@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -1,602 +1,452 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = exports.capabilities = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-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 _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _operators = require("rxjs/operators");
-
-var _util = require("../util");
-
-var _MismatchParser = require("../BamAdapter/MismatchParser");
-
-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 __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 __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+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 });
+exports.capabilities = void 0;
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var operators_1 = require("rxjs/operators");
+var util_1 = require("../util");
+var MismatchParser_1 = require("../BamAdapter/MismatchParser");
 function mismatchLen(mismatch) {
-  return !isInterbase(mismatch.type) ? mismatch.length : 1;
+    return !isInterbase(mismatch.type) ? mismatch.length : 1;
 }
-
 function isInterbase(type) {
-  return type === 'softclip' || type === 'hardclip' || type === 'insertion';
-} // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
+    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function inc(bin, strand, type, field) {
-  var thisBin = bin[type][field];
-
-  if (thisBin === undefined) {
-    thisBin = bin[type][field] = {
-      total: 0,
-      '-1': 0,
-      '0': 0,
-      '1': 0
-    };
-  }
-
-  thisBin.total++;
-  thisBin[strand]++;
+    var thisBin = bin[type][field];
+    if (thisBin === undefined) {
+        thisBin = bin[type][field] = {
+            total: 0,
+            '-1': 0,
+            '0': 0,
+            '1': 0,
+        };
+    }
+    thisBin.total++;
+    thisBin[strand]++;
 }
-
-var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(SNPCoverageAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(SNPCoverageAdapter);
-
-  function SNPCoverageAdapter() {
-    (0, _classCallCheck2.default)(this, SNPCoverageAdapter);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(SNPCoverageAdapter, [{
-    key: "configure",
-    value: function () {
-      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var _this$getSubAdapter, _this$getSubAdapter2;
-
-        var subadapterConfig, sequenceConf, dataAdapter, sequenceAdapter;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                subadapterConfig = this.getConf('subadapter');
-                sequenceConf = this.getConf(['subadapter', 'sequenceAdapter']);
-                _context.next = 4;
-                return (_this$getSubAdapter = this.getSubAdapter) === null || _this$getSubAdapter === void 0 ? void 0 : _this$getSubAdapter.call(this, subadapterConfig);
-
-              case 4:
-                dataAdapter = _context.sent;
-
-                if (!sequenceConf) {
-                  _context.next = 11;
-                  break;
+var SNPCoverageAdapter = /** @class */ (function (_super) {
+    __extends(SNPCoverageAdapter, _super);
+    function SNPCoverageAdapter() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    SNPCoverageAdapter.prototype.configure = function () {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function () {
+            var subadapterConfig, sequenceConf, dataAdapter, sequenceAdapter, _c;
+            return __generator(this, function (_d) {
+                switch (_d.label) {
+                    case 0:
+                        subadapterConfig = this.getConf('subadapter');
+                        sequenceConf = this.getConf(['subadapter', 'sequenceAdapter']);
+                        return [4 /*yield*/, ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, subadapterConfig))];
+                    case 1:
+                        dataAdapter = _d.sent();
+                        if (!sequenceConf) return [3 /*break*/, 3];
+                        return [4 /*yield*/, ((_b = this.getSubAdapter) === null || _b === void 0 ? void 0 : _b.call(this, sequenceConf))];
+                    case 2:
+                        _c = _d.sent();
+                        return [3 /*break*/, 4];
+                    case 3:
+                        _c = undefined;
+                        _d.label = 4;
+                    case 4:
+                        sequenceAdapter = _c;
+                        if (!dataAdapter) {
+                            throw new Error('Failed to get subadapter');
+                        }
+                        return [2 /*return*/, {
+                                subadapter: dataAdapter.dataAdapter,
+                                sequenceAdapter: sequenceAdapter === null || sequenceAdapter === void 0 ? void 0 : sequenceAdapter.dataAdapter,
+                            }];
                 }
-
-                _context.next = 8;
-                return (_this$getSubAdapter2 = this.getSubAdapter) === null || _this$getSubAdapter2 === void 0 ? void 0 : _this$getSubAdapter2.call(this, sequenceConf);
-
-              case 8:
-                _context.t0 = _context.sent;
-                _context.next = 12;
-                break;
-
-              case 11:
-                _context.t0 = undefined;
-
-              case 12:
-                sequenceAdapter = _context.t0;
-
-                if (dataAdapter) {
-                  _context.next = 15;
-                  break;
+            });
+        });
+    };
+    SNPCoverageAdapter.prototype.fetchSequence = function (region) {
+        return __awaiter(this, void 0, void 0, function () {
+            var sequenceAdapter;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        sequenceAdapter = (_a.sent()).sequenceAdapter;
+                        if (!sequenceAdapter) {
+                            return [2 /*return*/, undefined];
+                        }
+                        return [2 /*return*/, (0, util_1.fetchSequence)(region, sequenceAdapter)];
                 }
-
-                throw new Error('Failed to get subadapter');
-
-              case 15:
-                return _context.abrupt("return", {
-                  subadapter: dataAdapter.dataAdapter,
-                  sequenceAdapter: sequenceAdapter === null || sequenceAdapter === void 0 ? void 0 : sequenceAdapter.dataAdapter
-                });
-
-              case 16:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function configure() {
-        return _configure.apply(this, arguments);
-      }
-
-      return configure;
-    }()
-  }, {
-    key: "fetchSequence",
-    value: function () {
-      var _fetchSequence2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(region) {
-        var _yield$this$configure, sequenceAdapter;
-
-        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$configure = _context2.sent;
-                sequenceAdapter = _yield$this$configure.sequenceAdapter;
-
-                if (sequenceAdapter) {
-                  _context2.next = 6;
-                  break;
+            });
+        });
+    };
+    SNPCoverageAdapter.prototype.getFeatures = function (region, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var subadapter, feats, _a, bins, skipmap;
+            var _this = this;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        subadapter = (_b.sent()).subadapter;
+                        return [4 /*yield*/, subadapter
+                                .getFeatures(region, opts)
+                                .pipe((0, operators_1.toArray)())
+                                .toPromise()];
+                    case 2:
+                        feats = _b.sent();
+                        return [4 /*yield*/, this.generateCoverageBins(feats, region, opts)];
+                    case 3:
+                        _a = _b.sent(), bins = _a.bins, skipmap = _a.skipmap;
+                        bins.forEach(function (bin, index) {
+                            observer.next(new simpleFeature_1.default({
+                                id: "".concat(_this.id, "-").concat(region.start + index),
+                                data: {
+                                    score: bin.total,
+                                    snpinfo: bin,
+                                    start: region.start + index,
+                                    end: region.start + index + 1,
+                                    refName: region.refName,
+                                },
+                            }));
+                        });
+                        // make fake features from the coverage
+                        Object.entries(skipmap).forEach(function (_a) {
+                            var _b = __read(_a, 2), key = _b[0], skip = _b[1];
+                            observer.next(new simpleFeature_1.default({
+                                id: key,
+                                data: {
+                                    type: 'skip',
+                                    start: skip.start,
+                                    end: skip.end,
+                                    strand: skip.strand,
+                                    score: skip.score,
+                                    xs: skip.xs,
+                                },
+                            }));
+                        });
+                        observer.complete();
+                        return [2 /*return*/];
                 }
-
-                return _context2.abrupt("return", undefined);
-
-              case 6:
-                return _context2.abrupt("return", (0, _util.fetchSequence)(region, sequenceAdapter));
-
-              case 7:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function fetchSequence(_x) {
-        return _fetchSequence2.apply(this, arguments);
-      }
-
-      return fetchSequence;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(region) {
-      var _this = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(observer) {
-          var _yield$_this$configur, subadapter, feats, _yield$_this$generate, bins, skipmap;
-
-          return _regenerator.default.wrap(function _callee3$(_context3) {
-            while (1) {
-              switch (_context3.prev = _context3.next) {
-                case 0:
-                  _context3.next = 2;
-                  return _this.configure();
-
-                case 2:
-                  _yield$_this$configur = _context3.sent;
-                  subadapter = _yield$_this$configur.subadapter;
-                  _context3.next = 6;
-                  return subadapter.getFeatures(region, opts).pipe((0, _operators.toArray)()).toPromise();
-
-                case 6:
-                  feats = _context3.sent;
-                  _context3.next = 9;
-                  return _this.generateCoverageBins(feats, region, opts);
-
-                case 9:
-                  _yield$_this$generate = _context3.sent;
-                  bins = _yield$_this$generate.bins;
-                  skipmap = _yield$_this$generate.skipmap;
-                  bins.forEach(function (bin, index) {
-                    observer.next(new _simpleFeature.default({
-                      id: "".concat(_this.id, "-").concat(region.start + index),
-                      data: {
-                        score: bin.total,
-                        snpinfo: bin,
-                        start: region.start + index,
-                        end: region.start + index + 1,
-                        refName: region.refName
-                      }
-                    }));
-                  }); // make fake features from the coverage
-
-                  Object.entries(skipmap).forEach(function (_ref2) {
-                    var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
-                        key = _ref3[0],
-                        skip = _ref3[1];
-
-                    observer.next(new _simpleFeature.default({
-                      id: key,
-                      data: {
-                        type: 'skip',
-                        start: skip.start,
-                        end: skip.end,
-                        strand: skip.strand,
-                        score: skip.score,
-                        xs: skip.xs
-                      }
-                    }));
-                  });
-                  observer.complete();
-
-                case 15:
-                case "end":
-                  return _context3.stop();
-              }
-            }
-          }, _callee3);
-        }));
-
-        return function (_x2) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
-    }
-  }, {
-    key: "estimateRegionsStats",
-    value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(regions, opts) {
-        var _yield$this$configure2, subadapter;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure2 = _context4.sent;
-                subadapter = _yield$this$configure2.subadapter;
-                return _context4.abrupt("return", subadapter.estimateRegionsStats(regions, opts));
-
-              case 5:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function estimateRegionsStats(_x3, _x4) {
-        return _estimateRegionsStats.apply(this, arguments);
-      }
-
-      return estimateRegionsStats;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
-        var opts,
-            _yield$this$configure3,
-            subadapter,
-            _args5 = arguments;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                opts = _args5.length > 0 && _args5[0] !== undefined ? _args5[0] : {};
-                _context5.next = 3;
-                return this.configure();
-
-              case 3:
-                _yield$this$configure3 = _context5.sent;
-                subadapter = _yield$this$configure3.subadapter;
-                return _context5.abrupt("return", subadapter.getRefNames(opts));
-
-              case 6:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }, {
-    key: "generateCoverageBins",
-    value: function () {
-      var _generateCoverageBins = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(features, region, opts) {
-        var _opts$colorBy;
-
-        var colorBy, binMax, skipmap, regionSeq, bins, _loop, i;
-
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                colorBy = opts.colorBy;
-                binMax = Math.ceil(region.end - region.start);
-                skipmap = {}; // bins contain:
-                // - cov feature if they contribute to coverage
-                // - noncov are insertions/clip features that don't contribute to coverage
-                // - delskips deletions or introns that don't contribute to coverage
-
-                if (!(features.length && (0, _util.shouldFetchReferenceSequence)((_opts$colorBy = opts.colorBy) === null || _opts$colorBy === void 0 ? void 0 : _opts$colorBy.type))) {
-                  _context6.next = 9;
-                  break;
+            });
+        }); }, opts.signal);
+    };
+    SNPCoverageAdapter.prototype.estimateRegionsStats = function (regions, opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var subadapter;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        subadapter = (_a.sent()).subadapter;
+                        return [2 /*return*/, subadapter.estimateRegionsStats(regions, opts)];
                 }
-
-                _context6.next = 6;
-                return this.fetchSequence(region);
-
-              case 6:
-                _context6.t0 = _context6.sent;
-                _context6.next = 10;
-                break;
-
-              case 9:
-                _context6.t0 = undefined;
-
-              case 10:
-                regionSeq = _context6.t0;
-                bins = [];
-
-                _loop = function _loop(i) {
-                  var feature = features[i];
-                  var fstart = feature.get('start');
-                  var fend = feature.get('end');
-                  var fstrand = feature.get('strand');
-
-                  for (var j = fstart; j < fend + 1; j++) {
-                    var _i = j - region.start;
-
-                    if (_i >= 0 && _i < binMax) {
-                      if (bins[_i] === undefined) {
-                        bins[_i] = {
-                          total: 0,
-                          ref: 0,
-                          '-1': 0,
-                          '0': 0,
-                          '1': 0,
-                          lowqual: {},
-                          cov: {},
-                          delskips: {},
-                          noncov: {}
-                        };
-                      }
-
-                      if (j !== fend) {
-                        bins[_i].total++;
-                        bins[_i].ref++;
-                        bins[_i][fstrand]++;
-                      }
-                    }
-                  }
-
-                  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                    var seq = feature.get('seq');
-                    var mm = (0, _util.getTagAlt)(feature, 'MM', 'Mm') || '';
-                    var ops = (0, _MismatchParser.parseCigar)(feature.get('CIGAR'));
-
-                    var _fend = feature.get('end');
-
-                    (0, _MismatchParser.getModificationPositions)(mm, seq, fstrand).forEach(function (_ref4) {
-                      var type = _ref4.type,
-                          positions = _ref4.positions;
-                      var mod = "mod_".concat(type);
-
-                      var _iterator = _createForOfIteratorHelper((0, _MismatchParser.getNextRefPos)(ops, positions)),
-                          _step;
-
-                      try {
-                        for (_iterator.s(); !(_step = _iterator.n()).done;) {
-                          var pos = _step.value;
-                          var epos = pos + fstart - region.start;
-
-                          if (epos >= 0 && epos < bins.length && pos + fstart < _fend) {
-                            var bin = bins[epos];
-
-                            if (bin) {
-                              inc(bin, fstrand, 'cov', mod);
-                            } else {
-                              console.warn('Undefined position in modifications snpcoverage encountered');
+            });
+        });
+    };
+    SNPCoverageAdapter.prototype.getRefNames = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var subadapter;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        subadapter = (_a.sent()).subadapter;
+                        return [2 /*return*/, subadapter.getRefNames(opts)];
+                }
+            });
+        });
+    };
+    SNPCoverageAdapter.prototype.freeResources = function ( /* { region } */) { };
+    SNPCoverageAdapter.prototype.generateCoverageBins = function (features, region, opts) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function () {
+            var colorBy, binMax, skipmap, regionSeq, _b, bins, _loop_1, i;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        colorBy = opts.colorBy;
+                        binMax = Math.ceil(region.end - region.start);
+                        skipmap = {};
+                        if (!(features.length && (0, util_1.shouldFetchReferenceSequence)((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type))) return [3 /*break*/, 2];
+                        return [4 /*yield*/, this.fetchSequence(region)];
+                    case 1:
+                        _b = _c.sent();
+                        return [3 /*break*/, 3];
+                    case 2:
+                        _b = undefined;
+                        _c.label = 3;
+                    case 3:
+                        regionSeq = _b;
+                        bins = [];
+                        _loop_1 = function (i) {
+                            var feature = features[i];
+                            var fstart = feature.get('start');
+                            var fend = feature.get('end');
+                            var fstrand = feature.get('strand');
+                            for (var j = fstart; j < fend + 1; j++) {
+                                var i_1 = j - region.start;
+                                if (i_1 >= 0 && i_1 < binMax) {
+                                    if (bins[i_1] === undefined) {
+                                        bins[i_1] = {
+                                            total: 0,
+                                            all: 0,
+                                            ref: 0,
+                                            '-1': 0,
+                                            '0': 0,
+                                            '1': 0,
+                                            lowqual: {},
+                                            cov: {},
+                                            delskips: {},
+                                            noncov: {},
+                                        };
+                                    }
+                                    if (j !== fend) {
+                                        bins[i_1].total++;
+                                        bins[i_1].all++;
+                                        bins[i_1].ref++;
+                                        bins[i_1][fstrand]++;
+                                    }
+                                }
                             }
-                          }
-                        }
-                      } catch (err) {
-                        _iterator.e(err);
-                      } finally {
-                        _iterator.f();
-                      }
-                    });
-                  } // methylation based coloring takes into account both reference
-                  // sequence CpG detection and reads
-                  else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-                    if (!regionSeq) {
-                      throw new Error('no region sequence detected, need sequenceAdapter configuration');
-                    }
-
-                    var _seq = feature.get('seq');
-
-                    var _mm = (0, _util.getTagAlt)(feature, 'MM', 'Mm') || '';
-
-                    var methBins = new Array(region.end - region.start).fill(0);
-
-                    var _ops = (0, _MismatchParser.parseCigar)(feature.get('CIGAR'));
-
-                    (0, _MismatchParser.getModificationPositions)(_mm, _seq, fstrand).forEach(function (_ref5) {
-                      var type = _ref5.type,
-                          positions = _ref5.positions;
-
-                      // we are processing methylation
-                      if (type === 'm') {
-                        var _iterator2 = _createForOfIteratorHelper((0, _MismatchParser.getNextRefPos)(_ops, positions)),
-                            _step2;
-
-                        try {
-                          for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
-                            var pos = _step2.value;
-                            var epos = pos + fstart - region.start;
-
-                            if (epos >= 0 && epos < methBins.length) {
-                              methBins[epos] = 1;
+                            if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                                var seq = feature.get('seq');
+                                var mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+                                var ops_1 = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+                                var fend_1 = feature.get('end');
+                                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(function (_a) {
+                                    var e_1, _b;
+                                    var type = _a.type, positions = _a.positions;
+                                    var mod = "mod_".concat(type);
+                                    try {
+                                        for (var _c = (e_1 = void 0, __values((0, MismatchParser_1.getNextRefPos)(ops_1, positions))), _d = _c.next(); !_d.done; _d = _c.next()) {
+                                            var pos = _d.value;
+                                            var epos = pos + fstart - region.start;
+                                            if (epos >= 0 && epos < bins.length && pos + fstart < fend_1) {
+                                                var bin = bins[epos];
+                                                if (bin) {
+                                                    inc(bin, fstrand, 'cov', mod);
+                                                }
+                                                else {
+                                                    console.warn('Undefined position in modifications snpcoverage encountered');
+                                                }
+                                            }
+                                        }
+                                    }
+                                    catch (e_1_1) { e_1 = { error: e_1_1 }; }
+                                    finally {
+                                        try {
+                                            if (_d && !_d.done && (_b = _c.return)) _b.call(_c);
+                                        }
+                                        finally { if (e_1) throw e_1.error; }
+                                    }
+                                });
+                            }
+                            // methylation based coloring takes into account both reference
+                            // sequence CpG detection and reads
+                            else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
+                                if (!regionSeq) {
+                                    throw new Error('no region sequence detected, need sequenceAdapter configuration');
+                                }
+                                var seq = feature.get('seq');
+                                var mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+                                var methBins_1 = new Array(region.end - region.start).fill(0);
+                                var ops_2 = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+                                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(function (_a) {
+                                    var e_2, _b;
+                                    var type = _a.type, positions = _a.positions;
+                                    // we are processing methylation
+                                    if (type === 'm') {
+                                        try {
+                                            for (var _c = (e_2 = void 0, __values((0, MismatchParser_1.getNextRefPos)(ops_2, positions))), _d = _c.next(); !_d.done; _d = _c.next()) {
+                                                var pos = _d.value;
+                                                var epos = pos + fstart - region.start;
+                                                if (epos >= 0 && epos < methBins_1.length) {
+                                                    methBins_1[epos] = 1;
+                                                }
+                                            }
+                                        }
+                                        catch (e_2_1) { e_2 = { error: e_2_1 }; }
+                                        finally {
+                                            try {
+                                                if (_d && !_d.done && (_b = _c.return)) _b.call(_c);
+                                            }
+                                            finally { if (e_2) throw e_2.error; }
+                                        }
+                                    }
+                                });
+                                for (var j = fstart; j < fend; j++) {
+                                    var i_2 = j - region.start;
+                                    if (i_2 >= 0 && i_2 < bins.length - 1) {
+                                        var l1 = regionSeq[i_2].toLowerCase();
+                                        var l2 = regionSeq[i_2 + 1].toLowerCase();
+                                        var bin = bins[i_2];
+                                        var bin1 = bins[i_2 + 1];
+                                        // color
+                                        if (l1 === 'c' && l2 === 'g') {
+                                            if (methBins_1[i_2] || methBins_1[i_2 + 1]) {
+                                                inc(bin, fstrand, 'cov', 'meth');
+                                                inc(bin1, fstrand, 'cov', 'meth');
+                                                bins[i_2].ref--;
+                                                bins[i_2][fstrand]--;
+                                                bins[i_2 + 1].ref--;
+                                                bins[i_2 + 1][fstrand]--;
+                                            }
+                                            else {
+                                                inc(bin, fstrand, 'cov', 'unmeth');
+                                                inc(bin1, fstrand, 'cov', 'unmeth');
+                                                bins[i_2].ref--;
+                                                bins[i_2][fstrand]--;
+                                                bins[i_2 + 1].ref--;
+                                                bins[i_2 + 1][fstrand]--;
+                                            }
+                                        }
+                                    }
+                                }
+                            }
+                            // normal SNP based coloring
+                            var mismatches = feature.get('mismatches') || [];
+                            var colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
+                            for (var i_3 = 0; i_3 < mismatches.length; i_3++) {
+                                var mismatch = mismatches[i_3];
+                                var mstart = fstart + mismatch.start;
+                                var mlen = mismatchLen(mismatch);
+                                var mend = mstart + mlen;
+                                for (var j = mstart; j < mstart + mlen; j++) {
+                                    var epos = j - region.start;
+                                    if (epos >= 0 && epos < bins.length) {
+                                        var bin = bins[epos];
+                                        var base = mismatch.base, type = mismatch.type;
+                                        var interbase = isInterbase(type);
+                                        if (!interbase) {
+                                            bin.ref--;
+                                            bin[fstrand]--;
+                                        }
+                                        else {
+                                            inc(bin, fstrand, 'noncov', type);
+                                        }
+                                        if (type === 'deletion' || type === 'skip') {
+                                            inc(bin, fstrand, 'delskips', type);
+                                            bin.total--;
+                                        }
+                                        else if (!interbase && colorSNPs) {
+                                            inc(bin, fstrand, 'cov', base);
+                                            bin.refbase = mismatch.altbase;
+                                        }
+                                    }
+                                }
+                                if (mismatch.type === 'skip') {
+                                    var hash = "".concat(mstart, "_").concat(mend, "_").concat(fstrand);
+                                    if (skipmap[hash] === undefined) {
+                                        skipmap[hash] = {
+                                            feature: feature,
+                                            start: mstart,
+                                            end: mend,
+                                            strand: fstrand,
+                                            xs: (0, util_1.getTag)(feature, 'XS') || (0, util_1.getTag)(feature, 'TS'),
+                                            score: 0,
+                                        };
+                                    }
+                                    skipmap[hash].score++;
+                                }
                             }
-                          }
-                        } catch (err) {
-                          _iterator2.e(err);
-                        } finally {
-                          _iterator2.f();
-                        }
-                      }
-                    });
-
-                    for (var _j = fstart; _j < fend; _j++) {
-                      var _i2 = _j - region.start;
-
-                      if (_i2 >= 0 && _i2 < bins.length - 1) {
-                        var l1 = regionSeq[_i2].toLowerCase();
-
-                        var l2 = regionSeq[_i2 + 1].toLowerCase();
-
-                        var bin = bins[_i2];
-                        var bin1 = bins[_i2 + 1]; // color
-
-                        if (l1 === 'c' && l2 === 'g') {
-                          if (methBins[_i2] || methBins[_i2 + 1]) {
-                            inc(bin, fstrand, 'cov', 'meth');
-                            inc(bin1, fstrand, 'cov', 'meth');
-                            bins[_i2].ref--;
-                            bins[_i2][fstrand]--;
-                            bins[_i2 + 1].ref--;
-                            bins[_i2 + 1][fstrand]--;
-                          } else {
-                            inc(bin, fstrand, 'cov', 'unmeth');
-                            inc(bin1, fstrand, 'cov', 'unmeth');
-                            bins[_i2].ref--;
-                            bins[_i2][fstrand]--;
-                            bins[_i2 + 1].ref--;
-                            bins[_i2 + 1][fstrand]--;
-                          }
-                        }
-                      }
-                    }
-                  } // normal SNP based coloring
-
-
-                  var mismatches = feature.get('mismatches') || [];
-                  var colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
-
-                  for (var _i3 = 0; _i3 < mismatches.length; _i3++) {
-                    var mismatch = mismatches[_i3];
-                    var mstart = fstart + mismatch.start;
-                    var mlen = mismatchLen(mismatch);
-                    var mend = mstart + mlen;
-
-                    for (var _j2 = mstart; _j2 < mstart + mlen; _j2++) {
-                      var epos = _j2 - region.start;
-
-                      if (epos >= 0 && epos < bins.length) {
-                        var _bin = bins[epos];
-                        var base = mismatch.base,
-                            type = mismatch.type;
-                        var interbase = isInterbase(type);
-
-                        if (!interbase) {
-                          _bin.ref--;
-                          _bin[fstrand]--;
-                        } else {
-                          inc(_bin, fstrand, 'noncov', type);
-                        }
-
-                        if (type === 'deletion' || type === 'skip') {
-                          inc(_bin, fstrand, 'delskips', type);
-                          _bin.total--;
-                        } else if (!interbase && colorSNPs) {
-                          inc(_bin, fstrand, 'cov', base);
-                        }
-                      }
-                    }
-
-                    if (mismatch.type === 'skip') {
-                      var hash = "".concat(mstart, "_").concat(mend, "_").concat(fstrand);
-
-                      if (skipmap[hash] === undefined) {
-                        skipmap[hash] = {
-                          feature: feature,
-                          start: mstart,
-                          end: mend,
-                          strand: fstrand,
-                          xs: (0, _util.getTag)(feature, 'XS') || (0, _util.getTag)(feature, 'TS'),
-                          score: 0
                         };
-                      }
-
-                      skipmap[hash].score++;
-                    }
-                  }
-                };
-
-                for (i = 0; i < features.length; i++) {
-                  _loop(i);
+                        for (i = 0; i < features.length; i++) {
+                            _loop_1(i);
+                        }
+                        return [2 /*return*/, { bins: bins, skipmap: skipmap }];
                 }
-
-                return _context6.abrupt("return", {
-                  bins: bins,
-                  skipmap: skipmap
-                });
-
-              case 15:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function generateCoverageBins(_x5, _x6, _x7) {
-        return _generateCoverageBins.apply(this, arguments);
-      }
-
-      return generateCoverageBins;
-    }()
-  }]);
-  return SNPCoverageAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
+            });
+        });
+    };
+    return SNPCoverageAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
 exports.default = SNPCoverageAdapter;
 var capabilities = SNPCoverageAdapter.capabilities;
-exports.capabilities = capabilities;
+exports.capabilities = capabilities;
+//# sourceMappingURL=SNPCoverageAdapter.js.map