@jbrowse/plugin-bed 2.16.1 → 2.18.0

package/dist/util.js

@@ -1,179 +1,157 @@
 "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;
-    }
-    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,
-            });
+exports.featureData2 = featureData2;
+exports.arrayify = arrayify;
+const generateBedMethylFeature_1 = require("./generateBedMethylFeature");
+const generateRepeatMaskerFeature_1 = require("./generateRepeatMaskerFeature");
+const generateUcscTranscript_1 = require("./generateUcscTranscript");
+function defaultParser(fields, splitLine) {
+    let hasBlockCount = false;
+    const r = [];
+    for (let i = 0; i < splitLine.length; i++) {
+        if (fields[i] === 'blockCount') {
+            hasBlockCount = true;
         }
-        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),
-        thickStart: thickStart ? +thickStart : undefined,
-        thickEnd: thickEnd ? +thickEnd : undefined,
-        blockCount: blockCount ? +blockCount : undefined,
-    };
+        r.push([fields[i], splitLine[i]]);
+    }
+    const obj = Object.fromEntries(r);
+    if (hasBlockCount) {
+        const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
+        return {
+            ...rest,
+            blockStarts: arrayify(blockStarts),
+            chromStarts: arrayify(chromStarts),
+            blockSizes: arrayify(blockSizes),
+            thickStart: thickStart ? +thickStart : undefined,
+            thickEnd: thickEnd ? +thickEnd : undefined,
+            blockCount: blockCount ? +blockCount : undefined,
+        };
+    }
+    else {
+        return obj;
+    }
 }
 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',
-        });
+        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;
 }
-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 = Number.parseInt(splitLine[colStart], 10);
+    const end = Number.parseInt(splitLine[colEnd], 10) + (colStart === colEnd ? 1 : 0);
+    return featureData2({
+        splitLine,
+        refName,
+        start,
+        end,
+        parser,
+        uniqueId,
+        scoreColumn,
+        names,
+    });
+}
+function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
     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
+        ? defaultParser(names, splitLine)
+        : parser.parseLine(splitLine, { uniqueId });
+    const { strand: strand2, score: score2, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
+    const score = scoreColumn ? +data[scoreColumn] : score2 ? +score2 : undefined;
+    const strand = typeof strand2 === 'string' ? (strand2 === '-' ? -1 : 1) : strand2;
+    const subfeatures = rest.blockCount
         ? makeBlocks({
             start,
             uniqueId,
             refName,
+            chromStarts: rest.chromStarts,
+            blockCount: rest.blockCount,
+            blockSizes: rest.blockSizes,
+            blockStarts: rest.blockStarts,
+        })
+        : undefined;
+    if ((0, generateBedMethylFeature_1.isBedMethylFeature)({ splitLine, start, end })) {
+        return (0, generateBedMethylFeature_1.generateBedMethylFeature)({
+            splitLine,
+            uniqueId,
+            refName,
+            start,
+            end,
+        });
+    }
+    else if ((0, generateRepeatMaskerFeature_1.isRepeatMaskerDescriptionField)(rest.description)) {
+        const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
+        return (0, generateRepeatMaskerFeature_1.generateRepeatMaskerFeature)({
+            ...rest2,
+            uniqueId,
+            description,
+            type,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            subfeatures,
+        });
+    }
+    else if (subfeatures &&
+        (0, generateUcscTranscript_1.isUcscTranscript)({
+            strand,
+            blockCount: rest.blockCount,
+            thickStart: rest.thickStart,
+        })) {
+        const { chromStarts, blockSizes, type, blockCount, thickStart, thickEnd, description, } = rest;
+        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,
+            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.d.ts

@@ -1,7 +1,8 @@
-import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class BedAdapter extends BaseFeatureDataAdapter {
     protected bedFeatures?: Promise<{
         header: string;
@@ -16,12 +17,21 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
-    private loadData;
+    loadData(opts?: BaseOptions): Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        parser: BED;
+        columnNames: string[];
+        scoreColumn: string;
+        colRef: number;
+        colStart: number;
+        colEnd: number;
+    }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
-    private loadFeatureIntervalTree;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/esm/BedAdapter/BedAdapter.js

@@ -1,11 +1,9 @@
+import IntervalTree from '@flatten-js/interval-tree';
 import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { isGzip } 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 {
     constructor() {
@@ -15,9 +13,7 @@ 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;
-        // 512MB  max chrome string length is 512MB
+        const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, pm), opts);
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
         }
@@ -96,12 +92,20 @@ class BedAdapter extends BaseFeatureDataAdapter {
         }
         const names = await this.getNames();
         const intervalTree = new IntervalTree();
-        const ret = lines.map((f, i) => {
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i];
             const uniqueId = `${this.id}-${refName}-${i}`;
-            return featureData(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
-        });
-        for (const obj of ret) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            const feat = new SimpleFeature(featureData({
+                line,
+                colRef,
+                colStart,
+                colEnd,
+                scoreColumn,
+                parser,
+                uniqueId,
+                names,
+            }));
+            intervalTree.insert([feat.get('start'), feat.get('end')], feat);
         }
         return intervalTree;
     }
@@ -122,7 +126,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
                 observer.next(f);
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/esm/BedAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bedLocation: {
         type: string;
         defaultValue: {
@@ -9,49 +6,31 @@ declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;
         defaultValue: never[];
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     autoSql: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     colRef: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     colStart: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     colEnd: {
         type: string;
         description: string;

package/esm/BedAdapter/configSchema.js

@@ -1,59 +1,35 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config BedAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedAdapter = ConfigurationSchema('BedAdapter', {
-    /**
-     * #slot
-     */
     bedLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     autoSql: {
         type: 'string',
         description: 'The autoSql definition for the data fields in the file',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     colRef: {
         type: 'number',
         description: 'The column to use as a "refName" attribute',
         defaultValue: 0,
     },
-    /**
-     * #slot
-     */
     colStart: {
         type: 'number',
         description: 'The column to use as a "start" attribute',
         defaultValue: 1,
     },
-    /**
-     * #slot
-     */
     colEnd: {
         type: 'number',
         description: 'The column to use as a "end" attribute',

package/esm/BedAdapter/index.d.ts

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

package/esm/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -0,0 +1,24 @@
+import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
+export default class BedGraphAdapter extends BaseFeatureDataAdapter {
+    protected bedFeatures?: Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        columnNames: string[];
+    }>;
+    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    getNames(): Promise<string[] | undefined>;
+    private loadFeatureIntervalTreeHelper;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    private loadDataP;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
+    loadData(opts?: BaseOptions): Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        columnNames: string[];
+    }>;
+    getFeatures(query: Region, _opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}