@jbrowse/plugin-gtf 1.7.0 → 1.7.4

package/dist/GtfAdapter/GtfAdapter.d.ts

@@ -1,14 +1,14 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import IntervalTree from '@flatten-js/interval-tree';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-export default class extends BaseFeatureDataAdapter {
-    protected gtfFeatures?: Promise<{
-        intervalTree: Record<string, IntervalTree>;
-    }>;
-    private loadDataP;
-    private loadData;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
-}
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import IntervalTree from '@flatten-js/interval-tree';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class extends BaseFeatureDataAdapter {
+    protected gtfFeatures?: Promise<{
+        intervalTree: Record<string, IntervalTree>;
+    }>;
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/GtfAdapter/GtfAdapter.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -43,7 +43,7 @@ var _gtf = _interopRequireDefault(require("@gmod/gtf"));
 
 var _util = require("../util");
 
-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 _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; } }
 
@@ -52,32 +52,32 @@ function isGzip(buf) {
 }
 
 var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2["default"])(_default, _BaseFeatureDataAdapt);
+  (0, _inherits2.default)(_default, _BaseFeatureDataAdapt);
 
   var _super = _createSuper(_default);
 
   function _default() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, _default);
+    (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), "gtfFeatures", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "gtfFeatures", void 0);
     return _this;
   }
 
-  (0, _createClass2["default"])(_default, [{
+  (0, _createClass2.default)(_default, [{
     key: "loadDataP",
     value: function () {
-      var _loadDataP = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+      var _loadDataP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
         var _this2 = this;
 
         var buffer, buf, data, feats, intervalTree;
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -117,14 +117,14 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 data = new TextDecoder('utf8', {
                   fatal: true
                 }).decode(buf);
-                feats = _gtf["default"].parseStringSync(data, {
+                feats = _gtf.default.parseStringSync(data, {
                   parseFeatures: true,
                   parseComments: false,
                   parseDirectives: false,
                   parseSequences: false
                 });
                 intervalTree = feats.flat().map(function (f, i) {
-                  return new _simpleFeature["default"]({
+                  return new _simpleFeature.default({
                     data: (0, _util.featureData)(f),
                     id: "".concat(_this2.id, "-offset-").concat(i)
                   });
@@ -132,7 +132,7 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   var key = obj.get('refName');
 
                   if (!acc[key]) {
-                    acc[key] = new _intervalTree["default"]();
+                    acc[key] = new _intervalTree.default();
                   }
 
                   acc[key].insert([obj.get('start'), obj.get('end')], obj);
@@ -159,15 +159,15 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "loadData",
     value: function () {
-      var _loadData = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+      var _loadData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
         var _this3 = this;
 
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
                 if (!this.gtfFeatures) {
-                  this.gtfFeatures = this.loadDataP()["catch"](function (e) {
+                  this.gtfFeatures = this.loadDataP().catch(function (e) {
                     _this3.gtfFeatures = undefined;
                     throw e;
                   });
@@ -192,13 +192,13 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
         var opts,
             _yield$this$loadData,
             intervalTree,
             _args3 = arguments;
 
-        return _regenerator["default"].wrap(function _callee3$(_context3) {
+        return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
@@ -232,10 +232,10 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(observer) {
+        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
           var _intervalTree$refName, start, end, refName, _yield$_this4$loadDat, intervalTree;
 
-          return _regenerator["default"].wrap(function _callee4$(_context4) {
+          return _regenerator.default.wrap(function _callee4$(_context4) {
             while (1) {
               switch (_context4.prev = _context4.next) {
                 case 0:
@@ -281,4 +281,4 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   return _default;
 }(_BaseAdapter.BaseFeatureDataAdapter);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/GtfAdapter/GtfAdapter.test.js

@@ -18,15 +18,15 @@ window.TextDecoder = _webEncoding.TextDecoder;
 describe('adapter can fetch features from volvox.sorted.gtf', function () {
   var adapter;
   beforeEach(function () {
-    adapter = new _GtfAdapter["default"](_configSchema["default"].create({
+    adapter = new _GtfAdapter.default(_configSchema.default.create({
       gtfLocation: {
         localPath: require.resolve('../test_data/volvox.sorted.gtf')
       }
     }));
   });
-  it('test getfeatures on gtf plain text adapter', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  it('test getfeatures on gtf plain text adapter', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
     var features, featuresArray, featuresJsonArray;
-    return _regenerator["default"].wrap(function _callee$(_context) {
+    return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
@@ -69,13 +69,13 @@ describe('adapter can fetch features from volvox.sorted.gtf', function () {
     }, _callee);
   })));
 });
-test('can instantiate new GtfAdapter and check for demo data', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+test('can instantiate new GtfAdapter and check for demo data', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
   var demoAdapter, features, featuresArray, featuresJsonArray;
-  return _regenerator["default"].wrap(function _callee2$(_context2) {
+  return _regenerator.default.wrap(function _callee2$(_context2) {
     while (1) {
       switch (_context2.prev = _context2.next) {
         case 0:
-          demoAdapter = new _GtfAdapter["default"](_configSchema["default"].create({
+          demoAdapter = new _GtfAdapter.default(_configSchema.default.create({
             gtfLocation: {
               localPath: require.resolve('../test_data/demo.gtf')
             }

package/dist/GtfAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/GtfAdapter/configSchema.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _configuration = require("@jbrowse/core/configuration");
 
@@ -19,4 +19,4 @@ var _default = (0, _configuration.ConfigurationSchema)('GtfAdapter', {
   explicitlyTyped: true
 });
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/GtfAdapter/index.d.ts

@@ -1 +1 @@
-export { default as configSchema } from './configSchema';
+export { default as configSchema } from './configSchema';

package/dist/GtfAdapter/index.js

@@ -8,7 +8,7 @@ Object.defineProperty(exports, "__esModule", {
 Object.defineProperty(exports, "configSchema", {
   enumerable: true,
   get: function get() {
-    return _configSchema["default"];
+    return _configSchema.default;
   }
 });
 

package/dist/index.d.ts

@@ -1,6 +1,6 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import Plugin from '@jbrowse/core/Plugin';
-export default class GtfPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
+import PluginManager from '@jbrowse/core/PluginManager';
+import Plugin from '@jbrowse/core/Plugin';
+export default class GtfPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
@@ -33,43 +33,43 @@ 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 _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 _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 GtfPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2["default"])(GtfPlugin, _Plugin);
+  (0, _inherits2.default)(GtfPlugin, _Plugin);
 
   var _super = _createSuper(GtfPlugin);
 
   function GtfPlugin() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, GtfPlugin);
+    (0, _classCallCheck2.default)(this, GtfPlugin);
 
     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), "name", 'GTFPlugin');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'GTFPlugin');
     return _this;
   }
 
-  (0, _createClass2["default"])(GtfPlugin, [{
+  (0, _createClass2.default)(GtfPlugin, [{
     key: "install",
     value: function install(pluginManager) {
       pluginManager.addAdapterType(function () {
-        return new _AdapterType["default"]({
+        return new _AdapterType.default({
           name: 'GtfAdapter',
           configSchema: _GtfAdapter.configSchema,
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () {
               return _interopRequireWildcard(require('./GtfAdapter/GtfAdapter'));
             }).then(function (r) {
-              return r["default"];
+              return r.default;
             });
           }
         });
@@ -96,6 +96,6 @@ var GtfPlugin = /*#__PURE__*/function (_Plugin) {
     }
   }]);
   return GtfPlugin;
-}(_Plugin2["default"]);
+}(_Plugin2.default);
 
-exports["default"] = GtfPlugin;
+exports.default = GtfPlugin;

package/dist/util.d.ts

@@ -1,15 +1,15 @@
-export declare type Strand = '+' | '-' | '.' | '?';
-export interface FeatureLoc {
-    [key: string]: unknown;
-    start: number;
-    end: number;
-    strand: Strand;
-    seq_name: string;
-    child_features: FeatureLoc[][];
-    data: unknown;
-    derived_features: unknown;
-    attributes: {
-        [key: string]: unknown[];
-    };
-}
-export declare function featureData(data: FeatureLoc): Record<string, unknown>;
+export declare type Strand = '+' | '-' | '.' | '?';
+export interface FeatureLoc {
+    [key: string]: unknown;
+    start: number;
+    end: number;
+    strand: Strand;
+    seq_name: string;
+    child_features: FeatureLoc[][];
+    data: unknown;
+    derived_features: unknown;
+    attributes: {
+        [key: string]: unknown[];
+    };
+}
+export declare function featureData(data: FeatureLoc): Record<string, unknown>;

package/dist/util.js

@@ -11,7 +11,7 @@ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/de
 
 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 _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 featureData(data) {
   var f = _objectSpread({}, data);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "1.7.0",
+  "version": "1.7.4",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -29,9 +29,11 @@
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
+    "@babel/runtime": "^7.17.9",
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/gtf": "^0.0.6"
@@ -49,5 +51,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
+  "gitHead": "0a3e0c58055bbab8e3ab0270c139291b96eff403"
 }