@jbrowse/plugin-config 2.2.0 → 2.2.2

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.d.ts

@@ -19,7 +19,7 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter impleme
     }[]>;
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources(): void;

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.js

@@ -62,7 +62,7 @@ class FromConfigSequenceAdapter extends FromConfigAdapter_1.default {
     }
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources( /* { region } */) { }

package/dist/FromConfigAdapter/fromConfig.js

@@ -13,13 +13,6 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('FromConfigAdapter
         type: 'frozen',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
 }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
 exports.default = configSchema;
 //# sourceMappingURL=fromConfig.js.map

package/dist/FromConfigAdapter/fromConfig.js.map

@@ -1 +1 @@
-{"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,YAAY,CAAA"}
+{"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,YAAY,CAAA"}

package/dist/FromConfigAdapter/fromConfigRegions.js

@@ -14,13 +14,6 @@ const regionsConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfig
         type: 'frozen',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
 }, {
     explicitlyTyped: true,
     implicitIdentifier: 'adapterId',

package/dist/FromConfigAdapter/fromConfigRegions.js.map

@@ -1 +1 @@
-{"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,kBAAe,mBAAmB,CAAA"}
+{"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,kBAAe,mBAAmB,CAAA"}

package/dist/FromConfigAdapter/fromConfigSequence.js

@@ -13,13 +13,6 @@ const sequenceConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfi
         type: 'frozen',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
 }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
 exports.default = sequenceConfigSchema;
 //# sourceMappingURL=fromConfigSequence.js.map

package/dist/FromConfigAdapter/fromConfigSequence.js.map

@@ -1 +1 @@
-{"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,IAAA,mCAAmB,EAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,oBAAoB,CAAA"}
+{"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,IAAA,mCAAmB,EAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,oBAAoB,CAAA"}

package/dist/FromConfigAdapter/index.d.ts

@@ -2,5 +2,5 @@ export { default as AdapterClass } from './FromConfigAdapter';
 export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter';
 export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter';
 export { default as configSchema } from './fromConfig';
-export { default as regionsConfigSchema } from './fromConfig';
+export { default as regionsConfigSchema } from './fromConfigRegions';
 export { default as sequenceConfigSchema } from './fromConfigSequence';

package/dist/FromConfigAdapter/index.js

@@ -12,8 +12,8 @@ var FromConfigSequenceAdapter_1 = require("./FromConfigSequenceAdapter");
 Object.defineProperty(exports, "SequenceAdapterClass", { enumerable: true, get: function () { return __importDefault(FromConfigSequenceAdapter_1).default; } });
 var fromConfig_1 = require("./fromConfig");
 Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(fromConfig_1).default; } });
-var fromConfig_2 = require("./fromConfig");
-Object.defineProperty(exports, "regionsConfigSchema", { enumerable: true, get: function () { return __importDefault(fromConfig_2).default; } });
+var fromConfigRegions_1 = require("./fromConfigRegions");
+Object.defineProperty(exports, "regionsConfigSchema", { enumerable: true, get: function () { return __importDefault(fromConfigRegions_1).default; } });
 var fromConfigSequence_1 = require("./fromConfigSequence");
 Object.defineProperty(exports, "sequenceConfigSchema", { enumerable: true, get: function () { return __importDefault(fromConfigSequence_1).default; } });
 //# sourceMappingURL=index.js.map

package/dist/FromConfigAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,yDAA6D;AAApD,kIAAA,OAAO,OAAgB;AAChC,uEAA2E;AAAlE,gJAAA,OAAO,OAAuB;AACvC,yEAA6E;AAApE,kJAAA,OAAO,OAAwB;AACxC,2CAAsD;AAA7C,2HAAA,OAAO,OAAgB;AAChC,2CAA6D;AAApD,kIAAA,OAAO,OAAuB;AACvC,2DAAsE;AAA7D,2IAAA,OAAO,OAAwB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,yDAA6D;AAApD,kIAAA,OAAO,OAAgB;AAChC,uEAA2E;AAAlE,gJAAA,OAAO,OAAuB;AACvC,yEAA6E;AAApE,kJAAA,OAAO,OAAwB;AACxC,2CAAsD;AAA7C,2HAAA,OAAO,OAAgB;AAChC,yDAAoE;AAA3D,yIAAA,OAAO,OAAuB;AACvC,2DAAsE;AAA7D,2IAAA,OAAO,OAAwB"}

package/dist/RefNameAliasAdapter/configSchema.js

@@ -3,6 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 /**
  * #config RefNameAliasAdapter
+ * can read "chromAliases" type files from UCSC or any tab separated file of
+ * refName aliases
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAliasAdapter', {
@@ -18,6 +20,8 @@ const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAli
     },
     /**
      * #slot
+     * by default, the "ref names that match the fasta" are assumed to be in the
+     * first column (0), change this variable if needed
      */
     refNameColumn: {
         type: 'number',

package/dist/RefNameAliasAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;;;OAIG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}

package/esm/FromConfigAdapter/FromConfigSequenceAdapter.d.ts

@@ -19,7 +19,7 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter impleme
     }[]>;
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources(): void;

package/esm/FromConfigAdapter/FromConfigSequenceAdapter.js

@@ -57,7 +57,7 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter {
     }
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources( /* { region } */) { }

package/esm/FromConfigAdapter/fromConfig.js

@@ -11,13 +11,6 @@ const configSchema = ConfigurationSchema('FromConfigAdapter', {
         type: 'frozen',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
 }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
 export default configSchema;
 //# sourceMappingURL=fromConfig.js.map

package/esm/FromConfigAdapter/fromConfig.js.map

@@ -1 +1 @@
-{"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,YAAY,CAAA"}
+{"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,YAAY,CAAA"}

package/esm/FromConfigAdapter/fromConfigRegions.js

@@ -12,13 +12,6 @@ const regionsConfigSchema = ConfigurationSchema('FromConfigRegionsAdapter', {
         type: 'frozen',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
 }, {
     explicitlyTyped: true,
     implicitIdentifier: 'adapterId',

package/esm/FromConfigAdapter/fromConfigRegions.js.map

@@ -1 +1 @@
-{"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,eAAe,mBAAmB,CAAA"}
+{"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,eAAe,mBAAmB,CAAA"}

package/esm/FromConfigAdapter/fromConfigSequence.js

@@ -11,13 +11,6 @@ const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
         type: 'frozen',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
 }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
 export default sequenceConfigSchema;
 //# sourceMappingURL=fromConfigSequence.js.map

package/esm/FromConfigAdapter/fromConfigSequence.js.map

@@ -1 +1 @@
-{"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,mBAAmB,CAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,oBAAoB,CAAA"}
+{"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,mBAAmB,CAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,oBAAoB,CAAA"}

package/esm/FromConfigAdapter/index.d.ts

@@ -2,5 +2,5 @@ export { default as AdapterClass } from './FromConfigAdapter';
 export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter';
 export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter';
 export { default as configSchema } from './fromConfig';
-export { default as regionsConfigSchema } from './fromConfig';
+export { default as regionsConfigSchema } from './fromConfigRegions';
 export { default as sequenceConfigSchema } from './fromConfigSequence';

package/esm/FromConfigAdapter/index.js

@@ -2,6 +2,6 @@ export { default as AdapterClass } from './FromConfigAdapter';
 export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter';
 export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter';
 export { default as configSchema } from './fromConfig';
-export { default as regionsConfigSchema } from './fromConfig';
+export { default as regionsConfigSchema } from './fromConfigRegions';
 export { default as sequenceConfigSchema } from './fromConfigSequence';
 //# sourceMappingURL=index.js.map

package/esm/FromConfigAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,mBAAmB,EAAE,MAAM,4BAA4B,CAAA;AAC3E,OAAO,EAAE,OAAO,IAAI,oBAAoB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,cAAc,CAAA;AACtD,OAAO,EAAE,OAAO,IAAI,mBAAmB,EAAE,MAAM,cAAc,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,oBAAoB,EAAE,MAAM,sBAAsB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,mBAAmB,EAAE,MAAM,4BAA4B,CAAA;AAC3E,OAAO,EAAE,OAAO,IAAI,oBAAoB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,cAAc,CAAA;AACtD,OAAO,EAAE,OAAO,IAAI,mBAAmB,EAAE,MAAM,qBAAqB,CAAA;AACpE,OAAO,EAAE,OAAO,IAAI,oBAAoB,EAAE,MAAM,sBAAsB,CAAA"}

package/esm/RefNameAliasAdapter/configSchema.js

@@ -1,6 +1,8 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config RefNameAliasAdapter
+ * can read "chromAliases" type files from UCSC or any tab separated file of
+ * refName aliases
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
@@ -16,6 +18,8 @@ const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
     },
     /**
      * #slot
+     * by default, the "ref names that match the fasta" are assumed to be in the
+     * first column (0), change this variable if needed
      */
     refNameColumn: {
         type: 'number',

package/esm/RefNameAliasAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,mBAAmB,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;;;OAIG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,mBAAmB,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "2.2.0",
+  "version": "2.2.2",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -27,7 +27,7 @@
     "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/config",
     "prepublishOnly": "yarn test",
-    "prepack": "yarn build; yarn useDist",
+    "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
@@ -58,5 +58,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
+  "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
 }

package/src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap

@@ -1405,7 +1405,7 @@ exports[`ConfigurationEditor widget renders with defaults of the PileupTrack sch
                                   id="mui-18-helper-text"
                                 >
                                   <div>
-                                    read sequencer orienation. fr is normal "reads pointing at each other ---&gt; &lt;--- while some other sequencers can use other options
+                                    read sequencer orientation. fr is normal "reads pointing at each other ---&gt; &lt;--- while some other sequencers can use other options
                                   </div>
                                 </div>
                               </div>

package/src/FromConfigAdapter/FromConfigAdapter.test.ts

@@ -1,6 +1,6 @@
 import { toArray } from 'rxjs/operators'
 import Adapter from './FromConfigAdapter'
-import { configSchema } from './configSchema'
+import configSchema from './fromConfig'
 
 test('adapter can fetch features', async () => {
   const features = [

package/src/FromConfigAdapter/FromConfigSequenceAdapter.ts

@@ -74,7 +74,7 @@ export default class FromConfigSequenceAdapter
 
   /**
    * called to provide a hint that data tied to a certain region
-   * will not be needed for the forseeable future and can be purged
+   * will not be needed for the foreseeable future and can be purged
    * from caches, etc
    */
   freeResources(/* { region } */): void {}

package/src/FromConfigAdapter/fromConfig.ts

@@ -15,13 +15,6 @@ const configSchema = ConfigurationSchema(
       type: 'frozen',
       defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-      type: 'string',
-      defaultValue: 'SimpleFeature',
-    },
   },
   { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
 )

package/src/FromConfigAdapter/fromConfigRegions.ts

@@ -15,13 +15,6 @@ const regionsConfigSchema = ConfigurationSchema(
       type: 'frozen',
       defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-      type: 'string',
-      defaultValue: 'SimpleFeature',
-    },
   },
   {
     explicitlyTyped: true,

package/src/FromConfigAdapter/fromConfigSequence.ts

@@ -14,13 +14,6 @@ const sequenceConfigSchema = ConfigurationSchema(
       type: 'frozen',
       defaultValue: [],
     },
-    /**
-     * #slot
-     */
-    featureClass: {
-      type: 'string',
-      defaultValue: 'SimpleFeature',
-    },
   },
   { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
 )

package/src/FromConfigAdapter/index.ts

@@ -2,5 +2,5 @@ export { default as AdapterClass } from './FromConfigAdapter'
 export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter'
 export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter'
 export { default as configSchema } from './fromConfig'
-export { default as regionsConfigSchema } from './fromConfig'
+export { default as regionsConfigSchema } from './fromConfigRegions'
 export { default as sequenceConfigSchema } from './fromConfigSequence'

package/src/RefNameAliasAdapter/configSchema.ts

@@ -2,6 +2,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
 /**
  * #config RefNameAliasAdapter
+ * can read "chromAliases" type files from UCSC or any tab separated file of
+ * refName aliases
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
@@ -20,6 +22,8 @@ const RefNameAliasAdapter = ConfigurationSchema(
     },
     /**
      * #slot
+     * by default, the "ref names that match the fasta" are assumed to be in the
+     * first column (0), change this variable if needed
      */
     refNameColumn: {
       type: 'number',

package/src/__snapshots__/index.test.js.snap

@@ -1,9 +1,9 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`Config editing adds config editor widget 1`] = `Object {}`;
+exports[`Config editing adds config editor widget 1`] = `{}`;
 
 exports[`Config editing creates proper FromConfigAdapter 1`] = `
-Object {
+{
   "adapterId": "testFromConfigAdapterId",
   "type": "FromConfigAdapter",
 }

package/dist/FromConfigAdapter/configSchema.d.ts

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

package/dist/FromConfigAdapter/configSchema.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config FromConfigAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('FromConfigAdapter', {
-    /**
-     * #slot
-     */
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-//# sourceMappingURL=configSchema.js.map

package/dist/FromConfigAdapter/configSchema.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/configSchema.ts"],"names":[],"mappings":";;;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAE3D,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA"}

package/esm/FromConfigAdapter/configSchema.d.ts

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

package/esm/FromConfigAdapter/configSchema.js

@@ -1,22 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FromConfigAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-export const configSchema = ConfigurationSchema('FromConfigAdapter', {
-    /**
-     * #slot
-     */
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    /**
-     * #slot
-     */
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-//# sourceMappingURL=configSchema.js.map

package/esm/FromConfigAdapter/configSchema.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA"}

package/src/FromConfigAdapter/configSchema.ts

@@ -1,27 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config FromConfigAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export const configSchema = ConfigurationSchema(
-  'FromConfigAdapter',
-  {
-    /**
-     * #slot
-     */
-    features: {
-      type: 'frozen',
-      defaultValue: [],
-    },
-    /**
-     * #slot
-     */
-    featureClass: {
-      type: 'string',
-      defaultValue: 'SimpleFeature',
-    },
-  },
-  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
-)