@jbrowse/img 1.3.5 → 1.5.3

package/LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [2021] [Evolutionary Software Foundation]
+   Copyright [2020] [Evolutionary Software Foundation]
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

package/dist/bin.js

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

package/dist/index.js

@@ -2,8 +2,6 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
-
 var _fs = _interopRequireDefault(require("fs"));
 
 var _yargs = _interopRequireDefault(require("yargs"));
@@ -16,74 +14,76 @@ var _tmp = _interopRequireDefault(require("tmp"));
 
 var _child_process = require("child_process");
 
-_yargs.default.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",
+/* eslint-disable no-console */
+// eslint-disable-next-line no-unused-expressions
+_yargs.default.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"
+.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; //prints to stderr the time it takes to execute cb
+.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; // prints to stderr the time it takes to execute cb
 
 async function time(cb) {
   const start = +Date.now();
@@ -92,34 +92,34 @@ async function time(cb) {
   return ret;
 }
 
-const args = (0, _parseArgv.standardizeArgv)((0, _parseArgv.parseArgv)(process.argv.slice(2)), ["bam", "cram", "vcfgz", "hic", "bigwig", "bigbed", "bedgz", "gffgz", "configtracks"]);
+const args = (0, _parseArgv.standardizeArgv)((0, _parseArgv.parseArgv)(process.argv.slice(2)), ['bam', 'cram', 'vcfgz', 'hic', 'bigwig', 'bigbed', 'bedgz', 'gffgz', 'configtracks']);
 time(() => (0, _renderRegion.renderRegion)(args).then(result => {
-  const outfile = args.out || "out.svg";
+  const outfile = args.out || 'out.svg';
 
-  if (outfile.endsWith(".png")) {
+  if (outfile.endsWith('.png')) {
     const tmpobj = _tmp.default.fileSync({
       mode: 0o644,
-      prefix: "prefix-",
-      postfix: ".svg"
+      prefix: 'prefix-',
+      postfix: '.svg'
     });
 
     _fs.default.writeFileSync(tmpobj.name, result);
 
-    const ls = (0, _child_process.spawnSync)("rsvg-convert", ["-w", args.pngwidth || 2048, tmpobj.name, "-o", outfile]);
+    const ls = (0, _child_process.spawnSync)('rsvg-convert', ['-w', args.pngwidth || 2048, tmpobj.name, '-o', outfile]);
     console.log(`rsvg-convert stderr: ${ls.stderr.toString()}`);
     console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
 
     _fs.default.unlinkSync(tmpobj.name);
-  } else if (outfile.endsWith(".pdf")) {
+  } else if (outfile.endsWith('.pdf')) {
     const tmpobj = _tmp.default.fileSync({
       mode: 0o644,
-      prefix: "prefix-",
-      postfix: ".svg"
+      prefix: 'prefix-',
+      postfix: '.svg'
     });
 
     _fs.default.writeFileSync(tmpobj.name, result);
 
-    const ls = (0, _child_process.spawnSync)("rsvg-convert", ["-w", args.pngwidth || 2048, tmpobj.name, "-f", "pdf", "-o", outfile]);
+    const ls = (0, _child_process.spawnSync)('rsvg-convert', ['-w', args.pngwidth || 2048, tmpobj.name, '-f', 'pdf', '-o', outfile]);
     console.log(`rsvg-convert stderr: ${ls.stderr.toString()}`);
     console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
 

package/dist/index.testmod.js

@@ -0,0 +1,97 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _renderRegion = require("./renderRegion");
+
+var _fs = _interopRequireDefault(require("fs"));
+
+function hashCode(str) {
+  let hash = 0;
+  let chr;
+
+  if (str.length === 0) {
+    return hash;
+  }
+
+  for (let i = 0; i < str.length; i++) {
+    chr = str.charCodeAt(i);
+    hash = (hash << 5) - hash + chr;
+    hash |= 0; // Convert to 32bit integer
+  }
+
+  return hash;
+}
+
+const timeout = 20000; // commented out for using remote files currently
+
+xtest('renders a region with --session and --config args', async () => {
+  const result = await (0, _renderRegion.renderRegion)({
+    session: require.resolve('../test/clingen_session.json'),
+    config: require.resolve('../data/config.json')
+  });
+
+  _fs.default.writeFileSync('svg_from_config_and_session_param.svg', result);
+
+  expect(hashCode(result)).toMatchSnapshot();
+}, timeout); // commented out for using remote files currently
+
+xtest('renders a region with --session, --tracks, and --assembly args', async () => {
+  const result = await (0, _renderRegion.renderRegion)({
+    session: require.resolve('../test/clingen_session.json'),
+    tracks: require.resolve('../data/tracks.json'),
+    assembly: require.resolve('../data/assembly.json')
+  });
+
+  _fs.default.writeFileSync('svg_from_separate_session_and_tracks.svg', result);
+
+  expect(hashCode(result)).toMatchSnapshot();
+}, timeout);
+test('renders volvox with variety of args', async () => {
+  console.error = jest.fn();
+  const result = await (0, _renderRegion.renderRegion)({
+    fasta: require.resolve('../data/volvox/volvox.fa'),
+    trackList: [['bam', [require.resolve('../data/volvox/volvox-sorted.bam')]], ['cram', [require.resolve('../data/volvox/volvox-sorted.cram')]], ['bigwig', [require.resolve('../data/volvox/volvox-sorted.bam.coverage.bw')]], ['vcfgz', [require.resolve('../data/volvox/volvox.filtered.vcf.gz')]], ['gffgz', [require.resolve('../data/volvox/volvox.sort.gff3.gz')]], ['bigbed', [require.resolve('../data/volvox/volvox.bb')]], ['bedgz', [require.resolve('../data/volvox/volvox-bed12.bed.gz')]]],
+    loc: 'ctgA:1000-2000'
+  }); // can't do a snapshot test here, slightly inconsistent results(?)
+
+  _fs.default.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam.svg'), result);
+
+  expect(result).toBeTruthy();
+}, timeout); // commented out for using remote files currently
+
+xtest('configtracks arg with urls', async () => {
+  const result = await (0, _renderRegion.renderRegion)({
+    config: 'data/config.json',
+    trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
+    assembly: 'GRCh38',
+    loc: 'chr1:50,000-60,000'
+  }); // can't do a snapshot test here, slightly inconsistent results(?)
+
+  _fs.default.writeFileSync('svg_configtracks_simple.svg', result);
+
+  expect(result).toBeTruthy();
+}, timeout * 3);
+test('configtracks arg with local files', async () => {
+  const result = await (0, _renderRegion.renderRegion)({
+    config: require.resolve('../data/volvox/config.json'),
+    trackList: [['configtracks', ['volvox_sv']]],
+    assembly: 'volvox',
+    loc: 'ctgA:1-50,000'
+  }); // can't do a snapshot test here, slightly inconsistent results(?)
+
+  _fs.default.writeFileSync(require.resolve('../test/svg_configtracks_local.svg'), result);
+
+  expect(result).toBeTruthy();
+}, timeout * 3);
+xtest('renders --hic', async () => {
+  const result = await (0, _renderRegion.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.default.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result);
+
+  expect(result).toBeTruthy();
+}, 20000);

package/dist/parseArgv.js

@@ -12,7 +12,7 @@ function parseArgv(argv) {
   while (argv.length) {
     const val = argv[0].slice(2);
     argv = argv.slice(1);
-    const next = argv.findIndex(arg => arg.startsWith("-"));
+    const next = argv.findIndex(arg => arg.startsWith('-'));
 
     if (next !== -1) {
       map.push([val, argv.slice(0, next)]);

package/dist/parseArgv.testmod.js

@@ -0,0 +1,8 @@
+"use strict";
+
+var _parseArgv = 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.parseArgv)(args.split(' '))).toEqual([['bam', ['dad.bam', 'color:red']], ['vcf', ['variants.vcf']], ['bam', ['mom.bam']], ['defaultSession', []], ['out', ['out.svg']], ['noRasterize', []]]);
+});

package/dist/renderRegion.js

@@ -8,12 +8,8 @@ Object.defineProperty(exports, "__esModule", {
 exports.readData = readData;
 exports.renderRegion = renderRegion;
 
-require("regenerator-runtime/runtime");
-
 var _reactLinearGenomeView = require("@jbrowse/react-linear-genome-view");
 
-var _mobxStateTree = require("mobx-state-tree");
-
 var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
 
 var _mobx = require("mobx");
@@ -37,7 +33,7 @@ function read(file) {
 }
 
 function makeLocation(file) {
-  return file.startsWith("http") ? {
+  return file.startsWith('http') ? {
     uri: file
   } : {
     localPath: file
@@ -45,11 +41,11 @@ function makeLocation(file) {
 }
 
 function addRelativePaths(config, configPath) {
-  if (typeof config === "object") {
+  if (typeof config === 'object') {
     for (const key of Object.keys(config)) {
-      if (typeof config[key] === "object") {
+      if (typeof config[key] === 'object') {
         addRelativePaths(config[key], configPath);
-      } else if (key === "localPath") {
+      } else if (key === 'localPath') {
         config.localPath = _path.default.resolve(configPath, config.localPath);
       }
     }
@@ -95,37 +91,37 @@ function readData(opts) {
     configData.assembly = assemblyData;
   } // else check if it was an assembly name in a config file
   else if ((_configData$assemblie = configData.assemblies) !== null && _configData$assemblie !== void 0 && _configData$assemblie.length) {
-      configData.assembly = asm ? configData.assemblies.find(entry => entry.name === asm) : configData.assemblies[0];
-    } // else load fasta from command line
-    else if (fasta) {
-        const bgzip = fasta.endsWith("gz");
-        configData.assembly = {
-          name: _path.default.basename(fasta),
-          sequence: {
-            type: "ReferenceSequenceTrack",
-            trackId: "refseq",
-            adapter: {
-              type: bgzip ? "BgzipFastaAdapter" : "IndexedFastaAdapter",
-              fastaLocation: makeLocation(fasta),
-              faiLocation: makeLocation(fasta + ".fai"),
-              gziLocation: bgzip ? makeLocation(fasta + ".gzi") : undefined
-            }
-          }
-        };
-
-        if (aliases) {
-          configData.assembly.refNameAliases = {
-            adapter: {
-              type: "RefNameAliasAdapter",
-              location: makeLocation(aliases)
-            }
-          };
+    configData.assembly = asm ? configData.assemblies.find(entry => entry.name === asm) : configData.assemblies[0];
+  } // else load fasta from command line
+  else if (fasta) {
+    const bgzip = fasta.endsWith('gz');
+    configData.assembly = {
+      name: _path.default.basename(fasta),
+      sequence: {
+        type: 'ReferenceSequenceTrack',
+        trackId: 'refseq',
+        adapter: {
+          type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
+          fastaLocation: makeLocation(fasta),
+          faiLocation: makeLocation(fasta + '.fai'),
+          gziLocation: bgzip ? makeLocation(fasta + '.gzi') : undefined
+        }
+      }
+    };
+
+    if (aliases) {
+      configData.assembly.refNameAliases = {
+        adapter: {
+          type: 'RefNameAliasAdapter',
+          location: makeLocation(aliases)
         }
-      } // throw if still no assembly
+      };
+    }
+  } // throw if still no assembly
 
 
   if (!configData.assembly) {
-    throw new Error("no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config");
+    throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
   }
 
   if (tracksData) {
@@ -135,122 +131,122 @@ function readData(opts) {
   }
 
   trackList.forEach(track => {
-    const [type, [file, opts]] = track;
+    const [type, [file]] = track;
 
-    if (type === "bam") {
+    if (type === 'bam') {
       configData.tracks = [...configData.tracks, {
-        type: "AlignmentsTrack",
+        type: 'AlignmentsTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "BamAdapter",
+          type: 'BamAdapter',
           bamLocation: makeLocation(file),
           index: {
-            location: makeLocation(file + ".bai")
+            location: makeLocation(file + '.bai')
           },
           sequenceAdapter: configData.assembly.sequence.adapter
         }
       }];
     }
 
-    if (type === "cram") {
+    if (type === 'cram') {
       configData.tracks = [...configData.tracks, {
-        type: "AlignmentsTrack",
+        type: 'AlignmentsTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "CramAdapter",
+          type: 'CramAdapter',
           cramLocation: makeLocation(file),
-          craiLocation: makeLocation(file + ".crai"),
+          craiLocation: makeLocation(file + '.crai'),
           sequenceAdapter: configData.assembly.sequence.adapter
         }
       }];
     }
 
-    if (type === "bigwig") {
+    if (type === 'bigwig') {
       configData.tracks = [...configData.tracks, {
-        type: "QuantitativeTrack",
+        type: 'QuantitativeTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "BigWigAdapter",
+          type: 'BigWigAdapter',
           bigWigLocation: makeLocation(file)
         }
       }];
     }
 
-    if (type === "vcfgz") {
+    if (type === 'vcfgz') {
       configData.tracks = [...configData.tracks, {
-        type: "VariantTrack",
+        type: 'VariantTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "VcfTabixAdapter",
+          type: 'VcfTabixAdapter',
           vcfGzLocation: makeLocation(file),
           index: {
-            location: makeLocation(file + ".tbi")
+            location: makeLocation(file + '.tbi')
           }
         }
       }];
     }
 
-    if (type === "gffgz") {
+    if (type === 'gffgz') {
       configData.tracks = [...configData.tracks, {
-        type: "FeatureTrack",
+        type: 'FeatureTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "Gff3TabixAdapter",
+          type: 'Gff3TabixAdapter',
           gffGzLocation: makeLocation(file),
           index: {
-            location: makeLocation(file + ".tbi")
+            location: makeLocation(file + '.tbi')
           }
         }
       }];
     }
 
-    if (type === "hic") {
+    if (type === 'hic') {
       configData.tracks = [...configData.tracks, {
-        type: "HicTrack",
+        type: 'HicTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "HicAdapter",
+          type: 'HicAdapter',
           hicLocation: makeLocation(file)
         }
       }];
     }
 
-    if (type === "bigbed") {
+    if (type === 'bigbed') {
       configData.tracks = [...configData.tracks, {
-        type: "FeatureTrack",
+        type: 'FeatureTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "BigBedAdapter",
+          type: 'BigBedAdapter',
           bigBedLocation: makeLocation(file)
         }
       }];
     }
 
-    if (type === "bedgz") {
+    if (type === 'bedgz') {
       configData.tracks = [...configData.tracks, {
-        type: "FeatureTrack",
+        type: 'FeatureTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
         assemblyNames: [configData.assembly.name],
         adapter: {
-          type: "BedTabixAdapter",
+          type: 'BedTabixAdapter',
           bedGzLocation: makeLocation(file),
           index: {
-            location: makeLocation(file + ".tbi")
+            location: makeLocation(file + '.tbi')
           }
         }
       }];
@@ -291,7 +287,9 @@ async function renderRegion(opts = {}) {
   } = model;
   view.setWidth(width);
   await (0, _mobx.when)(() => {
-    return assemblyManager.allPossibleRefNames && assemblyManager.allPossibleRefNames.length && model.session.view.initialized;
+    var _assemblyManager$allP;
+
+    return ((_assemblyManager$allP = assemblyManager.allPossibleRefNames) === null || _assemblyManager$allP === void 0 ? void 0 : _assemblyManager$allP.length) && model.session.view.initialized;
   });
 
   if (loc) {
@@ -302,13 +300,13 @@ async function renderRegion(opts = {}) {
       view.setDisplayedRegions([region]);
     }
 
-    if (loc === "all") {
+    if (loc === 'all') {
       view.showAllRegionsInAssembly(assembly.name);
     } else {
       view.navToLocString(loc);
     }
   } else if (!sessionParam && !defaultSession) {
-    console.warn("No loc specified");
+    console.warn('No loc specified');
   }
 
   function process(trackEntry, extra = () => {}) {
@@ -317,65 +315,65 @@ async function renderRegion(opts = {}) {
     const display = currentTrack.displays[0];
     opts.forEach(opt => {
       // apply height to any track
-      if (opt.startsWith("height:")) {
-        const [, height] = opt.split(":");
+      if (opt.startsWith('height:')) {
+        const [, height] = opt.split(':');
         display.setHeight(+height);
       } // apply sort to pileup
-      else if (opt.startsWith("sort:")) {
-          const [, type, tag] = opt.split(":");
-          display.PileupDisplay.setSortedBy(type, tag);
-        } // apply color scheme to pileup
-        else if (opt.startsWith("color:")) {
-            const [, type, tag] = opt.split(":");
-
-            if (display.PileupDisplay) {
-              display.PileupDisplay.setColorScheme({
-                type,
-                tag
-              });
-            } else {
-              display.setColor(type);
-            }
-          } // force track to render even if maxbpperpx limit hit...
-          else if (opt.startsWith("force:")) {
-              const [, force] = opt.split(":");
-
-              if (Boolean(force)) {
-                display.setUserBpPerPxLimit(Number.MAX_VALUE);
-              }
-            } // apply wiggle autoscale
-            else if (opt.startsWith("autoscale:")) {
-                const [, autoscale] = opt.split(":");
-                display.setAutoscale(autoscale);
-              } // apply min and max score to wiggle
-              else if (opt.startsWith("minmax:")) {
-                  const [, min, max] = opt.split(":");
-                  display.setMinScore(+min);
-                  display.setMaxScore(+max);
-                } // apply linear or log scale to wiggle
-                else if (opt.startsWith("scaletype:")) {
-                    const [, scaletype] = opt.split(":");
-                    display.setScaleType(scaletype);
-                  } // draw crosshatches on wiggle
-                  else if (opt.startsWith("crosshatch:")) {
-                      const [, val] = opt.split(":");
-                      display.setCrossHatches((0, _util.booleanize)(val));
-                    } // turn off fill on bigwig with fill:false
-                    else if (opt.startsWith("fill:")) {
-                        const [, val] = opt.split(":");
-                        display.setFill((0, _util.booleanize)(val));
-                      } // set resolution:superfine to use finer bigwig bin size
-                      else if (opt.startsWith("resolution:")) {
-                          let [, val] = opt.split(":");
-
-                          if (val === "fine") {
-                            val = 10;
-                          } else if (val === "superfine") {
-                            val = 100;
-                          }
-
-                          display.setResolution(val);
-                        }
+      else if (opt.startsWith('sort:')) {
+        const [, type, tag] = opt.split(':');
+        display.PileupDisplay.setSortedBy(type, tag);
+      } // apply color scheme to pileup
+      else if (opt.startsWith('color:')) {
+        const [, type, tag] = opt.split(':');
+
+        if (display.PileupDisplay) {
+          display.PileupDisplay.setColorScheme({
+            type,
+            tag
+          });
+        } else {
+          display.setColor(type);
+        }
+      } // force track to render even if maxbpperpx limit hit...
+      else if (opt.startsWith('force:')) {
+        const [, force] = opt.split(':');
+
+        if (Boolean(force)) {
+          display.setUserBpPerPxLimit(Number.MAX_VALUE);
+        }
+      } // apply wiggle autoscale
+      else if (opt.startsWith('autoscale:')) {
+        const [, autoscale] = opt.split(':');
+        display.setAutoscale(autoscale);
+      } // apply min and max score to wiggle
+      else if (opt.startsWith('minmax:')) {
+        const [, min, max] = opt.split(':');
+        display.setMinScore(+min);
+        display.setMaxScore(+max);
+      } // apply linear or log scale to wiggle
+      else if (opt.startsWith('scaletype:')) {
+        const [, scaletype] = opt.split(':');
+        display.setScaleType(scaletype);
+      } // draw crosshatches on wiggle
+      else if (opt.startsWith('crosshatch:')) {
+        const [, val] = opt.split(':');
+        display.setCrossHatches((0, _util.booleanize)(val));
+      } // turn off fill on bigwig with fill:false
+      else if (opt.startsWith('fill:')) {
+        const [, val] = opt.split(':');
+        display.setFill((0, _util.booleanize)(val));
+      } // set resolution:superfine to use finer bigwig bin size
+      else if (opt.startsWith('resolution:')) {
+        let [, val] = opt.split(':');
+
+        if (val === 'fine') {
+          val = 10;
+        } else if (val === 'superfine') {
+          val = 100;
+        }
+
+        display.setResolution(val);
+      }
     });
   }
 

package/dist/util.js

@@ -6,6 +6,6 @@ Object.defineProperty(exports, "__esModule", {
 exports.booleanize = void 0;
 
 // nice helper function from https://stackoverflow.com/questions/263965/
-const booleanize = string => string === "false" ? false : !!string;
+const booleanize = string => string === 'false' ? false : !!string;
 
 exports.booleanize = booleanize;

package/package.json

@@ -1,17 +1,9 @@
 {
   "name": "@jbrowse/img",
-  "version": "1.3.5",
+  "version": "1.5.3",
   "main": "index.js",
   "author": "JBrowse Team",
   "license": "Apache-2.0",
-  "devDependencies": {
-    "@babel/cli": "^7.12.17",
-    "@babel/core": "^7.12.17",
-    "@babel/plugin-transform-runtime": "^7.12.17",
-    "@babel/preset-env": "^7.12.17",
-    "@babel/preset-react": "^7.12.13",
-    "jest": "^26.6.3"
-  },
   "bin": {
     "jb2export": "./dist/bin.js"
   },
@@ -19,6 +11,7 @@
     "dist"
   ],
   "scripts": {
+    "pretest": "cd ../jbrowse-react-linear-genome-view; yarn build; cd ../jb2export",
     "test": "jest",
     "prebuild": "rm -rf dist",
     "build": "babel src -d dist",
@@ -27,12 +20,14 @@
     "snappng": "npm run build && node dist/index.js --config data/config.json --defaultSession --out out.png",
     "snappdf": "npm run build && node dist/index.js --config data/config.json --defaultSession --out out.pdf",
     "snapjpg": "npm run build && node dist/index.js --config data/config.json --defaultSession --out out.jpg",
-    "tiny": "npm run build && node dist/index.js --fasta data/volvox/volvox.fa --bam data/volvox/volvox-sorted.bam --loc ctgA:1-5000",
+    "tiny": "npm run build && node dist/index.js --fasta data/volvox/volvox.fa --bam data/volvox/volvox-sorted.bam --loc ctgA:1-5000 --out tiny.svg",
     "tinypng": "npm run build && node dist/index.js --fasta data/volvox/volvox.fa --bam data/volvox/volvox-sorted.bam --loc ctgA:1-5000 --out out.png",
     "postversion": "git push --follow-tags"
   },
   "dependencies": {
-    "@jbrowse/react-linear-genome-view": "^1.3.5",
+    "@jbrowse/plugin-linear-genome-view": "^1.5.3",
+    "@jbrowse/react-linear-genome-view": "^1.5.3",
+    "mobx": "^5.10.1",
     "react": "^17.0.1",
     "react-dom": "^17.0.1",
     "tmp": "^0.2.1",
@@ -40,5 +35,6 @@
   },
   "publishConfig": {
     "access": "public"
-  }
+  },
+  "gitHead": "cea9023ebce8bbe5c08ae9e00c4e74fe3f02a7f1"
 }

package/dist/index.test.js

@@ -1,91 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _renderRegion = require("./renderRegion");
-
-var _fs = _interopRequireDefault(require("fs"));
-
-function hashCode(str) {
-  var hash = 0;
-  let chr;
-  if (str.length === 0) return hash;
-
-  for (let i = 0; i < str.length; i++) {
-    chr = str.charCodeAt(i);
-    hash = (hash << 5) - hash + chr;
-    hash |= 0; // Convert to 32bit integer
-  }
-
-  return hash;
-}
-
-const timeout = 20000;
-test("renders a region with --session and --config args", async () => {
-  const result = await (0, _renderRegion.renderRegion)({
-    session: "test/clingen_session.json",
-    config: "data/config.json"
-  });
-
-  _fs.default.writeFileSync("test/svg_from_config_and_session_param.svg", result);
-
-  expect(hashCode(result)).toMatchSnapshot();
-}, timeout);
-test("renders a region with --session, --tracks, and --assembly args", async () => {
-  const result = await (0, _renderRegion.renderRegion)({
-    session: "test/clingen_session.json",
-    tracks: "data/tracks.json",
-    assembly: "data/assembly.json"
-  });
-
-  _fs.default.writeFileSync("test/svg_from_separate_session_and_tracks.svg", result);
-
-  expect(hashCode(result)).toMatchSnapshot();
-}, timeout);
-test("renders volvox with variety of args", async () => {
-  console.error = jest.fn();
-  const result = await (0, _renderRegion.renderRegion)({
-    fasta: "data/volvox/volvox.fa",
-    trackList: [["bam", ["data/volvox/volvox-sorted.bam"]], ["cram", ["data/volvox/volvox-sorted.cram"]], ["bigwig", ["data/volvox/volvox-sorted.bam.coverage.bw"]], ["vcfgz", ["data/volvox/volvox.filtered.vcf.gz"]], ["gffgz", ["data/volvox/volvox.sort.gff3.gz"]], ["bigbed", ["data/volvox/volvox.bb"]], ["bedgz", ["data/volvox/volvox-bed12.bed.gz"]]],
-    loc: "ctgA:1000-2000"
-  }); // can't do a snapshot test here, slightly inconsistent results(?)
-
-  _fs.default.writeFileSync("test/svg_from_volvox_fasta_and_bam.svg", result);
-
-  expect(result).toBeTruthy();
-}, timeout);
-test("configtracks arg with urls", async () => {
-  const result = await (0, _renderRegion.renderRegion)({
-    config: "data/config.json",
-    trackList: [["configtracks", ["ncbi_refseq_109_hg38"]]],
-    assembly: "GRCh38",
-    loc: "chr1:50,000-60,000"
-  }); // can't do a snapshot test here, slightly inconsistent results(?)
-
-  _fs.default.writeFileSync("test/svg_configtracks_simple.svg", result);
-
-  expect(result).toBeTruthy();
-}, timeout * 3);
-test("configtracks arg with local files", async () => {
-  const result = await (0, _renderRegion.renderRegion)({
-    config: "data/volvox/config.json",
-    trackList: [["configtracks", ["volvox_sv"]]],
-    assembly: "volvox",
-    loc: "ctgA:1-50,000"
-  }); // can't do a snapshot test here, slightly inconsistent results(?)
-
-  _fs.default.writeFileSync("test/svg_configtracks_local.svg", result);
-
-  expect(result).toBeTruthy();
-}, timeout * 3);
-xtest("renders --hic", async () => {
-  const result = await (0, _renderRegion.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.default.writeFileSync("test/svg_from_human_hic.svg", result);
-
-  expect(result).toBeTruthy();
-}, 20000);

package/dist/parseArgv.test.js

@@ -1,8 +0,0 @@
-"use strict";
-
-var _parseArgv = 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.parseArgv)(args.split(" "))).toEqual([["bam", ["dad.bam", "color:red"]], ["vcf", ["variants.vcf"]], ["bam", ["mom.bam"]], ["defaultSession", []], ["out", ["out.svg"]], ["noRasterize", []]]);
-});