@jbrowse/plugin-sequence 1.7.11 → 2.1.0

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -1,261 +1,194 @@
 "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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _operators = require("rxjs/operators");
-
-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 _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(_default, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(_default);
-
-  function _default() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, _default);
-
-    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 };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var configuration_1 = require("@jbrowse/core/configuration");
+var operators_1 = require("rxjs/operators");
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.windowSize = 1000;
+        _this.windowDelta = 1000;
+        _this.gcMode = 'content';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "windowSize", 1000);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "windowDelta", 1000);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "gcMode", 'content');
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    key: "configure",
-    value: function () {
-      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var _this$getSubAdapter;
-
-        var sequenceAdapter, dataAdapter;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                // instantiate the sequence adapter
-                sequenceAdapter = (0, _configuration.readConfObject)(this.config, 'sequenceAdapter');
-                _context.next = 3;
-                return (_this$getSubAdapter = this.getSubAdapter) === null || _this$getSubAdapter === void 0 ? void 0 : _this$getSubAdapter.call(this, sequenceAdapter);
-
-              case 3:
-                dataAdapter = _context.sent;
-
-                if (dataAdapter) {
-                  _context.next = 6;
-                  break;
+    default_1.prototype.configure = function () {
+        var _a;
+        return __awaiter(this, void 0, void 0, function () {
+            var sequenceAdapter, dataAdapter;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        sequenceAdapter = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
+                        return [4 /*yield*/, ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, sequenceAdapter))];
+                    case 1:
+                        dataAdapter = _b.sent();
+                        if (!dataAdapter) {
+                            throw new Error('Error getting subadapter');
+                        }
+                        return [2 /*return*/, dataAdapter.dataAdapter];
                 }
-
-                throw new Error('Error getting subadapter');
-
-              case 6:
-                return _context.abrupt("return", dataAdapter.dataAdapter);
-
-              case 7:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function configure() {
-        return _configure.apply(this, arguments);
-      }
-
-      return configure;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var sequenceAdapter;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.configure();
-
-              case 2:
-                sequenceAdapter = _context2.sent;
-                return _context2.abrupt("return", sequenceAdapter.getRefNames());
-
-              case 4:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
+            });
+        });
+    };
+    default_1.prototype.getRefNames = function () {
+        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();
+                        return [2 /*return*/, sequenceAdapter.getRefNames()];
+                }
+            });
+        });
+    };
     /**
      * Fetch features for a certain region
      * @param param -
      * @returns Observable of Feature objects in the region
      */
-
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(query, opts) {
-      var _this2 = this;
-
-      this.windowSize = 1000;
-      this.windowDelta = 1000;
-      this.gcMode = 'content';
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(observer) {
-          var _feats$;
-
-          var sequenceAdapter, hw, f, queryStart, queryEnd, ret, feats, residues, i, r, nc, ng, len, j, pos, score;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
-            while (1) {
-              switch (_context3.prev = _context3.next) {
-                case 0:
-                  _context3.next = 2;
-                  return _this2.configure();
-
-                case 2:
-                  sequenceAdapter = _context3.sent;
-                  hw = _this2.windowSize === 1 ? 1 : _this2.windowSize / 2; // Half the window size
-
-                  f = _this2.windowSize === 1;
-                  queryStart = query.start, queryEnd = query.end;
-                  queryStart = Math.max(0, queryStart - hw);
-                  queryEnd += hw;
-
-                  if (!(queryEnd < 0 || queryStart > queryEnd)) {
-                    _context3.next = 11;
-                    break;
-                  }
-
-                  observer.complete();
-                  return _context3.abrupt("return");
-
-                case 11:
-                  ret = sequenceAdapter.getFeatures(_objectSpread(_objectSpread({}, query), {}, {
-                    start: queryStart,
-                    end: queryEnd
-                  }));
-                  _context3.next = 14;
-                  return ret.pipe((0, _operators.toArray)()).toPromise();
-
-                case 14:
-                  feats = _context3.sent;
-                  residues = ((_feats$ = feats[0]) === null || _feats$ === void 0 ? void 0 : _feats$.get('seq')) || '';
-
-                  for (i = hw; i < residues.length - hw; i += _this2.windowDelta) {
-                    r = f ? residues[i] : residues.slice(i - hw, i + hw);
-                    nc = 0;
-                    ng = 0;
-                    len = 0;
-
-                    for (j = 0; j < r.length; j++) {
-                      if (r[j] === 'c' || r[j] === 'C') {
-                        nc++;
-                      } else if (r[j] === 'g' || r[j] === 'G') {
-                        ng++;
-                      }
-
-                      if (r[j] !== 'N') {
-                        len++;
-                      }
-                    }
-
-                    pos = queryStart;
-                    score = void 0;
-
-                    if (_this2.gcMode === 'content') {
-                      score = (ng + nc) / (len || 1);
-                    } else if (_this2.gcMode === 'skew') {
-                      score = (ng - nc) / (ng + nc || 1);
-                    }
-
-                    observer.next(new _simpleFeature.default({
-                      uniqueId: "".concat(_this2.id, "_").concat(pos + i),
-                      start: pos + i,
-                      end: pos + i + _this2.windowDelta,
-                      score: score
-                    }));
-                  }
-
-                  observer.complete();
-
-                case 18:
-                case "end":
-                  return _context3.stop();
-              }
-            }
-          }, _callee3);
-        }));
-
-        return function (_x) {
-          return _ref.apply(this, arguments);
-        };
-      }());
-    }
+    default_1.prototype.getFeatures = function (query, opts) {
+        var _this = this;
+        this.windowSize = 1000;
+        this.windowDelta = 1000;
+        this.gcMode = 'content';
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var sequenceAdapter, hw, f, queryStart, queryEnd, ret, feats, residues, i, r, nc, ng, len, j, pos, score;
+            var _a;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        sequenceAdapter = _b.sent();
+                        hw = this.windowSize === 1 ? 1 : this.windowSize / 2 // Half the window size
+                        ;
+                        f = this.windowSize === 1;
+                        queryStart = query.start, queryEnd = query.end;
+                        queryStart = Math.max(0, queryStart - hw);
+                        queryEnd += hw;
+                        if (queryEnd < 0 || queryStart > queryEnd) {
+                            observer.complete();
+                            return [2 /*return*/];
+                        }
+                        ret = sequenceAdapter.getFeatures(__assign(__assign({}, query), { start: queryStart, end: queryEnd }));
+                        return [4 /*yield*/, ret.pipe((0, operators_1.toArray)()).toPromise()];
+                    case 2:
+                        feats = _b.sent();
+                        residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
+                        for (i = hw; i < residues.length - hw; i += this.windowDelta) {
+                            r = f ? residues[i] : residues.slice(i - hw, i + hw);
+                            nc = 0;
+                            ng = 0;
+                            len = 0;
+                            for (j = 0; j < r.length; j++) {
+                                if (r[j] === 'c' || r[j] === 'C') {
+                                    nc++;
+                                }
+                                else if (r[j] === 'g' || r[j] === 'G') {
+                                    ng++;
+                                }
+                                if (r[j] !== 'N') {
+                                    len++;
+                                }
+                            }
+                            pos = queryStart;
+                            score = void 0;
+                            if (this.gcMode === 'content') {
+                                score = (ng + nc) / (len || 1);
+                            }
+                            else if (this.gcMode === 'skew') {
+                                score = (ng - nc) / (ng + nc || 1);
+                            }
+                            observer.next(new simpleFeature_1.default({
+                                uniqueId: "".concat(this.id, "_").concat(pos + i),
+                                start: pos + i,
+                                end: pos + i + this.windowDelta,
+                                score: score,
+                            }));
+                        }
+                        observer.complete();
+                        return [2 /*return*/];
+                }
+            });
+        }); });
+    };
     /**
      * called to provide a hint that data tied to a certain region
      * will not be needed for the forseeable future and can be purged
      * from caches, etc
      */
-
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return _default;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = _default;
-(0, _defineProperty2.default)(_default, "capabilities", ['hasLocalStats']);
+    default_1.prototype.freeResources = function ( /* { region } */) { };
+    default_1.capabilities = ['hasLocalStats'];
+    return default_1;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = default_1;
+//# sourceMappingURL=GCContentAdapter.js.map

package/dist/GCContentAdapter/GCContentAdapter.js.map

@@ -0,0 +1 @@
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package/dist/GCContentAdapter/configSchema.js

@@ -1,18 +1,9 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (function (pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('GCContentAdapter', {
+        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    }, { explicitlyTyped: true });
 });
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = function _default(pluginManager) {
-  return (0, _configuration.ConfigurationSchema)('GCContentAdapter', {
-    sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter')
-  }, {
-    explicitlyTyped: true
-  });
-};
-
-exports.default = _default;
+//# sourceMappingURL=configSchema.js.map

package/dist/GCContentAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/GCContentAdapter/configSchema.ts"],"names":[],"mappings":";;AACA,6DAAiE;AAEjE,mBAAe,UAAC,aAA4B;IAC1C,OAAO,IAAA,mCAAmB,EACxB,kBAAkB,EAClB;QACE,eAAe,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;KACpE,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACH,CAAC,EAAA"}

package/dist/GCContentAdapter/index.js

@@ -1,31 +1,36 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2.default)(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-var _default = function _default(pluginManager) {
-  return {
-    configSchema: pluginManager.load(_configSchema.default),
-    getAdapterClass: function getAdapterClass() {
-      return Promise.resolve().then(function () {
-        return _interopRequireWildcard(require('./GCContentAdapter'));
-      }).then(function (r) {
-        return r.default;
-      });
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
     }
-  };
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
 };
-
-exports.default = _default;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (function (pluginManager) {
+    return {
+        configSchema: pluginManager.load(configSchema_1.default),
+        getAdapterClass: function () { return Promise.resolve().then(function () { return __importStar(require('./GCContentAdapter')); }).then(function (r) { return r.default; }); },
+    };
+});
+//# sourceMappingURL=index.js.map

package/dist/GCContentAdapter/index.js.map

@@ -0,0 +1 @@
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