@jbrowse/plugin-bed 2.11.2 → 2.12.1

package/dist/BedAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BedAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function BedAdapterF(pluginManager) {
@@ -36,4 +37,3 @@ function BedAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedAdapter'))).then(r => r.default),
     }));
 }
-exports.default = BedAdapterF;

package/dist/BedTabixAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BedTabixAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function BedTabixAdapterF(pluginManager) {
@@ -36,4 +37,3 @@ function BedTabixAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedTabixAdapter'))).then(r => r.default),
     }));
 }
-exports.default = BedTabixAdapterF;

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.featureData = void 0;
+exports.featureData = featureData;
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
@@ -46,7 +46,6 @@ function featureData(line, uniqueId, flip, names) {
         mate: { refName: ref2, start: start2, end: end2, strand: strand2 },
     });
 }
-exports.featureData = featureData;
 function parseStrand(strand) {
     if (strand === '+') {
         return 1;

package/dist/BedpeAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BedpeAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function BedpeAdapterF(pluginManager) {
@@ -36,4 +37,3 @@ function BedpeAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedpeAdapter'))).then(r => r.default),
     }));
 }
-exports.default = BedpeAdapterF;

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,29 +1,31 @@
-import { BigBed, Header } from '@gmod/bbi';
+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/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
+import { Observer } from 'rxjs';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cached?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: Header;
+        header: import("@gmod/bbi").Header;
         parser: BED;
     }>;
     configure(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: Header;
+        header: Awaited<ReturnType<BigBed["getHeader"]>>;
         parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<{
-        version: any;
+        version: number;
         fileType: string;
         autoSql: {};
         fields: {
             [k: string]: string;
         };
     }>;
-    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeaturesHelper(query: Region, opts: BaseOptions | undefined, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -8,10 +8,9 @@ const bed_1 = __importDefault(require("@gmod/bed"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const operators_1 = require("rxjs/operators");
+const util_1 = require("@jbrowse/core/util");
 // locals
-const util_1 = require("../util");
+const util_2 = require("../util");
 class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre(opts) {
         const pm = this.pluginManager;
@@ -37,7 +36,6 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getHeader(opts) {
         const { parser, header } = await this.configure(opts);
-        // @ts-expect-error
         const { version, fileType } = header;
         const { fields, ...rest } = parser.autoSql;
         return {
@@ -47,68 +45,121 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
         };
     }
-    getFeatures(region, opts = {}) {
+    async getFeaturesHelper(query, opts = {}, observer, allowRedispatch, originalQuery = query) {
         const { signal } = opts;
         const scoreColumn = this.getConf('scoreColumn');
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            try {
-                const { parser, bigbed } = await this.configure(opts);
-                const ob = await bigbed.getFeatureStream(region.refName, region.start, region.end, {
-                    signal,
-                    basesPerSpan: region.end - region.start,
+        const aggregateField = this.getConf('aggregateField');
+        const { parser, bigbed } = await this.configure(opts);
+        const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
+            signal,
+            basesPerSpan: query.end - query.start,
+        });
+        if (allowRedispatch && feats.length) {
+            let minStart = Infinity;
+            let maxEnd = -Infinity;
+            for (const feat of feats) {
+                if (feat.start < minStart) {
+                    minStart = feat.start;
+                }
+                if (feat.end > maxEnd) {
+                    maxEnd = feat.end;
+                }
+            }
+            if (maxEnd > query.end || minStart < query.start) {
+                await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, observer, false, query);
+                return;
+            }
+        }
+        const parentAggregation = {};
+        if (feats.some(f => f.uniqueId === undefined)) {
+            throw new Error('found uniqueId undefined');
+        }
+        for (const feat of feats) {
+            const data = parser.parseLine(`${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, { uniqueId: feat.uniqueId });
+            const aggr = data[aggregateField];
+            if (!parentAggregation[aggr]) {
+                parentAggregation[aggr] = [];
+            }
+            const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
+            const subfeatures = blockCount
+                ? (0, util_2.makeBlocks)({
+                    chromStarts,
+                    blockStarts,
+                    blockCount,
+                    blockSizes,
+                    uniqueId,
+                    refName: query.refName,
+                    start: feat.start,
+                })
+                : [];
+            if ((0, util_2.isUcscProcessedTranscript)(data)) {
+                const f = (0, util_2.ucscProcessedTranscript)({
+                    ...rest,
+                    uniqueId,
+                    type,
+                    start: feat.start,
+                    end: feat.end,
+                    refName: query.refName,
+                    score: scoreColumn ? +data[scoreColumn] : score,
+                    chromStarts,
+                    blockCount,
+                    blockSizes,
+                    thickStart,
+                    thickEnd,
+                    subfeatures,
                 });
-                ob.pipe((0, operators_1.mergeAll)(), (0, operators_1.map)(feat => {
-                    const data = parser.parseLine(`${region.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, {
-                        uniqueId: feat.uniqueId,
-                    });
-                    if (feat.uniqueId === undefined) {
-                        throw new Error('invalid bbi feature');
+                if (aggr) {
+                    parentAggregation[aggr].push(f);
+                }
+                else {
+                    if ((0, util_1.doesIntersect2)(f.start, f.end, originalQuery.start, originalQuery.end)) {
+                        observer.next(new util_1.SimpleFeature({ id: `${this.id}-${uniqueId}`, data: f }));
                     }
-                    const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
-                    const subfeatures = blockCount
-                        ? (0, util_1.makeBlocks)({
-                            chromStarts,
-                            blockStarts,
-                            blockCount,
-                            blockSizes,
+                }
+            }
+            else {
+                if ((0, util_1.doesIntersect2)(feat.start, feat.end, originalQuery.start, originalQuery.end)) {
+                    observer.next(new util_1.SimpleFeature({
+                        id: `${this.id}-${uniqueId}`,
+                        data: {
+                            ...rest,
                             uniqueId,
-                            refName: region.refName,
+                            type,
                             start: feat.start,
-                        })
-                        : [];
-                    // collection of heuristics for suggesting that this feature should
-                    // be converted to a gene, CNV bigbed has many gene like features
-                    // including thickStart and blockCount but no strand
-                    return new simpleFeature_1.default({
-                        id: `${this.id}-${uniqueId}`,
-                        data: (0, util_1.isUCSC)(data)
-                            ? (0, util_1.ucscProcessedTranscript)({
-                                ...rest,
-                                uniqueId,
-                                type,
-                                start: feat.start,
-                                end: feat.end,
-                                refName: region.refName,
-                                score: scoreColumn ? +data[scoreColumn] : score,
-                                chromStarts,
-                                blockCount,
-                                blockSizes,
-                                thickStart,
-                                thickEnd,
-                                subfeatures,
-                            })
-                            : {
-                                ...rest,
-                                uniqueId,
-                                type,
-                                start: feat.start,
-                                score: scoreColumn ? +data[scoreColumn] : score,
-                                end: feat.end,
-                                refName: region.refName,
-                                subfeatures,
-                            },
-                    });
-                })).subscribe(observer);
+                            score: scoreColumn ? +data[scoreColumn] : score,
+                            end: feat.end,
+                            refName: query.refName,
+                            subfeatures,
+                        },
+                    }));
+                }
+            }
+        }
+        Object.entries(parentAggregation).map(([name, subfeatures]) => {
+            const s = (0, util_1.min)(subfeatures.map(f => f.start));
+            const e = (0, util_1.max)(subfeatures.map(f => f.end));
+            if ((0, util_1.doesIntersect2)(s, e, originalQuery.start, originalQuery.end)) {
+                const { uniqueId, strand } = subfeatures[0];
+                observer.next(new util_1.SimpleFeature({
+                    id: `${this.id}-${uniqueId}-parent`,
+                    data: {
+                        type: 'gene',
+                        subfeatures,
+                        strand,
+                        name,
+                        start: s,
+                        end: e,
+                        refName: query.refName,
+                    },
+                }));
+            }
+        });
+        observer.complete();
+    }
+    getFeatures(query, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            try {
+                await this.getFeaturesHelper(query, opts, observer, true);
             }
             catch (e) {
                 observer.error(e);

package/dist/BigBedAdapter/configSchema.d.ts

@@ -17,5 +17,13 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
         description: string;
         defaultValue: string;
     };
+    /**
+     * #slot
+     */
+    aggregateField: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BigBedAdapter;

package/dist/BigBedAdapter/configSchema.js

@@ -21,5 +21,13 @@ const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
+    aggregateField: {
+        type: 'string',
+        description: 'An attribute to aggregate features with',
+        defaultValue: 'geneName',
+    },
 }, { explicitlyTyped: true });
 exports.default = BigBedAdapter;

package/dist/BigBedAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BigBedAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function BigBedAdapterF(pluginManager) {
@@ -36,4 +37,3 @@ function BigBedAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigBedAdapter'))).then(r => r.default),
     }));
 }
-exports.default = BigBedAdapterF;

package/dist/util.d.ts

@@ -1,12 +1,13 @@
 import BED from '@gmod/bed';
 import { SimpleFeature } from '@jbrowse/core/util';
-interface MinimalFeature {
+export interface MinimalFeature {
     type: string;
     start: number;
     end: number;
     refName: string;
+    [key: string]: unknown;
 }
-interface TranscriptFeat {
+export interface TranscriptFeat extends MinimalFeature {
     thickStart: number;
     thickEnd: number;
     blockCount: number;
@@ -15,13 +16,14 @@ interface TranscriptFeat {
     refName: string;
     strand?: number;
     subfeatures: MinimalFeature[];
-    [key: string]: unknown;
 }
 export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
     strand: number;
     type: string;
     refName: string;
     subfeatures: MinimalFeature[];
+    start: number;
+    end: number;
 };
 export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
     blockCount: number;
@@ -39,9 +41,8 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
     type: string;
 }[];
 export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
-export declare function isUCSC(f: {
+export declare function isUcscProcessedTranscript(f: {
     thickStart?: number;
     blockCount?: number;
     strand?: number;
 }): boolean | 0 | undefined;
-export {};

package/dist/util.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isUCSC = exports.featureData = exports.makeBlocks = exports.ucscProcessedTranscript = void 0;
+exports.ucscProcessedTranscript = ucscProcessedTranscript;
+exports.makeBlocks = makeBlocks;
+exports.featureData = featureData;
+exports.isUcscProcessedTranscript = isUcscProcessedTranscript;
 const util_1 = require("@jbrowse/core/util");
 function ucscProcessedTranscript(feature) {
     var _a;
@@ -97,7 +100,6 @@ function ucscProcessedTranscript(feature) {
     });
     return { ...rest, strand, type: 'mRNA', refName, subfeatures };
 }
-exports.ucscProcessedTranscript = ucscProcessedTranscript;
 function defaultParser(fields, line) {
     const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
     return {
@@ -126,7 +128,6 @@ function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSi
     }
     return subfeatures;
 }
-exports.makeBlocks = makeBlocks;
 function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
     const l = line.split('\t');
     const refName = l[colRef];
@@ -160,7 +161,7 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
     };
     return new util_1.SimpleFeature({
         id: uniqueId,
-        data: isUCSC(data)
+        data: isUcscProcessedTranscript(data)
             ? ucscProcessedTranscript({
                 thickStart,
                 thickEnd,
@@ -172,8 +173,6 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
             : f,
     });
 }
-exports.featureData = featureData;
-function isUCSC(f) {
+function isUcscProcessedTranscript(f) {
     return f.thickStart && f.blockCount && f.strand !== 0;
 }
-exports.isUCSC = isUCSC;

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,29 +1,31 @@
-import { BigBed, Header } from '@gmod/bbi';
+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/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
+import { Observer } from 'rxjs';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cached?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: Header;
+        header: import("@gmod/bbi").Header;
         parser: BED;
     }>;
     configure(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: Header;
+        header: Awaited<ReturnType<BigBed["getHeader"]>>;
         parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<{
-        version: any;
+        version: number;
         fileType: string;
         autoSql: {};
         fields: {
             [k: string]: string;
         };
     }>;
-    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeaturesHelper(query: Region, opts: BaseOptions | undefined, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -3,10 +3,9 @@ import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { map, mergeAll } from 'rxjs/operators';
+import { doesIntersect2, max, min, SimpleFeature, } from '@jbrowse/core/util';
 // locals
-import { isUCSC, makeBlocks, ucscProcessedTranscript } from '../util';
+import { isUcscProcessedTranscript, makeBlocks, ucscProcessedTranscript, } from '../util';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     async configurePre(opts) {
         const pm = this.pluginManager;
@@ -32,7 +31,6 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     }
     async getHeader(opts) {
         const { parser, header } = await this.configure(opts);
-        // @ts-expect-error
         const { version, fileType } = header;
         const { fields, ...rest } = parser.autoSql;
         return {
@@ -42,68 +40,121 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
         };
     }
-    getFeatures(region, opts = {}) {
+    async getFeaturesHelper(query, opts = {}, observer, allowRedispatch, originalQuery = query) {
         const { signal } = opts;
         const scoreColumn = this.getConf('scoreColumn');
-        return ObservableCreate(async (observer) => {
-            try {
-                const { parser, bigbed } = await this.configure(opts);
-                const ob = await bigbed.getFeatureStream(region.refName, region.start, region.end, {
-                    signal,
-                    basesPerSpan: region.end - region.start,
+        const aggregateField = this.getConf('aggregateField');
+        const { parser, bigbed } = await this.configure(opts);
+        const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
+            signal,
+            basesPerSpan: query.end - query.start,
+        });
+        if (allowRedispatch && feats.length) {
+            let minStart = Infinity;
+            let maxEnd = -Infinity;
+            for (const feat of feats) {
+                if (feat.start < minStart) {
+                    minStart = feat.start;
+                }
+                if (feat.end > maxEnd) {
+                    maxEnd = feat.end;
+                }
+            }
+            if (maxEnd > query.end || minStart < query.start) {
+                await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, observer, false, query);
+                return;
+            }
+        }
+        const parentAggregation = {};
+        if (feats.some(f => f.uniqueId === undefined)) {
+            throw new Error('found uniqueId undefined');
+        }
+        for (const feat of feats) {
+            const data = parser.parseLine(`${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, { uniqueId: feat.uniqueId });
+            const aggr = data[aggregateField];
+            if (!parentAggregation[aggr]) {
+                parentAggregation[aggr] = [];
+            }
+            const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
+            const subfeatures = blockCount
+                ? makeBlocks({
+                    chromStarts,
+                    blockStarts,
+                    blockCount,
+                    blockSizes,
+                    uniqueId,
+                    refName: query.refName,
+                    start: feat.start,
+                })
+                : [];
+            if (isUcscProcessedTranscript(data)) {
+                const f = ucscProcessedTranscript({
+                    ...rest,
+                    uniqueId,
+                    type,
+                    start: feat.start,
+                    end: feat.end,
+                    refName: query.refName,
+                    score: scoreColumn ? +data[scoreColumn] : score,
+                    chromStarts,
+                    blockCount,
+                    blockSizes,
+                    thickStart,
+                    thickEnd,
+                    subfeatures,
                 });
-                ob.pipe(mergeAll(), map(feat => {
-                    const data = parser.parseLine(`${region.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, {
-                        uniqueId: feat.uniqueId,
-                    });
-                    if (feat.uniqueId === undefined) {
-                        throw new Error('invalid bbi feature');
+                if (aggr) {
+                    parentAggregation[aggr].push(f);
+                }
+                else {
+                    if (doesIntersect2(f.start, f.end, originalQuery.start, originalQuery.end)) {
+                        observer.next(new SimpleFeature({ id: `${this.id}-${uniqueId}`, data: f }));
                     }
-                    const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
-                    const subfeatures = blockCount
-                        ? makeBlocks({
-                            chromStarts,
-                            blockStarts,
-                            blockCount,
-                            blockSizes,
+                }
+            }
+            else {
+                if (doesIntersect2(feat.start, feat.end, originalQuery.start, originalQuery.end)) {
+                    observer.next(new SimpleFeature({
+                        id: `${this.id}-${uniqueId}`,
+                        data: {
+                            ...rest,
                             uniqueId,
-                            refName: region.refName,
+                            type,
                             start: feat.start,
-                        })
-                        : [];
-                    // collection of heuristics for suggesting that this feature should
-                    // be converted to a gene, CNV bigbed has many gene like features
-                    // including thickStart and blockCount but no strand
-                    return new SimpleFeature({
-                        id: `${this.id}-${uniqueId}`,
-                        data: isUCSC(data)
-                            ? ucscProcessedTranscript({
-                                ...rest,
-                                uniqueId,
-                                type,
-                                start: feat.start,
-                                end: feat.end,
-                                refName: region.refName,
-                                score: scoreColumn ? +data[scoreColumn] : score,
-                                chromStarts,
-                                blockCount,
-                                blockSizes,
-                                thickStart,
-                                thickEnd,
-                                subfeatures,
-                            })
-                            : {
-                                ...rest,
-                                uniqueId,
-                                type,
-                                start: feat.start,
-                                score: scoreColumn ? +data[scoreColumn] : score,
-                                end: feat.end,
-                                refName: region.refName,
-                                subfeatures,
-                            },
-                    });
-                })).subscribe(observer);
+                            score: scoreColumn ? +data[scoreColumn] : score,
+                            end: feat.end,
+                            refName: query.refName,
+                            subfeatures,
+                        },
+                    }));
+                }
+            }
+        }
+        Object.entries(parentAggregation).map(([name, subfeatures]) => {
+            const s = min(subfeatures.map(f => f.start));
+            const e = max(subfeatures.map(f => f.end));
+            if (doesIntersect2(s, e, originalQuery.start, originalQuery.end)) {
+                const { uniqueId, strand } = subfeatures[0];
+                observer.next(new SimpleFeature({
+                    id: `${this.id}-${uniqueId}-parent`,
+                    data: {
+                        type: 'gene',
+                        subfeatures,
+                        strand,
+                        name,
+                        start: s,
+                        end: e,
+                        refName: query.refName,
+                    },
+                }));
+            }
+        });
+        observer.complete();
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            try {
+                await this.getFeaturesHelper(query, opts, observer, true);
             }
             catch (e) {
                 observer.error(e);

package/esm/BigBedAdapter/configSchema.d.ts

@@ -17,5 +17,13 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
         description: string;
         defaultValue: string;
     };
+    /**
+     * #slot
+     */
+    aggregateField: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BigBedAdapter;

package/esm/BigBedAdapter/configSchema.js

@@ -19,5 +19,13 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
+    aggregateField: {
+        type: 'string',
+        description: 'An attribute to aggregate features with',
+        defaultValue: 'geneName',
+    },
 }, { explicitlyTyped: true });
 export default BigBedAdapter;

package/esm/util.d.ts

@@ -1,12 +1,13 @@
 import BED from '@gmod/bed';
 import { SimpleFeature } from '@jbrowse/core/util';
-interface MinimalFeature {
+export interface MinimalFeature {
     type: string;
     start: number;
     end: number;
     refName: string;
+    [key: string]: unknown;
 }
-interface TranscriptFeat {
+export interface TranscriptFeat extends MinimalFeature {
     thickStart: number;
     thickEnd: number;
     blockCount: number;
@@ -15,13 +16,14 @@ interface TranscriptFeat {
     refName: string;
     strand?: number;
     subfeatures: MinimalFeature[];
-    [key: string]: unknown;
 }
 export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
     strand: number;
     type: string;
     refName: string;
     subfeatures: MinimalFeature[];
+    start: number;
+    end: number;
 };
 export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
     blockCount: number;
@@ -39,9 +41,8 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
     type: string;
 }[];
 export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
-export declare function isUCSC(f: {
+export declare function isUcscProcessedTranscript(f: {
     thickStart?: number;
     blockCount?: number;
     strand?: number;
 }): boolean | 0 | undefined;
-export {};

package/esm/util.js

@@ -155,7 +155,7 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
     };
     return new SimpleFeature({
         id: uniqueId,
-        data: isUCSC(data)
+        data: isUcscProcessedTranscript(data)
             ? ucscProcessedTranscript({
                 thickStart,
                 thickEnd,
@@ -167,6 +167,6 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
             : f,
     });
 }
-export function isUCSC(f) {
+export function isUcscProcessedTranscript(f) {
     return f.thickStart && f.blockCount && f.strand !== 0;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.11.2",
+  "version": "2.12.1",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
+  "gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
 }