@jbrowse/plugin-sequence 1.7.11 → 2.0.0

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -1,70 +1,52 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-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 _indexedfasta = require("@gmod/indexedfasta");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _IndexedFastaAdapter = _interopRequireDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
-
-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 (_IndexedFasta) {
-  (0, _inherits2.default)(_default, _IndexedFasta);
-
-  var _super = _createSuper(_default);
-
-  function _default(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, _default);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    var fastaLocation = (0, _configuration.readConfObject)(config, 'fastaLocation');
-    var faiLocation = (0, _configuration.readConfObject)(config, 'faiLocation');
-    var gziLocation = (0, _configuration.readConfObject)(config, 'gziLocation');
-
-    if (!fastaLocation) {
-      throw new Error('must provide fastaLocation');
-    }
-
-    if (!faiLocation) {
-      throw new Error('must provide faiLocation');
-    }
-
-    if (!gziLocation) {
-      throw new Error('must provide gziLocation');
-    }
-
-    var fastaOpts = {
-      fasta: (0, _io.openLocation)(fastaLocation, _this.pluginManager),
-      fai: (0, _io.openLocation)(faiLocation, _this.pluginManager),
-      gzi: (0, _io.openLocation)(gziLocation, _this.pluginManager)
+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);
     };
-    _this.fasta = new _indexedfasta.BgzipIndexedFasta(fastaOpts);
-    return _this;
-  }
-
-  return (0, _createClass2.default)(_default);
-}(_IndexedFastaAdapter.default);
-
-exports.default = _default;
+    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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var indexedfasta_1 = require("@gmod/indexedfasta");
+var io_1 = require("@jbrowse/core/util/io");
+var configuration_1 = require("@jbrowse/core/configuration");
+var IndexedFastaAdapter_1 = __importDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        var fastaLocation = (0, configuration_1.readConfObject)(config, 'fastaLocation');
+        var faiLocation = (0, configuration_1.readConfObject)(config, 'faiLocation');
+        var gziLocation = (0, configuration_1.readConfObject)(config, 'gziLocation');
+        if (!fastaLocation) {
+            throw new Error('must provide fastaLocation');
+        }
+        if (!faiLocation) {
+            throw new Error('must provide faiLocation');
+        }
+        if (!gziLocation) {
+            throw new Error('must provide gziLocation');
+        }
+        var fastaOpts = {
+            fasta: (0, io_1.openLocation)(fastaLocation, _this.pluginManager),
+            fai: (0, io_1.openLocation)(faiLocation, _this.pluginManager),
+            gzi: (0, io_1.openLocation)(gziLocation, _this.pluginManager),
+        };
+        _this.fasta = new indexedfasta_1.BgzipIndexedFasta(fastaOpts);
+        return _this;
+    }
+    return default_1;
+}(IndexedFastaAdapter_1.default));
+exports.default = default_1;
+//# sourceMappingURL=BgzipFastaAdapter.js.map

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"BgzipFastaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/BgzipFastaAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,mDAAsD;AAEtD,4CAAoD;AACpD,6DAA4D;AAE5D,mGAAqE;AAIrE;IAA6B,6BAAY;IACvC,mBACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAH/B,YAKE,kBAAM,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,SAoB5C;QAnBC,IAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,IAAM,WAAW,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,aAAa,CAAC,CAAA;QACzD,IAAM,WAAW,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,aAAa,CAAC,CAAA;QACzD,IAAI,CAAC,aAAa,EAAE;YAClB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;SAC9C;QACD,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,IAAM,SAAS,GAAG;YAChB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAA6B,EAAE,KAAI,CAAC,aAAa,CAAC;YACtE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,KAAI,CAAC,aAAa,CAAC;YAClE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,KAAI,CAAC,aAAa,CAAC;SACnE,CAAA;QAED,KAAI,CAAC,KAAK,GAAG,IAAI,gCAAiB,CAAC,SAAS,CAAC,CAAA;;IAC/C,CAAC;IACH,gBAAC;AAAD,CAAC,AA3BD,CAA6B,6BAAY,GA2BxC"}

package/dist/BgzipFastaAdapter/configSchema.js

@@ -1,44 +1,32 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('BgzipFastaAdapter', {
-  fastaLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/seq.fa.gz',
-      locationType: 'UriLocation'
-    }
-  },
-  faiLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/seq.fa.gz.fai',
-      locationType: 'UriLocation'
-    }
-  },
-  metadataLocation: {
-    description: 'Optional metadata file',
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/fa.metadata.yaml',
-      locationType: 'UriLocation'
-    }
-  },
-  gziLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/seq.fa.gz.gzi',
-      locationType: 'UriLocation'
-    }
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter', {
+    fastaLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
+    },
+    faiLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/seq.fa.gz.fai',
+            locationType: 'UriLocation',
+        },
+    },
+    metadataLocation: {
+        description: 'Optional metadata file',
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/fa.metadata.yaml',
+            locationType: 'UriLocation',
+        },
+    },
+    gziLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/seq.fa.gz.gzi',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/BgzipFastaAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,mBAAmB,EACnB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,gBAAgB,EAAE;QAChB,WAAW,EAAE,wBAAwB;QACrC,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,2BAA2B;YAChC,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/BgzipFastaAdapter/index.js

@@ -1,15 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/BgzipFastaAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,170 +1,136 @@
 "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 _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 _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 _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-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 (_BaseAdapter) {
-  (0, _inherits2.default)(_default, _BaseAdapter);
-
-  var _super = _createSuper(_default);
-
-  // the map of refSeq to length
-  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), "refSeqs", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "source", void 0);
-    var chromSizesLocation = (0, _configuration.readConfObject)(config, 'chromSizesLocation');
-
-    if (!chromSizesLocation) {
-      throw new Error('must provide chromSizesLocation');
-    }
-
-    var file = (0, _io.openLocation)(chromSizesLocation, _this.pluginManager);
-    _this.source = file.toString();
-    _this.refSeqs = _this.init(file);
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    key: "init",
-    value: function () {
-      var _init = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(file) {
-        var data, refSeqs;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return file.readFile('utf8');
-
-              case 2:
-                data = _context.sent;
-                refSeqs = {};
-
-                if (data.length) {
-                  _context.next = 6;
-                  break;
-                }
-
-                throw new Error("Could not read file ".concat(file.toString()));
-
-              case 6:
-                data.split('\n').forEach(function (line) {
-                  if (line.length) {
-                    var _line$split = line.split('\t'),
-                        _line$split2 = (0, _slicedToArray2.default)(_line$split, 2),
-                        name = _line$split2[0],
-                        length = _line$split2[1];
-
-                    refSeqs[name] = +length;
-                  }
-                });
-                return _context.abrupt("return", refSeqs);
-
-              case 8:
-              case "end":
-                return _context.stop();
+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;
             }
-          }
-        }, _callee);
-      }));
-
-      function init(_x) {
-        return _init.apply(this, arguments);
-      }
-
-      return init;
-    }()
-  }, {
-    key: "getRegions",
-    value: function () {
-      var _getRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var refSeqs;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.refSeqs;
-
-              case 2:
-                refSeqs = _context2.sent;
-                return _context2.abrupt("return", Object.keys(refSeqs).map(function (refName) {
-                  return {
-                    refName: refName,
-                    start: 0,
-                    end: refSeqs[refName]
-                  };
-                }));
-
-              case 4:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getRegions() {
-        return _getRegions.apply(this, arguments);
-      }
-
-      return getRegions;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures() {
-      throw new Error('sequence not available');
+            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);
     }
-  }, {
-    key: "getHeader",
-    value: function getHeader() {
-      return {};
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
     }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return _default;
-}(_BaseAdapter2.BaseAdapter);
-
-exports.default = _default;
+    return ar;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var io_1 = require("@jbrowse/core/util/io");
+var configuration_1 = require("@jbrowse/core/configuration");
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        var chromSizesLocation = (0, configuration_1.readConfObject)(config, 'chromSizesLocation');
+        if (!chromSizesLocation) {
+            throw new Error('must provide chromSizesLocation');
+        }
+        var file = (0, io_1.openLocation)(chromSizesLocation, _this.pluginManager);
+        _this.source = file.toString();
+        _this.refSeqs = _this.init(file);
+        return _this;
+    }
+    default_1.prototype.init = function (file) {
+        return __awaiter(this, void 0, void 0, function () {
+            var data, refSeqs;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, file.readFile('utf8')];
+                    case 1:
+                        data = _a.sent();
+                        refSeqs = {};
+                        if (!data.length) {
+                            throw new Error("Could not read file ".concat(file.toString()));
+                        }
+                        data.split('\n').forEach(function (line) {
+                            if (line.length) {
+                                var _a = __read(line.split('\t'), 2), name_1 = _a[0], length_1 = _a[1];
+                                refSeqs[name_1] = +length_1;
+                            }
+                        });
+                        return [2 /*return*/, refSeqs];
+                }
+            });
+        });
+    };
+    default_1.prototype.getRegions = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var refSeqs;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.refSeqs];
+                    case 1:
+                        refSeqs = _a.sent();
+                        return [2 /*return*/, Object.keys(refSeqs).map(function (refName) { return ({
+                                refName: refName,
+                                start: 0,
+                                end: refSeqs[refName],
+                            }); })];
+                }
+            });
+        });
+    };
+    default_1.prototype.getFeatures = function () {
+        throw new Error('sequence not available');
+    };
+    default_1.prototype.getHeader = function () {
+        return {};
+    };
+    default_1.prototype.freeResources = function ( /* { region } */) { };
+    return default_1;
+}(BaseAdapter_1.BaseAdapter));
+exports.default = default_1;
+//# sourceMappingURL=ChromSizesAdapter.js.map

package/dist/ChromSizesAdapter/ChromSizesAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ChromSizesAdapter.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/ChromSizesAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uEAGgD;AAEhD,4CAAoD;AAEpD,6DAA4D;AAM5D;IAA6B,6BAAW;IAMtC,mBACE,MAAuC,EACvC,aAAiC,EACjC,aAA6B;QAH/B,YAKE,kBAAM,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,SAW5C;QAVC,IAAM,kBAAkB,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QACvE,IAAI,CAAC,kBAAkB,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;SACnD;QACD,IAAM,IAAI,GAAG,IAAA,iBAAY,EACvB,kBAAkC,EAClC,KAAI,CAAC,aAAa,CACnB,CAAA;QACD,KAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAA;QAC7B,KAAI,CAAC,OAAO,GAAG,KAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;;IAChC,CAAC;IAEa,wBAAI,GAAlB,UAAmB,IAAuB;;;;;4BAC3B,qBAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAA;;wBAAlC,IAAI,GAAG,SAA2B;wBAClC,OAAO,GAA8B,EAAE,CAAA;wBAC7C,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;4BAChB,MAAM,IAAI,KAAK,CAAC,8BAAuB,IAAI,CAAC,QAAQ,EAAE,CAAE,CAAC,CAAA;yBAC1D;wBACD,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,UAAC,IAAY;4BACpC,IAAI,IAAI,CAAC,MAAM,EAAE;gCACT,IAAA,KAAA,OAAiB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAA,EAAhC,MAAI,QAAA,EAAE,QAAM,QAAoB,CAAA;gCACvC,OAAO,CAAC,MAAI,CAAC,GAAG,CAAC,QAAM,CAAA;6BACxB;wBACH,CAAC,CAAC,CAAA;wBACF,sBAAO,OAAO,EAAA;;;;KACf;IAEY,8BAAU,GAAvB;;;;;4BACkB,qBAAM,IAAI,CAAC,OAAO,EAAA;;wBAA5B,OAAO,GAAG,SAAkB;wBAClC,sBAAO,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,UAAA,OAAO,IAAI,OAAA,CAAC;gCAC1C,OAAO,SAAA;gCACP,KAAK,EAAE,CAAC;gCACR,GAAG,EAAE,OAAO,CAAC,OAAO,CAAC;6BACtB,CAAC,EAJyC,CAIzC,CAAC,EAAA;;;;KACJ;IAEM,+BAAW,GAAlB;QACE,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAA;IAC3C,CAAC;IAEM,6BAAS,GAAhB;QACE,OAAO,EAAE,CAAA;IACX,CAAC;IAEM,iCAAa,GAApB,WAAqB,gBAAgB,IAAS,CAAC;IACjD,gBAAC;AAAD,CAAC,AAzDD,CAA6B,yBAAW,GAyDvC"}

package/dist/ChromSizesAdapter/configSchema.js

@@ -1,22 +1,13 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('ChromSizesAdapter', {
-  chromSizesLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/species.chrom.sizes',
-      locationType: 'UriLocation'
-    }
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('ChromSizesAdapter', {
+    chromSizesLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/species.chrom.sizes',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/ChromSizesAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,mBAAmB,EACnB;IACE,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/ChromSizesAdapter/index.js

@@ -1,15 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/ChromSizesAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}