@jbrowse/plugin-gtf 1.7.11 → 2.1.0

package/dist/GtfAdapter/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)('GtfAdapter', {
-  gtfLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.gtf',
-      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)('GtfAdapter', {
+    gtfLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.gtf', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/GtfAdapter/configSchema.js.map

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

package/dist/GtfAdapter/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/GtfAdapter/index.js.map

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

package/dist/index.js

@@ -1,101 +1,87 @@
 "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 _GtfAdapter = require("./GtfAdapter");
-
-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 GtfPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(GtfPlugin, _Plugin);
-
-  var _super = _createSuper(GtfPlugin);
-
-  function GtfPlugin() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, GtfPlugin);
-
-    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 GtfAdapter_1 = require("./GtfAdapter");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var GtfPlugin = /** @class */ (function (_super) {
+    __extends(GtfPlugin, _super);
+    function GtfPlugin() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'GTFPlugin';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'GTFPlugin');
-    return _this;
-  }
-
-  (0, _createClass2.default)(GtfPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addAdapterType(function () {
-        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;
+    GtfPlugin.prototype.install = function (pluginManager) {
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'GtfAdapter',
+                configSchema: GtfAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./GtfAdapter/GtfAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.gtf(\.gz)?$/i;
-          var adapterName = 'GtfAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var obj = {
-            type: adapterName,
-            gtfLocation: file
-          };
-
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj;
-          } else if (adapterHint === adapterName) {
-            return obj;
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-    }
-  }]);
-  return GtfPlugin;
-}(_Plugin2.default);
-
-exports.default = GtfPlugin;
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.gtf(\.gz)?$/i;
+                var adapterName = 'GtfAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var obj = {
+                    type: adapterName,
+                    gtfLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+    };
+    return GtfPlugin;
+}(Plugin_1.default));
+exports.default = GtfPlugin;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gGAAyE;AAEzE,gEAAyC;AACzC,2CAAqE;AAErE,oDAAuE;AAEvE;IAAuC,6BAAM;IAA7C;QAAA,qEAuCC;QAtCC,UAAI,GAAG,WAAW,CAAA;;IAsCpB,CAAC;IApCC,2BAAO,GAAP,UAAQ,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B;YACE,OAAA,IAAI,qBAAW,CAAC;gBACd,IAAI,EAAE,YAAY;gBAClB,YAAY,EAAE,yBAAsB;gBACpC,eAAe,EAAE;oBACf,OAAA,iEAAO,yBAAyB,OAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,OAAO,EAAT,CAAS,CAAC;gBAAtD,CAAsD;aACzD,CAAC;QALF,CAKE,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,UAAC,cAA8B;YAC7B,OAAO,UACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB;gBAEpB,IAAM,UAAU,GAAG,gBAAgB,CAAA;gBACnC,IAAM,WAAW,GAAG,YAAY,CAAA;gBAChC,IAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAElC,IAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;iBAClB,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;IACH,gBAAC;AAAD,CAAC,AAvCD,CAAuC,gBAAM,GAuC5C"}

package/dist/util.js

@@ -1,87 +1,77 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.featureData = featureData;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-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; }
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.featureData = void 0;
 function featureData(data) {
-  var f = _objectSpread({}, data);
-
-  f.start -= 1; // convert to interbase
-
-  f.strand = {
-    '+': 1,
-    '-': -1,
-    '.': 0,
-    '?': undefined
-  }[data.strand]; // convert strand
-
-  f.phase = Number(data.frame);
-  f.refName = data.seq_name;
-
-  if (data.score === null) {
-    delete f.score;
-  }
-
-  if (data.frame === null) {
-    delete f.score;
-  }
-
-  var defaultFields = ['start', 'end', 'seq_name', 'score', 'featureType', 'source', 'frame', 'strand'];
-  Object.keys(data.attributes).forEach(function (a) {
-    var b = a.toLowerCase();
-
-    if (defaultFields.includes(b)) {
-      // add "suffix" to tag name if it already exists
-      // reproduces behavior of NCList
-      b += '2';
+    var f = __assign({}, data);
+    f.start -= 1; // convert to interbase
+    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand]; // convert strand
+    f.phase = Number(data.frame);
+    f.refName = data.seq_name;
+    if (data.score === null) {
+        delete f.score;
+    }
+    if (data.frame === null) {
+        delete f.score;
     }
-
-    if (data.attributes[a] !== null) {
-      var attr = data.attributes[a];
-
-      if (Array.isArray(attr) && attr.length === 1) {
-        // gtf uses double quotes for text values in the attributes column, remove them
-        var formattedAttr = attr[0].replace(/^"|"$/g, '');
-        attr = formattedAttr;
-      }
-
-      f[b] = attr;
+    var defaultFields = [
+        'start',
+        'end',
+        'seq_name',
+        'score',
+        'featureType',
+        'source',
+        'frame',
+        'strand',
+    ];
+    Object.keys(data.attributes).forEach(function (a) {
+        var b = a.toLowerCase();
+        if (defaultFields.includes(b)) {
+            // add "suffix" to tag name if it already exists
+            // reproduces behavior of NCList
+            b += '2';
+        }
+        if (data.attributes[a] !== null) {
+            var attr = data.attributes[a];
+            if (Array.isArray(attr) && attr.length === 1) {
+                // gtf uses double quotes for text values in the attributes column, remove them
+                var formattedAttr = attr[0].replace(/^"|"$/g, '');
+                attr = formattedAttr;
+            }
+            f[b] = attr;
+        }
+    });
+    f.refName = f.seq_name;
+    f.type = f.featureType;
+    // the SimpleFeature constructor takes care of recursively inflating subfeatures
+    if (data.child_features && data.child_features.length) {
+        f.subfeatures = data.child_features
+            .map(function (childLocs) { return childLocs.map(function (childLoc) { return featureData(childLoc); }); })
+            .flat();
     }
-  });
-  f.refName = f.seq_name;
-  f.type = f.featureType; // the SimpleFeature constructor takes care of recursively inflating subfeatures
-
-  if (data.child_features && data.child_features.length) {
-    f.subfeatures = data.child_features.map(function (childLocs) {
-      return childLocs.map(function (childLoc) {
-        return featureData(childLoc);
-      });
-    }).flat();
-  }
-
-  delete f.child_features;
-  delete f.data;
-  delete f.derived_features; // eslint-disable-next-line no-underscore-dangle
-
-  delete f._linehash;
-  delete f.attributes;
-  delete f.seq_name;
-  delete f.featureType;
-  delete f.frame;
-
-  if (f.transcript_id) {
-    f.name = f.transcript_id;
-  }
-
-  return f;
-}
+    delete f.child_features;
+    delete f.data;
+    delete f.derived_features;
+    // eslint-disable-next-line no-underscore-dangle
+    delete f._linehash;
+    delete f.attributes;
+    delete f.seq_name;
+    delete f.featureType;
+    delete f.frame;
+    if (f.transcript_id) {
+        f.name = f.transcript_id;
+    }
+    return f;
+}
+exports.featureData = featureData;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/esm/GtfAdapter/GtfAdapter.d.ts

@@ -0,0 +1,21 @@
+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<{
+        feats: {
+            [key: string]: string[];
+        };
+    }>;
+    protected intervalTrees: {
+        [key: string]: Promise<IntervalTree | undefined> | undefined;
+    };
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    private loadFeatureIntervalTreeHelper;
+    private loadFeatureIntervalTree;
+    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/GtfAdapter/GtfAdapter.js

@@ -0,0 +1,102 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import IntervalTree from '@flatten-js/interval-tree';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { unzip } from '@gmod/bgzf-filehandle';
+import gtf from '@gmod/gtf';
+import { featureData } from '../util';
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export default class extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.intervalTrees = {};
+    }
+    async loadDataP(opts = {}) {
+        const gtfLoc = this.getConf('gtfLocation');
+        const buffer = await openLocation(gtfLoc, this.pluginManager).readFile(opts);
+        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        // 512MB  max chrome string length is 512MB
+        if (buf.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const data = new TextDecoder('utf8', { fatal: true }).decode(buf);
+        const lines = data.split('\n').filter(f => !!f && !f.startsWith('#'));
+        const feats = {};
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i];
+            if (line.startsWith('#')) {
+                continue;
+            }
+            const tab = line.indexOf('\t');
+            const refName = line.slice(0, tab);
+            if (!feats[refName]) {
+                feats[refName] = [];
+            }
+            feats[refName].push(lines[i]);
+        }
+        return { feats };
+    }
+    async loadData(opts = {}) {
+        if (!this.gtfFeatures) {
+            this.gtfFeatures = this.loadDataP(opts).catch(e => {
+                this.gtfFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.gtfFeatures;
+    }
+    async getRefNames(opts = {}) {
+        const { feats } = await this.loadData(opts);
+        return Object.keys(feats);
+    }
+    async loadFeatureIntervalTreeHelper(refName) {
+        const { feats } = await this.loadData();
+        const lines = feats[refName];
+        if (!lines) {
+            return undefined;
+        }
+        const data = gtf.parseStringSync(lines.join('\n'), {
+            parseFeatures: true,
+            parseComments: false,
+            parseDirectives: false,
+            parseSequences: false,
+        });
+        const intervalTree = new IntervalTree();
+        const ret = data.flat().map((f, i) => new SimpleFeature({
+            data: featureData(f),
+            id: `${this.id}-${refName}-${i}`,
+        }));
+        for (let i = 0; i < ret.length; i++) {
+            const obj = ret[i];
+            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        }
+        return intervalTree;
+    }
+    async loadFeatureIntervalTree(refName) {
+        if (!this.intervalTrees[refName]) {
+            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(e => {
+                this.intervalTrees[refName] = undefined;
+                throw e;
+            });
+        }
+        return this.intervalTrees[refName];
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            try {
+                const { start, end, refName } = query;
+                const intervalTree = await this.loadFeatureIntervalTree(refName);
+                intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => observer.next(f));
+                observer.complete();
+            }
+            catch (e) {
+                observer.error(e);
+            }
+        }, opts.signal);
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=GtfAdapter.js.map

package/esm/GtfAdapter/GtfAdapter.js.map

@@ -0,0 +1 @@
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package/esm/GtfAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/GtfAdapter/configSchema.js

@@ -0,0 +1,8 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('GtfAdapter', {
+    gtfLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.gtf', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/GtfAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/GtfAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/GtfAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/GtfAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/GtfAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GtfAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +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;
+}

package/esm/index.js

@@ -0,0 +1,36 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import Plugin from '@jbrowse/core/Plugin';
+import { configSchema as gtfAdapterConfigSchema } from './GtfAdapter';
+import { getFileName } from '@jbrowse/core/util/tracks';
+export default class GtfPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'GTFPlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'GtfAdapter',
+            configSchema: gtfAdapterConfigSchema,
+            getAdapterClass: () => import('./GtfAdapter/GtfAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.gtf(\.gz)?$/i;
+                const adapterName = 'GtfAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    gtfLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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