@jbrowse/plugin-gtf 1.6.7 → 1.7.0

package/dist/GtfAdapter/GtfAdapter.js

@@ -0,0 +1,284 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _intervalTree = _interopRequireDefault(require("@flatten-js/interval-tree"));
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
+
+var _gtf = _interopRequireDefault(require("@gmod/gtf"));
+
+var _util = require("../util");
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+function isGzip(buf) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+
+var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(_default, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(_default);
+
+  function _default() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "gtfFeatures", void 0);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "loadDataP",
+    value: function () {
+      var _loadDataP = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var _this2 = this;
+
+        var buffer, buf, data, feats, intervalTree;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                _context.next = 2;
+                return (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'gtfLocation'), this.pluginManager).readFile();
+
+              case 2:
+                buffer = _context.sent;
+
+                if (!isGzip(buffer)) {
+                  _context.next = 9;
+                  break;
+                }
+
+                _context.next = 6;
+                return (0, _bgzfFilehandle.unzip)(buffer);
+
+              case 6:
+                _context.t0 = _context.sent;
+                _context.next = 10;
+                break;
+
+              case 9:
+                _context.t0 = buffer;
+
+              case 10:
+                buf = _context.t0;
+
+                if (!(buf.length > 536870888)) {
+                  _context.next = 13;
+                  break;
+                }
+
+                throw new Error('Data exceeds maximum string length (512MB)');
+
+              case 13:
+                data = new TextDecoder('utf8', {
+                  fatal: true
+                }).decode(buf);
+                feats = _gtf["default"].parseStringSync(data, {
+                  parseFeatures: true,
+                  parseComments: false,
+                  parseDirectives: false,
+                  parseSequences: false
+                });
+                intervalTree = feats.flat().map(function (f, i) {
+                  return new _simpleFeature["default"]({
+                    data: (0, _util.featureData)(f),
+                    id: "".concat(_this2.id, "-offset-").concat(i)
+                  });
+                }).reduce(function (acc, obj) {
+                  var key = obj.get('refName');
+
+                  if (!acc[key]) {
+                    acc[key] = new _intervalTree["default"]();
+                  }
+
+                  acc[key].insert([obj.get('start'), obj.get('end')], obj);
+                  return acc;
+                }, {});
+                return _context.abrupt("return", {
+                  intervalTree: intervalTree
+                });
+
+              case 17:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function loadDataP() {
+        return _loadDataP.apply(this, arguments);
+      }
+
+      return loadDataP;
+    }()
+  }, {
+    key: "loadData",
+    value: function () {
+      var _loadData = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var _this3 = this;
+
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                if (!this.gtfFeatures) {
+                  this.gtfFeatures = this.loadDataP()["catch"](function (e) {
+                    _this3.gtfFeatures = undefined;
+                    throw e;
+                  });
+                }
+
+                return _context2.abrupt("return", this.gtfFeatures);
+
+              case 2:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function loadData() {
+        return _loadData.apply(this, arguments);
+      }
+
+      return loadData;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+        var opts,
+            _yield$this$loadData,
+            intervalTree,
+            _args3 = arguments;
+
+        return _regenerator["default"].wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
+                _context3.next = 3;
+                return this.loadData();
+
+              case 3:
+                _yield$this$loadData = _context3.sent;
+                intervalTree = _yield$this$loadData.intervalTree;
+                return _context3.abrupt("return", Object.keys(intervalTree));
+
+              case 6:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(query) {
+      var _this4 = this;
+
+      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(observer) {
+          var _intervalTree$refName, start, end, refName, _yield$_this4$loadDat, intervalTree;
+
+          return _regenerator["default"].wrap(function _callee4$(_context4) {
+            while (1) {
+              switch (_context4.prev = _context4.next) {
+                case 0:
+                  _context4.prev = 0;
+                  start = query.start, end = query.end, refName = query.refName;
+                  _context4.next = 4;
+                  return _this4.loadData();
+
+                case 4:
+                  _yield$_this4$loadDat = _context4.sent;
+                  intervalTree = _yield$_this4$loadDat.intervalTree;
+                  (_intervalTree$refName = intervalTree[refName]) === null || _intervalTree$refName === void 0 ? void 0 : _intervalTree$refName.search([start, end]).forEach(function (f) {
+                    return observer.next(f);
+                  });
+                  observer.complete();
+                  _context4.next = 13;
+                  break;
+
+                case 10:
+                  _context4.prev = 10;
+                  _context4.t0 = _context4["catch"](0);
+                  observer.error(_context4.t0);
+
+                case 13:
+                case "end":
+                  return _context4.stop();
+              }
+            }
+          }, _callee4, null, [[0, 10]]);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return _default;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = _default;

package/dist/GtfAdapter/GtfAdapter.test.js

@@ -0,0 +1,127 @@
+"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 _operators = require("rxjs/operators");
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _GtfAdapter = _interopRequireDefault(require("./GtfAdapter"));
+
+var _webEncoding = require("web-encoding");
+
+window.TextDecoder = _webEncoding.TextDecoder;
+describe('adapter can fetch features from volvox.sorted.gtf', function () {
+  var adapter;
+  beforeEach(function () {
+    adapter = new _GtfAdapter["default"](_configSchema["default"].create({
+      gtfLocation: {
+        localPath: require.resolve('../test_data/volvox.sorted.gtf')
+      }
+    }));
+  });
+  it('test getfeatures on gtf plain text adapter', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+    var features, featuresArray, featuresJsonArray;
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            features = adapter.getFeatures({
+              refName: 'ctgA',
+              start: 0,
+              end: 100000
+            });
+            _context.t0 = expect;
+            _context.next = 4;
+            return adapter.hasDataForRefName('ctgA');
+
+          case 4:
+            _context.t1 = _context.sent;
+            (0, _context.t0)(_context.t1).toBe(true);
+            _context.t2 = expect;
+            _context.next = 9;
+            return adapter.hasDataForRefName('ctgB');
+
+          case 9:
+            _context.t3 = _context.sent;
+            (0, _context.t2)(_context.t3).toBe(false);
+            _context.next = 13;
+            return features.pipe((0, _operators.toArray)()).toPromise();
+
+          case 13:
+            featuresArray = _context.sent;
+            // There are only 4 features in ctgB
+            expect(featuresArray.length).toBe(6);
+            featuresJsonArray = featuresArray.map(function (f) {
+              return f.toJSON();
+            });
+            expect(featuresJsonArray).toMatchSnapshot();
+
+          case 17:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  })));
+});
+test('can instantiate new GtfAdapter and check for demo data', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+  var demoAdapter, features, featuresArray, featuresJsonArray;
+  return _regenerator["default"].wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          demoAdapter = new _GtfAdapter["default"](_configSchema["default"].create({
+            gtfLocation: {
+              localPath: require.resolve('../test_data/demo.gtf')
+            }
+          }));
+          _context2.t0 = expect;
+          _context2.next = 4;
+          return demoAdapter.hasDataForRefName('GeneScaffold_1');
+
+        case 4:
+          _context2.t1 = _context2.sent;
+          (0, _context2.t0)(_context2.t1).toBe(true);
+          _context2.t2 = expect;
+          _context2.next = 9;
+          return demoAdapter.hasDataForRefName('GeneScaffold_10');
+
+        case 9:
+          _context2.t3 = _context2.sent;
+          (0, _context2.t2)(_context2.t3).toBe(true);
+          _context2.t4 = expect;
+          _context2.next = 14;
+          return demoAdapter.hasDataForRefName('GeneScaffold_11');
+
+        case 14:
+          _context2.t5 = _context2.sent;
+          (0, _context2.t4)(_context2.t5).toBe(false);
+          features = demoAdapter.getFeatures({
+            refName: 'GeneScaffold_1',
+            start: 0,
+            end: 1100000
+          });
+          _context2.next = 19;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 19:
+          featuresArray = _context2.sent;
+          featuresJsonArray = featuresArray.map(function (f) {
+            return f.toJSON();
+          }); // ENSVPAT00000000407
+
+          expect(featuresArray.length).toEqual(1);
+          expect(featuresJsonArray).toMatchSnapshot();
+
+        case 23:
+        case "end":
+          return _context2.stop();
+      }
+    }
+  }, _callee2);
+})));

package/dist/GtfAdapter/configSchema.js

@@ -0,0 +1,22 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('GtfAdapter', {
+  gtfLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.gtf',
+      locationType: 'UriLocation'
+    }
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/GtfAdapter/index.js

@@ -0,0 +1,15 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema["default"];
+  }
+});
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));

package/dist/declare.d.js

@@ -0,0 +1 @@
+"use strict";

package/dist/index.js

@@ -1,8 +1,101 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-gtf.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-gtf.cjs.development.js')
-}
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _GtfAdapter = require("./GtfAdapter");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+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; }
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+var GtfPlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(GtfPlugin, _Plugin);
+
+  var _super = _createSuper(GtfPlugin);
+
+  function GtfPlugin() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, GtfPlugin);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'GTFPlugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(GtfPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'GtfAdapter',
+          configSchema: _GtfAdapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./GtfAdapter/GtfAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.gtf(\.gz)?$/i;
+          var adapterName = 'GtfAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var obj = {
+            type: adapterName,
+            gtfLocation: file
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+    }
+  }]);
+  return GtfPlugin;
+}(_Plugin2["default"]);
+
+exports["default"] = GtfPlugin;

package/dist/util.js

@@ -0,0 +1,87 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.featureData = featureData;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+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 featureData(data) {
+  var f = _objectSpread({}, data);
+
+  f.start -= 1; // convert to interbase
+
+  f.strand = {
+    '+': 1,
+    '-': -1,
+    '.': 0,
+    '?': undefined
+  }[data.strand]; // convert strand
+
+  f.phase = Number(data.frame);
+  f.refName = data.seq_name;
+
+  if (data.score === null) {
+    delete f.score;
+  }
+
+  if (data.frame === null) {
+    delete f.score;
+  }
+
+  var defaultFields = ['start', 'end', 'seq_name', 'score', 'featureType', 'source', 'frame', 'strand'];
+  Object.keys(data.attributes).forEach(function (a) {
+    var b = a.toLowerCase();
+
+    if (defaultFields.includes(b)) {
+      // add "suffix" to tag name if it already exists
+      // reproduces behavior of NCList
+      b += '2';
+    }
+
+    if (data.attributes[a] !== null) {
+      var attr = data.attributes[a];
+
+      if (Array.isArray(attr) && attr.length === 1) {
+        // gtf uses double quotes for text values in the attributes column, remove them
+        var formattedAttr = attr[0].replace(/^"|"$/g, '');
+        attr = formattedAttr;
+      }
+
+      f[b] = attr;
+    }
+  });
+  f.refName = f.seq_name;
+  f.type = f.featureType; // the SimpleFeature constructor takes care of recursively inflating subfeatures
+
+  if (data.child_features && data.child_features.length) {
+    f.subfeatures = data.child_features.map(function (childLocs) {
+      return childLocs.map(function (childLoc) {
+        return featureData(childLoc);
+      });
+    }).flat();
+  }
+
+  delete f.child_features;
+  delete f.data;
+  delete f.derived_features; // eslint-disable-next-line no-underscore-dangle
+
+  delete f._linehash;
+  delete f.attributes;
+  delete f.seq_name;
+  delete f.featureType;
+  delete f.frame;
+
+  if (f.transcript_id) {
+    f.name = f.transcript_id;
+  }
+
+  return f;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "1.6.7",
+  "version": "1.7.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,12 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-gtf.esm.js",
-  "module": "dist/plugin-gtf.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "test": "cd ../..; jest plugins/gtf --passWithNoTests",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -52,5 +49,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02012ec299c36647f755316571775d36b0fee5ec"
+  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
 }