@jbrowse/plugin-gff3 1.7.11 → 2.0.0

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js.map

@@ -0,0 +1 @@
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package/dist/Gff3TabixAdapter/configSchema.js

@@ -1,42 +1,29 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('Gff3TabixAdapter', {
-  gffGzLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.gff.gz',
-      locationType: 'UriLocation'
-    }
-  },
-  index: (0, _configuration.ConfigurationSchema)('Gff3TabixIndex', {
-    indexType: {
-      model: _mobxStateTree.types.enumeration('IndexType', ['TBI', 'CSI']),
-      type: 'stringEnum',
-      defaultValue: 'TBI'
+Object.defineProperty(exports, "__esModule", { value: true });
+var mobx_state_tree_1 = require("mobx-state-tree");
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
+    gffGzLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
     },
-    location: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/my.gff.gz.tbi',
-        locationType: 'UriLocation'
-      }
-    }
-  }),
-  dontRedispatch: {
-    type: 'stringArray',
-    defaultValue: ['chromosome', 'region']
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+    index: (0, configuration_1.ConfigurationSchema)('Gff3TabixIndex', {
+        indexType: {
+            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.gff.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    dontRedispatch: {
+        type: 'stringArray',
+        defaultValue: ['chromosome', 'region'],
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/Gff3TabixAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/Gff3TabixAdapter/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/Gff3TabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/index.js

@@ -1,138 +1,117 @@
 "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 _Gff3TabixAdapter = require("./Gff3TabixAdapter");
-
-var _tracks = require("@jbrowse/core/util/tracks");
-
-var _Gff3Adapter = require("./Gff3Adapter");
-
-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 _default = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(_default, _Plugin);
-
-  var _super = _createSuper(_default);
-
-  function _default() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, _default);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+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 Gff3TabixAdapter_1 = require("./Gff3TabixAdapter");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var Gff3Adapter_1 = require("./Gff3Adapter");
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'GFF3Plugin';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'GFF3Plugin');
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'Gff3TabixAdapter',
-          configSchema: _Gff3TabixAdapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./Gff3TabixAdapter/Gff3TabixAdapter'));
-            }).then(function (r) {
-              return r.default;
+    default_1.prototype.install = function (pluginManager) {
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'Gff3TabixAdapter',
+                configSchema: Gff3TabixAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./Gff3TabixAdapter/Gff3TabixAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.gff3?\.b?gz$/i;
-          var adapterName = 'Gff3TabixAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var indexName = index && (0, _tracks.getFileName)(index);
-
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bamLocation: file,
-              gffGzLocation: file,
-              index: {
-                location: index || (0, _tracks.makeIndex)(file, '.tbi'),
-                indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'TBI')
-              }
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.gff3?\.b?gz$/i;
+                var adapterName = 'Gff3TabixAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var indexName = index && (0, tracks_1.getFileName)(index);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bamLocation: file,
+                        gffGzLocation: 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.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'Gff3Adapter',
-          configSchema: _Gff3Adapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./Gff3Adapter/Gff3Adapter'));
-            }).then(function (r) {
-              return r.default;
+        });
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'Gff3Adapter',
+                configSchema: Gff3Adapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./Gff3Adapter/Gff3Adapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.gff3?$/i;
-          var adapterName = 'Gff3Adapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var obj = {
-            type: adapterName,
-            gffLocation: file
-          };
-
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj;
-          } else if (adapterHint === adapterName) {
-            return obj;
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-    }
-  }]);
-  return _default;
-}(_Plugin2.default);
-
-exports.default = _default;
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.gff3?$/i;
+                var adapterName = 'Gff3Adapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var obj = {
+                    type: adapterName,
+                    gffLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+    };
+    return default_1;
+}(Plugin_1.default));
+exports.default = default_1;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/esm/Gff3Adapter/Gff3Adapter.d.ts

@@ -0,0 +1,17 @@
+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 gffFeatures?: Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree>;
+    }>;
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(): Promise<string>;
+    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    private featureData;
+    freeResources(): void;
+}

package/esm/Gff3Adapter/Gff3Adapter.js

@@ -0,0 +1,146 @@
+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 gff from '@gmod/gff';
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export default class extends BaseFeatureDataAdapter {
+    async loadDataP() {
+        const pm = this.pluginManager;
+        const buf = await openLocation(this.getConf('gffLocation'), pm).readFile();
+        const buffer = isGzip(buf) ? await unzip(buf) : buf;
+        // 512MB  max chrome string length is 512MB
+        if (buffer.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const lines = data.split('\n');
+        const headerLines = [];
+        for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
+            headerLines.push(lines[i]);
+        }
+        const header = headerLines.join('\n');
+        const feats = gff.parseStringSync(data, {
+            parseFeatures: true,
+            parseComments: false,
+            parseDirectives: false,
+            parseSequences: false,
+        });
+        const intervalTree = feats
+            .flat()
+            .map((f, i) => new SimpleFeature({
+            data: this.featureData(f),
+            id: `${this.id}-offset-${i}`,
+        }))
+            .reduce((acc, obj) => {
+            const key = obj.get('refName');
+            if (!acc[key]) {
+                acc[key] = new IntervalTree();
+            }
+            acc[key].insert([obj.get('start'), obj.get('end')], obj);
+            return acc;
+        }, {});
+        return { header, intervalTree };
+    }
+    async loadData() {
+        if (!this.gffFeatures) {
+            this.gffFeatures = this.loadDataP().catch(e => {
+                this.gffFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.gffFeatures;
+    }
+    async getRefNames(opts = {}) {
+        const { intervalTree } = await this.loadData();
+        return Object.keys(intervalTree);
+    }
+    async getHeader() {
+        const { header } = await this.loadData();
+        return header;
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            var _a;
+            try {
+                const { start, end, refName } = query;
+                const { intervalTree } = await this.loadData();
+                (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(f));
+                observer.complete();
+            }
+            catch (e) {
+                observer.error(e);
+            }
+        }, opts.signal);
+    }
+    featureData(data) {
+        const f = { ...data };
+        f.start -= 1; // convert to interbase
+        if (data.strand === '+') {
+            f.strand = 1;
+        }
+        else if (data.strand === '-') {
+            f.strand = -1;
+        }
+        else if (data.strand === '.') {
+            f.strand = 0;
+        }
+        else {
+            f.strand = undefined;
+        }
+        f.phase = Number(data.phase);
+        f.refName = data.seq_id;
+        if (data.score === null) {
+            delete f.score;
+        }
+        if (data.phase === null) {
+            delete f.score;
+        }
+        const defaultFields = [
+            'start',
+            'end',
+            'seq_id',
+            'score',
+            'type',
+            'source',
+            'phase',
+            'strand',
+        ];
+        const dataAttributes = data.attributes || {};
+        Object.keys(dataAttributes).forEach(a => {
+            let b = a.toLowerCase();
+            if (defaultFields.includes(b)) {
+                // add "suffix" to tag name if it already exists
+                // reproduces behavior of NCList
+                b += '2';
+            }
+            if (dataAttributes[a] !== null) {
+                let attr = dataAttributes[a];
+                if (Array.isArray(attr) && attr.length === 1) {
+                    ;
+                    [attr] = attr;
+                }
+                f[b] = attr;
+            }
+        });
+        f.refName = f.seq_id;
+        // the SimpleFeature constructor takes care of recursively inflating subfeatures
+        if (data.child_features && data.child_features.length) {
+            f.subfeatures = data.child_features
+                .map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
+                .flat();
+        }
+        delete f.child_features;
+        delete f.data;
+        delete f.derived_features;
+        delete f.attributes;
+        delete f.seq_id;
+        return f;
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=Gff3Adapter.js.map

package/esm/Gff3Adapter/Gff3Adapter.js.map

@@ -0,0 +1 @@
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package/esm/Gff3Adapter/configSchema.d.ts

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

package/esm/Gff3Adapter/configSchema.js

@@ -0,0 +1,8 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('Gff3Adapter', {
+    gffLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/Gff3Adapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3Adapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,aAAa,EACb;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/Gff3Adapter/index.d.ts

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

package/esm/Gff3Adapter/index.js

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

package/esm/Gff3Adapter/index.js.map

@@ -0,0 +1 @@
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package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -0,0 +1,20 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { TabixIndexedFile } from '@gmod/tabix';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends BaseFeatureDataAdapter {
+    protected gff: TabixIndexedFile;
+    protected dontRedispatch: string[];
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(opts?: BaseOptions): Promise<any>;
+    getHeader(): Promise<string>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    private getFeaturesHelper;
+    private parseLine;
+    private formatFeatures;
+    private featureData;
+    freeResources(): void;
+}