@jbrowse/plugin-bed 1.7.11 → 2.1.0

package/dist/BedTabixAdapter/index.js

@@ -1,15 +1,9 @@
 "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"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/BedTabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,35 +1,19 @@
 import { BigBed } from '@gmod/bbi';
+import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-interface BEDFeature {
-    chrom: string;
-    chromStart: number;
-    chromEnd: number;
-    [key: string]: any;
-}
-interface Parser {
-    parseLine: (line: string, opts: {
-        uniqueId: string | number;
-    }) => BEDFeature;
-    autoSql: {
-        fields: {
-            name: string;
-            comment: string;
-        }[];
-    };
-}
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cached?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: any;
-        parser: Parser;
+        header: import("@gmod/bbi").Header;
+        parser: BED;
     }>;
     configure(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
         header: any;
-        parser: Parser;
+        parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<{
@@ -43,4 +27,3 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }
-export {};

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -1,341 +1,234 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
-
-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 _bbi = require("@gmod/bbi");
-
-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 _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _operators = require("rxjs/operators");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _util = require("../util");
-
-var _excluded = ["fields"],
-    _excluded2 = ["chromStart", "chromEnd", "chrom"];
-
-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 _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 __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+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 __rest = (this && this.__rest) || function (s, e) {
+    var t = {};
+    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
+        t[p] = s[p];
+    if (s != null && typeof Object.getOwnPropertySymbols === "function")
+        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
+            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
+                t[p[i]] = s[p[i]];
+        }
+    return t;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/no-explicit-any */
+var bbi_1 = require("@gmod/bbi");
+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 simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var operators_1 = require("rxjs/operators");
+var configuration_1 = require("@jbrowse/core/configuration");
+var util_1 = require("../util");
 function isUCSC(f) {
-  return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
+    return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
 }
-
-var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(BigBedAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(BigBedAdapter);
-
-  function BigBedAdapter() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BigBedAdapter);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+var BigBedAdapter = /** @class */ (function (_super) {
+    __extends(BigBedAdapter, _super);
+    function BigBedAdapter() {
+        return _super !== null && _super.apply(this, arguments) || this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "cached", void 0);
-    return _this;
-  }
-
-  (0, _createClass2.default)(BigBedAdapter, [{
-    key: "configurePre",
-    value: function () {
-      var _configurePre = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(opts) {
-        var bigbed, header, parser;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                bigbed = new _bbi.BigBed({
-                  filehandle: (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'bigBedLocation'), this.pluginManager)
-                });
-                _context.next = 3;
-                return bigbed.getHeader(opts);
-
-              case 3:
-                header = _context.sent;
-                parser = new _bed.default({
-                  autoSql: header.autoSql
-                });
-                return _context.abrupt("return", {
-                  bigbed: bigbed,
-                  header: header,
-                  parser: parser
-                });
-
-              case 6:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function configurePre(_x) {
-        return _configurePre.apply(this, arguments);
-      }
-
-      return configurePre;
-    }()
-  }, {
-    key: "configure",
-    value: function () {
-      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
-        var _this2 = this;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                if (!this.cached) {
-                  this.cached = this.configurePre(opts).catch(function (e) {
-                    _this2.cached = undefined;
-                    throw e;
-                  });
+    BigBedAdapter.prototype.configurePre = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var bigbed, header, parser;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        bigbed = new bbi_1.BigBed({
+                            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'bigBedLocation'), this.pluginManager),
+                        });
+                        return [4 /*yield*/, bigbed.getHeader(opts)];
+                    case 1:
+                        header = _a.sent();
+                        parser = new bed_1.default({ autoSql: header.autoSql });
+                        return [2 /*return*/, { bigbed: bigbed, header: header, parser: parser }];
                 }
-
-                return _context2.abrupt("return", this.cached);
-
-              case 2:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function configure(_x2) {
-        return _configure.apply(this, arguments);
-      }
-
-      return configure;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(opts) {
-        var _yield$this$configure, header;
-
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.configure(opts);
-
-              case 2:
-                _yield$this$configure = _context3.sent;
-                header = _yield$this$configure.header;
-                return _context3.abrupt("return", Object.keys(header.refsByName));
-
-              case 5:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRefNames(_x3) {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
-        var _yield$this$configure2, parser, header, version, fileType, _parser$autoSql, fields, rest;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.configure(opts);
-
-              case 2:
-                _yield$this$configure2 = _context4.sent;
-                parser = _yield$this$configure2.parser;
-                header = _yield$this$configure2.header;
-                version = header.version, fileType = header.fileType;
-                _parser$autoSql = parser.autoSql, fields = _parser$autoSql.fields, rest = (0, _objectWithoutProperties2.default)(_parser$autoSql, _excluded);
-                return _context4.abrupt("return", {
-                  version: version,
-                  fileType: fileType,
-                  autoSql: _objectSpread({}, rest),
-                  fields: Object.fromEntries(fields.map(function (_ref) {
-                    var name = _ref.name,
-                        comment = _ref.comment;
-                    return [name, comment];
-                  }))
-                });
-
-              case 8:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function getHeader(_x4) {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(region) {
-      var _this3 = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      var refName = region.refName,
-          start = region.start,
-          end = region.end;
-      var signal = opts.signal;
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(observer) {
-          var _yield$_this3$configu, parser, bigbed, ob;
-
-          return _regenerator.default.wrap(function _callee5$(_context5) {
-            while (1) {
-              switch (_context5.prev = _context5.next) {
-                case 0:
-                  _context5.prev = 0;
-                  _context5.next = 3;
-                  return _this3.configure(opts);
-
-                case 3:
-                  _yield$_this3$configu = _context5.sent;
-                  parser = _yield$_this3$configu.parser;
-                  bigbed = _yield$_this3$configu.bigbed;
-                  _context5.next = 8;
-                  return bigbed.getFeatureStream(refName, start, end, {
-                    signal: signal,
-                    basesPerSpan: end - start
-                  });
-
-                case 8:
-                  ob = _context5.sent;
-                  ob.pipe((0, _operators.mergeAll)(), (0, _operators.map)(function (r) {
-                    var data = parser.parseLine("".concat(refName, "\t").concat(r.start, "\t").concat(r.end, "\t").concat(r.rest), {
-                      uniqueId: r.uniqueId
+            });
+        });
+    };
+    BigBedAdapter.prototype.configure = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
+                if (!this.cached) {
+                    this.cached = this.configurePre(opts).catch(function (e) {
+                        _this.cached = undefined;
+                        throw e;
                     });
-                    var blockCount = data.blockCount,
-                        blockSizes = data.blockSizes,
-                        blockStarts = data.blockStarts,
-                        chromStarts = data.chromStarts;
-
-                    if (blockCount) {
-                      var starts = chromStarts || blockStarts || [];
-                      var sizes = blockSizes;
-                      var blocksOffset = r.start;
-                      data.subfeatures = [];
-
-                      for (var b = 0; b < blockCount; b += 1) {
-                        var bmin = (starts[b] || 0) + blocksOffset;
-                        var bmax = bmin + (sizes[b] || 0);
-                        data.subfeatures.push({
-                          uniqueId: "".concat(r.uniqueId, "-").concat(b),
-                          start: bmin,
-                          end: bmax,
-                          type: 'block'
-                        });
-                      }
-                    }
-
-                    if (r.uniqueId === undefined) {
-                      throw new Error('invalid bbi feature');
-                    }
-
-                    var chromStart = data.chromStart,
-                        chromEnd = data.chromEnd,
-                        chrom = data.chrom,
-                        rest = (0, _objectWithoutProperties2.default)(data, _excluded2);
-                    var f = new _simpleFeature.default({
-                      id: "".concat(_this3.id, "-").concat(r.uniqueId),
-                      data: _objectSpread(_objectSpread({}, rest), {}, {
-                        start: r.start,
-                        end: r.end,
-                        refName: refName
-                      })
-                    }); // collection of heuristics for suggesting that this feature
-                    // should be converted to a gene, CNV bigbed has many gene like
-                    // features including thickStart and blockCount but no strand
-
-                    return isUCSC(f) ? (0, _util.ucscProcessedTranscript)(f) : f;
-                  })).subscribe(observer);
-                  _context5.next = 15;
-                  break;
-
-                case 12:
-                  _context5.prev = 12;
-                  _context5.t0 = _context5["catch"](0);
-                  observer.error(_context5.t0);
-
-                case 15:
-                case "end":
-                  return _context5.stop();
-              }
-            }
-          }, _callee5, null, [[0, 12]]);
-        }));
-
-        return function (_x5) {
-          return _ref2.apply(this, arguments);
-        };
-      }(), opts.signal);
-    }
-  }, {
-    key: "freeResources",
-    value: function freeResources() {}
-  }]);
-  return BigBedAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = BigBedAdapter;
+                }
+                return [2 /*return*/, this.cached];
+            });
+        });
+    };
+    BigBedAdapter.prototype.getRefNames = function (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.configure(opts)];
+                    case 1:
+                        header = (_a.sent()).header;
+                        return [2 /*return*/, Object.keys(header.refsByName)];
+                }
+            });
+        });
+    };
+    BigBedAdapter.prototype.getHeader = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, parser, header, version, fileType, _b, fields, rest;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0: return [4 /*yield*/, this.configure(opts)];
+                    case 1:
+                        _a = _c.sent(), parser = _a.parser, header = _a.header;
+                        version = header.version, fileType = header.fileType;
+                        _b = parser.autoSql, fields = _b.fields, rest = __rest(_b, ["fields"]);
+                        return [2 /*return*/, {
+                                version: version,
+                                fileType: fileType,
+                                autoSql: __assign({}, rest),
+                                fields: Object.fromEntries(fields.map(function (_a) {
+                                    var name = _a.name, comment = _a.comment;
+                                    return [name, comment];
+                                })),
+                            }];
+                }
+            });
+        });
+    };
+    BigBedAdapter.prototype.getFeatures = function (region, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        var refName = region.refName, start = region.start, end = region.end;
+        var signal = opts.signal;
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var _a, parser_1, bigbed, ob, e_1;
+            var _this = this;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _b.trys.push([0, 3, , 4]);
+                        return [4 /*yield*/, this.configure(opts)];
+                    case 1:
+                        _a = _b.sent(), parser_1 = _a.parser, bigbed = _a.bigbed;
+                        return [4 /*yield*/, bigbed.getFeatureStream(refName, start, end, {
+                                signal: signal,
+                                basesPerSpan: end - start,
+                            })];
+                    case 2:
+                        ob = _b.sent();
+                        ob.pipe((0, operators_1.mergeAll)(), (0, operators_1.map)(function (r) {
+                            var data = parser_1.parseLine("".concat(refName, "\t").concat(r.start, "\t").concat(r.end, "\t").concat(r.rest), {
+                                uniqueId: r.uniqueId,
+                            });
+                            var blockCount = data.blockCount, blockSizes = data.blockSizes, blockStarts = data.blockStarts, chromStarts = data.chromStarts;
+                            if (blockCount) {
+                                var starts = chromStarts || blockStarts || [];
+                                var sizes = blockSizes;
+                                var blocksOffset = r.start;
+                                data.subfeatures = [];
+                                for (var b = 0; b < blockCount; b += 1) {
+                                    var bmin = (starts[b] || 0) + blocksOffset;
+                                    var bmax = bmin + (sizes[b] || 0);
+                                    data.subfeatures.push({
+                                        uniqueId: "".concat(r.uniqueId, "-").concat(b),
+                                        start: bmin,
+                                        end: bmax,
+                                        type: 'block',
+                                    });
+                                }
+                            }
+                            if (r.uniqueId === undefined) {
+                                throw new Error('invalid bbi feature');
+                            }
+                            var chromStart = data.chromStart, chromEnd = data.chromEnd, chrom = data.chrom, rest = __rest(data, ["chromStart", "chromEnd", "chrom"]);
+                            var f = new simpleFeature_1.default({
+                                id: "".concat(_this.id, "-").concat(r.uniqueId),
+                                data: __assign(__assign({}, rest), { start: r.start, end: r.end, refName: refName }),
+                            });
+                            // collection of heuristics for suggesting that this feature
+                            // should be converted to a gene, CNV bigbed has many gene like
+                            // features including thickStart and blockCount but no strand
+                            return isUCSC(f) ? (0, util_1.ucscProcessedTranscript)(f) : f;
+                        })).subscribe(observer);
+                        return [3 /*break*/, 4];
+                    case 3:
+                        e_1 = _b.sent();
+                        observer.error(e_1);
+                        return [3 /*break*/, 4];
+                    case 4: return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    BigBedAdapter.prototype.freeResources = function () { };
+    return BigBedAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = BigBedAdapter;
+//# sourceMappingURL=BigBedAdapter.js.map