@jbrowse/plugin-bed 2.17.0 → 2.18.0

package/dist/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/dist/util.js

@@ -5,61 +5,60 @@ exports.featureData = featureData;
 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;
+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;
+        }
+        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,
-    };
-}
 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;
 }
 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,
@@ -69,34 +68,35 @@ function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniq
         names,
     });
 }
-function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
-    const splitLine = line.split('\t');
+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 ((0, generateBedMethylFeature_1.isBedMethylFeature)({ splitLine, start, end })) {
         return (0, generateBedMethylFeature_1.generateBedMethylFeature)({
-            line,
+            splitLine,
             uniqueId,
             refName,
             start,
             end,
         });
     }
-    else if ((0, generateRepeatMaskerFeature_1.isRepeatMaskerDescriptionField)(description)) {
+    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,
@@ -110,7 +110,13 @@ function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn
             subfeatures,
         });
     }
-    else if ((0, generateUcscTranscript_1.isUcscTranscript)({ strand, blockCount, thickStart })) {
+    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,
@@ -133,8 +139,6 @@ function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn
         return {
             ...rest,
             uniqueId,
-            description,
-            type,
             score,
             start,
             end,

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

@@ -1,10 +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 { fetchAndMaybeUnzip, SimpleFeature, } from '@jbrowse/core/util';
-import IntervalTree from '@flatten-js/interval-tree';
-// locals
 import { featureData } from '../util';
 class BedAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -15,7 +14,6 @@ class BedAdapter extends BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedLocation');
         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)');
         }
@@ -94,9 +92,10 @@ class BedAdapter extends BaseFeatureDataAdapter {
         }
         const names = await this.getNames();
         const intervalTree = new IntervalTree();
-        const ret = lines.map((line, i) => {
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i];
             const uniqueId = `${this.id}-${refName}-${i}`;
-            return new SimpleFeature(featureData({
+            const feat = new SimpleFeature(featureData({
                 line,
                 colRef,
                 colStart,
@@ -106,9 +105,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
                 uniqueId,
                 names,
             }));
-        });
-        for (const obj of ret) {
-            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            intervalTree.insert([feat.get('start'), feat.get('end')], feat);
         }
         return intervalTree;
     }
@@ -129,7 +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;
+}