@jbrowse/plugin-bed 2.17.0 → 3.0.0

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -0,0 +1,105 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+export default class BedGraphAdapter extends BaseFeatureDataAdapter {
+    async configurePre() {
+        const pm = this.pluginManager;
+        const bedGraphGzLocation = this.getConf('bedGraphGzLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const filehandle = openLocation(bedGraphGzLocation, pm);
+        const isCSI = indexType === 'CSI';
+        const bedGraph = new TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
+            tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+        const columnNames = this.getConf('columnNames');
+        const header = await bedGraph.getHeader();
+        return {
+            columnNames,
+            bedGraph,
+            header,
+        };
+    }
+    async configure() {
+        if (!this.configured) {
+            this.configured = this.configurePre().catch((e) => {
+                this.configured = undefined;
+                throw e;
+            });
+        }
+        return this.configured;
+    }
+    async getNames() {
+        const { bedGraph, columnNames } = await this.configure();
+        if (columnNames.length) {
+            return columnNames;
+        }
+        const header = await bedGraph.getHeader();
+        const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
+        const defline = defs.at(-1);
+        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+            ? defline
+                .slice(1)
+                .split('\t')
+                .map(f => f.trim())
+            : undefined;
+    }
+    async getRefNames(opts = {}) {
+        const { bedGraph } = await this.configure();
+        return bedGraph.getReferenceSequenceNames(opts);
+    }
+    async getHeader() {
+        const { bedGraph } = await this.configure();
+        return bedGraph.getHeader();
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            var _a;
+            const { bedGraph } = await this.configure();
+            const meta = await bedGraph.getMetadata();
+            const { columnNumbers } = meta;
+            const colRef = columnNumbers.ref - 1;
+            const colStart = columnNumbers.start - 1;
+            const colEnd = columnNumbers.end - 1;
+            const same = colStart === colEnd;
+            const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(same ? 2 : 3)) || [];
+            await bedGraph.getLines(query.refName, query.start + (same ? -1 : 0), query.end, {
+                lineCallback: (line, fileOffset) => {
+                    const cols = line.split('\t');
+                    const refName = cols[colRef];
+                    const start = +cols[colStart];
+                    const end = +(same ? start + 1 : cols[colEnd]);
+                    const rest = cols.slice(colEnd + 1);
+                    if (Number.isNaN(start) || Number.isNaN(end)) {
+                        throw new Error(`start/end NaN on line "${line}", with colStart:${colStart} and colEnd:${colEnd}. run "tabix -p bed" to ensure bed preset`);
+                    }
+                    for (let j = 0; j < rest.length; j++) {
+                        const uniqueId = `${this.id}-${fileOffset}-${j}`;
+                        const score = Math.abs(+rest[j]);
+                        const source = names[j] || `col${j}`;
+                        if (score) {
+                            observer.next(new SimpleFeature({
+                                id: uniqueId,
+                                data: {
+                                    refName,
+                                    start,
+                                    end,
+                                    score,
+                                    source,
+                                },
+                            }));
+                        }
+                    }
+                },
+                ...opts,
+            });
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}

package/esm/BedGraphTabixAdapter/configSchema.d.ts

@@ -0,0 +1,29 @@
+declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    bedGraphGzLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    columnNames: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default BedGraphTabixAdapter;

package/esm/BedGraphTabixAdapter/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+function x() { }
+const BedGraphTabixAdapter = ConfigurationSchema('BedGraphTabixAdapter', {
+    bedGraphGzLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bedgraph',
+            locationType: 'UriLocation',
+        },
+    },
+    index: ConfigurationSchema('VcfIndex', {
+        indexType: {
+            model: types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.vcf.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+export default BedGraphTabixAdapter;

package/esm/BedGraphTabixAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function BedGraphTabixAdapterF(pluginManager: PluginManager): void;

package/esm/BedGraphTabixAdapter/index.js

@@ -0,0 +1,10 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default function BedGraphTabixAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BedGraphTabixAdapter',
+        displayName: 'BedGraphTabix adapter',
+        configSchema,
+        getAdapterClass: () => import('./BedGraphTabixAdapter').then(r => r.default),
+    }));
+}

package/esm/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -1,9 +1,10 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     private parser;
     protected bed: TabixIndexedFile;

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -1,10 +1,10 @@
 import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, } from '@jbrowse/core/util';
-import { TabixIndexedFile } from '@gmod/tabix';
-// locals
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { featureData } from '../util';
 class BedTabixAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
@@ -45,6 +45,7 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
             : undefined;
     }
     getFeatures(query, opts = {}) {
+        const { stopToken } = opts;
         return ObservableCreate(async (observer) => {
             const meta = await this.bed.getMetadata();
             const { columnNumbers } = meta;
@@ -52,8 +53,14 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
             const colStart = columnNumbers.start - 1;
             const colEnd = columnNumbers.end - 1;
             const names = await this.getNames();
+            let start = performance.now();
+            checkStopToken(stopToken);
             await this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
+                    if (performance.now() - start > 200) {
+                        checkStopToken(stopToken);
+                        start = performance.now();
+                    }
                     observer.next(new SimpleFeature(featureData({
                         line,
                         colRef,
@@ -65,10 +72,10 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
                         names,
                     })));
                 },
-                signal: opts.signal,
+                stopToken: opts.stopToken,
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/esm/BedTabixAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bedGzLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {
@@ -29,25 +20,16 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;
         defaultValue: never[];
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     autoSql: {
         type: string;
         description: string;

package/esm/BedTabixAdapter/configSchema.js

@@ -1,29 +1,17 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-/**
- * #config BedTabixAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
-    /**
-     * #slot
-     */
     bedGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -32,25 +20,16 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
             },
         },
     }),
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     autoSql: {
         type: 'string',
         description: 'The autoSql definition for the data fields in the file',

package/esm/BedTabixAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function BedTabixAdapterF(pluginManager: PluginManager): void;

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,7 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature, SimpleFeature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
-export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
     protected bedpeFeatures?: Promise<{
         header: string;

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -1,72 +1,16 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, fetchAndMaybeUnzip, } from '@jbrowse/core/util';
-import IntervalTree from '@flatten-js/interval-tree';
-const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
-export function featureData(line, uniqueId, flip, names) {
-    const l = line.split('\t');
-    const ref1 = l[flip ? 3 : 0];
-    const start1 = +l[flip ? 4 : 1];
-    const end1 = +l[flip ? 5 : 2];
-    const ref2 = l[!flip ? 3 : 0];
-    const start2 = +l[!flip ? 4 : 1];
-    const end2 = +l[!flip ? 5 : 2];
-    const name = l[6];
-    const score = +l[7];
-    const strand1 = parseStrand(l[8]);
-    const strand2 = parseStrand(l[9]);
-    const extra = l.slice(10);
-    const rest = names
-        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
-        : extra;
-    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
-    return new SimpleFeature({
-        ...rest,
-        start: start1,
-        end: end1,
-        type: 'paired_feature',
-        refName: ref1,
-        strand: strand1,
-        name,
-        score,
-        uniqueId,
-        mate: {
-            refName: ref2,
-            start: start2,
-            end: end2,
-            strand: strand2,
-        },
-        ...(ALT ? { ALT: [ALT] } : {}), // ALT is an array in VCF
-    });
-}
-function parseStrand(strand) {
-    if (strand === '+') {
-        return 1;
-    }
-    if (strand === '-') {
-        return -1;
-    }
-    if (strand === '.') {
-        return 0;
-    }
-    return undefined;
-}
+import { featureData } from './util';
 class BedpeAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
         this.intervalTrees = {};
     }
     async loadDataP(opts) {
-        const pm = this.pluginManager;
-        const bedLoc = this.getConf('bedpeLocation');
-        const loc = openLocation(bedLoc, pm);
-        const buffer = await fetchAndMaybeUnzip(loc, opts);
-        // 512MB  max chrome string length is 512MB
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const data = await fetchAndMaybeUnzipText(openLocation(this.getConf('bedpeLocation'), this.pluginManager), opts);
         const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
         const headerLines = [];
         let i = 0;
@@ -158,7 +102,7 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
                 observer.next(f);
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/esm/BedpeAdapter/configSchema.d.ts

@@ -1,8 +1,4 @@
 declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * can be plaintext or gzipped, not indexed so loaded into memory on startup
-     */
     bedpeLocation: {
         type: string;
         defaultValue: {
@@ -10,9 +6,6 @@ declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;

package/esm/BedpeAdapter/configSchema.js

@@ -1,14 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config BedpeAdapter
- * intended for SVs in a single assembly
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
-    /**
-     * #slot
-     * can be plaintext or gzipped, not indexed so loaded into memory on startup
-     */
     bedpeLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,9 +8,6 @@ const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',

package/esm/BedpeAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function BedpeAdapterF(pluginManager: PluginManager): void;

package/esm/BedpeAdapter/util.d.ts

@@ -0,0 +1,2 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;

package/esm/BedpeAdapter/util.js

@@ -0,0 +1,52 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
+export function featureData(line, uniqueId, flip, names) {
+    const l = line.split('\t');
+    const ref1 = l[flip ? 3 : 0];
+    const start1 = +l[flip ? 4 : 1];
+    const end1 = +l[flip ? 5 : 2];
+    const ref2 = l[!flip ? 3 : 0];
+    const start2 = +l[!flip ? 4 : 1];
+    const end2 = +l[!flip ? 5 : 2];
+    const name = l[6];
+    const score = +l[7];
+    const strand1 = parseStrand(l[8]);
+    const strand2 = parseStrand(l[9]);
+    const extra = l.slice(10);
+    const rest = names
+        ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
+        : {};
+    const ALT = svTypes.has(extra[0]) ? `<${extra[0]}>` : undefined;
+    return new SimpleFeature({
+        ...rest,
+        start: start1,
+        end: end1,
+        type: 'paired_feature',
+        refName: ref1,
+        strand: strand1,
+        name,
+        score,
+        uniqueId,
+        mate: {
+            refName: ref2,
+            start: start2,
+            end: end2,
+            strand: strand2,
+        },
+        ...(ALT ? { ALT: [ALT] } : {}),
+    });
+}
+function parseStrand(strand) {
+    if (strand === '+') {
+        return 1;
+    }
+    else if (strand === '-') {
+        return -1;
+    }
+    else if (strand === '.') {
+        return 0;
+    }
+    else {
+        return undefined;
+    }
+}

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,9 +1,10 @@
 import { BigBed } from '@gmod/bbi';
 import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { Observer } from 'rxjs';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
+import type { Observer } from 'rxjs';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cachedP?;
     configurePre(opts?: BaseOptions): Promise<{

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -1,11 +1,10 @@
 import { BigBed } from '@gmod/bbi';
 import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, doesIntersect2, max, min } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { doesIntersect2, max, min, SimpleFeature, } from '@jbrowse/core/util';
 import { firstValueFrom, toArray } from 'rxjs';
-// locals
 import { featureData2 } from '../util';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     async configurePre(opts) {
@@ -62,12 +61,13 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         };
     }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        const { signal } = opts;
+        var _a;
+        const { stopToken } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
         const { parser, bigbed } = await this.configure(opts);
         const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
-            signal,
+            stopToken,
             basesPerSpan: query.end - query.start,
         });
         if (allowRedispatch && feats.length) {
@@ -101,8 +101,13 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             throw new Error('found uniqueId undefined');
         }
         for (const feat of feats) {
-            const line = `${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`;
-            const data = parser.parseLine(line, { uniqueId: feat.uniqueId });
+            const splitLine = [
+                query.refName,
+                `${feat.start}`,
+                `${feat.end}`,
+                ...(((_a = feat.rest) === null || _a === void 0 ? void 0 : _a.split('\t')) || []),
+            ];
+            const data = parser.parseLine(splitLine, { uniqueId: feat.uniqueId });
             const aggr = data[aggregateField];
             if (!parentAggregation[aggr]) {
                 parentAggregation[aggr] = [];
@@ -111,7 +116,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             const f = featureData2({
                 ...rest,
                 scoreColumn,
-                line,
+                splitLine,
                 parser,
                 uniqueId,
                 start: feat.start,
@@ -164,7 +169,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }