@jbrowse/plugin-gff3 5.0.0-beta.8 → 5.0.0-beta.9

package/esm/Gff3Adapter/Gff3Adapter.js

@@ -59,6 +59,6 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
                 }
             }
             observer.complete();
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/Gff3Adapter/configSchema.d.ts

@@ -17,18 +17,16 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const Gff3Adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the GFF3 file. May be gzipped; it is decompressed and parsed
-     * in full on first use, so the file has to fit in memory.
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly gffLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.gff";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-}, 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 Gff3AdapterConfig = Instance<typeof Gff3Adapter>;
 export default Gff3Adapter;

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -1,7 +1,6 @@
 import { TabixIndexedFile } from '@gmod/tabix';
 import { BaseFeatureDataAdapter, cachedSetup, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { 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 { doesIntersect2 } from '@jbrowse/core/util/range';
@@ -17,7 +16,6 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                 filehandle: openLocation(this.getConf('gffGzLocation'), this.pluginManager),
                 ...openTabixIndexFilehandle(this.getConf(['index', 'location']), this.getConf(['index', 'indexType']), this.pluginManager),
                 chunkCacheBudget: decompressedBytesBudget,
-                bgzfWorkerPool: sharedBgzfWorkerPool(),
             });
             return {
                 gff,
@@ -80,6 +78,6 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/Gff3TabixAdapter/configSchema.d.ts

@@ -19,55 +19,37 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  */
 declare const Gff3TabixAdapter: 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 GFF3, sorted by position. Must be bgzip
-     * rather than plain gzip, which tabix cannot index.
-     */
     readonly gffGzLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.gff.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 Gff3TabixAdapter 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 GFF3 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;
     };
-}, 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 Gff3TabixAdapterConfig = Instance<typeof Gff3TabixAdapter>;
 export default Gff3TabixAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "5.0.0-beta.8",
+  "version": "5.0.0-beta.9",
   "type": "module",
   "description": "JBrowse 2 gff3.",
   "keywords": [
@@ -21,12 +21,12 @@
     "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",
     "gff-nostream": "^5.4.0",
     "mobx": "^7.0.3",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.8"
+    "@jbrowse/core": "^5.0.0-beta.9"
   },
   "publishConfig": {
     "access": "public"