@jbrowse/plugin-bed 1.7.11 → 2.1.0

package/dist/BigBedAdapter/BigBedAdapter.js.map

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

@@ -1,22 +1,10 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('BigBedAdapter', {
-  bigBedLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.bb',
-      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)('BigBedAdapter', {
+    bigBedLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/BigBedAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/BigBedAdapter/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/BigBedAdapter/index.js.map

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

package/dist/index.js

@@ -1,168 +1,140 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+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 __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;
 });
-exports.default = void 0;
-
-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 _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-
-var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _BigBedAdapter = require("./BigBedAdapter");
-
-var _BedTabixAdapter = require("./BedTabixAdapter");
-
-var _BedAdapter = require("./BedAdapter");
-
-var _tracks = require("@jbrowse/core/util/tracks");
-
-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 || _typeof(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; }
-
-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 BedPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(BedPlugin, _Plugin);
-
-  var _super = _createSuper(BedPlugin);
-
-  function BedPlugin() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BedPlugin);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+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;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+var BigBedAdapter_1 = require("./BigBedAdapter");
+var BedTabixAdapter_1 = require("./BedTabixAdapter");
+var BedAdapter_1 = require("./BedAdapter");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var BedPlugin = /** @class */ (function (_super) {
+    __extends(BedPlugin, _super);
+    function BedPlugin() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'BedPlugin';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'BedPlugin');
-    return _this;
-  }
-
-  (0, _createClass2.default)(BedPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'BigBedAdapter',
-          configSchema: _BigBedAdapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./BigBedAdapter/BigBedAdapter'));
-            }).then(function (r) {
-              return r.default;
+    BedPlugin.prototype.install = function (pluginManager) {
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'BigBedAdapter',
+                configSchema: BigBedAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./BigBedAdapter/BigBedAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.(bb|bigbed)$/i;
-          var adapterName = 'BigBedAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var obj = {
-            type: adapterName,
-            bigBedLocation: file
-          };
-
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj;
-          } else if (adapterHint === adapterName) {
-            return obj;
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'BedTabixAdapter',
-          configSchema: _BedTabixAdapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./BedTabixAdapter/BedTabixAdapter'));
-            }).then(function (r) {
-              return r.default;
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.(bb|bigbed)$/i;
+                var adapterName = 'BigBedAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var obj = {
+                    type: adapterName,
+                    bigBedLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'BedTabixAdapter',
+                configSchema: BedTabixAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./BedTabixAdapter/BedTabixAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'BedAdapter',
-          configSchema: _BedAdapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./BedAdapter/BedAdapter'));
-            }).then(function (r) {
-              return r.default;
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'BedAdapter',
+                configSchema: BedAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./BedAdapter/BedAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.bed\.b?gz$/i;
-          var adapterName = 'BedTabixAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var indexName = index && (0, _tracks.getFileName)(index);
-
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bedGzLocation: file,
-              index: {
-                location: index || (0, _tracks.makeIndex)(file, '.tbi'),
-                indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'TBI')
-              }
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.bed\.b?gz$/i;
+                var adapterName = 'BedTabixAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var indexName = index && (0, tracks_1.getFileName)(index);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bedGzLocation: file,
+                        index: {
+                            location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                            indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                        },
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
             };
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.bed$/i;
-          var adapterName = 'BedAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bedLocation: file
+        });
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.bed$/i;
+                var adapterName = 'BedAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bedLocation: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
             };
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-    }
-  }]);
-  return BedPlugin;
-}(_Plugin2.default);
-
-exports.default = BedPlugin;
+        });
+    };
+    return BedPlugin;
+}(Plugin_1.default));
+exports.default = BedPlugin;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/util.d.ts

@@ -1,4 +1,4 @@
 import { SimpleFeature, Feature } from '@jbrowse/core/util';
 import BED from '@gmod/bed';
 export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
-export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: typeof BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;
+export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;