDir));
-        app.use((0, cors_1.default)());
-        // POST route to save config
-        app.use(express_1.default.json({ limit: bodySizeLimit }));
-        app.post('/updateConfig', async (req, res) => {
-            if (adminKey === req.body.adminKey) {
-                this.debug('Admin key matches');
-                try {
-                    // use directory traversal prevention
-                    // https://nodejs.org/en/knowledge/file-system/security/introduction/#preventing-directory-traversal
-                    const filename = req.body.configPath
-                        ? path_1.default.join(baseDir, req.body.configPath)
-                        : outFile;
-                    if (!filename.startsWith(baseDir)) {
-                        throw new Error(`Cannot perform directory traversal outside of ${baseDir}`);
-                    }
-                    await this.writeJsonFile(filename, req.body.config);
-                    res.send('Config written to disk');
-                }
-                catch (e) {
-                    res.status(500).send(`Could not write config file ${e}`);
-                }
-            }
-            else {
-                res.status(403).send('Admin key does not match');
-            }
-        });
-        app.post('/shutdown', async (req, res) => {
-            this.debug('Req body: ', req.body);
-            if (req.body.adminKey === adminKey) {
-                this.debug('Admin key matches');
-                res.send('Exiting');
-                server.close();
-            }
-            else {
-                res.status(403).send('Admin key does not match');
-            }
-        });
-        const adminKey = generateKey();
-        const server = app.listen(port);
-        // Server message adapted from `serve`
-        // https://github.com/vercel/serve/blob/f65ac293c20058f809769a4dbf4951acc21df6df/bin/serve.js
-        const details = server.address();
-        let localAddress = '';
-        let networkAddress = '';
-        if (typeof details === 'string') {
-            localAddress = details;
-        }
-        else if (details && typeof details === 'object') {
-            const address = details.address === '::' ? 'localhost' : details.address;
-            const ip = getNetworkAddress();
-            localAddress = `http://${address}:${details.port}?adminKey=${adminKey}`;
-            if (ip) {
-                networkAddress = `http://${ip}:${details.port}?adminKey=${adminKey}`;
-            }
-        }
-        let message = chalk_1.default.green('Now serving JBrowse\nNavigate to the below URL to configure');
-        if (localAddress) {
-            const prefix = networkAddress ? '- ' : '';
-            const space = networkAddress ? '            ' : '  ';
-            message += `\n\n${chalk_1.default.bold(`${prefix}Local:`)}${space}${localAddress}`;
-        }
-        if (networkAddress) {
-            message += `\n${chalk_1.default.bold('- On Your Network:')}  ${networkAddress}`;
-        }
-        this.log((0, boxen_1.default)(message, { padding: 1, borderColor: 'blue', margin: 1 }));
-        this.log(`If you are running yarn start you can launch http://localhost:3000?adminKey=${adminKey}&adminServer=http://localhost:${port}/updateConfig`);
-    }
-}
-AdminServer.description = 'Start up a small admin server for JBrowse configuration';
-AdminServer.examples = ['$ jbrowse admin-server', '$ jbrowse admin-server -p 8888'];
-AdminServer.flags = {
-    port: core_1.Flags.string({
-        char: 'p',
-        description: 'Specifified port to start the server on;\nDefault is 9090.',
-    }),
-    root: core_1.Flags.string({
-        description: 'path to the root of the JB2 installation.\nCreates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json',
-    }),
-    bodySizeLimit: core_1.Flags.string({
-        description: 'Size limit of the update message; may need to increase if config is large.\nArgument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.',
-        default: '25mb',
-    }),
-    help: core_1.Flags.help({ char: 'h' }),
-};
-exports.default = AdminServer;
-function getNetworkAddress() {
-    for (const network of Object.values(os_1.default.networkInterfaces())) {
-        for (const networkInterface of network || []) {
-            const { address, family, internal } = networkInterface;
-            if (family === 'IPv4' && !internal) {
-                return address;
-            }
-        }
-    }
-    return undefined;
-}

package/lib/commands/create.js

@@ -1,111 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const fs_1 = __importDefault(require("fs"));
-const core_1 = require("@oclif/core");
-const decompress_1 = __importDefault(require("decompress"));
-const base_1 = __importDefault(require("../base"));
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
-const fsPromises = fs_1.default.promises;
-class Create extends base_1.default {
-    async run() {
-        const { args: runArgs, flags: runFlags } = await this.parse(Create);
-        const { localPath: argsPath } = runArgs;
-        this.debug(`Want to install path at: ${argsPath}`);
-        const { force, url, listVersions, tag, branch, nightly } = runFlags;
-        if (listVersions) {
-            const versions = (await this.fetchGithubVersions()).map(version => version.tag_name);
-            this.log(`All JBrowse versions:\n${versions.join('\n')}`);
-            this.exit();
-        }
-        // mkdir will do nothing if dir exists
-        await fsPromises.mkdir(argsPath, { recursive: true });
-        if (!force) {
-            await this.checkPath(argsPath);
-        }
-        const locationUrl = url ||
-            (nightly ? await this.getBranch('main') : '') ||
-            (branch ? await this.getBranch(branch) : '') ||
-            (tag ? await this.getTag(tag) : await this.getLatest());
-        this.log(`Fetching ${locationUrl}...`);
-        const response = await (0, fetchWithProxy_1.default)(locationUrl);
-        if (!response.ok) {
-            this.error(`Failed to fetch: ${response.statusText}`, { exit: 100 });
-        }
-        const type = response.headers.get('content-type');
-        if (url &&
-            type !== 'application/zip' &&
-            type !== 'application/octet-stream') {
-            this.error('The URL provided does not seem to be a JBrowse installation URL');
-        }
-        await (0, decompress_1.default)(Buffer.from(await response.arrayBuffer()), argsPath);
-        this.log(`Unpacked ${locationUrl} at ${argsPath}`);
-    }
-    async checkPath(userPath) {
-        const allFiles = await fsPromises.readdir(userPath);
-        if (allFiles.length > 0) {
-            this.error(`This directory (${userPath}) has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files`, { exit: 120 });
-        }
-    }
-    async catch(error) {
-        // @ts-expect-error
-        if (error.parse?.output.flags.listVersions) {
-            const versions = (await this.fetchGithubVersions()).map(version => version.tag_name);
-            this.log(`All JBrowse versions:\n${versions.join('\n')}`);
-            this.exit();
-        }
-        throw error;
-    }
-}
-Create.description = 'Downloads and installs the latest JBrowse 2 release';
-Create.examples = [
-    '# Download latest release from github, and put in specific path',
-    '$ 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',
-    '',
-    '# List available versions',
-    '$ jbrowse create --listVersions',
-];
-Create.args = {
-    localPath: core_1.Args.string({
-        required: true,
-        description: 'Location where JBrowse 2 will be installed',
-    }),
-};
-Create.flags = {
-    help: core_1.Flags.help({ char: 'h' }),
-    force: core_1.Flags.boolean({
-        char: 'f',
-        description: 'Overwrites existing JBrowse 2 installation if present in path',
-    }),
-    // will need to account for pagination once there is a lot of releases
-    listVersions: core_1.Flags.boolean({
-        char: 'l',
-        description: 'Lists out all versions of JBrowse 2',
-    }),
-    branch: core_1.Flags.string({
-        description: 'Download a development build from a named git branch',
-    }),
-    nightly: core_1.Flags.boolean({
-        description: 'Download the latest development build from the main branch',
-    }),
-    url: core_1.Flags.string({
-        char: 'u',
-        description: 'A direct URL to a JBrowse 2 release',
-    }),
-    tag: core_1.Flags.string({
-        char: 't',
-        description: 'Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest',
-    }),
-};
-exports.default = Create;

package/lib/commands/make-pif.js

@@ -1,116 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.flipCigar = flipCigar;
-exports.swapIndelCigar = swapIndelCigar;
-exports.createPIF = createPIF;
-const child_process_1 = require("child_process");
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-const core_1 = require("@oclif/core");
-const command_exists_1 = require("command-exists");
-const base_1 = __importDefault(require("../base"));
-const cigarRegex = new RegExp(/([MIDNSHPX=])/);
-function getReadline(filename) {
-    const stream = fs_1.default.createReadStream(filename);
-    return readline_1.default.createInterface({
-        input: /.b?gz$/.exec(filename) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
-    });
-}
-function getStdReadline() {
-    return readline_1.default.createInterface({
-        input: process.stdin,
-    });
-}
-function parseCigar(cigar = '') {
-    return cigar.split(cigarRegex).slice(0, -1);
-}
-function flipCigar(cigar) {
-    const arr = [];
-    for (let i = cigar.length - 2; i >= 0; i -= 2) {
-        arr.push(cigar[i]);
-        const op = cigar[i + 1];
-        if (op === 'D') {
-            arr.push('I');
-        }
-        else if (op === 'I') {
-            arr.push('D');
-        }
-        else {
-            arr.push(op);
-        }
-    }
-    return arr;
-}
-function swapIndelCigar(cigar) {
-    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
-}
-async function createPIF(filename, stream) {
-    const rl1 = filename ? getReadline(filename) : getStdReadline();
-    for await (const line of rl1) {
-        const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t');
-        stream.write(`${[`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t')}\n`);
-        const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'));
-        const CIGAR = rest[cigarIdx];
-        if (CIGAR) {
-            rest[cigarIdx] = `cg:Z:${strand === '-'
-                ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
-                : swapIndelCigar(CIGAR.slice(5))}`;
-        }
-        stream.write(`${[`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t')}\n`);
-    }
-    rl1.close();
-}
-class MakePIF extends base_1.default {
-    async run() {
-        const { args: { file }, flags: { out, csi }, } = await this.parse(MakePIF);
-        if ((0, command_exists_1.sync)('sh') &&
-            (0, command_exists_1.sync)('sort') &&
-            (0, command_exists_1.sync)('grep') &&
-            (0, command_exists_1.sync)('tabix') &&
-            (0, command_exists_1.sync)('bgzip')) {
-            const fn = out || `${path_1.default.basename(file || 'output', '.paf')}.pif.gz`;
-            const child = (0, child_process_1.spawn)('sh', [
-                '-c',
-                `sort -t"\`printf '\t'\`" -k1,1 -k3,3n | bgzip > ${fn}; tabix ${csi ? '-C ' : ''}-s1 -b3 -e4 -0 ${fn}`,
-            ], {
-                env: { ...process.env, LC_ALL: 'C' },
-                stdio: ['pipe', process.stdout, process.stderr],
-            });
-            await createPIF(file, child.stdin);
-            child.stdin.end();
-            await new Promise(resolve => {
-                child.on('close', resolve);
-            });
-        }
-        else {
-            throw new Error('Unable to sort, requires unix type environment with sort, grep, bgzip, tabix');
-        }
-    }
-}
-MakePIF.description = 'creates pairwise indexed PAF (PIF), with bgzip and tabix';
-MakePIF.examples = [
-    '$ jbrowse pif input.paf # creates input.pif.gz in same directory',
-    '',
-    '$ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
-];
-MakePIF.flags = {
-    out: core_1.Flags.string({
-        description: 'Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi',
-    }),
-    csi: core_1.Flags.boolean({
-        description: 'Create a CSI index for the PIF file instead of TBI',
-    }),
-    help: core_1.Flags.help({ char: 'h' }),
-};
-MakePIF.args = {
-    file: core_1.Args.string({
-        required: true,
-        description: 'PAF file as input',
-    }),
-};
-exports.default = MakePIF;

package/lib/commands/remove-track.js

@@ -1,37 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const fs_1 = require("fs");
-const core_1 = require("@oclif/core");
-const base_1 = __importDefault(require("../base"));
-class RemoveTrackJson extends base_1.default {
-    async run() {
-        const { args, flags: runFlags } = await this.parse(RemoveTrackJson);
-        const output = runFlags.target || runFlags.out || '.';
-        const isDir = (await fs_1.promises.lstat(output)).isDirectory();
-        this.target = isDir ? `${output}/config.json` : output;
-        const { track: inputId } = args;
-        const config = await this.readJsonFile(this.target);
-        config.tracks = config.tracks?.filter(({ trackId }) => trackId !== inputId);
-        await this.writeJsonFile(this.target, config);
-    }
-}
-RemoveTrackJson.description = 'Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!';
-RemoveTrackJson.examples = ['$ jbrowse remove-track-json trackId'];
-RemoveTrackJson.args = {
-    track: core_1.Args.string({
-        required: true,
-        description: 'track JSON file or command line arg blob',
-    }),
-};
-RemoveTrackJson.flags = {
-    target: core_1.Flags.string({
-        description: 'path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent',
-    }),
-    out: core_1.Flags.string({
-        description: 'synonym for target',
-    }),
-};
-exports.default = RemoveTrackJson;

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

@@ -1,98 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const fs_1 = __importDefault(require("fs"));
-const core_1 = require("@oclif/core");
-const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const base_1 = __importDefault(require("../base"));
-const fsPromises = fs_1.default.promises;
-class SetDefaultSession extends base_1.default {
-    async run() {
-        const { flags: runFlags } = await this.parse(SetDefaultSession);
-        const { session, currentSession, delete: deleteDefaultSession } = runFlags;
-        const output = runFlags.target || runFlags.out || '.';
-        const isDir = (await fsPromises.lstat(output)).isDirectory();
-        this.target = isDir ? `${output}/config.json` : output;
-        const configContents = await this.readJsonFile(this.target);
-        if (deleteDefaultSession) {
-            configContents.defaultSession = undefined;
-            await this.writeJsonFile(this.target, configContents);
-        }
-        else if (currentSession) {
-            this.log(`The current default session is ${JSON.stringify(configContents.defaultSession)}`);
-            this.exit();
-        }
-        else if (!session) {
-            this.error('Please provide a --session file', { exit: 120 });
-        }
-        else if (session) {
-            await this.writeJsonFile(this.target, {
-                ...configContents,
-                defaultSession: await this.readDefaultSessionFile(session),
-            });
-        }
-    }
-    async readDefaultSessionFile(defaultSessionFile) {
-        let defaultSessionJson;
-        try {
-            defaultSessionJson = await fsPromises.readFile(defaultSessionFile, {
-                encoding: 'utf8',
-            });
-        }
-        catch (error) {
-            return this.error('Could not read the provided file', { exit: 150 });
-        }
-        try {
-            const session = (0, json_parse_better_errors_1.default)(defaultSessionJson);
-            // return top-level "session" if it exists, such as in files created by
-            // "File -> Export session"
-            return session.session || session;
-        }
-        catch (error) {
-            return this.error('Could not parse the given default session file', {
-                exit: 160,
-            });
-        }
-    }
-}
-SetDefaultSession.description = 'Set a default session with views and tracks';
-SetDefaultSession.examples = [
-    '# set default session for the config.json in your current directory',
-    '$ jbrowse set-default-session --session /path/to/default/session.json',
-    '',
-    '# make session.json the defaultSession on the specified target config.json file',
-    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json',
-    '',
-    '# print current default session',
-    '$ jbrowse set-default-session --currentSession # Prints out current default session',
-];
-SetDefaultSession.flags = {
-    session: core_1.Flags.string({
-        char: 's',
-        description: 'set path to a file containing session in json format (required, unless using delete/currentSession flags)',
-    }),
-    name: core_1.Flags.string({
-        char: 'n',
-        description: 'Give a name for the default session',
-        default: 'New Default Session',
-    }),
-    currentSession: core_1.Flags.boolean({
-        char: 'c',
-        description: 'List out the current default session',
-    }),
-    target: core_1.Flags.string({
-        description: 'path to config file in JB2 installation directory to write out to',
-    }),
-    out: core_1.Flags.string({
-        description: 'synonym for target',
-    }),
-    delete: core_1.Flags.boolean({
-        description: 'Delete any existing default session.',
-    }),
-    help: core_1.Flags.help({
-        char: 'h',
-    }),
-};
-exports.default = SetDefaultSession;

package/lib/commands/sort-bed.js

@@ -1,45 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const child_process_1 = require("child_process");
-const core_1 = require("@oclif/core");
-const command_exists_1 = require("command-exists");
-const base_1 = __importDefault(require("../base"));
-class SortGff extends base_1.default {
-    async run() {
-        const { args: { file }, } = await this.parse(SortGff);
-        if ((0, command_exists_1.sync)('sh') &&
-            (0, command_exists_1.sync)('sort') &&
-            (0, command_exists_1.sync)('grep')) {
-            // this command comes from the tabix docs http://www.htslib.org/doc/tabix.html
-            (0, child_process_1.spawn)('sh', [
-                '-c',
-                `(grep "^#" "${file}"; grep -v "^#" "${file}" | sort -t"\`printf '\t'\`" -k1,1 -k2,2n)`,
-            ], {
-                env: { ...process.env, LC_ALL: 'C' },
-                stdio: 'inherit',
-            });
-        }
-        else {
-            throw new Error('Unable to sort, requires unix type environment with sort, grep');
-        }
-    }
-}
-SortGff.description = 'Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep';
-SortGff.examples = [
-    '# sort gff and pipe to bgzip',
-    '$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz',
-    '$ tabix sorted.gff.gz',
-];
-SortGff.args = {
-    file: core_1.Args.string({
-        required: true,
-        description: 'GFF file',
-    }),
-};
-SortGff.flags = {
-    help: core_1.Flags.help({ char: 'h' }),
-};
-exports.default = SortGff;

package/lib/commands/sort-gff.js

@@ -1,45 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const child_process_1 = require("child_process");
-const core_1 = require("@oclif/core");
-const command_exists_1 = require("command-exists");
-const base_1 = __importDefault(require("../base"));
-class SortGff extends base_1.default {
-    async run() {
-        const { args: { file }, } = await this.parse(SortGff);
-        if ((0, command_exists_1.sync)('sh') &&
-            (0, command_exists_1.sync)('sort') &&
-            (0, command_exists_1.sync)('grep')) {
-            // this command comes from the tabix docs http://www.htslib.org/doc/tabix.html
-            (0, child_process_1.spawn)('sh', [
-                '-c',
-                `(grep "^#" "${file}"; grep -v "^#" "${file}" | sort -t"\`printf '\t'\`" -k1,1 -k4,4n)`,
-            ], {
-                env: { ...process.env, LC_ALL: 'C' },
-                stdio: 'inherit',
-            });
-        }
-        else {
-            throw new Error('Unable to sort, requires unix type environment with sort, grep');
-        }
-    }
-}
-SortGff.description = 'Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep';
-SortGff.examples = [
-    '# sort gff and pipe to bgzip',
-    '$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz',
-    '$ tabix sorted.gff.gz',
-];
-SortGff.args = {
-    file: core_1.Args.string({
-        required: true,
-        description: 'GFF file',
-    }),
-};
-SortGff.flags = {
-    help: core_1.Flags.help({ char: 'h' }),
-};
-exports.default = SortGff;