@jbrowse/core 2.13.1 → 2.14.0

package/assemblyManager/assemblyManager.d.ts

@@ -18,16 +18,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
         error: unknown;
-        loaded: boolean;
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
+    } & {
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         getConf(arg: string): any;
     } & {
@@ -50,13 +50,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setLoaded({ regions, refNameAliases, cytobands, }: {
+            regions: import("../util").Region[];
+            refNameAliases: {
+                [x: string]: string;
+            };
+            cytobands: import("../util").Feature[];
+        }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -69,29 +73,29 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
-    readonly assemblyNameMap: Record<string, ({
+    readonly assemblyNameMap: Record<string, {
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: unknown;
-        loaded: boolean;
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
+    } & {
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         getConf(arg: string): any;
     } & {
@@ -114,13 +118,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setLoaded({ regions, refNameAliases, cytobands, }: {
+            regions: import("../util").Region[];
+            refNameAliases: {
+                [x: string]: string;
+            };
+            cytobands: import("../util").Feature[];
+        }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -133,27 +141,27 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
         error: unknown;
-        loaded: boolean;
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
+    } & {
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         getConf(arg: string): any;
     } & {
@@ -176,13 +184,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setLoaded({ regions, refNameAliases, cytobands, }: {
+            regions: import("../util").Region[];
+            refNameAliases: {
+                [x: string]: string;
+            };
+            cytobands: import("../util").Feature[];
+        }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -195,14 +207,14 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
 } & {
     /**
      * #method
@@ -211,16 +223,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: unknown;
-        loaded: boolean;
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
+    } & {
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         getConf(arg: string): any;
     } & {
@@ -243,13 +255,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setLoaded({ regions, refNameAliases, cytobands, }: {
+            regions: import("../util").Region[];
+            refNameAliases: {
+                [x: string]: string;
+            };
+            cytobands: import("../util").Feature[];
+        }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -262,27 +278,27 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
         error: unknown;
-        loaded: boolean;
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
+    } & {
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         getConf(arg: string): any;
     } & {
@@ -305,13 +321,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setLoaded({ regions, refNameAliases, cytobands, }: {
+            regions: import("../util").Region[];
+            refNameAliases: {
+                [x: string]: string;
+            };
+            cytobands: import("../util").Feature[];
+        }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -324,12 +344,12 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     /**
@@ -353,16 +373,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: unknown;
-        loaded: boolean;
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
+    } & {
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         getConf(arg: string): any;
     } & {
@@ -385,13 +405,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setLoaded({ regions, refNameAliases, cytobands, }: {
+            regions: import("../util").Region[];
+            refNameAliases: {
+                [x: string]: string;
+            };
+            cytobands: import("../util").Feature[];
+        }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -404,27 +428,27 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
         error: unknown;
-        loaded: boolean;
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
+    } & {
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         getConf(arg: string): any;
     } & {
@@ -447,13 +471,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setLoaded({ regions, refNameAliases, cytobands, }: {
+            regions: import("../util").Region[];
+            refNameAliases: {
+                [x: string]: string;
+            };
+            cytobands: import("../util").Feature[];
+        }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
+            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -466,12 +494,12 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
     /**
@@ -481,7 +509,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{
-        [x: string]: string | undefined;
+        [x: string]: string;
     } | undefined>;
     /**
      * #method
@@ -490,7 +518,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{
-        [x: string]: string | undefined;
+        [x: string]: string;
     } | undefined>;
     /**
      * #method

package/assemblyManager/assemblyManager.js

@@ -54,9 +54,7 @@ function assemblyManagerFactory(conf, pm) {
         get assemblyList() {
             // name is the explicit identifier and can be accessed without getConf,
             // hence the union with {name:string}
-            const { jbrowse: { assemblies }, session: { sessionAssemblies = [], temporaryAssemblies = [] } = {},
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-             } = (0, mobx_state_tree_1.getParent)(self);
+            const { jbrowse: { assemblies }, session: { sessionAssemblies = [], temporaryAssemblies = [] } = {}, } = (0, mobx_state_tree_1.getParent)(self);
             return [
                 ...assemblies,
                 ...sessionAssemblies,
@@ -64,7 +62,6 @@ function assemblyManagerFactory(conf, pm) {
             ];
         },
         get rpcManager() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             return (0, mobx_state_tree_1.getParent)(self).rpcManager;
         },
     }))
@@ -92,9 +89,9 @@ function assemblyManagerFactory(conf, pm) {
                 return undefined;
             }
             await assembly.load();
-            await (0, util_1.when)(() => !!((assembly === null || assembly === void 0 ? void 0 : assembly.regions) && assembly.refNameAliases) ||
-                !!(assembly === null || assembly === void 0 ? void 0 : assembly.error));
+            await (0, util_1.when)(() => !!(assembly.regions && assembly.refNameAliases) || !!assembly.error);
             if (assembly.error) {
+                // eslint-disable-next-line @typescript-eslint/only-throw-error
                 throw assembly.error;
             }
             return assembly;

package/configuration/configurationSchema.d.ts

@@ -13,7 +13,7 @@ export interface ConfigurationSchemaOptions<BASE_SCHEMA extends AnyConfiguration
     actions?: (self: unknown) => any;
     views?: (self: unknown) => any;
     extend?: (self: unknown) => any;
-    preProcessSnapshot?: (snapshot: {}) => {};
+    preProcessSnapshot?: (snapshot: Record<string, unknown>) => Record<string, unknown>;
 }
 declare function makeConfigurationSchemaModel<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions<any, any>>(modelName: string, schemaDefinition: DEFINITION, options: OPTIONS): import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<Record<string, any>, {
     setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({

package/configuration/configurationSchema.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ConfigurationSchema = ConfigurationSchema;
 exports.ConfigurationReference = ConfigurationReference;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("../util/types/mst");
 const configurationSlot_1 = __importDefault(require("./configurationSlot"));
@@ -37,7 +36,7 @@ function preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition
             ...inputOptions.baseConfiguration.jbrowseSchemaOptions,
             ...inputOptions,
         };
-        delete options.baseConfiguration;
+        options.baseConfiguration = undefined;
     }
     return { schemaDefinition, options };
 }

package/configuration/configurationSlot.js

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = ConfigSlot;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const mobx_state_tree_1 = require("mobx-state-tree");
 const jexlStrings_1 = require("../util/jexlStrings");
 const mst_1 = require("../util/types/mst");
@@ -182,9 +181,11 @@ function ConfigSlot(slotName, { description = '', model, type, defaultValue, con
             if (self.isCallback) {
                 // compile as jexl function
                 const { pluginManager } = (0, util_1.getEnv)(self);
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 if (!pluginManager && typeof jest === 'undefined') {
                     console.warn('no pluginManager detected on config env (if you dynamically instantiate a config, for example in renderProps for your display model, check that you add the env argument)');
                 }
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 return (0, jexlStrings_1.stringToJexlExpression)(String(self.value), pluginManager === null || pluginManager === void 0 ? void 0 : pluginManager.jexl);
             }
             return { evalSync: () => self.value };
@@ -244,15 +245,13 @@ function ConfigSlot(slotName, { description = '', model, type, defaultValue, con
                 /* ignore */
             }
             self.value = defaultValue;
-            // if it is still a callback (happens if the defaultValue is a callback),
-            // then use the last-resort fallback default
+            // if it is still a callback (happens if the defaultValue is a
+            // callback), then use the last-resort fallback default
             // if defaultValue has jexl: string, run this part
-            if (self.isCallback) {
-                if (!(type in fallbackDefaults)) {
-                    throw new Error(`no fallbackDefault defined for type ${type}`);
-                }
-                self.value = fallbackDefaults[type];
+            if (!(type in fallbackDefaults)) {
+                throw new Error(`no fallbackDefault defined for type ${type}`);
             }
+            self.value = fallbackDefaults[type];
         },
     }));
     // if there are any type-specific extensions (views or actions)

package/configuration/util.js

@@ -7,7 +7,6 @@ exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
 exports.isConfigurationSchemaType = isConfigurationSchemaType;
 exports.isConfigurationModel = isConfigurationModel;
 exports.isConfigurationSlotType = isConfigurationSlotType;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_reflection_1 = require("../util/mst-reflection");
 /**
@@ -20,9 +19,6 @@ const mst_reflection_1 = require("../util/mst-reflection");
  *  will be sent to each of the slotNames
  */
 function readConfObject(confObject, slotPath, args = {}) {
-    if (!confObject) {
-        throw new TypeError('must provide conf object to read');
-    }
     if (!slotPath) {
         return JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(confObject)));
     }
@@ -78,9 +74,6 @@ function readConfObject(confObject, slotPath, args = {}) {
  *   will be sent to each of the slotNames
  */
 function getConf(model, slotPath, args) {
-    if (!model) {
-        throw new TypeError('must provide a model object');
-    }
     const { configuration } = model;
     if (isConfigurationModel(configuration)) {
         return readConfObject(configuration, slotPath, args);

package/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts

@@ -105,9 +105,9 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
      * Derived classes can override this to return alternative calculations for
      * featureDensity, or they can also return an object containing a byte size
      * calculation with the format \{bytes:number, fetchSizeLimit:number\} where
-     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too much
-     * data' (e.g. CRAM and
-     * BAM may vary on what they think too much data is)
+     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too
+     * much data' (e.g. CRAM and BAM may vary on what they think too much data
+     * is)
      */
     getRegionFeatureDensityStats(region: Region, opts?: BaseOptions): Promise<FeatureDensityStats>;
     /**
@@ -120,9 +120,9 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
      * Derived classes can override this to return alternative calculations for
      * featureDensity, or they can also return an object containing a byte size
      * calculation with the format \{bytes:number, fetchSizeLimit:number\} where
-     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too much
-     * data' (e.g. CRAM and
-     * BAM may vary on what they think too much data is)
+     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too
+     * much data' (e.g. CRAM and BAM may vary on what they think too much data
+     * is)
      */
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<FeatureDensityStats>;
 }

package/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js

@@ -116,9 +116,9 @@ class BaseFeatureDataAdapter extends BaseAdapter_1.BaseAdapter {
      * Derived classes can override this to return alternative calculations for
      * featureDensity, or they can also return an object containing a byte size
      * calculation with the format \{bytes:number, fetchSizeLimit:number\} where
-     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too much
-     * data' (e.g. CRAM and
-     * BAM may vary on what they think too much data is)
+     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too
+     * much data' (e.g. CRAM and BAM may vary on what they think too much data
+     * is)
      */
     getRegionFeatureDensityStats(region, opts) {
         let lastTime = +Date.now();
@@ -160,9 +160,9 @@ class BaseFeatureDataAdapter extends BaseAdapter_1.BaseAdapter {
      * Derived classes can override this to return alternative calculations for
      * featureDensity, or they can also return an object containing a byte size
      * calculation with the format \{bytes:number, fetchSizeLimit:number\} where
-     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too much
-     * data' (e.g. CRAM and
-     * BAM may vary on what they think too much data is)
+     * fetchSizeLimit is the adapter-defined limit for what it thinks is 'too
+     * much data' (e.g. CRAM and BAM may vary on what they think too much data
+     * is)
      */
     async getMultiRegionFeatureDensityStats(regions, opts) {
         if (!regions.length) {

package/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts

@@ -3,6 +3,7 @@ import { BaseOptions } from './types';
 export interface Alias {
     refName: string;
     aliases: string[];
+    override?: boolean;
 }
 export interface BaseRefNameAliasAdapter extends BaseAdapter {
     getRefNameAliases(opts: BaseOptions): Promise<Alias[]>;

package/data_adapters/CytobandAdapter/CytobandAdapter.d.ts

@@ -1,6 +1,5 @@
 import { SimpleFeature } from '../../util';
 import { BaseAdapter } from '../BaseAdapter';
-export declare function isGzip(buf: Buffer): boolean;
 export default class CytobandAdapter extends BaseAdapter {
     getData(): Promise<SimpleFeature[]>;
     freeResources(): void;

package/data_adapters/CytobandAdapter/CytobandAdapter.js

@@ -1,14 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isGzip = isGzip;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 // locals
 const util_1 = require("../../util");
 const io_1 = require("../../util/io");
 const BaseAdapter_1 = require("../BaseAdapter");
-function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
 class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
     async getData() {
         const pm = this.pluginManager;
@@ -17,7 +13,7 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
             return [];
         }
         const buffer = await (0, io_1.openLocation)(loc, pm).readFile();
-        const buf = isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
         const text = new TextDecoder('utf8', { fatal: true }).decode(buf);
         return text
             .split(/\n|\r\n|\r/)
@@ -26,11 +22,11 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
             const [refName, start, end, name, type] = line.split('\t');
             return new util_1.SimpleFeature({
                 uniqueId: `${i}`,
-                refName,
+                refName: refName,
                 start: +start,
                 end: +end,
-                name,
-                type,
+                name: name,
+                type: type,
             });
         });
     }