@jbrowse/img 2.2.1 → 2.3.0

package/README.md

@@ -4,7 +4,9 @@ Static exports of JBrowse 2 rendering.
 
 ## Prerequisites
 
-You don't need to have JBrowse 2 installed to use this tool. The tool can generate images using files on your hard drive or from remote files. So, all you need to run this tool is
+You don't need to have JBrowse 2 installed to use this tool. The tool can
+generate images using files on your hard drive or from remote files. So, all you
+need to run this tool is
 
 - NodeJS v12+
 
@@ -16,24 +18,27 @@ More examples [EXAMPLES.md](EXAMPLES.md)
 
 ## Setup
 
-You can install the `@jbrowse/img` package from npm, which, if your node is configured in a typical configuration, will then have a command `jb2export` in your path
+You can install the `@jbrowse/img` package from npm, which, if your node is
+configured in a typical configuration, will then have a command `jb2export` in
+your path
 
 ```bash
 npm install -g @jbrowse/img
 ```
 
-If you are using npm version 7+ (released 2021) you may also need to add `--legacy-peer-deps`
+If you are using npm version 7+ (released 2021) you may also need to add
+`--legacy-peer-deps`
 
-If you are a developer and want to modify the code, see [developer
-guide](DEVELOPER.md) for details
+If you are a developer and want to modify the code, see
+[developer guide](DEVELOPER.md) for details
 
 ## Example usages
 
 ### Use with local files
 
 We can call this script on local files, and it doesn't require a web browser,
-not even a headless webbrowser, it just runs a node script and React SSR is
-used to create the SVG
+not even a headless webbrowser, it just runs a node script and React SSR is used
+to create the SVG
 
 ```bash
 ## generate an indexed fasta e.g. fai file
@@ -52,7 +57,8 @@ If `--out` is not specified it writes to out.svg
 ### Generate PNG instead of SVG
 
 Supply a file with the png extension to `--out`, uses rsvg-convert so you will
-need to install rsvg-convert to your system e.g. with `sudo apt install librsvg2-bin`
+need to install rsvg-convert to your system e.g. with
+`sudo apt install librsvg2-bin`
 
 ```bash
 jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.png
@@ -61,7 +67,8 @@ jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000
 ### Generate PDF instead of SVG
 
 Supply a file with the pdf extension to `--out`, uses rsvg-convert so you will
-need to install rsvg-convert to your system e.g. with `sudo apt install librsvg2-bin`
+need to install rsvg-convert to your system e.g. with
+`sudo apt install librsvg2-bin`
 
 ```bash
 jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.pdf
@@ -122,9 +129,9 @@ jb2export --fasta data/volvox/volvox.fa --configtracks refseq --loc ctgA:1-100
 
 ### Use with a jbrowse config.json (remote files in the config.json)
 
-A config.json can be specified, and then we just refer to trackIds in this
-file, and extra tracks can also be supplied that are outside of the config e.g.
-with --bam
+A config.json can be specified, and then we just refer to trackIds in this file,
+and extra tracks can also be supplied that are outside of the config e.g. with
+--bam
 
 ```bash
 jb2export --config data/config.json \
@@ -184,8 +191,8 @@ jb2export --loc all \
 
 ### Use with a jbrowse config.json (local files in the config.json)
 
-The jbrowse CLI tool (e.g. npm install -g @jbrowse/cli) refers to "uri" paths
-by default, but you replace them with localPath like this
+The jbrowse CLI tool (e.g. npm install -g @jbrowse/cli) refers to "uri" paths by
+default, but you replace them with localPath like this
 
 ```js
 
@@ -209,8 +216,8 @@ jb2export --config data/volvox/config.json \
   --loc ctgA:1-50,000
 ```
 
-The localPaths will be resolved relative to the file that is supplied so in
-this example we would resolve data/volvox/volvox.dup.vcf.gz if "localPath":
+The localPaths will be resolved relative to the file that is supplied so in this
+example we would resolve data/volvox/volvox.dup.vcf.gz if "localPath":
 "volvox.dup.vcf.gz" is used, and `--config data/volvox/config.json` is passed
 
 See data/volvox/config.json for a config that contains localPaths, or
@@ -337,13 +344,13 @@ convert -size 2048x out.svg out.png
 ### I don't get any outputted svg and no message
 
 The error reporting from the app is not very good at the moment so often has
-silent failures. Confirm that your fasta file to your pass to --fasta is
-indexed in this case e.g. `samtools faidx yourfile.fa` so that your have a
+silent failures. Confirm that your fasta file to your pass to --fasta is indexed
+in this case e.g. `samtools faidx yourfile.fa` so that your have a
 yourfile.fa.fai alongside yourfile.fa
 
 ### I get a lot of warnings during npm install -g @jbrowse/img
 
 There are some new features in the latest NPM (2021, v7) related to
 peerDependencies that may produce some warnings. It should work even despite
-making warnings, but you can use yarn to install or use legacy peer
-dependencies if you want to avoid install time warningsvg
+making warnings, but you can use yarn to install or use legacy peer dependencies
+if you want to avoid install time warningsvg

package/dist/index.js

@@ -83,6 +83,7 @@ console.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_1.default
     .command('jb2export', 'Creates a jbrowse 2 image snapshot')
     .option('config', {

package/dist/index.js.map

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package/esm/index.js

@@ -55,6 +55,7 @@ console.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', {

package/esm/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "2.2.1",
+  "version": "2.3.0",
   "main": "dist/index.js",
   "module": "esm/index.js",
   "author": "JBrowse Team",
@@ -29,11 +29,11 @@
     "@babel/runtime": "^7.17.9",
     "@emotion/cache": "^11.7.1",
     "@emotion/react": "^11.9.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.2.1",
-    "@jbrowse/react-linear-genome-view": "^2.2.1",
+    "@jbrowse/plugin-linear-genome-view": "^2.3.0",
+    "@jbrowse/react-linear-genome-view": "^2.3.0",
     "abortcontroller-polyfill": "^1.7.3",
     "canvas": "^2.9.1",
-    "jsdom": "^19.0.0",
+    "jsdom": "^20.0.3",
     "mobx": "^6.6.0",
     "node-fetch": "^2.6.7",
     "react": "^17.0.0",
@@ -44,5 +44,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
+  "gitHead": "a85b280a8af4d1a11e81ab42913f5f6049e6e580"
 }

package/src/{index.testmod.js → index.test.js}

@@ -1,4 +1,11 @@
+/**
+ * @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 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
@@ -17,8 +24,8 @@ global.nodeCreateCanvas = createCanvas
 
 xtest('renders a region with --session and --config args', async () => {
   const result = await renderRegion({
-    session: require.resolve('../test/clingen_session.json'),
-    config: require.resolve('../data/config.json'),
+    session: path.join(__dirname, '../test/clingen_session.json'),
+    config: path.join(__dirname, '../data/config.json'),
   })
   fs.writeFileSync('svg_from_config_and_session_param.svg', result)
   expect(result).toMatchSnapshot()
@@ -26,16 +33,16 @@ xtest('renders a region with --session and --config args', async () => {
 
 xtest('renders a region with --session, --tracks, and --assembly args', async () => {
   const result = await renderRegion({
-    session: require.resolve('../test/clingen_session.json'),
-    tracks: require.resolve('../data/tracks.json'),
-    assembly: require.resolve('../data/assembly.json'),
+    session: path.join(__dirname, '../test/clingen_session.json'),
+    tracks: path.join(__dirname, '../data/tracks.json'),
+    assembly: path.join(__dirname, '../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 => require.resolve('../data/volvox/' + f)
+  const fp = f => path.join(__dirname, '../data/volvox/' + f)
   console.error = jest.fn()
   const result = await renderRegion({
     fasta: fp('volvox.fa'),
@@ -51,7 +58,7 @@ test('renders volvox with variety of args', async () => {
     loc: 'ctgA:1000-2000',
   })
   fs.writeFileSync(
-    require.resolve('../test/svg_from_volvox_fasta_and_bam.svg'),
+    path.join(__dirname, '../test/svg_from_volvox_fasta_and_bam.svg'),
     result,
   )
   expect(result).toBeTruthy()
@@ -72,7 +79,7 @@ xtest('renders human large region with remote urls', async () => {
     loc: '1:10,000,000-10,030,000',
   })
   fs.writeFileSync(
-    require.resolve('../test/human_remote_urls_large_region.svg'),
+    path.join(__dirname, '../test/human_remote_urls_large_region.svg'),
     result,
   )
   expect(result).toBeTruthy()
@@ -91,12 +98,15 @@ xtest('renders volvox with remote urls', async () => {
     ],
     loc: 'ctgA:1-1000',
   })
-  fs.writeFileSync(require.resolve('../test/volvox_remote_region.svg'), result)
+  fs.writeFileSync(
+    path.join(__dirname, '../test/volvox_remote_region.svg'),
+    result,
+  )
   expect(result).toBeTruthy()
 }, 20000)
 
 test('renders volvox with variety of args (noRasterize)', async () => {
-  const fp = f => require.resolve('../data/volvox/' + f)
+  const fp = f => path.join(__dirname, '../data/volvox/' + f)
   console.error = jest.fn()
   const result = await renderRegion({
     fasta: fp('volvox.fa'),
@@ -113,7 +123,10 @@ test('renders volvox with variety of args (noRasterize)', async () => {
     noRasterize: true,
   })
   fs.writeFileSync(
-    require.resolve('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'),
+    path.join(
+      __dirname,
+      '../test/svg_from_volvox_fasta_and_bam_norasterize.svg',
+    ),
     result,
   )
   expect(result).toBeTruthy()
@@ -133,13 +146,13 @@ xtest('configtracks arg with urls', async () => {
 
 test('configtracks arg with local files', async () => {
   const result = await renderRegion({
-    config: require.resolve('../data/volvox/config.json'),
+    config: path.join(__dirname, '../data/volvox/config.json'),
     trackList: [['configtracks', ['volvox_sv']]],
     assembly: 'volvox',
     loc: 'ctgA:1-50,000',
   })
   fs.writeFileSync(
-    require.resolve('../test/svg_configtracks_local.svg'),
+    path.join(__dirname, '../test/svg_configtracks_local.svg'),
     result,
   )
   expect(result).toBeTruthy()
@@ -158,6 +171,9 @@ xtest('renders --hic', async () => {
     ],
     loc: '1:2,000,000-10,000,000',
   })
-  fs.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result)
+  fs.writeFileSync(
+    path.join(__dirname, '../test/svg_from_human_hic.svg'),
+    result,
+  )
   expect(result).toBeTruthy()
 }, 20000)

package/src/index.ts

@@ -63,7 +63,7 @@ console.warn = (...p: unknown[]) => {
 
 // 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', {
@@ -186,6 +186,7 @@ const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
   'configtracks',
 ])
 
+// eslint-disable-next-line @typescript-eslint/no-floating-promises
 ;(async () => {
   try {
     const result = await renderRegion(args as Opts)

package/dist/index.testmod.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/index.testmod.js

@@ -1,169 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const renderRegion_1 = require("./renderRegion");
-const fs_1 = __importDefault(require("fs"));
-const jsdom_1 = require("jsdom");
-require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
-const canvas_1 = require("canvas");
-const node_fetch_1 = __importStar(require("node-fetch"));
-global.fetch = node_fetch_1.default;
-global.Headers = node_fetch_1.Headers;
-global.Response = node_fetch_1.Response;
-global.Request = node_fetch_1.Request;
-const { document } = new jsdom_1.JSDOM(`...`).window;
-global.document = document;
-global.nodeImage = canvas_1.Image;
-global.nodeCreateCanvas = canvas_1.createCanvas;
-xtest('renders a region with --session and --config args', async () => {
-    const result = await (0, renderRegion_1.renderRegion)({
-        session: require.resolve('../test/clingen_session.json'),
-        config: require.resolve('../data/config.json'),
-    });
-    fs_1.default.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 (0, renderRegion_1.renderRegion)({
-        session: require.resolve('../test/clingen_session.json'),
-        tracks: require.resolve('../data/tracks.json'),
-        assembly: require.resolve('../data/assembly.json'),
-    });
-    fs_1.default.writeFileSync('svg_from_separate_session_and_tracks.svg', result);
-    expect(result).toMatchSnapshot();
-}, 40000);
-test('renders volvox with variety of args', async () => {
-    const fp = f => require.resolve('../data/volvox/' + f);
-    console.error = jest.fn();
-    const result = await (0, renderRegion_1.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_1.default.writeFileSync(require.resolve('../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 (0, renderRegion_1.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_1.default.writeFileSync(require.resolve('../test/human_remote_urls_large_region.svg'), result);
-    expect(result).toBeTruthy();
-}, 120000);
-xtest('renders volvox with remote urls', async () => {
-    const result = await (0, renderRegion_1.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_1.default.writeFileSync(require.resolve('../test/volvox_remote_region.svg'), result);
-    expect(result).toBeTruthy();
-}, 20000);
-test('renders volvox with variety of args (noRasterize)', async () => {
-    const fp = f => require.resolve('../data/volvox/' + f);
-    console.error = jest.fn();
-    const result = await (0, renderRegion_1.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_1.default.writeFileSync(require.resolve('../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 (0, renderRegion_1.renderRegion)({
-        config: 'data/config.json',
-        trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
-        assembly: 'GRCh38',
-        loc: 'chr1:50,000-60,000',
-    });
-    fs_1.default.writeFileSync('svg_configtracks_simple.svg', result);
-    expect(result).toBeTruthy();
-}, 40000);
-test('configtracks arg with local files', async () => {
-    const result = await (0, renderRegion_1.renderRegion)({
-        config: require.resolve('../data/volvox/config.json'),
-        trackList: [['configtracks', ['volvox_sv']]],
-        assembly: 'volvox',
-        loc: 'ctgA:1-50,000',
-    });
-    fs_1.default.writeFileSync(require.resolve('../test/svg_configtracks_local.svg'), result);
-    expect(result).toBeTruthy();
-}, 40000);
-xtest('renders --hic', async () => {
-    const result = await (0, renderRegion_1.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_1.default.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result);
-    expect(result).toBeTruthy();
-}, 20000);
-//# sourceMappingURL=index.testmod.js.map

package/dist/index.testmod.js.map

@@ -1 +0,0 @@
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package/dist/parseArgv.testmod.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/parseArgv.testmod.js

@@ -1,26 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const parseArgv_1 = require("./parseArgv");
-test('parse', () => {
-    const args = '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize';
-    expect((0, parseArgv_1.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((0, parseArgv_1.parseArgv)(args.split(' '))).toEqual([
-        ['bam', ['dad.bam', 'color:red']],
-        ['vcf', ['variants.vcf']],
-        ['bam', ['mom.bam', 'force:true']],
-        ['defaultSession', []],
-        ['out', ['out.svg']],
-        ['noRasterize', []],
-    ]);
-});
-//# sourceMappingURL=parseArgv.testmod.js.map

package/dist/parseArgv.testmod.js.map

@@ -1 +0,0 @@
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package/esm/index.testmod.d.ts

@@ -1 +0,0 @@
-export {};

package/esm/index.testmod.js

@@ -1,141 +0,0 @@
-import { renderRegion } from './renderRegion';
-import fs from 'fs';
-import { JSDOM } from 'jsdom';
-import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only';
-import { Image, createCanvas } from 'canvas';
-import fetch, { Headers, Response, Request } from 'node-fetch';
-global.fetch = fetch;
-global.Headers = Headers;
-global.Response = Response;
-global.Request = Request;
-const { document } = new JSDOM(`...`).window;
-global.document = document;
-global.nodeImage = Image;
-global.nodeCreateCanvas = createCanvas;
-xtest('renders a region with --session and --config args', async () => {
-    const result = await renderRegion({
-        session: require.resolve('../test/clingen_session.json'),
-        config: require.resolve('../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: require.resolve('../test/clingen_session.json'),
-        tracks: require.resolve('../data/tracks.json'),
-        assembly: require.resolve('../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 => require.resolve('../data/volvox/' + f);
-    console.error = jest.fn();
-    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(require.resolve('../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(require.resolve('../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(require.resolve('../test/volvox_remote_region.svg'), result);
-    expect(result).toBeTruthy();
-}, 20000);
-test('renders volvox with variety of args (noRasterize)', async () => {
-    const fp = f => require.resolve('../data/volvox/' + f);
-    console.error = jest.fn();
-    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(require.resolve('../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: require.resolve('../data/volvox/config.json'),
-        trackList: [['configtracks', ['volvox_sv']]],
-        assembly: 'volvox',
-        loc: 'ctgA:1-50,000',
-    });
-    fs.writeFileSync(require.resolve('../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(require.resolve('../test/svg_from_human_hic.svg'), result);
-    expect(result).toBeTruthy();
-}, 20000);
-//# sourceMappingURL=index.testmod.js.map

package/esm/index.testmod.js.map

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package/esm/parseArgv.testmod.d.ts

@@ -1 +0,0 @@
-export {};

package/esm/parseArgv.testmod.js

@@ -1,24 +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', []],
-    ]);
-});
-//# sourceMappingURL=parseArgv.testmod.js.map

package/esm/parseArgv.testmod.js.map

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