@jbrowse/plugin-gtf 5.0.0-beta.8 → 5.0.0-beta.9

package/esm/GtfAdapter/GtfAdapter.js

@@ -54,6 +54,6 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/GtfAdapter/configSchema.d.ts

@@ -18,25 +18,21 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly gtfLocation: {
-        readonly type: "fileLocation";
-        readonly description: "path to gtf file, also allows for gzipped gtf";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.gtf";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly aggregateField: {
-        readonly type: "string";
-        readonly description: "attribute naming the parent gene that transcripts are aggregated into. transcripts are grouped by gene_id where the file has one (gene names are not unique within a reference), so this is the gene label, and the grouping key only for files with no gene_id";
-        readonly defaultValue: "gene_name";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
 export type GtfAdapterConfig = Instance<typeof GtfAdapter>;
 export default GtfAdapter;

package/esm/GtfTabixAdapter/GtfTabixAdapter.js

@@ -1,7 +1,6 @@
 import { TabixIndexedFile } from '@gmod/tabix';
 import { BaseFeatureDataAdapter, cachedSetup, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, downloadStatus } from '@jbrowse/core/util';
-import { sharedBgzfWorkerPool } from '@jbrowse/core/util/bgzfWorkerPool';
 import { decompressedBytesBudget } from '@jbrowse/core/util/cacheBudgets';
 import { openLocation, openTabixIndexFilehandle } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
@@ -15,7 +14,6 @@ export default class GtfTabixAdapter extends BaseFeatureDataAdapter {
                 filehandle: openLocation(this.getConf('gtfGzLocation'), this.pluginManager),
                 ...openTabixIndexFilehandle(this.getConf(['index', 'location']), this.getConf(['index', 'indexType']), this.pluginManager),
                 chunkCacheBudget: decompressedBytesBudget,
-                bgzfWorkerPool: sharedBgzfWorkerPool(),
             });
             return {
                 gtf,
@@ -74,6 +72,6 @@ export default class GtfTabixAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/GtfTabixAdapter/configSchema.d.ts

@@ -19,63 +19,42 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  */
 declare const GtfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly densityAdapter: {
-        readonly type: 'frozen';
-        readonly defaultValue: null;
-        readonly description: 'optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; null disables it';
+        type: "maybeFrozen";
+    };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     * location of the bgzip-compressed GTF, sorted by position. Must be bgzip
-     * rather than plain gzip, which tabix cannot index.
-     */
     readonly gtfGzLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.gtf.gz";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
     readonly index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly indexType: {
-            readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"CSI" | "TBI">;
-            readonly type: 'stringEnum';
-            readonly defaultValue: 'TBI';
-            readonly description: '`TBI` is the usual `tabix` output. `CSI` is required for a reference longer than 512 Mb, which TBI cannot address.';
+            type: "stringEnum";
+        } & {
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<"CSI" | "TBI">;
+        } & {
+            defaultValue: string;
         };
         readonly location: {
-            readonly type: 'fileLocation';
-            readonly defaultValue: {
-                readonly uri: '/path/to/my.gz.tbi';
-                readonly locationType: 'UriLocation';
-            };
-            readonly description: 'location of the tabix index. Only needed when it is not named `<file>.tbi`, which is what the `uri` shorthand assumes — a `.csi` beside the file is reached with `csi: true` rather than by spelling this out.';
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     * the GtfTabixAdapter has to "redispatch" if it fetches a region and
-     * features it finds inside that region extend outside the region we
-     * requested. you can disable this for certain feature types to avoid
-     * fetching e.g. the entire chromosome
-     *
-     * the defaults are the whole-sequence records the common annotation sources
-     * emit: `region` (NCBI), `supercontig`/`scaffold` (Ensembl, for
-     * non-chromosomal sequences), plus `chromosome` and `contig`. They span an
-     * entire reference and have no children, so letting one expand the fetch
-     * would pull a whole chromosome to gain nothing
-     */
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly dontRedispatch: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly ["chromosome", "region", "contig", "supercontig", "scaffold"];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly aggregateField: {
-        readonly type: "string";
-        readonly description: "attribute naming the parent gene that transcripts are aggregated into. transcripts are grouped by gene_id where the file has one (gene names are not unique within a reference), so this is the gene label, and the grouping key only for files with no gene_id";
-        readonly defaultValue: "gene_name";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
 export type GtfTabixAdapterConfig = Instance<typeof GtfTabixAdapter>;
 export default GtfTabixAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "5.0.0-beta.8",
+  "version": "5.0.0-beta.9",
   "type": "module",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
@@ -21,10 +21,10 @@
     "esm"
   ],
   "dependencies": {
-    "@gmod/tabix": "^3.8.2",
-    "@jbrowse/mobx-state-tree": "^6.5.1",
+    "@gmod/tabix": "^3.8.3",
+    "@jbrowse/mobx-state-tree": "^6.5.2",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.8"
+    "@jbrowse/core": "^5.0.0-beta.9"
   },
   "peerDependencies": {
     "react": ">=19.0.0"