@jbrowse/plugin-bed 1.7.11 → 2.0.0

package/dist/BedAdapter/BedAdapter.js

@@ -1,498 +1,273 @@
 "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 _bed = _interopRequireDefault(require("@gmod/bed"));
-
-var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _util = require("../util");
-
-var _intervalTree = _interopRequireDefault(require("@flatten-js/interval-tree"));
-
-var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
-
-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 __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var bed_1 = __importDefault(require("@gmod/bed"));
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var io_1 = require("@jbrowse/core/util/io");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var util_1 = require("../util");
+var interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 function isGzip(buf) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-
-var BedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(BedAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(BedAdapter);
-
-  function BedAdapter() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BedAdapter);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+var BedAdapter = /** @class */ (function (_super) {
+    __extends(BedAdapter, _super);
+    function BedAdapter() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.intervalTrees = {};
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "bedFeatures", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "intervalTrees", {});
-    return _this;
-  }
-
-  (0, _createClass2.default)(BedAdapter, [{
-    key: "loadDataP",
-    value: function () {
-      var _loadDataP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var opts,
-            pm,
-            bedLoc,
-            buf,
-            buffer,
-            data,
-            lines,
-            headerLines,
-            i,
-            header,
-            features,
-            line,
-            tab,
-            refName,
-            autoSql,
-            parser,
-            columnNames,
-            scoreColumn,
-            colRef,
-            colStart,
-            colEnd,
-            _args = arguments;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
-                pm = this.pluginManager;
-                bedLoc = this.getConf('bedLocation');
-                _context.next = 5;
-                return (0, _io.openLocation)(bedLoc, pm).readFile(opts);
-
-              case 5:
-                buf = _context.sent;
-
-                if (!isGzip(buf)) {
-                  _context.next = 12;
-                  break;
-                }
-
-                _context.next = 9;
-                return (0, _bgzfFilehandle.unzip)(buf);
-
-              case 9:
-                _context.t0 = _context.sent;
-                _context.next = 13;
-                break;
-
-              case 12:
-                _context.t0 = buf;
-
-              case 13:
-                buffer = _context.t0;
-
-                if (!(buffer.length > 536870888)) {
-                  _context.next = 16;
-                  break;
-                }
-
-                throw new Error('Data exceeds maximum string length (512MB)');
-
-              case 16:
-                data = new TextDecoder('utf8', {
-                  fatal: true
-                }).decode(buffer);
-                lines = data.split('\n').filter(function (f) {
-                  return !!f;
-                });
-                headerLines = [];
-                i = 0;
-
-                for (; i < lines.length && lines[i].startsWith('#'); i++) {
-                  headerLines.push(lines[i]);
+    BedAdapter.prototype.loadDataP = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var pm, bedLoc, buf, buffer, _a, data, lines, headerLines, i, header, features, line, tab, refName, autoSql, parser, columnNames, scoreColumn, colRef, colStart, colEnd;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        pm = this.pluginManager;
+                        bedLoc = this.getConf('bedLocation');
+                        return [4 /*yield*/, (0, io_1.openLocation)(bedLoc, pm).readFile(opts)];
+                    case 1:
+                        buf = _b.sent();
+                        if (!isGzip(buf)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buf)];
+                    case 2:
+                        _a = _b.sent();
+                        return [3 /*break*/, 4];
+                    case 3:
+                        _a = buf;
+                        _b.label = 4;
+                    case 4:
+                        buffer = _a;
+                        // 512MB  max chrome string length is 512MB
+                        if (buffer.length > 536870888) {
+                            throw new Error('Data exceeds maximum string length (512MB)');
+                        }
+                        data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+                        lines = data.split('\n').filter(function (f) { return !!f; });
+                        headerLines = [];
+                        i = 0;
+                        for (; i < lines.length && lines[i].startsWith('#'); i++) {
+                            headerLines.push(lines[i]);
+                        }
+                        header = headerLines.join('\n');
+                        features = {};
+                        for (; i < lines.length; i++) {
+                            line = lines[i];
+                            tab = line.indexOf('\t');
+                            refName = line.slice(0, tab);
+                            if (!features[refName]) {
+                                features[refName] = [];
+                            }
+                            features[refName].push(line);
+                        }
+                        autoSql = this.getConf('autoSql');
+                        parser = new bed_1.default({ autoSql: autoSql });
+                        columnNames = this.getConf('columnNames');
+                        scoreColumn = this.getConf('scoreColumn');
+                        colRef = this.getConf('colRef');
+                        colStart = this.getConf('colStart');
+                        colEnd = this.getConf('colEnd');
+                        return [2 /*return*/, {
+                                header: header,
+                                features: features,
+                                parser: parser,
+                                columnNames: columnNames,
+                                scoreColumn: scoreColumn,
+                                colRef: colRef,
+                                colStart: colStart,
+                                colEnd: colEnd,
+                            }];
                 }
-
-                header = headerLines.join('\n');
-                features = {};
-
-                for (; i < lines.length; i++) {
-                  line = lines[i];
-                  tab = line.indexOf('\t');
-                  refName = line.slice(0, tab);
-
-                  if (!features[refName]) {
-                    features[refName] = [];
-                  }
-
-                  features[refName].push(line);
-                }
-
-                autoSql = this.getConf('autoSql');
-                parser = new _bed.default({
-                  autoSql: autoSql
-                });
-                columnNames = this.getConf('columnNames');
-                scoreColumn = this.getConf('scoreColumn');
-                colRef = this.getConf('colRef');
-                colStart = this.getConf('colStart');
-                colEnd = this.getConf('colEnd');
-                return _context.abrupt("return", {
-                  header: header,
-                  features: features,
-                  parser: parser,
-                  columnNames: columnNames,
-                  scoreColumn: scoreColumn,
-                  colRef: colRef,
-                  colStart: colStart,
-                  colEnd: colEnd
-                });
-
-              case 32:
-              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 _this2 = this;
-
-        var opts,
-            _args2 = arguments;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                opts = _args2.length > 0 && _args2[0] !== undefined ? _args2[0] : {};
-
+            });
+        });
+    };
+    BedAdapter.prototype.loadData = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.bedFeatures) {
-                  this.bedFeatures = this.loadDataP(opts).catch(function (e) {
-                    _this2.bedFeatures = undefined;
-                    throw e;
-                  });
+                    this.bedFeatures = this.loadDataP(opts).catch(function (e) {
+                        _this.bedFeatures = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context2.abrupt("return", this.bedFeatures);
-
-              case 3:
-              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,
-            features,
-            _args3 = arguments;
-
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
-                _context3.next = 3;
-                return this.loadData(opts);
-
-              case 3:
-                _yield$this$loadData = _context3.sent;
-                features = _yield$this$loadData.features;
-                return _context3.abrupt("return", Object.keys(features));
-
-              case 6:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-        var opts,
-            _yield$this$loadData2,
-            header,
-            _args4 = arguments;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                opts = _args4.length > 0 && _args4[0] !== undefined ? _args4[0] : {};
-                _context4.next = 3;
-                return this.loadData(opts);
-
-              case 3:
-                _yield$this$loadData2 = _context4.sent;
-                header = _yield$this$loadData2.header;
-                return _context4.abrupt("return", header);
-
-              case 6:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "getNames",
-    value: function () {
-      var _getNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
-        var _yield$this$loadData3, header, columnNames, defs, defline;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _context5.next = 2;
-                return this.loadData();
-
-              case 2:
-                _yield$this$loadData3 = _context5.sent;
-                header = _yield$this$loadData3.header;
-                columnNames = _yield$this$loadData3.columnNames;
-
-                if (!columnNames.length) {
-                  _context5.next = 7;
-                  break;
+                return [2 /*return*/, this.bedFeatures];
+            });
+        });
+    };
+    BedAdapter.prototype.getRefNames = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var features;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.loadData(opts)];
+                    case 1:
+                        features = (_a.sent()).features;
+                        return [2 /*return*/, Object.keys(features)];
                 }
-
-                return _context5.abrupt("return", columnNames);
-
-              case 7:
-                defs = header.split('\n').filter(function (f) {
-                  return !!f;
-                });
-                defline = defs[defs.length - 1];
-                return _context5.abrupt("return", defline !== null && defline !== void 0 && defline.includes('\t') ? defline.slice(1).split('\t').map(function (field) {
-                  return field.trim();
-                }) : undefined);
-
-              case 10:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function getNames() {
-        return _getNames.apply(this, arguments);
-      }
-
-      return getNames;
-    }()
-  }, {
-    key: "loadFeatureIntervalTreeHelper",
-    value: function () {
-      var _loadFeatureIntervalTreeHelper = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(refName) {
-        var _this3 = this;
-
-        var _yield$this$loadData4, colRef, colStart, colEnd, features, parser, scoreColumn, lines, names, intervalTree, ret, i, obj;
-
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                _context6.next = 2;
-                return this.loadData();
-
-              case 2:
-                _yield$this$loadData4 = _context6.sent;
-                colRef = _yield$this$loadData4.colRef;
-                colStart = _yield$this$loadData4.colStart;
-                colEnd = _yield$this$loadData4.colEnd;
-                features = _yield$this$loadData4.features;
-                parser = _yield$this$loadData4.parser;
-                scoreColumn = _yield$this$loadData4.scoreColumn;
-                lines = features[refName];
-
-                if (lines) {
-                  _context6.next = 12;
-                  break;
+            });
+        });
+    };
+    BedAdapter.prototype.getHeader = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.loadData(opts)];
+                    case 1:
+                        header = (_a.sent()).header;
+                        return [2 /*return*/, header];
                 }
-
-                return _context6.abrupt("return", undefined);
-
-              case 12:
-                _context6.next = 14;
-                return this.getNames();
-
-              case 14:
-                names = _context6.sent;
-                intervalTree = new _intervalTree.default();
-                ret = lines.map(function (f, i) {
-                  var uniqueId = "".concat(_this3.id, "-").concat(refName, "-").concat(i);
-                  return (0, _util.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
-                });
-
-                for (i = 0; i < ret.length; i++) {
-                  obj = ret[i];
-                  intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            });
+        });
+    };
+    BedAdapter.prototype.getNames = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, header, columnNames, defs, defline;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0: return [4 /*yield*/, this.loadData()];
+                    case 1:
+                        _a = _b.sent(), header = _a.header, columnNames = _a.columnNames;
+                        if (columnNames.length) {
+                            return [2 /*return*/, columnNames];
+                        }
+                        defs = header.split('\n').filter(function (f) { return !!f; });
+                        defline = defs[defs.length - 1];
+                        return [2 /*return*/, (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+                                ? defline
+                                    .slice(1)
+                                    .split('\t')
+                                    .map(function (field) { return field.trim(); })
+                                : undefined];
                 }
-
-                return _context6.abrupt("return", intervalTree);
-
-              case 19:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function loadFeatureIntervalTreeHelper(_x) {
-        return _loadFeatureIntervalTreeHelper.apply(this, arguments);
-      }
-
-      return loadFeatureIntervalTreeHelper;
-    }()
-  }, {
-    key: "loadFeatureIntervalTree",
-    value: function () {
-      var _loadFeatureIntervalTree = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(refName) {
-        var _this4 = this;
-
-        return _regenerator.default.wrap(function _callee7$(_context7) {
-          while (1) {
-            switch (_context7.prev = _context7.next) {
-              case 0:
+            });
+        });
+    };
+    BedAdapter.prototype.loadFeatureIntervalTreeHelper = function (refName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, colRef, colStart, colEnd, features, parser, scoreColumn, lines, names, intervalTree, ret, i, obj;
+            var _this = this;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0: return [4 /*yield*/, this.loadData()];
+                    case 1:
+                        _a = _b.sent(), colRef = _a.colRef, colStart = _a.colStart, colEnd = _a.colEnd, features = _a.features, parser = _a.parser, scoreColumn = _a.scoreColumn;
+                        lines = features[refName];
+                        if (!lines) {
+                            return [2 /*return*/, undefined];
+                        }
+                        return [4 /*yield*/, this.getNames()];
+                    case 2:
+                        names = _b.sent();
+                        intervalTree = new interval_tree_1.default();
+                        ret = lines.map(function (f, i) {
+                            var uniqueId = "".concat(_this.id, "-").concat(refName, "-").concat(i);
+                            return (0, util_1.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
+                        });
+                        for (i = 0; i < ret.length; i++) {
+                            obj = ret[i];
+                            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+                        }
+                        return [2 /*return*/, intervalTree];
+                }
+            });
+        });
+    };
+    BedAdapter.prototype.loadFeatureIntervalTree = function (refName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.intervalTrees[refName]) {
-                  this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(function (e) {
-                    _this4.intervalTrees[refName] = undefined;
-                    throw e;
-                  });
+                    this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(function (e) {
+                        _this.intervalTrees[refName] = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context7.abrupt("return", this.intervalTrees[refName]);
-
-              case 2:
-              case "end":
-                return _context7.stop();
-            }
-          }
-        }, _callee7, this);
-      }));
-
-      function loadFeatureIntervalTree(_x2) {
-        return _loadFeatureIntervalTree.apply(this, arguments);
-      }
-
-      return loadFeatureIntervalTree;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(query) {
-      var _this5 = 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 _callee8(observer) {
-          var start, end, refName, intervalTree;
-          return _regenerator.default.wrap(function _callee8$(_context8) {
-            while (1) {
-              switch (_context8.prev = _context8.next) {
-                case 0:
-                  start = query.start, end = query.end, refName = query.refName;
-                  _context8.next = 3;
-                  return _this5.loadFeatureIntervalTree(refName);
-
-                case 3:
-                  intervalTree = _context8.sent;
-                  intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(function (f) {
-                    return observer.next(f);
-                  });
-                  observer.complete();
-
-                case 6:
-                case "end":
-                  return _context8.stop();
-              }
-            }
-          }, _callee8);
-        }));
-
-        return function (_x3) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
-    }
-  }, {
-    key: "freeResources",
-    value: function freeResources() {}
-  }]);
-  return BedAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
+                return [2 /*return*/, this.intervalTrees[refName]];
+            });
+        });
+    };
+    BedAdapter.prototype.getFeatures = function (query, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var start, end, refName, intervalTree;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        start = query.start, end = query.end, refName = query.refName;
+                        return [4 /*yield*/, this.loadFeatureIntervalTree(refName)];
+                    case 1:
+                        intervalTree = _a.sent();
+                        intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(function (f) { return observer.next(f); });
+                        observer.complete();
+                        return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    BedAdapter.prototype.freeResources = function () { };
+    BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
+    return BedAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
 exports.default = BedAdapter;
-(0, _defineProperty2.default)(BedAdapter, "capabilities", ['getFeatures', 'getRefNames']);
+//# sourceMappingURL=BedAdapter.js.map