@jbrowse/plugin-gtf 5.0.0-beta.1 → 5.0.0-beta.10

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>, any>>;
 export type GtfAdapterConfig = Instance<typeof GtfAdapter>;
 export default GtfAdapter;

package/esm/GtfAdapter/configSchema.js

@@ -1,14 +1,6 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, expandUriShorthand, } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
-    return snap.uri
-        ? {
-            ...snap,
-            gtfLocation: {
-                uri: snap.uri,
-                baseUri: snap.baseUri,
-            },
-        }
-        : snap;
+    return expandUriShorthand(snap, 'gtfLocation');
 }
 /**
  * #config 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,
@@ -45,7 +43,18 @@ 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,
@@ -63,6 +72,6 @@ export default class GtfTabixAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/GtfTabixAdapter/configSchema.d.ts

@@ -18,59 +18,43 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const GtfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the bgzip-compressed GTF, sorted by position. Must be bgzip
-     * rather than plain gzip, which tabix cannot index.
-     */
+    readonly densityAdapter: {
+        type: "maybeFrozen";
+    };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     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` (or `.csi`), which is what the `uri` shorthand assumes.';
+            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>, any>>;
     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>, any>>;
 export type GtfTabixAdapterConfig = Instance<typeof GtfTabixAdapter>;
 export default GtfTabixAdapter;

package/esm/GtfTabixAdapter/configSchema.js

@@ -1,4 +1,5 @@
-import { ConfigurationSchema, expandTabixShorthand, tabixIndexFields, } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, expandTabixShorthand, tabixIndexSchema, } from '@jbrowse/core/configuration';
+import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
 export function normalizeSnapshot(snap) {
     return expandTabixShorthand(snap, 'gtfGzLocation');
 }
@@ -32,7 +33,12 @@ const GtfTabixAdapter = ConfigurationSchema('GtfTabixAdapter', {
             locationType: 'UriLocation',
         },
     },
-    index: ConfigurationSchema('TabixIndex', { ...tabixIndexFields }),
+    /**
+     * #slot
+     * where the tabix index is and which kind it is. The `uri` shorthand derives
+     * both, so a config using it states neither.
+     */
+    index: tabixIndexSchema(),
     /**
      * #slot
      * the GtfTabixAdapter has to "redispatch" if it fetches a region and
@@ -64,6 +70,7 @@ 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.10",
   "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": "^6.6.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.1"
+    "@jbrowse/core": "^5.0.0-beta.10"
   },
   "peerDependencies": {
     "react": ">=19.0.0"