@jbrowse/img 2.1.7 → 2.2.1

package/dist/renderRegion.js

@@ -1,474 +1,374 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-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 _reactLinearGenomeView = require("@jbrowse/react-linear-genome-view");
-
-var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
-
-var _mobx = require("mobx");
-
-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; }
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderRegion = exports.muiCache = exports.readData = void 0;
+const react_1 = __importDefault(require("react"));
+const react_linear_genome_view_1 = require("@jbrowse/react-linear-genome-view");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const cache_1 = __importDefault(require("@emotion/cache"));
+const react_2 = require("@emotion/react");
+const path_1 = __importDefault(require("path"));
+const fs_1 = __importDefault(require("fs"));
+const util_1 = require("./util");
 function read(file) {
-  var res;
-
-  try {
-    res = JSON.parse(_fs.default.readFileSync(file));
-  } catch (e) {
-    throw new Error("Failed to parse ".concat(file, " as JSON, use --fasta if you mean to pass a FASTA file"));
-  }
-
-  return res;
+    let res;
+    try {
+        res = JSON.parse(fs_1.default.readFileSync(file, 'utf8'));
+    }
+    catch (e) {
+        throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`);
+    }
+    return res;
 }
-
 function makeLocation(file) {
-  return file.startsWith('http') ? {
-    uri: file
-  } : {
-    localPath: file
-  };
+    return file.startsWith('http') ? { uri: file } : { localPath: file };
 }
-
 function addRelativePaths(config, configPath) {
-  if ((0, _typeof2.default)(config) === 'object') {
-    for (var _i = 0, _Object$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') {
-        config.localPath = _path.default.resolve(configPath, config.localPath);
-      }
+    if (typeof config === 'object') {
+        for (const key of Object.keys(config)) {
+            if (typeof config[key] === 'object') {
+                addRelativePaths(config[key], configPath);
+            }
+            else if (key === 'localPath') {
+                config.localPath = path_1.default.resolve(configPath, config.localPath);
+            }
+        }
     }
-  }
 }
-
-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;
-  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"
-  // 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
-
-
-  if ((_sessionData2 = sessionData) !== null && _sessionData2 !== void 0 && _sessionData2.views) {
-    sessionData.view = sessionData.views[0];
-  } // 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 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 if (fasta) {
-    var 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
+function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList = [], }) {
+    var _a;
+    const assemblyData = asm && fs_1.default.existsSync(asm) ? read(asm) : undefined;
+    const tracksData = tracks ? read(tracks) : undefined;
+    const configData = (config ? read(config) : {});
+    let sessionData = session ? read(session) : undefined;
+    if (config) {
+        addRelativePaths(configData, path_1.default.dirname(path_1.default.resolve(config)));
+    }
+    // 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 === null || sessionData === void 0 ? void 0 : sessionData.session) {
+        sessionData = sessionData.session;
+    }
+    // only export first view
+    if (sessionData === null || sessionData === void 0 ? void 0 : sessionData.views) {
+        sessionData.view = sessionData.views[0];
+    }
+    // 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 if ((_a = configData.assemblies) === null || _a === void 0 ? void 0 : _a.length) {
+        configData.assemblies.find(entry => entry.name === asm);
+        if (asm) {
+            const assembly = configData.assemblies.find(entry => entry.name === asm);
+            if (!assembly) {
+                throw new Error(`assembly ${asm} not found in config`);
+            }
+            configData.assembly = assembly;
         }
-      }
-    };
-
-    if (aliases) {
-      configData.assembly.refNameAliases = {
-        adapter: {
-          type: 'RefNameAliasAdapter',
-          location: makeLocation(aliases)
+        else {
+            configData.assembly = configData.assemblies[0];
         }
-      };
     }
-  } // throw if still no assembly
-
-
-  if (!configData.assembly) {
-    throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
-  }
-
-  if (tracksData) {
-    configData.tracks = tracksData;
-  } else if (!configData.tracks) {
-    configData.tracks = [];
-  }
-
-  trackList.forEach(function (track) {
-    var _track = (0, _slicedToArray2.default)(track, 2),
-        type = _track[0],
-        _track$ = (0, _slicedToArray2.default)(_track[1], 1),
-        file = _track$[0];
-
-    if (type === 'bam') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'AlignmentsTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'BamAdapter',
-          bamLocation: makeLocation(file),
-          index: {
-            location: makeLocation(file + '.bai')
-          },
-          sequenceAdapter: configData.assembly.sequence.adapter
+    // else load fasta from command line
+    else if (fasta) {
+        const bgzip = fasta.endsWith('gz');
+        configData.assembly = {
+            name: path_1.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),
+                },
+            };
         }
-      }]);
-    }
-
-    if (type === 'cram') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'AlignmentsTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'CramAdapter',
-          cramLocation: makeLocation(file),
-          craiLocation: makeLocation(file + '.crai'),
-          sequenceAdapter: configData.assembly.sequence.adapter
+        if (cytobands) {
+            configData.assembly.cytobands = {
+                adapter: {
+                    type: 'CytobandAdapter',
+                    location: makeLocation(cytobands),
+                },
+            };
         }
-      }]);
     }
-
-    if (type === 'bigwig') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'QuantitativeTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'BigWigAdapter',
-          bigWigLocation: makeLocation(file)
-        }
-      }]);
+    // 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 (type === 'vcfgz') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'VariantTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'VcfTabixAdapter',
-          vcfGzLocation: makeLocation(file),
-          index: {
-            location: makeLocation(file + '.tbi')
-          }
-        }
-      }]);
+    if (tracksData) {
+        configData.tracks = tracksData;
     }
-
-    if (type === 'gffgz') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'FeatureTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'Gff3TabixAdapter',
-          gffGzLocation: makeLocation(file),
-          index: {
-            location: makeLocation(file + '.tbi')
-          }
-        }
-      }]);
+    else if (!configData.tracks) {
+        configData.tracks = [];
     }
-
-    if (type === 'hic') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'HicTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'HicAdapter',
-          hicLocation: makeLocation(file)
+    trackList.forEach(track => {
+        const [type, [file]] = track;
+        if (type === 'bam') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'AlignmentsTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BamAdapter',
+                        bamLocation: makeLocation(file),
+                        index: { location: makeLocation(file + '.bai') },
+                        sequenceAdapter: configData.assembly.sequence.adapter,
+                    },
+                },
+            ];
         }
-      }]);
-    }
-
-    if (type === 'bigbed') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'FeatureTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: makeLocation(file)
+        if (type === 'cram') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'AlignmentsTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'CramAdapter',
+                        cramLocation: makeLocation(file),
+                        craiLocation: makeLocation(file + '.crai'),
+                        sequenceAdapter: configData.assembly.sequence.adapter,
+                    },
+                },
+            ];
         }
-      }]);
-    }
-
-    if (type === 'bedgz') {
-      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
-        type: 'FeatureTrack',
-        trackId: _path.default.basename(file),
-        name: _path.default.basename(file),
-        assemblyNames: [configData.assembly.name],
-        adapter: {
-          type: 'BedTabixAdapter',
-          bedGzLocation: makeLocation(file),
-          index: {
-            location: makeLocation(file + '.tbi')
-          }
+        if (type === 'bigwig') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'QuantitativeTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BigWigAdapter',
+                        bigWigLocation: makeLocation(file),
+                    },
+                },
+            ];
+        }
+        if (type === 'vcfgz') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'VariantTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'VcfTabixAdapter',
+                        vcfGzLocation: makeLocation(file),
+                        index: {
+                            location: makeLocation(file + '.tbi'),
+                        },
+                    },
+                },
+            ];
+        }
+        if (type === 'gffgz') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'FeatureTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'Gff3TabixAdapter',
+                        gffGzLocation: makeLocation(file),
+                        index: {
+                            location: makeLocation(file + '.tbi'),
+                        },
+                    },
+                },
+            ];
+        }
+        if (type === 'hic') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'HicTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'HicAdapter',
+                        hicLocation: makeLocation(file),
+                    },
+                },
+            ];
+        }
+        if (type === 'bigbed') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'FeatureTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BigBedAdapter',
+                        bigBedLocation: makeLocation(file),
+                    },
+                },
+            ];
+        }
+        if (type === 'bedgz') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'FeatureTrack',
+                    trackId: path_1.default.basename(file),
+                    name: path_1.default.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BedTabixAdapter',
+                        bedGzLocation: makeLocation(file),
+                        index: {
+                            location: makeLocation(file + '.tbi'),
+                        },
+                    },
+                },
+            ];
         }
-      }]);
+    });
+    if (!defaultSession) {
+        // don't use defaultSession from config.json file, can result in assembly
+        // name confusion
+        delete configData.defaultSession;
     }
-  });
-
-  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
-
-
-  if (sessionData) {
-    configData.defaultSession = sessionData;
-  }
-
-  return configData;
-}
-
-function renderRegion() {
-  return _renderRegion.apply(this, arguments);
+    // only allow an external manually specified session
+    if (sessionData) {
+        configData.defaultSession = sessionData;
+    }
+    return configData;
 }
-
-function _renderRegion() {
-  _renderRegion = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var opts,
-        model,
-        loc,
-        _opts$width,
-        width,
-        _opts$trackList2,
-        trackList,
-        sessionParam,
-        defaultSession,
-        session,
-        view,
-        assemblyManager,
-        assembly,
-        region,
-        process,
-        _args = arguments;
-
-    return _regenerator.default.wrap(function _callee$(_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);
-
-              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];
-
-                  display.setHeight(+height);
-                } // 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$split4[2];
-
-                  display.PileupDisplay.setSortedBy(type, tag);
-                } // apply color scheme to pileup
-                else if (opt.startsWith('color:')) {
-                  var _opt$split5 = opt.split(':'),
-                      _opt$split6 = (0, _slicedToArray2.default)(_opt$split5, 3),
-                      _type = _opt$split6[1],
-                      _tag = _opt$split6[2];
-
-                  if (display.PileupDisplay) {
-                    display.PileupDisplay.setColorScheme({
-                      type: _type,
-                      tag: _tag
-                    });
-                  } else {
-                    display.setColor(_type);
-                  }
-                } // 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];
-
-                  if (force) {
-                    display.setUserFeatureScreenDensity(Number.MAX_VALUE);
-                  }
-                } // 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];
-
-                  display.setAutoscale(autoscale);
-                } // 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$split12[2];
-
-                  display.setMinScore(+min);
-                  display.setMaxScore(+max);
-                } // apply linear or log scale to wiggle
-                else if (opt.startsWith('scaletype:')) {
-                  var _opt$split13 = opt.split(':'),
-                      _opt$split14 = (0, _slicedToArray2.default)(_opt$split13, 2),
-                      scaletype = _opt$split14[1];
-
-                  display.setScaleType(scaletype);
-                } // draw crosshatches on wiggle
-                else if (opt.startsWith('crosshatch:')) {
-                  var _opt$split15 = opt.split(':'),
-                      _opt$split16 = (0, _slicedToArray2.default)(_opt$split15, 2),
-                      val = _opt$split16[1];
-
-                  display.setCrossHatches((0, _util.booleanize)(val));
-                } // turn off fill on bigwig with fill:false
-                else if (opt.startsWith('fill:')) {
-                  var _opt$split17 = opt.split(':'),
-                      _opt$split18 = (0, _slicedToArray2.default)(_opt$split17, 2),
-                      _val = _opt$split18[1];
-
-                  display.setFill((0, _util.booleanize)(_val));
-                } // set resolution:superfine to use finer bigwig bin size
-                else if (opt.startsWith('resolution:')) {
-                  var _opt$split19 = opt.split(':'),
-                      _opt$split20 = (0, _slicedToArray2.default)(_opt$split19, 2),
-                      _val2 = _opt$split20[1];
-
-                  if (_val2 === 'fine') {
-                    _val2 = 10;
-                  } else if (_val2 === 'superfine') {
-                    _val2 = 100;
-                  }
-
-                  display.setResolution(_val2);
-                }
-              });
-            };
-
-            opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
-            model = (0, _reactLinearGenomeView.createViewState)(readData(opts));
-            loc = opts.loc, _opts$width = opts.width, width = _opts$width === void 0 ? 1500 : _opts$width, _opts$trackList2 = opts.trackList, trackList = _opts$trackList2 === void 0 ? [] : _opts$trackList2, sessionParam = opts.session, defaultSession = opts.defaultSession;
-            session = model.session;
-            view = session.view;
-            assemblyManager = model.assemblyManager;
-            view.setWidth(width);
-            _context.next = 10;
-            return (0, _mobx.when)(function () {
-              var _assemblyManager$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) {
-              console.warn('No loc specified');
+exports.readData = readData;
+// without this, the styles can become messed up especially in lgv header
+// xref https://github.com/garronej/tss-react/issues/25
+exports.muiCache = (0, cache_1.default)({
+    key: 'mui',
+    prepend: true,
+});
+function process(trackEntry, view, extra = c => c) {
+    const [, [track, ...opts]] = trackEntry;
+    const currentTrack = view.showTrack(extra(track));
+    const display = currentTrack.displays[0];
+    opts.forEach(opt => {
+        // apply height to any track
+        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 });
             }
-
-            trackList.forEach(function (track) {
-              return process(track, function (extra) {
-                return _path.default.basename(extra);
-              });
-            });
-            return _context.abrupt("return", (0, _pluginLinearGenomeView.renderToSvg)(view, _objectSpread({
-              rasterizeLayers: !opts.noRasterize
-            }, opts)));
-
-          case 13:
-          case "end":
-            return _context.stop();
+            else {
+                display.setColor(type);
+            }
+        }
+        // force track to render even if maxbpperpx limit hit...
+        else if (opt.startsWith('force:')) {
+            const [, force] = opt.split(':');
+            if (force) {
+                display.updateStatsLimit({ bytes: 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);
         }
-      }
-    }, _callee);
-  }));
-  return _renderRegion.apply(this, arguments);
-}
+        // draw crosshatches on wiggle
+        else if (opt.startsWith('crosshatch:')) {
+            const [, val] = opt.split(':');
+            display.setCrossHatches((0, util_1.booleanize)(val));
+        }
+        // turn off fill on bigwig with fill:false
+        else if (opt.startsWith('fill:')) {
+            const [, val] = opt.split(':');
+            display.setFill((0, util_1.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);
+        }
+    });
+}
+async function renderRegion(opts) {
+    const model = (0, react_linear_genome_view_1.createViewState)(readData(opts));
+    const { loc, width = 1500, trackList = [], session: sessionParam, defaultSession, } = opts;
+    const { session } = model;
+    const { view } = session;
+    const { assemblyManager } = model;
+    view.setWidth(width);
+    if (loc) {
+        const [assembly] = assemblyManager.assemblies;
+        if (loc === 'all') {
+            view.showAllRegionsInAssembly(assembly.name);
+        }
+        else {
+            await view.navToLocString(loc, assembly.name);
+        }
+    }
+    else if (!sessionParam && !defaultSession) {
+        console.warn('No loc specified');
+    }
+    trackList.forEach(track => {
+        process(track, view, extra => path_1.default.basename(extra));
+    });
+    return (0, plugin_linear_genome_view_1.renderToSvg)(view, {
+        rasterizeLayers: !opts.noRasterize,
+        ...opts,
+        Wrapper: ({ children }) => (react_1.default.createElement(react_2.CacheProvider, { value: exports.muiCache }, children)),
+    });
+}
+exports.renderRegion = renderRegion;
+//# sourceMappingURL=renderRegion.js.map