@jbrowse/plugin-sequence 1.6.9 → 1.7.3

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -0,0 +1,261 @@
+"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];
+    }
+
+    _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$getSubAdapter.call(this, sequenceAdapter);
+
+              case 3:
+                dataAdapter = _context.sent;
+
+                if (dataAdapter) {
+                  _context.next = 6;
+                  break;
+                }
+
+                throw new Error('Error getting subadapter');
+
+              case 6:
+                return _context.abrupt("return", dataAdapter.dataAdapter);
+
+              case 7:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function configure() {
+        return _configure.apply(this, arguments);
+      }
+
+      return configure;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var sequenceAdapter;
+        return _regenerator["default"].wrap(function _callee2$(_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;
+    }()
+    /**
+     * 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);
+        };
+      }());
+    }
+    /**
+     * 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']);

package/dist/GCContentAdapter/configSchema.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/GCContentAdapter/configSchema.js

@@ -0,0 +1,18 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: 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;

package/dist/GCContentAdapter/index.d.ts

@@ -1,6 +1,6 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => {
-    configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    getAdapterClass: () => Promise<typeof import("./GCContentAdapter").default>;
-};
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => {
+    configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    getAdapterClass: () => Promise<typeof import("./GCContentAdapter").default>;
+};
+export default _default;

package/dist/GCContentAdapter/index.js

@@ -0,0 +1,31 @@
+"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"];
+      });
+    }
+  };
+};
+
+exports["default"] = _default;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -1,25 +1,25 @@
-import { IndexedFasta } from '@gmod/indexedfasta';
-import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class extends BaseSequenceAdapter {
-    protected fasta: IndexedFasta;
-    private seqCache;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getRegions(opts?: BaseOptions): Promise<{
-        refName: string;
-        start: number;
-        end: number;
-    }[]>;
-    getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * 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
-     */
-    freeResources(): void;
-}
+import { IndexedFasta } from '@gmod/indexedfasta';
+import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends BaseSequenceAdapter {
+    protected fasta: IndexedFasta;
+    private seqCache;
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getRegions(opts?: BaseOptions): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * 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
+     */
+    freeResources(): void;
+}

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -0,0 +1,228 @@
+"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 _indexedfasta = require("@gmod/indexedfasta");
+
+var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
+
+var _QuickLRU = _interopRequireDefault(require("@jbrowse/core/util/QuickLRU"));
+
+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 (_BaseSequenceAdapter) {
+  (0, _inherits2["default"])(_default, _BaseSequenceAdapter);
+
+  var _super = _createSuper(_default);
+
+  function _default(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "fasta", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "seqCache", new _abortablePromiseCache["default"]({
+      cache: new _QuickLRU["default"]({
+        maxSize: 200
+      }),
+      fill: function () {
+        var _fill = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(args, signal) {
+          var refName, start, end;
+          return _regenerator["default"].wrap(function _callee$(_context) {
+            while (1) {
+              switch (_context.prev = _context.next) {
+                case 0:
+                  refName = args.refName, start = args.start, end = args.end;
+                  return _context.abrupt("return", _this.fasta.getSequence(refName, start, end, _objectSpread(_objectSpread({}, args), {}, {
+                    signal: signal
+                  })));
+
+                case 2:
+                case "end":
+                  return _context.stop();
+              }
+            }
+          }, _callee);
+        }));
+
+        function fill(_x, _x2) {
+          return _fill.apply(this, arguments);
+        }
+
+        return fill;
+      }()
+    }));
+    var fastaLocation = (0, _configuration.readConfObject)(config, 'fastaLocation');
+    var faiLocation = (0, _configuration.readConfObject)(config, 'faiLocation');
+    var fastaOpts = {
+      fasta: (0, _io.openLocation)(fastaLocation, _this.pluginManager),
+      fai: (0, _io.openLocation)(faiLocation, _this.pluginManager)
+    };
+    _this.fasta = new _indexedfasta.IndexedFasta(fastaOpts);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "getRefNames",
+    value: function getRefNames(opts) {
+      return this.fasta.getSequenceNames(opts);
+    }
+  }, {
+    key: "getRegions",
+    value: function () {
+      var _getRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(opts) {
+        var seqSizes;
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                _context2.next = 2;
+                return this.fasta.getSequenceSizes(opts);
+
+              case 2:
+                seqSizes = _context2.sent;
+                return _context2.abrupt("return", Object.keys(seqSizes).map(function (refName) {
+                  return {
+                    refName: refName,
+                    start: 0,
+                    end: seqSizes[refName]
+                  };
+                }));
+
+              case 4:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getRegions(_x3) {
+        return _getRegions.apply(this, arguments);
+      }
+
+      return getRegions;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(region, opts) {
+      var _this2 = this;
+
+      var refName = region.refName,
+          start = region.start,
+          end = region.end;
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(observer) {
+          var size, regionEnd, chunks, chunkSize, s, e, chunkStart, r, seq;
+          return _regenerator["default"].wrap(function _callee3$(_context3) {
+            while (1) {
+              switch (_context3.prev = _context3.next) {
+                case 0:
+                  _context3.next = 2;
+                  return _this2.fasta.getSequenceSize(refName, opts);
+
+                case 2:
+                  size = _context3.sent;
+                  regionEnd = size !== undefined ? Math.min(size, end) : end;
+                  chunks = [];
+                  chunkSize = 128000;
+                  s = start - start % chunkSize;
+                  e = end + (chunkSize - end % chunkSize);
+
+                  for (chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
+                    r = {
+                      refName: refName,
+                      start: chunkStart,
+                      end: chunkStart + chunkSize
+                    };
+                    chunks.push(_this2.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+                  }
+
+                  _context3.next = 11;
+                  return Promise.all(chunks);
+
+                case 11:
+                  seq = _context3.sent.join('').slice(start - s).slice(0, end - start);
+
+                  if (seq) {
+                    observer.next(new _simpleFeature["default"]({
+                      id: "".concat(refName, " ").concat(start, "-").concat(regionEnd),
+                      data: {
+                        refName: refName,
+                        start: start,
+                        end: regionEnd,
+                        seq: seq
+                      }
+                    }));
+                  }
+
+                  observer.complete();
+
+                case 14:
+                case "end":
+                  return _context3.stop();
+              }
+            }
+          }, _callee3);
+        }));
+
+        return function (_x4) {
+          return _ref.apply(this, arguments);
+        };
+      }());
+    }
+    /**
+     * 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.BaseSequenceAdapter);
+
+exports["default"] = _default;