@jbrowse/plugin-bed 5.0.0-beta.13 → 5.0.0-beta.14

package/esm/BedAdapter/BedAdapter.d.ts

@@ -10,6 +10,17 @@ export default class BedAdapter extends BaseFeatureDataAdapter<BedAdapterConfig>
     private getParser;
     static capabilities: string[];
     private loadDataP;
+    /** Each column the parser reads, as its autoSql or the header declares it. */
+    getAutoSqlFields(): Promise<{
+        isArray: boolean;
+        arrayIsNumeric: boolean;
+        isNumeric: boolean;
+        size?: number | string;
+        type: string;
+        name: string;
+        comment: string;
+        vals?: string[];
+    }[]>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getNames(): Promise<string[] | undefined>;

package/esm/BedAdapter/BedAdapter.js

@@ -19,6 +19,10 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
         const buffer = await fetchAndMaybeUnzip(openLocation(this.getConf('bedLocation'), this.pluginManager), opts);
         return bucketBedLines(buffer, opts?.statusCallback);
     }
+    /** Each column the parser reads, as its autoSql or the header declares it. */
+    async getAutoSqlFields() {
+        return (await this.getParser()).autoSql.fields;
+    }
     async getRefNames(opts = {}) {
         const { features } = await this.loadData(opts);
         return Object.keys(features);

package/esm/BedAdapter/configSchema.d.ts

@@ -11,8 +11,8 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ... and a jexl callback reading `feature.itemRgb` gets `undefined`. Set
  * `columnNames` to refer to them by name.
  *
- * used to load plain-text BED files. Loads the whole file into memory, so
- * prefer the BedTabixAdapter for large files.
+ * Reads plain-text BED files. The adapter loads the whole file into memory, so
+ * use `BedTabixAdapter` for large files.
  *
  * #example
  * ```js

package/esm/BedAdapter/configSchema.js

@@ -13,8 +13,8 @@ export function normalizeSnapshot(snap) {
  * ... and a jexl callback reading `feature.itemRgb` gets `undefined`. Set
  * `columnNames` to refer to them by name.
  *
- * used to load plain-text BED files. Loads the whole file into memory, so
- * prefer the BedTabixAdapter for large files.
+ * Reads plain-text BED files. The adapter loads the whole file into memory, so
+ * use `BedTabixAdapter` for large files.
  *
  * #example
  * ```js
@@ -94,6 +94,7 @@ const BedAdapter = ConfigurationSchema('BedAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/BedGraphAdapter/configSchema.d.ts

@@ -4,8 +4,9 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #config BedGraphAdapter
  * #trackType QuantitativeTrack
  * #fileFormat quantitative | BedGraph (plain) | Loaded entirely into memory; for small files
- * used to load plain-text bedGraph signal files. Loads the whole file into
- * memory, so prefer the BedGraphTabixAdapter for large files.
+ * Reads plain-text bedGraph signal files. The adapter loads the whole file into
+ * memory, so use `BedGraphTabixAdapter` for large files.
+ *
  * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
  * one value column each, named by the header, or a `source` column naming each
  * row's, which is the form Save track data writes.

package/esm/BedGraphAdapter/configSchema.js

@@ -6,8 +6,9 @@ export function normalizeSnapshot(snap) {
  * #config BedGraphAdapter
  * #trackType QuantitativeTrack
  * #fileFormat quantitative | BedGraph (plain) | Loaded entirely into memory; for small files
- * used to load plain-text bedGraph signal files. Loads the whole file into
- * memory, so prefer the BedGraphTabixAdapter for large files.
+ * Reads plain-text bedGraph signal files. The adapter loads the whole file into
+ * memory, so use `BedGraphTabixAdapter` for large files.
+ *
  * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
  * one value column each, named by the header, or a `source` column naming each
  * row's, which is the form Save track data writes.
@@ -43,6 +44,7 @@ const BedGraphAdapter = ConfigurationSchema('BedGraphAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -4,6 +4,8 @@ import type { BedGraphTabixAdapterConfig } from './configSchema.ts';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
 export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter<BedGraphTabixAdapterConfig> {
+    private file?;
+    freeResources(): void;
     protected configure: (opts?: BaseOptions) => Promise<{
         columnNames: string[];
         bedGraph: TabixIndexedFile;

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -9,6 +9,11 @@ import { readTabixHeaderLines } from '@jbrowse/core/util/tabix';
 import { makeBedGraphFeature } from '../bedGraphUtil.js';
 import { parseNamesFromHeader } from '../util.js';
 export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
+    // set once the file is open, for dataAdapterCache's eviction to clear
+    file;
+    freeResources() {
+        this.file?.clearChunkCache();
+    }
     // `label` because the index setup narrates nothing itself; the helper shows
     // it only while the first attempt is in flight, so pan/zoom re-entry (every
     // getFeatures/byte-estimate awaits it) doesn't re-flash "Downloading index"
@@ -27,6 +32,7 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
             chunkCacheBudget: decompressedBytesBudget,
             bgzfWorkerPool: sharedBgzfWorkerPool(),
         });
+        this.file = bedGraph;
         const columnNames = this.getConf('columnNames');
         // Not bedGraph.getHeader(): that returns only a `#`-commented header, so a
         // file whose header is a plain row skipped via `tabix -S 1` reported none
@@ -53,8 +59,7 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { bedGraph } = await this.configure(opts);
-            const meta = await bedGraph.getMetadata();
-            const { columnNumbers } = meta;
+            const { columnNumbers } = await bedGraph.getMetadata();
             const colRef = columnNumbers.ref - 1;
             const colStart = columnNumbers.start - 1;
             const colEnd = columnNumbers.end - 1;

package/esm/BedGraphTabixAdapter/configSchema.d.ts

@@ -4,7 +4,8 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #config BedGraphTabixAdapter
  * #trackType QuantitativeTrack
  * #fileFormat quantitative | BedGraph (tabix)
- * used to load bgzip-compressed, tabix-indexed bedGraph signal files.
+ * Reads bgzip-compressed, tabix-indexed bedGraph signal files.
+ *
  * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
  * one value column each, named by the header, or a `source` column naming each
  * row's, which is the form Save track data writes.

package/esm/BedGraphTabixAdapter/configSchema.js

@@ -6,7 +6,8 @@ export function normalizeSnapshot(snap) {
  * #config BedGraphTabixAdapter
  * #trackType QuantitativeTrack
  * #fileFormat quantitative | BedGraph (tabix)
- * used to load bgzip-compressed, tabix-indexed bedGraph signal files.
+ * Reads bgzip-compressed, tabix-indexed bedGraph signal files.
+ *
  * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
  * one value column each, named by the header, or a `source` column naming each
  * row's, which is the form Save track data writes.
@@ -36,7 +37,7 @@ const BedGraphTabixAdapter = ConfigurationSchema('BedGraphTabixAdapter', {
     },
     /**
      * #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(),
@@ -50,6 +51,7 @@ const BedGraphTabixAdapter = ConfigurationSchema('BedGraphTabixAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -34,6 +34,18 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter<BedTabixAdap
     }>;
     getNames: (opts?: BaseOptions) => Promise<string[] | undefined>;
     constructor(config: BedTabixAdapterConfig, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    freeResources(): void;
+    /** Each column the parser reads, as its autoSql or the header declares it. */
+    getAutoSqlFields(): Promise<{
+        isArray: boolean;
+        arrayIsNumeric: boolean;
+        isNumeric: boolean;
+        size?: number | string;
+        type: string;
+        name: string;
+        comment: string;
+        vals?: string[];
+    }[]>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     /**

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -47,6 +47,13 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             bgzfWorkerPool: sharedBgzfWorkerPool(),
         });
     }
+    freeResources() {
+        this.bed.clearChunkCache();
+    }
+    /** Each column the parser reads, as its autoSql or the header declares it. */
+    async getAutoSqlFields() {
+        return (await this.getParser()).autoSql.fields;
+    }
     async getRefNames(opts = {}) {
         return downloadStatus('Downloading index', opts.statusCallback, onProgress => this.bed.getReferenceSequenceNames({ ...opts, onProgress }));
     }
@@ -77,37 +84,54 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             // warms the index under its own status label — getLines would otherwise
             // download it under "Downloading features"
             await this.getMetadata(opts);
-            const names = await this.getNames();
-            const parser = await this.getParser();
             const scoreColumn = readConfObject(this.config, 'scoreColumn');
             const disableGeneHeuristic = readConfObject(this.config, 'disableGeneHeuristic');
+            let ready;
+            const early = [];
+            const emit = ({ names, parser }, { splitLine, start, end, offset }) => {
+                observer.next(new SimpleFeature(featureData({
+                    splitLine,
+                    refName: query.refName,
+                    start,
+                    end,
+                    scoreColumn,
+                    parser,
+                    uniqueId: `${this.id}-${offset}`,
+                    names,
+                    disableGeneHeuristic,
+                })));
+            };
+            const loaded = Promise.all([this.getNames(), this.getParser()]).then(([names, parser]) => {
+                ready = { names, parser };
+                for (const row of early.splice(0)) {
+                    emit(ready, row);
+                }
+            });
             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
-            // 1-based-closed preset) and its no-end-column convention (a single
-            // position becomes start..start+1). refName is likewise the query's
-            // — 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) => {
-                    checkAbortSignal(signal);
-                    const splitLine = line.split('\t');
-                    observer.next(new SimpleFeature(featureData({
-                        splitLine,
-                        refName: query.refName,
-                        start,
-                        end,
-                        scoreColumn,
-                        parser,
-                        uniqueId: `${this.id}-${fileOffset}`,
-                        names,
-                        disableGeneHeuristic,
-                    })));
-                },
-                onProgress,
-                signal,
-            }));
+            await Promise.all([
+                loaded,
+                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
+                // 1-based-closed preset) and its no-end-column convention (a single
+                // position becomes start..start+1). refName is likewise the query's
+                // — getLines only calls back for lines whose ref column matches it.
+                this.bed.getLines(query.refName, query.start, query.end, {
+                    lineCallback: (line, offset, start, end) => {
+                        checkAbortSignal(signal);
+                        const row = { splitLine: line.split('\t'), start, end, offset };
+                        if (ready) {
+                            emit(ready, row);
+                        }
+                        else {
+                            early.push(row);
+                        }
+                    },
+                    onProgress,
+                    signal,
+                })),
+            ]);
             observer.complete();
         }, signal);
     }

package/esm/BedTabixAdapter/configSchema.d.ts

@@ -4,6 +4,7 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #config BedTabixAdapter
  * #trackType FeatureTrack
  * #fileFormat feature | BED (tabix)
+ * Reads bgzip-compressed, tabix-indexed BED files.
  *
  * #example
  * The `uri` shorthand auto-resolves the `.tbi` index; add `csi: true` for a
@@ -16,9 +17,6 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    readonly densityAdapter: {
-        type: "maybeFrozen";
-    };
     type: {
         type: "string";
     } & {

package/esm/BedTabixAdapter/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, 'bedGzLocation');
 }
@@ -7,6 +6,7 @@ export function normalizeSnapshot(snap) {
  * #config BedTabixAdapter
  * #trackType FeatureTrack
  * #fileFormat feature | BED (tabix)
+ * Reads bgzip-compressed, tabix-indexed BED files.
  *
  * #example
  * The `uri` shorthand auto-resolves the `.tbi` index; add `csi: true` for a
@@ -33,7 +33,7 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
     },
     /**
      * #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(),
@@ -69,9 +69,9 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
         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)',
         defaultValue: false,
     },
-    ...densityAdapterConfigSchemaFields,
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/BedpeAdapter/configSchema.d.ts

@@ -4,7 +4,8 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #config BedpeAdapter
  * #trackType VariantTrack
  * #fileFormat variants | BEDPE | Paired/breakend records, e.g. SV calls or Hi-C loops
- * intended for SVs in a single assembly
+ * Reads BEDPE files of paired breakends, such as structural variant calls
+ * within a single assembly.
  *
  * #example
  * ```js

package/esm/BedpeAdapter/configSchema.js

@@ -6,7 +6,8 @@ export function normalizeSnapshot(snap) {
  * #config BedpeAdapter
  * #trackType VariantTrack
  * #fileFormat variants | BEDPE | Paired/breakend records, e.g. SV calls or Hi-C loops
- * intended for SVs in a single assembly
+ * Reads BEDPE files of paired breakends, such as structural variant calls
+ * within a single assembly.
  *
  * #example
  * ```js
@@ -38,6 +39,7 @@ const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -11,13 +11,21 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter<BigBedAdapterC
         bigbed: BigBed;
         header: import("@gmod/bbi").BigWigHeaderWithRefNames;
         parser: BED;
+        positionalItemRgb: string | undefined;
     }>;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
         header: import("@gmod/bbi").BigWigHeaderWithRefNames;
         parser: BED;
+        positionalItemRgb: string | undefined;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
+    /** Each contig's length off the chrom table, which lists empty contigs too. */
+    getContigs(opts?: BaseOptions): Promise<{
+        refName: string;
+        length: number | undefined;
+        hasData: null;
+    }[]>;
     getRegionByteSize(regions: Region[], opts?: BaseOptions): Promise<number>;
     getRefNameAliases(opts?: BaseOptions): Promise<{
         refName: unknown;
@@ -28,11 +36,26 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter<BigBedAdapterC
     getHeader(opts?: BaseOptions): Promise<{
         version: number;
         fileType: "bigbed" | "bigwig";
-        autoSql: {};
+        autoSql: {
+            type?: string;
+            name?: string;
+            comment?: string;
+        };
         fields: {
             [k: string]: string;
         };
     }>;
+    /** Each column the file's autoSql declares, with its type and comment. */
+    getAutoSqlFields(opts?: BaseOptions): Promise<{
+        isArray: boolean;
+        arrayIsNumeric: boolean;
+        isNumeric: boolean;
+        size?: number | string;
+        type: string;
+        name: string;
+        comment: string;
+        vals?: string[];
+    }[]>;
     getMetadata(opts?: BaseOptions): Promise<{
         [k: string]: string;
     }>;

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -6,6 +6,12 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { firstValueFrom, toArray } from 'rxjs';
 import { featureData } from '../util.js';
+// UCSC reads column 9 of a bed9+ bigBed as itemRgb whatever its autoSql calls
+// it (spliceVarDb calls it `color`); colorBits reads only the standard names.
+function positionalItemRgbField(definedFieldCount, fields) {
+    const name = definedFieldCount >= 9 ? fields[8]?.name : undefined;
+    return name && name !== 'itemRgb' && name !== 'reserved' ? name : undefined;
+}
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     // `label` on cachedSetup so "Downloading header" shows only while the first
     // fetch is in flight; every later getFeatures resolves from the memo with no
@@ -27,12 +33,22 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             bigbed,
             header,
             parser,
+            positionalItemRgb: positionalItemRgbField(header.definedFieldCount, parser.autoSql.fields),
         };
     }
     async getRefNames(opts) {
         const { header } = await this.configure(opts);
         return Object.keys(header.refsByName);
     }
+    /** Each contig's length off the chrom table, which lists empty contigs too. */
+    async getContigs(opts) {
+        const { header } = await this.configure(opts);
+        return Object.entries(header.refsByName).map(([refName, id]) => ({
+            refName,
+            length: header.refsByNumber[id]?.length,
+            hasData: null,
+        }));
+    }
     // Compressed download-size estimate straight from the bbi R-tree index (block
     // byte lengths, no data blocks read), so a display can byte-gate an over-large
     // BigBed fetch before it starts. Overrides the base no-estimate default, which
@@ -81,6 +97,11 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             fields: await this.getMetadata(opts),
         };
     }
+    /** Each column the file's autoSql declares, with its type and comment. */
+    async getAutoSqlFields(opts) {
+        const { parser } = await this.configure(opts);
+        return parser.autoSql.fields;
+    }
     async getMetadata(opts) {
         const { parser } = await this.configure(opts);
         const { fields } = parser.autoSql;
@@ -91,7 +112,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
         const disableGeneHeuristic = this.getConf('disableGeneHeuristic');
-        const { parser, bigbed } = await this.configure(opts);
+        const { parser, bigbed, positionalItemRgb } = await this.configure(opts);
         // downloadStatus, not updateStatus: bbi knows the total block bytes up front
         // (they come from the R-tree index) so this reports a determinate fraction
         // rather than an indeterminate spinner. Matters most here — BigBed is a
@@ -121,6 +142,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                     refName: query.refName,
                     disableGeneHeuristic,
                 });
+                if (positionalItemRgb) {
+                    f.itemRgb ??= f[positionalItemRgb];
+                }
                 const aggr = f[aggregateField];
                 const aggrIsNotNone = typeof aggr === 'string' && aggr && aggr !== 'none';
                 if (aggrIsNotNone) {

package/esm/BigBedAdapter/configSchema.d.ts

@@ -4,6 +4,7 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #config BigBedAdapter
  * #trackType FeatureTrack
  * #fileFormat feature | BigBed
+ * Reads BigBed files, the indexed binary form of BED.
  *
  * #example
  * ```js
@@ -14,9 +15,6 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    readonly densityAdapter: {
-        type: "maybeFrozen";
-    };
     type: {
         type: "string";
     } & {

package/esm/BigBedAdapter/configSchema.js

@@ -1,5 +1,4 @@
 import { ConfigurationSchema, expandUriShorthand, } from '@jbrowse/core/configuration';
-import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
 export function normalizeSnapshot(snap) {
     return expandUriShorthand(snap, 'bigBedLocation');
 }
@@ -7,6 +6,7 @@ export function normalizeSnapshot(snap) {
  * #config BigBedAdapter
  * #trackType FeatureTrack
  * #fileFormat feature | BigBed
+ * Reads BigBed files, the indexed binary form of BED.
  *
  * #example
  * ```js
@@ -53,9 +53,9 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
         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)',
         defaultValue: false,
     },
-    ...densityAdapterConfigSchemaFields,
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/StarFusionAdapter/configSchema.d.ts

@@ -4,7 +4,8 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #config StarFusionAdapter
  * #trackType VariantTrack
  * #fileFormat variants | STAR-Fusion
- * used to load STAR-Fusion `star-fusion.fusion_predictions.tsv` output
+ * Reads the gene fusions that STAR-Fusion predicts, from its
+ * `star-fusion.fusion_predictions.tsv` output.
  *
  * #example
  * ```js

package/esm/StarFusionAdapter/configSchema.js

@@ -6,7 +6,8 @@ export function normalizeSnapshot(snap) {
  * #config StarFusionAdapter
  * #trackType VariantTrack
  * #fileFormat variants | STAR-Fusion
- * used to load STAR-Fusion `star-fusion.fusion_predictions.tsv` output
+ * Reads the gene fusions that STAR-Fusion predicts, from its
+ * `star-fusion.fusion_predictions.tsv` output.
  *
  * #example
  * ```js
@@ -30,6 +31,7 @@ const StarFusionAdapter = ConfigurationSchema('StarFusionAdapter', {
     },
 }, {
     explicitlyTyped: true,
+    closed: true,
     /**
      * #preProcessSnapshot
      *

package/esm/generateUcscTranscript.js

@@ -1,4 +1,5 @@
 import { copyExcept } from './copyExcept.js';
+import { toNumberList } from './numberColumns.js';
 // type guard: narrows input fields to required when true
 // strand===0 means unstranded — likely not a gene
 //
@@ -42,11 +43,6 @@ function calculatePhasesFromCds(cdsRegions, strand) {
 function frameToPhase(frame) {
     return (3 - frame) % 3;
 }
-function parseFrames(frames) {
-    return typeof frames === 'string'
-        ? frames.replace(/,$/, '').split(',').map(Number)
-        : frames;
-}
 const TRANSCRIPT_OWN = new Set([
     'strand',
     'uniqueId',
@@ -70,7 +66,7 @@ export function generateUcscTranscript(data) {
     // exonFrames from bigGenePred - the @gmod/bed parser returns it in genomic order.
     // _exonFrames fallback supports BED files that use the underscore-prefixed column
     // name, which the parser leaves as raw text because it is not a standard column.
-    const exonFrames = parseFrames(rest.exonFrames ?? rest._exonFrames);
+    const exonFrames = toNumberList((rest.exonFrames ?? rest._exonFrames));
     const feats = oldSubfeatures
         .filter(child => child.type === 'block')
         .sort((a, b) => a.start - b.start);

package/esm/numberColumns.d.ts

@@ -0,0 +1,4 @@
+export type NumberColumn = number | string;
+export type NumberListColumn = number[] | string[] | string;
+export declare function toNumber(value: NumberColumn | undefined): number | undefined;
+export declare function toNumberList(value: NumberListColumn | undefined): number[] | undefined;

package/esm/numberColumns.js

@@ -0,0 +1,17 @@
+export function toNumber(value) {
+    if (value === undefined || value === '') {
+        return undefined;
+    }
+    const n = Number(value);
+    return Number.isNaN(n) ? undefined : n;
+}
+export function toNumberList(value) {
+    return typeof value === 'string'
+        ? value
+            .split(',')
+            .filter(s => s !== '')
+            .map(Number)
+        : typeof value?.[0] === 'string'
+            ? value.map(Number)
+            : value;
+}

package/esm/util.js

@@ -5,6 +5,7 @@ import { generateBedMethylFeature, isBedMethylFeature, } from './generateBedMeth
 import { generateRastairMethylFeature, isRastairMethylFeature, } from './generateRastairMethylFeature.js';
 import { parseRepeatMaskerDescription } from './generateRepeatMaskerFeature.js';
 import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript.js';
+import { toNumber, toNumberList } from './numberColumns.js';
 // Heuristically split features and header from a buffered BED file, bucketing
 // data lines by the first tab-separated column (refName).
 export function bucketBedLines(buffer, statusCallback) {
@@ -151,22 +152,23 @@ export function featureData({ splitLine, refName, start, end, parser, uniqueId,
         };
     }
     const rest = copyExcept(data, BED_OWN);
-    const subfeatures = data.blockCount
+    const blockCount = toNumber(data.blockCount);
+    const subfeatures = blockCount
         ? makeBlocks({
             start,
             uniqueId,
             refName,
-            chromStarts: data.chromStarts,
-            blockCount: data.blockCount,
-            blockSizes: data.blockSizes,
-            blockStarts: data.blockStarts,
+            chromStarts: toNumberList(data.chromStarts),
+            blockCount,
+            blockSizes: toNumberList(data.blockSizes),
+            blockStarts: toNumberList(data.blockStarts),
         })
         : undefined;
     const transcriptCheck = {
         strand,
-        blockCount: data.blockCount,
-        thickStart: data.thickStart,
-        thickEnd: data.thickEnd,
+        blockCount,
+        thickStart: toNumber(data.thickStart),
+        thickEnd: toNumber(data.thickEnd),
     };
     if (!disableGeneHeuristic &&
         subfeatures &&

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "5.0.0-beta.13",
+  "version": "5.0.0-beta.14",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -21,14 +21,14 @@
     "esm"
   ],
   "dependencies": {
-    "@gmod/bbi": "^11.3.0",
-    "@gmod/bed": "^2.3.1",
-    "@gmod/tabix": "^3.9.1",
-    "@gmod/trix": "^3.0.22",
-    "@jbrowse/mobx-state-tree": "^6.7.0",
+    "@gmod/bbi": "^11.3.2",
+    "@gmod/bed": "^2.3.3",
+    "@gmod/tabix": "^3.11.0",
+    "@gmod/trix": "^3.1.0",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
     "mobx": "^7.0.6",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.13"
+    "@jbrowse/core": "^5.0.0-beta.14"
   },
   "peerDependencies": {
     "react": ">=19.0.0",