@jbrowse/img 1.5.8 → 1.6.5

package/dist/index.js

@@ -2,6 +2,10 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
+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"));
@@ -85,46 +89,72 @@ _yargs.default.command('jb2export', 'Creates a jbrowse 2 image snapshot').option
   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();
-  const ret = await cb();
-  console.log(`Finished rendering: ${(+Date.now() - start) / 1000}s`);
-  return ret;
+function time(_x) {
+  return _time.apply(this, arguments);
+}
+
+function _time() {
+  _time = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(cb) {
+    var start, ret;
+    return _regenerator.default.wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            start = +Date.now();
+            _context.next = 3;
+            return cb();
+
+          case 3:
+            ret = _context.sent;
+            console.log("Finished rendering: ".concat((+Date.now() - start) / 1000, "s"));
+            return _context.abrupt("return", ret);
+
+          case 6:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  }));
+  return _time.apply(this, arguments);
 }
 
-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';
-
-  if (outfile.endsWith('.png')) {
-    const tmpobj = _tmp.default.fileSync({
-      mode: 0o644,
-      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]);
-    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')) {
-    const tmpobj = _tmp.default.fileSync({
-      mode: 0o644,
-      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]);
-    console.log(`rsvg-convert stderr: ${ls.stderr.toString()}`);
-    console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
-
-    _fs.default.unlinkSync(tmpobj.name);
-  } else {
-    _fs.default.writeFileSync(outfile, result);
-  }
-}, console.error));
+var args = (0, _parseArgv.standardizeArgv)((0, _parseArgv.parseArgv)(process.argv.slice(2)), ['bam', 'cram', 'vcfgz', 'hic', 'bigwig', 'bigbed', 'bedgz', 'gffgz', 'configtracks']);
+time(function () {
+  return (0, _renderRegion.renderRegion)(args).then(function (result) {
+    var outfile = args.out || 'out.svg';
+
+    if (outfile.endsWith('.png')) {
+      var tmpobj = _tmp.default.fileSync({
+        mode: 420,
+        prefix: 'prefix-',
+        postfix: '.svg'
+      });
+
+      _fs.default.writeFileSync(tmpobj.name, result);
+
+      var 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')) {
+      var _tmpobj = _tmp.default.fileSync({
+        mode: 420,
+        prefix: 'prefix-',
+        postfix: '.svg'
+      });
+
+      _fs.default.writeFileSync(_tmpobj.name, result);
+
+      var _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);
+    }
+  }, console.error);
+});

package/dist/index.testmod.js

@@ -2,19 +2,23 @@
 
 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"));
 
 function hashCode(str) {
-  let hash = 0;
-  let chr;
+  var hash = 0;
+  var chr;
 
   if (str.length === 0) {
     return hash;
   }
 
-  for (let i = 0; i < str.length; i++) {
+  for (var i = 0; i < str.length; i++) {
     chr = str.charCodeAt(i);
     hash = (hash << 5) - hash + chr;
     hash |= 0; // Convert to 32bit integer
@@ -23,75 +27,174 @@ function hashCode(str) {
   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);
+var timeout = 20000; // 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$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          _context.next = 2;
+          return (0, _renderRegion.renderRegion)({
+            session: require.resolve('../test/clingen_session.json'),
+            config: require.resolve('../data/config.json')
+          });
+
+        case 2:
+          result = _context.sent;
+
+          _fs.default.writeFileSync('svg_from_config_and_session_param.svg', result);
+
+          expect(hashCode(result)).toMatchSnapshot();
+
+        case 5:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})), timeout); // commented out for using remote files currently
+
+xtest('renders a region with --session, --tracks, and --assembly args', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+  var result;
+  return _regenerator.default.wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          _context2.next = 2;
+          return (0, _renderRegion.renderRegion)({
+            session: require.resolve('../test/clingen_session.json'),
+            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();
+      }
+    }
+  }, _callee2);
+})), timeout);
+test('renders volvox with variety of args', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+  var result;
+  return _regenerator.default.wrap(function _callee3$(_context3) {
+    while (1) {
+      switch (_context3.prev = _context3.next) {
+        case 0:
+          console.error = jest.fn();
+          _context3.next = 3;
+          return (0, _renderRegion.renderRegion)({
+            fasta: require.resolve('../data/volvox/volvox.fa'),
+            trackList: [['bam', [require.resolve('../data/volvox/volvox-sorted.bam')]], ['cram', [require.resolve('../data/volvox/volvox-sorted.cram')]], ['bigwig', [require.resolve('../data/volvox/volvox-sorted.bam.coverage.bw')]], ['vcfgz', [require.resolve('../data/volvox/volvox.filtered.vcf.gz')]], ['gffgz', [require.resolve('../data/volvox/volvox.sort.gff3.gz')]], ['bigbed', [require.resolve('../data/volvox/volvox.bb')]], ['bedgz', [require.resolve('../data/volvox/volvox-bed12.bed.gz')]]],
+            loc: 'ctgA:1000-2000'
+          });
+
+        case 3:
+          result = _context3.sent;
+
+          // can't do a snapshot test here, slightly inconsistent results(?)
+          _fs.default.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam.svg'), result);
+
+          expect(result).toBeTruthy();
+
+        case 6:
+        case "end":
+          return _context3.stop();
+      }
+    }
+  }, _callee3);
+})), timeout); // commented out for using remote files currently
+
+xtest('configtracks arg with urls', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
+  var result;
+  return _regenerator.default.wrap(function _callee4$(_context4) {
+    while (1) {
+      switch (_context4.prev = _context4.next) {
+        case 0:
+          _context4.next = 2;
+          return (0, _renderRegion.renderRegion)({
+            config: 'data/config.json',
+            trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
+            assembly: 'GRCh38',
+            loc: 'chr1:50,000-60,000'
+          });
+
+        case 2:
+          result = _context4.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 _context4.stop();
+      }
+    }
+  }, _callee4);
+})), timeout * 3);
+test('configtracks arg with local files', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
+  var result;
+  return _regenerator.default.wrap(function _callee5$(_context5) {
+    while (1) {
+      switch (_context5.prev = _context5.next) {
+        case 0:
+          _context5.next = 2;
+          return (0, _renderRegion.renderRegion)({
+            config: require.resolve('../data/volvox/config.json'),
+            trackList: [['configtracks', ['volvox_sv']]],
+            assembly: 'volvox',
+            loc: 'ctgA:1-50,000'
+          });
+
+        case 2:
+          result = _context5.sent;
+
+          // can't do a snapshot test here, slightly inconsistent results(?)
+          _fs.default.writeFileSync(require.resolve('../test/svg_configtracks_local.svg'), result);
+
+          expect(result).toBeTruthy();
+
+        case 5:
+        case "end":
+          return _context5.stop();
+      }
+    }
+  }, _callee5);
+})), timeout * 3);
+xtest('renders --hic', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6() {
+  var result;
+  return _regenerator.default.wrap(function _callee6$(_context6) {
+    while (1) {
+      switch (_context6.prev = _context6.next) {
+        case 0:
+          _context6.next = 2;
+          return (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'
+          });
+
+        case 2:
+          result = _context6.sent;
+
+          _fs.default.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result);
+
+          expect(result).toBeTruthy();
+
+        case 5:
+        case "end":
+          return _context6.stop();
+      }
+    }
+  }, _callee6);
+})), 20000);

package/dist/parseArgv.js

@@ -7,12 +7,14 @@ exports.parseArgv = parseArgv;
 exports.standardizeArgv = standardizeArgv;
 
 function parseArgv(argv) {
-  const map = [];
+  var map = [];
 
   while (argv.length) {
-    const val = argv[0].slice(2);
+    var val = argv[0].slice(2);
     argv = argv.slice(1);
-    const next = argv.findIndex(arg => arg.startsWith('-'));
+    var next = argv.findIndex(function (arg) {
+      return arg.startsWith('-');
+    });
 
     if (next !== -1) {
       map.push([val, argv.slice(0, next)]);
@@ -27,10 +29,10 @@ function parseArgv(argv) {
 }
 
 function standardizeArgv(args, trackTypes) {
-  const result = {
+  var result = {
     trackList: []
   };
-  args.forEach(arg => {
+  args.forEach(function (arg) {
     if (trackTypes.includes(arg[0])) {
       result.trackList.push(arg);
     } else {

package/dist/parseArgv.testmod.js

@@ -2,7 +2,7 @@
 
 var _parseArgv = require("./parseArgv");
 
-test('parse', () => {
-  const args = '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize';
+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

@@ -8,6 +8,20 @@ Object.defineProperty(exports, "__esModule", {
 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");
@@ -20,13 +34,17 @@ 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) {
-  let res;
+  var res;
 
   try {
     res = JSON.parse(_fs.default.readFileSync(file));
   } catch (e) {
-    throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`);
+    throw new Error("Failed to parse ".concat(file, " as JSON, use --fasta if you mean to pass a FASTA file"));
   }
 
   return res;
@@ -41,9 +59,11 @@ function makeLocation(file) {
 }
 
 function addRelativePaths(config, configPath) {
-  if (typeof config === 'object') {
-    for (const key of Object.keys(config)) {
-      if (typeof config[key] === 'object') {
+  if ((0, _typeof2.default)(config) === 'object') {
+    for (var _i = 0, _Object$keys = Object.keys(config); _i < _Object$keys.length; _i++) {
+      var key = _Object$keys[_i];
+
+      if ((0, _typeof2.default)(config[key]) === 'object') {
         addRelativePaths(config[key], configPath);
       } else if (key === 'localPath') {
         config.localPath = _path.default.resolve(configPath, config.localPath);
@@ -55,20 +75,19 @@ function addRelativePaths(config, configPath) {
 function readData(opts) {
   var _sessionData, _sessionData2, _configData$assemblie;
 
-  const {
-    assembly: asm,
-    config,
-    session,
-    fasta,
-    aliases,
-    defaultSession,
-    trackList = [],
-    tracks
-  } = opts;
-  const assemblyData = asm && _fs.default.existsSync(asm) ? read(asm) : undefined;
-  const tracksData = tracks ? read(tracks) : undefined;
-  const configData = config ? read(config) : {};
-  let sessionData = session ? read(session) : undefined;
+  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)));
@@ -91,10 +110,12 @@ 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];
+    configData.assembly = asm ? configData.assemblies.find(function (entry) {
+      return entry.name === asm;
+    }) : configData.assemblies[0];
   } // else load fasta from command line
   else if (fasta) {
-    const bgzip = fasta.endsWith('gz');
+    var bgzip = fasta.endsWith('gz');
     configData.assembly = {
       name: _path.default.basename(fasta),
       sequence: {
@@ -130,11 +151,14 @@ function readData(opts) {
     configData.tracks = [];
   }
 
-  trackList.forEach(track => {
-    const [type, [file]] = track;
+  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 = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'AlignmentsTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -147,11 +171,11 @@ function readData(opts) {
           },
           sequenceAdapter: configData.assembly.sequence.adapter
         }
-      }];
+      }]);
     }
 
     if (type === 'cram') {
-      configData.tracks = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'AlignmentsTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -162,11 +186,11 @@ function readData(opts) {
           craiLocation: makeLocation(file + '.crai'),
           sequenceAdapter: configData.assembly.sequence.adapter
         }
-      }];
+      }]);
     }
 
     if (type === 'bigwig') {
-      configData.tracks = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'QuantitativeTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -175,11 +199,11 @@ function readData(opts) {
           type: 'BigWigAdapter',
           bigWigLocation: makeLocation(file)
         }
-      }];
+      }]);
     }
 
     if (type === 'vcfgz') {
-      configData.tracks = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'VariantTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -191,11 +215,11 @@ function readData(opts) {
             location: makeLocation(file + '.tbi')
           }
         }
-      }];
+      }]);
     }
 
     if (type === 'gffgz') {
-      configData.tracks = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'FeatureTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -207,11 +231,11 @@ function readData(opts) {
             location: makeLocation(file + '.tbi')
           }
         }
-      }];
+      }]);
     }
 
     if (type === 'hic') {
-      configData.tracks = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'HicTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -220,11 +244,11 @@ function readData(opts) {
           type: 'HicAdapter',
           hicLocation: makeLocation(file)
         }
-      }];
+      }]);
     }
 
     if (type === 'bigbed') {
-      configData.tracks = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'FeatureTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -233,11 +257,11 @@ function readData(opts) {
           type: 'BigBedAdapter',
           bigBedLocation: makeLocation(file)
         }
-      }];
+      }]);
     }
 
     if (type === 'bedgz') {
-      configData.tracks = [...configData.tracks, {
+      configData.tracks = [].concat((0, _toConsumableArray2.default)(configData.tracks), [{
         type: 'FeatureTrack',
         trackId: _path.default.basename(file),
         name: _path.default.basename(file),
@@ -249,7 +273,7 @@ function readData(opts) {
             location: makeLocation(file + '.tbi')
           }
         }
-      }];
+      }]);
     }
   });
 
@@ -267,119 +291,184 @@ function readData(opts) {
   return configData;
 }
 
-async function renderRegion(opts = {}) {
-  const model = (0, _reactLinearGenomeView.createViewState)(readData(opts));
-  const {
-    loc,
-    width = 1500,
-    trackList = [],
-    session: sessionParam,
-    defaultSession
-  } = opts;
-  const {
-    session
-  } = model;
-  const {
-    view
-  } = session;
-  const {
-    assemblyManager
-  } = model;
-  view.setWidth(width);
-  await (0, _mobx.when)(() => {
-    var _assemblyManager$allP;
-
-    return ((_assemblyManager$allP = assemblyManager.allPossibleRefNames) === null || _assemblyManager$allP === void 0 ? void 0 : _assemblyManager$allP.length) && model.session.view.initialized;
-  });
-
-  if (loc) {
-    const assembly = assemblyManager.assemblies[0];
-    const 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');
-  }
-
-  function process(trackEntry, extra = () => {}) {
-    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
-          });
-        } else {
-          display.setColor(type);
-        }
-      } // force track to render even if maxbpperpx limit hit...
-      else if (opt.startsWith('force:')) {
-        const [, force] = opt.split(':');
+function renderRegion() {
+  return _renderRegion.apply(this, arguments);
+}
 
-        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;
+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 (Boolean(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');
+            }
+
+            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();
         }
-
-        display.setResolution(val);
       }
-    });
-  }
-
-  trackList.forEach(track => process(track, extra => _path.default.basename(extra)));
-  return (0, _pluginLinearGenomeView.renderToSvg)(view, {
-    rasterizeLayers: !opts.noRasterize,
-    ...opts
-  });
+    }, _callee);
+  }));
+  return _renderRegion.apply(this, arguments);
 }

package/dist/util.js

@@ -6,6 +6,8 @@ Object.defineProperty(exports, "__esModule", {
 exports.booleanize = void 0;
 
 // nice helper function from https://stackoverflow.com/questions/263965/
-const booleanize = string => string === 'false' ? false : !!string;
+var booleanize = function booleanize(string) {
+  return string === 'false' ? false : !!string;
+};
 
 exports.booleanize = booleanize;

package/package.json

@@ -1,9 +1,10 @@
 {
   "name": "@jbrowse/img",
-  "version": "1.5.8",
+  "version": "1.6.5",
   "main": "index.js",
   "author": "JBrowse Team",
   "license": "Apache-2.0",
+  "engines": ">=16",
   "bin": {
     "jb2export": "./dist/bin.js"
   },
@@ -14,7 +15,7 @@
     "pretest": "cd ../jbrowse-react-linear-genome-view; yarn build; cd ../jb2export",
     "test": "jest",
     "prebuild": "rm -rf dist",
-    "build": "babel src -d 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",
@@ -25,8 +26,8 @@
     "postversion": "git push --follow-tags"
   },
   "dependencies": {
-    "@jbrowse/plugin-linear-genome-view": "^1.5.8",
-    "@jbrowse/react-linear-genome-view": "^1.5.8",
+    "@jbrowse/plugin-linear-genome-view": "^1.6.5",
+    "@jbrowse/react-linear-genome-view": "^1.6.5",
     "mobx": "^5.10.1",
     "react": "^17.0.1",
     "react-dom": "^17.0.1",
@@ -36,5 +37,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f16afc382629a4a830f9040410a9ff1a3a328918"
+  "gitHead": "ab41f017840ffef09f5d60b008281cedaa5abe26"
 }