@jbrowse/img 2.5.0 → 2.6.2
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.
- package/dist/bin.js +0 -1
- package/dist/index.js +0 -1
- package/dist/parseArgv.js +0 -1
- package/dist/renderRegion.js +0 -1
- package/dist/util.js +0 -1
- package/esm/bin.js +0 -1
- package/esm/index.js +0 -1
- package/esm/parseArgv.js +0 -1
- package/esm/renderRegion.js +0 -1
- package/esm/util.js +0 -1
- package/package.json +7 -8
- package/dist/bin.js.map +0 -1
- package/dist/index.js.map +0 -1
- package/dist/parseArgv.js.map +0 -1
- package/dist/renderRegion.js.map +0 -1
- package/dist/util.js.map +0 -1
- package/esm/bin.js.map +0 -1
- package/esm/index.js.map +0 -1
- package/esm/parseArgv.js.map +0 -1
- package/esm/renderRegion.js.map +0 -1
- package/esm/util.js.map +0 -1
- package/src/bin.js +0 -2
- package/src/index.test.ts +0 -171
- package/src/index.ts +0 -210
- package/src/parseArgv.test.ts +0 -29
- package/src/parseArgv.ts +0 -48
- package/src/renderRegion.tsx +0 -456
- package/src/util.ts +0 -32
package/dist/bin.js
CHANGED
package/dist/index.js
CHANGED
package/dist/parseArgv.js
CHANGED
package/dist/renderRegion.js
CHANGED
package/dist/util.js
CHANGED
package/esm/bin.js
CHANGED
package/esm/index.js
CHANGED
package/esm/parseArgv.js
CHANGED
package/esm/renderRegion.js
CHANGED
package/esm/util.js
CHANGED
package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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{
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"name": "@jbrowse/img",
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"version": "2.
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"version": "2.6.2",
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"main": "dist/index.js",
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"module": "esm/index.js",
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"author": "JBrowse Team",
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@@ -13,8 +13,7 @@
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},
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"files": [
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"dist",
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"esm"
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"src"
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"esm"
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],
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"scripts": {
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"test": "cd ../../; jest --env node --testMatch '**/*testmod.js' products/jbrowse-img",
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@@ -22,18 +21,18 @@
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"prebuild": "yarn clean",
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"build": "npm-run-all build:*",
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"build:esm": "tsc --build tsconfig.build.esm.json",
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-
"build:
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"build:commonjs": "tsc --build tsconfig.build.commonjs.json",
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"preversion": "npm run build"
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},
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"dependencies": {
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"@babel/runtime": "^7.17.9",
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"@emotion/cache": "^11.7.1",
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"@emotion/react": "^11.9.0",
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32
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-
"@jbrowse/plugin-linear-genome-view": "^2.
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-
"@jbrowse/react-linear-genome-view": "^2.
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"@jbrowse/plugin-linear-genome-view": "^2.6.2",
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"@jbrowse/react-linear-genome-view": "^2.6.2",
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"abortcontroller-polyfill": "^1.7.3",
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"canvas": "^2.9.1",
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-
"jsdom": "^
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"jsdom": "^22.1.0",
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"mobx": "^6.6.0",
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"node-fetch": "^2.6.7",
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"react": "^17.0.0",
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@@ -44,5 +43,5 @@
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"publishConfig": {
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"access": "public"
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},
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-
"gitHead": "
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+
"gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
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}
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package/dist/bin.js.map
DELETED
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@@ -1 +0,0 @@
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1
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{"version":3,"file":"bin.js","sourceRoot":"","sources":["../src/bin.js"],"names":[],"mappings":";;AACA,OAAO,CAAC,YAAY,CAAC,CAAA"}
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package/dist/index.js.map
DELETED
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@@ -1 +0,0 @@
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package/dist/parseArgv.js.map
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package/dist/renderRegion.js.map
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package/esm/util.js.map
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{"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
DELETED
package/src/index.test.ts
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@@ -1,171 +0,0 @@
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/* eslint-disable tsdoc/syntax */
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/**
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* @jest-environment node
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*/
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// the above jest-environment node is important to check true usage
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// as a CLI tool
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import { renderRegion } from './renderRegion'
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import path from 'path'
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import fs from 'fs'
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import { JSDOM } from 'jsdom'
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import { Image, createCanvas } from 'canvas'
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import fetch, { Headers, Response, Request } from 'node-fetch'
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// @ts-expect-error
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global.fetch = fetch
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// @ts-expect-error
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global.Headers = Headers
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// @ts-expect-error
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global.Response = Response
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// @ts-expect-error
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global.Request = Request
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const { document } = new JSDOM(`...`).window
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global.document = document
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// @ts-expect-error
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global.nodeImage = Image
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// @ts-expect-error
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global.nodeCreateCanvas = createCanvas
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function pa(s: string) {
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return path.join(__dirname, s)
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}
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xtest('renders a region with --session and --config args', async () => {
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const result = await renderRegion({
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session: pa('../test/clingen_session.json'),
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config: pa('../data/config.json'),
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})
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fs.writeFileSync('svg_from_config_and_session_param.svg', result)
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expect(result).toMatchSnapshot()
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}, 40000)
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xtest('renders a region with --session, --tracks, and --assembly args', async () => {
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const result = await renderRegion({
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session: pa('../test/clingen_session.json'),
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tracks: pa('../data/tracks.json'),
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assembly: pa('../data/assembly.json'),
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})
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fs.writeFileSync('svg_from_separate_session_and_tracks.svg', result)
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expect(result).toMatchSnapshot()
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}, 40000)
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test('renders volvox with variety of args', async () => {
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const fp = (f: string) => pa('../data/volvox/' + f)
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const result = await renderRegion({
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fasta: fp('volvox.fa'),
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trackList: [
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['bam', [fp('volvox-sorted.bam')]],
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['cram', [fp('volvox-sorted.cram')]],
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['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
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['vcfgz', [fp('volvox.filtered.vcf.gz')]],
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['gffgz', [fp('volvox.sort.gff3.gz')]],
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['bigbed', [fp('volvox.bb')]],
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['bedgz', [fp('volvox-bed12.bed.gz')]],
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],
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loc: 'ctgA:1000-2000',
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})
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fs.writeFileSync(pa('../test/svg_from_volvox_fasta_and_bam.svg'), result)
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expect(result).toBeTruthy()
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}, 40000)
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-
xtest('renders human large region with remote urls', async () => {
|
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const result = await renderRegion({
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fasta: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
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trackList: [
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[
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'cram',
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[
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'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/skbr3.ont.sort.mod.cram',
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'force:true',
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],
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],
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],
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loc: '1:10,000,000-10,030,000',
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})
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fs.writeFileSync(pa('../test/human_remote_urls_large_region.svg'), result)
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90
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expect(result).toBeTruthy()
|
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91
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-
}, 120000)
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92
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-
|
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93
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-
xtest('renders volvox with remote urls', async () => {
|
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94
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-
const result = await renderRegion({
|
|
95
|
-
fasta: 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa',
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trackList: [
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97
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[
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'bam',
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[
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'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam',
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],
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],
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],
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loc: 'ctgA:1-1000',
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})
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fs.writeFileSync(pa('../test/volvox_remote_region.svg'), result)
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expect(result).toBeTruthy()
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108
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}, 20000)
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109
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-
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110
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test('renders volvox with variety of args (noRasterize)', async () => {
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const fp = (f: string) => pa('../data/volvox/' + f)
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const result = await renderRegion({
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fasta: fp('volvox.fa'),
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trackList: [
|
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['bam', [fp('volvox-sorted.bam')]],
|
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['cram', [fp('volvox-sorted.cram')]],
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['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
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['vcfgz', [fp('volvox.filtered.vcf.gz')]],
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['gffgz', [fp('volvox.sort.gff3.gz')]],
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['bigbed', [fp('volvox.bb')]],
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['bedgz', [fp('volvox-bed12.bed.gz')]],
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],
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loc: 'ctgA:1000-2000',
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noRasterize: true,
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})
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126
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fs.writeFileSync(
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pa('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'),
|
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result,
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)
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expect(result).toBeTruthy()
|
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-
}, 40000)
|
|
132
|
-
|
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133
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-
// commented out for using remote files currently
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134
|
-
xtest('configtracks arg with urls', async () => {
|
|
135
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-
const result = await renderRegion({
|
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-
config: 'data/config.json',
|
|
137
|
-
trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
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assembly: 'GRCh38',
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loc: 'chr1:50,000-60,000',
|
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140
|
-
})
|
|
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|
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fs.writeFileSync('svg_configtracks_simple.svg', result)
|
|
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|
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expect(result).toBeTruthy()
|
|
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|
-
}, 40000)
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|
|
145
|
-
test('configtracks arg with local files', async () => {
|
|
146
|
-
const result = await renderRegion({
|
|
147
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-
config: pa('../data/volvox/config.json'),
|
|
148
|
-
trackList: [['configtracks', ['volvox_sv']]],
|
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-
assembly: 'volvox',
|
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150
|
-
loc: 'ctgA:1-50,000',
|
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-
})
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fs.writeFileSync(pa('../test/svg_configtracks_local.svg'), result)
|
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expect(result).toBeTruthy()
|
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154
|
-
}, 40000)
|
|
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|
-
|
|
156
|
-
xtest('renders --hic', async () => {
|
|
157
|
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const result = await renderRegion({
|
|
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fasta: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz',
|
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159
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-
trackList: [
|
|
160
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-
[
|
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161
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-
'hic',
|
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|
-
[
|
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163
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'https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic',
|
|
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|
-
],
|
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165
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-
],
|
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|
-
],
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167
|
-
loc: '1:2,000,000-10,000,000',
|
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168
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-
})
|
|
169
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-
fs.writeFileSync(pa('../test/svg_from_human_hic.svg'), result)
|
|
170
|
-
expect(result).toBeTruthy()
|
|
171
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-
}, 20000)
|
package/src/index.ts
DELETED
|
@@ -1,210 +0,0 @@
|
|
|
1
|
-
import fs from 'fs'
|
|
2
|
-
import yargs from 'yargs'
|
|
3
|
-
import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
|
|
4
|
-
import fetch, { Headers, Response, Request } from 'node-fetch'
|
|
5
|
-
import { JSDOM } from 'jsdom'
|
|
6
|
-
import { Image, createCanvas } from 'canvas'
|
|
7
|
-
|
|
8
|
-
// locals
|
|
9
|
-
import { standardizeArgv, parseArgv } from './parseArgv'
|
|
10
|
-
import { renderRegion, Opts } from './renderRegion'
|
|
11
|
-
import { convert } from './util'
|
|
12
|
-
|
|
13
|
-
// @ts-expect-error
|
|
14
|
-
global.nodeImage = Image
|
|
15
|
-
// @ts-expect-error
|
|
16
|
-
global.nodeCreateCanvas = createCanvas
|
|
17
|
-
|
|
18
|
-
const { document } = new JSDOM(`...`).window
|
|
19
|
-
global.document = document
|
|
20
|
-
|
|
21
|
-
// force use of node-fetch polyfill, even if node 18+ fetch is available.
|
|
22
|
-
// native node 18+ fetch currently gives errors related to unidici and
|
|
23
|
-
// Uint8Array:
|
|
24
|
-
//
|
|
25
|
-
//
|
|
26
|
-
// % node --version
|
|
27
|
-
// v18.12.1
|
|
28
|
-
//
|
|
29
|
-
// % 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
|
|
30
|
-
// [
|
|
31
|
-
// '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
|
|
32
|
-
// '(Use `node --trace-warnings ...` to show where the warning was created)'
|
|
33
|
-
// ]
|
|
34
|
-
// [
|
|
35
|
-
// RangeError: offset is out of bounds
|
|
36
|
-
// at Uint8Array.set (<anonymous>)
|
|
37
|
-
// at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
|
|
38
|
-
// at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
|
|
39
|
-
// ]
|
|
40
|
-
|
|
41
|
-
// @ts-expect-error
|
|
42
|
-
global.fetch = fetch
|
|
43
|
-
// @ts-expect-error
|
|
44
|
-
global.Headers = Headers
|
|
45
|
-
// @ts-expect-error
|
|
46
|
-
global.Response = Response
|
|
47
|
-
// @ts-expect-error
|
|
48
|
-
global.Request = Request
|
|
49
|
-
|
|
50
|
-
const err = console.error
|
|
51
|
-
console.error = (...p: unknown[]) => {
|
|
52
|
-
if (!`${p[0]}`.match('useLayoutEffect')) {
|
|
53
|
-
err(p)
|
|
54
|
-
}
|
|
55
|
-
}
|
|
56
|
-
|
|
57
|
-
const warn = console.warn
|
|
58
|
-
console.warn = (...p: unknown[]) => {
|
|
59
|
-
if (!`${p[0]}`.match('estimation reached timeout')) {
|
|
60
|
-
warn(p)
|
|
61
|
-
}
|
|
62
|
-
}
|
|
63
|
-
|
|
64
|
-
// note: yargs is actually unused except for printing help
|
|
65
|
-
// we do custom command line parsing, see parseArgv.ts
|
|
66
|
-
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
67
|
-
yargs
|
|
68
|
-
.command('jb2export', 'Creates a jbrowse 2 image snapshot')
|
|
69
|
-
.option('config', {
|
|
70
|
-
description: 'Path to config file',
|
|
71
|
-
type: 'string',
|
|
72
|
-
})
|
|
73
|
-
.option('session', {
|
|
74
|
-
description: 'Path to session file',
|
|
75
|
-
type: 'string',
|
|
76
|
-
})
|
|
77
|
-
.option('assembly', {
|
|
78
|
-
description:
|
|
79
|
-
'Path to an assembly configuration, or a name of an assembly in the configFile',
|
|
80
|
-
type: 'string',
|
|
81
|
-
})
|
|
82
|
-
.option('tracks', {
|
|
83
|
-
description: 'Path to tracks portion of a session',
|
|
84
|
-
type: 'string',
|
|
85
|
-
})
|
|
86
|
-
.option('loc', {
|
|
87
|
-
description:
|
|
88
|
-
'A locstring to navigate to, or --loc all to view the whole genome',
|
|
89
|
-
type: 'string',
|
|
90
|
-
})
|
|
91
|
-
.option('fasta', {
|
|
92
|
-
description: 'Supply a fasta for the assembly',
|
|
93
|
-
type: 'string',
|
|
94
|
-
})
|
|
95
|
-
.option('aliases', {
|
|
96
|
-
description:
|
|
97
|
-
'Supply aliases for the assembly, e.g. mapping of 1 to chr1. Tab separated file where column 1 matches the names from the FASTA',
|
|
98
|
-
type: 'string',
|
|
99
|
-
})
|
|
100
|
-
.option('width', {
|
|
101
|
-
description:
|
|
102
|
-
'Set the width of the window that jbrowse renders to, default: 1500px',
|
|
103
|
-
type: 'number',
|
|
104
|
-
})
|
|
105
|
-
.option('pngwidth', {
|
|
106
|
-
description:
|
|
107
|
-
'Set the width of the png canvas if using png output, default 2048px',
|
|
108
|
-
type: 'number',
|
|
109
|
-
default: 2048,
|
|
110
|
-
})
|
|
111
|
-
// track types
|
|
112
|
-
.option('configtracks', {
|
|
113
|
-
description: 'A list of track labels from a config file',
|
|
114
|
-
type: 'array',
|
|
115
|
-
})
|
|
116
|
-
.option('bam', {
|
|
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|
-
description:
|
|
118
|
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'A bam file, flag --bam can be used multiple times to specify multiple bam files',
|
|
119
|
-
type: 'array',
|
|
120
|
-
})
|
|
121
|
-
.option('bigwig', {
|
|
122
|
-
description:
|
|
123
|
-
'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
|
|
124
|
-
type: 'array',
|
|
125
|
-
})
|
|
126
|
-
.option('cram', {
|
|
127
|
-
description:
|
|
128
|
-
'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
|
|
129
|
-
type: 'array',
|
|
130
|
-
})
|
|
131
|
-
.option('vcfgz', {
|
|
132
|
-
description:
|
|
133
|
-
'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
|
|
134
|
-
type: 'array',
|
|
135
|
-
})
|
|
136
|
-
.option('gffgz', {
|
|
137
|
-
description:
|
|
138
|
-
'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
|
|
139
|
-
type: 'array',
|
|
140
|
-
})
|
|
141
|
-
.option('hic', {
|
|
142
|
-
description:
|
|
143
|
-
'A .hic file, the --hic can be used multiple times to specify multiple hic files',
|
|
144
|
-
type: 'array',
|
|
145
|
-
})
|
|
146
|
-
.option('bigbed', {
|
|
147
|
-
description:
|
|
148
|
-
'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
|
|
149
|
-
type: 'array',
|
|
150
|
-
})
|
|
151
|
-
.option('bedgz', {
|
|
152
|
-
description:
|
|
153
|
-
'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
|
|
154
|
-
type: 'array',
|
|
155
|
-
})
|
|
156
|
-
|
|
157
|
-
// other
|
|
158
|
-
.option('out', {
|
|
159
|
-
description:
|
|
160
|
-
'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',
|
|
161
|
-
type: 'string',
|
|
162
|
-
default: 'out.svg',
|
|
163
|
-
})
|
|
164
|
-
.option('noRasterize', {
|
|
165
|
-
description:
|
|
166
|
-
'Use full SVG rendering with no rasterized layers, this can substantially increase filesize',
|
|
167
|
-
type: 'boolean',
|
|
168
|
-
})
|
|
169
|
-
.option('defaultSession', {
|
|
170
|
-
description: 'Use the defaultSession from config.json',
|
|
171
|
-
type: 'boolean',
|
|
172
|
-
})
|
|
173
|
-
.help()
|
|
174
|
-
.alias('help', 'h')
|
|
175
|
-
.alias('width', 'w').argv
|
|
176
|
-
|
|
177
|
-
const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
|
|
178
|
-
'bam',
|
|
179
|
-
'cram',
|
|
180
|
-
'vcfgz',
|
|
181
|
-
'hic',
|
|
182
|
-
'bigwig',
|
|
183
|
-
'bigbed',
|
|
184
|
-
'bedgz',
|
|
185
|
-
'gffgz',
|
|
186
|
-
'configtracks',
|
|
187
|
-
])
|
|
188
|
-
|
|
189
|
-
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
190
|
-
;(async () => {
|
|
191
|
-
try {
|
|
192
|
-
const result = await renderRegion(args as Opts)
|
|
193
|
-
const { out = 'out.svg', pngwidth = '2048' } = args
|
|
194
|
-
if (out.endsWith('.png')) {
|
|
195
|
-
convert(result, { out, pngwidth })
|
|
196
|
-
} else if (out.endsWith('.pdf')) {
|
|
197
|
-
convert(result, { out, pngwidth }, ['-f', 'pdf'])
|
|
198
|
-
} else {
|
|
199
|
-
fs.writeFileSync(out, result)
|
|
200
|
-
}
|
|
201
|
-
|
|
202
|
-
// manually exit the process after done rendering because autoruns or
|
|
203
|
-
// something similar otherwise keeps the nodejs process alive xref
|
|
204
|
-
// https://github.com/GMOD/jb2export/issues/6
|
|
205
|
-
process.exit(0)
|
|
206
|
-
} catch (e) {
|
|
207
|
-
console.error(e)
|
|
208
|
-
process.exit(1)
|
|
209
|
-
}
|
|
210
|
-
})()
|
package/src/parseArgv.test.ts
DELETED
|
@@ -1,29 +0,0 @@
|
|
|
1
|
-
import { parseArgv } from './parseArgv'
|
|
2
|
-
|
|
3
|
-
test('parse', () => {
|
|
4
|
-
const args =
|
|
5
|
-
'--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize'
|
|
6
|
-
|
|
7
|
-
expect(parseArgv(args.split(' '))).toEqual([
|
|
8
|
-
['bam', ['dad.bam', 'color:red']],
|
|
9
|
-
['vcf', ['variants.vcf']],
|
|
10
|
-
['bam', ['mom.bam']],
|
|
11
|
-
['defaultSession', []],
|
|
12
|
-
['out', ['out.svg']],
|
|
13
|
-
['noRasterize', []],
|
|
14
|
-
])
|
|
15
|
-
})
|
|
16
|
-
|
|
17
|
-
test('parse', () => {
|
|
18
|
-
const args =
|
|
19
|
-
'--bam dad.bam color:red --vcf variants.vcf --bam mom.bam force:true --defaultSession --out out.svg --noRasterize'
|
|
20
|
-
|
|
21
|
-
expect(parseArgv(args.split(' '))).toEqual([
|
|
22
|
-
['bam', ['dad.bam', 'color:red']],
|
|
23
|
-
['vcf', ['variants.vcf']],
|
|
24
|
-
['bam', ['mom.bam', 'force:true']],
|
|
25
|
-
['defaultSession', []],
|
|
26
|
-
['out', ['out.svg']],
|
|
27
|
-
['noRasterize', []],
|
|
28
|
-
])
|
|
29
|
-
})
|
package/src/parseArgv.ts
DELETED
|
@@ -1,48 +0,0 @@
|
|
|
1
|
-
export type Entry = [string, string[]]
|
|
2
|
-
|
|
3
|
-
// example (see parseArgv.test.js):
|
|
4
|
-
// const args =
|
|
5
|
-
// '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize'
|
|
6
|
-
//
|
|
7
|
-
// expect(parseArgv(args.split(' '))).toEqual([
|
|
8
|
-
// ['bam', ['dad.bam', 'color:red']],
|
|
9
|
-
// ['vcf', ['variants.vcf']],
|
|
10
|
-
// ['bam', ['mom.bam']],
|
|
11
|
-
// ['defaultSession', []],
|
|
12
|
-
// ['out', ['out.svg']],
|
|
13
|
-
// ['noRasterize', []],
|
|
14
|
-
// ])
|
|
15
|
-
export function parseArgv(argv: string[]) {
|
|
16
|
-
const map = [] as Entry[]
|
|
17
|
-
while (argv.length) {
|
|
18
|
-
const val = argv[0].slice(2)
|
|
19
|
-
argv = argv.slice(1)
|
|
20
|
-
const next = argv.findIndex(arg => arg.startsWith('-'))
|
|
21
|
-
|
|
22
|
-
if (next !== -1) {
|
|
23
|
-
map.push([val, argv.slice(0, next)])
|
|
24
|
-
argv = argv.slice(next)
|
|
25
|
-
} else {
|
|
26
|
-
map.push([val, argv])
|
|
27
|
-
break
|
|
28
|
-
}
|
|
29
|
-
}
|
|
30
|
-
return map
|
|
31
|
-
}
|
|
32
|
-
|
|
33
|
-
export function standardizeArgv(args: Entry[], trackTypes: string[]) {
|
|
34
|
-
const result = { trackList: [] } as {
|
|
35
|
-
trackList: Entry[]
|
|
36
|
-
out?: string
|
|
37
|
-
pngwidth?: string
|
|
38
|
-
[key: string]: unknown
|
|
39
|
-
}
|
|
40
|
-
args.forEach(arg => {
|
|
41
|
-
if (trackTypes.includes(arg[0])) {
|
|
42
|
-
result.trackList.push(arg)
|
|
43
|
-
} else {
|
|
44
|
-
result[arg[0]] = arg[1][0] || true
|
|
45
|
-
}
|
|
46
|
-
})
|
|
47
|
-
return result
|
|
48
|
-
}
|
package/src/renderRegion.tsx
DELETED
|
@@ -1,456 +0,0 @@
|
|
|
1
|
-
import React from 'react'
|
|
2
|
-
import { createViewState } from '@jbrowse/react-linear-genome-view'
|
|
3
|
-
import {
|
|
4
|
-
LinearGenomeViewModel,
|
|
5
|
-
renderToSvg,
|
|
6
|
-
} from '@jbrowse/plugin-linear-genome-view'
|
|
7
|
-
import createCache from '@emotion/cache'
|
|
8
|
-
import { CacheProvider } from '@emotion/react'
|
|
9
|
-
import path from 'path'
|
|
10
|
-
import fs from 'fs'
|
|
11
|
-
|
|
12
|
-
// local
|
|
13
|
-
import { Entry } from './parseArgv'
|
|
14
|
-
import { booleanize } from './util'
|
|
15
|
-
|
|
16
|
-
export interface Opts {
|
|
17
|
-
noRasterize?: boolean
|
|
18
|
-
loc?: string
|
|
19
|
-
width?: number
|
|
20
|
-
session?: string
|
|
21
|
-
assembly?: string
|
|
22
|
-
config?: string
|
|
23
|
-
fasta?: string
|
|
24
|
-
aliases?: string
|
|
25
|
-
cytobands?: string
|
|
26
|
-
defaultSession?: string
|
|
27
|
-
trackList?: Entry[]
|
|
28
|
-
tracks?: string
|
|
29
|
-
}
|
|
30
|
-
|
|
31
|
-
function read(file: string) {
|
|
32
|
-
let res
|
|
33
|
-
try {
|
|
34
|
-
res = JSON.parse(fs.readFileSync(file, 'utf8'))
|
|
35
|
-
} catch (e) {
|
|
36
|
-
throw new Error(
|
|
37
|
-
`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`,
|
|
38
|
-
)
|
|
39
|
-
}
|
|
40
|
-
return res
|
|
41
|
-
}
|
|
42
|
-
function makeLocation(file: string) {
|
|
43
|
-
return file.startsWith('http') ? { uri: file } : { localPath: file }
|
|
44
|
-
}
|
|
45
|
-
|
|
46
|
-
function addRelativePaths(config: Record<string, unknown>, configPath: string) {
|
|
47
|
-
if (typeof config === 'object') {
|
|
48
|
-
for (const key of Object.keys(config)) {
|
|
49
|
-
if (typeof config[key] === 'object') {
|
|
50
|
-
addRelativePaths(config[key] as Record<string, unknown>, configPath)
|
|
51
|
-
} else if (key === 'localPath') {
|
|
52
|
-
config.localPath = path.resolve(configPath, config.localPath as string)
|
|
53
|
-
}
|
|
54
|
-
}
|
|
55
|
-
}
|
|
56
|
-
}
|
|
57
|
-
|
|
58
|
-
interface Assembly {
|
|
59
|
-
name: string
|
|
60
|
-
sequence: Record<string, unknown>
|
|
61
|
-
refNameAliases?: Record<string, unknown>
|
|
62
|
-
cytobands?: Record<string, unknown>
|
|
63
|
-
}
|
|
64
|
-
|
|
65
|
-
interface Track {
|
|
66
|
-
trackId: string
|
|
67
|
-
[key: string]: unknown
|
|
68
|
-
}
|
|
69
|
-
interface Config {
|
|
70
|
-
assemblies: Assembly[]
|
|
71
|
-
assembly: Assembly
|
|
72
|
-
tracks: Track[]
|
|
73
|
-
[key: string]: unknown
|
|
74
|
-
}
|
|
75
|
-
|
|
76
|
-
export function readData({
|
|
77
|
-
assembly: asm,
|
|
78
|
-
config,
|
|
79
|
-
session,
|
|
80
|
-
fasta,
|
|
81
|
-
aliases,
|
|
82
|
-
cytobands,
|
|
83
|
-
defaultSession,
|
|
84
|
-
tracks,
|
|
85
|
-
trackList = [],
|
|
86
|
-
}: Opts) {
|
|
87
|
-
const assemblyData = asm && fs.existsSync(asm) ? read(asm) : undefined
|
|
88
|
-
const tracksData = tracks ? read(tracks) : undefined
|
|
89
|
-
const configData = (config ? read(config) : {}) as Config
|
|
90
|
-
let sessionData = session ? read(session) : undefined
|
|
91
|
-
|
|
92
|
-
if (config) {
|
|
93
|
-
addRelativePaths(configData, path.dirname(path.resolve(config)))
|
|
94
|
-
}
|
|
95
|
-
|
|
96
|
-
// the session.json can be a raw session or a json file with a "session"
|
|
97
|
-
// attribute, which is what is exported via the "File->Export session" in
|
|
98
|
-
// jbrowse-web
|
|
99
|
-
if (sessionData?.session) {
|
|
100
|
-
sessionData = sessionData.session
|
|
101
|
-
}
|
|
102
|
-
|
|
103
|
-
// only export first view
|
|
104
|
-
if (sessionData?.views) {
|
|
105
|
-
sessionData.view = sessionData.views[0]
|
|
106
|
-
}
|
|
107
|
-
|
|
108
|
-
// use assembly from file if a file existed
|
|
109
|
-
if (assemblyData) {
|
|
110
|
-
configData.assembly = assemblyData
|
|
111
|
-
}
|
|
112
|
-
// else check if it was an assembly name in a config file
|
|
113
|
-
else if (configData.assemblies?.length) {
|
|
114
|
-
configData.assemblies.find(entry => entry.name === asm)
|
|
115
|
-
if (asm) {
|
|
116
|
-
const assembly = configData.assemblies.find(entry => entry.name === asm)
|
|
117
|
-
if (!assembly) {
|
|
118
|
-
throw new Error(`assembly ${asm} not found in config`)
|
|
119
|
-
}
|
|
120
|
-
configData.assembly = assembly
|
|
121
|
-
} else {
|
|
122
|
-
configData.assembly = configData.assemblies[0]
|
|
123
|
-
}
|
|
124
|
-
}
|
|
125
|
-
// else load fasta from command line
|
|
126
|
-
else if (fasta) {
|
|
127
|
-
const bgzip = fasta.endsWith('gz')
|
|
128
|
-
|
|
129
|
-
configData.assembly = {
|
|
130
|
-
name: path.basename(fasta),
|
|
131
|
-
sequence: {
|
|
132
|
-
type: 'ReferenceSequenceTrack',
|
|
133
|
-
trackId: 'refseq',
|
|
134
|
-
adapter: {
|
|
135
|
-
type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
|
|
136
|
-
fastaLocation: makeLocation(fasta),
|
|
137
|
-
faiLocation: makeLocation(fasta + '.fai'),
|
|
138
|
-
gziLocation: bgzip ? makeLocation(fasta + '.gzi') : undefined,
|
|
139
|
-
},
|
|
140
|
-
},
|
|
141
|
-
}
|
|
142
|
-
if (aliases) {
|
|
143
|
-
configData.assembly.refNameAliases = {
|
|
144
|
-
adapter: {
|
|
145
|
-
type: 'RefNameAliasAdapter',
|
|
146
|
-
location: makeLocation(aliases),
|
|
147
|
-
},
|
|
148
|
-
}
|
|
149
|
-
}
|
|
150
|
-
if (cytobands) {
|
|
151
|
-
configData.assembly.cytobands = {
|
|
152
|
-
adapter: {
|
|
153
|
-
type: 'CytobandAdapter',
|
|
154
|
-
location: makeLocation(cytobands),
|
|
155
|
-
},
|
|
156
|
-
}
|
|
157
|
-
}
|
|
158
|
-
}
|
|
159
|
-
|
|
160
|
-
// throw if still no assembly
|
|
161
|
-
if (!configData.assembly) {
|
|
162
|
-
throw new Error(
|
|
163
|
-
'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',
|
|
164
|
-
)
|
|
165
|
-
}
|
|
166
|
-
|
|
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if (tracksData) {
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} else if (!configData.tracks) {
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}
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|
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173
|
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trackList.forEach(track => {
|
|
174
|
-
const [type, [file]] = track
|
|
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|
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|
|
176
|
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if (type === 'bam') {
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177
|
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configData.tracks = [
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{
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type: 'AlignmentsTrack',
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|
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trackId: path.basename(file),
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name: path.basename(file),
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assemblyNames: [configData.assembly.name],
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adapter: {
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type: 'BamAdapter',
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bamLocation: makeLocation(file),
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index: { location: makeLocation(file + '.bai') },
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sequenceAdapter: configData.assembly.sequence.adapter,
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},
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},
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]
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}
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if (type === 'cram') {
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configData.tracks = [
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{
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type: 'AlignmentsTrack',
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trackId: path.basename(file),
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name: path.basename(file),
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assemblyNames: [configData.assembly.name],
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adapter: {
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type: 'CramAdapter',
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cramLocation: makeLocation(file),
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craiLocation: makeLocation(file + '.crai'),
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sequenceAdapter: configData.assembly.sequence.adapter,
|
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|
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},
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},
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]
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}
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if (type === 'bigwig') {
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configData.tracks = [
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{
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type: 'QuantitativeTrack',
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trackId: path.basename(file),
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name: path.basename(file),
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|
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assemblyNames: [configData.assembly.name],
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adapter: {
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type: 'BigWigAdapter',
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bigWigLocation: makeLocation(file),
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},
|
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|
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},
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|
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]
|
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|
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}
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|
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|
-
|
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226
|
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if (type === 'vcfgz') {
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|
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configData.tracks = [
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|
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...configData.tracks,
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|
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{
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|
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type: 'VariantTrack',
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|
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trackId: path.basename(file),
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|
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name: path.basename(file),
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|
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assemblyNames: [configData.assembly.name],
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|
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adapter: {
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|
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type: 'VcfTabixAdapter',
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|
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vcfGzLocation: makeLocation(file),
|
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|
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index: {
|
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238
|
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location: makeLocation(file + '.tbi'),
|
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|
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},
|
|
240
|
-
},
|
|
241
|
-
},
|
|
242
|
-
]
|
|
243
|
-
}
|
|
244
|
-
|
|
245
|
-
if (type === 'gffgz') {
|
|
246
|
-
configData.tracks = [
|
|
247
|
-
...configData.tracks,
|
|
248
|
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{
|
|
249
|
-
type: 'FeatureTrack',
|
|
250
|
-
trackId: path.basename(file),
|
|
251
|
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name: path.basename(file),
|
|
252
|
-
assemblyNames: [configData.assembly.name],
|
|
253
|
-
adapter: {
|
|
254
|
-
type: 'Gff3TabixAdapter',
|
|
255
|
-
gffGzLocation: makeLocation(file),
|
|
256
|
-
index: {
|
|
257
|
-
location: makeLocation(file + '.tbi'),
|
|
258
|
-
},
|
|
259
|
-
},
|
|
260
|
-
},
|
|
261
|
-
]
|
|
262
|
-
}
|
|
263
|
-
|
|
264
|
-
if (type === 'hic') {
|
|
265
|
-
configData.tracks = [
|
|
266
|
-
...configData.tracks,
|
|
267
|
-
{
|
|
268
|
-
type: 'HicTrack',
|
|
269
|
-
trackId: path.basename(file),
|
|
270
|
-
name: path.basename(file),
|
|
271
|
-
assemblyNames: [configData.assembly.name],
|
|
272
|
-
adapter: {
|
|
273
|
-
type: 'HicAdapter',
|
|
274
|
-
hicLocation: makeLocation(file),
|
|
275
|
-
},
|
|
276
|
-
},
|
|
277
|
-
]
|
|
278
|
-
}
|
|
279
|
-
if (type === 'bigbed') {
|
|
280
|
-
configData.tracks = [
|
|
281
|
-
...configData.tracks,
|
|
282
|
-
{
|
|
283
|
-
type: 'FeatureTrack',
|
|
284
|
-
trackId: path.basename(file),
|
|
285
|
-
name: path.basename(file),
|
|
286
|
-
assemblyNames: [configData.assembly.name],
|
|
287
|
-
adapter: {
|
|
288
|
-
type: 'BigBedAdapter',
|
|
289
|
-
bigBedLocation: makeLocation(file),
|
|
290
|
-
},
|
|
291
|
-
},
|
|
292
|
-
]
|
|
293
|
-
}
|
|
294
|
-
if (type === 'bedgz') {
|
|
295
|
-
configData.tracks = [
|
|
296
|
-
...configData.tracks,
|
|
297
|
-
{
|
|
298
|
-
type: 'FeatureTrack',
|
|
299
|
-
trackId: path.basename(file),
|
|
300
|
-
name: path.basename(file),
|
|
301
|
-
assemblyNames: [configData.assembly.name],
|
|
302
|
-
adapter: {
|
|
303
|
-
type: 'BedTabixAdapter',
|
|
304
|
-
bedGzLocation: makeLocation(file),
|
|
305
|
-
index: {
|
|
306
|
-
location: makeLocation(file + '.tbi'),
|
|
307
|
-
},
|
|
308
|
-
},
|
|
309
|
-
},
|
|
310
|
-
]
|
|
311
|
-
}
|
|
312
|
-
})
|
|
313
|
-
|
|
314
|
-
if (!defaultSession) {
|
|
315
|
-
// don't use defaultSession from config.json file, can result in assembly
|
|
316
|
-
// name confusion
|
|
317
|
-
delete configData.defaultSession
|
|
318
|
-
}
|
|
319
|
-
|
|
320
|
-
// only allow an external manually specified session
|
|
321
|
-
if (sessionData) {
|
|
322
|
-
configData.defaultSession = sessionData
|
|
323
|
-
}
|
|
324
|
-
|
|
325
|
-
return configData
|
|
326
|
-
}
|
|
327
|
-
|
|
328
|
-
// without this, the styles can become messed up especially in lgv header
|
|
329
|
-
// xref https://github.com/garronej/tss-react/issues/25
|
|
330
|
-
export const muiCache = createCache({
|
|
331
|
-
key: 'mui',
|
|
332
|
-
prepend: true,
|
|
333
|
-
})
|
|
334
|
-
|
|
335
|
-
function process(
|
|
336
|
-
trackEntry: Entry,
|
|
337
|
-
view: LinearGenomeViewModel,
|
|
338
|
-
extra: (arg: string) => string = c => c,
|
|
339
|
-
) {
|
|
340
|
-
const [, [track, ...opts]] = trackEntry
|
|
341
|
-
const currentTrack = view.showTrack(extra(track))
|
|
342
|
-
const display = currentTrack.displays[0]
|
|
343
|
-
opts.forEach(opt => {
|
|
344
|
-
// apply height to any track
|
|
345
|
-
if (opt.startsWith('height:')) {
|
|
346
|
-
const [, height] = opt.split(':')
|
|
347
|
-
display.setHeight(+height)
|
|
348
|
-
}
|
|
349
|
-
|
|
350
|
-
// apply sort to pileup
|
|
351
|
-
else if (opt.startsWith('sort:')) {
|
|
352
|
-
const [, type, tag] = opt.split(':')
|
|
353
|
-
display.PileupDisplay.setSortedBy(type, tag)
|
|
354
|
-
}
|
|
355
|
-
|
|
356
|
-
// apply color scheme to pileup
|
|
357
|
-
else if (opt.startsWith('color:')) {
|
|
358
|
-
const [, type, tag] = opt.split(':')
|
|
359
|
-
if (display.PileupDisplay) {
|
|
360
|
-
display.PileupDisplay.setColorScheme({ type, tag })
|
|
361
|
-
} else {
|
|
362
|
-
display.setColor(type)
|
|
363
|
-
}
|
|
364
|
-
}
|
|
365
|
-
|
|
366
|
-
// force track to render even if maxbpperpx limit hit...
|
|
367
|
-
else if (opt.startsWith('force:')) {
|
|
368
|
-
const [, force] = opt.split(':')
|
|
369
|
-
if (force) {
|
|
370
|
-
display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE })
|
|
371
|
-
}
|
|
372
|
-
}
|
|
373
|
-
|
|
374
|
-
// apply wiggle autoscale
|
|
375
|
-
else if (opt.startsWith('autoscale:')) {
|
|
376
|
-
const [, autoscale] = opt.split(':')
|
|
377
|
-
display.setAutoscale(autoscale)
|
|
378
|
-
}
|
|
379
|
-
|
|
380
|
-
// apply min and max score to wiggle
|
|
381
|
-
else if (opt.startsWith('minmax:')) {
|
|
382
|
-
const [, min, max] = opt.split(':')
|
|
383
|
-
display.setMinScore(+min)
|
|
384
|
-
display.setMaxScore(+max)
|
|
385
|
-
}
|
|
386
|
-
|
|
387
|
-
// apply linear or log scale to wiggle
|
|
388
|
-
else if (opt.startsWith('scaletype:')) {
|
|
389
|
-
const [, scaletype] = opt.split(':')
|
|
390
|
-
display.setScaleType(scaletype)
|
|
391
|
-
}
|
|
392
|
-
|
|
393
|
-
// draw crosshatches on wiggle
|
|
394
|
-
else if (opt.startsWith('crosshatch:')) {
|
|
395
|
-
const [, val] = opt.split(':')
|
|
396
|
-
display.setCrossHatches(booleanize(val))
|
|
397
|
-
}
|
|
398
|
-
|
|
399
|
-
// turn off fill on bigwig with fill:false
|
|
400
|
-
else if (opt.startsWith('fill:')) {
|
|
401
|
-
const [, val] = opt.split(':')
|
|
402
|
-
display.setFill(booleanize(val))
|
|
403
|
-
}
|
|
404
|
-
|
|
405
|
-
// set resolution:superfine to use finer bigwig bin size
|
|
406
|
-
else if (opt.startsWith('resolution:')) {
|
|
407
|
-
let [, val] = opt.split(':')
|
|
408
|
-
if (val === 'fine') {
|
|
409
|
-
val = '10'
|
|
410
|
-
} else if (val === 'superfine') {
|
|
411
|
-
val = '100'
|
|
412
|
-
}
|
|
413
|
-
display.setResolution(+val)
|
|
414
|
-
}
|
|
415
|
-
})
|
|
416
|
-
}
|
|
417
|
-
|
|
418
|
-
export async function renderRegion(opts: Opts) {
|
|
419
|
-
const model = createViewState(readData(opts))
|
|
420
|
-
const {
|
|
421
|
-
loc,
|
|
422
|
-
width = 1500,
|
|
423
|
-
trackList = [],
|
|
424
|
-
session: sessionParam,
|
|
425
|
-
defaultSession,
|
|
426
|
-
} = opts
|
|
427
|
-
|
|
428
|
-
const { session } = model
|
|
429
|
-
const { view } = session
|
|
430
|
-
const { assemblyManager } = model
|
|
431
|
-
|
|
432
|
-
view.setWidth(width)
|
|
433
|
-
|
|
434
|
-
if (loc) {
|
|
435
|
-
const [assembly] = assemblyManager.assemblies
|
|
436
|
-
if (loc === 'all') {
|
|
437
|
-
view.showAllRegionsInAssembly(assembly.name)
|
|
438
|
-
} else {
|
|
439
|
-
await view.navToLocString(loc, assembly.name)
|
|
440
|
-
}
|
|
441
|
-
} else if (!sessionParam && !defaultSession) {
|
|
442
|
-
console.warn('No loc specified')
|
|
443
|
-
}
|
|
444
|
-
|
|
445
|
-
trackList.forEach(track => {
|
|
446
|
-
process(track, view, extra => path.basename(extra))
|
|
447
|
-
})
|
|
448
|
-
|
|
449
|
-
return renderToSvg(view, {
|
|
450
|
-
rasterizeLayers: !opts.noRasterize,
|
|
451
|
-
...opts,
|
|
452
|
-
Wrapper: ({ children }) => (
|
|
453
|
-
<CacheProvider value={muiCache}>{children}</CacheProvider>
|
|
454
|
-
),
|
|
455
|
-
})
|
|
456
|
-
}
|
package/src/util.ts
DELETED
|
@@ -1,32 +0,0 @@
|
|
|
1
|
-
import fs from 'fs'
|
|
2
|
-
import tmp from 'tmp'
|
|
3
|
-
import { spawnSync } from 'child_process'
|
|
4
|
-
|
|
5
|
-
// nice helper function from https://stackoverflow.com/questions/263965/
|
|
6
|
-
export function booleanize(str: string) {
|
|
7
|
-
return str === 'false' ? false : !!str
|
|
8
|
-
}
|
|
9
|
-
|
|
10
|
-
function createTmp() {
|
|
11
|
-
return tmp.fileSync({
|
|
12
|
-
mode: 0o644,
|
|
13
|
-
prefix: 'prefix-',
|
|
14
|
-
postfix: '.svg',
|
|
15
|
-
})
|
|
16
|
-
}
|
|
17
|
-
|
|
18
|
-
export function convert(
|
|
19
|
-
result: string,
|
|
20
|
-
args: { out: string; pngwidth?: string },
|
|
21
|
-
spawnArgs: string[] = [],
|
|
22
|
-
) {
|
|
23
|
-
const { name } = createTmp()
|
|
24
|
-
const { pngwidth = '2048', out } = args
|
|
25
|
-
fs.writeFileSync(name, result)
|
|
26
|
-
const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs] as string[]
|
|
27
|
-
const ls = spawnSync('rsvg-convert', a)
|
|
28
|
-
|
|
29
|
-
console.error(`rsvg-convert stderr: ${ls.stderr.toString()}`)
|
|
30
|
-
console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`) // eslint-disable-line no-console
|
|
31
|
-
fs.unlinkSync(name)
|
|
32
|
-
}
|