@jbrowse/img 2.6.1 → 2.6.3

package/dist/bin.js

@@ -1,4 +1,3 @@
 #!/usr/bin/env node
 "use strict";
 require('./index.js');
-//# sourceMappingURL=bin.js.map

package/dist/index.js

@@ -211,4 +211,3 @@ const args = (0, parseArgv_1.standardizeArgv)((0, parseArgv_1.parseArgv)(process
         process.exit(1);
     }
 })();
-//# sourceMappingURL=index.js.map

package/dist/parseArgv.js

@@ -44,4 +44,3 @@ function standardizeArgv(args, trackTypes) {
     return result;
 }
 exports.standardizeArgv = standardizeArgv;
-//# sourceMappingURL=parseArgv.js.map

package/dist/renderRegion.js

@@ -371,4 +371,3 @@ async function renderRegion(opts) {
     });
 }
 exports.renderRegion = renderRegion;
-//# sourceMappingURL=renderRegion.js.map

package/dist/util.js

@@ -30,4 +30,3 @@ function convert(result, args, spawnArgs = []) {
     fs_1.default.unlinkSync(name);
 }
 exports.convert = convert;
-//# sourceMappingURL=util.js.map

package/esm/bin.js

@@ -1,4 +1,3 @@
 #!/usr/bin/env node
 "use strict";
 require('./index.js');
-//# sourceMappingURL=bin.js.map

package/esm/index.js

@@ -183,4 +183,3 @@ const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
         process.exit(1);
     }
 })();
-//# sourceMappingURL=index.js.map

package/esm/parseArgv.js

@@ -39,4 +39,3 @@ export function standardizeArgv(args, trackTypes) {
     });
     return result;
 }
-//# sourceMappingURL=parseArgv.js.map

package/esm/renderRegion.js

@@ -363,4 +363,3 @@ export async function renderRegion(opts) {
         Wrapper: ({ children }) => (React.createElement(CacheProvider, { value: muiCache }, children)),
     });
 }
-//# sourceMappingURL=renderRegion.js.map

package/esm/util.js

@@ -22,4 +22,3 @@ export function convert(result, args, spawnArgs = []) {
     console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`); // eslint-disable-line no-console
     fs.unlinkSync(name);
 }
-//# sourceMappingURL=util.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "main": "dist/index.js",
   "module": "esm/index.js",
   "author": "JBrowse Team",
@@ -13,8 +13,7 @@
   },
   "files": [
     "dist",
-    "esm",
-    "src"
+    "esm"
   ],
   "scripts": {
     "test": "cd ../../; jest --env node --testMatch '**/*testmod.js' products/jbrowse-img",
@@ -22,15 +21,15 @@
     "prebuild": "yarn clean",
     "build": "npm-run-all build:*",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "preversion": "npm run build"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
     "@emotion/cache": "^11.7.1",
     "@emotion/react": "^11.9.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.6.1",
-    "@jbrowse/react-linear-genome-view": "^2.6.1",
+    "@jbrowse/plugin-linear-genome-view": "^2.6.3",
+    "@jbrowse/react-linear-genome-view": "^2.6.3",
     "abortcontroller-polyfill": "^1.7.3",
     "canvas": "^2.9.1",
     "jsdom": "^22.1.0",
@@ -44,5 +43,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/bin.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"bin.js","sourceRoot":"","sources":["../src/bin.js"],"names":[],"mappings":";;AACA,OAAO,CAAC,YAAY,CAAC,CAAA"}

package/dist/index.js.map

@@ -1 +0,0 @@
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package/dist/parseArgv.js.map

@@ -1 +0,0 @@
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package/dist/renderRegion.js.map

@@ -1 +0,0 @@
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package/dist/util.js.map

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package/esm/bin.js.map

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package/esm/parseArgv.js.map

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package/esm/renderRegion.js.map

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package/esm/util.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAA;AACnB,OAAO,GAAG,MAAM,KAAK,CAAA;AACrB,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEzC,wEAAwE;AACxE,MAAM,UAAU,UAAU,CAAC,GAAW;IACpC,OAAO,GAAG,KAAK,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;AACxC,CAAC;AAED,SAAS,SAAS;IAChB,OAAO,GAAG,CAAC,QAAQ,CAAC;QAClB,IAAI,EAAE,KAAK;QACX,MAAM,EAAE,SAAS;QACjB,OAAO,EAAE,MAAM;KAChB,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,OAAO,CACrB,MAAc,EACd,IAAwC,EACxC,YAAsB,EAAE;IAExB,MAAM,EAAE,IAAI,EAAE,GAAG,SAAS,EAAE,CAAA;IAC5B,MAAM,EAAE,QAAQ,GAAG,MAAM,EAAE,GAAG,EAAE,GAAG,IAAI,CAAA;IACvC,EAAE,CAAC,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;IAC9B,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,SAAS,CAAa,CAAA;IACrE,MAAM,EAAE,GAAG,SAAS,CAAC,cAAc,EAAE,CAAC,CAAC,CAAA;IAEvC,OAAO,CAAC,KAAK,CAAC,wBAAwB,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;IAC7D,OAAO,CAAC,GAAG,CAAC,wBAAwB,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA,CAAC,iCAAiC;IAC7F,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;AACrB,CAAC"}

package/src/bin.js

@@ -1,2 +0,0 @@
-#!/usr/bin/env node
-require('./index.js')

package/src/index.test.ts

@@ -1,171 +0,0 @@
-/* eslint-disable tsdoc/syntax */
-/**
- * @jest-environment node
- */
-
-// the above jest-environment node is important to check true usage
-// as a CLI tool
-
-import { renderRegion } from './renderRegion'
-import path from 'path'
-import fs from 'fs'
-import { JSDOM } from 'jsdom'
-import { Image, createCanvas } from 'canvas'
-import fetch, { Headers, Response, Request } from 'node-fetch'
-
-// @ts-expect-error
-global.fetch = fetch
-// @ts-expect-error
-global.Headers = Headers
-// @ts-expect-error
-global.Response = Response
-// @ts-expect-error
-global.Request = Request
-
-const { document } = new JSDOM(`...`).window
-global.document = document
-
-// @ts-expect-error
-global.nodeImage = Image
-// @ts-expect-error
-global.nodeCreateCanvas = createCanvas
-
-function pa(s: string) {
-  return path.join(__dirname, s)
-}
-
-xtest('renders a region with --session and --config args', async () => {
-  const result = await renderRegion({
-    session: pa('../test/clingen_session.json'),
-    config: pa('../data/config.json'),
-  })
-  fs.writeFileSync('svg_from_config_and_session_param.svg', result)
-  expect(result).toMatchSnapshot()
-}, 40000)
-
-xtest('renders a region with --session, --tracks, and --assembly args', async () => {
-  const result = await renderRegion({
-    session: pa('../test/clingen_session.json'),
-    tracks: pa('../data/tracks.json'),
-    assembly: pa('../data/assembly.json'),
-  })
-  fs.writeFileSync('svg_from_separate_session_and_tracks.svg', result)
-  expect(result).toMatchSnapshot()
-}, 40000)
-
-test('renders volvox with variety of args', async () => {
-  const fp = (f: string) => pa('../data/volvox/' + f)
-  const result = await renderRegion({
-    fasta: fp('volvox.fa'),
-    trackList: [
-      ['bam', [fp('volvox-sorted.bam')]],
-      ['cram', [fp('volvox-sorted.cram')]],
-      ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
-      ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
-      ['gffgz', [fp('volvox.sort.gff3.gz')]],
-      ['bigbed', [fp('volvox.bb')]],
-      ['bedgz', [fp('volvox-bed12.bed.gz')]],
-    ],
-    loc: 'ctgA:1000-2000',
-  })
-  fs.writeFileSync(pa('../test/svg_from_volvox_fasta_and_bam.svg'), result)
-  expect(result).toBeTruthy()
-}, 40000)
-
-xtest('renders human large region with remote urls', async () => {
-  const result = await renderRegion({
-    fasta: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
-    trackList: [
-      [
-        'cram',
-        [
-          'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/skbr3.ont.sort.mod.cram',
-          'force:true',
-        ],
-      ],
-    ],
-    loc: '1:10,000,000-10,030,000',
-  })
-  fs.writeFileSync(pa('../test/human_remote_urls_large_region.svg'), result)
-  expect(result).toBeTruthy()
-}, 120000)
-
-xtest('renders volvox with remote urls', async () => {
-  const result = await renderRegion({
-    fasta: 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa',
-    trackList: [
-      [
-        'bam',
-        [
-          'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam',
-        ],
-      ],
-    ],
-    loc: 'ctgA:1-1000',
-  })
-  fs.writeFileSync(pa('../test/volvox_remote_region.svg'), result)
-  expect(result).toBeTruthy()
-}, 20000)
-
-test('renders volvox with variety of args (noRasterize)', async () => {
-  const fp = (f: string) => pa('../data/volvox/' + f)
-  const result = await renderRegion({
-    fasta: fp('volvox.fa'),
-    trackList: [
-      ['bam', [fp('volvox-sorted.bam')]],
-      ['cram', [fp('volvox-sorted.cram')]],
-      ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
-      ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
-      ['gffgz', [fp('volvox.sort.gff3.gz')]],
-      ['bigbed', [fp('volvox.bb')]],
-      ['bedgz', [fp('volvox-bed12.bed.gz')]],
-    ],
-    loc: 'ctgA:1000-2000',
-    noRasterize: true,
-  })
-  fs.writeFileSync(
-    pa('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'),
-    result,
-  )
-  expect(result).toBeTruthy()
-}, 40000)
-
-// commented out for using remote files currently
-xtest('configtracks arg with urls', async () => {
-  const result = await renderRegion({
-    config: 'data/config.json',
-    trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
-    assembly: 'GRCh38',
-    loc: 'chr1:50,000-60,000',
-  })
-  fs.writeFileSync('svg_configtracks_simple.svg', result)
-  expect(result).toBeTruthy()
-}, 40000)
-
-test('configtracks arg with local files', async () => {
-  const result = await renderRegion({
-    config: pa('../data/volvox/config.json'),
-    trackList: [['configtracks', ['volvox_sv']]],
-    assembly: 'volvox',
-    loc: 'ctgA:1-50,000',
-  })
-  fs.writeFileSync(pa('../test/svg_configtracks_local.svg'), result)
-  expect(result).toBeTruthy()
-}, 40000)
-
-xtest('renders --hic', async () => {
-  const result = await renderRegion({
-    fasta: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz',
-    trackList: [
-      [
-        'hic',
-        [
-          'https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic',
-        ],
-      ],
-    ],
-    loc: '1:2,000,000-10,000,000',
-  })
-  fs.writeFileSync(pa('../test/svg_from_human_hic.svg'), result)
-  expect(result).toBeTruthy()
-}, 20000)

package/src/index.ts

@@ -1,210 +0,0 @@
-import fs from 'fs'
-import yargs from 'yargs'
-import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
-import fetch, { Headers, Response, Request } from 'node-fetch'
-import { JSDOM } from 'jsdom'
-import { Image, createCanvas } from 'canvas'
-
-// locals
-import { standardizeArgv, parseArgv } from './parseArgv'
-import { renderRegion, Opts } from './renderRegion'
-import { convert } from './util'
-
-// @ts-expect-error
-global.nodeImage = Image
-// @ts-expect-error
-global.nodeCreateCanvas = createCanvas
-
-const { document } = new JSDOM(`...`).window
-global.document = document
-
-// force use of node-fetch polyfill, even if node 18+ fetch is available.
-// native node 18+ fetch currently gives errors related to unidici and
-// Uint8Array:
-//
-//
-// % node --version
-// v18.12.1
-//
-// % jb2export --fasta https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa --bam https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam --loc ctgA:1-1000 --out out4.svg
-// [
-//   '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
-//     '(Use `node --trace-warnings ...` to show where the warning was created)'
-// ]
-// [
-//   RangeError: offset is out of bounds
-//       at Uint8Array.set (<anonymous>)
-//       at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
-//       at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
-// ]
-
-// @ts-expect-error
-global.fetch = fetch
-// @ts-expect-error
-global.Headers = Headers
-// @ts-expect-error
-global.Response = Response
-// @ts-expect-error
-global.Request = Request
-
-const err = console.error
-console.error = (...p: unknown[]) => {
-  if (!`${p[0]}`.match('useLayoutEffect')) {
-    err(p)
-  }
-}
-
-const warn = console.warn
-console.warn = (...p: unknown[]) => {
-  if (!`${p[0]}`.match('estimation reached timeout')) {
-    warn(p)
-  }
-}
-
-// note: yargs is actually unused except for printing help
-// we do custom command line parsing, see parseArgv.ts
-// eslint-disable-next-line @typescript-eslint/no-floating-promises
-yargs
-  .command('jb2export', 'Creates a jbrowse 2 image snapshot')
-  .option('config', {
-    description: 'Path to config file',
-    type: 'string',
-  })
-  .option('session', {
-    description: 'Path to session file',
-    type: 'string',
-  })
-  .option('assembly', {
-    description:
-      'Path to an assembly configuration, or a name of an assembly in the configFile',
-    type: 'string',
-  })
-  .option('tracks', {
-    description: 'Path to tracks portion of a session',
-    type: 'string',
-  })
-  .option('loc', {
-    description:
-      'A locstring to navigate to, or --loc all to view the whole genome',
-    type: 'string',
-  })
-  .option('fasta', {
-    description: 'Supply a fasta for the assembly',
-    type: 'string',
-  })
-  .option('aliases', {
-    description:
-      'Supply aliases for the assembly, e.g. mapping of 1 to chr1. Tab separated file where column 1 matches the names from the FASTA',
-    type: 'string',
-  })
-  .option('width', {
-    description:
-      'Set the width of the window that jbrowse renders to, default: 1500px',
-    type: 'number',
-  })
-  .option('pngwidth', {
-    description:
-      'Set the width of the png canvas if using png output, default 2048px',
-    type: 'number',
-    default: 2048,
-  })
-  // track types
-  .option('configtracks', {
-    description: 'A list of track labels from a config file',
-    type: 'array',
-  })
-  .option('bam', {
-    description:
-      'A bam file, flag --bam can be used multiple times to specify multiple bam files',
-    type: 'array',
-  })
-  .option('bigwig', {
-    description:
-      'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
-    type: 'array',
-  })
-  .option('cram', {
-    description:
-      'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
-    type: 'array',
-  })
-  .option('vcfgz', {
-    description:
-      'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
-    type: 'array',
-  })
-  .option('gffgz', {
-    description:
-      'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
-    type: 'array',
-  })
-  .option('hic', {
-    description:
-      'A .hic file, the --hic can be used multiple times to specify multiple hic files',
-    type: 'array',
-  })
-  .option('bigbed', {
-    description:
-      'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
-    type: 'array',
-  })
-  .option('bedgz', {
-    description:
-      'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
-    type: 'array',
-  })
-
-  // other
-  .option('out', {
-    description:
-      'File to output to. Default: out.svg. If a filename with extension .png is supplied the program will try to automatically execute rsvg-convert to convert it to png',
-    type: 'string',
-    default: 'out.svg',
-  })
-  .option('noRasterize', {
-    description:
-      'Use full SVG rendering with no rasterized layers, this can substantially increase filesize',
-    type: 'boolean',
-  })
-  .option('defaultSession', {
-    description: 'Use the defaultSession from config.json',
-    type: 'boolean',
-  })
-  .help()
-  .alias('help', 'h')
-  .alias('width', 'w').argv
-
-const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
-  'bam',
-  'cram',
-  'vcfgz',
-  'hic',
-  'bigwig',
-  'bigbed',
-  'bedgz',
-  'gffgz',
-  'configtracks',
-])
-
-// eslint-disable-next-line @typescript-eslint/no-floating-promises
-;(async () => {
-  try {
-    const result = await renderRegion(args as Opts)
-    const { out = 'out.svg', pngwidth = '2048' } = args
-    if (out.endsWith('.png')) {
-      convert(result, { out, pngwidth })
-    } else if (out.endsWith('.pdf')) {
-      convert(result, { out, pngwidth }, ['-f', 'pdf'])
-    } else {
-      fs.writeFileSync(out, result)
-    }
-
-    // manually exit the process after done rendering because autoruns or
-    // something similar otherwise keeps the nodejs process alive xref
-    // https://github.com/GMOD/jb2export/issues/6
-    process.exit(0)
-  } catch (e) {
-    console.error(e)
-    process.exit(1)
-  }
-})()

package/src/parseArgv.test.ts

@@ -1,29 +0,0 @@
-import { parseArgv } from './parseArgv'
-
-test('parse', () => {
-  const args =
-    '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize'
-
-  expect(parseArgv(args.split(' '))).toEqual([
-    ['bam', ['dad.bam', 'color:red']],
-    ['vcf', ['variants.vcf']],
-    ['bam', ['mom.bam']],
-    ['defaultSession', []],
-    ['out', ['out.svg']],
-    ['noRasterize', []],
-  ])
-})
-
-test('parse', () => {
-  const args =
-    '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam force:true --defaultSession --out out.svg --noRasterize'
-
-  expect(parseArgv(args.split(' '))).toEqual([
-    ['bam', ['dad.bam', 'color:red']],
-    ['vcf', ['variants.vcf']],
-    ['bam', ['mom.bam', 'force:true']],
-    ['defaultSession', []],
-    ['out', ['out.svg']],
-    ['noRasterize', []],
-  ])
-})

package/src/parseArgv.ts

@@ -1,48 +0,0 @@
-export type Entry = [string, string[]]
-
-// example (see parseArgv.test.js):
-// const args =
-//   '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize'
-//
-// expect(parseArgv(args.split(' '))).toEqual([
-//   ['bam', ['dad.bam', 'color:red']],
-//   ['vcf', ['variants.vcf']],
-//   ['bam', ['mom.bam']],
-//   ['defaultSession', []],
-//   ['out', ['out.svg']],
-//   ['noRasterize', []],
-// ])
-export function parseArgv(argv: string[]) {
-  const map = [] as Entry[]
-  while (argv.length) {
-    const val = argv[0].slice(2)
-    argv = argv.slice(1)
-    const next = argv.findIndex(arg => arg.startsWith('-'))
-
-    if (next !== -1) {
-      map.push([val, argv.slice(0, next)])
-      argv = argv.slice(next)
-    } else {
-      map.push([val, argv])
-      break
-    }
-  }
-  return map
-}
-
-export function standardizeArgv(args: Entry[], trackTypes: string[]) {
-  const result = { trackList: [] } as {
-    trackList: Entry[]
-    out?: string
-    pngwidth?: string
-    [key: string]: unknown
-  }
-  args.forEach(arg => {
-    if (trackTypes.includes(arg[0])) {
-      result.trackList.push(arg)
-    } else {
-      result[arg[0]] = arg[1][0] || true
-    }
-  })
-  return result
-}

package/src/renderRegion.tsx

@@ -1,456 +0,0 @@
-import React from 'react'
-import { createViewState } from '@jbrowse/react-linear-genome-view'
-import {
-  LinearGenomeViewModel,
-  renderToSvg,
-} from '@jbrowse/plugin-linear-genome-view'
-import createCache from '@emotion/cache'
-import { CacheProvider } from '@emotion/react'
-import path from 'path'
-import fs from 'fs'
-
-// local
-import { Entry } from './parseArgv'
-import { booleanize } from './util'
-
-export interface Opts {
-  noRasterize?: boolean
-  loc?: string
-  width?: number
-  session?: string
-  assembly?: string
-  config?: string
-  fasta?: string
-  aliases?: string
-  cytobands?: string
-  defaultSession?: string
-  trackList?: Entry[]
-  tracks?: string
-}
-
-function read(file: string) {
-  let res
-  try {
-    res = JSON.parse(fs.readFileSync(file, 'utf8'))
-  } catch (e) {
-    throw new Error(
-      `Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`,
-    )
-  }
-  return res
-}
-function makeLocation(file: string) {
-  return file.startsWith('http') ? { uri: file } : { localPath: file }
-}
-
-function addRelativePaths(config: Record<string, unknown>, configPath: string) {
-  if (typeof config === 'object') {
-    for (const key of Object.keys(config)) {
-      if (typeof config[key] === 'object') {
-        addRelativePaths(config[key] as Record<string, unknown>, configPath)
-      } else if (key === 'localPath') {
-        config.localPath = path.resolve(configPath, config.localPath as string)
-      }
-    }
-  }
-}
-
-interface Assembly {
-  name: string
-  sequence: Record<string, unknown>
-  refNameAliases?: Record<string, unknown>
-  cytobands?: Record<string, unknown>
-}
-
-interface Track {
-  trackId: string
-  [key: string]: unknown
-}
-interface Config {
-  assemblies: Assembly[]
-  assembly: Assembly
-  tracks: Track[]
-  [key: string]: unknown
-}
-
-export function readData({
-  assembly: asm,
-  config,
-  session,
-  fasta,
-  aliases,
-  cytobands,
-  defaultSession,
-  tracks,
-  trackList = [],
-}: Opts) {
-  const assemblyData = asm && fs.existsSync(asm) ? read(asm) : undefined
-  const tracksData = tracks ? read(tracks) : undefined
-  const configData = (config ? read(config) : {}) as Config
-  let sessionData = session ? read(session) : undefined
-
-  if (config) {
-    addRelativePaths(configData, path.dirname(path.resolve(config)))
-  }
-
-  // the session.json can be a raw session or a json file with a "session"
-  // attribute, which is what is exported via the "File->Export session" in
-  // jbrowse-web
-  if (sessionData?.session) {
-    sessionData = sessionData.session
-  }
-
-  // only export first view
-  if (sessionData?.views) {
-    sessionData.view = sessionData.views[0]
-  }
-
-  // use assembly from file if a file existed
-  if (assemblyData) {
-    configData.assembly = assemblyData
-  }
-  // else check if it was an assembly name in a config file
-  else if (configData.assemblies?.length) {
-    configData.assemblies.find(entry => entry.name === asm)
-    if (asm) {
-      const assembly = configData.assemblies.find(entry => entry.name === asm)
-      if (!assembly) {
-        throw new Error(`assembly ${asm} not found in config`)
-      }
-      configData.assembly = assembly
-    } else {
-      configData.assembly = configData.assemblies[0]
-    }
-  }
-  // else load fasta from command line
-  else if (fasta) {
-    const bgzip = fasta.endsWith('gz')
-
-    configData.assembly = {
-      name: path.basename(fasta),
-      sequence: {
-        type: 'ReferenceSequenceTrack',
-        trackId: 'refseq',
-        adapter: {
-          type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
-          fastaLocation: makeLocation(fasta),
-          faiLocation: makeLocation(fasta + '.fai'),
-          gziLocation: bgzip ? makeLocation(fasta + '.gzi') : undefined,
-        },
-      },
-    }
-    if (aliases) {
-      configData.assembly.refNameAliases = {
-        adapter: {
-          type: 'RefNameAliasAdapter',
-          location: makeLocation(aliases),
-        },
-      }
-    }
-    if (cytobands) {
-      configData.assembly.cytobands = {
-        adapter: {
-          type: 'CytobandAdapter',
-          location: makeLocation(cytobands),
-        },
-      }
-    }
-  }
-
-  // throw if still no assembly
-  if (!configData.assembly) {
-    throw new Error(
-      'no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config',
-    )
-  }
-
-  if (tracksData) {
-    configData.tracks = tracksData
-  } else if (!configData.tracks) {
-    configData.tracks = []
-  }
-
-  trackList.forEach(track => {
-    const [type, [file]] = track
-
-    if (type === 'bam') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'AlignmentsTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'BamAdapter',
-            bamLocation: makeLocation(file),
-            index: { location: makeLocation(file + '.bai') },
-            sequenceAdapter: configData.assembly.sequence.adapter,
-          },
-        },
-      ]
-    }
-    if (type === 'cram') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'AlignmentsTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'CramAdapter',
-            cramLocation: makeLocation(file),
-            craiLocation: makeLocation(file + '.crai'),
-            sequenceAdapter: configData.assembly.sequence.adapter,
-          },
-        },
-      ]
-    }
-    if (type === 'bigwig') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'QuantitativeTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'BigWigAdapter',
-            bigWigLocation: makeLocation(file),
-          },
-        },
-      ]
-    }
-
-    if (type === 'vcfgz') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'VariantTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'VcfTabixAdapter',
-            vcfGzLocation: makeLocation(file),
-            index: {
-              location: makeLocation(file + '.tbi'),
-            },
-          },
-        },
-      ]
-    }
-
-    if (type === 'gffgz') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'FeatureTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'Gff3TabixAdapter',
-            gffGzLocation: makeLocation(file),
-            index: {
-              location: makeLocation(file + '.tbi'),
-            },
-          },
-        },
-      ]
-    }
-
-    if (type === 'hic') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'HicTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'HicAdapter',
-            hicLocation: makeLocation(file),
-          },
-        },
-      ]
-    }
-    if (type === 'bigbed') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'FeatureTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'BigBedAdapter',
-            bigBedLocation: makeLocation(file),
-          },
-        },
-      ]
-    }
-    if (type === 'bedgz') {
-      configData.tracks = [
-        ...configData.tracks,
-        {
-          type: 'FeatureTrack',
-          trackId: path.basename(file),
-          name: path.basename(file),
-          assemblyNames: [configData.assembly.name],
-          adapter: {
-            type: 'BedTabixAdapter',
-            bedGzLocation: makeLocation(file),
-            index: {
-              location: makeLocation(file + '.tbi'),
-            },
-          },
-        },
-      ]
-    }
-  })
-
-  if (!defaultSession) {
-    // don't use defaultSession from config.json file, can result in assembly
-    // name confusion
-    delete configData.defaultSession
-  }
-
-  // only allow an external manually specified session
-  if (sessionData) {
-    configData.defaultSession = sessionData
-  }
-
-  return configData
-}
-
-// without this, the styles can become messed up especially in lgv header
-// xref https://github.com/garronej/tss-react/issues/25
-export const muiCache = createCache({
-  key: 'mui',
-  prepend: true,
-})
-
-function process(
-  trackEntry: Entry,
-  view: LinearGenomeViewModel,
-  extra: (arg: string) => string = c => c,
-) {
-  const [, [track, ...opts]] = trackEntry
-  const currentTrack = view.showTrack(extra(track))
-  const display = currentTrack.displays[0]
-  opts.forEach(opt => {
-    // apply height to any track
-    if (opt.startsWith('height:')) {
-      const [, height] = opt.split(':')
-      display.setHeight(+height)
-    }
-
-    // apply sort to pileup
-    else if (opt.startsWith('sort:')) {
-      const [, type, tag] = opt.split(':')
-      display.PileupDisplay.setSortedBy(type, tag)
-    }
-
-    // apply color scheme to pileup
-    else if (opt.startsWith('color:')) {
-      const [, type, tag] = opt.split(':')
-      if (display.PileupDisplay) {
-        display.PileupDisplay.setColorScheme({ type, tag })
-      } else {
-        display.setColor(type)
-      }
-    }
-
-    // force track to render even if maxbpperpx limit hit...
-    else if (opt.startsWith('force:')) {
-      const [, force] = opt.split(':')
-      if (force) {
-        display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE })
-      }
-    }
-
-    // apply wiggle autoscale
-    else if (opt.startsWith('autoscale:')) {
-      const [, autoscale] = opt.split(':')
-      display.setAutoscale(autoscale)
-    }
-
-    // apply min and max score to wiggle
-    else if (opt.startsWith('minmax:')) {
-      const [, min, max] = opt.split(':')
-      display.setMinScore(+min)
-      display.setMaxScore(+max)
-    }
-
-    // apply linear or log scale to wiggle
-    else if (opt.startsWith('scaletype:')) {
-      const [, scaletype] = opt.split(':')
-      display.setScaleType(scaletype)
-    }
-
-    // draw crosshatches on wiggle
-    else if (opt.startsWith('crosshatch:')) {
-      const [, val] = opt.split(':')
-      display.setCrossHatches(booleanize(val))
-    }
-
-    // turn off fill on bigwig with fill:false
-    else if (opt.startsWith('fill:')) {
-      const [, val] = opt.split(':')
-      display.setFill(booleanize(val))
-    }
-
-    // set resolution:superfine to use finer bigwig bin size
-    else if (opt.startsWith('resolution:')) {
-      let [, val] = opt.split(':')
-      if (val === 'fine') {
-        val = '10'
-      } else if (val === 'superfine') {
-        val = '100'
-      }
-      display.setResolution(+val)
-    }
-  })
-}
-
-export async function renderRegion(opts: Opts) {
-  const model = createViewState(readData(opts))
-  const {
-    loc,
-    width = 1500,
-    trackList = [],
-    session: sessionParam,
-    defaultSession,
-  } = opts
-
-  const { session } = model
-  const { view } = session
-  const { assemblyManager } = model
-
-  view.setWidth(width)
-
-  if (loc) {
-    const [assembly] = assemblyManager.assemblies
-    if (loc === 'all') {
-      view.showAllRegionsInAssembly(assembly.name)
-    } else {
-      await view.navToLocString(loc, assembly.name)
-    }
-  } else if (!sessionParam && !defaultSession) {
-    console.warn('No loc specified')
-  }
-
-  trackList.forEach(track => {
-    process(track, view, extra => path.basename(extra))
-  })
-
-  return renderToSvg(view, {
-    rasterizeLayers: !opts.noRasterize,
-    ...opts,
-    Wrapper: ({ children }) => (
-      <CacheProvider value={muiCache}>{children}</CacheProvider>
-    ),
-  })
-}

package/src/util.ts

@@ -1,32 +0,0 @@
-import fs from 'fs'
-import tmp from 'tmp'
-import { spawnSync } from 'child_process'
-
-// nice helper function from https://stackoverflow.com/questions/263965/
-export function booleanize(str: string) {
-  return str === 'false' ? false : !!str
-}
-
-function createTmp() {
-  return tmp.fileSync({
-    mode: 0o644,
-    prefix: 'prefix-',
-    postfix: '.svg',
-  })
-}
-
-export function convert(
-  result: string,
-  args: { out: string; pngwidth?: string },
-  spawnArgs: string[] = [],
-) {
-  const { name } = createTmp()
-  const { pngwidth = '2048', out } = args
-  fs.writeFileSync(name, result)
-  const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs] as string[]
-  const ls = spawnSync('rsvg-convert', a)
-
-  console.error(`rsvg-convert stderr: ${ls.stderr.toString()}`)
-  console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`) // eslint-disable-line no-console
-  fs.unlinkSync(name)
-}