@jbrowse/plugin-sequence 1.4.1 → 1.5.2

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,5 +1,7 @@
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends IndexedFasta {
-    constructor(config: AnyConfigurationModel);
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
 }

package/dist/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,10 +1,12 @@
 import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Instance } from 'mobx-state-tree';
 import MyConfigSchema from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseAdapter implements RegionsAdapter {
     protected refSeqs: Promise<Record<string, number>>;
     protected source: string;
-    constructor(config: Instance<typeof MyConfigSchema>);
+    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     private init;
     getRegions(): Promise<{
         refName: string;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -3,10 +3,12 @@ import { BaseFeatureDataAdapter, SequenceAdapter, BaseOptions } from '@jbrowse/c
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseFeatureDataAdapter implements SequenceAdapter {
     protected fasta: typeof IndexedFasta;
     private seqCache;
-    constructor(config: AnyConfigurationModel);
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): any;
     getRegions(opts?: BaseOptions): Promise<{
         refName: string;

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -28,7 +28,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
         layout: any;
         status: string;
-        error: Error | undefined;
+        error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
@@ -48,7 +48,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
-        setError(error: Error): void;
+        setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -62,7 +62,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     height: import("mobx-state-tree").IType<number | undefined, number, number>;
 }, {
     rendererTypeName: string;
-    error: Error | undefined;
+    error: unknown;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -71,14 +71,14 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }> & {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -90,14 +90,14 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }> & {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -109,7 +109,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): undefined;
 } & {
-    setError(error?: Error | undefined): void;
+    setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {

package/dist/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -2,11 +2,13 @@ import { BaseFeatureDataAdapter, SequenceAdapter } from '@jbrowse/core/data_adap
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class TwoBitAdapter extends BaseFeatureDataAdapter implements SequenceAdapter {
     private twobit;
     protected chromSizesData: Promise<Record<string, number> | undefined>;
     private initChromSizes;
-    constructor(config: AnyConfigurationModel);
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(): Promise<any>;
     getRegions(): Promise<NoAssemblyRegion[]>;
     /**

package/dist/plugin-sequence.cjs.development.js

@@ -10,6 +10,7 @@ var FeatureRendererType = _interopDefault(require('@jbrowse/core/pluggableElemen
 var TrackType = _interopDefault(require('@jbrowse/core/pluggableElementTypes/TrackType'));
 var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
 var pluginLinearGenomeView = require('@jbrowse/plugin-linear-genome-view');
+var tracks = require('@jbrowse/core/util/tracks');
 var configuration = require('@jbrowse/core/configuration');
 var color = require('@jbrowse/core/util/color');
 var ui = require('@jbrowse/core/ui');
@@ -193,6 +194,8 @@ function _assertThisInitialized(self) {
 function _possibleConstructorReturn(self, call) {
   if (call && (typeof call === "object" || typeof call === "function")) {
     return call;
+  } else if (call !== void 0) {
+    throw new TypeError("Derived constructors may only return object or undefined");
   }
 
   return _assertThisInitialized(self);
@@ -296,19 +299,22 @@ var bgzipFastaAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSche
   fastaLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.gz'
+      uri: '/path/to/seq.fa.gz',
+      locationType: 'UriLocation'
     }
   },
   faiLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.gz.fai'
+      uri: '/path/to/seq.fa.gz.fai',
+      locationType: 'UriLocation'
     }
   },
   gziLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.gz.gzi'
+      uri: '/path/to/seq.fa.gz.gzi',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -319,7 +325,8 @@ var chromSizesAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSche
   chromSizesLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/species.chrom.sizes'
+      uri: '/path/to/species.chrom.sizes',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -551,13 +558,15 @@ var indexedFastaAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSc
   fastaLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa'
+      uri: '/path/to/seq.fa',
+      locationType: 'UriLocation'
     }
   },
   faiLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.fai'
+      uri: '/path/to/seq.fa.fai',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -594,9 +603,7 @@ function modelFactory(configSchema) {
           showTranslation: showTranslation
         });
       },
-      regionCannotBeRendered: function regionCannotBeRendered()
-      /* region */
-      {
+      regionCannotBeRendered: function regionCannotBeRendered() {
         var view = util.getContainingView(self);
 
         if (view && view.bpPerPx >= 1) {
@@ -657,13 +664,15 @@ var twoBitAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSchema('
   twoBitLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.2bit'
+      uri: '/path/to/my.2bit',
+      locationType: 'UriLocation'
     }
   },
   chromSizesLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/default.chrom.sizes'
+      uri: '/path/to/default.chrom.sizes',
+      locationType: 'UriLocation'
     },
     description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time'
   }
@@ -813,6 +822,12 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         return new AdapterType({
           name: 'TwoBitAdapter',
           configSchema: twoBitAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return TwoBitAdapter$1; }).then(function (r) {
               return r["default"];
@@ -820,10 +835,41 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.2bit$/i;
+          var adapterName = 'TwoBitAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              twoBitLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'TwoBitAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'ChromSizesAdapter',
           configSchema: chromSizesAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return ChromSizesAdapter; }).then(function (r) {
               return r["default"];
@@ -835,6 +881,12 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         return new AdapterType({
           name: 'IndexedFastaAdapter',
           configSchema: indexedFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return IndexedFastaAdapter; }).then(function (r) {
               return r["default"];
@@ -842,10 +894,42 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
+          var adapterName = 'IndexedFastaAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              fastaLocation: file,
+              faiLocation: index || tracks.makeIndex(file, '.fai')
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'IndexedFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'BgzipFastaAdapter',
           configSchema: bgzipFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return BgzipFastaAdapter; }).then(function (r) {
               return r["default"];
@@ -853,9 +937,41 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
+          var adapterName = 'BgzipFastaAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              faiLocation: tracks.makeIndex(file, '.fai'),
+              gziLocation: tracks.makeIndex(file, '.gzi')
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'BgzipFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType(_objectSpread2({
-          name: 'GCContentAdapter'
+          name: 'GCContentAdapter',
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
         }, pluginManager.load(GCContentAdapterF)));
       });
       pluginManager.addTrackType(function () {
@@ -988,11 +1104,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
 
 
     var IteratorPrototype = {};
-
-    IteratorPrototype[iteratorSymbol] = function () {
+    define(IteratorPrototype, iteratorSymbol, function () {
       return this;
-    };
-
+    });
     var getProto = Object.getPrototypeOf;
     var NativeIteratorPrototype = getProto && getProto(getProto(values([])));
 
@@ -1003,8 +1117,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     }
 
     var Gp = GeneratorFunctionPrototype.prototype = Generator.prototype = Object.create(IteratorPrototype);
-    GeneratorFunction.prototype = Gp.constructor = GeneratorFunctionPrototype;
-    GeneratorFunctionPrototype.constructor = GeneratorFunction;
+    GeneratorFunction.prototype = GeneratorFunctionPrototype;
+    define(Gp, "constructor", GeneratorFunctionPrototype);
+    define(GeneratorFunctionPrototype, "constructor", GeneratorFunction);
     GeneratorFunction.displayName = define(GeneratorFunctionPrototype, toStringTagSymbol, "GeneratorFunction"); // Helper for defining the .next, .throw, and .return methods of the
     // Iterator interface in terms of a single ._invoke method.
 
@@ -1109,11 +1224,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     }
 
     defineIteratorMethods(AsyncIterator.prototype);
-
-    AsyncIterator.prototype[asyncIteratorSymbol] = function () {
+    define(AsyncIterator.prototype, asyncIteratorSymbol, function () {
       return this;
-    };
-
+    });
     exports.AsyncIterator = AsyncIterator; // Note that simple async functions are implemented on top of
     // AsyncIterator objects; they just return a Promise for the value of
     // the final result produced by the iterator.
@@ -1290,13 +1403,12 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     // object to not be returned from this call. This ensures that doesn't happen.
     // See https://github.com/facebook/regenerator/issues/274 for more details.
 
-    Gp[iteratorSymbol] = function () {
+    define(Gp, iteratorSymbol, function () {
       return this;
-    };
-
-    Gp.toString = function () {
+    });
+    define(Gp, "toString", function () {
       return "[object Generator]";
-    };
+    });
 
     function pushTryEntry(locs) {
       var entry = {
@@ -1608,14 +1720,19 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
   } catch (accidentalStrictMode) {
     // This module should not be running in strict mode, so the above
     // assignment should always work unless something is misconfigured. Just
-    // in case runtime.js accidentally runs in strict mode, we can escape
+    // in case runtime.js accidentally runs in strict mode, in modern engines
+    // we can explicitly access globalThis. In older engines we can escape
     // strict mode using a global Function call. This could conceivably fail
     // if a Content Security Policy forbids using Function, but in that case
     // the proper solution is to fix the accidental strict mode problem. If
     // you've misconfigured your bundler to force strict mode and applied a
     // CSP to forbid Function, and you're not willing to fix either of those
     // problems, please detail your unique predicament in a GitHub issue.
-    Function("r", "regeneratorRuntime = r")(runtime);
+    if (typeof globalThis === "object") {
+      globalThis.regeneratorRuntime = runtime;
+    } else {
+      Function("r", "regeneratorRuntime = r")(runtime);
+    }
   }
 });
 
@@ -1824,9 +1941,9 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return default_1;
@@ -1843,15 +1960,15 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   var _super = /*#__PURE__*/_createSuper(TwoBitAdapter);
 
-  function TwoBitAdapter(config) {
+  function TwoBitAdapter(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, TwoBitAdapter);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     _this.chromSizesData = _this.initChromSizes();
     _this.twobit = new twobit.TwoBitFile({
-      filehandle: io.openLocation(configuration.readConfObject(config, 'twoBitLocation'))
+      filehandle: io.openLocation(configuration.readConfObject(config, 'twoBitLocation'), _this.pluginManager)
     });
     return _this;
   }
@@ -1874,7 +1991,7 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   break;
                 }
 
-                file = io.openLocation(conf);
+                file = io.openLocation(conf, this.pluginManager);
                 _context.next = 5;
                 return file.readFile('utf8');
 
@@ -2071,9 +2188,9 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return TwoBitAdapter;
@@ -2089,19 +2206,19 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
-  function _default(config) {
+  function _default(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, _default);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     var chromSizesLocation = configuration.readConfObject(config, 'chromSizesLocation');
 
     if (!chromSizesLocation) {
       throw new Error('must provide chromSizesLocation');
     }
 
-    var file = io.openLocation(chromSizesLocation);
+    var file = io.openLocation(chromSizesLocation, _this.pluginManager);
     _this.source = file.toString();
     _this.refSeqs = _this.init(file);
     return _this;
@@ -2200,9 +2317,9 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
     }
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2218,12 +2335,12 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
-  function _default(config) {
+  function _default(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, _default);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     _this.seqCache = new AbortablePromiseCache({
       cache: new LRU({
         maxSize: 200
@@ -2258,8 +2375,8 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     var fastaLocation = configuration.readConfObject(config, 'fastaLocation');
     var faiLocation = configuration.readConfObject(config, 'faiLocation');
     var fastaOpts = {
-      fasta: io.openLocation(fastaLocation),
-      fai: io.openLocation(faiLocation)
+      fasta: io.openLocation(fastaLocation, _this.pluginManager),
+      fai: io.openLocation(faiLocation, _this.pluginManager)
     };
     _this.fasta = new indexedfasta.IndexedFasta(fastaOpts);
     return _this;
@@ -2388,9 +2505,9 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2406,12 +2523,12 @@ var _default$2 = /*#__PURE__*/function (_IndexedFasta) {
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
-  function _default(config) {
+  function _default(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, _default);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     var fastaLocation = configuration.readConfObject(config, 'fastaLocation');
     var faiLocation = configuration.readConfObject(config, 'faiLocation');
     var gziLocation = configuration.readConfObject(config, 'gziLocation');
@@ -2429,9 +2546,9 @@ var _default$2 = /*#__PURE__*/function (_IndexedFasta) {
     }
 
     var fastaOpts = {
-      fasta: io.openLocation(fastaLocation),
-      fai: io.openLocation(faiLocation),
-      gzi: io.openLocation(gziLocation)
+      fasta: io.openLocation(fastaLocation, _this.pluginManager),
+      fai: io.openLocation(faiLocation, _this.pluginManager),
+      gzi: io.openLocation(gziLocation, _this.pluginManager)
     };
     _this.fasta = new indexedfasta.BgzipIndexedFasta(fastaOpts);
     return _this;