@jbrowse/img 2.1.6 → 2.2.0

package/dist/index.js

@@ -1,77 +1,56 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 var _typeof = require("@babel/runtime/helpers/typeof");
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
 var _fs = _interopRequireDefault(require("fs"));
-
 var _yargs = _interopRequireDefault(require("yargs"));
-
 var _parseArgv = require("./parseArgv");
-
 var _renderRegion = require("./renderRegion");
-
 var _tmp = _interopRequireDefault(require("tmp"));
-
 require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
-
 var _child_process = require("child_process");
-
 var _nodeFetch = _interopRequireWildcard(require("node-fetch"));
-
 var _jsdom = require("jsdom");
-
 var _canvas = require("canvas");
-
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
 /* eslint-disable no-console */
+
 global.nodeImage = _canvas.Image;
 global.nodeCreateCanvas = _canvas.createCanvas;
 var document = new _jsdom.JSDOM("...").window.document;
 global.document = document;
-
 if (!global.fetch) {
   global.fetch = _nodeFetch.default;
   global.Headers = _nodeFetch.Headers;
   global.Response = _nodeFetch.Response;
   global.Request = _nodeFetch.Request;
 }
-
 var err = console.error;
-
 console.error = function () {
   for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
     args[_key] = arguments[_key];
   }
-
   if ("".concat(args[0]).match('useLayoutEffect')) {
     return null;
   } else {
     err(args);
   }
 };
-
 console.warn = function () {
   for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
     args[_key2] = arguments[_key2];
   }
-
   if ("".concat(args[0]).match('estimation reached timeout')) {
     return null;
   } else {
     err(args);
   }
-}; // eslint-disable-next-line no-unused-expressions
-
+};
 
+// 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'
@@ -100,7 +79,8 @@ _yargs.default.command('jb2export', 'Creates a jbrowse 2 image snapshot').option
   description: 'Set the width of the png canvas if using png output, default 2048px',
   type: 'number',
   default: 2048
-}) // track types
+})
+// track types
 .option('configtracks', {
   description: 'A list of track labels from a config file',
   type: 'array'
@@ -128,7 +108,9 @@ _yargs.default.command('jb2export', 'Creates a jbrowse 2 image snapshot').option
 }).option('bedgz', {
   description: 'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
   type: 'array'
-}) // other
+})
+
+// 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',
@@ -139,12 +121,12 @@ _yargs.default.command('jb2export', 'Creates a jbrowse 2 image snapshot').option
 }).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
+}).help().alias('help', 'h').alias('width', 'w').argv;
 
+// prints to stderr the time it takes to execute cb
 function time(_x) {
   return _time.apply(this, arguments);
 }
-
 function _time() {
   _time = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(cb) {
     var start, ret;
@@ -155,12 +137,10 @@ function _time() {
             start = +Date.now();
             _context2.next = 3;
             return cb();
-
           case 3:
             ret = _context2.sent;
             console.log("Finished rendering: ".concat((+Date.now() - start) / 1000, "s"));
             return _context2.abrupt("return", ret);
-
           case 6:
           case "end":
             return _context2.stop();
@@ -170,11 +150,9 @@ function _time() {
   }));
   return _time.apply(this, arguments);
 }
-
 var args = (0, _parseArgv.standardizeArgv)((0, _parseArgv.parseArgv)(process.argv.slice(2)), ['bam', 'cram', 'vcfgz', 'hic', 'bigwig', 'bigbed', 'bedgz', 'gffgz', 'configtracks']);
 time( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
   var result, outfile, tmpobj, ls, _tmpobj, _ls;
-
   return _regenerator.default.wrap(function _callee$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
@@ -182,24 +160,19 @@ time( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.de
           _context.prev = 0;
           _context.next = 3;
           return (0, _renderRegion.renderRegion)(args);
-
         case 3:
           result = _context.sent;
           outfile = args.out || 'out.svg';
-
           if (outfile.endsWith('.png')) {
             tmpobj = _tmp.default.fileSync({
               mode: 420,
               prefix: 'prefix-',
               postfix: '.svg'
             });
-
             _fs.default.writeFileSync(tmpobj.name, result);
-
             ls = (0, _child_process.spawnSync)('rsvg-convert', ['-w', args.pngwidth || 2048, tmpobj.name, '-o', outfile]);
             console.log("rsvg-convert stderr: ".concat(ls.stderr.toString()));
             console.log("rsvg-convert stdout: ".concat(ls.stdout.toString()));
-
             _fs.default.unlinkSync(tmpobj.name);
           } else if (outfile.endsWith('.pdf')) {
             _tmpobj = _tmp.default.fileSync({
@@ -207,31 +180,26 @@ time( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.de
               prefix: 'prefix-',
               postfix: '.svg'
             });
-
             _fs.default.writeFileSync(_tmpobj.name, result);
-
             _ls = (0, _child_process.spawnSync)('rsvg-convert', ['-w', args.pngwidth || 2048, _tmpobj.name, '-f', 'pdf', '-o', outfile]);
             console.log("rsvg-convert stderr: ".concat(_ls.stderr.toString()));
             console.log("rsvg-convert stdout: ".concat(_ls.stdout.toString()));
-
             _fs.default.unlinkSync(_tmpobj.name);
           } else {
             _fs.default.writeFileSync(outfile, result);
-          } // manually exit the process after done rendering because autoruns or
+          }
+
+          // 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);
           _context.next = 13;
           break;
-
         case 9:
           _context.prev = 9;
           _context.t0 = _context["catch"](0);
           console.error(_context.t0);
           process.exit(1);
-
         case 13:
         case "end":
           return _context.stop();

package/dist/index.testmod.js

@@ -1,34 +1,23 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
 var _renderRegion = require("./renderRegion");
-
 var _fs = _interopRequireDefault(require("fs"));
-
 var _jsdom = require("jsdom");
-
 require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
-
 var _canvas = require("canvas");
-
 var document = new _jsdom.JSDOM("...").window.document;
 global.document = document;
 global.nodeImage = _canvas.Image;
 global.nodeCreateCanvas = _canvas.createCanvas;
-
 function hashCode(str) {
   var hash = 0;
   var chr;
-
   if (str.length === 0) {
     return hash;
   }
-
   for (var i = 0; i < str.length; i++) {
     chr = str.charCodeAt(i);
     hash = (hash << 5) - hash + chr;
@@ -37,9 +26,9 @@ function hashCode(str) {
 
   return hash;
 }
+var timeout = 20000;
 
-var timeout = 20000; // commented out for using remote files currently
-
+// commented out for using remote files currently
 xtest('renders a region with --session and --config args', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
   var result;
   return _regenerator.default.wrap(function _callee$(_context) {
@@ -51,22 +40,19 @@ xtest('renders a region with --session and --config args', /*#__PURE__*/(0, _asy
             session: require.resolve('../test/clingen_session.json'),
             config: require.resolve('../data/config.json')
           });
-
         case 2:
           result = _context.sent;
-
           _fs.default.writeFileSync('svg_from_config_and_session_param.svg', result);
-
           expect(hashCode(result)).toMatchSnapshot();
-
         case 5:
         case "end":
           return _context.stop();
       }
     }
   }, _callee);
-})), timeout); // commented out for using remote files currently
+})), timeout);
 
+// commented out for using remote files currently
 xtest('renders a region with --session, --tracks, and --assembly args', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
   var result;
   return _regenerator.default.wrap(function _callee2$(_context2) {
@@ -79,14 +65,10 @@ xtest('renders a region with --session, --tracks, and --assembly args', /*#__PUR
             tracks: require.resolve('../data/tracks.json'),
             assembly: require.resolve('../data/assembly.json')
           });
-
         case 2:
           result = _context2.sent;
-
           _fs.default.writeFileSync('svg_from_separate_session_and_tracks.svg', result);
-
           expect(hashCode(result)).toMatchSnapshot();
-
         case 5:
         case "end":
           return _context2.stop();
@@ -103,7 +85,6 @@ test('renders volvox with variety of args', /*#__PURE__*/(0, _asyncToGenerator2.
           fp = function fp(f) {
             return require.resolve('../data/volvox/' + f);
           };
-
           console.error = jest.fn();
           _context3.next = 4;
           return (0, _renderRegion.renderRegion)({
@@ -111,15 +92,11 @@ test('renders volvox with variety of args', /*#__PURE__*/(0, _asyncToGenerator2.
             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'
           });
-
         case 4:
           result = _context3.sent;
-
           // 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();
-
         case 7:
         case "end":
           return _context3.stop();
@@ -136,7 +113,6 @@ test('renders volvox with variety of args (noRasterize)', /*#__PURE__*/(0, _asyn
           fp = function fp(f) {
             return require.resolve('../data/volvox/' + f);
           };
-
           console.error = jest.fn();
           _context4.next = 4;
           return (0, _renderRegion.renderRegion)({
@@ -145,23 +121,20 @@ test('renders volvox with variety of args (noRasterize)', /*#__PURE__*/(0, _asyn
             loc: 'ctgA:1000-2000',
             noRasterize: true
           });
-
         case 4:
           result = _context4.sent;
-
           // can't do a snapshot test here, slightly inconsistent results(?)
           _fs.default.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'), result);
-
           expect(result).toBeTruthy();
-
         case 7:
         case "end":
           return _context4.stop();
       }
     }
   }, _callee4);
-})), timeout); // commented out for using remote files currently
+})), timeout);
 
+// commented out for using remote files currently
 xtest('configtracks arg with urls', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
   var result;
   return _regenerator.default.wrap(function _callee5$(_context5) {
@@ -175,15 +148,11 @@ xtest('configtracks arg with urls', /*#__PURE__*/(0, _asyncToGenerator2.default)
             assembly: 'GRCh38',
             loc: 'chr1:50,000-60,000'
           });
-
         case 2:
           result = _context5.sent;
-
           // can't do a snapshot test here, slightly inconsistent results(?)
           _fs.default.writeFileSync('svg_configtracks_simple.svg', result);
-
           expect(result).toBeTruthy();
-
         case 5:
         case "end":
           return _context5.stop();
@@ -204,15 +173,11 @@ test('configtracks arg with local files', /*#__PURE__*/(0, _asyncToGenerator2.de
             assembly: 'volvox',
             loc: 'ctgA:1-50,000'
           });
-
         case 2:
           result = _context6.sent;
-
           // can't do a snapshot test here, slightly inconsistent results(?)
           _fs.default.writeFileSync(require.resolve('../test/svg_configtracks_local.svg'), result);
-
           expect(result).toBeTruthy();
-
         case 5:
         case "end":
           return _context6.stop();
@@ -232,14 +197,10 @@ xtest('renders --hic', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__
             trackList: [['hic', ['https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic']]],
             loc: '1:2,000,000-10,000,000'
           });
-
         case 2:
           result = _context7.sent;
-
           _fs.default.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result);
-
           expect(result).toBeTruthy();
-
         case 5:
         case "end":
           return _context7.stop();

package/dist/parseArgv.js

@@ -5,17 +5,14 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.parseArgv = parseArgv;
 exports.standardizeArgv = standardizeArgv;
-
 function parseArgv(argv) {
   var map = [];
-
   while (argv.length) {
     var val = argv[0].slice(2);
     argv = argv.slice(1);
     var next = argv.findIndex(function (arg) {
       return arg.startsWith('-');
     });
-
     if (next !== -1) {
       map.push([val, argv.slice(0, next)]);
       argv = argv.slice(next);
@@ -24,10 +21,8 @@ function parseArgv(argv) {
       break;
     }
   }
-
   return map;
 }
-
 function standardizeArgv(args, trackTypes) {
   var result = {
     trackList: []

package/dist/parseArgv.testmod.js

@@ -1,7 +1,6 @@
 "use strict";
 
 var _parseArgv = require("./parseArgv");
-
 test('parse', function () {
   var 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

@@ -1,55 +1,38 @@
 "use strict";
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.muiCache = void 0;
 exports.readData = readData;
 exports.renderRegion = renderRegion;
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
 var _toArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toArray"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
+var _react = _interopRequireDefault(require("react"));
 var _reactLinearGenomeView = require("@jbrowse/react-linear-genome-view");
-
 var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
-
-var _mobx = require("mobx");
-
+var _cache = _interopRequireDefault(require("@emotion/cache"));
+var _react2 = require("@emotion/react");
 var _path = _interopRequireDefault(require("path"));
-
 var _fs = _interopRequireDefault(require("fs"));
-
 var _util = require("./util");
-
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
 function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
 function read(file) {
   var res;
-
   try {
-    res = JSON.parse(_fs.default.readFileSync(file));
+    res = JSON.parse(_fs.default.readFileSync(file, 'utf8'));
   } catch (e) {
     throw new Error("Failed to parse ".concat(file, " as JSON, use --fasta if you mean to pass a FASTA file"));
   }
-
   return res;
 }
-
 function makeLocation(file) {
   return file.startsWith('http') ? {
     uri: file
@@ -57,12 +40,10 @@ function makeLocation(file) {
     localPath: file
   };
 }
-
 function addRelativePaths(config, configPath) {
   if ((0, _typeof2.default)(config) === 'object') {
     for (var _i = 0, _Object$keys = Object.keys(config); _i < _Object$keys.length; _i++) {
       var key = _Object$keys[_i];
-
       if ((0, _typeof2.default)(config[key]) === 'object') {
         addRelativePaths(config[key], configPath);
       } else if (key === 'localPath') {
@@ -71,49 +52,48 @@ function addRelativePaths(config, configPath) {
     }
   }
 }
-
 function readData(opts) {
   var _sessionData, _sessionData2, _configData$assemblie;
-
   var asm = opts.assembly,
-      config = opts.config,
-      session = opts.session,
-      fasta = opts.fasta,
-      aliases = opts.aliases,
-      defaultSession = opts.defaultSession,
-      _opts$trackList = opts.trackList,
-      trackList = _opts$trackList === void 0 ? [] : _opts$trackList,
-      tracks = opts.tracks;
+    config = opts.config,
+    session = opts.session,
+    fasta = opts.fasta,
+    aliases = opts.aliases,
+    defaultSession = opts.defaultSession,
+    _opts$trackList = opts.trackList,
+    trackList = _opts$trackList === void 0 ? [] : _opts$trackList,
+    tracks = opts.tracks;
   var assemblyData = asm && _fs.default.existsSync(asm) ? read(asm) : undefined;
   var tracksData = tracks ? read(tracks) : undefined;
   var configData = config ? read(config) : {};
   var sessionData = session ? read(session) : undefined;
-
   if (config) {
     addRelativePaths(configData, _path.default.dirname(_path.default.resolve(config)));
-  } // the session.json can be a raw session or a json file with a "session"
+  }
+
+  // the session.json can be a raw session or a json file with a "session"
   // attribute, which is what is exported via the "File->Export session" in
   // jbrowse-web
-
-
   if ((_sessionData = sessionData) !== null && _sessionData !== void 0 && _sessionData.session) {
     sessionData = sessionData.session;
-  } // only export first view
-
+  }
 
+  // only export first view
   if ((_sessionData2 = sessionData) !== null && _sessionData2 !== void 0 && _sessionData2.views) {
     sessionData.view = sessionData.views[0];
-  } // use assembly from file if a file existed
-
+  }
 
+  // use assembly from file if a file existed
   if (assemblyData) {
     configData.assembly = assemblyData;
-  } // else check if it was an assembly name in a config file
+  }
+  // else 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(function (entry) {
       return entry.name === asm;
     }) : configData.assemblies[0];
-  } // else load fasta from command line
+  }
+  // else load fasta from command line
   else if (fasta) {
     var bgzip = fasta.endsWith('gz');
     configData.assembly = {
@@ -129,7 +109,6 @@ function readData(opts) {
         }
       }
     };
-
     if (aliases) {
       configData.assembly.refNameAliases = {
         adapter: {
@@ -138,25 +117,22 @@ function readData(opts) {
         }
       };
     }
-  } // 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');
   }
-
   if (tracksData) {
     configData.tracks = tracksData;
   } else if (!configData.tracks) {
     configData.tracks = [];
   }
-
   trackList.forEach(function (track) {
     var _track = (0, _slicedToArray2.default)(track, 2),
-        type = _track[0],
-        _track$ = (0, _slicedToArray2.default)(_track[1], 1),
-        file = _track$[0];
-
+      type = _track[0],
+      _track$ = (0, _slicedToArray2.default)(_track[1], 1),
+      file = _track$[0];
     if (type === 'bam') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'AlignmentsTrack',
@@ -173,7 +149,6 @@ function readData(opts) {
         }
       }]);
     }
-
     if (type === 'cram') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'AlignmentsTrack',
@@ -188,7 +163,6 @@ function readData(opts) {
         }
       }]);
     }
-
     if (type === 'bigwig') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'QuantitativeTrack',
@@ -201,7 +175,6 @@ function readData(opts) {
         }
       }]);
     }
-
     if (type === 'vcfgz') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'VariantTrack',
@@ -217,7 +190,6 @@ function readData(opts) {
         }
       }]);
     }
-
     if (type === 'gffgz') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'FeatureTrack',
@@ -233,7 +205,6 @@ function readData(opts) {
         }
       }]);
     }
-
     if (type === 'hic') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'HicTrack',
@@ -246,7 +217,6 @@ function readData(opts) {
         }
       }]);
     }
-
     if (type === 'bigbed') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'FeatureTrack',
@@ -259,7 +229,6 @@ function readData(opts) {
         }
       }]);
     }
-
     if (type === 'bedgz') {
       configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'FeatureTrack',
@@ -276,81 +245,83 @@ function readData(opts) {
       }]);
     }
   });
-
   if (!defaultSession) {
     // don't use defaultSession from config.json file, can result in assembly
     // name confusion
     delete configData.defaultSession;
-  } // only allow an external manually specified session
-
+  }
 
+  // only allow an external manually specified session
   if (sessionData) {
     configData.defaultSession = sessionData;
   }
-
   return configData;
 }
 
+// without this, the styles can become messed up especially in lgv header
+// xref https://github.com/garronej/tss-react/issues/25
+var muiCache = (0, _cache.default)({
+  key: 'mui',
+  prepend: true
+});
+exports.muiCache = muiCache;
 function renderRegion() {
   return _renderRegion.apply(this, arguments);
 }
-
 function _renderRegion() {
   _renderRegion = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
     var opts,
-        model,
-        loc,
-        _opts$width,
-        width,
-        _opts$trackList2,
-        trackList,
-        sessionParam,
-        defaultSession,
-        session,
-        view,
-        assemblyManager,
-        assembly,
-        region,
-        process,
-        _args = arguments;
-
+      model,
+      loc,
+      _opts$width,
+      width,
+      _opts$trackList2,
+      trackList,
+      sessionParam,
+      defaultSession,
+      session,
+      view,
+      assemblyManager,
+      _assemblyManager$asse,
+      assembly,
+      process,
+      _args = arguments;
     return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
             process = function _process(trackEntry) {
               var extra = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : function () {};
-
               var _trackEntry = (0, _slicedToArray2.default)(trackEntry, 2),
-                  _trackEntry$ = (0, _toArray2.default)(_trackEntry[1]),
-                  track = _trackEntry$[0],
-                  opts = _trackEntry$.slice(1);
-
+                _trackEntry$ = (0, _toArray2.default)(_trackEntry[1]),
+                track = _trackEntry$[0],
+                opts = _trackEntry$.slice(1);
               var currentTrack = view.showTrack(extra(track));
               var display = currentTrack.displays[0];
               opts.forEach(function (opt) {
                 // apply height to any track
                 if (opt.startsWith('height:')) {
                   var _opt$split = opt.split(':'),
-                      _opt$split2 = (0, _slicedToArray2.default)(_opt$split, 2),
-                      height = _opt$split2[1];
-
+                    _opt$split2 = (0, _slicedToArray2.default)(_opt$split, 2),
+                    height = _opt$split2[1];
                   display.setHeight(+height);
-                } // apply sort to pileup
+                }
+
+                // apply sort to pileup
                 else if (opt.startsWith('sort:')) {
                   var _opt$split3 = opt.split(':'),
-                      _opt$split4 = (0, _slicedToArray2.default)(_opt$split3, 3),
-                      type = _opt$split4[1],
-                      tag = _opt$split4[2];
-
+                    _opt$split4 = (0, _slicedToArray2.default)(_opt$split3, 3),
+                    type = _opt$split4[1],
+                    tag = _opt$split4[2];
                   display.PileupDisplay.setSortedBy(type, tag);
-                } // apply color scheme to pileup
+                }
+
+                // apply color scheme to pileup
                 else if (opt.startsWith('color:')) {
                   var _opt$split5 = opt.split(':'),
-                      _opt$split6 = (0, _slicedToArray2.default)(_opt$split5, 3),
-                      _type = _opt$split6[1],
-                      _tag = _opt$split6[2];
-
+                    _opt$split6 = (0, _slicedToArray2.default)(_opt$split5, 3),
+                    _type = _opt$split6[1],
+                    _tag = _opt$split6[2];
                   if (display.PileupDisplay) {
                     display.PileupDisplay.setColorScheme({
                       type: _type,
@@ -359,69 +330,74 @@ function _renderRegion() {
                   } else {
                     display.setColor(_type);
                   }
-                } // force track to render even if maxbpperpx limit hit...
+                }
+
+                // force track to render even if maxbpperpx limit hit...
                 else if (opt.startsWith('force:')) {
                   var _opt$split7 = opt.split(':'),
-                      _opt$split8 = (0, _slicedToArray2.default)(_opt$split7, 2),
-                      force = _opt$split8[1];
-
+                    _opt$split8 = (0, _slicedToArray2.default)(_opt$split7, 2),
+                    force = _opt$split8[1];
                   if (force) {
                     display.setUserFeatureScreenDensity(Number.MAX_VALUE);
                   }
-                } // apply wiggle autoscale
+                }
+
+                // apply wiggle autoscale
                 else if (opt.startsWith('autoscale:')) {
                   var _opt$split9 = opt.split(':'),
-                      _opt$split10 = (0, _slicedToArray2.default)(_opt$split9, 2),
-                      autoscale = _opt$split10[1];
-
+                    _opt$split10 = (0, _slicedToArray2.default)(_opt$split9, 2),
+                    autoscale = _opt$split10[1];
                   display.setAutoscale(autoscale);
-                } // apply min and max score to wiggle
+                }
+
+                // apply min and max score to wiggle
                 else if (opt.startsWith('minmax:')) {
                   var _opt$split11 = opt.split(':'),
-                      _opt$split12 = (0, _slicedToArray2.default)(_opt$split11, 3),
-                      min = _opt$split12[1],
-                      max = _opt$split12[2];
-
+                    _opt$split12 = (0, _slicedToArray2.default)(_opt$split11, 3),
+                    min = _opt$split12[1],
+                    max = _opt$split12[2];
                   display.setMinScore(+min);
                   display.setMaxScore(+max);
-                } // apply linear or log scale to wiggle
+                }
+
+                // apply linear or log scale to wiggle
                 else if (opt.startsWith('scaletype:')) {
                   var _opt$split13 = opt.split(':'),
-                      _opt$split14 = (0, _slicedToArray2.default)(_opt$split13, 2),
-                      scaletype = _opt$split14[1];
-
+                    _opt$split14 = (0, _slicedToArray2.default)(_opt$split13, 2),
+                    scaletype = _opt$split14[1];
                   display.setScaleType(scaletype);
-                } // draw crosshatches on wiggle
+                }
+
+                // draw crosshatches on wiggle
                 else if (opt.startsWith('crosshatch:')) {
                   var _opt$split15 = opt.split(':'),
-                      _opt$split16 = (0, _slicedToArray2.default)(_opt$split15, 2),
-                      val = _opt$split16[1];
-
+                    _opt$split16 = (0, _slicedToArray2.default)(_opt$split15, 2),
+                    val = _opt$split16[1];
                   display.setCrossHatches((0, _util.booleanize)(val));
-                } // turn off fill on bigwig with fill:false
+                }
+
+                // turn off fill on bigwig with fill:false
                 else if (opt.startsWith('fill:')) {
                   var _opt$split17 = opt.split(':'),
-                      _opt$split18 = (0, _slicedToArray2.default)(_opt$split17, 2),
-                      _val = _opt$split18[1];
-
+                    _opt$split18 = (0, _slicedToArray2.default)(_opt$split17, 2),
+                    _val = _opt$split18[1];
                   display.setFill((0, _util.booleanize)(_val));
-                } // set resolution:superfine to use finer bigwig bin size
+                }
+
+                // set resolution:superfine to use finer bigwig bin size
                 else if (opt.startsWith('resolution:')) {
                   var _opt$split19 = opt.split(':'),
-                      _opt$split20 = (0, _slicedToArray2.default)(_opt$split19, 2),
-                      _val2 = _opt$split20[1];
-
+                    _opt$split20 = (0, _slicedToArray2.default)(_opt$split19, 2),
+                    _val2 = _opt$split20[1];
                   if (_val2 === 'fine') {
                     _val2 = 10;
                   } else if (_val2 === 'superfine') {
                     _val2 = 100;
                   }
-
                   display.setResolution(_val2);
                 }
               });
             };
-
             opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
             model = (0, _reactLinearGenomeView.createViewState)(readData(opts));
             loc = opts.loc, _opts$width = opts.width, width = _opts$width === void 0 ? 1500 : _opts$width, _opts$trackList2 = opts.trackList, trackList = _opts$trackList2 === void 0 ? [] : _opts$trackList2, sessionParam = opts.session, defaultSession = opts.defaultSession;
@@ -429,41 +405,45 @@ function _renderRegion() {
             view = session.view;
             assemblyManager = model.assemblyManager;
             view.setWidth(width);
-            _context.next = 10;
-            return (0, _mobx.when)(function () {
-              var _assemblyManager$allP;
-
-              return ((_assemblyManager$allP = assemblyManager.allPossibleRefNames) === null || _assemblyManager$allP === void 0 ? void 0 : _assemblyManager$allP.length) && model.session.view.initialized;
-            });
-
-          case 10:
-            if (loc) {
-              assembly = assemblyManager.assemblies[0];
-              region = assembly.regions[0];
-
-              if (region) {
-                view.setDisplayedRegions([region]);
-              }
-
-              if (loc === 'all') {
-                view.showAllRegionsInAssembly(assembly.name);
-              } else {
-                view.navToLocString(loc);
-              }
-            } else if (!sessionParam && !defaultSession) {
+            if (!loc) {
+              _context.next = 18;
+              break;
+            }
+            _assemblyManager$asse = (0, _slicedToArray2.default)(assemblyManager.assemblies, 1), assembly = _assemblyManager$asse[0];
+            if (!(loc === 'all')) {
+              _context.next = 14;
+              break;
+            }
+            view.showAllRegionsInAssembly(assembly.name);
+            _context.next = 16;
+            break;
+          case 14:
+            _context.next = 16;
+            return view.navToLocString(loc, assembly.name);
+          case 16:
+            _context.next = 19;
+            break;
+          case 18:
+            if (!sessionParam && !defaultSession) {
               console.warn('No loc specified');
             }
-
+          case 19:
             trackList.forEach(function (track) {
               return process(track, function (extra) {
                 return _path.default.basename(extra);
               });
             });
-            return _context.abrupt("return", (0, _pluginLinearGenomeView.renderToSvg)(view, _objectSpread({
+            return _context.abrupt("return", (0, _pluginLinearGenomeView.renderToSvg)(view, _objectSpread(_objectSpread({
               rasterizeLayers: !opts.noRasterize
-            }, opts)));
-
-          case 13:
+            }, opts), {}, {
+              Wrapper: function Wrapper(_ref) {
+                var children = _ref.children;
+                return /*#__PURE__*/_react.default.createElement(_react2.CacheProvider, {
+                  value: muiCache
+                }, children);
+              }
+            })));
+          case 21:
           case "end":
             return _context.stop();
         }

package/dist/util.js

@@ -4,10 +4,8 @@ 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;
 };
-
 exports.booleanize = booleanize;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "2.1.6",
+  "version": "2.2.0",
   "main": "index.js",
   "author": "JBrowse Team",
   "license": "Apache-2.0",
@@ -18,18 +18,14 @@
     "test": "jest",
     "prebuild": "rm -rf dist",
     "build": "babel --root-mode upward src -d dist",
-    "preversion": "npm run build",
-    "snap": "npm run build && node dist/index.js --config data/config.json --defaultSession --out out.svg",
-    "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 --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"
+    "preversion": "npm run build"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
-    "@jbrowse/plugin-linear-genome-view": "^2.1.6",
-    "@jbrowse/react-linear-genome-view": "^2.1.6",
+    "@emotion/cache": "^11.7.1",
+    "@emotion/react": "^11.9.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.2.0",
+    "@jbrowse/react-linear-genome-view": "^2.2.0",
     "abortcontroller-polyfill": "^1.7.3",
     "canvas": "^2.9.1",
     "jsdom": "^19.0.0",
@@ -43,5 +39,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
+  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
 }