@jbrowse/img 2.2.0 → 2.2.1

package/dist/renderRegion.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"renderRegion.js","sourceRoot":"","sources":["../src/renderRegion.tsx"],"names":[],"mappings":";;;;;;AAAA,kDAAyB;AACzB,gFAAmE;AACnE,kFAG2C;AAC3C,2DAAwC;AACxC,0CAA8C;AAC9C,gDAAuB;AACvB,4CAAmB;AAInB,iCAAmC;AAiBnC,SAAS,IAAI,CAAC,IAAY;IACxB,IAAI,GAAG,CAAA;IACP,IAAI;QACF,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,YAAE,CAAC,YAAY,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC,CAAA;KAChD;IAAC,OAAO,CAAC,EAAE;QACV,MAAM,IAAI,KAAK,CACb,mBAAmB,IAAI,wDAAwD,CAChF,CAAA;KACF;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AACD,SAAS,YAAY,CAAC,IAAY;IAChC,OAAO,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAA;AACtE,CAAC;AAED,SAAS,gBAAgB,CAAC,MAA+B,EAAE,UAAkB;IAC3E,IAAI,OAAO,MAAM,KAAK,QAAQ,EAAE;QAC9B,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;YACrC,IAAI,OAAO,MAAM,CAAC,GAAG,CAAC,KAAK,QAAQ,EAAE;gBACnC,gBAAgB,CAAC,MAAM,CAAC,GAAG,CAA4B,EAAE,UAAU,CAAC,CAAA;aACrE;iBAAM,IAAI,GAAG,KAAK,WAAW,EAAE;gBAC9B,MAAM,CAAC,SAAS,GAAG,cAAI,CAAC,OAAO,CAAC,UAAU,EAAE,MAAM,CAAC,SAAmB,CAAC,CAAA;aACxE;SACF;KACF;AACH,CAAC;AAoBD,SAAgB,QAAQ,CAAC,EACvB,QAAQ,EAAE,GAAG,EACb,MAAM,EACN,OAAO,EACP,KAAK,EACL,OAAO,EACP,SAAS,EACT,cAAc,EACd,MAAM,EACN,SAAS,GAAG,EAAE,GACT;;IACL,MAAM,YAAY,GAAG,GAAG,IAAI,YAAE,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACtE,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACpD,MAAM,UAAU,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CAAW,CAAA;IACzD,IAAI,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAErD,IAAI,MAAM,EAAE;QACV,gBAAgB,CAAC,UAAU,EAAE,cAAI,CAAC,OAAO,CAAC,cAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;KACjE;IAED,wEAAwE;IACxE,yEAAyE;IACzE,cAAc;IACd,IAAI,WAAW,aAAX,WAAW,uBAAX,WAAW,CAAE,OAAO,EAAE;QACxB,WAAW,GAAG,WAAW,CAAC,OAAO,CAAA;KAClC;IAED,yBAAyB;IACzB,IAAI,WAAW,aAAX,WAAW,uBAAX,WAAW,CAAE,KAAK,EAAE;QACtB,WAAW,CAAC,IAAI,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;KACxC;IAED,2CAA2C;IAC3C,IAAI,YAAY,EAAE;QAChB,UAAU,CAAC,QAAQ,GAAG,YAAY,CAAA;KACnC;IACD,yDAAyD;SACpD,IAAI,MAAA,UAAU,CAAC,UAAU,0CAAE,MAAM,EAAE;QACtC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,KAAK,GAAG,CAAC,CAAA;QACvD,IAAI,GAAG,EAAE;YACP,MAAM,QAAQ,GAAG,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,KAAK,GAAG,CAAC,CAAA;YACxE,IAAI,CAAC,QAAQ,EAAE;gBACb,MAAM,IAAI,KAAK,CAAC,YAAY,GAAG,sBAAsB,CAAC,CAAA;aACvD;YACD,UAAU,CAAC,QAAQ,GAAG,QAAQ,CAAA;SAC/B;aAAM;YACL,UAAU,CAAC,QAAQ,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;SAC/C;KACF;IACD,oCAAoC;SAC/B,IAAI,KAAK,EAAE;QACd,MAAM,KAAK,GAAG,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAElC,UAAU,CAAC,QAAQ,GAAG;YACpB,IAAI,EAAE,cAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;YAC1B,QAAQ,EAAE;gBACR,IAAI,EAAE,wBAAwB;gBAC9B,OAAO,EAAE,QAAQ;gBACjB,OAAO,EAAE;oBACP,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,qBAAqB;oBACzD,aAAa,EAAE,YAAY,CAAC,KAAK,CAAC;oBAClC,WAAW,EAAE,YAAY,CAAC,KAAK,GAAG,MAAM,CAAC;oBACzC,WAAW,EAAE,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS;iBAC9D;aACF;SACF,CAAA;QACD,IAAI,OAAO,EAAE;YACX,UAAU,CAAC,QAAQ,CAAC,cAAc,GAAG;gBACnC,OAAO,EAAE;oBACP,IAAI,EAAE,qBAAqB;oBAC3B,QAAQ,EAAE,YAAY,CAAC,OAAO,CAAC;iBAChC;aACF,CAAA;SACF;QACD,IAAI,SAAS,EAAE;YACb,UAAU,CAAC,QAAQ,CAAC,SAAS,GAAG;gBAC9B,OAAO,EAAE;oBACP,IAAI,EAAE,iBAAiB;oBACvB,QAAQ,EAAE,YAAY,CAAC,SAAS,CAAC;iBAClC;aACF,CAAA;SACF;KACF;IAED,6BAA6B;IAC7B,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE;QACxB,MAAM,IAAI,KAAK,CACb,0KAA0K,CAC3K,CAAA;KACF;IAED,IAAI,UAAU,EAAE;QACd,UAAU,CAAC,MAAM,GAAG,UAAU,CAAA;KAC/B;SAAM,IAAI,CAAC,UAAU,CAAC,MAAM,EAAE;QAC7B,UAAU,CAAC,MAAM,GAAG,EAAE,CAAA;KACvB;IAED,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACxB,MAAM,CAAC,IAAI,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAA;QAE5B,IAAI,IAAI,KAAK,KAAK,EAAE;YAClB,UAAU,CAAC,MAAM,GAAG;gBAClB,GAAG,UAAU,CAAC,MAAM;gBACpB;oBACE,IAAI,EAAE,iBAAiB;oBACvB,OAAO,EAAE,cAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;oBAC5B,IAAI,EAAE,cAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;oBACzB,aAAa,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC;oBACzC,OAAO,EAAE;wBACP,IAAI,EAAE,YAAY;wBAClB,WAAW,EAAE,YAAY,CAAC,IAAI,CAAC;wBAC/B,KAAK,EAAE,EAAE,QAAQ,EAAE,YAAY,CAAC,IAAI,GAAG,MAAM,CAAC,EAAE;wBAChD,eAAe,EAAE,UAAU,CAAC,QAAQ,CAAC,QAAQ,CAAC,OAAO;qBACtD;iBACF;aACF,CAAA;SACF;QACD,IAAI,IAAI,KAAK,MAAM,EAAE;YACnB,UAAU,CAAC,MAAM,GAAG;gBAClB,GAAG,UAAU,CAAC,MAAM;gBACpB;oBACE,IAAI,EAAE,iBAAiB;oBACvB,OAAO,EAAE,cAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;oBAC5B,IAAI,EAAE,cAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;oBACzB,aAAa,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC;oBACzC,OAAO,EAAE;wBACP,IAAI,EAAE,aAAa;wBACnB,YAAY,EAAE,YAAY,CAAC,IAAI,CAAC;wBAChC,YAAY,EAAE,YAAY,CAAC,IAAI,GAAG,OAAO,CAAC;wBAC1C,eAAe,EAAE,UAAU,CAAC,QAAQ,CAAC,QAAQ,CAAC,OAAO;qBACtD;iBACF;aACF,CAAA;SACF;QACD,IAAI,IAAI,KAAK,QAAQ,EAAE;YACrB,UAAU,CAAC,MAAM,GAAG;gBAClB,GAAG,UAAU,CAAC,MAAM;gBACpB;oBACE,IAAI,EAAE,mBAAmB;oBACzB,OAAO,EAAE,cAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;oBAC5B,IAAI,EAAE,cAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;oBACzB,aAAa,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC;oBACzC,OAAO,EAAE;wBACP,IAAI,EAAE,eAAe;wBACrB,cAAc,EAAE,YAAY,CAAC,IAAI,CAAC;qBACnC;iBACF;aACF,CAAA;SACF;QAED,IAAI,IAAI,KAAK,OAAO,EAAE;YACpB,UAAU,CAAC,MAAM,G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package/dist/util.d.ts

@@ -0,0 +1,5 @@
+export declare function booleanize(str: string): boolean;
+export declare function convert(result: string, args: {
+    out: string;
+    pngwidth?: string;
+}, spawnArgs?: string[]): void;

package/dist/util.js

@@ -1,11 +1,33 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.booleanize = void 0;
-// nice helper function from https://stackoverflow.com/questions/263965/
-var booleanize = function booleanize(string) {
-  return string === 'false' ? false : !!string;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
 };
-exports.booleanize = booleanize;
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.convert = exports.booleanize = void 0;
+const fs_1 = __importDefault(require("fs"));
+const tmp_1 = __importDefault(require("tmp"));
+const child_process_1 = require("child_process");
+// nice helper function from https://stackoverflow.com/questions/263965/
+function booleanize(str) {
+    return str === 'false' ? false : !!str;
+}
+exports.booleanize = booleanize;
+function createTmp() {
+    return tmp_1.default.fileSync({
+        mode: 0o644,
+        prefix: 'prefix-',
+        postfix: '.svg',
+    });
+}
+function convert(result, args, spawnArgs = []) {
+    const { name } = createTmp();
+    const { pngwidth = '2048', out } = args;
+    fs_1.default.writeFileSync(name, result);
+    const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs];
+    const ls = (0, child_process_1.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_1.default.unlinkSync(name);
+}
+exports.convert = convert;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;AAAA,4CAAmB;AACnB,8CAAqB;AACrB,iDAAyC;AAEzC,wEAAwE;AACxE,SAAgB,UAAU,CAAC,GAAW;IACpC,OAAO,GAAG,KAAK,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;AACxC,CAAC;AAFD,gCAEC;AAED,SAAS,SAAS;IAChB,OAAO,aAAG,CAAC,QAAQ,CAAC;QAClB,IAAI,EAAE,KAAK;QACX,MAAM,EAAE,SAAS;QACjB,OAAO,EAAE,MAAM;KAChB,CAAC,CAAA;AACJ,CAAC;AAED,SAAgB,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,YAAE,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,IAAA,yBAAS,EAAC,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,YAAE,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;AACrB,CAAC;AAdD,0BAcC"}

package/esm/bin.d.ts

@@ -0,0 +1,2 @@
+#!/usr/bin/env node
+export {};

package/esm/bin.js

@@ -0,0 +1,4 @@
+#!/usr/bin/env node
+"use strict";
+require('./index.js');
+//# sourceMappingURL=bin.js.map

package/esm/bin.js.map

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

package/esm/index.d.ts

@@ -0,0 +1 @@
+import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only';

package/esm/index.js

@@ -0,0 +1,185 @@
+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 } from './renderRegion';
+import { convert } from './util';
+// @ts-ignore
+global.nodeImage = Image;
+// @ts-ignore
+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-ignore
+global.fetch = fetch;
+// @ts-ignore
+global.Headers = Headers;
+// @ts-ignore
+global.Response = Response;
+// @ts-ignore
+global.Request = Request;
+const err = console.error;
+console.error = (...p) => {
+    if (!`${p[0]}`.match('useLayoutEffect')) {
+        err(p);
+    }
+};
+const warn = console.warn;
+console.warn = (...p) => {
+    if (!`${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
+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',
+]);
+(async () => {
+    try {
+        const result = await renderRegion(args);
+        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);
+    }
+})();
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

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

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

package/esm/index.testmod.js

@@ -0,0 +1,141 @@
+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

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

@@ -0,0 +1,8 @@
+export type Entry = [string, string[]];
+export declare function parseArgv(argv: string[]): Entry[];
+export declare function standardizeArgv(args: Entry[], trackTypes: string[]): {
+    [key: string]: unknown;
+    trackList: Entry[];
+    out?: string | undefined;
+    pngwidth?: string | undefined;
+};

package/esm/parseArgv.js

@@ -0,0 +1,42 @@
+// 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) {
+    const map = [];
+    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, trackTypes) {
+    const result = { trackList: [] };
+    args.forEach(arg => {
+        if (trackTypes.includes(arg[0])) {
+            result.trackList.push(arg);
+        }
+        else {
+            result[arg[0]] = arg[1][0] || true;
+        }
+    });
+    return result;
+}
+//# sourceMappingURL=parseArgv.js.map

package/esm/parseArgv.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"parseArgv.js","sourceRoot":"","sources":["../src/parseArgv.ts"],"names":[],"mappings":"AAEA,mCAAmC;AACnC,eAAe;AACf,4GAA4G;AAC5G,EAAE;AACF,+CAA+C;AAC/C,uCAAuC;AACvC,+BAA+B;AAC/B,0BAA0B;AAC1B,4BAA4B;AAC5B,0BAA0B;AAC1B,yBAAyB;AACzB,KAAK;AACL,MAAM,UAAU,SAAS,CAAC,IAAc;IACtC,MAAM,GAAG,GAAG,EAAa,CAAA;IACzB,OAAO,IAAI,CAAC,MAAM,EAAE;QAClB,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAC5B,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACpB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAA;QAEvD,IAAI,IAAI,KAAK,CAAC,CAAC,EAAE;YACf,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;SACxB;aAAM;YACL,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CAAA;YACrB,MAAK;SACN;KACF;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAa,EAAE,UAAoB;IACjE,MAAM,MAAM,GAAG,EAAE,SAAS,EAAE,EAAE,EAK7B,CAAA;IACD,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE;QACjB,IAAI,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE;YAC/B,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;SAC3B;aAAM;YACL,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;SACnC;IACH,CAAC,CAAC,CAAA;IACF,OAAO,MAAM,CAAA;AACf,CAAC"}

package/esm/parseArgv.testmod.d.ts

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

package/esm/parseArgv.testmod.js

@@ -0,0 +1,24 @@
+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

@@ -0,0 +1 @@
+{"version":3,"file":"parseArgv.testmod.js","sourceRoot":"","sources":["../src/parseArgv.testmod.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAA;AAEvC,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE;IACjB,MAAM,IAAI,GACR,uGAAuG,CAAA;IAEzG,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;QACzC,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;QACjC,CAAC,KAAK,EAAE,CAAC,cAAc,CAAC,CAAC;QACzB,CAAC,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC;QACpB,CAAC,gBAAgB,EAAE,EAAE,CAAC;QACtB,CAAC,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC;QACpB,CAAC,aAAa,EAAE,EAAE,CAAC;KACpB,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE;IACjB,MAAM,IAAI,GACR,kHAAkH,CAAA;IAEpH,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;QACzC,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;QACjC,CAAC,KAAK,EAAE,CAAC,cAAc,CAAC,CAAC;QACzB,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC;QAClC,CAAC,gBAAgB,EAAE,EAAE,CAAC;QACtB,CAAC,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC;QACpB,CAAC,aAAa,EAAE,EAAE,CAAC;KACpB,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

package/esm/renderRegion.d.ts

@@ -0,0 +1,35 @@
+import { Entry } from './parseArgv';
+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;
+}
+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 declare function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList, }: Opts): Config;
+export declare const muiCache: import("@emotion/utils").EmotionCache;
+export declare function renderRegion(opts: Opts): Promise<string>;
+export {};