@jbrowse/plugin-bed 2.16.0 → 2.17.0

package/dist/util.d.ts

@@ -1,37 +1,12 @@
 import BED from '@gmod/bed';
-import { SimpleFeature } from '@jbrowse/core/util';
-export interface MinimalFeature {
-    type: string;
-    start: number;
-    end: number;
-    refName: string;
-    [key: string]: unknown;
-}
-export interface TranscriptFeat extends MinimalFeature {
-    thickStart: number;
-    thickEnd: number;
-    blockCount: number;
-    blockSizes: number[];
-    chromStarts: number[];
-    refName: string;
-    strand?: number;
-    subfeatures: MinimalFeature[];
-}
-export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
-    strand: number;
-    type: string;
-    refName: string;
-    subfeatures: MinimalFeature[];
-    start: number;
-    end: number;
-};
+import { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
     blockCount: number;
     start: number;
     uniqueId: string;
     refName: string;
     chromStarts?: number[];
-    blockSizes: number[];
+    blockSizes?: number[];
     blockStarts?: number[];
 }): {
     uniqueId: string;
@@ -40,9 +15,24 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
     refName: string;
     type: string;
 }[];
-export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
-export declare function isUcscProcessedTranscript(f: {
-    thickStart?: number;
-    blockCount?: number;
-    strand?: number;
-}): boolean | 0 | undefined;
+export declare function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, }: {
+    line: string;
+    colRef: number;
+    colStart: number;
+    colEnd: number;
+    scoreColumn: string;
+    parser: BED;
+    uniqueId: string;
+    names?: string[];
+}): SimpleFeatureSerialized;
+export declare function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
+    line: string;
+    refName: string;
+    start: number;
+    end: number;
+    parser: BED;
+    uniqueId: string;
+    scoreColumn: string;
+    names?: string[];
+}): SimpleFeatureSerialized;
+export declare function arrayify(f?: string | number[]): number[] | undefined;

package/dist/util.js

@@ -1,179 +1,153 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ucscProcessedTranscript = ucscProcessedTranscript;
 exports.makeBlocks = makeBlocks;
 exports.featureData = featureData;
-exports.isUcscProcessedTranscript = isUcscProcessedTranscript;
-const util_1 = require("@jbrowse/core/util");
-function ucscProcessedTranscript(feature) {
-    const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, blockSizes, chromStarts, refName, strand = 0, ...rest } = feature;
-    if (!thickStart || !thickEnd || !strand) {
-        return feature;
+exports.featureData2 = featureData2;
+exports.arrayify = arrayify;
+const generateBedMethylFeature_1 = require("./generateBedMethylFeature");
+const generateUcscTranscript_1 = require("./generateUcscTranscript");
+const generateRepeatMaskerFeature_1 = require("./generateRepeatMaskerFeature");
+function stringToStrand(f) {
+    if (f === '-1') {
+        return -1;
+    }
+    else if (f === '+') {
+        return 1;
+    }
+    else {
+        return 0;
     }
-    const subfeatures = [];
-    oldSubfeatures
-        .filter(child => child.type === 'block')
-        .sort((a, b) => a.start - b.start)
-        .forEach(block => {
-        const start = block.start;
-        const end = block.end;
-        if (thickStart >= end) {
-            // left-side UTR
-            const prime = strand > 0 ? 'five' : 'three';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd >= end) {
-            // UTR | CDS
-            const prime = strand > 0 ? 'five' : 'three';
-            subfeatures.push({
-                type: `${prime}_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
-            const leftPrime = strand > 0 ? 'five' : 'three';
-            const rightPrime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: `${leftPrime}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                start: thickStart,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${rightPrime}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-            // CDS | UTR
-            const prime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: 'CDS',
-                start,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${prime}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickEnd <= start) {
-            // right-side UTR
-            const prime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-    });
-    return { ...rest, strand, type: 'mRNA', refName, subfeatures };
 }
 function defaultParser(fields, line) {
     const obj = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
     const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
     return {
         ...rest,
-        blockStarts: blockStarts === null || blockStarts === void 0 ? void 0 : blockStarts.split(',').map(r => +r),
-        chromStarts: chromStarts === null || chromStarts === void 0 ? void 0 : chromStarts.split(',').map(r => +r),
-        blockSizes: blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes.split(',').map(r => +r),
+        blockStarts: arrayify(blockStarts),
+        chromStarts: arrayify(chromStarts),
+        blockSizes: arrayify(blockSizes),
         thickStart: thickStart ? +thickStart : undefined,
         thickEnd: thickEnd ? +thickEnd : undefined,
         blockCount: blockCount ? +blockCount : undefined,
     };
 }
 function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
-    const subfeatures = [];
-    const starts = chromStarts || blockStarts || [];
-    for (let b = 0; b < blockCount; b++) {
-        const bmin = (starts[b] || 0) + start;
-        const bmax = bmin + (blockSizes[b] || 0);
-        subfeatures.push({
-            uniqueId: `${uniqueId}-${b}`,
-            start: bmin,
-            end: bmax,
-            refName,
-            type: 'block',
-        });
+    if (blockCount) {
+        const subfeatures = [];
+        const starts = chromStarts || blockStarts || [];
+        for (let b = 0; b < blockCount; b++) {
+            const bmin = (starts[b] || 0) + start;
+            const bsize = blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b];
+            if (bsize && bsize > 0) {
+                const bmax = bmin + bsize;
+                subfeatures.push({
+                    uniqueId: `${uniqueId}-${b}`,
+                    start: bmin,
+                    end: bmax,
+                    refName,
+                    type: 'block',
+                });
+            }
+        }
+        return subfeatures;
     }
-    return subfeatures;
+    return [];
 }
-function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
-    const l = line.split('\t');
-    const refName = l[colRef];
-    const start = +l[colStart];
-    const colSame = colStart === colEnd ? 1 : 0;
-    const end = +l[colEnd] + colSame;
+function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, }) {
+    const splitLine = line.split('\t');
+    const refName = splitLine[colRef];
+    const start = +splitLine[colStart];
+    const end = +splitLine[colEnd] + (colStart === colEnd ? 1 : 0);
+    return featureData2({
+        line,
+        refName,
+        start,
+        end,
+        parser,
+        uniqueId,
+        scoreColumn,
+        names,
+    });
+}
+function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
+    const splitLine = line.split('\t');
     const data = names
         ? defaultParser(names, line)
         : parser.parseLine(line, { uniqueId });
-    const { blockCount, blockSizes, blockStarts, chromStarts, thickStart, thickEnd, type, score, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
-    const subfeatures = blockCount
-        ? makeBlocks({
+    const { strand: strand2, score: score2, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
+    const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
+    const score = scoreColumn ? +data[scoreColumn] : score2 ? +score2 : undefined;
+    const strand = typeof strand2 === 'string' ? stringToStrand(strand2) : strand2;
+    const subfeatures = makeBlocks({
+        start,
+        uniqueId,
+        refName,
+        chromStarts,
+        blockCount,
+        blockSizes,
+        blockStarts,
+    });
+    if ((0, generateBedMethylFeature_1.isBedMethylFeature)({ splitLine, start, end })) {
+        return (0, generateBedMethylFeature_1.generateBedMethylFeature)({
+            line,
+            uniqueId,
+            refName,
             start,
+            end,
+        });
+    }
+    else if ((0, generateRepeatMaskerFeature_1.isRepeatMaskerDescriptionField)(description)) {
+        return (0, generateRepeatMaskerFeature_1.generateRepeatMaskerFeature)({
+            ...rest2,
             uniqueId,
+            description,
+            type,
+            score,
+            start,
+            end,
+            strand,
             refName,
+            subfeatures,
+        });
+    }
+    else if ((0, generateUcscTranscript_1.isUcscTranscript)({ strand, blockCount, thickStart })) {
+        return (0, generateUcscTranscript_1.generateUcscTranscript)({
+            ...rest,
+            description,
             chromStarts,
-            blockCount,
+            thickStart,
+            thickEnd,
             blockSizes,
-            blockStarts,
-        })
-        : [];
-    const f = {
-        ...rest,
-        type,
-        score: scoreColumn ? +data[scoreColumn] : score,
-        start,
-        end,
-        refName,
-        uniqueId,
-        subfeatures,
-    };
-    return new util_1.SimpleFeature({
-        id: uniqueId,
-        data: isUcscProcessedTranscript(data)
-            ? ucscProcessedTranscript({
-                thickStart: thickStart,
-                thickEnd: thickEnd,
-                blockCount: blockCount,
-                blockSizes: blockSizes,
-                chromStarts: chromStarts,
-                ...f,
-            })
-            : f,
-    });
+            blockCount,
+            type,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            uniqueId,
+            subfeatures,
+        });
+    }
+    else {
+        return {
+            ...rest,
+            uniqueId,
+            description,
+            type,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            subfeatures,
+        };
+    }
 }
-function isUcscProcessedTranscript(f) {
-    return f.thickStart && f.blockCount && f.strand !== 0;
+function arrayify(f) {
+    return f !== undefined
+        ? typeof f === 'string'
+            ? f.split(',').map(f => +f)
+            : f
+        : undefined;
 }

package/esm/BedAdapter/BedAdapter.js

@@ -2,9 +2,8 @@ import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { isGzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip, SimpleFeature, } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
-import { unzip } from '@gmod/bgzf-filehandle';
 // locals
 import { featureData } from '../util';
 class BedAdapter extends BaseFeatureDataAdapter {
@@ -15,8 +14,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
     async loadDataP(opts = {}) {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedLocation');
-        const buf = await openLocation(bedLoc, pm).readFile(opts);
-        const buffer = isGzip(buf) ? await unzip(buf) : buf;
+        const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, pm), opts);
         // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
@@ -96,9 +94,18 @@ class BedAdapter extends BaseFeatureDataAdapter {
         }
         const names = await this.getNames();
         const intervalTree = new IntervalTree();
-        const ret = lines.map((f, i) => {
+        const ret = lines.map((line, i) => {
             const uniqueId = `${this.id}-${refName}-${i}`;
-            return featureData(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
+            return new SimpleFeature(featureData({
+                line,
+                colRef,
+                colStart,
+                colEnd,
+                scoreColumn,
+                parser,
+                uniqueId,
+                names,
+            }));
         });
         for (const obj of ret) {
             intervalTree.insert([obj.get('start'), obj.get('end')], obj);

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -2,6 +2,7 @@ import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { SimpleFeature, } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 // locals
 import { featureData } from '../util';
@@ -50,13 +51,19 @@ class BedTabixAdapter extends 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(featureData(line, colRef, colStart, colEnd, this.scoreColumn, this.parser, `${this.id}-${fileOffset}`, names));
+                    observer.next(new SimpleFeature(featureData({
+                        line,
+                        colRef,
+                        colStart,
+                        colEnd,
+                        scoreColumn: this.scoreColumn,
+                        parser: this.parser,
+                        uniqueId: `${this.id}-${fileOffset}`,
+                        names,
+                    })));
                 },
                 signal: opts.signal,
             });

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -1,9 +1,8 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, isGzip } from '@jbrowse/core/util';
+import { SimpleFeature, fetchAndMaybeUnzip, } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
-import { unzip } from '@gmod/bgzf-filehandle';
 const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
 export function featureData(line, uniqueId, flip, names) {
     const l = line.split('\t');
@@ -58,11 +57,11 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
         super(...arguments);
         this.intervalTrees = {};
     }
-    async loadDataP(opts = {}) {
+    async loadDataP(opts) {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedpeLocation');
-        const buf = await openLocation(bedLoc, pm).readFile(opts);
-        const buffer = isGzip(buf) ? await unzip(buf) : buf;
+        const loc = openLocation(bedLoc, pm);
+        const buffer = await fetchAndMaybeUnzip(loc, opts);
         // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');

package/esm/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;
 }