@jbrowse/plugin-bed 3.3.0 → 3.5.0

package/dist/BedAdapter/BedAdapter.d.ts

@@ -33,5 +33,4 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     private loadFeatureIntervalTreeHelper;
     loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedAdapter/BedAdapter.js

@@ -15,31 +15,41 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         super(...arguments);
         this.intervalTrees = {};
     }
-    async loadDataP(opts = {}) {
-        const pm = this.pluginManager;
+    async loadDataP(opts) {
+        const { statusCallback = () => { } } = opts || {};
         const bedLoc = this.getConf('bedLocation');
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, pm), opts);
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
-        const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, this.pluginManager), opts);
         const headerLines = [];
-        let i = 0;
-        for (; i < lines.length && lines[i].startsWith('#'); i++) {
-            headerLines.push(lines[i]);
-        }
-        const header = headerLines.join('\n');
         const features = {};
-        for (; i < lines.length; i++) {
-            const line = lines[i];
-            const tab = line.indexOf('\t');
-            const refName = line.slice(0, tab);
-            if (!features[refName]) {
-                features[refName] = [];
+        let blockStart = 0;
+        let i = 0;
+        const decoder = new TextDecoder('utf8');
+        while (blockStart < buffer.length) {
+            const n = buffer.indexOf(10, blockStart);
+            const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
+            const line = decoder.decode(b).trim();
+            if (line) {
+                if (line.startsWith('#')) {
+                    headerLines.push(line);
+                }
+                else if (line.startsWith('>')) {
+                    break;
+                }
+                else {
+                    const tab = line.indexOf('\t');
+                    const refName = line.slice(0, tab);
+                    if (!features[refName]) {
+                        features[refName] = [];
+                    }
+                    features[refName].push(line);
+                }
             }
-            features[refName].push(line);
+            if (i++ % 10000 === 0) {
+                statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
+            }
+            blockStart = n + 1;
         }
+        const header = headerLines.join('\n');
         const autoSql = this.getConf('autoSql');
         const parser = new bed_1.default({ autoSql });
         const columnNames = this.getConf('columnNames');
@@ -136,7 +146,6 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedAdapter;

package/dist/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -20,5 +20,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         columnNames: string[];
     }>;
     getFeatures(query: Region, _opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedGraphAdapter/BedGraphAdapter.js

@@ -125,6 +125,5 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 exports.default = BedGraphAdapter;

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -14,5 +14,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(): Promise<string>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -103,6 +103,5 @@ class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 exports.default = BedGraphAdapter;

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -19,5 +19,4 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
     private loadFeatureTreeP;
     private loadFeatureTree;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -109,7 +109,6 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedpeAdapter;

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -32,6 +32,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
+    getMetadata(opts?: BaseOptions): Promise<{
+        [k: string]: string;
+    }>;
     getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
         query: Region;
         opts: BaseOptions;
@@ -40,5 +43,4 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         originalQuery?: Region;
     }): Promise<void>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -42,9 +42,9 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getRefNameAliases(opts) {
         const { header } = await this.configure(opts);
-        const ret = await Promise.all(Object.keys(header.refsByName).map(async (r) => (await (0, rxjs_2.firstValueFrom)(this.getFeatures({
+        const ret = await Promise.all(Object.keys(header.refsByName).map(async (refName) => (await (0, rxjs_2.firstValueFrom)(this.getFeatures({
             assemblyName: '',
-            refName: r,
+            refName,
             start: 0,
             end: 1,
         }).pipe((0, rxjs_2.toArray)())))[0]));
@@ -73,16 +73,20 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async getHeader(opts) {
         const { parser, header } = await this.configure(opts);
         const { version, fileType } = header;
-        const { fields, ...rest } = parser.autoSql;
+        const { fields, ...autoSql } = parser.autoSql;
         return {
             version,
             fileType,
-            autoSql: { ...rest },
-            fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
+            autoSql,
+            fields: await this.getMetadata(opts),
         };
     }
+    async getMetadata(opts) {
+        const { parser } = await this.configure(opts);
+        const { fields } = parser.autoSql;
+        return Object.fromEntries(fields.map(({ name, comment }) => [name, comment]));
+    }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        var _a;
         const { statusCallback = () => { } } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
@@ -90,94 +94,98 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const feats = await (0, util_1.updateStatus)('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
             basesPerSpan: query.end - query.start,
         }));
-        const parentAggregation = {};
-        const parentAggregationFlat = [];
-        if (feats.some(f => f.uniqueId === undefined)) {
-            throw new Error('found uniqueId undefined');
-        }
-        for (const feat of feats) {
-            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] = [];
+        await (0, util_1.updateStatus)('Processing features', statusCallback, async () => {
+            var _a;
+            const parentAggregation = {};
+            const parentAggregationFlat = [];
+            if (feats.some(f => f.uniqueId === undefined)) {
+                throw new Error('found uniqueId undefined');
             }
-            const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
-            const f = (0, util_2.featureData2)({
-                ...rest,
-                scoreColumn,
-                splitLine,
-                parser,
-                uniqueId,
-                start: feat.start,
-                end: feat.end,
-                refName: query.refName,
-            });
-            if (aggr) {
-                parentAggregation[aggr].push(f);
-                parentAggregationFlat.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,
-                    }));
+            for (const feat of feats) {
+                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];
+                const aggrIsNotNone = aggr && aggr !== 'none';
+                if (aggrIsNotNone && !parentAggregation[aggr]) {
+                    parentAggregation[aggr] = [];
                 }
-            }
-        }
-        if (allowRedispatch && parentAggregationFlat.length) {
-            let minStart = Number.POSITIVE_INFINITY;
-            let maxEnd = Number.NEGATIVE_INFINITY;
-            for (const feat of parentAggregationFlat) {
-                if (feat.start < minStart) {
-                    minStart = feat.start;
+                const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
+                const f = (0, util_2.featureData2)({
+                    ...rest,
+                    scoreColumn,
+                    splitLine,
+                    parser,
+                    uniqueId,
+                    start: feat.start,
+                    end: feat.end,
+                    refName: query.refName,
+                });
+                if (aggrIsNotNone) {
+                    parentAggregation[aggr].push(f);
+                    parentAggregationFlat.push(f);
                 }
-                if (feat.end > maxEnd) {
-                    maxEnd = feat.end;
+                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,
+                        }));
+                    }
                 }
             }
-            if (maxEnd > query.end || minStart < query.start) {
-                await this.getFeaturesHelper({
-                    query: {
-                        ...query,
-                        start: minStart - 500000,
-                        end: maxEnd + 500000,
-                    },
-                    opts,
-                    observer,
-                    allowRedispatch: false,
-                    originalQuery: query,
-                });
-                return;
-            }
-        }
-        Object.entries(parentAggregation).map(([name, subfeatures]) => {
-            var _a, _b;
-            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 subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
-                observer.next(new util_1.SimpleFeature({
-                    id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
-                    data: {
-                        type: 'gene',
-                        subfeatures: subs,
-                        strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
-                        name,
-                        start: s,
-                        end: e,
-                        refName: query.refName,
-                    },
-                }));
+            if (allowRedispatch && parentAggregationFlat.length) {
+                let minStart = Number.POSITIVE_INFINITY;
+                let maxEnd = Number.NEGATIVE_INFINITY;
+                for (const feat of parentAggregationFlat) {
+                    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: {
+                            ...query,
+                            start: minStart - 500000,
+                            end: maxEnd + 500000,
+                        },
+                        opts,
+                        observer,
+                        allowRedispatch: false,
+                        originalQuery: query,
+                    });
+                    return;
+                }
             }
+            Object.entries(parentAggregation).map(([name, subfeatures]) => {
+                var _a, _b;
+                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 subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
+                    observer.next(new util_1.SimpleFeature({
+                        id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
+                        data: {
+                            type: 'gene',
+                            subfeatures: subs,
+                            strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
+                            name,
+                            start: s,
+                            end: e,
+                            refName: query.refName,
+                        },
+                    }));
+                }
+            });
         });
         observer.complete();
     }
@@ -200,6 +208,5 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             }
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 exports.default = BigBedAdapter;

package/dist/generateUcscTranscript.d.ts

@@ -1,4 +1,4 @@
-import type { MinimalFeature, TranscriptFeat } from './types';
+import type { TranscriptFeat } from './types';
 export declare function isUcscTranscript({ thickStart, blockCount, strand, }: {
     thickStart?: number;
     blockCount?: number;
@@ -9,7 +9,12 @@ export declare function generateUcscTranscript(data: TranscriptFeat): {
     strand: number;
     type: string;
     refName: string;
-    subfeatures: MinimalFeature[];
+    subfeatures: {
+        type: string;
+        start: number;
+        end: number;
+        refName: string;
+    }[];
     start: number;
     end: number;
 };

package/dist/generateUcscTranscript.js

@@ -12,81 +12,105 @@ function generateUcscTranscript(data) {
     const feats = oldSubfeatures
         .filter(child => child.type === 'block')
         .sort((a, b) => a.start - b.start);
-    for (const block of feats) {
-        const start = block.start;
-        const end = block.end;
-        if (thickStart >= end) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd >= end) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                phase: 0,
-                start: thickStart,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd >= end) {
-            subfeatures.push({
-                type: 'CDS',
-                phase: 0,
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd < end) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                phase: 0,
-                start: thickStart,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-            subfeatures.push({
-                type: 'CDS',
-                phase: 0,
-                start,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickEnd <= start) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
+    const { cdsEndStat, cdsStartStat } = rest2;
+    if (cdsStartStat === 'none' && cdsEndStat === 'none') {
+        return {
+            ...rest2,
+            uniqueId,
+            strand,
+            type: 'transcript',
+            refName,
+            subfeatures: feats.map(e => ({
+                ...e,
+                type: 'exon',
+            })),
+        };
+    }
+    else {
+        for (const block of feats) {
+            const start = block.start;
+            const end = block.end;
+            if (thickStart >= end) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                    start,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart > start && thickStart < end && thickEnd >= end) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                    start,
+                    end: thickStart,
+                    refName,
+                }, {
+                    type: 'CDS',
+                    phase: 0,
+                    start: thickStart,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart <= start && thickEnd >= end) {
+                subfeatures.push({
+                    type: 'CDS',
+                    phase: 0,
+                    start,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart > start && thickStart < end && thickEnd < end) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                    start,
+                    end: thickStart,
+                    refName,
+                }, {
+                    type: 'CDS',
+                    phase: 0,
+                    start: thickStart,
+                    end: thickEnd,
+                    refName,
+                }, {
+                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                    start: thickEnd,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+                subfeatures.push({
+                    type: 'CDS',
+                    phase: 0,
+                    start,
+                    end: thickEnd,
+                    refName,
+                }, {
+                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                    start: thickEnd,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickEnd <= start) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                    start,
+                    end,
+                    refName,
+                });
+            }
         }
+        return {
+            ...rest2,
+            uniqueId,
+            strand,
+            type: 'mRNA',
+            refName,
+            subfeatures,
+        };
     }
     return {
         ...rest2,

package/dist/util.d.ts

@@ -89,7 +89,12 @@ export declare function featureData({ line, colRef, colStart, colEnd, scoreColum
     strand: number;
     type: string;
     refName: string;
-    subfeatures: import("./types").MinimalFeature[];
+    subfeatures: {
+        type: string;
+        start: number;
+        end: number;
+        refName: string;
+    }[];
     start: number;
     end: number;
 } | {
@@ -182,7 +187,12 @@ export declare function featureData2({ splitLine, refName, start, end, parser, u
     strand: number;
     type: string;
     refName: string;
-    subfeatures: import("./types").MinimalFeature[];
+    subfeatures: {
+        type: string;
+        start: number;
+        end: number;
+        refName: string;
+    }[];
     start: number;
     end: number;
 } | {

package/esm/BedAdapter/BedAdapter.d.ts

@@ -33,5 +33,4 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     private loadFeatureIntervalTreeHelper;
     loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedAdapter/BedAdapter.js

@@ -1,7 +1,7 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { SimpleFeature, fetchAndMaybeUnzip, getProgressDisplayStr, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { featureData } from '../util';
@@ -10,31 +10,41 @@ class BedAdapter extends BaseFeatureDataAdapter {
         super(...arguments);
         this.intervalTrees = {};
     }
-    async loadDataP(opts = {}) {
-        const pm = this.pluginManager;
+    async loadDataP(opts) {
+        const { statusCallback = () => { } } = opts || {};
         const bedLoc = this.getConf('bedLocation');
-        const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, pm), opts);
-        if (buffer.length > 536870888) {
-            throw new Error('Data exceeds maximum string length (512MB)');
-        }
-        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
-        const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
+        const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, this.pluginManager), opts);
         const headerLines = [];
-        let i = 0;
-        for (; i < lines.length && lines[i].startsWith('#'); i++) {
-            headerLines.push(lines[i]);
-        }
-        const header = headerLines.join('\n');
         const features = {};
-        for (; i < lines.length; i++) {
-            const line = lines[i];
-            const tab = line.indexOf('\t');
-            const refName = line.slice(0, tab);
-            if (!features[refName]) {
-                features[refName] = [];
+        let blockStart = 0;
+        let i = 0;
+        const decoder = new TextDecoder('utf8');
+        while (blockStart < buffer.length) {
+            const n = buffer.indexOf(10, blockStart);
+            const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
+            const line = decoder.decode(b).trim();
+            if (line) {
+                if (line.startsWith('#')) {
+                    headerLines.push(line);
+                }
+                else if (line.startsWith('>')) {
+                    break;
+                }
+                else {
+                    const tab = line.indexOf('\t');
+                    const refName = line.slice(0, tab);
+                    if (!features[refName]) {
+                        features[refName] = [];
+                    }
+                    features[refName].push(line);
+                }
             }
-            features[refName].push(line);
+            if (i++ % 10000 === 0) {
+                statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
+            }
+            blockStart = n + 1;
         }
+        const header = headerLines.join('\n');
         const autoSql = this.getConf('autoSql');
         const parser = new BED({ autoSql });
         const columnNames = this.getConf('columnNames');
@@ -131,7 +141,6 @@ class BedAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedAdapter;

package/esm/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -20,5 +20,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         columnNames: string[];
     }>;
     getFeatures(query: Region, _opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedGraphAdapter/BedGraphAdapter.js

@@ -120,5 +120,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -14,5 +14,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(): Promise<string>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -101,5 +101,4 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -19,5 +19,4 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
     private loadFeatureTreeP;
     private loadFeatureTree;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -104,7 +104,6 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.stopToken);
     }
-    freeResources() { }
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedpeAdapter;

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -32,6 +32,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
+    getMetadata(opts?: BaseOptions): Promise<{
+        [k: string]: string;
+    }>;
     getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
         query: Region;
         opts: BaseOptions;
@@ -40,5 +43,4 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         originalQuery?: Region;
     }): Promise<void>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -37,9 +37,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     }
     async getRefNameAliases(opts) {
         const { header } = await this.configure(opts);
-        const ret = await Promise.all(Object.keys(header.refsByName).map(async (r) => (await firstValueFrom(this.getFeatures({
+        const ret = await Promise.all(Object.keys(header.refsByName).map(async (refName) => (await firstValueFrom(this.getFeatures({
             assemblyName: '',
-            refName: r,
+            refName,
             start: 0,
             end: 1,
         }).pipe(toArray())))[0]));
@@ -68,16 +68,20 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     async getHeader(opts) {
         const { parser, header } = await this.configure(opts);
         const { version, fileType } = header;
-        const { fields, ...rest } = parser.autoSql;
+        const { fields, ...autoSql } = parser.autoSql;
         return {
             version,
             fileType,
-            autoSql: { ...rest },
-            fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
+            autoSql,
+            fields: await this.getMetadata(opts),
         };
     }
+    async getMetadata(opts) {
+        const { parser } = await this.configure(opts);
+        const { fields } = parser.autoSql;
+        return Object.fromEntries(fields.map(({ name, comment }) => [name, comment]));
+    }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        var _a;
         const { statusCallback = () => { } } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
@@ -85,94 +89,98 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         const feats = await updateStatus('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
             basesPerSpan: query.end - query.start,
         }));
-        const parentAggregation = {};
-        const parentAggregationFlat = [];
-        if (feats.some(f => f.uniqueId === undefined)) {
-            throw new Error('found uniqueId undefined');
-        }
-        for (const feat of feats) {
-            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] = [];
+        await updateStatus('Processing features', statusCallback, async () => {
+            var _a;
+            const parentAggregation = {};
+            const parentAggregationFlat = [];
+            if (feats.some(f => f.uniqueId === undefined)) {
+                throw new Error('found uniqueId undefined');
             }
-            const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
-            const f = featureData2({
-                ...rest,
-                scoreColumn,
-                splitLine,
-                parser,
-                uniqueId,
-                start: feat.start,
-                end: feat.end,
-                refName: query.refName,
-            });
-            if (aggr) {
-                parentAggregation[aggr].push(f);
-                parentAggregationFlat.push(f);
-            }
-            else {
-                if (doesIntersect2(f.start, f.end, originalQuery.start, originalQuery.end)) {
-                    observer.next(new SimpleFeature({
-                        id: `${this.id}-${uniqueId}`,
-                        data: f,
-                    }));
+            for (const feat of feats) {
+                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];
+                const aggrIsNotNone = aggr && aggr !== 'none';
+                if (aggrIsNotNone && !parentAggregation[aggr]) {
+                    parentAggregation[aggr] = [];
                 }
-            }
-        }
-        if (allowRedispatch && parentAggregationFlat.length) {
-            let minStart = Number.POSITIVE_INFINITY;
-            let maxEnd = Number.NEGATIVE_INFINITY;
-            for (const feat of parentAggregationFlat) {
-                if (feat.start < minStart) {
-                    minStart = feat.start;
+                const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
+                const f = featureData2({
+                    ...rest,
+                    scoreColumn,
+                    splitLine,
+                    parser,
+                    uniqueId,
+                    start: feat.start,
+                    end: feat.end,
+                    refName: query.refName,
+                });
+                if (aggrIsNotNone) {
+                    parentAggregation[aggr].push(f);
+                    parentAggregationFlat.push(f);
                 }
-                if (feat.end > maxEnd) {
-                    maxEnd = feat.end;
+                else {
+                    if (doesIntersect2(f.start, f.end, originalQuery.start, originalQuery.end)) {
+                        observer.next(new SimpleFeature({
+                            id: `${this.id}-${uniqueId}`,
+                            data: f,
+                        }));
+                    }
                 }
             }
-            if (maxEnd > query.end || minStart < query.start) {
-                await this.getFeaturesHelper({
-                    query: {
-                        ...query,
-                        start: minStart - 500000,
-                        end: maxEnd + 500000,
-                    },
-                    opts,
-                    observer,
-                    allowRedispatch: false,
-                    originalQuery: query,
-                });
-                return;
-            }
-        }
-        Object.entries(parentAggregation).map(([name, subfeatures]) => {
-            var _a, _b;
-            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 subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
-                observer.next(new SimpleFeature({
-                    id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
-                    data: {
-                        type: 'gene',
-                        subfeatures: subs,
-                        strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
-                        name,
-                        start: s,
-                        end: e,
-                        refName: query.refName,
-                    },
-                }));
+            if (allowRedispatch && parentAggregationFlat.length) {
+                let minStart = Number.POSITIVE_INFINITY;
+                let maxEnd = Number.NEGATIVE_INFINITY;
+                for (const feat of parentAggregationFlat) {
+                    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: {
+                            ...query,
+                            start: minStart - 500000,
+                            end: maxEnd + 500000,
+                        },
+                        opts,
+                        observer,
+                        allowRedispatch: false,
+                        originalQuery: query,
+                    });
+                    return;
+                }
             }
+            Object.entries(parentAggregation).map(([name, subfeatures]) => {
+                var _a, _b;
+                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 subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
+                    observer.next(new SimpleFeature({
+                        id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
+                        data: {
+                            type: 'gene',
+                            subfeatures: subs,
+                            strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
+                            name,
+                            start: s,
+                            end: e,
+                            refName: query.refName,
+                        },
+                    }));
+                }
+            });
         });
         observer.complete();
     }
@@ -195,5 +203,4 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             }
         }, opts.stopToken);
     }
-    freeResources() { }
 }

package/esm/generateUcscTranscript.d.ts

@@ -1,4 +1,4 @@
-import type { MinimalFeature, TranscriptFeat } from './types';
+import type { TranscriptFeat } from './types';
 export declare function isUcscTranscript({ thickStart, blockCount, strand, }: {
     thickStart?: number;
     blockCount?: number;
@@ -9,7 +9,12 @@ export declare function generateUcscTranscript(data: TranscriptFeat): {
     strand: number;
     type: string;
     refName: string;
-    subfeatures: MinimalFeature[];
+    subfeatures: {
+        type: string;
+        start: number;
+        end: number;
+        refName: string;
+    }[];
     start: number;
     end: number;
 };

package/esm/generateUcscTranscript.js

@@ -8,81 +8,105 @@ export function generateUcscTranscript(data) {
     const feats = oldSubfeatures
         .filter(child => child.type === 'block')
         .sort((a, b) => a.start - b.start);
-    for (const block of feats) {
-        const start = block.start;
-        const end = block.end;
-        if (thickStart >= end) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd >= end) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                phase: 0,
-                start: thickStart,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd >= end) {
-            subfeatures.push({
-                type: 'CDS',
-                phase: 0,
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd < end) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                phase: 0,
-                start: thickStart,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-            subfeatures.push({
-                type: 'CDS',
-                phase: 0,
-                start,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickEnd <= start) {
-            subfeatures.push({
-                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
+    const { cdsEndStat, cdsStartStat } = rest2;
+    if (cdsStartStat === 'none' && cdsEndStat === 'none') {
+        return {
+            ...rest2,
+            uniqueId,
+            strand,
+            type: 'transcript',
+            refName,
+            subfeatures: feats.map(e => ({
+                ...e,
+                type: 'exon',
+            })),
+        };
+    }
+    else {
+        for (const block of feats) {
+            const start = block.start;
+            const end = block.end;
+            if (thickStart >= end) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                    start,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart > start && thickStart < end && thickEnd >= end) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                    start,
+                    end: thickStart,
+                    refName,
+                }, {
+                    type: 'CDS',
+                    phase: 0,
+                    start: thickStart,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart <= start && thickEnd >= end) {
+                subfeatures.push({
+                    type: 'CDS',
+                    phase: 0,
+                    start,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart > start && thickStart < end && thickEnd < end) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                    start,
+                    end: thickStart,
+                    refName,
+                }, {
+                    type: 'CDS',
+                    phase: 0,
+                    start: thickStart,
+                    end: thickEnd,
+                    refName,
+                }, {
+                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                    start: thickEnd,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+                subfeatures.push({
+                    type: 'CDS',
+                    phase: 0,
+                    start,
+                    end: thickEnd,
+                    refName,
+                }, {
+                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                    start: thickEnd,
+                    end,
+                    refName,
+                });
+            }
+            else if (thickEnd <= start) {
+                subfeatures.push({
+                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                    start,
+                    end,
+                    refName,
+                });
+            }
         }
+        return {
+            ...rest2,
+            uniqueId,
+            strand,
+            type: 'mRNA',
+            refName,
+            subfeatures,
+        };
     }
     return {
         ...rest2,

package/esm/util.d.ts

@@ -89,7 +89,12 @@ export declare function featureData({ line, colRef, colStart, colEnd, scoreColum
     strand: number;
     type: string;
     refName: string;
-    subfeatures: import("./types").MinimalFeature[];
+    subfeatures: {
+        type: string;
+        start: number;
+        end: number;
+        refName: string;
+    }[];
     start: number;
     end: number;
 } | {
@@ -182,7 +187,12 @@ export declare function featureData2({ splitLine, refName, start, end, parser, u
     strand: number;
     type: string;
     refName: string;
-    subfeatures: import("./types").MinimalFeature[];
+    subfeatures: {
+        type: string;
+        start: number;
+        end: number;
+        refName: string;
+    }[];
     start: number;
     end: number;
 } | {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "3.3.0",
+  "version": "3.5.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,11 +37,11 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^6.0.0",
+    "@gmod/bbi": "^7.0.0",
     "@gmod/bed": "^2.1.2",
-    "@gmod/bgzf-filehandle": "^2.0.1",
-    "@gmod/tabix": "^2.0.0",
-    "@jbrowse/core": "^3.3.0",
+    "@gmod/bgzf-filehandle": "^4.0.0",
+    "@gmod/tabix": "^3.0.1",
+    "@jbrowse/core": "^3.5.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -53,5 +53,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
+  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
 }