@jbrowse/plugin-bed 5.0.0-beta.7 → 5.0.0-beta.9

package/esm/BedAdapter/configSchema.d.ts

@@ -23,73 +23,51 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedLocation: {
-        readonly type: "fileLocation";
-        readonly description: "path to bed file, also allows gzipped bed";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bed.gz";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly scoreColumn: {
-        readonly type: "string";
-        readonly description: "The column to use as a \"score\" attribute";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly autoSql: {
-        readonly type: "string";
-        readonly description: "The autoSql definition for the data fields in the file";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly colRef: {
-        readonly type: "number";
-        readonly description: "The column to use as a \"refName\" attribute";
-        readonly defaultValue: 0;
+        type: "number";
+    } & {
+        defaultValue: number;
     };
-    /**
-     * #slot
-     */
     readonly colStart: {
-        readonly type: "number";
-        readonly description: "The column to use as a \"start\" attribute";
-        readonly defaultValue: 1;
+        type: "number";
+    } & {
+        defaultValue: number;
     };
-    /**
-     * #slot
-     */
     readonly colEnd: {
-        readonly type: "number";
-        readonly description: "The column to use as a \"end\" attribute";
-        readonly defaultValue: 2;
+        type: "number";
+    } & {
+        defaultValue: number;
     };
-    /**
-     * #slot
-     */
     readonly disableGeneHeuristic: {
-        readonly type: "boolean";
-        readonly description: "Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-}, 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 BedAdapterConfig = Instance<typeof BedAdapter>;
 export default BedAdapter;

package/esm/BedGraphAdapter/configSchema.d.ts

@@ -16,26 +16,21 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedGraphAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the plain-text bedGraph (`chrom start end value`, one line
-     * per interval). May be gzipped.
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedGraphLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bedgraph";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names";
-        readonly defaultValue: readonly [];
+        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 BedGraphAdapterConfig = Instance<typeof BedGraphAdapter>;
 export default BedGraphAdapter;

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -5,7 +5,6 @@ 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';
-import { withStopTokenSignal } from '@jbrowse/core/util/stopToken';
 import { readTabixHeaderLines } from '@jbrowse/core/util/tabix';
 import { makeBedGraphFeature } from '../bedGraphUtil.js';
 import { parseNamesFromHeader } from '../util.js';
@@ -61,7 +60,7 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
             const colEnd = columnNumbers.end - 1;
             const same = colStart === colEnd;
             const names = (await this.getNames())?.slice(same ? 2 : 3) ?? [];
-            await withStopTokenSignal(opts.stopToken, signal => downloadStatus('Downloading features', opts.statusCallback, onProgress => 
+            await downloadStatus('Downloading features', opts.statusCallback, onProgress => 
             // `same` is a single-coordinate file — a GWAS-style txt with only a
             // start column, indexed `-b N -e N`. The widening is not slop: the
             // column value is used below as an interbase start (point p is
@@ -101,9 +100,8 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
                 },
                 ...opts,
                 onProgress,
-                signal,
-            })));
+            }));
             observer.complete();
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/BedGraphTabixAdapter/configSchema.d.ts

@@ -16,43 +16,35 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the bgzip-compressed bedGraph (`chrom start end value`,
-     * sorted by position). Must be bgzip rather than plain gzip, which tabix
-     * cannot index.
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedGraphGzLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bedgraph";
-            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
-     */
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names";
-        readonly defaultValue: readonly [];
+        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 BedGraphTabixAdapterConfig = Instance<typeof BedGraphTabixAdapter>;
 export default BedGraphTabixAdapter;

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -2,11 +2,11 @@ import { TabixIndexedFile } from '@gmod/tabix';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseFeatureDataAdapter, cachedSetup, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, downloadStatus } from '@jbrowse/core/util';
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
 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';
-import { checkStopTokenThrottled, checkStopToken, createStopTokenChecker, withStopTokenSignal, } from '@jbrowse/core/util/stopToken';
 import { readTabixHeaderLines } from '@jbrowse/core/util/tabix';
 import { featureData, makeParser, parseNamesFromHeader } from '../util.js';
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
@@ -72,7 +72,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
         return parseNamesFromHeader((await readTabixHeaderLines(this.bed)).join('\n'));
     }
     getFeatures(query, opts) {
-        const { stopToken, statusCallback } = opts ?? {};
+        const { signal, statusCallback } = opts ?? {};
         return ObservableCreate(async (observer) => {
             // warms the index under its own status label — getLines would otherwise
             // download it under "Downloading features"
@@ -81,9 +81,8 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             const parser = await this.getParser();
             const scoreColumn = readConfObject(this.config, 'scoreColumn');
             const disableGeneHeuristic = readConfObject(this.config, 'disableGeneHeuristic');
-            const stopTokenCheck = createStopTokenChecker(stopToken);
-            checkStopToken(stopToken);
-            await withStopTokenSignal(stopToken, signal => downloadStatus('Downloading features', statusCallback, onProgress => 
+            checkAbortSignal(signal);
+            await downloadStatus('Downloading features', statusCallback, onProgress => 
             // start/end come from @gmod/tabix rather than being re-derived from
             // the line: it located the coordinate columns to find these lines at
             // all, and already applied the index's coordinate offset (-1 for a
@@ -92,7 +91,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             // — getLines only calls back for lines whose ref column matches it.
             this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset, start, end) => {
-                    checkStopTokenThrottled(stopTokenCheck);
+                    checkAbortSignal(signal);
                     const splitLine = line.split('\t');
                     observer.next(new SimpleFeature(featureData({
                         splitLine,
@@ -108,8 +107,8 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
                 },
                 onProgress,
                 signal,
-            })));
+            }));
             observer.complete();
-        }, stopToken);
+        }, signal);
     }
 }

package/esm/BedTabixAdapter/configSchema.d.ts

@@ -17,70 +17,52 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  */
 declare const BedTabixAdapter: 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 BED, sorted by position. Must be bgzip
-     * rather than plain gzip, which tabix cannot index.
-     */
     readonly bedGzLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bed.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
-     */
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly scoreColumn: {
-        readonly type: "string";
-        readonly description: "The column to use as a \"score\" attribute";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly autoSql: {
-        readonly type: "string";
-        readonly description: "The autoSql definition for the data fields in the file";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly disableGeneHeuristic: {
-        readonly type: "boolean";
-        readonly description: "Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-}, 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 BedTabixAdapterConfig = Instance<typeof BedTabixAdapter>;
 export default BedTabixAdapter;

package/esm/BedpeAdapter/configSchema.d.ts

@@ -15,25 +15,21 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedpeLocation: {
-        readonly type: "fileLocation";
-        readonly description: "can be plaintext or gzipped, not indexed so loaded into memory on startup";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bedpe.gz";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names";
-        readonly defaultValue: readonly [];
+        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 BedpeAdapterConfig = Instance<typeof BedpeAdapter>;
 export default BedpeAdapter;

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -4,7 +4,6 @@ import { BaseFeatureDataAdapter, cachedSetup, } from '@jbrowse/core/data_adapter
 import { SimpleFeature, doesIntersect2, downloadStatus, max, min, updateStatus, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { withStopTokenSignal } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { featureData } from '../util.js';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
@@ -97,11 +96,11 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         // (they come from the R-tree index) so this reports a determinate fraction
         // rather than an indeterminate spinner. Matters most here — BigBed is a
         // full-feature download, which is why getRegionByteSize gates it above.
-        const feats = await withStopTokenSignal(opts.stopToken, signal => downloadStatus('Downloading features', statusCallback, onProgress => bigbed.getFeatures(query.refName, query.start, query.end, {
+        const feats = await downloadStatus('Downloading features', statusCallback, onProgress => bigbed.getFeatures(query.refName, query.start, query.end, {
             basesPerSpan: query.end - query.start,
             onProgress,
-            signal,
-        })));
+            signal: opts.signal,
+        }));
         await updateStatus('Processing features', statusCallback, async () => {
             const parentAggregation = {};
             const singletons = [];
@@ -214,6 +213,6 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/BigBedAdapter/configSchema.d.ts

@@ -15,46 +15,33 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  */
 declare const BigBedAdapter: 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 BigBed file. It carries its own index and summary zoom
-     * levels, so there is no separate index to configure.
-     */
     readonly bigBedLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bb";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly scoreColumn: {
-        readonly type: "string";
-        readonly description: "The column to use as a \"score\" attribute";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly aggregateField: {
-        readonly type: "string";
-        readonly description: "An attribute to aggregate features with";
-        readonly defaultValue: "geneName2";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly disableGeneHeuristic: {
-        readonly type: "boolean";
-        readonly description: "Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-}, 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 BigBedAdapterConfig = Instance<typeof BigBedAdapter>;
 export default BigBedAdapter;

package/esm/StarFusionAdapter/configSchema.d.ts

@@ -15,17 +15,16 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const StarFusionAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly starFusionLocation: {
-        readonly type: "fileLocation";
-        readonly description: "STAR-Fusion TSV output file (plain text or gzipped)";
-        readonly defaultValue: {
-            readonly uri: "/path/to/star-fusion.fusion_predictions.tsv";
-            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 StarFusionAdapterConfig = Instance<typeof StarFusionAdapter>;
 export default StarFusionAdapter;

package/esm/adapterUtil.js

@@ -9,7 +9,7 @@ export function intervalTreeFeatures(query, opts, loadTree) {
             observer.next(f);
         }
         observer.complete();
-    }, opts.stopToken);
+    }, opts.signal);
 }
 // Build one interval tree for a refName from paired-feature buckets, inserting
 // the records that start on this ref (feats1, flip=false) and those whose mate

package/esm/generateUcscTranscript.js

@@ -61,9 +61,18 @@ export function generateUcscTranscript(data) {
     // below cannot express that: a thick point inside a block would emit a
     // zero-length CDS carrying a phase, and one outside every block would make
     // the whole transcript UTR.
+    //
+    // cdsStartStat and cdsEndStat `none` alone do not mean non-coding: UCSC's
+    // GENCODE bigGenePred (gencodeV44.bb through V50) writes `none` on every
+    // transcript, and reading it as non-coding stripped the CDS from all 370,886
+    // of V50's coding ones, TP53 included. exonFrames tells them apart there:
+    // every coding transcript has a block with a frame, every other one has -1
+    // throughout.
     const { cdsEndStat, cdsStartStat } = rest;
     if (thickStart === thickEnd ||
-        (cdsStartStat === 'none' && cdsEndStat === 'none')) {
+        (cdsStartStat === 'none' &&
+            cdsEndStat === 'none' &&
+            !exonFrames?.some(frame => frame >= 0))) {
         return {
             ...rest,
             uniqueId,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "5.0.0-beta.7",
+  "version": "5.0.0-beta.9",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -23,11 +23,11 @@
   "dependencies": {
     "@gmod/bbi": "^11.2.3",
     "@gmod/bed": "^2.3.0",
-    "@gmod/tabix": "^3.8.2",
-    "@jbrowse/mobx-state-tree": "^6.5.1",
+    "@gmod/tabix": "^3.8.3",
+    "@jbrowse/mobx-state-tree": "^6.5.2",
     "mobx": "^7.0.3",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.7"
+    "@jbrowse/core": "^5.0.0-beta.9"
   },
   "publishConfig": {
     "access": "public"