@jbrowse/plugin-bed 2.16.1 → 2.18.0

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/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,11 +1,12 @@
 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 cached?;
+    private cachedP?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
         header: import("@gmod/bbi").Header;
@@ -17,6 +18,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getData(): Promise<Feature[]>;
     getHeader(opts?: BaseOptions): Promise<{
         version: number;
         fileType: string;
@@ -25,7 +27,13 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
-    getFeaturesHelper(query: Region, opts: BaseOptions, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
+    getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
+        query: Region;
+        opts: BaseOptions;
+        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

@@ -1,11 +1,11 @@
 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';
-// locals
-import { isUcscProcessedTranscript, makeBlocks, ucscProcessedTranscript, } from '../util';
+import { firstValueFrom, toArray } from 'rxjs';
+import { featureData2 } from '../util';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     async configurePre(opts) {
         const pm = this.pluginManager;
@@ -13,22 +13,42 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             filehandle: openLocation(this.getConf('bigBedLocation'), pm),
         });
         const header = await bigbed.getHeader(opts);
-        const parser = new BED({ autoSql: header.autoSql });
-        return { bigbed, header, parser };
+        const parser = new BED({
+            autoSql: header.autoSql,
+        });
+        return {
+            bigbed,
+            header,
+            parser,
+        };
     }
     async configure(opts) {
-        if (!this.cached) {
-            this.cached = this.configurePre(opts).catch((e) => {
-                this.cached = undefined;
+        if (!this.cachedP) {
+            this.cachedP = this.configurePre(opts).catch((e) => {
+                this.cachedP = undefined;
                 throw e;
             });
         }
-        return this.cached;
+        return this.cachedP;
     }
     async getRefNames(opts) {
         const { header } = await this.configure(opts);
         return Object.keys(header.refsByName);
     }
+    async getData() {
+        const refNames = await this.getRefNames();
+        const features = [];
+        for (const refName of refNames) {
+            const f = await firstValueFrom(this.getFeatures({
+                assemblyName: 'unknown',
+                refName,
+                start: 0,
+                end: Number.MAX_SAFE_INTEGER,
+            }).pipe(toArray()));
+            features.push(f);
+        }
+        return features.flat();
+    }
     async getHeader(opts) {
         const { parser, header } = await this.configure(opts);
         const { version, fileType } = header;
@@ -40,13 +60,14 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
         };
     }
-    async getFeaturesHelper(query, opts, observer, allowRedispatch, originalQuery = query) {
-        const { signal } = opts;
+    async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
+        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) {
@@ -61,7 +82,17 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                 }
             }
             if (maxEnd > query.end || minStart < query.start) {
-                await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, observer, false, query);
+                await this.getFeaturesHelper({
+                    query: {
+                        ...query,
+                        start: minStart,
+                        end: maxEnd,
+                    },
+                    opts,
+                    observer,
+                    allowRedispatch: false,
+                    originalQuery: query,
+                });
                 return;
             }
         }
@@ -70,62 +101,36 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             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 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] = [];
             }
-            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,
-                });
-                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, 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);
             }
             else {
-                if (doesIntersect2(feat.start, feat.end, originalQuery.start, originalQuery.end)) {
+                if (doesIntersect2(f.start, f.end, originalQuery.start, originalQuery.end)) {
                     observer.next(new SimpleFeature({
                         id: `${this.id}-${uniqueId}`,
-                        data: {
-                            ...rest,
-                            uniqueId,
-                            type,
-                            start: feat.start,
-                            score: scoreColumn ? +data[scoreColumn] : score,
-                            end: feat.end,
-                            refName: query.refName,
-                            subfeatures,
-                        },
+                        data: f,
                     }));
                 }
             }
@@ -154,12 +159,17 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
             try {
-                await this.getFeaturesHelper(query, opts, observer, true);
+                await this.getFeaturesHelper({
+                    query,
+                    opts,
+                    observer,
+                    allowRedispatch: true,
+                });
             }
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/esm/BigBedAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bigBedLocation: {
         type: string;
         defaultValue: {
@@ -9,17 +6,11 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     aggregateField: {
         type: string;
         description: string;

package/esm/BigBedAdapter/configSchema.js

@@ -1,27 +1,15 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config BigBedAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
-    /**
-     * #slot
-     */
     bigBedLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     aggregateField: {
         type: 'string',
         description: 'An attribute to aggregate features with',

package/esm/BigBedAdapter/index.d.ts

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

package/esm/generateBedMethylFeature.d.ts

@@ -0,0 +1,31 @@
+export declare function isBedMethylFeature({ splitLine, start, end, }: {
+    splitLine: string[];
+    start: number;
+    end: number;
+}): boolean;
+export declare function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }: {
+    splitLine: string[];
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+}): {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    code: string | undefined;
+    score: number;
+    strand: string | undefined;
+    color: string | undefined;
+    source: string | undefined;
+    n_valid_cov: string | undefined;
+    fraction_modified: string | undefined;
+    n_mod: string | undefined;
+    n_canonical: string | undefined;
+    n_other_mod: string | undefined;
+    n_delete: string | undefined;
+    n_fail: string | undefined;
+    n_diff: string | undefined;
+    n_nocall: string | undefined;
+};

package/esm/generateBedMethylFeature.js

@@ -0,0 +1,26 @@
+export function isBedMethylFeature({ splitLine, start, end, }) {
+    return +(splitLine[6] || 0) === start && +(splitLine[7] || 0) === end;
+}
+export function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }) {
+    const [, , , code, , strand, , , color, n_valid_cov, fraction_modified, n_mod, n_canonical, n_other_mod, n_delete, n_fail, n_diff, n_nocall,] = splitLine;
+    return {
+        uniqueId,
+        refName,
+        start,
+        end,
+        code,
+        score: +fraction_modified || 0,
+        strand,
+        color,
+        source: code,
+        n_valid_cov,
+        fraction_modified,
+        n_mod,
+        n_canonical,
+        n_other_mod,
+        n_delete,
+        n_fail,
+        n_diff,
+        n_nocall,
+    };
+}

package/esm/generateRepeatMaskerFeature.d.ts

@@ -0,0 +1,51 @@
+export declare function isRepeatMaskerDescriptionField(desc?: string): desc is string;
+export declare function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }: {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    description: string;
+    [key: string]: unknown;
+}): {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    bitsw_score: string | undefined;
+    percent_div: string | undefined;
+    percent_del: string | undefined;
+    percent_ins: string | undefined;
+    query_chr: string | undefined;
+    query_begin: string | undefined;
+    query_end: string | undefined;
+    query_remaining: string | undefined;
+    orientation: string | undefined;
+    matching_repeat_name: string | undefined;
+    matching_repeat_class: string | undefined;
+    matching_repeat_begin: string | undefined;
+    matching_repeat_end: string | undefined;
+    matching_repeat_remaining: string | undefined;
+    repeat_id: string | undefined;
+    description?: undefined;
+} | {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    description: undefined;
+    bitsw_score?: undefined;
+    percent_div?: undefined;
+    percent_del?: undefined;
+    percent_ins?: undefined;
+    query_chr?: undefined;
+    query_begin?: undefined;
+    query_end?: undefined;
+    query_remaining?: undefined;
+    orientation?: undefined;
+    matching_repeat_name?: undefined;
+    matching_repeat_class?: undefined;
+    matching_repeat_begin?: undefined;
+    matching_repeat_end?: undefined;
+    matching_repeat_remaining?: undefined;
+    repeat_id?: undefined;
+};

package/esm/generateRepeatMaskerFeature.js

@@ -0,0 +1,37 @@
+export function isRepeatMaskerDescriptionField(desc) {
+    const ret = desc === null || desc === void 0 ? void 0 : desc.trim().split(' ');
+    return [0, 1, 2, 3, 5, 6].every(s => (ret === null || ret === void 0 ? void 0 : ret[s]) !== undefined ? !Number.isNaN(+ret[s]) : false);
+}
+function makeRepeatTrackDescription(description) {
+    if (isRepeatMaskerDescriptionField(description)) {
+        const [bitsw_score, percent_div, percent_del, percent_ins, query_chr, query_begin, query_end, query_remaining, orientation, matching_repeat_name, matching_repeat_class, matching_repeat_begin, matching_repeat_end, matching_repeat_remaining, repeat_id,] = description.trim().split(' ');
+        return {
+            bitsw_score,
+            percent_div,
+            percent_del,
+            percent_ins,
+            query_chr,
+            query_begin,
+            query_end,
+            query_remaining,
+            orientation,
+            matching_repeat_name,
+            matching_repeat_class,
+            matching_repeat_begin,
+            matching_repeat_end,
+            matching_repeat_remaining,
+            repeat_id,
+        };
+    }
+    return { description };
+}
+export function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }) {
+    return {
+        ...rest,
+        ...makeRepeatTrackDescription(description),
+        uniqueId,
+        refName,
+        start,
+        end,
+    };
+}

package/esm/generateUcscTranscript.d.ts

@@ -0,0 +1,15 @@
+import type { MinimalFeature, TranscriptFeat } from './types';
+export declare function isUcscTranscript({ thickStart, blockCount, strand, }: {
+    thickStart?: number;
+    blockCount?: number;
+    strand?: number;
+}): boolean | 0 | undefined;
+export declare function generateUcscTranscript(data: TranscriptFeat): {
+    uniqueId: string;
+    strand: number;
+    type: string;
+    refName: string;
+    subfeatures: MinimalFeature[];
+    start: number;
+    end: number;
+};

package/esm/generateUcscTranscript.js

@@ -0,0 +1,91 @@
+export function isUcscTranscript({ thickStart, blockCount, strand, }) {
+    return thickStart && blockCount && strand !== 0;
+}
+export function generateUcscTranscript(data) {
+    const { strand = 0, chrom: _1, chromStart: _2, chromEnd: _3, chromStarts, blockStarts, blockSizes, uniqueId, ...rest } = data;
+    const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, refName, ...rest2 } = rest;
+    const subfeatures = [];
+    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',
+                start: thickStart,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart <= start && thickEnd >= end) {
+            subfeatures.push({
+                type: 'CDS',
+                start,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd < end) {
+            subfeatures.push({
+                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                start,
+                end: thickStart,
+                refName,
+            }, {
+                type: 'CDS',
+                start: thickStart,
+                end: thickEnd,
+                refName,
+            }, {
+                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                start: thickEnd,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+            subfeatures.push({
+                type: 'CDS',
+                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,
+    };
+}

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class BedPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,9 +1,11 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BigBedAdapterF from './BigBedAdapter';
-import BedpeAdapterF from './BedpeAdapter';
-import BedTabixAdapterF from './BedTabixAdapter';
-import BedAdapterF from './BedAdapter';
 import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
+import BedAdapterF from './BedAdapter';
+import BedGraphAdapterF from './BedGraphAdapter';
+import BedGraphTabixAdapterF from './BedGraphTabixAdapter';
+import BedTabixAdapterF from './BedTabixAdapter';
+import BedpeAdapterF from './BedpeAdapter';
+import BigBedAdapterF from './BigBedAdapter';
 export default class BedPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -14,6 +16,8 @@ export default class BedPlugin extends Plugin {
         BedAdapterF(pluginManager);
         BedpeAdapterF(pluginManager);
         BedTabixAdapterF(pluginManager);
+        BedGraphAdapterF(pluginManager);
+        BedGraphTabixAdapterF(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\.(bb|bigbed)$/i;

package/esm/types.d.ts

@@ -0,0 +1,18 @@
+export interface MinimalFeature {
+    type: string;
+    start: number;
+    end: number;
+    refName: string;
+    [key: string]: unknown;
+}
+export interface TranscriptFeat extends MinimalFeature {
+    uniqueId: string;
+    thickStart: number;
+    thickEnd: number;
+    blockCount: number;
+    blockSizes: number[];
+    chromStarts: number[];
+    refName: string;
+    strand?: number;
+    subfeatures: MinimalFeature[];
+}

package/esm/types.js

@@ -0,0 +1 @@
+export {};