@jbrowse/plugin-gtf 5.0.0-beta.11 → 5.0.0-beta.14

package/esm/GtfAdapter/configSchema.d.ts

@@ -5,8 +5,8 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #category adapter
  * #trackType FeatureTrack
  * #fileFormat feature | GTF (plain) | Loaded entirely into memory; for small files
- * used to load plain-text GTF files (optionally gzipped). Loads the whole file
- * into memory, so prefer the GtfTabixAdapter for large files.
+ * Reads plain-text GTF files, optionally gzipped. The adapter loads the whole
+ * file into memory, so use `GtfTabixAdapter` for large files.
  *
  * #example
  * The `uri` shorthand works for plain or gzipped GTF:

package/esm/GtfAdapter/configSchema.js

@@ -7,8 +7,8 @@ export function normalizeSnapshot(snap) {
  * #category adapter
  * #trackType FeatureTrack
  * #fileFormat feature | GTF (plain) | Loaded entirely into memory; for small files
- * used to load plain-text GTF files (optionally gzipped). Loads the whole file
- * into memory, so prefer the GtfTabixAdapter for large files.
+ * Reads plain-text GTF files, optionally gzipped. The adapter loads the whole
+ * file into memory, so use `GtfTabixAdapter` for large files.
  *
  * #example
  * The `uri` shorthand works for plain or gzipped GTF:
@@ -41,6 +41,7 @@ const GtfAdapter = ConfigurationSchema('GtfAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/GtfTabixAdapter/GtfTabixAdapter.d.ts

@@ -4,6 +4,8 @@ import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
 export default class GtfTabixAdapter extends BaseFeatureDataAdapter<GtfTabixAdapterConfig> {
+    private file?;
+    freeResources(): void;
     private configure;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;

package/esm/GtfTabixAdapter/GtfTabixAdapter.js

@@ -7,6 +7,11 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { readTabixLinesRedispatched } from '@jbrowse/core/util/tabix';
 import { aggregateGtfFeatures, parseGtfToFeatures } from '../util.js';
 export default class GtfTabixAdapter extends BaseFeatureDataAdapter {
+    // set once the file is open, for dataAdapterCache's eviction to clear
+    file;
+    freeResources() {
+        this.file?.clearChunkCache();
+    }
     configure = cachedSetup({
         label: 'Downloading index',
         setup: async (opts, onProgress) => {
@@ -15,6 +20,7 @@ export default class GtfTabixAdapter extends BaseFeatureDataAdapter {
                 ...openTabixIndexFilehandle(this.getConf(['index', 'location']), this.getConf(['index', 'indexType']), this.pluginManager),
                 chunkCacheBudget: decompressedBytesBudget,
             });
+            this.file = gtf;
             return {
                 gtf,
                 dontRedispatchSet: new Set(this.getConf('dontRedispatch')),

package/esm/GtfTabixAdapter/configSchema.d.ts

@@ -5,7 +5,7 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #category adapter
  * #trackType FeatureTrack
  * #fileFormat feature | GTF (tabix)
- * used to load bgzip-compressed, tabix-indexed GTF files
+ * Reads bgzip-compressed, tabix-indexed GTF files.
  *
  * #example
  * The `uri` shorthand auto-resolves the `.tbi` index; add `csi: true` for a
@@ -18,9 +18,6 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const GtfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    readonly densityAdapter: {
-        type: "maybeFrozen";
-    };
     type: {
         type: "string";
     } & {

package/esm/GtfTabixAdapter/configSchema.js

@@ -1,5 +1,4 @@
 import { ConfigurationSchema, expandTabixShorthand, tabixIndexSchema, } from '@jbrowse/core/configuration';
-import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
 export function normalizeSnapshot(snap) {
     return expandTabixShorthand(snap, 'gtfGzLocation');
 }
@@ -8,7 +7,7 @@ export function normalizeSnapshot(snap) {
  * #category adapter
  * #trackType FeatureTrack
  * #fileFormat feature | GTF (tabix)
- * used to load bgzip-compressed, tabix-indexed GTF files
+ * Reads bgzip-compressed, tabix-indexed GTF files.
  *
  * #example
  * The `uri` shorthand auto-resolves the `.tbi` index; add `csi: true` for a
@@ -35,7 +34,7 @@ const GtfTabixAdapter = ConfigurationSchema('GtfTabixAdapter', {
     },
     /**
      * #slot
-     * where the tabix index is and which kind it is. The `uri` shorthand derives
+     * The tabix index location and its kind. The `uri` shorthand derives
      * both, so a config using it states neither.
      */
     index: tabixIndexSchema(),
@@ -70,9 +69,9 @@ const GtfTabixAdapter = ConfigurationSchema('GtfTabixAdapter', {
         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',
         defaultValue: 'gene_name',
     },
-    ...densityAdapterConfigSchemaFields,
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/util.d.ts

@@ -21,7 +21,7 @@ export interface GtfLineRecord {
  * A top-level parsed feature paired with the record it came from. The parser
  * stamps no identity onto the feature; callers that need a stable per-feature
  * id (e.g. a tabix byte offset) read it off their own `record`. Mirrors
- * gff-nostream's `ParsedRecord`.
+ * @gmod/gff-nostream's `ParsedRecord`.
  */
 export interface ParsedGtfRecord<R extends GtfLineRecord = GtfLineRecord> {
     feature: FeatureLoc;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "5.0.0-beta.11",
+  "version": "5.0.0-beta.14",
   "type": "module",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
@@ -21,11 +21,11 @@
     "esm"
   ],
   "dependencies": {
-    "@gmod/tabix": "^3.9.1",
-    "@jbrowse/mobx-state-tree": "^6.7.0",
-    "mobx": "^7.0.5",
+    "@gmod/tabix": "^3.11.0",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
+    "mobx": "^7.0.6",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.11"
+    "@jbrowse/core": "^5.0.0-beta.14"
   },
   "peerDependencies": {
     "react": ">=19.0.0",