@jbrowse/plugin-alignments 1.7.11 → 2.0.0

package/dist/BamAdapter/BamAdapter.js

@@ -1,598 +1,358 @@
 "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 _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
-
-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 _bam = require("@gmod/bam");
-
-var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _util = require("@jbrowse/core/util");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _operators = require("rxjs/operators");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _BamSlightlyLazyFeature = _interopRequireDefault(require("./BamSlightlyLazyFeature"));
-
-function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
-
-function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-
-function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
-
-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 BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(BamAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(BamAdapter);
-
-  function BamAdapter() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BamAdapter);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+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 __values = (this && this.__values) || function(o) {
+    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
+    if (m) return m.call(o);
+    if (o && typeof o.length === "number") return {
+        next: function () {
+            if (o && i >= o.length) o = void 0;
+            return { value: o && o[i++], done: !o };
+        }
+    };
+    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var bam_1 = require("@gmod/bam");
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var util_1 = require("@jbrowse/core/util");
+var io_1 = require("@jbrowse/core/util/io");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var operators_1 = require("rxjs/operators");
+var configuration_1 = require("@jbrowse/core/configuration");
+var BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
+var BamAdapter = /** @class */ (function (_super) {
+    __extends(BamAdapter, _super);
+    function BamAdapter() {
+        return _super !== null && _super.apply(this, arguments) || this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "samHeader", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "setupP", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configured", void 0);
-    return _this;
-  }
-
-  (0, _createClass2.default)(BamAdapter, [{
-    key: "configure",
-    value: // derived classes may not use the same configuration so a custom
+    // derived classes may not use the same configuration so a custom
     // configure method allows derived classes to override this behavior
-    function () {
-      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var bamLocation, location, indexType, bam, adapterConfig;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
+    BamAdapter.prototype.configure = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var bamLocation, location_1, indexType, bam_2, adapterConfig;
+            return __generator(this, function (_a) {
                 if (!this.configured) {
-                  bamLocation = (0, _configuration.readConfObject)(this.config, 'bamLocation');
-                  location = (0, _configuration.readConfObject)(this.config, ['index', 'location']);
-                  indexType = (0, _configuration.readConfObject)(this.config, ['index', 'indexType']);
-                  bam = new _bam.BamFile({
-                    bamFilehandle: (0, _io.openLocation)(bamLocation, this.pluginManager),
-                    csiFilehandle: indexType === 'CSI' ? (0, _io.openLocation)(location, this.pluginManager) : undefined,
-                    baiFilehandle: indexType !== 'CSI' ? (0, _io.openLocation)(location, this.pluginManager) : undefined,
-                    // chunkSizeLimit and fetchSizeLimit are more troublesome than
-                    // helpful, and have given overly large values on the ultra long
-                    // nanopore reads even with 500MB limits, so disabled with infinity
-                    chunkSizeLimit: Infinity,
-                    fetchSizeLimit: Infinity,
-                    yieldThreadTime: Infinity
-                  });
-                  adapterConfig = (0, _configuration.readConfObject)(this.config, 'sequenceAdapter');
-
-                  if (adapterConfig && this.getSubAdapter) {
-                    this.configured = this.getSubAdapter(adapterConfig).then(function (_ref) {
-                      var dataAdapter = _ref.dataAdapter;
-                      return {
-                        bam: bam,
-                        sequenceAdapter: dataAdapter
-                      };
-                    });
-                  } else {
-                    this.configured = Promise.resolve({
-                      bam: bam
+                    bamLocation = (0, configuration_1.readConfObject)(this.config, 'bamLocation');
+                    location_1 = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
+                    indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
+                    bam_2 = new bam_1.BamFile({
+                        bamFilehandle: (0, io_1.openLocation)(bamLocation, this.pluginManager),
+                        csiFilehandle: indexType === 'CSI'
+                            ? (0, io_1.openLocation)(location_1, this.pluginManager)
+                            : undefined,
+                        baiFilehandle: indexType !== 'CSI'
+                            ? (0, io_1.openLocation)(location_1, this.pluginManager)
+                            : undefined,
+                        // chunkSizeLimit and fetchSizeLimit are more troublesome than
+                        // helpful, and have given overly large values on the ultra long
+                        // nanopore reads even with 500MB limits, so disabled with infinity
+                        chunkSizeLimit: Infinity,
+                        fetchSizeLimit: Infinity,
+                        yieldThreadTime: Infinity,
                     });
-                  }
-                }
-
-                return _context.abrupt("return", this.configured);
-
-              case 2:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function configure() {
-        return _configure.apply(this, arguments);
-      }
-
-      return configure;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
-        var _yield$this$configure, bam;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure = _context2.sent;
-                bam = _yield$this$configure.bam;
-                return _context2.abrupt("return", bam.getHeaderText(opts));
-
-              case 5:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getHeader(_x) {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "setupPre",
-    value: function () {
-      var _setupPre = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
-        var _ref2, _ref2$statusCallback, statusCallback, _yield$this$configure2, bam;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _ref2 = opts || {}, _ref2$statusCallback = _ref2.statusCallback, statusCallback = _ref2$statusCallback === void 0 ? function () {} : _ref2$statusCallback;
-                _context4.next = 3;
-                return this.configure();
-
-              case 3:
-                _yield$this$configure2 = _context4.sent;
-                bam = _yield$this$configure2.bam;
-                _context4.next = 7;
-                return (0, _util.updateStatus)('Downloading index', statusCallback, /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-                  var samHeader, idToName, nameToId;
-                  return _regenerator.default.wrap(function _callee3$(_context3) {
-                    while (1) {
-                      switch (_context3.prev = _context3.next) {
-                        case 0:
-                          _context3.next = 2;
-                          return bam.getHeader(opts);
-
-                        case 2:
-                          samHeader = _context3.sent;
-                          // use the @SQ lines in the header to figure out the
-                          // mapping between ref ref ID numbers and names
-                          idToName = [];
-                          nameToId = {};
-                          samHeader.filter(function (l) {
-                            return l.tag === 'SQ';
-                          }).forEach(function (sqLine, refId) {
-                            sqLine.data.forEach(function (item) {
-                              if (item.tag === 'SN') {
-                                // this is the ref name
-                                var refName = item.value;
-                                nameToId[refName] = refId;
-                                idToName[refId] = refName;
-                              }
+                    adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
+                    if (adapterConfig && this.getSubAdapter) {
+                        this.configured = this.getSubAdapter(adapterConfig).then(function (_a) {
+                            var dataAdapter = _a.dataAdapter;
+                            return ({
+                                bam: bam_2,
+                                sequenceAdapter: dataAdapter,
                             });
-                          });
-                          return _context3.abrupt("return", {
-                            idToName: idToName,
-                            nameToId: nameToId
-                          });
-
-                        case 7:
-                        case "end":
-                          return _context3.stop();
-                      }
+                        });
                     }
-                  }, _callee3);
-                })));
-
-              case 7:
-                this.samHeader = _context4.sent;
-                return _context4.abrupt("return", this.samHeader);
-
-              case 9:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function setupPre(_x2) {
-        return _setupPre.apply(this, arguments);
-      }
-
-      return setupPre;
-    }()
-  }, {
-    key: "setup",
-    value: function () {
-      var _setup = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(opts) {
-        var _this2 = this;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
+                    else {
+                        this.configured = Promise.resolve({ bam: bam_2 });
+                    }
+                }
+                return [2 /*return*/, this.configured];
+            });
+        });
+    };
+    BamAdapter.prototype.getHeader = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var bam;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        bam = (_a.sent()).bam;
+                        return [2 /*return*/, bam.getHeaderText(opts)];
+                }
+            });
+        });
+    };
+    BamAdapter.prototype.setupPre = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, statusCallback, bam, _b;
+            var _this = this;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        _a = (opts || {}).statusCallback, statusCallback = _a === void 0 ? function () { } : _a;
+                        return [4 /*yield*/, this.configure()];
+                    case 1:
+                        bam = (_c.sent()).bam;
+                        _b = this;
+                        return [4 /*yield*/, (0, util_1.updateStatus)('Downloading index', statusCallback, function () { return __awaiter(_this, void 0, void 0, function () {
+                                var samHeader, idToName, nameToId;
+                                return __generator(this, function (_a) {
+                                    switch (_a.label) {
+                                        case 0: return [4 /*yield*/, bam.getHeader(opts)
+                                            // use the @SQ lines in the header to figure out the
+                                            // mapping between ref ref ID numbers and names
+                                        ];
+                                        case 1:
+                                            samHeader = _a.sent();
+                                            idToName = [];
+                                            nameToId = {};
+                                            samHeader
+                                                .filter(function (l) { return l.tag === 'SQ'; })
+                                                .forEach(function (sqLine, refId) {
+                                                sqLine.data.forEach(function (item) {
+                                                    if (item.tag === 'SN') {
+                                                        // this is the ref name
+                                                        var refName = item.value;
+                                                        nameToId[refName] = refId;
+                                                        idToName[refId] = refName;
+                                                    }
+                                                });
+                                            });
+                                            return [2 /*return*/, { idToName: idToName, nameToId: nameToId }];
+                                    }
+                                });
+                            }); })];
+                    case 2:
+                        _b.samHeader = _c.sent();
+                        return [2 /*return*/, this.samHeader];
+                }
+            });
+        });
+    };
+    BamAdapter.prototype.setup = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.setupP) {
-                  this.setupP = this.setupPre(opts).catch(function (e) {
-                    _this2.setupP = undefined;
-                    throw e;
-                  });
+                    this.setupP = this.setupPre(opts).catch(function (e) {
+                        _this.setupP = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context5.abrupt("return", this.setupP);
-
-              case 2:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function setup(_x3) {
-        return _setup.apply(this, arguments);
-      }
-
-      return setup;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(opts) {
-        var _yield$this$setup, idToName;
-
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                _context6.next = 2;
-                return this.setup(opts);
-
-              case 2:
-                _yield$this$setup = _context6.sent;
-                idToName = _yield$this$setup.idToName;
-                return _context6.abrupt("return", idToName);
-
-              case 5:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function getRefNames(_x4) {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "seqFetch",
-    value: function () {
-      var _seqFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(refName, start, end) {
-        var _yield$this$configure3, sequenceAdapter, refSeqStore, features, seqChunks, sequence;
-
-        return _regenerator.default.wrap(function _callee7$(_context7) {
-          while (1) {
-            switch (_context7.prev = _context7.next) {
-              case 0:
-                _context7.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure3 = _context7.sent;
-                sequenceAdapter = _yield$this$configure3.sequenceAdapter;
-                refSeqStore = sequenceAdapter;
-
-                if (refSeqStore) {
-                  _context7.next = 7;
-                  break;
+                return [2 /*return*/, this.setupP];
+            });
+        });
+    };
+    BamAdapter.prototype.getRefNames = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var idToName;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.setup(opts)];
+                    case 1:
+                        idToName = (_a.sent()).idToName;
+                        return [2 /*return*/, idToName];
                 }
-
-                return _context7.abrupt("return", undefined);
-
-              case 7:
-                if (refName) {
-                  _context7.next = 9;
-                  break;
+            });
+        });
+    };
+    BamAdapter.prototype.seqFetch = function (refName, start, end) {
+        return __awaiter(this, void 0, void 0, function () {
+            var sequenceAdapter, refSeqStore, features, seqChunks, sequence;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        sequenceAdapter = (_a.sent()).sequenceAdapter;
+                        refSeqStore = sequenceAdapter;
+                        if (!refSeqStore) {
+                            return [2 /*return*/, undefined];
+                        }
+                        if (!refName) {
+                            return [2 /*return*/, undefined];
+                        }
+                        features = refSeqStore.getFeatures({
+                            refName: refName,
+                            start: start,
+                            end: end,
+                            assemblyName: '',
+                        });
+                        return [4 /*yield*/, features.pipe((0, operators_1.toArray)()).toPromise()];
+                    case 2:
+                        seqChunks = _a.sent();
+                        sequence = '';
+                        seqChunks
+                            .sort(function (a, b) { return a.get('start') - b.get('start'); })
+                            .forEach(function (chunk) {
+                            var chunkStart = chunk.get('start');
+                            var chunkEnd = chunk.get('end');
+                            var trimStart = Math.max(start - chunkStart, 0);
+                            var trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
+                            var trimLength = trimEnd - trimStart;
+                            var chunkSeq = chunk.get('seq') || chunk.get('residues');
+                            sequence += chunkSeq.substr(trimStart, trimLength);
+                        });
+                        if (sequence.length !== end - start) {
+                            throw new Error("sequence fetch failed: fetching ".concat(refName, ":").concat((start - 1).toLocaleString(), "-").concat(end.toLocaleString(), " returned ").concat(sequence.length.toLocaleString(), " bases, but should have returned ").concat((end - start).toLocaleString()));
+                        }
+                        return [2 /*return*/, sequence];
                 }
-
-                return _context7.abrupt("return", undefined);
-
-              case 9:
-                features = refSeqStore.getFeatures({
-                  refName: refName,
-                  start: start,
-                  end: end,
-                  assemblyName: ''
-                });
-                _context7.next = 12;
-                return features.pipe((0, _operators.toArray)()).toPromise();
-
-              case 12:
-                seqChunks = _context7.sent;
-                sequence = '';
-                seqChunks.sort(function (a, b) {
-                  return a.get('start') - b.get('start');
-                }).forEach(function (chunk) {
-                  var chunkStart = chunk.get('start');
-                  var chunkEnd = chunk.get('end');
-                  var trimStart = Math.max(start - chunkStart, 0);
-                  var trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
-                  var trimLength = trimEnd - trimStart;
-                  var chunkSeq = chunk.get('seq') || chunk.get('residues');
-                  sequence += chunkSeq.substr(trimStart, trimLength);
-                });
-
-                if (!(sequence.length !== end - start)) {
-                  _context7.next = 17;
-                  break;
+            });
+        });
+    };
+    BamAdapter.prototype.getFeatures = function (region, opts) {
+        var _this = this;
+        var refName = region.refName, start = region.start, end = region.end, originalRefName = region.originalRefName;
+        var _a = opts || {}, signal = _a.signal, filterBy = _a.filterBy, _b = _a.statusCallback, statusCallback = _b === void 0 ? function () { } : _b;
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var bam, records, _a, _b, flagInclude, _c, flagExclude, tagFilter, readName, records_1, records_1_1, record, ref, flags, val, e_1_1;
+            var e_1, _d;
+            return __generator(this, function (_e) {
+                switch (_e.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        bam = (_e.sent()).bam;
+                        return [4 /*yield*/, this.setup(opts)];
+                    case 2:
+                        _e.sent();
+                        statusCallback('Downloading alignments');
+                        return [4 /*yield*/, bam.getRecordsForRange(refName, start, end, opts)];
+                    case 3:
+                        records = _e.sent();
+                        _a = filterBy || {}, _b = _a.flagInclude, flagInclude = _b === void 0 ? 0 : _b, _c = _a.flagExclude, flagExclude = _c === void 0 ? 0 : _c, tagFilter = _a.tagFilter, readName = _a.readName;
+                        _e.label = 4;
+                    case 4:
+                        _e.trys.push([4, 10, 11, 12]);
+                        records_1 = __values(records), records_1_1 = records_1.next();
+                        _e.label = 5;
+                    case 5:
+                        if (!!records_1_1.done) return [3 /*break*/, 9];
+                        record = records_1_1.value;
+                        ref = void 0;
+                        if (!!record.get('MD')) return [3 /*break*/, 7];
+                        return [4 /*yield*/, this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'))];
+                    case 6:
+                        ref = _e.sent();
+                        _e.label = 7;
+                    case 7:
+                        flags = record.flags;
+                        if (!((flags & flagInclude) === flagInclude && !(flags & flagExclude))) {
+                            return [3 /*break*/, 8];
+                        }
+                        if (tagFilter) {
+                            val = record.get(tagFilter.tag);
+                            if (!(val === '*' ? val !== undefined : val === tagFilter.value)) {
+                                return [3 /*break*/, 8];
+                            }
+                        }
+                        if (readName && record.get('name') !== readName) {
+                            return [3 /*break*/, 8];
+                        }
+                        observer.next(new BamSlightlyLazyFeature_1.default(record, this, ref));
+                        _e.label = 8;
+                    case 8:
+                        records_1_1 = records_1.next();
+                        return [3 /*break*/, 5];
+                    case 9: return [3 /*break*/, 12];
+                    case 10:
+                        e_1_1 = _e.sent();
+                        e_1 = { error: e_1_1 };
+                        return [3 /*break*/, 12];
+                    case 11:
+                        try {
+                            if (records_1_1 && !records_1_1.done && (_d = records_1.return)) _d.call(records_1);
+                        }
+                        finally { if (e_1) throw e_1.error; }
+                        return [7 /*endfinally*/];
+                    case 12:
+                        statusCallback('');
+                        observer.complete();
+                        return [2 /*return*/];
                 }
-
-                throw new Error("sequence fetch failed: fetching ".concat(refName, ":").concat((start - 1).toLocaleString(), "-").concat(end.toLocaleString(), " returned ").concat(sequence.length.toLocaleString(), " bases, but should have returned ").concat((end - start).toLocaleString()));
-
-              case 17:
-                return _context7.abrupt("return", sequence);
-
-              case 18:
-              case "end":
-                return _context7.stop();
-            }
-          }
-        }, _callee7, this);
-      }));
-
-      function seqFetch(_x5, _x6, _x7) {
-        return _seqFetch.apply(this, arguments);
-      }
-
-      return seqFetch;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(region, opts) {
-      var _this3 = this;
-
-      var refName = region.refName,
-          start = region.start,
-          end = region.end,
-          originalRefName = region.originalRefName;
-
-      var _ref4 = opts || {},
-          signal = _ref4.signal,
-          filterBy = _ref4.filterBy,
-          _ref4$statusCallback = _ref4.statusCallback,
-          statusCallback = _ref4$statusCallback === void 0 ? function () {} : _ref4$statusCallback;
-
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref5 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(observer) {
-          var _yield$_this3$configu, bam, records, _ref6, _ref6$flagInclude, flagInclude, _ref6$flagExclude, flagExclude, tagFilter, readName, _iterator, _step, record, ref, flags, val;
-
-          return _regenerator.default.wrap(function _callee8$(_context8) {
-            while (1) {
-              switch (_context8.prev = _context8.next) {
-                case 0:
-                  _context8.next = 2;
-                  return _this3.configure();
-
-                case 2:
-                  _yield$_this3$configu = _context8.sent;
-                  bam = _yield$_this3$configu.bam;
-                  _context8.next = 6;
-                  return _this3.setup(opts);
-
-                case 6:
-                  statusCallback('Downloading alignments');
-                  _context8.next = 9;
-                  return bam.getRecordsForRange(refName, start, end, opts);
-
-                case 9:
-                  records = _context8.sent;
-                  _ref6 = filterBy || {}, _ref6$flagInclude = _ref6.flagInclude, flagInclude = _ref6$flagInclude === void 0 ? 0 : _ref6$flagInclude, _ref6$flagExclude = _ref6.flagExclude, flagExclude = _ref6$flagExclude === void 0 ? 0 : _ref6$flagExclude, tagFilter = _ref6.tagFilter, readName = _ref6.readName;
-                  _iterator = _createForOfIteratorHelper(records);
-                  _context8.prev = 12;
-
-                  _iterator.s();
-
-                case 14:
-                  if ((_step = _iterator.n()).done) {
-                    _context8.next = 33;
-                    break;
-                  }
-
-                  record = _step.value;
-                  ref = void 0;
-
-                  if (record.get('MD')) {
-                    _context8.next = 21;
-                    break;
-                  }
-
-                  _context8.next = 20;
-                  return _this3.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
-
-                case 20:
-                  ref = _context8.sent;
-
-                case 21:
-                  flags = record.flags;
-
-                  if ((flags & flagInclude) === flagInclude && !(flags & flagExclude)) {
-                    _context8.next = 24;
-                    break;
-                  }
-
-                  return _context8.abrupt("continue", 31);
-
-                case 24:
-                  if (!tagFilter) {
-                    _context8.next = 28;
-                    break;
-                  }
-
-                  val = record.get(tagFilter.tag);
-
-                  if (val === '*' ? val !== undefined : val === tagFilter.value) {
-                    _context8.next = 28;
-                    break;
-                  }
-
-                  return _context8.abrupt("continue", 31);
-
-                case 28:
-                  if (!(readName && record.get('name') !== readName)) {
-                    _context8.next = 30;
-                    break;
-                  }
-
-                  return _context8.abrupt("continue", 31);
-
-                case 30:
-                  observer.next(new _BamSlightlyLazyFeature.default(record, _this3, ref));
-
-                case 31:
-                  _context8.next = 14;
-                  break;
-
-                case 33:
-                  _context8.next = 38;
-                  break;
-
-                case 35:
-                  _context8.prev = 35;
-                  _context8.t0 = _context8["catch"](12);
-
-                  _iterator.e(_context8.t0);
-
-                case 38:
-                  _context8.prev = 38;
-
-                  _iterator.f();
-
-                  return _context8.finish(38);
-
-                case 41:
-                  statusCallback('');
-                  observer.complete();
-
-                case 43:
-                case "end":
-                  return _context8.stop();
-              }
-            }
-          }, _callee8, null, [[12, 35, 38, 41]]);
-        }));
-
-        return function (_x8) {
-          return _ref5.apply(this, arguments);
-        };
-      }(), signal);
-    }
-  }, {
-    key: "estimateRegionsStats",
-    value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee9(regions, opts) {
-        var _yield$this$configure4, bam, bytes, fetchSizeLimit;
-
-        return _regenerator.default.wrap(function _callee9$(_context9) {
-          while (1) {
-            switch (_context9.prev = _context9.next) {
-              case 0:
-                _context9.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure4 = _context9.sent;
-                bam = _yield$this$configure4.bam;
-
-                if (!(bam.index.filehandle !== '?')) {
-                  _context9.next = 12;
-                  break;
+            });
+        }); }, signal);
+    };
+    BamAdapter.prototype.estimateRegionsStats = function (regions, opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var bam, bytes, fetchSizeLimit;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()
+                        // this is a method to avoid calling on htsget adapters
+                        // @ts-ignore
+                    ];
+                    case 1:
+                        bam = (_a.sent()).bam;
+                        if (!(bam.index.filehandle !== '?')) return [3 /*break*/, 3];
+                        return [4 /*yield*/, (0, util_1.bytesForRegions)(regions, bam)];
+                    case 2:
+                        bytes = _a.sent();
+                        fetchSizeLimit = (0, configuration_1.readConfObject)(this.config, 'fetchSizeLimit');
+                        return [2 /*return*/, { bytes: bytes, fetchSizeLimit: fetchSizeLimit }];
+                    case 3: return [2 /*return*/, _super.prototype.estimateRegionsStats.call(this, regions, opts)];
                 }
-
-                _context9.next = 7;
-                return (0, _util.bytesForRegions)(regions, bam);
-
-              case 7:
-                bytes = _context9.sent;
-                fetchSizeLimit = (0, _configuration.readConfObject)(this.config, 'fetchSizeLimit');
-                return _context9.abrupt("return", {
-                  bytes: bytes,
-                  fetchSizeLimit: fetchSizeLimit
-                });
-
-              case 12:
-                return _context9.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(BamAdapter.prototype), "estimateRegionsStats", this).call(this, regions, opts));
-
-              case 13:
-              case "end":
-                return _context9.stop();
-            }
-          }
-        }, _callee9, this);
-      }));
-
-      function estimateRegionsStats(_x9, _x10) {
-        return _estimateRegionsStats.apply(this, arguments);
-      }
-
-      return estimateRegionsStats;
-    }()
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {} // depends on setup being called before the BAM constructor
-
-  }, {
-    key: "refIdToName",
-    value: function refIdToName(refId) {
-      var _this$samHeader;
-
-      return (_this$samHeader = this.samHeader) === null || _this$samHeader === void 0 ? void 0 : _this$samHeader.idToName[refId];
-    }
-  }]);
-  return BamAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = BamAdapter;
+            });
+        });
+    };
+    BamAdapter.prototype.freeResources = function ( /* { region } */) { };
+    // depends on setup being called before the BAM constructor
+    BamAdapter.prototype.refIdToName = function (refId) {
+        var _a;
+        return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];
+    };
+    return BamAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = BamAdapter;
+//# sourceMappingURL=BamAdapter.js.map