@jbrowse/cli 3.7.0 → 4.0.1

package/dist/commands/upgrade.js

@@ -8,8 +8,8 @@ const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const util_1 = require("util");
 const decompress_1 = __importDefault(require("decompress"));
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
-const utils_1 = require("../utils");
+const fetchWithProxy_ts_1 = __importDefault(require("../fetchWithProxy.js"));
+const utils_ts_1 = require("../utils.js");
 const description = 'Upgrades JBrowse 2 to latest version';
 const examples = [
     '# Upgrades current directory to latest jbrowse release',
@@ -74,7 +74,7 @@ async function run(args) {
     const argsPath = positionals[0];
     const { clean, listVersions, tag, url, branch, nightly } = runFlags;
     if (runFlags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             options,
             examples,
             usage: 'jbrowse upgrade [localPath] [options]',
@@ -83,7 +83,7 @@ async function run(args) {
         return;
     }
     if (listVersions) {
-        const versions = (await (0, utils_1.fetchGithubVersions)()).map(v => v.tag_name);
+        const versions = (await (0, utils_ts_1.fetchGithubVersions)()).map(v => v.tag_name);
         console.log(`All JBrowse versions:\n${versions.join('\n')}`);
         process.exit(0);
     }
@@ -95,11 +95,11 @@ async function run(args) {
         existing jbrowse 2 installation?`);
     }
     const locationUrl = url ||
-        (nightly ? await (0, utils_1.getBranch)('main') : '') ||
-        (branch ? await (0, utils_1.getBranch)(branch) : '') ||
-        (tag ? await (0, utils_1.getTag)(tag) : await (0, utils_1.getLatest)());
+        (nightly ? await (0, utils_ts_1.getBranch)('main') : '') ||
+        (branch ? await (0, utils_ts_1.getBranch)(branch) : '') ||
+        (tag ? await (0, utils_ts_1.getTag)(tag) : await (0, utils_ts_1.getLatest)());
     console.log(`Fetching ${locationUrl}...`);
-    const response = await (0, fetchWithProxy_1.default)(locationUrl);
+    const response = await (0, fetchWithProxy_ts_1.default)(locationUrl);
     if (!response.ok) {
         throw new Error(`HTTP ${response.status} fetching ${locationUrl}: ${response.statusText}`);
     }

package/dist/index.js

@@ -9,33 +9,33 @@ const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const util_1 = require("util");
 // Command imports
-const add_assembly_1 = require("./commands/add-assembly");
-const add_connection_1 = require("./commands/add-connection");
-const add_track_1 = require("./commands/add-track");
-const add_track_json_1 = require("./commands/add-track-json");
-const admin_server_1 = require("./commands/admin-server");
-const create_1 = require("./commands/create");
-const make_pif_1 = require("./commands/make-pif");
-const remove_track_1 = require("./commands/remove-track");
-const set_default_session_1 = require("./commands/set-default-session");
-const sort_bed_1 = require("./commands/sort-bed");
-const sort_gff_1 = require("./commands/sort-gff");
-const text_index_1 = require("./commands/text-index");
-const upgrade_1 = require("./commands/upgrade");
+const index_ts_1 = require("./commands/add-assembly/index.js");
+const add_connection_ts_1 = require("./commands/add-connection.js");
+const add_track_json_ts_1 = require("./commands/add-track-json.js");
+const add_track_ts_1 = require("./commands/add-track.js");
+const index_ts_2 = require("./commands/admin-server/index.js");
+const create_ts_1 = require("./commands/create.js");
+const index_ts_3 = require("./commands/make-pif/index.js");
+const remove_track_ts_1 = require("./commands/remove-track.js");
+const set_default_session_ts_1 = require("./commands/set-default-session.js");
+const sort_bed_ts_1 = require("./commands/sort-bed.js");
+const sort_gff_ts_1 = require("./commands/sort-gff.js");
+const index_ts_4 = require("./commands/text-index/index.js");
+const upgrade_ts_1 = require("./commands/upgrade.js");
 const commands = {
-    create: create_1.run,
-    'add-assembly': add_assembly_1.run,
-    'add-track': add_track_1.run,
-    'text-index': text_index_1.run,
-    'admin-server': admin_server_1.run,
-    upgrade: upgrade_1.run,
-    'make-pif': make_pif_1.run,
-    'sort-gff': sort_gff_1.run,
-    'sort-bed': sort_bed_1.run,
-    'add-connection': add_connection_1.run,
-    'add-track-json': add_track_json_1.run,
-    'remove-track': remove_track_1.run,
-    'set-default-session': set_default_session_1.run,
+    create: create_ts_1.run,
+    'add-assembly': index_ts_1.run,
+    'add-track': add_track_ts_1.run,
+    'text-index': index_ts_4.run,
+    'admin-server': index_ts_2.run,
+    upgrade: upgrade_ts_1.run,
+    'make-pif': index_ts_3.run,
+    'sort-gff': sort_gff_ts_1.run,
+    'sort-bed': sort_bed_ts_1.run,
+    'add-connection': add_connection_ts_1.run,
+    'add-track-json': add_track_json_ts_1.run,
+    'remove-track': remove_track_ts_1.run,
+    'set-default-session': set_default_session_ts_1.run,
 };
 async function main(args) {
     try {
@@ -84,7 +84,19 @@ async function main(args) {
         await command(commandArgs);
     }
     catch (error) {
-        console.error('Error:', error instanceof Error ? error.message : error);
+        const message = error instanceof Error ? error.message : String(error);
+        const code = error instanceof Error ? error.code : undefined;
+        console.error('Error:', message);
+        if (code === 'EPIPE' || code === 'ENOSPC' || message.includes('EPIPE')) {
+            console.error(`
+This error may be caused by running out of space in the temporary directory.
+Try setting a custom TMPDIR with more available space:
+
+  mkdir mytmpdir
+  TMPDIR=mytmpdir jbrowse text-index ...
+
+`);
+        }
         process.exit(1);
     }
 }

package/dist/types/common.js

@@ -10,9 +10,9 @@ exports.supported = supported;
 exports.generateMeta = generateMeta;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
+const fetchWithProxy_ts_1 = __importDefault(require("../fetchWithProxy.js"));
 async function createRemoteStream(urlIn) {
-    const res = await (0, fetchWithProxy_1.default)(urlIn);
+    const res = await (0, fetchWithProxy_ts_1.default)(urlIn);
     if (!res.ok) {
         throw new Error(`Failed to fetch ${urlIn} status ${res.status} ${await res.text()}`);
     }
@@ -105,13 +105,14 @@ function guessAdapterFromFileName(filePath) {
         throw new Error(`Unsupported file type ${filePath}`);
     }
 }
+const SUPPORTED_ADAPTERS = new Set([
+    'Gff3TabixAdapter',
+    'VcfTabixAdapter',
+    'Gff3Adapter',
+    'VcfAdapter',
+]);
 function supported(type = '') {
-    return [
-        'Gff3TabixAdapter',
-        'VcfTabixAdapter',
-        'Gff3Adapter',
-        'VcfAdapter',
-    ].includes(type);
+    return SUPPORTED_ADAPTERS.has(type);
 }
 async function generateMeta({ trackConfigs, attributes, outLocation, name, typesToExclude, assemblyNames, }) {
     const tracks = trackConfigs.map(({ adapter, textSearching, trackId }) => ({

package/dist/types/gff3Adapter.js

@@ -1,35 +1,18 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexGff3 = indexGff3;
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-const cli_progress_1 = require("cli-progress");
-const util_1 = require("../util");
+const util_ts_1 = require("../util.js");
+const streamUtils_ts_1 = require("./streamUtils.js");
 async function* indexGff3({ config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, }) {
     const { trackId } = config;
-    // 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({
-        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
-        etaBuffer: 2000,
-    }, cli_progress_1.Presets.shades_classic);
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, util_1.getLocalOrRemoteStream)(inLocation, outLocation);
-    if (!quiet) {
-        progressBar.start(totalBytes, 0);
-    }
-    // @ts-expect-error
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        progressBar.update(receivedBytes);
-    });
-    const rl = readline_1.default.createInterface({
-        // @ts-expect-error
-        input: /.b?gz$/.exec(inLocation) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+    const { rl, progressBar } = await (0, streamUtils_ts_1.createIndexingStream)({
+        inLocation,
+        outLocation,
+        trackId,
+        quiet,
     });
+    const excludeSet = new Set(typesToExclude);
+    const encodedTrackId = encodeURIComponent(trackId);
     for await (const line of rl) {
         if (!line.trim()) {
             continue;
@@ -41,31 +24,17 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
             break;
         }
         const [seq_id, , type, start, end, , , , col9] = line.split('\t');
-        const locStr = `${seq_id}:${start}..${end}`;
-        if (!typesToExclude.includes(type)) {
-            // turns gff3 attrs into a map, and converts the arrays into space
-            // separated strings
-            const col9attrs = Object.fromEntries(col9
-                .split(';')
-                .map(f => f.trim())
-                .filter(f => !!f)
-                .map(f => f.split('='))
-                .map(([key, val]) => [
-                key.trim(),
-                val
-                    ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
-                    : undefined,
-            ]));
+        if (!excludeSet.has(type)) {
+            const col9attrs = (0, streamUtils_ts_1.parseAttributes)(col9, util_ts_1.decodeURIComponentNoThrow);
             const attrs = attributesToIndex
                 .map(attr => col9attrs[attr])
                 .filter((f) => !!f);
-            if (attrs.length) {
-                const record = JSON.stringify([
-                    encodeURIComponent(locStr),
-                    encodeURIComponent(trackId),
-                    ...attrs.map(a => encodeURIComponent(a)),
-                ]).replaceAll(',', '|');
-                yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
+            if (attrs.length > 0) {
+                const locStr = `${seq_id}:${start}..${end}`;
+                const encodedAttrs = attrs.map(a => `"${encodeURIComponent(a)}"`);
+                const record = `["${encodeURIComponent(locStr)}"|"${encodedTrackId}"|${encodedAttrs.join('|')}]`;
+                const uniqueAttrs = [...new Set(attrs)];
+                yield `${record} ${uniqueAttrs.join(' ')}\n`;
             }
         }
     }

package/dist/types/streamUtils.js

@@ -0,0 +1,66 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createIndexingStream = createIndexingStream;
+exports.parseAttributes = parseAttributes;
+const cli_progress_1 = require("cli-progress");
+const util_ts_1 = require("../util.js");
+async function* readLines(reader, progressBar) {
+    const decoder = new TextDecoder();
+    let buffer = '';
+    let receivedBytes = 0;
+    try {
+        let result = await reader.read();
+        while (!result.done) {
+            receivedBytes += result.value.length;
+            progressBar.update(receivedBytes);
+            buffer += decoder.decode(result.value, { stream: true });
+            const lines = buffer.split('\n');
+            buffer = lines.pop();
+            for (const line of lines) {
+                yield line;
+            }
+            result = await reader.read();
+        }
+    }
+    finally {
+        reader.releaseLock();
+    }
+    buffer += decoder.decode();
+    if (buffer) {
+        yield buffer;
+    }
+}
+async function createIndexingStream({ inLocation, outLocation, trackId, quiet, }) {
+    const progressBar = new cli_progress_1.SingleBar({
+        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
+        etaBuffer: 2000,
+    }, cli_progress_1.Presets.shades_classic);
+    const { totalBytes, stream } = await (0, util_ts_1.getLocalOrRemoteStream)(inLocation, outLocation);
+    if (!quiet) {
+        progressBar.start(totalBytes, 0);
+    }
+    if (!stream) {
+        throw new Error(`Failed to fetch ${inLocation}: no response body`);
+    }
+    const inputStream = /.b?gz$/.exec(inLocation)
+        ? // @ts-ignore root tsconfig includes DOM lib which has incompatible stream types
+            stream.pipeThrough(new DecompressionStream('gzip'))
+        : stream;
+    const rl = readLines(inputStream.getReader(), progressBar);
+    return { rl, progressBar };
+}
+function parseAttributes(infoString, decodeFunc) {
+    const result = {};
+    for (const field of infoString.split(';')) {
+        const trimmed = field.trim();
+        if (trimmed) {
+            const eqIdx = trimmed.indexOf('=');
+            if (eqIdx !== -1) {
+                const key = trimmed.slice(0, eqIdx).trim();
+                const val = trimmed.slice(eqIdx + 1);
+                result[key] = decodeFunc(val).trim().replaceAll(',', ' ');
+            }
+        }
+    }
+    return result;
+}

package/dist/types/vcfAdapter.js

@@ -1,75 +1,38 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexVcf = indexVcf;
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-const cli_progress_1 = require("cli-progress");
-const util_1 = require("../util");
+const util_ts_1 = require("../util.js");
+const streamUtils_ts_1 = require("./streamUtils.js");
 async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }) {
     const { trackId } = config;
-    // 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({
-        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
-        etaBuffer: 2000,
-    }, cli_progress_1.Presets.shades_classic);
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, util_1.getLocalOrRemoteStream)(inLocation, outLocation);
-    if (!quiet) {
-        progressBar.start(totalBytes, 0);
-    }
-    // @ts-expect-error
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        progressBar.update(receivedBytes);
-    });
-    const gzStream = /.b?gz$/.exec(inLocation)
-        ? // @ts-expect-error
-            stream.pipe((0, zlib_1.createGunzip)())
-        : stream;
-    const rl = readline_1.default.createInterface({
-        input: gzStream,
+    const { rl, progressBar } = await (0, streamUtils_ts_1.createIndexingStream)({
+        inLocation,
+        outLocation,
+        trackId,
+        quiet,
     });
+    const encodedTrackId = encodeURIComponent(trackId);
     for await (const line of rl) {
         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
-                ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
-                : undefined,
-        ]));
-        const end = fields.END;
-        const locStr = `${ref}:${pos}..${end || +pos + 1}`;
         if (id === '.') {
             continue;
         }
+        const fields = (0, streamUtils_ts_1.parseAttributes)(info, util_ts_1.decodeURIComponentNoThrow);
+        const end = fields.END;
+        const locStr = `${ref}:${pos}..${end || +pos + 1}`;
+        const encodedLocStr = encodeURIComponent(locStr);
         const infoAttrs = attributesToIndex
             .map(attr => fields[attr])
             .filter((f) => !!f);
-        const ids = id.split(',');
-        for (const id of ids) {
-            const attrs = [id];
-            const record = JSON.stringify([
-                encodeURIComponent(locStr),
-                encodeURIComponent(trackId),
-                encodeURIComponent(id || ''),
-                ...infoAttrs.map(a => encodeURIComponent(a || '')),
-            ]).replaceAll(',', '|');
-            yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
+        const encodedInfoAttrs = infoAttrs.map(a => `"${encodeURIComponent(a)}"`);
+        for (const variantId of id.split(',')) {
+            const encodedId = encodeURIComponent(variantId);
+            const record = `["${encodedLocStr}"|"${encodedTrackId}"|"${encodedId}"${encodedInfoAttrs.length > 0 ? `|${encodedInfoAttrs.join('|')}` : ''}]`;
+            yield `${record} ${variantId}\n`;
         }
     }
     progressBar.stop();

package/dist/util.js

@@ -5,12 +5,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
 exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
-const fs_1 = __importDefault(require("fs"));
+const fs_1 = require("fs");
+const promises_1 = require("fs/promises");
 const path_1 = __importDefault(require("path"));
-const common_1 = require("./types/common");
+const stream_1 = require("stream");
+const common_ts_1 = require("./types/common.js");
 async function getLocalOrRemoteStream(uri, out) {
-    if ((0, common_1.isURL)(uri)) {
-        const result = await (0, common_1.createRemoteStream)(uri);
+    if ((0, common_ts_1.isURL)(uri)) {
+        const result = await (0, common_ts_1.createRemoteStream)(uri);
         return {
             totalBytes: +(result.headers.get('Content-Length') || 0),
             stream: result.body,
@@ -18,17 +20,22 @@ async function getLocalOrRemoteStream(uri, out) {
     }
     else {
         const filename = path_1.default.isAbsolute(uri) ? uri : path_1.default.join(out, uri);
+        const stats = await (0, promises_1.stat)(filename);
+        const nodeStream = (0, fs_1.createReadStream)(filename);
         return {
-            totalBytes: fs_1.default.statSync(filename).size,
-            stream: fs_1.default.createReadStream(filename),
+            totalBytes: stats.size,
+            stream: stream_1.Readable.toWeb(nodeStream),
         };
     }
 }
 function decodeURIComponentNoThrow(uri) {
+    if (!uri.includes('%')) {
+        return uri;
+    }
     try {
         return decodeURIComponent(uri);
     }
-    catch (e) {
+    catch {
         // avoid throwing exception on a failure to decode URI component
         return uri;
     }

package/dist/utils.js

@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.debug = debug;
+exports.resolveConfigPath = resolveConfigPath;
 exports.readFile = readFile;
 exports.readJsonFile = readJsonFile;
 exports.writeJsonFile = writeJsonFile;
@@ -18,12 +19,17 @@ exports.printHelp = printHelp;
 const fs_1 = require("fs");
 const path_1 = __importDefault(require("path"));
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const fetchWithProxy_1 = __importDefault(require("./fetchWithProxy"));
+const fetchWithProxy_ts_1 = __importDefault(require("./fetchWithProxy.js"));
 function debug(message) {
     if (process.env.DEBUG) {
         console.log(`DEBUG: ${message}`);
     }
 }
+async function resolveConfigPath(target, out) {
+    const output = target || out || '.';
+    const stat = await fs_1.promises.lstat(output);
+    return stat.isDirectory() ? `${output}/config.json` : output;
+}
 async function readFile(location) {
     return fs_1.promises.readFile(location, { encoding: 'utf8' });
 }
@@ -45,8 +51,7 @@ async function resolveFileLocation(location, check = true, inPlace = false) {
     }
     if (locationUrl) {
         if (check) {
-            // @ts-expect-error
-            const response = await (0, fetchWithProxy_1.default)(locationUrl, { method: 'HEAD' });
+            const response = await (0, fetchWithProxy_ts_1.default)(locationUrl, { method: 'HEAD' });
             if (!response.ok) {
                 throw new Error(`${locationUrl} result ${response.statusText}`);
             }
@@ -112,7 +117,7 @@ async function* fetchVersions() {
     let result;
     do {
         const url = `https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`;
-        const response = await (0, fetchWithProxy_1.default)(url);
+        const response = await (0, fetchWithProxy_ts_1.default)(url);
         if (response.ok) {
             result = (await response.json());
             yield result.filter(release => release.tag_name.startsWith('v'));
@@ -124,7 +129,7 @@ async function* fetchVersions() {
     } while (result.length);
 }
 async function getTag(tag) {
-    const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
+    const response = await (0, fetchWithProxy_ts_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
     if (response.ok) {
         const result = (await response.json());
         const file = result.assets?.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -27,27 +27,24 @@
   "engines": {
     "node": ">=18.3.0"
   },
-  "scripts": {
-    "prebuild": "npm run clean",
-    "build": "tsc --build && webpack",
-    "clean": "rimraf dist bundle",
-    "prepack": "npm run clean  && npm run docs",
-    "predocs": "npm run build",
-    "docs": "./generate_readme.sh > README.md"
-  },
   "dependencies": {
-    "cli-progress": "^3.9.0",
+    "cli-progress": "^3.12.0",
     "command-exists": "^1.2.9",
     "cors": "^2.8.5",
-    "decompress": "^4.0.0",
-    "express": "^5.1.0",
-    "ixixx": "^2.0.1",
+    "decompress": "^4.2.1",
+    "express": "^5.2.1",
+    "ixixx": "^3.0.2",
     "json-parse-better-errors": "^1.0.2",
-    "node-fetch-native": "^1.6.4",
-    "tmp": "^0.2.1"
+    "node-fetch-native": "^1.6.7",
+    "tmp": "^0.2.5"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "scripts": {
+    "prebuild": "pnpm clean",
+    "build": "tsc && webpack",
+    "clean": "rimraf bundle",
+    "generate-readme": "./generate_readme.sh > README.md"
+  }
+}

package/dist/commands/make-pif-utils/validators.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateFileArgument = validateFileArgument;
-exports.validateRequiredCommands = validateRequiredCommands;
-const command_exists_1 = require("command-exists");
-function validateFileArgument(file) {
-    // Allow no file argument for stdin input
-    if (!file && process.stdin.isTTY) {
-        console.error('Error: Missing required argument: file');
-        console.error('Usage: jbrowse make-pif <file> [options]');
-        console.error('       OR pipe data via stdin: cat file.paf | jbrowse make-pif');
-        process.exit(1);
-    }
-}
-function validateRequiredCommands() {
-    const requiredCommands = ['sh', 'sort', 'grep', 'tabix', 'bgzip'];
-    const missingCommands = requiredCommands.filter(cmd => !(0, command_exists_1.sync)(cmd));
-    if (missingCommands.length > 0) {
-        console.error('Error: Unable to sort, requires unix type environment with sort, grep, bgzip, tabix');
-        process.exit(1);
-    }
-}

package/dist/commands/sort-bed-utils/constants.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.REQUIRED_COMMANDS = exports.SORT_BED_EXAMPLES = exports.SORT_BED_DESCRIPTION = void 0;
-exports.SORT_BED_DESCRIPTION = 'Helper utility to sort BED 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';
-exports.SORT_BED_EXAMPLES = [
-    '# sort bed and pipe to bgzip',
-    '$ jbrowse sort-bed input.bed | bgzip > sorted.bed.gz',
-    '$ tabix sorted.bed.gz',
-    '',
-    '# OR pipe data via stdin: cat file.bed | jbrowse sort-bed | bgzip > sorted.bed.gz',
-];
-exports.REQUIRED_COMMANDS = ['sh', 'sort', 'grep'];

package/dist/commands/sort-bed-utils/sort-utils.js

@@ -1,24 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getMinimalEnvironment = getMinimalEnvironment;
-exports.createSortCommandForFile = createSortCommandForFile;
-exports.spawnSortProcess = spawnSortProcess;
-const child_process_1 = require("child_process");
-function getMinimalEnvironment() {
-    return {
-        ...process.env,
-        LC_ALL: 'C',
-    };
-}
-function createSortCommandForFile(file) {
-    // BED files use columns 1,2 (0-based) for chromosome and start position
-    return `(grep "^#" "${file}"; grep -v "^#" "${file}" | sort -t"\`printf '\\t'\`" -k1,1 -k2,2n)`;
-}
-function spawnSortProcess(options) {
-    const command = createSortCommandForFile(options.file);
-    const env = getMinimalEnvironment();
-    return (0, child_process_1.spawn)('sh', ['-c', command], {
-        env,
-        stdio: 'inherit',
-    });
-}

package/dist/commands/sort-bed-utils/validators.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateFileArgument = validateFileArgument;
-exports.validateRequiredCommands = validateRequiredCommands;
-const command_exists_1 = require("command-exists");
-function validateFileArgument(file) {
-    // Allow no file argument for stdin input
-    if (!file && process.stdin.isTTY) {
-        console.error('Error: Missing required argument: file');
-        console.error('Usage: jbrowse sort-bed <file>');
-        console.error('       OR pipe data via stdin: cat file.bed | jbrowse sort-bed');
-        process.exit(1);
-    }
-}
-function validateRequiredCommands() {
-    const requiredCommands = ['sh', 'sort', 'grep'];
-    const missingCommands = requiredCommands.filter(cmd => !(0, command_exists_1.sync)(cmd));
-    if (missingCommands.length > 0) {
-        console.error('Error: Unable to sort, requires unix type environment with sort, grep');
-        process.exit(1);
-    }
-}

package/dist/commands/sort-gff-utils/constants.js

@@ -1,13 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.REQUIRED_COMMANDS = exports.SORT_GFF_EXAMPLES = exports.SORT_GFF_DESCRIPTION = void 0;
-exports.SORT_GFF_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';
-exports.SORT_GFF_EXAMPLES = [
-    '# sort gff and pipe to bgzip',
-    '$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz',
-    '$ tabix sorted.gff.gz',
-    '',
-    '# sort gff from stdin',
-    '$ cat input.gff | jbrowse sort-gff | bgzip > sorted.gff.gz',
-];
-exports.REQUIRED_COMMANDS = ['sh', 'sort', 'grep'];