@jbrowse/plugin-gtf 5.0.0-beta.1 → 5.0.0-beta.3

package/esm/GtfTabixAdapter/GtfTabixAdapter.js

@@ -45,7 +45,18 @@ export default class GtfTabixAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             try {
                 const { gtf, dontRedispatchSet } = await this.configure(opts);
-                const lines = await readTabixLinesRedispatched(gtf, query, dontRedispatchSet, opts);
+                // The type list alone, and `opts.topLevelOnly` is deliberately not
+                // honoured — both for the same reason. A GTF line has no `ID`/`Parent`,
+                // so there is no cheap "can this have children"; and a GTF top-level
+                // feature is not a line at all, it is synthesized by
+                // `aggregateGtfFeatures` from the transcripts in the FETCHED set, whose
+                // span it takes from them. So the argument that lets GFF3 skip the
+                // flanks — a top-level feature overlapping the query is already in the
+                // query's own read — does not transfer, and a narrower bound could draw
+                // a gene short rather than merely flat. Nothing is lost by declining:
+                // no GTF record shape makes this bound expensive (the fixtures top out
+                // at 19 kb, against GFF3's chromosome-long `match`).
+                const lines = await readTabixLinesRedispatched(gtf, query, line => !dontRedispatchSet.has(line.type), opts);
                 const feats = parseGtfToFeatures(lines, record => `${this.id}-offset-${record.offset}`);
                 const aggregated = aggregateGtfFeatures({
                     feats,

package/esm/GtfTabixAdapter/configSchema.d.ts

@@ -18,6 +18,11 @@ 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';
+    };
     /**
      * #slot
      * location of the bgzip-compressed GTF, sorted by position. Must be bgzip
@@ -43,7 +48,7 @@ declare const GtfTabixAdapter: import("@jbrowse/core/configuration/configuration
                 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` (or `.csi`), which is what the `uri` shorthand assumes.';
+            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.';
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     /**

package/esm/GtfTabixAdapter/configSchema.js

@@ -1,4 +1,5 @@
 import { ConfigurationSchema, expandTabixShorthand, tabixIndexFields, } from '@jbrowse/core/configuration';
+import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
 export function normalizeSnapshot(snap) {
     return expandTabixShorthand(snap, 'gtfGzLocation');
 }
@@ -64,6 +65,7 @@ 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,
     /**

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "5.0.0-beta.1",
+  "version": "5.0.0-beta.3",
   "type": "module",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
@@ -24,7 +24,7 @@
     "@gmod/tabix": "^3.8.2",
     "@jbrowse/mobx-state-tree": "^6.5.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.1"
+    "@jbrowse/core": "^5.0.0-beta.3"
   },
   "peerDependencies": {
     "react": ">=19.0.0"