@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/CramAdapter/CramAdapter.js

@@ -1,660 +1,392 @@
 "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 _cram = require("@gmod/cram");
-
-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 _CramSlightlyLazyFeature = _interopRequireDefault(require("./CramSlightlyLazyFeature"));
-
-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 CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(CramAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(CramAdapter);
-
-  function CramAdapter() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, CramAdapter);
-
-    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 __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 };
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "samHeader", {});
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "setupP", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "seqIdToRefName", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "seqIdToOriginalRefName", []);
-    return _this;
-  }
-
-  (0, _createClass2.default)(CramAdapter, [{
-    key: "configure",
-    value: function () {
-      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var cramLocation, craiLocation, cram, sequenceAdapterType, seqConf, _yield$this$getSubAda, sequenceAdapter;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                cramLocation = this.getConf('cramLocation');
-                craiLocation = this.getConf('craiLocation');
-
-                if (cramLocation) {
-                  _context.next = 4;
-                  break;
-                }
-
-                throw new Error('missing cramLocation argument');
-
-              case 4:
-                if (craiLocation) {
-                  _context.next = 6;
-                  break;
-                }
-
-                throw new Error('missing craiLocation argument');
-
-              case 6:
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                cram = new _cram.IndexedCramFile({
-                  cramFilehandle: (0, _io.openLocation)(cramLocation, this.pluginManager),
-                  index: new _cram.CraiIndex({
-                    filehandle: (0, _io.openLocation)(craiLocation, this.pluginManager)
-                  }),
-                  seqFetch: this.seqFetch.bind(this),
-                  checkSequenceMD5: false,
-                  fetchSizeLimit: 200000000 // just make this a large size to avoid hitting it
-
-                }); // instantiate the sequence adapter
-
-                sequenceAdapterType = this.getConf(['sequenceAdapter', 'type']);
-
-                if (this.getSubAdapter) {
-                  _context.next = 10;
-                  break;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var cram_1 = require("@gmod/cram");
+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 CramSlightlyLazyFeature_1 = __importDefault(require("./CramSlightlyLazyFeature"));
+var CramAdapter = /** @class */ (function (_super) {
+    __extends(CramAdapter, _super);
+    function CramAdapter() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.samHeader = {};
+        // maps a seqId to original refname, passed specially to render args, to a seqid
+        _this.seqIdToOriginalRefName = [];
+        return _this;
+    }
+    CramAdapter.prototype.configure = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var cramLocation, craiLocation, cram, sequenceAdapterType, seqConf, sequenceAdapter;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        cramLocation = this.getConf('cramLocation');
+                        craiLocation = this.getConf('craiLocation');
+                        if (!cramLocation) {
+                            throw new Error('missing cramLocation argument');
+                        }
+                        if (!craiLocation) {
+                            throw new Error('missing craiLocation argument');
+                        }
+                        cram = new cram_1.IndexedCramFile({
+                            cramFilehandle: (0, io_1.openLocation)(cramLocation, this.pluginManager),
+                            index: new cram_1.CraiIndex({
+                                filehandle: (0, io_1.openLocation)(craiLocation, this.pluginManager),
+                            }),
+                            seqFetch: this.seqFetch.bind(this),
+                            checkSequenceMD5: false,
+                            fetchSizeLimit: 200000000, // just make this a large size to avoid hitting it
+                        });
+                        sequenceAdapterType = this.getConf(['sequenceAdapter', 'type']);
+                        if (!this.getSubAdapter) {
+                            throw new Error('Error getting subadapter');
+                        }
+                        seqConf = this.getConf('sequenceAdapter');
+                        return [4 /*yield*/, this.getSubAdapter(seqConf)];
+                    case 1:
+                        sequenceAdapter = (_a.sent()).dataAdapter;
+                        if (!(sequenceAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter)) {
+                            throw new Error("CRAM feature adapters cannot use sequence adapters of type '".concat(sequenceAdapterType, "'"));
+                        }
+                        return [2 /*return*/, { cram: cram, sequenceAdapter: sequenceAdapter }];
                 }
-
-                throw new Error('Error getting subadapter');
-
-              case 10:
-                seqConf = this.getConf('sequenceAdapter');
-                _context.next = 13;
-                return this.getSubAdapter(seqConf);
-
-              case 13:
-                _yield$this$getSubAda = _context.sent;
-                sequenceAdapter = _yield$this$getSubAda.dataAdapter;
-
-                if (sequenceAdapter instanceof _BaseAdapter.BaseFeatureDataAdapter) {
-                  _context.next = 17;
-                  break;
+            });
+        });
+    };
+    CramAdapter.prototype.getHeader = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var cram;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        cram = (_a.sent()).cram;
+                        return [2 /*return*/, cram.cram.getHeaderText(opts)];
                 }
-
-                throw new Error("CRAM feature adapters cannot use sequence adapters of type '".concat(sequenceAdapterType, "'"));
-
-              case 17:
-                return _context.abrupt("return", {
-                  cram: cram,
-                  sequenceAdapter: sequenceAdapter
-                });
-
-              case 18:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function configure() {
-        return _configure.apply(this, arguments);
-      }
-
-      return configure;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
-        var _yield$this$configure, cram;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure = _context2.sent;
-                cram = _yield$this$configure.cram;
-                return _context2.abrupt("return", cram.cram.getHeaderText(opts));
-
-              case 5:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getHeader(_x) {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "seqFetch",
-    value: function () {
-      var _seqFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(seqId, start, end) {
-        var _yield$this$configure2, sequenceAdapter, refName, seqChunks, sequence;
-
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                start -= 1; // convert from 1-based closed to interbase
-
-                _context3.next = 3;
-                return this.configure();
-
-              case 3:
-                _yield$this$configure2 = _context3.sent;
-                sequenceAdapter = _yield$this$configure2.sequenceAdapter;
-                refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
-
-                if (refName) {
-                  _context3.next = 8;
-                  break;
+            });
+        });
+    };
+    CramAdapter.prototype.seqFetch = function (seqId, start, end) {
+        return __awaiter(this, void 0, void 0, function () {
+            var sequenceAdapter, refName, seqChunks, sequence;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        start -= 1; // convert from 1-based closed to interbase
+                        return [4 /*yield*/, this.configure()];
+                    case 1:
+                        sequenceAdapter = (_a.sent()).sequenceAdapter;
+                        refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
+                        if (!refName) {
+                            return [2 /*return*/, undefined];
+                        }
+                        return [4 /*yield*/, sequenceAdapter
+                                .getFeatures({
+                                refName: refName,
+                                start: start,
+                                end: end,
+                                assemblyName: '',
+                            })
+                                .pipe((0, operators_1.toArray)())
+                                .toPromise()];
+                    case 2:
+                        seqChunks = _a.sent();
+                        sequence = seqChunks
+                            .sort(function (a, b) { return a.get('start') - b.get('start'); })
+                            .map(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');
+                            return chunkSeq.substr(trimStart, trimLength);
+                        })
+                            .join('');
+                        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 _context3.abrupt("return", undefined);
-
-              case 8:
-                _context3.next = 10;
-                return sequenceAdapter.getFeatures({
-                  refName: refName,
-                  start: start,
-                  end: end,
-                  assemblyName: ''
-                }).pipe((0, _operators.toArray)()).toPromise();
-
-              case 10:
-                seqChunks = _context3.sent;
-                sequence = seqChunks.sort(function (a, b) {
-                  return a.get('start') - b.get('start');
-                }).map(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');
-                  return chunkSeq.substr(trimStart, trimLength);
-                }).join('');
-
-                if (!(sequence.length !== end - start)) {
-                  _context3.next = 14;
-                  break;
+            });
+        });
+    };
+    CramAdapter.prototype.setupPre = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, statusCallback, configured, cram, samHeader, idToName, nameToId, readGroups, data;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = (opts || {}).statusCallback, statusCallback = _a === void 0 ? function () { } : _a;
+                        return [4 /*yield*/, this.configure()];
+                    case 1:
+                        configured = _b.sent();
+                        statusCallback('Downloading index');
+                        cram = configured.cram;
+                        return [4 /*yield*/, cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal)
+                            // use the @SQ lines in the header to figure out the
+                            // mapping between ref ID numbers and names
+                        ];
+                    case 2:
+                        samHeader = _b.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;
+                                }
+                            });
+                        });
+                        readGroups = samHeader
+                            .filter(function (l) { return l.tag === 'RG'; })
+                            .map(function (rgLine) { var _a; return (_a = rgLine.data.find(function (item) { return item.tag === 'ID'; })) === null || _a === void 0 ? void 0 : _a.value; });
+                        data = { idToName: idToName, nameToId: nameToId, readGroups: readGroups };
+                        statusCallback('');
+                        this.samHeader = data;
+                        return [2 /*return*/, __assign({ samHeader: data }, configured)];
                 }
-
-                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 14:
-                return _context3.abrupt("return", sequence);
-
-              case 15:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function seqFetch(_x2, _x3, _x4) {
-        return _seqFetch.apply(this, arguments);
-      }
-
-      return seqFetch;
-    }()
-  }, {
-    key: "setupPre",
-    value: function () {
-      var _setupPre = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
-        var _ref, _ref$statusCallback, statusCallback, configured, cram, samHeader, idToName, nameToId, readGroups, data;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _ref = opts || {}, _ref$statusCallback = _ref.statusCallback, statusCallback = _ref$statusCallback === void 0 ? function () {} : _ref$statusCallback;
-                _context4.next = 3;
-                return this.configure();
-
-              case 3:
-                configured = _context4.sent;
-                statusCallback('Downloading index');
-                cram = configured.cram;
-                _context4.next = 8;
-                return cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
-
-              case 8:
-                samHeader = _context4.sent;
-                // use the @SQ lines in the header to figure out the
-                // mapping between 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;
-                    }
-                  });
-                });
-                readGroups = samHeader.filter(function (l) {
-                  return l.tag === 'RG';
-                }).map(function (rgLine) {
-                  var _rgLine$data$find;
-
-                  return (_rgLine$data$find = rgLine.data.find(function (item) {
-                    return item.tag === 'ID';
-                  })) === null || _rgLine$data$find === void 0 ? void 0 : _rgLine$data$find.value;
-                });
-                data = {
-                  idToName: idToName,
-                  nameToId: nameToId,
-                  readGroups: readGroups
-                };
-                statusCallback('');
-                this.samHeader = data;
-                return _context4.abrupt("return", _objectSpread({
-                  samHeader: data
-                }, configured));
-
-              case 17:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function setupPre(_x5) {
-        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$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
+            });
+        });
+    };
+    CramAdapter.prototype.setup = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.setupP) {
-                  this.setupP = this.setupPre(opts).catch(function (e) {
-                    _this2.setupP = undefined;
-                    throw e;
-                  });
+                    this.setupP = this.setupPre(opts).catch(function (e) {
+                        _this.setupP = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context5.abrupt("return", this.setupP);
-
-              case 2:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function setup(_x6) {
-        return _setup.apply(this, arguments);
-      }
-
-      return setup;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(opts) {
-        var _yield$this$setup, samHeader;
-
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                _context6.next = 2;
-                return this.setup(opts);
-
-              case 2:
-                _yield$this$setup = _context6.sent;
-                samHeader = _yield$this$setup.samHeader;
-
-                if (samHeader.idToName) {
-                  _context6.next = 6;
-                  break;
+                return [2 /*return*/, this.setupP];
+            });
+        });
+    };
+    CramAdapter.prototype.getRefNames = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var samHeader;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.setup(opts)];
+                    case 1:
+                        samHeader = (_a.sent()).samHeader;
+                        if (!samHeader.idToName) {
+                            throw new Error('CRAM file has no header lines');
+                        }
+                        return [2 /*return*/, samHeader.idToName];
                 }
-
-                throw new Error('CRAM file has no header lines');
-
-              case 6:
-                return _context6.abrupt("return", samHeader.idToName);
-
-              case 7:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function getRefNames(_x7) {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }() // use info from the SAM header if possible, but fall back to using
+            });
+        });
+    };
+    // use info from the SAM header if possible, but fall back to using
     // the ref seq order from when the browser's refseqs were loaded
-
-  }, {
-    key: "refNameToId",
-    value: function refNameToId(refName) {
-      if (this.samHeader.nameToId) {
-        return this.samHeader.nameToId[refName];
-      }
-
-      if (this.seqIdToRefName) {
-        return this.seqIdToRefName.indexOf(refName);
-      }
-
-      return undefined;
-    } // use info from the SAM header if possible, but fall back to using
+    CramAdapter.prototype.refNameToId = function (refName) {
+        if (this.samHeader.nameToId) {
+            return this.samHeader.nameToId[refName];
+        }
+        if (this.seqIdToRefName) {
+            return this.seqIdToRefName.indexOf(refName);
+        }
+        return undefined;
+    };
+    // use info from the SAM header if possible, but fall back to using
     // the ref seq order from when the browser's refseqs were loaded
-
-  }, {
-    key: "refIdToName",
-    value: function refIdToName(refId) {
-      if (this.samHeader.idToName) {
-        return this.samHeader.idToName[refId];
-      }
-
-      if (this.seqIdToRefName) {
-        return this.seqIdToRefName[refId];
-      }
-
-      return undefined;
-    }
-  }, {
-    key: "refIdToOriginalName",
-    value: function refIdToOriginalName(refId) {
-      return this.seqIdToOriginalRefName[refId];
-    }
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(region, opts) {
-      var _this3 = this;
-
-      var _ref2 = opts || {},
-          signal = _ref2.signal,
-          filterBy = _ref2.filterBy,
-          _ref2$statusCallback = _ref2.statusCallback,
-          statusCallback = _ref2$statusCallback === void 0 ? function () {} : _ref2$statusCallback;
-
-      var refName = region.refName,
-          start = region.start,
-          end = region.end,
-          originalRefName = region.originalRefName;
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref3 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(observer) {
-          var _yield$_this3$setup, cram, sequenceAdapter, refId, records, _ref4, _ref4$flagInclude, flagInclude, _ref4$flagExclude, flagExclude, tagFilter, readName, filtered;
-
-          return _regenerator.default.wrap(function _callee7$(_context7) {
-            while (1) {
-              switch (_context7.prev = _context7.next) {
-                case 0:
-                  _context7.next = 2;
-                  return _this3.setup(opts);
-
-                case 2:
-                  _yield$_this3$setup = _context7.sent;
-                  cram = _yield$_this3$setup.cram;
-                  sequenceAdapter = _yield$_this3$setup.sequenceAdapter;
-                  statusCallback('Downloading alignments');
-
-                  if (_this3.seqIdToRefName) {
-                    _context7.next = 10;
-                    break;
-                  }
-
-                  _context7.next = 9;
-                  return sequenceAdapter.getRefNames(opts);
-
-                case 9:
-                  _this3.seqIdToRefName = _context7.sent;
-
-                case 10:
-                  refId = _this3.refNameToId(refName);
-
-                  if (!(refId !== undefined)) {
-                    _context7.next = 24;
-                    break;
-                  }
-
-                  if (originalRefName) {
-                    _this3.seqIdToOriginalRefName[refId] = originalRefName;
-                  }
-
-                  _context7.next = 15;
-                  return cram.getRecordsForRange(refId, start, end, opts);
-
-                case 15:
-                  records = _context7.sent;
-                  (0, _util.checkAbortSignal)(signal);
-                  _ref4 = filterBy || {}, _ref4$flagInclude = _ref4.flagInclude, flagInclude = _ref4$flagInclude === void 0 ? 0 : _ref4$flagInclude, _ref4$flagExclude = _ref4.flagExclude, flagExclude = _ref4$flagExclude === void 0 ? 0 : _ref4$flagExclude, tagFilter = _ref4.tagFilter, readName = _ref4.readName; // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-                  filtered = records.filter(function (record) {
-                    var flags = record.flags;
-                    return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
-                  });
-
-                  if (tagFilter) {
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    filtered = filtered.filter(function (record) {
-                      var val = record[tagFilter.tag];
-                      return val === '*' ? val !== undefined : val === tagFilter.value;
-                    });
-                  }
-
-                  if (readName) {
-                    filtered = filtered.filter( // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    function (record) {
-                      return record.readName === readName;
-                    });
-                  } // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
-                  filtered.forEach(function (record) {
-                    observer.next(_this3.cramRecordToFeature(record));
-                  });
-                  _context7.next = 25;
-                  break;
-
-                case 24:
-                  console.warn('Unknown refName', refName);
-
-                case 25:
-                  statusCallback('');
-                  observer.complete();
-
-                case 27:
-                case "end":
-                  return _context7.stop();
-              }
-            }
-          }, _callee7);
-        }));
-
-        return function (_x8) {
-          return _ref3.apply(this, arguments);
-        };
-      }(), signal);
-    }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }, {
-    key: "cramRecordToFeature",
-    value: function cramRecordToFeature(record) {
-      return new _CramSlightlyLazyFeature.default(record, this);
-    } // we return the configured fetchSizeLimit, and the bytes for the region
-
-  }, {
-    key: "estimateRegionsStats",
-    value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(regions, opts) {
-        var bytes, fetchSizeLimit;
-        return _regenerator.default.wrap(function _callee8$(_context8) {
-          while (1) {
-            switch (_context8.prev = _context8.next) {
-              case 0:
-                _context8.next = 2;
-                return this.bytesForRegions(regions, opts);
-
-              case 2:
-                bytes = _context8.sent;
-                fetchSizeLimit = this.getConf('fetchSizeLimit');
-                return _context8.abrupt("return", {
-                  bytes: bytes,
-                  fetchSizeLimit: fetchSizeLimit
-                });
-
-              case 5:
-              case "end":
-                return _context8.stop();
-            }
-          }
-        }, _callee8, this);
-      }));
-
-      function estimateRegionsStats(_x9, _x10) {
-        return _estimateRegionsStats.apply(this, arguments);
-      }
-
-      return estimateRegionsStats;
-    }()
+    CramAdapter.prototype.refIdToName = function (refId) {
+        if (this.samHeader.idToName) {
+            return this.samHeader.idToName[refId];
+        }
+        if (this.seqIdToRefName) {
+            return this.seqIdToRefName[refId];
+        }
+        return undefined;
+    };
+    CramAdapter.prototype.refIdToOriginalName = function (refId) {
+        return this.seqIdToOriginalRefName[refId];
+    };
+    CramAdapter.prototype.getFeatures = function (region, opts) {
+        var _this = this;
+        var _a = opts || {}, signal = _a.signal, filterBy = _a.filterBy, _b = _a.statusCallback, statusCallback = _b === void 0 ? function () { } : _b;
+        var refName = region.refName, start = region.start, end = region.end, originalRefName = region.originalRefName;
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var _a, cram, sequenceAdapter, _b, refId, records, _c, _d, flagInclude_1, _e, flagExclude_1, tagFilter_1, readName_1, filtered;
+            var _this = this;
+            return __generator(this, function (_f) {
+                switch (_f.label) {
+                    case 0: return [4 /*yield*/, this.setup(opts)];
+                    case 1:
+                        _a = _f.sent(), cram = _a.cram, sequenceAdapter = _a.sequenceAdapter;
+                        statusCallback('Downloading alignments');
+                        if (!!this.seqIdToRefName) return [3 /*break*/, 3];
+                        _b = this;
+                        return [4 /*yield*/, sequenceAdapter.getRefNames(opts)];
+                    case 2:
+                        _b.seqIdToRefName = _f.sent();
+                        _f.label = 3;
+                    case 3:
+                        refId = this.refNameToId(refName);
+                        if (!(refId !== undefined)) return [3 /*break*/, 5];
+                        if (originalRefName) {
+                            this.seqIdToOriginalRefName[refId] = originalRefName;
+                        }
+                        return [4 /*yield*/, cram.getRecordsForRange(refId, start, end, opts)];
+                    case 4:
+                        records = _f.sent();
+                        (0, util_1.checkAbortSignal)(signal);
+                        _c = filterBy || {}, _d = _c.flagInclude, flagInclude_1 = _d === void 0 ? 0 : _d, _e = _c.flagExclude, flagExclude_1 = _e === void 0 ? 0 : _e, tagFilter_1 = _c.tagFilter, readName_1 = _c.readName;
+                        filtered = records.filter(function (record) {
+                            var flags = record.flags;
+                            return (flags & flagInclude_1) === flagInclude_1 && !(flags & flagExclude_1);
+                        });
+                        if (tagFilter_1) {
+                            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                            filtered = filtered.filter(function (record) {
+                                var val = record[tagFilter_1.tag];
+                                return val === '*' ? val !== undefined : val === tagFilter_1.value;
+                            });
+                        }
+                        if (readName_1) {
+                            filtered = filtered.filter(
+                            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                            function (record) { return record.readName === readName_1; });
+                        }
+                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                        filtered.forEach(function (record) {
+                            observer.next(_this.cramRecordToFeature(record));
+                        });
+                        return [3 /*break*/, 6];
+                    case 5:
+                        console.warn('Unknown refName', refName);
+                        _f.label = 6;
+                    case 6:
+                        statusCallback('');
+                        observer.complete();
+                        return [2 /*return*/];
+                }
+            });
+        }); }, signal);
+    };
+    CramAdapter.prototype.freeResources = function ( /* { region } */) { };
+    CramAdapter.prototype.cramRecordToFeature = function (record) {
+        return new CramSlightlyLazyFeature_1.default(record, this);
+    };
+    // we return the configured fetchSizeLimit, and the bytes for the region
+    CramAdapter.prototype.estimateRegionsStats = function (regions, opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var bytes, fetchSizeLimit;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.bytesForRegions(regions, opts)];
+                    case 1:
+                        bytes = _a.sent();
+                        fetchSizeLimit = this.getConf('fetchSizeLimit');
+                        return [2 /*return*/, {
+                                bytes: bytes,
+                                fetchSizeLimit: fetchSizeLimit,
+                            }];
+                }
+            });
+        });
+    };
     /**
      * get the approximate number of bytes queried from the file for the given
      * query regions
      * @param regions - list of query regions
      */
-
-  }, {
-    key: "bytesForRegions",
-    value: function () {
-      var _bytesForRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee9(regions, _opts) {
-        var _this4 = this;
-
-        var _yield$this$configure3, cram, blockResults;
-
-        return _regenerator.default.wrap(function _callee9$(_context9) {
-          while (1) {
-            switch (_context9.prev = _context9.next) {
-              case 0:
-                _context9.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure3 = _context9.sent;
-                cram = _yield$this$configure3.cram;
-                _context9.next = 6;
-                return Promise.all(regions.map(function (region) {
-                  var refName = region.refName,
-                      start = region.start,
-                      end = region.end;
-
-                  var chrId = _this4.refNameToId(refName);
-
-                  return cram.index.getEntriesForRange(chrId, start, end);
-                }));
-
-              case 6:
-                blockResults = _context9.sent;
-                return _context9.abrupt("return", blockResults.flat().reduce(function (a, b) {
-                  return a + b.sliceBytes;
-                }, 0));
-
-              case 8:
-              case "end":
-                return _context9.stop();
-            }
-          }
-        }, _callee9, this);
-      }));
-
-      function bytesForRegions(_x11, _x12) {
-        return _bytesForRegions.apply(this, arguments);
-      }
-
-      return bytesForRegions;
-    }()
-  }]);
-  return CramAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = CramAdapter;
+    CramAdapter.prototype.bytesForRegions = function (regions, _opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var cram, blockResults;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        cram = (_a.sent()).cram;
+                        return [4 /*yield*/, Promise.all(regions.map(function (region) {
+                                var refName = region.refName, start = region.start, end = region.end;
+                                var chrId = _this.refNameToId(refName);
+                                return cram.index.getEntriesForRange(chrId, start, end);
+                            }))];
+                    case 2:
+                        blockResults = _a.sent();
+                        return [2 /*return*/, blockResults.flat().reduce(function (a, b) { return a + b.sliceBytes; }, 0)];
+                }
+            });
+        });
+    };
+    return CramAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = CramAdapter;
+//# sourceMappingURL=CramAdapter.js.map