@jbrowse/cli 4.0.4 → 4.1.3

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

@@ -1,13 +1,8 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseCigar = parseCigar;
-exports.flipCigar = flipCigar;
-exports.swapIndelCigar = swapIndelCigar;
 const cigarRegex = new RegExp(/([MIDNSHPX=])/);
-function parseCigar(cigar = '') {
+export function parseCigar(cigar = '') {
     return cigar.split(cigarRegex).slice(0, -1);
 }
-function flipCigar(cigar) {
+export function flipCigar(cigar) {
     const arr = [];
     for (let i = cigar.length - 2; i >= 0; i -= 2) {
         arr.push(cigar[i]);
@@ -24,6 +19,6 @@ function flipCigar(cigar) {
     }
     return arr;
 }
-function swapIndelCigar(cigar) {
+export function swapIndelCigar(cigar) {
     return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
 }

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

@@ -1,26 +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.getReadline = getReadline;
-exports.getStdReadline = getStdReadline;
-exports.createWriteWithBackpressure = createWriteWithBackpressure;
-const fs_1 = __importDefault(require("fs"));
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-function getReadline(filename) {
-    const stream = fs_1.default.createReadStream(filename);
-    return readline_1.default.createInterface({
-        input: /.b?gz$/.exec(filename) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+import fs from 'fs';
+import readline from 'readline';
+import { createGunzip } from 'zlib';
+export function getReadline(filename) {
+    const stream = fs.createReadStream(filename);
+    return readline.createInterface({
+        input: /.b?gz$/.exec(filename) ? stream.pipe(createGunzip()) : stream,
     });
 }
-function getStdReadline() {
-    return readline_1.default.createInterface({
+export function getStdReadline() {
+    return readline.createInterface({
         input: process.stdin,
     });
 }
-function createWriteWithBackpressure(stream) {
+export function createWriteWithBackpressure(stream) {
     return (data) => {
         // If the stream buffer is full (write returns false), we need to wait for drain
         if (!stream.write(data)) {

package/dist/commands/make-pif/index.js

@@ -1,11 +1,8 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const util_1 = require("util");
-const pif_generator_ts_1 = require("./pif-generator.js");
-const utils_ts_1 = require("../../utils.js");
-const validators_ts_1 = require("../shared/validators.js");
-async function run(args) {
+import { parseArgs } from 'util';
+import { createPIF, getOutputFilename, spawnSortProcess, waitForProcessClose, } from "./pif-generator.js";
+import { printHelp } from "../../utils.js";
+import { validateFileArgument, validateRequiredCommands, } from "../shared/validators.js";
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
@@ -20,7 +17,7 @@ async function run(args) {
             description: 'Create a CSI index for the PIF file instead of TBI',
         },
     };
-    const { values: flags, positionals } = (0, util_1.parseArgs)({
+    const { values: flags, positionals } = parseArgs({
         args,
         options,
         allowPositionals: true,
@@ -32,7 +29,7 @@ async function run(args) {
         '$ jbrowse make-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
     ];
     if (flags.help) {
-        (0, utils_ts_1.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse make-pif <file> [options]',
@@ -41,12 +38,12 @@ async function run(args) {
         return;
     }
     const file = positionals[0];
-    (0, validators_ts_1.validateFileArgument)(file, 'make-pif', 'paf');
-    (0, validators_ts_1.validateRequiredCommands)(['sh', 'sort', 'grep', 'tabix', 'bgzip']);
+    validateFileArgument(file, 'make-pif', 'paf');
+    validateRequiredCommands(['sh', 'sort', 'grep', 'tabix', 'bgzip']);
     const { out, csi = false } = flags;
-    const outputFile = (0, pif_generator_ts_1.getOutputFilename)(file, out);
-    const child = (0, pif_generator_ts_1.spawnSortProcess)(outputFile, csi);
-    await (0, pif_generator_ts_1.createPIF)(file, child.stdin);
+    const outputFile = getOutputFilename(file, out);
+    const child = spawnSortProcess(outputFile, csi);
+    await createPIF(file, child.stdin);
     child.stdin.end();
-    await (0, pif_generator_ts_1.waitForProcessClose)(child);
+    await waitForProcessClose(child);
 }

package/dist/commands/make-pif/pif-generator.js

@@ -1,19 +1,10 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.createPIF = createPIF;
-exports.spawnSortProcess = spawnSortProcess;
-exports.getOutputFilename = getOutputFilename;
-exports.waitForProcessClose = waitForProcessClose;
-const child_process_1 = require("child_process");
-const path_1 = __importDefault(require("path"));
-const cigar_utils_ts_1 = require("./cigar-utils.js");
-const file_utils_ts_1 = require("./file-utils.js");
-async function createPIF(filename, stream) {
-    const rl1 = filename ? (0, file_utils_ts_1.getReadline)(filename) : (0, file_utils_ts_1.getStdReadline)();
-    const writeWithBackpressure = (0, file_utils_ts_1.createWriteWithBackpressure)(stream);
+import { spawn } from 'child_process';
+import path from 'path';
+import { flipCigar, parseCigar, swapIndelCigar } from "./cigar-utils.js";
+import { createWriteWithBackpressure, getReadline, getStdReadline, } from "./file-utils.js";
+export async function createPIF(filename, stream) {
+    const rl1 = filename ? getReadline(filename) : getStdReadline();
+    const writeWithBackpressure = createWriteWithBackpressure(stream);
     // Process the file line by line with backpressure handling
     try {
         for await (const line of rl1) {
@@ -24,8 +15,8 @@ async function createPIF(filename, stream) {
             const CIGAR = rest[cigarIdx];
             if (CIGAR) {
                 rest[cigarIdx] = `cg:Z:${strand === '-'
-                    ? (0, cigar_utils_ts_1.flipCigar)((0, cigar_utils_ts_1.parseCigar)(CIGAR.slice(5))).join('')
-                    : (0, cigar_utils_ts_1.swapIndelCigar)(CIGAR.slice(5))}`;
+                    ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
+                    : swapIndelCigar(CIGAR.slice(5))}`;
             }
             // Write the second line and handle backpressure
             await writeWithBackpressure(`${[`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t')}\n`);
@@ -39,7 +30,7 @@ async function createPIF(filename, stream) {
         rl1.close();
     }
 }
-function spawnSortProcess(outputFile, useCsi) {
+export function spawnSortProcess(outputFile, useCsi) {
     // Use a more portable approach to avoid E2BIG errors
     const sortCmd = `sort -t"\`printf '\\t'\`" -k1,1 -k3,3n`;
     const bgzipCommand = `bgzip > "${outputFile}"`;
@@ -49,15 +40,15 @@ function spawnSortProcess(outputFile, useCsi) {
         ...process.env,
         LC_ALL: 'C',
     };
-    return (0, child_process_1.spawn)('sh', ['-c', fullCommand], {
+    return spawn('sh', ['-c', fullCommand], {
         env: minimalEnv,
         stdio: ['pipe', process.stdout, process.stderr],
     });
 }
-function getOutputFilename(file, out) {
-    return out || `${path_1.default.basename(file || 'output', '.paf')}.pif.gz`;
+export function getOutputFilename(file, out) {
+    return out || `${path.basename(file || 'output', '.paf')}.pif.gz`;
 }
-async function waitForProcessClose(child) {
+export async function waitForProcessClose(child) {
     return new Promise(resolve => {
         child.on('close', resolve);
     });

package/dist/commands/process-utils.js

@@ -1,7 +1,4 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.waitForProcessClose = waitForProcessClose;
-async function waitForProcessClose(child) {
+export async function waitForProcessClose(child) {
     return new Promise((resolve, reject) => {
         child.on('close', code => {
             resolve(code);

package/dist/commands/remove-track.js

@@ -1,9 +1,6 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const util_1 = require("util");
-const utils_ts_1 = require("../utils.js");
-async function run(args) {
+import { parseArgs } from 'util';
+import { printHelp, readJsonFile, resolveConfigPath, writeJsonFile, } from "../utils.js";
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
@@ -18,7 +15,7 @@ async function run(args) {
             description: 'Synonym for target',
         },
     };
-    const { values: flags, positionals } = (0, util_1.parseArgs)({
+    const { values: flags, positionals } = parseArgs({
         args,
         options,
         allowPositionals: true,
@@ -26,7 +23,7 @@ async function run(args) {
     const 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!';
     const examples = ['$ jbrowse remove-track trackId'];
     if (flags.help) {
-        (0, utils_ts_1.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse remove-track <trackId> [options]',
@@ -38,8 +35,8 @@ async function run(args) {
     if (!trackId) {
         throw new Error('Missing required argument: trackId\nUsage: jbrowse remove-track <trackId> [options]');
     }
-    const target = await (0, utils_ts_1.resolveConfigPath)(flags.target, flags.out);
-    const config = await (0, utils_ts_1.readJsonFile)(target);
+    const target = await resolveConfigPath(flags.target, flags.out);
+    const config = await readJsonFile(target);
     const originalLength = config.tracks?.length || 0;
     config.tracks = config.tracks?.filter(({ trackId: id }) => id !== trackId);
     const newLength = config.tracks?.length || 0;
@@ -47,7 +44,7 @@ async function run(args) {
         console.log(`No track found with trackId: ${trackId}`);
     }
     else {
-        await (0, utils_ts_1.writeJsonFile)(target, config);
+        await writeJsonFile(target, config);
         console.log(`Removed track with trackId: ${trackId} from ${target}`);
     }
 }

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

@@ -1,13 +1,7 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const fs_1 = require("fs");
-const util_1 = require("util");
-const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const utils_ts_1 = require("../utils.js");
+import { promises as fsPromises } from 'fs';
+import { parseArgs } from 'util';
+import parseJSON from 'json-parse-better-errors';
+import { printHelp, readJsonFile, resolveConfigPath, writeJsonFile, } from "../utils.js";
 const description = 'Set a default session with views and tracks';
 const examples = [
     '# set default session for the config.json in your current directory',
@@ -47,10 +41,10 @@ const options = {
     },
     help: { type: 'boolean', short: 'h', description: 'Show help' },
 };
-async function run(args) {
-    const { values: runFlags } = (0, util_1.parseArgs)({ options, args });
+export async function run(args) {
+    const { values: runFlags } = parseArgs({ options, args });
     if (runFlags.help) {
-        (0, utils_ts_1.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse add-track <track> [options]',
@@ -59,11 +53,11 @@ async function run(args) {
         return;
     }
     const { session, currentSession, delete: deleteDefaultSession } = runFlags;
-    const target = await (0, utils_ts_1.resolveConfigPath)(runFlags.target, runFlags.out);
-    const configContents = await (0, utils_ts_1.readJsonFile)(target);
+    const target = await resolveConfigPath(runFlags.target, runFlags.out);
+    const configContents = await readJsonFile(target);
     if (deleteDefaultSession) {
         configContents.defaultSession = undefined;
-        await (0, utils_ts_1.writeJsonFile)(target, configContents);
+        await writeJsonFile(target, configContents);
     }
     else if (currentSession) {
         console.log(`The current default session is ${JSON.stringify(configContents.defaultSession)}`);
@@ -72,7 +66,7 @@ async function run(args) {
         throw new Error('Please provide a --session file');
     }
     else if (session) {
-        await (0, utils_ts_1.writeJsonFile)(target, {
+        await writeJsonFile(target, {
             ...configContents,
             defaultSession: await readDefaultSessionFile(session),
         });
@@ -81,7 +75,7 @@ async function run(args) {
 async function readDefaultSessionFile(defaultSessionFile) {
     let defaultSessionJson;
     try {
-        defaultSessionJson = await fs_1.promises.readFile(defaultSessionFile, {
+        defaultSessionJson = await fsPromises.readFile(defaultSessionFile, {
             encoding: 'utf8',
         });
     }
@@ -89,7 +83,7 @@ async function readDefaultSessionFile(defaultSessionFile) {
         throw new Error('Could not read the provided file');
     }
     try {
-        const session = (0, json_parse_better_errors_1.default)(defaultSessionJson);
+        const session = parseJSON(defaultSessionJson);
         // return top-level "session" if it exists, such as in files created by
         // "File -> Export session"
         return session.session || session;

package/dist/commands/shared/config-operations.js

@@ -1,19 +1,15 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.findAndUpdateOrAdd = findAndUpdateOrAdd;
-exports.saveConfigAndReport = saveConfigAndReport;
-const utils_ts_1 = require("../../utils.js");
+import { debug, writeJsonFile } from "../../utils.js";
 /**
  * Generic function to find and update or add an item to a config array
  * Returns the updated config and whether an item was overwritten
  */
-function findAndUpdateOrAdd({ items, newItem, idField, getId, allowOverwrite, itemType, }) {
+export function findAndUpdateOrAdd({ items, newItem, idField, getId, allowOverwrite, itemType, }) {
     const newId = getId(newItem);
     const idx = items.findIndex(item => getId(item) === newId);
     if (idx !== -1) {
-        (0, utils_ts_1.debug)(`Found existing ${itemType} ${newId} in configuration`);
+        debug(`Found existing ${itemType} ${newId} in configuration`);
         if (allowOverwrite) {
-            (0, utils_ts_1.debug)(`Overwriting ${itemType} ${newId} in configuration`);
+            debug(`Overwriting ${itemType} ${newId} in configuration`);
             const updatedItems = [...items];
             updatedItems[idx] = newItem;
             return { updatedItems, wasOverwritten: true };
@@ -29,9 +25,9 @@ function findAndUpdateOrAdd({ items, newItem, idField, getId, allowOverwrite, it
 /**
  * Saves a config file and reports the result to the user
  */
-async function saveConfigAndReport({ config, target, itemType, itemName, itemId, wasOverwritten, }) {
-    (0, utils_ts_1.debug)(`Writing configuration to file ${target}`);
-    await (0, utils_ts_1.writeJsonFile)(target, config);
+export async function saveConfigAndReport({ config, target, itemType, itemName, itemId, wasOverwritten, }) {
+    debug(`Writing configuration to file ${target}`);
+    await writeJsonFile(target, config);
     const idPart = itemId ? ` and ${itemType}Id "${itemId}"` : '';
     console.log(`${wasOverwritten ? 'Overwrote' : 'Added'} ${itemType} with name "${itemName}"${idPart} ${wasOverwritten ? 'in' : 'to'} ${target}`);
 }

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

@@ -1,13 +1,6 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.GFF_CONFIG = exports.BED_CONFIG = void 0;
-exports.spawnSortProcess = spawnSortProcess;
-const child_process_1 = require("child_process");
-const tmp_1 = __importDefault(require("tmp"));
-exports.BED_CONFIG = {
+import { spawn } from 'child_process';
+import tmp from 'tmp';
+export const BED_CONFIG = {
     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',
     examples: [
         '# sort bed and pipe to bgzip',
@@ -19,7 +12,7 @@ exports.BED_CONFIG = {
     sortColumn: 2,
     fileType: 'bed',
 };
-exports.GFF_CONFIG = {
+export const GFF_CONFIG = {
     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',
     examples: [
         '# sort gff and pipe to bgzip',
@@ -39,18 +32,18 @@ function getMinimalEnvironment() {
     };
 }
 function createSortCommandForStdin(sortColumn) {
-    const tmpFile = tmp_1.default.fileSync({ prefix: 'jbrowse-sort' }).name;
+    const tmpFile = tmp.fileSync({ prefix: 'jbrowse-sort' }).name;
     const sortCmd = `sort -t"\`printf '\\t'\`" -k1,1 -k${sortColumn},${sortColumn}n`;
     return `cat > ${tmpFile} && (grep "^#" ${tmpFile}; grep -v "^#" ${tmpFile} | ${sortCmd}) && rm -f ${tmpFile}`;
 }
 function createSortCommandForFile(file, sortColumn) {
     return `(grep "^#" "${file}"; grep -v "^#" "${file}" | sort -t"\`printf '\\t'\`" -k1,1 -k${sortColumn},${sortColumn}n)`;
 }
-function spawnSortProcess(file, sortColumn) {
+export function spawnSortProcess(file, sortColumn) {
     const command = file
         ? createSortCommandForFile(file, sortColumn)
         : createSortCommandForStdin(sortColumn);
-    return (0, child_process_1.spawn)('sh', ['-c', command], {
+    return spawn('sh', ['-c', command], {
         env: getMinimalEnvironment(),
         stdio: 'inherit',
     });

package/dist/commands/shared/validators.js

@@ -1,17 +1,13 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateFileArgument = validateFileArgument;
-exports.validateRequiredCommands = validateRequiredCommands;
-const command_exists_1 = require("command-exists");
-function validateFileArgument(file, commandName, fileType) {
+import { sync as commandExistsSync } from 'command-exists';
+export function validateFileArgument(file, commandName, fileType) {
     if (!file && process.stdin.isTTY) {
         throw new Error(`Missing required argument: file\n` +
             `Usage: jbrowse ${commandName} <file>\n` +
             `       OR pipe data via stdin: cat file.${fileType} | jbrowse ${commandName}`);
     }
 }
-function validateRequiredCommands(requiredCommands) {
-    const missingCommands = requiredCommands.filter(cmd => !(0, command_exists_1.sync)(cmd));
+export function validateRequiredCommands(requiredCommands) {
+    const missingCommands = requiredCommands.filter(cmd => !commandExistsSync(cmd));
     if (missingCommands.length > 0) {
         throw new Error(`Unable to run command, requires unix type environment with: ${requiredCommands.join(', ')}`);
     }

package/dist/commands/sort-bed.js

@@ -1,37 +1,34 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const util_1 = require("util");
-const utils_ts_1 = require("../utils.js");
-const process_utils_ts_1 = require("./process-utils.js");
-const sort_utils_ts_1 = require("./shared/sort-utils.js");
-const validators_ts_1 = require("./shared/validators.js");
-async function run(args) {
+import { parseArgs } from 'util';
+import { printHelp } from "../utils.js";
+import { waitForProcessClose } from "./process-utils.js";
+import { BED_CONFIG, spawnSortProcess } from "./shared/sort-utils.js";
+import { validateFileArgument, validateRequiredCommands, } from "./shared/validators.js";
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
             short: 'h',
         },
     };
-    const { values: flags, positionals } = (0, util_1.parseArgs)({
+    const { values: flags, positionals } = parseArgs({
         args,
         options,
         allowPositionals: true,
     });
     if (flags.help) {
-        (0, utils_ts_1.printHelp)({
-            description: sort_utils_ts_1.BED_CONFIG.description,
-            examples: sort_utils_ts_1.BED_CONFIG.examples,
+        printHelp({
+            description: BED_CONFIG.description,
+            examples: BED_CONFIG.examples,
             usage: 'jbrowse sort-bed [file] [options]',
             options,
         });
         return;
     }
     const file = positionals[0];
-    (0, validators_ts_1.validateFileArgument)(file, 'sort-bed', 'bed');
-    (0, validators_ts_1.validateRequiredCommands)(['sh', 'sort', 'grep']);
-    const child = (0, sort_utils_ts_1.spawnSortProcess)(file, sort_utils_ts_1.BED_CONFIG.sortColumn);
-    const exitCode = await (0, process_utils_ts_1.waitForProcessClose)(child);
+    validateFileArgument(file, 'sort-bed', 'bed');
+    validateRequiredCommands(['sh', 'sort', 'grep']);
+    const child = spawnSortProcess(file, BED_CONFIG.sortColumn);
+    const exitCode = await waitForProcessClose(child);
     if (exitCode !== 0) {
         throw new Error(`Sort process exited with code ${exitCode}`);
     }

package/dist/commands/sort-gff.js

@@ -1,37 +1,34 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const util_1 = require("util");
-const utils_ts_1 = require("../utils.js");
-const process_utils_ts_1 = require("./process-utils.js");
-const sort_utils_ts_1 = require("./shared/sort-utils.js");
-const validators_ts_1 = require("./shared/validators.js");
-async function run(args) {
+import { parseArgs } from 'util';
+import { printHelp } from "../utils.js";
+import { waitForProcessClose } from "./process-utils.js";
+import { GFF_CONFIG, spawnSortProcess } from "./shared/sort-utils.js";
+import { validateFileArgument, validateRequiredCommands, } from "./shared/validators.js";
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
             short: 'h',
         },
     };
-    const { values: flags, positionals } = (0, util_1.parseArgs)({
+    const { values: flags, positionals } = parseArgs({
         args,
         options,
         allowPositionals: true,
     });
     if (flags.help) {
-        (0, utils_ts_1.printHelp)({
-            description: sort_utils_ts_1.GFF_CONFIG.description,
-            examples: sort_utils_ts_1.GFF_CONFIG.examples,
+        printHelp({
+            description: GFF_CONFIG.description,
+            examples: GFF_CONFIG.examples,
             usage: 'jbrowse sort-gff [file] [options]',
             options,
         });
         return;
     }
     const file = positionals[0];
-    (0, validators_ts_1.validateFileArgument)(file, 'sort-gff', 'gff');
-    (0, validators_ts_1.validateRequiredCommands)(['sh', 'sort', 'grep']);
-    const child = (0, sort_utils_ts_1.spawnSortProcess)(file, sort_utils_ts_1.GFF_CONFIG.sortColumn);
-    const exitCode = await (0, process_utils_ts_1.waitForProcessClose)(child);
+    validateFileArgument(file, 'sort-gff', 'gff');
+    validateRequiredCommands(['sh', 'sort', 'grep']);
+    const child = spawnSortProcess(file, GFF_CONFIG.sortColumn);
+    const exitCode = await waitForProcessClose(child);
     if (exitCode !== 0) {
         throw new Error(`Sort process exited with code ${exitCode}`);
     }

package/dist/commands/text-index/adapter-utils.js

@@ -1,14 +1,9 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getLoc = getLoc;
-exports.createTrixAdapter = createTrixAdapter;
-exports.getAdapterLocation = getAdapterLocation;
-const config_utils_ts_1 = require("./config-utils.js");
-function getLoc(elt) {
+import { sanitizeNameForPath } from "./config-utils.js";
+export function getLoc(elt) {
     return elt.locationType === 'LocalPathLocation' ? elt.localPath : elt.uri;
 }
-function createTrixAdapter(name, assemblyNames, idSuffix = 'index') {
-    const safeName = (0, config_utils_ts_1.sanitizeNameForPath)(name);
+export function createTrixAdapter(name, assemblyNames, idSuffix = 'index') {
+    const safeName = sanitizeNameForPath(name);
     return {
         type: 'TrixTextSearchAdapter',
         textSearchAdapterId: `${safeName}-${idSuffix}`,
@@ -33,7 +28,7 @@ const ADAPTER_LOCATION_KEYS = {
     VcfAdapter: 'vcfLocation',
     VcfTabixAdapter: 'vcfGzLocation',
 };
-function getAdapterLocation(adapter) {
+export function getAdapterLocation(adapter) {
     const key = ADAPTER_LOCATION_KEYS[adapter?.type ?? ''];
     return key
         ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition

package/dist/commands/text-index/aggregate.js

@@ -1,17 +1,14 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.aggregateIndex = aggregateIndex;
-const adapter_utils_ts_1 = require("./adapter-utils.js");
-const config_utils_ts_1 = require("./config-utils.js");
-const indexing_utils_ts_1 = require("./indexing-utils.js");
-const utils_ts_1 = require("../../utils.js");
-async function aggregateIndex(flags) {
+import { createTrixAdapter } from "./adapter-utils.js";
+import { getAssemblyNames, getTrackConfigs, loadConfigForIndexing, parseCommaSeparatedString, prepareIndexDriverFlags, writeConf, } from "./config-utils.js";
+import { indexDriver } from "./indexing-utils.js";
+import { resolveConfigPath } from "../../utils.js";
+export async function aggregateIndex(flags) {
     const { out, target, tracks, excludeTracks, assemblies, attributes, quiet, force, exclude, dryrun, prefixSize, } = flags;
-    const { config, configPath, outLocation } = await (0, config_utils_ts_1.loadConfigForIndexing)(target, out, utils_ts_1.resolveConfigPath);
+    const { config, configPath, outLocation } = await loadConfigForIndexing(target, out, resolveConfigPath);
     const aggregateTextSearchAdapters = config.aggregateTextSearchAdapters || [];
-    const asms = (0, config_utils_ts_1.getAssemblyNames)(config, assemblies);
+    const asms = getAssemblyNames(config, assemblies);
     for (const asm of asms) {
-        const trackConfigs = (0, config_utils_ts_1.getTrackConfigs)(config, (0, config_utils_ts_1.parseCommaSeparatedString)(tracks), asm, (0, config_utils_ts_1.parseCommaSeparatedString)(excludeTracks));
+        const trackConfigs = getTrackConfigs(config, parseCommaSeparatedString(tracks), asm, parseCommaSeparatedString(excludeTracks));
         if (!trackConfigs.length) {
             console.log(`Indexing assembly ${asm}...(no tracks found)...`);
             continue;
@@ -27,14 +24,14 @@ async function aggregateIndex(flags) {
                 console.log(`Note: ${asm} has already been indexed with this configuration, use --force to overwrite this assembly. Skipping for now`);
                 continue;
             }
-            await (0, indexing_utils_ts_1.indexDriver)({
+            await indexDriver({
                 trackConfigs,
                 outLocation,
                 name: asm,
                 assemblyNames: [asm],
-                ...(0, config_utils_ts_1.prepareIndexDriverFlags)({ attributes, exclude, quiet, prefixSize }),
+                ...prepareIndexDriverFlags({ attributes, exclude, quiet, prefixSize }),
             });
-            const trixConf = (0, adapter_utils_ts_1.createTrixAdapter)(asm, [asm]);
+            const trixConf = createTrixAdapter(asm, [asm]);
             if (idx === -1) {
                 aggregateTextSearchAdapters.push(trixConf);
             }
@@ -44,7 +41,7 @@ async function aggregateIndex(flags) {
         }
     }
     if (!dryrun) {
-        (0, config_utils_ts_1.writeConf)({
+        writeConf({
             ...config,
             aggregateTextSearchAdapters,
         }, configPath);