@jbrowse/plugin-bed 2.17.0 → 2.18.0

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,9 +1,10 @@
 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 cachedP?;
     configurePre(opts?: BaseOptions): Promise<{

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -1,11 +1,10 @@
 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';
 import { firstValueFrom, toArray } from 'rxjs';
-// locals
 import { featureData2 } from '../util';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     async configurePre(opts) {
@@ -62,12 +61,13 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         };
     }
     async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
-        const { signal } = opts;
+        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) {
@@ -101,8 +101,13 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             throw new Error('found uniqueId undefined');
         }
         for (const feat of feats) {
-            const line = `${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`;
-            const data = parser.parseLine(line, { 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] = [];
@@ -111,7 +116,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             const f = featureData2({
                 ...rest,
                 scoreColumn,
-                line,
+                splitLine,
                 parser,
                 uniqueId,
                 start: feat.start,
@@ -164,7 +169,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             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

@@ -3,8 +3,8 @@ export declare function isBedMethylFeature({ splitLine, start, end, }: {
     start: number;
     end: number;
 }): boolean;
-export declare function generateBedMethylFeature({ line, uniqueId, refName, start, end, }: {
-    line: string;
+export declare function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }: {
+    splitLine: string[];
     uniqueId: string;
     refName: string;
     start: number;
@@ -15,7 +15,7 @@ export declare function generateBedMethylFeature({ line, uniqueId, refName, star
     start: number;
     end: number;
     code: string | undefined;
-    score: string | undefined;
+    score: number;
     strand: string | undefined;
     color: string | undefined;
     source: string | undefined;

package/esm/generateBedMethylFeature.js

@@ -1,17 +1,15 @@
 export function isBedMethylFeature({ splitLine, start, end, }) {
     return +(splitLine[6] || 0) === start && +(splitLine[7] || 0) === end;
 }
-export 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');
+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,
+        score: +fraction_modified || 0,
         strand,
         color,
         source: code,

package/esm/generateUcscTranscript.d.ts

@@ -1,4 +1,4 @@
-import { MinimalFeature, TranscriptFeat } from './types';
+import type { MinimalFeature, TranscriptFeat } from './types';
 export declare function isUcscTranscript({ thickStart, blockCount, strand, }: {
     thickStart?: number;
     blockCount?: number;

package/esm/generateUcscTranscript.js

@@ -12,7 +12,6 @@ export function generateUcscTranscript(data) {
         const start = block.start;
         const end = block.end;
         if (thickStart >= end) {
-            // left-side UTR
             subfeatures.push({
                 type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
                 start,
@@ -21,7 +20,6 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickStart > start && thickStart < end && thickEnd >= end) {
-            // UTR | CDS
             subfeatures.push({
                 type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
                 start,
@@ -35,7 +33,6 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickStart <= start && thickEnd >= end) {
-            // CDS
             subfeatures.push({
                 type: 'CDS',
                 start,
@@ -44,7 +41,6 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickStart > start && thickStart < end && thickEnd < end) {
-            // UTR | CDS | UTR
             subfeatures.push({
                 type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
                 start,
@@ -63,7 +59,6 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-            // CDS | UTR
             subfeatures.push({
                 type: 'CDS',
                 start,
@@ -77,7 +72,6 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickEnd <= start) {
-            // right-side UTR
             subfeatures.push({
                 type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
                 start,

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/util.d.ts

@@ -1,5 +1,4 @@
-import BED from '@gmod/bed';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import type BED from '@gmod/bed';
 export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
     blockCount: number;
     start: number;
@@ -24,9 +23,92 @@ export declare function featureData({ line, colRef, colStart, colEnd, scoreColum
     parser: BED;
     uniqueId: string;
     names?: string[];
-}): SimpleFeatureSerialized;
-export declare function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
-    line: string;
+}): {
+    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;
+} | {
+    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;
+} | {
+    uniqueId: string;
+    strand: number;
+    type: string;
+    refName: string;
+    subfeatures: import("./types").MinimalFeature[];
+    start: number;
+    end: number;
+} | {
+    uniqueId: string;
+    score: number | undefined;
+    start: number;
+    end: number;
+    strand: any;
+    refName: string;
+    subfeatures: {
+        uniqueId: string;
+        start: number;
+        end: number;
+        refName: string;
+        type: string;
+    }[] | undefined;
+};
+export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
+    splitLine: string[];
     refName: string;
     start: number;
     end: number;
@@ -34,5 +116,88 @@ export declare function featureData2({ line, refName, start, end, parser, unique
     uniqueId: string;
     scoreColumn: string;
     names?: string[];
-}): SimpleFeatureSerialized;
+}): {
+    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;
+} | {
+    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;
+} | {
+    uniqueId: string;
+    strand: number;
+    type: string;
+    refName: string;
+    subfeatures: import("./types").MinimalFeature[];
+    start: number;
+    end: number;
+} | {
+    uniqueId: string;
+    score: number | undefined;
+    start: number;
+    end: number;
+    strand: any;
+    refName: string;
+    subfeatures: {
+        uniqueId: string;
+        start: number;
+        end: number;
+        refName: string;
+        type: string;
+    }[] | undefined;
+};
 export declare function arrayify(f?: string | number[]): number[] | undefined;

package/esm/util.js

@@ -1,59 +1,58 @@
 import { generateBedMethylFeature, isBedMethylFeature, } from './generateBedMethylFeature';
-import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript';
 import { generateRepeatMaskerFeature, isRepeatMaskerDescriptionField, } from './generateRepeatMaskerFeature';
-function stringToStrand(f) {
-    if (f === '-1') {
-        return -1;
+import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript';
+function defaultParser(fields, splitLine) {
+    let hasBlockCount = false;
+    const r = [];
+    for (let i = 0; i < splitLine.length; i++) {
+        if (fields[i] === 'blockCount') {
+            hasBlockCount = true;
+        }
+        r.push([fields[i], splitLine[i]]);
     }
-    else if (f === '+') {
-        return 1;
+    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 0;
+        return obj;
     }
 }
-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: arrayify(blockStarts),
-        chromStarts: arrayify(chromStarts),
-        blockSizes: arrayify(blockSizes),
-        thickStart: thickStart ? +thickStart : undefined,
-        thickEnd: thickEnd ? +thickEnd : undefined,
-        blockCount: blockCount ? +blockCount : undefined,
-    };
-}
 export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
-    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',
-                });
-            }
+    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 [];
+    return subfeatures;
 }
 export 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);
+    const start = Number.parseInt(splitLine[colStart], 10);
+    const end = Number.parseInt(splitLine[colEnd], 10) + (colStart === colEnd ? 1 : 0);
     return featureData2({
-        line,
+        splitLine,
         refName,
         start,
         end,
@@ -63,34 +62,35 @@ export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parse
         names,
     });
 }
-export function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
-    const splitLine = line.split('\t');
+export function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
     const data = names
-        ? defaultParser(names, line)
-        : parser.parseLine(line, { uniqueId });
+        ? defaultParser(names, splitLine)
+        : parser.parseLine(splitLine, { uniqueId });
     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,
-    });
+    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 (isBedMethylFeature({ splitLine, start, end })) {
         return generateBedMethylFeature({
-            line,
+            splitLine,
             uniqueId,
             refName,
             start,
             end,
         });
     }
-    else if (isRepeatMaskerDescriptionField(description)) {
+    else if (isRepeatMaskerDescriptionField(rest.description)) {
+        const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
         return generateRepeatMaskerFeature({
             ...rest2,
             uniqueId,
@@ -104,7 +104,13 @@ export function featureData2({ line, refName, start, end, parser, uniqueId, scor
             subfeatures,
         });
     }
-    else if (isUcscTranscript({ strand, blockCount, thickStart })) {
+    else if (subfeatures &&
+        isUcscTranscript({
+            strand,
+            blockCount: rest.blockCount,
+            thickStart: rest.thickStart,
+        })) {
+        const { chromStarts, blockSizes, type, blockCount, thickStart, thickEnd, description, } = rest;
         return generateUcscTranscript({
             ...rest,
             description,
@@ -127,8 +133,6 @@ export function featureData2({ line, refName, start, end, parser, uniqueId, scor
         return {
             ...rest,
             uniqueId,
-            description,
-            type,
             score,
             start,
             end,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.17.0",
+  "version": "2.18.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }