@jbrowse/plugin-bed 2.16.1 → 2.17.0

package/dist/BedAdapter/BedAdapter.js

@@ -9,7 +9,6 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 // locals
 const util_2 = require("../util");
 class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -20,8 +19,7 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async loadDataP(opts = {}) {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedLocation');
-        const buf = await (0, io_1.openLocation)(bedLoc, pm).readFile(opts);
-        const buffer = (0, util_1.isGzip)(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, pm), opts);
         // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
@@ -101,9 +99,18 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         const names = await this.getNames();
         const intervalTree = new interval_tree_1.default();
-        const ret = lines.map((f, i) => {
+        const ret = lines.map((line, i) => {
             const uniqueId = `${this.id}-${refName}-${i}`;
-            return (0, util_2.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
+            return new util_1.SimpleFeature((0, util_2.featureData)({
+                line,
+                colRef,
+                colStart,
+                colEnd,
+                scoreColumn,
+                parser,
+                uniqueId,
+                names,
+            }));
         });
         for (const obj of ret) {
             intervalTree.insert([obj.get('start'), obj.get('end')], obj);

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -7,9 +7,10 @@ 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 util_1 = require("@jbrowse/core/util");
 const tabix_1 = require("@gmod/tabix");
 // locals
-const util_1 = require("../util");
+const util_2 = require("../util");
 class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -55,13 +56,19 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const colRef = columnNumbers.ref - 1;
             const colStart = columnNumbers.start - 1;
             const colEnd = columnNumbers.end - 1;
-            // colSame handles special case for tabix where a single column is both
-            // the start and end, this is assumed to be covering the base at this
-            // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same
             const names = await this.getNames();
             await this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
-                    observer.next((0, util_1.featureData)(line, colRef, colStart, colEnd, this.scoreColumn, this.parser, `${this.id}-${fileOffset}`, names));
+                    observer.next(new util_1.SimpleFeature((0, util_2.featureData)({
+                        line,
+                        colRef,
+                        colStart,
+                        colEnd,
+                        scoreColumn: this.scoreColumn,
+                        parser: this.parser,
+                        uniqueId: `${this.id}-${fileOffset}`,
+                        names,
+                    })));
                 },
                 signal: opts.signal,
             });

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -9,7 +9,6 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
 function featureData(line, uniqueId, flip, names) {
     const l = line.split('\t');
@@ -64,11 +63,11 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         super(...arguments);
         this.intervalTrees = {};
     }
-    async loadDataP(opts = {}) {
+    async loadDataP(opts) {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedpeLocation');
-        const buf = await (0, io_1.openLocation)(bedLoc, pm).readFile(opts);
-        const buffer = (0, util_1.isGzip)(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
+        const loc = (0, io_1.openLocation)(bedLoc, pm);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -5,7 +5,7 @@ import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
 import { 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 +17,7 @@ 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 +26,13 @@ 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/dist/BigBedAdapter/BigBedAdapter.js

@@ -9,6 +9,7 @@ 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 util_1 = require("@jbrowse/core/util");
+const rxjs_2 = require("rxjs");
 // locals
 const util_2 = require("../util");
 class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -18,22 +19,42 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             filehandle: (0, io_1.openLocation)(this.getConf('bigBedLocation'), pm),
         });
         const header = await bigbed.getHeader(opts);
-        const parser = new bed_1.default({ autoSql: header.autoSql });
-        return { bigbed, header, parser };
+        const parser = new bed_1.default({
+            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 (0, rxjs_2.firstValueFrom)(this.getFeatures({
+                assemblyName: 'unknown',
+                refName,
+                start: 0,
+                end: Number.MAX_SAFE_INTEGER,
+            }).pipe((0, rxjs_2.toArray)()));
+            features.push(f);
+        }
+        return features.flat();
+    }
     async getHeader(opts) {
         const { parser, header } = await this.configure(opts);
         const { version, fileType } = header;
@@ -45,7 +66,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
         };
     }
-    async getFeaturesHelper(query, opts, observer, allowRedispatch, originalQuery = query) {
+    async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
         const { signal } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
@@ -66,7 +87,17 @@ class BigBedAdapter extends BaseAdapter_1.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;
             }
         }
@@ -75,62 +106,31 @@ class BigBedAdapter extends BaseAdapter_1.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 line = `${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`;
+            const data = parser.parseLine(line, { 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,
-                });
-                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, 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,
+                line,
+                parser,
+                uniqueId,
+                start: feat.start,
+                end: feat.end,
+                refName: query.refName,
+            });
+            if (aggr) {
+                parentAggregation[aggr].push(f);
             }
             else {
-                if ((0, util_1.doesIntersect2)(feat.start, feat.end, originalQuery.start, originalQuery.end)) {
+                if ((0, util_1.doesIntersect2)(f.start, f.end, originalQuery.start, originalQuery.end)) {
                     observer.next(new util_1.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,
                     }));
                 }
             }
@@ -159,7 +159,12 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             try {
-                await this.getFeaturesHelper(query, opts, observer, true);
+                await this.getFeaturesHelper({
+                    query,
+                    opts,
+                    observer,
+                    allowRedispatch: true,
+                });
             }
             catch (e) {
                 observer.error(e);

package/dist/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({ line, uniqueId, refName, start, end, }: {
+    line: string;
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+}): {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    code: string | undefined;
+    score: string | undefined;
+    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/dist/generateBedMethylFeature.js

@@ -0,0 +1,32 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isBedMethylFeature = isBedMethylFeature;
+exports.generateBedMethylFeature = generateBedMethylFeature;
+function isBedMethylFeature({ splitLine, start, end, }) {
+    return +(splitLine[6] || 0) === start && +(splitLine[7] || 0) === end;
+}
+function generateBedMethylFeature({ line, uniqueId, refName, start, end, }) {
+    // see
+    // https://github.com/nanoporetech/modkit?tab=readme-ov-file#description-of-bedmethyl-output
+    const [, , , code, , strand, , , color, n_valid_cov, fraction_modified, n_mod, n_canonical, n_other_mod, n_delete, n_fail, n_diff, n_nocall,] = line.split('\t');
+    return {
+        uniqueId,
+        refName,
+        start,
+        end,
+        code,
+        score: fraction_modified,
+        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/dist/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/dist/generateRepeatMaskerFeature.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isRepeatMaskerDescriptionField = isRepeatMaskerDescriptionField;
+exports.generateRepeatMaskerFeature = generateRepeatMaskerFeature;
+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 };
+}
+function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }) {
+    return {
+        ...rest,
+        ...makeRepeatTrackDescription(description),
+        uniqueId,
+        refName,
+        start,
+        end,
+    };
+}

package/dist/generateUcscTranscript.d.ts

@@ -0,0 +1,15 @@
+import { 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/dist/generateUcscTranscript.js

@@ -0,0 +1,101 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isUcscTranscript = isUcscTranscript;
+exports.generateUcscTranscript = generateUcscTranscript;
+function isUcscTranscript({ thickStart, blockCount, strand, }) {
+    return thickStart && blockCount && strand !== 0;
+}
+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) {
+            // left-side UTR
+            subfeatures.push({
+                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                start,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd >= end) {
+            // UTR | CDS
+            subfeatures.push({
+                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                start,
+                end: thickStart,
+                refName,
+            }, {
+                type: 'CDS',
+                start: thickStart,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart <= start && thickEnd >= end) {
+            // CDS
+            subfeatures.push({
+                type: 'CDS',
+                start,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd < end) {
+            // UTR | CDS | UTR
+            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) {
+            // CDS | UTR
+            subfeatures.push({
+                type: 'CDS',
+                start,
+                end: thickEnd,
+                refName,
+            }, {
+                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                start: thickEnd,
+                end,
+                refName,
+            });
+        }
+        else if (thickEnd <= start) {
+            // right-side UTR
+            subfeatures.push({
+                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                start,
+                end,
+                refName,
+            });
+        }
+    }
+    return {
+        ...rest2,
+        uniqueId,
+        strand,
+        type: 'mRNA',
+        refName,
+        subfeatures,
+    };
+}

package/dist/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/dist/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });