@jbrowse/core 1.5.3 → 1.5.7

package/data_adapters/BaseAdapter.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -12,23 +12,19 @@ exports.isRegionsAdapter = isRegionsAdapter;
 exports.isSequenceAdapter = isSequenceAdapter;
 exports.isTextSearchAdapter = isTextSearchAdapter;
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _inherits2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/inherits.js"));
 
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+var _createSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
 
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
 var _rxjs = require("rxjs");
 
@@ -46,27 +42,21 @@ var _stats = require("../util/stats");
 
 var _idMaker = _interopRequireDefault(require("../util/idMaker"));
 
-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 BaseAdapter = function BaseAdapter() {
+var BaseAdapter = /*#__PURE__*/(0, _createClass2["default"])(function BaseAdapter() {
   var config = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : (0, _configurationSchema.ConfigurationSchema)('empty', {}).create();
   var getSubAdapter = arguments.length > 1 ? arguments[1] : undefined;
   var pluginManager = arguments.length > 2 ? arguments[2] : undefined;
-  (0, _classCallCheck2.default)(this, BaseAdapter);
-  (0, _defineProperty2.default)(this, "id", void 0);
-  (0, _defineProperty2.default)(this, "config", void 0);
-  (0, _defineProperty2.default)(this, "getSubAdapter", void 0);
-  (0, _defineProperty2.default)(this, "pluginManager", void 0);
+  (0, _classCallCheck2["default"])(this, BaseAdapter);
   this.config = config;
   this.getSubAdapter = getSubAdapter;
-  this.pluginManager = pluginManager; // note: we use switch on jest here for more simple feature IDs
-  // in test environment
+  this.pluginManager = pluginManager;
+  this.id = void 0;
 
+  // note: we use switch on jest here for more simple feature IDs
+  // in test environment
   if (typeof jest === 'undefined') {
     var data = (0, _mobxStateTree.isStateTreeNode)(config) ? (0, _mobxStateTree.getSnapshot)(config) : config;
-    this.id = "".concat((0, _idMaker.default)(data));
+    this.id = "".concat((0, _idMaker["default"])(data));
   } else {
     this.id = 'test';
   }
@@ -76,27 +66,26 @@ var BaseAdapter = function BaseAdapter() {
  * needed for the forseeable future and can be purged from caches, etc
  * @param region - Region
  */
-;
+);
 /**
  * Base class for feature adapters to extend. Defines some methods that
  * subclasses must implement.
  */
 
-
 exports.BaseAdapter = BaseAdapter;
-(0, _defineProperty2.default)(BaseAdapter, "capabilities", []);
+BaseAdapter.capabilities = [];
 
 var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2.default)(BaseFeatureDataAdapter, _BaseAdapter);
+  (0, _inherits2["default"])(BaseFeatureDataAdapter, _BaseAdapter);
 
-  var _super = _createSuper(BaseFeatureDataAdapter);
+  var _super = (0, _createSuper2["default"])(BaseFeatureDataAdapter);
 
   function BaseFeatureDataAdapter() {
-    (0, _classCallCheck2.default)(this, BaseFeatureDataAdapter);
+    (0, _classCallCheck2["default"])(this, BaseFeatureDataAdapter);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2.default)(BaseFeatureDataAdapter, [{
+  (0, _createClass2["default"])(BaseFeatureDataAdapter, [{
     key: "getHeader",
     value: // public abstract getFeatures(
     //   region: Region,
@@ -119,8 +108,8 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
      * object
      */
     function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(_opts) {
-        return _regenerator.default.wrap(function _callee$(_context) {
+      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(_opts) {
+        return _index["default"].wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -148,8 +137,8 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getMetadata",
     value: function () {
-      var _getMetadata = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(_opts) {
-        return _regenerator.default.wrap(function _callee2$(_context2) {
+      var _getMetadata = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(_opts) {
+        return _index["default"].wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -181,9 +170,9 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return (0, _rxjs2.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(observer) {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3(observer) {
           var hasData;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
+          return _index["default"].wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
                 case 0:
@@ -237,11 +226,11 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
 
-      var obs = _rxjs.merge.apply(void 0, (0, _toConsumableArray2.default)(regions.map(function (region) {
+      var obs = _rxjs.merge.apply(void 0, (0, _toConsumableArray2["default"])(regions.map(function (region) {
         return (0, _rxjs2.ObservableCreate)( /*#__PURE__*/function () {
-          var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
+          var _ref2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee4(observer) {
             var hasData;
-            return _regenerator.default.wrap(function _callee4$(_context4) {
+            return _index["default"].wrap(function _callee4$(_context4) {
               while (1) {
                 switch (_context4.prev = _context4.next) {
                   case 0:
@@ -288,11 +277,11 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "hasDataForRefName",
     value: function () {
-      var _hasDataForRefName = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(refName) {
+      var _hasDataForRefName = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee5(refName) {
         var opts,
             refNames,
             _args5 = arguments;
-        return _regenerator.default.wrap(function _callee5$(_context5) {
+        return _index["default"].wrap(function _callee5$(_context5) {
           while (1) {
             switch (_context5.prev = _context5.next) {
               case 0:
@@ -321,9 +310,9 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getRegionStats",
     value: function () {
-      var _getRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(region, opts) {
+      var _getRegionStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee6(region, opts) {
         var feats;
-        return _regenerator.default.wrap(function _callee6$(_context6) {
+        return _index["default"].wrap(function _callee6$(_context6) {
           while (1) {
             switch (_context6.prev = _context6.next) {
               case 0:
@@ -347,7 +336,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
   }, {
     key: "getMultiRegionStats",
     value: function () {
-      var _getMultiRegionStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7() {
+      var _getMultiRegionStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee7() {
         var _this3 = this;
 
         var regions,
@@ -360,7 +349,7 @@ var BaseFeatureDataAdapter = /*#__PURE__*/function (_BaseAdapter) {
             featureCount,
             basesCovered,
             _args7 = arguments;
-        return _regenerator.default.wrap(function _callee7$(_context7) {
+        return _index["default"].wrap(function _callee7$(_context7) {
           while (1) {
             switch (_context7.prev = _context7.next) {
               case 0:

package/data_adapters/BaseAdapter.test.js

@@ -1,20 +1,18 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+var _inherits2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/inherits.js"));
 
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+var _createSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
 
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
 var _operators = require("rxjs/operators");
 
@@ -26,32 +24,28 @@ var _simpleFeature = _interopRequireDefault(require("../util/simpleFeature"));
 
 var _configurationSchema = require("../configuration/configurationSchema");
 
-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; } }
-
 describe('base data adapter', function () {
-  it('properly propagates errors in feature fetching', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+  it('properly propagates errors in feature fetching', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2() {
     var Adapter, adapter, features, featuresArray;
-    return _regenerator.default.wrap(function _callee2$(_context2) {
+    return _index["default"].wrap(function _callee2$(_context2) {
       while (1) {
         switch (_context2.prev = _context2.next) {
           case 0:
             Adapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-              (0, _inherits2.default)(Adapter, _BaseFeatureDataAdapt);
+              (0, _inherits2["default"])(Adapter, _BaseFeatureDataAdapt);
 
-              var _super = _createSuper(Adapter);
+              var _super = (0, _createSuper2["default"])(Adapter);
 
               function Adapter() {
-                (0, _classCallCheck2.default)(this, Adapter);
+                (0, _classCallCheck2["default"])(this, Adapter);
                 return _super.apply(this, arguments);
               }
 
-              (0, _createClass2.default)(Adapter, [{
+              (0, _createClass2["default"])(Adapter, [{
                 key: "getRefNames",
                 value: function () {
-                  var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-                    return _regenerator.default.wrap(function _callee$(_context) {
+                  var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
+                    return _index["default"].wrap(function _callee$(_context) {
                       while (1) {
                         switch (_context.prev = _context.next) {
                           case 0:
@@ -102,27 +96,27 @@ describe('base data adapter', function () {
       }
     }, _callee2);
   })));
-  it('retrieves features', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
+  it('retrieves features', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee4() {
     var Adapter, adapter, features, featuresArray, features2, featuresArray2;
-    return _regenerator.default.wrap(function _callee4$(_context4) {
+    return _index["default"].wrap(function _callee4$(_context4) {
       while (1) {
         switch (_context4.prev = _context4.next) {
           case 0:
             Adapter = /*#__PURE__*/function (_BaseFeatureDataAdapt2) {
-              (0, _inherits2.default)(Adapter, _BaseFeatureDataAdapt2);
+              (0, _inherits2["default"])(Adapter, _BaseFeatureDataAdapt2);
 
-              var _super2 = _createSuper(Adapter);
+              var _super2 = (0, _createSuper2["default"])(Adapter);
 
               function Adapter() {
-                (0, _classCallCheck2.default)(this, Adapter);
+                (0, _classCallCheck2["default"])(this, Adapter);
                 return _super2.apply(this, arguments);
               }
 
-              (0, _createClass2.default)(Adapter, [{
+              (0, _createClass2["default"])(Adapter, [{
                 key: "getRefNames",
                 value: function () {
-                  var _getRefNames2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-                    return _regenerator.default.wrap(function _callee3$(_context3) {
+                  var _getRefNames2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3() {
+                    return _index["default"].wrap(function _callee3$(_context3) {
                       while (1) {
                         switch (_context3.prev = _context3.next) {
                           case 0:
@@ -147,7 +141,7 @@ describe('base data adapter', function () {
                 value: function getFeatures(region) {
                   return (0, _rxjs.ObservableCreate)(function (observer) {
                     if (region.refName === 'ctgA') {
-                      observer.next(new _simpleFeature.default({
+                      observer.next(new _simpleFeature["default"]({
                         uniqueId: 'testFeature',
                         start: 100,
                         end: 200

package/data_adapters/CytobandAdapter.js

@@ -1,27 +1,25 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.configSchema = exports.DataAdapter = void 0;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _slicedToArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+var _inherits2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/inherits.js"));
 
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+var _createSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
 
 var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
 
@@ -31,10 +29,6 @@ var _io = require("@jbrowse/core/util/io");
 
 var _BaseAdapter2 = require("./BaseAdapter");
 
-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 configSchema = (0, _configuration.ConfigurationSchema)('CytobandAdapter', {
   cytobandLocation: {
     type: 'fileLocation',
@@ -48,21 +42,21 @@ var configSchema = (0, _configuration.ConfigurationSchema)('CytobandAdapter', {
 exports.configSchema = configSchema;
 
 var CytobandAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2.default)(CytobandAdapter, _BaseAdapter);
+  (0, _inherits2["default"])(CytobandAdapter, _BaseAdapter);
 
-  var _super = _createSuper(CytobandAdapter);
+  var _super = (0, _createSuper2["default"])(CytobandAdapter);
 
   function CytobandAdapter() {
-    (0, _classCallCheck2.default)(this, CytobandAdapter);
+    (0, _classCallCheck2["default"])(this, CytobandAdapter);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2.default)(CytobandAdapter, [{
+  (0, _createClass2["default"])(CytobandAdapter, [{
     key: "getData",
     value: function () {
-      var _getData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+      var _getData = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
         var loc, data;
-        return _regenerator.default.wrap(function _callee$(_context) {
+        return _index["default"].wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -85,14 +79,14 @@ var CytobandAdapter = /*#__PURE__*/function (_BaseAdapter) {
                   return !!f.trim();
                 }).map(function (line) {
                   var _line$split = line.split('\t'),
-                      _line$split2 = (0, _slicedToArray2.default)(_line$split, 5),
+                      _line$split2 = (0, _slicedToArray2["default"])(_line$split, 5),
                       refName = _line$split2[0],
                       start = _line$split2[1],
                       end = _line$split2[2],
                       name = _line$split2[3],
                       type = _line$split2[4];
 
-                  return new _simpleFeature.default({
+                  return new _simpleFeature["default"]({
                     uniqueId: line,
                     refName: refName,
                     start: +start,

package/data_adapters/dataAdapterCache.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -9,16 +9,16 @@ exports.clearAdapterCache = clearAdapterCache;
 exports.freeAdapterResources = freeAdapterResources;
 exports.getAdapter = getAdapter;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _slicedToArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
 var _idMaker = _interopRequireDefault(require("../util/idMaker"));
 
 function adapterConfigCacheKey(adapterConfig) {
-  return "".concat((0, _idMaker.default)(adapterConfig));
+  return "".concat((0, _idMaker["default"])(adapterConfig));
 }
 
 var adapterCache = {};
@@ -43,9 +43,9 @@ function getAdapter(_x, _x2, _x3) {
 
 
 function _getAdapter() {
-  _getAdapter = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(pluginManager, sessionId, adapterConfigSnapshot) {
+  _getAdapter = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(pluginManager, sessionId, adapterConfigSnapshot) {
     var cacheKey, adapterType, dataAdapterType, adapterConfig, getSubAdapter, AdapterClass, getAdapterClass, CLASS, dataAdapter, cacheEntry;
-    return _regenerator.default.wrap(function _callee$(_context) {
+    return _index["default"].wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
@@ -144,11 +144,11 @@ function freeAdapterResources(specification) {
   if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
     var sessionId = specification.sessionId;
     Object.entries(adapterCache).forEach(function (_ref) {
-      var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
+      var _ref2 = (0, _slicedToArray2["default"])(_ref, 2),
           cacheKey = _ref2[0],
           cacheEntry = _ref2[1];
 
-      cacheEntry.sessionIds.delete(sessionId);
+      cacheEntry.sessionIds["delete"](sessionId);
 
       if (cacheEntry.sessionIds.size === 0) {
         deleteCount += 1;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.5.3",
+  "version": "1.5.7",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -26,11 +26,11 @@
     "clean": "rimraf dist",
     "prebuild": "yarn clean",
     "prepack": "yarn build",
-    "build": "NODE_ENV=production babel . --out-dir dist --extensions '.ts,.js,.tsx,.jsx' && cp package.json README.md ../../LICENSE dist/ && tsc",
+    "build": "NODE_ENV=production babel . --root-mode upward --out-dir dist --extensions '.ts,.js,.tsx,.jsx' && cp package.json README.md ../../LICENSE dist/ && tsc",
     "postpublish": "git push origin main --follow-tags"
   },
   "dependencies": {
-    "@babel/runtime": "^7.15.3",
+    "@babel/runtime": "^7.16.3",
     "@material-ui/icons": "^4.0.1",
     "abortable-promise-cache": "^1.1.3",
     "base64-js": "^1.3.0",
@@ -40,7 +40,7 @@
     "copy-to-clipboard": "^3.3.1",
     "deepmerge": "^4.2.2",
     "detect-node": "^2.1.0",
-    "dompurify": "^2.0.11",
+    "dompurify": "^2.3.4",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "file-uri-to-path": "^1.0.0",
@@ -54,13 +54,13 @@
     "object.fromentries": "^2.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
-    "react-intersection-observer": "^8.31.0",
+    "react-intersection-observer": "^8.32.5",
     "react-measure": "^2.3.0",
     "sanitize-filename": "^1.6.3",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0",
     "tenacious-fetch": "^2.1.0",
-    "util.promisify": "^1.0.0"
+    "util.promisify": "^1.1.1"
   },
   "peerDependencies": {
     "@material-ui/core": "^4.12.2",
@@ -78,5 +78,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "cea9023ebce8bbe5c08ae9e00c4e74fe3f02a7f1"
+  "gitHead": "b9b69276a6760ca01c7c7d905e2172b4adf9df8d"
 }

package/pluggableElementTypes/AdapterType.js

@@ -1,54 +1,47 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
-var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+var _inherits2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/inherits.js"));
 
-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 _createSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
 
 var _PluggableElementBase2 = _interopRequireDefault(require("./PluggableElementBase"));
 
-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; } }
-
+/* eslint curly:error */
 var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
-  (0, _inherits2.default)(AdapterType, _PluggableElementBase);
+  (0, _inherits2["default"])(AdapterType, _PluggableElementBase);
 
-  var _super = _createSuper(AdapterType);
+  var _super = (0, _createSuper2["default"])(AdapterType);
 
   function AdapterType(stuff) {
     var _this;
 
-    (0, _classCallCheck2.default)(this, AdapterType);
+    (0, _classCallCheck2["default"])(this, AdapterType);
     _this = _super.call(this, stuff);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "AdapterClass", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "getAdapterClass", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configSchema", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "adapterCapabilities", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "adapterMetadata", void 0);
+    _this.AdapterClass = void 0;
+    _this.getAdapterClass = void 0;
+    _this.configSchema = void 0;
+    _this.adapterCapabilities = void 0;
+    _this.adapterMetadata = void 0;
 
     if ('AdapterClass' in stuff) {
       _this.AdapterClass = stuff.AdapterClass;
-      _this.getAdapterClass = /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        return _regenerator.default.wrap(function _callee$(_context) {
+      _this.getAdapterClass = /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
+        return _index["default"].wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -73,7 +66,7 @@ var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
     return _this;
   }
 
-  return AdapterType;
-}(_PluggableElementBase2.default);
+  return (0, _createClass2["default"])(AdapterType);
+}(_PluggableElementBase2["default"]);
 
-exports.default = AdapterType;
+exports["default"] = AdapterType;