@jbrowse/img 4.1.3 → 4.1.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. package/esm/bin.js +118 -14
  2. package/package.json +7 -7
  3. package/esm/cli.d.ts +0 -1
  4. package/esm/cli.js +0 -95
package/esm/bin.js CHANGED
@@ -1,15 +1,119 @@
1
1
  #!/usr/bin/env node
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- const { registerHooks } = await import('node:module');
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- registerHooks({
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- load(url, context, nextLoad) {
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- return url.endsWith('.css')
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- ? { url, format: 'module', source: '', shortCircuit: true }
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- : nextLoad(url, context);
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- },
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- });
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- const { main } = await import('./cli.js');
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- main().catch((error) => {
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- console.error(error);
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- process.exit(1);
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- });
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- export {};
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+ import fs from 'fs';
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+ import yargs from 'yargs';
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+ import { hideBin } from 'yargs/helpers';
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+ import { convert, parseArgv, renderRegion, setupEnv, standardizeArgv, } from './index.js';
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+ const trackTypes = [
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+ 'bam',
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+ 'cram',
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+ 'bigwig',
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+ 'vcfgz',
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+ 'gffgz',
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+ 'hic',
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+ 'bigbed',
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+ 'bedgz',
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+ ];
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+ const knownOptions = new Set([
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+ ...trackTypes,
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+ 'fasta',
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+ 'aliases',
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+ 'assembly',
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+ 'config',
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+ 'session',
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+ 'loc',
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+ 'out',
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+ 'width',
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+ 'noRasterize',
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+ 'defaultSession',
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+ 'tracks',
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+ 'cytobands',
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+ 'help',
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+ 'version',
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+ ]);
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+ const yargsInstance = yargs(hideBin(process.argv))
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+ .scriptName('jb2export')
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+ .usage('$0 [options]')
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+ .option('fasta', {
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+ type: 'string',
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+ description: 'Path to indexed FASTA file',
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+ })
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+ .option('aliases', {
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+ type: 'string',
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+ description: 'Path to reference name aliases file',
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+ })
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+ .option('assembly', {
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+ type: 'string',
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+ description: 'Path to assembly JSON or name in config',
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+ })
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+ .option('config', {
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+ type: 'string',
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+ description: 'Path to JBrowse config.json',
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+ })
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+ .option('session', {
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+ type: 'string',
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+ description: 'Path to session JSON',
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+ })
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+ .option('loc', {
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+ type: 'string',
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+ description: 'Location to render (e.g., chr1:1-1000 or "all")',
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+ })
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+ .option('out', {
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+ type: 'string',
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+ description: 'Output file path (SVG or PNG)',
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+ })
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+ .option('width', {
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+ type: 'number',
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+ description: 'Width of output in pixels',
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+ default: 1500,
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+ })
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+ .option('noRasterize', {
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+ type: 'boolean',
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+ description: 'Disable rasterization of pileup/coverage',
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+ default: false,
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+ })
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+ .option('defaultSession', {
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+ type: 'boolean',
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+ description: 'Use default session from config',
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+ default: false,
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+ })
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+ .example('$0 --fasta ref.fa --bam reads.bam --loc chr1:1-10000 --out out.svg', 'Render BAM alignments')
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+ .example('$0 --fasta ref.fa --vcfgz variants.vcf.gz --loc chr1:1-50000 --out out.png', 'Render VCF variants')
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+ .epilogue('Track options: --bam, --cram, --bigwig, --vcfgz, --gffgz, --hic, --bigbed, --bedgz')
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+ .strict(false)
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+ .help();
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+ async function main() {
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+ const argv = await yargsInstance.argv;
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+ setupEnv();
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+ const args = process.argv.slice(2);
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+ const parsed = parseArgv(args);
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+ const standardized = standardizeArgv(parsed, trackTypes);
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+ for (const [key] of parsed) {
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+ if (!knownOptions.has(key)) {
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+ console.warn(`Warning: unknown option "--${key}"`);
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+ }
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+ }
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+ const opts = {
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+ fasta: argv.fasta,
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+ aliases: argv.aliases,
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+ assembly: argv.assembly,
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+ config: argv.config,
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+ session: argv.session,
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+ loc: argv.loc,
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+ width: argv.width,
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+ noRasterize: argv.noRasterize,
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+ defaultSession: argv.defaultSession ? 'true' : undefined,
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+ trackList: standardized.trackList,
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+ };
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+ const result = await renderRegion(opts);
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+ const outFile = argv.out || standardized.out;
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+ if (!outFile) {
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+ console.log(result);
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+ }
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+ else if (outFile.endsWith('.png')) {
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+ convert(result, { out: outFile, pngwidth: String(argv.width || 2048) });
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+ }
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+ else {
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+ fs.writeFileSync(outFile, result);
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+ }
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+ }
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+ await main();
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/img",
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- "version": "4.1.3",
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+ "version": "4.1.5",
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  "main": "esm/index.js",
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  "types": "esm/index.d.ts",
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  "type": "module",
@@ -25,16 +25,16 @@
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  "dependencies": {
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  "@emotion/cache": "^11.14.0",
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  "@emotion/react": "^11.14.0",
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- "@types/jsdom": "^21.1.7",
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+ "@types/jsdom": "^27.0.0",
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  "@types/yargs": "^17.0.35",
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  "canvas": "^3.2.1",
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- "jsdom": "27.0.0",
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- "react": "^19.2.3",
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- "react-dom": "^19.2.3",
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+ "jsdom": "28.0.0",
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+ "react": "^19.2.4",
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+ "react-dom": "^19.2.4",
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  "tmp": "^0.2.5",
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  "yargs": "^18.0.0",
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- "@jbrowse/react-linear-genome-view2": "^4.1.3",
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- "@jbrowse/plugin-linear-genome-view": "^4.1.3"
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+ "@jbrowse/plugin-linear-genome-view": "^4.1.5",
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+ "@jbrowse/react-linear-genome-view2": "^4.1.5"
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  },
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  "publishConfig": {
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  "access": "public"
package/esm/cli.d.ts DELETED
@@ -1 +0,0 @@
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- export declare function main(): Promise<void>;
package/esm/cli.js DELETED
@@ -1,95 +0,0 @@
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- import fs from 'fs';
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- import yargs from 'yargs';
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- import { hideBin } from 'yargs/helpers';
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- import { convert, parseArgv, renderRegion, setupEnv, standardizeArgv, } from './index.js';
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- const trackTypes = [
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- 'bam',
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- 'cram',
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- 'bigwig',
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- 'vcfgz',
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- 'gffgz',
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- 'hic',
12
- 'bigbed',
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- 'bedgz',
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- ];
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- const yargsInstance = yargs(hideBin(process.argv))
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- .scriptName('jb2export')
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- .usage('$0 [options]')
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- .option('fasta', {
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- type: 'string',
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- description: 'Path to indexed FASTA file',
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- })
22
- .option('aliases', {
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- type: 'string',
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- description: 'Path to reference name aliases file',
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- })
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- .option('assembly', {
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- type: 'string',
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- description: 'Path to assembly JSON or name in config',
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- })
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- .option('config', {
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- type: 'string',
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- description: 'Path to JBrowse config.json',
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- })
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- .option('session', {
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- type: 'string',
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- description: 'Path to session JSON',
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- })
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- .option('loc', {
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- type: 'string',
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- description: 'Location to render (e.g., chr1:1-1000 or "all")',
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- })
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- .option('out', {
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- type: 'string',
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- description: 'Output file path (SVG or PNG)',
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- })
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- .option('width', {
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- type: 'number',
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- description: 'Width of output in pixels',
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- default: 1500,
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- })
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- .option('noRasterize', {
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- type: 'boolean',
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- description: 'Disable rasterization of pileup/coverage',
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- default: false,
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- })
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- .option('defaultSession', {
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- type: 'boolean',
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- description: 'Use default session from config',
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- default: false,
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- })
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- .example('$0 --fasta ref.fa --bam reads.bam --loc chr1:1-10000 --out out.svg', 'Render BAM alignments')
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- .example('$0 --fasta ref.fa --vcfgz variants.vcf.gz --loc chr1:1-50000 --out out.png', 'Render VCF variants')
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- .epilogue('Track options: --bam, --cram, --bigwig, --vcfgz, --gffgz, --hic, --bigbed, --bedgz')
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- .strict(false)
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- .help();
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- export async function main() {
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- const argv = await yargsInstance.argv;
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- setupEnv();
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- const args = process.argv.slice(2);
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- const parsed = parseArgv(args);
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- const standardized = standardizeArgv(parsed, trackTypes);
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- const opts = {
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- fasta: argv.fasta,
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- aliases: argv.aliases,
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- assembly: argv.assembly,
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- config: argv.config,
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- session: argv.session,
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- loc: argv.loc,
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- width: argv.width,
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- noRasterize: argv.noRasterize,
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- defaultSession: argv.defaultSession ? 'true' : undefined,
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- trackList: standardized.trackList,
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- };
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- const result = await renderRegion(opts);
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- const outFile = argv.out || standardized.out;
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- if (!outFile) {
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- console.log(result);
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- }
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- else if (outFile.endsWith('.png')) {
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- convert(result, { out: outFile, pngwidth: String(argv.width || 2048) });
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- }
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- else {
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- fs.writeFileSync(outFile, result);
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- }
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- }