@jbrowse/plugin-bed 2.11.2 → 2.12.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BigBedAdapter/BigBedAdapter.d.ts +8 -6
- package/dist/BigBedAdapter/BigBedAdapter.js +111 -60
- package/dist/BigBedAdapter/configSchema.d.ts +8 -0
- package/dist/BigBedAdapter/configSchema.js +8 -0
- package/dist/util.d.ts +6 -5
- package/dist/util.js +4 -4
- package/esm/BigBedAdapter/BigBedAdapter.d.ts +8 -6
- package/esm/BigBedAdapter/BigBedAdapter.js +111 -60
- package/esm/BigBedAdapter/configSchema.d.ts +8 -0
- package/esm/BigBedAdapter/configSchema.js +8 -0
- package/esm/util.d.ts +6 -5
- package/esm/util.js +2 -2
- package/package.json +2 -2
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@@ -1,29 +1,31 @@
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import { BigBed
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import { BigBed } from '@gmod/bbi';
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import BED from '@gmod/bed';
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import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { Region } from '@jbrowse/core/util/types';
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import { Feature } from '@jbrowse/core/util
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import { Feature } from '@jbrowse/core/util';
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import { Observer } from 'rxjs';
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export default class BigBedAdapter extends BaseFeatureDataAdapter {
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private cached?;
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configurePre(opts?: BaseOptions): Promise<{
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bigbed: BigBed;
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header: Header;
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header: import("@gmod/bbi").Header;
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parser: BED;
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}>;
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configure(opts?: BaseOptions): Promise<{
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bigbed: BigBed;
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header: Header;
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header: import("@gmod/bbi").Header;
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parser: BED;
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}>;
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getRefNames(opts?: BaseOptions): Promise<string[]>;
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getHeader(opts?: BaseOptions): Promise<{
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version:
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version: number;
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fileType: string;
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autoSql: {};
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fields: {
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[k: string]: string;
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};
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}>;
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getFeaturesHelper(query: Region, opts: BaseOptions | undefined, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
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getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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freeResources(): void;
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}
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@@ -8,10 +8,9 @@ const bed_1 = __importDefault(require("@gmod/bed"));
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const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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const io_1 = require("@jbrowse/core/util/io");
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const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const
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const operators_1 = require("rxjs/operators");
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const util_1 = require("@jbrowse/core/util");
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// locals
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const
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const util_2 = require("../util");
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class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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async configurePre(opts) {
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const pm = this.pluginManager;
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@@ -37,7 +36,6 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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}
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async getHeader(opts) {
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const { parser, header } = await this.configure(opts);
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// @ts-expect-error
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const { version, fileType } = header;
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const { fields, ...rest } = parser.autoSql;
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return {
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@@ -47,68 +45,121 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
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};
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}
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async getFeaturesHelper(query, opts = {}, observer, allowRedispatch, originalQuery = query) {
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const { signal } = opts;
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const scoreColumn = this.getConf('scoreColumn');
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const aggregateField = this.getConf('aggregateField');
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const { parser, bigbed } = await this.configure(opts);
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const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
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signal,
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basesPerSpan: query.end - query.start,
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});
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if (allowRedispatch && feats.length) {
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let minStart = Infinity;
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let maxEnd = -Infinity;
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for (const feat of feats) {
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if (feat.start < minStart) {
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minStart = feat.start;
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}
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if (feat.end > maxEnd) {
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maxEnd = feat.end;
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}
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}
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if (maxEnd > query.end || minStart < query.start) {
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await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, observer, false, query);
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return;
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}
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}
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const parentAggregation = {};
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if (feats.some(f => f.uniqueId === undefined)) {
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throw new Error('found uniqueId undefined');
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}
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for (const feat of feats) {
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const data = parser.parseLine(`${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, { uniqueId: feat.uniqueId });
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const aggr = data[aggregateField];
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if (!parentAggregation[aggr]) {
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parentAggregation[aggr] = [];
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}
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const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
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const subfeatures = blockCount
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? (0, util_2.makeBlocks)({
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chromStarts,
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blockStarts,
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blockCount,
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blockSizes,
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uniqueId,
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refName: query.refName,
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start: feat.start,
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})
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: [];
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if ((0, util_2.isUcscProcessedTranscript)(data)) {
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const f = (0, util_2.ucscProcessedTranscript)({
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...rest,
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uniqueId,
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type,
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start: feat.start,
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end: feat.end,
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refName: query.refName,
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score: scoreColumn ? +data[scoreColumn] : score,
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chromStarts,
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blockCount,
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blockSizes,
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thickStart,
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thickEnd,
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subfeatures,
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});
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if (
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if (aggr) {
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parentAggregation[aggr].push(f);
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}
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else {
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if ((0, util_1.doesIntersect2)(f.start, f.end, originalQuery.start, originalQuery.end)) {
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observer.next(new util_1.SimpleFeature({ id: `${this.id}-${uniqueId}`, data: f }));
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}
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}
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}
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else {
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if ((0, util_1.doesIntersect2)(feat.start, feat.end, originalQuery.start, originalQuery.end)) {
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observer.next(new util_1.SimpleFeature({
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id: `${this.id}-${uniqueId}`,
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data: {
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...rest,
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uniqueId,
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type,
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start: feat.start,
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})).subscribe(observer);
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score: scoreColumn ? +data[scoreColumn] : score,
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end: feat.end,
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refName: query.refName,
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subfeatures,
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},
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}));
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}
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}
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}
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Object.entries(parentAggregation).map(([name, subfeatures]) => {
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const s = (0, util_1.min)(subfeatures.map(f => f.start));
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const e = (0, util_1.max)(subfeatures.map(f => f.end));
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if ((0, util_1.doesIntersect2)(s, e, originalQuery.start, originalQuery.end)) {
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const { uniqueId, strand } = subfeatures[0];
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observer.next(new util_1.SimpleFeature({
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id: `${this.id}-${uniqueId}-parent`,
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data: {
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type: 'gene',
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subfeatures,
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strand,
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name,
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start: s,
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end: e,
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refName: query.refName,
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},
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}));
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}
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});
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observer.complete();
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}
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getFeatures(query, opts = {}) {
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return (0, rxjs_1.ObservableCreate)(async (observer) => {
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try {
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await this.getFeaturesHelper(query, opts, observer, true);
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}
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catch (e) {
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observer.error(e);
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description: string;
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defaultValue: string;
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};
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/**
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* #slot
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*/
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aggregateField: {
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type: string;
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description: string;
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defaultValue: string;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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export default BigBedAdapter;
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description: 'The column to use as a "score" attribute',
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defaultValue: '',
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},
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/**
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*/
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aggregateField: {
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type: 'string',
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description: 'An attribute to aggregate features with',
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defaultValue: 'geneName',
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},
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}, { explicitlyTyped: true });
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exports.default = BigBedAdapter;
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package/dist/util.d.ts
CHANGED
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import BED from '@gmod/bed';
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import { SimpleFeature } from '@jbrowse/core/util';
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interface MinimalFeature {
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export interface MinimalFeature {
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type: string;
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end: number;
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refName: string;
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[key: string]: unknown;
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}
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interface TranscriptFeat {
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export interface TranscriptFeat extends MinimalFeature {
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thickEnd: number;
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blockCount: number;
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refName: string;
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strand?: number;
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subfeatures: MinimalFeature[];
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[key: string]: unknown;
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}
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export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
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strand: number;
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type: string;
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refName: string;
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subfeatures: MinimalFeature[];
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start: number;
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end: number;
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};
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export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
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blockCount: number;
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}[];
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export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
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export declare function
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export declare function isUcscProcessedTranscript(f: {
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thickStart?: number;
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blockCount?: number;
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strand?: number;
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}): boolean | 0 | undefined;
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export {};
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package/dist/util.js
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exports.
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exports.isUcscProcessedTranscript = exports.featureData = exports.makeBlocks = exports.ucscProcessedTranscript = void 0;
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const util_1 = require("@jbrowse/core/util");
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function ucscProcessedTranscript(feature) {
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var _a;
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return new util_1.SimpleFeature({
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id: uniqueId,
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data:
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data: isUcscProcessedTranscript(data)
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? ucscProcessedTranscript({
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thickEnd,
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}
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exports.featureData = featureData;
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function
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function isUcscProcessedTranscript(f) {
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return f.thickStart && f.blockCount && f.strand !== 0;
|
|
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|
}
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|
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|
-
exports.
|
|
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|
+
exports.isUcscProcessedTranscript = isUcscProcessedTranscript;
|
|
@@ -1,29 +1,31 @@
|
|
|
1
|
-
import { BigBed
|
|
1
|
+
import { BigBed } from '@gmod/bbi';
|
|
2
2
|
import BED from '@gmod/bed';
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3
3
|
import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
|
|
4
4
|
import { Region } from '@jbrowse/core/util/types';
|
|
5
|
-
import { Feature } from '@jbrowse/core/util
|
|
5
|
+
import { Feature } from '@jbrowse/core/util';
|
|
6
|
+
import { Observer } from 'rxjs';
|
|
6
7
|
export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
7
8
|
private cached?;
|
|
8
9
|
configurePre(opts?: BaseOptions): Promise<{
|
|
9
10
|
bigbed: BigBed;
|
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10
|
-
header: Header;
|
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11
|
+
header: import("@gmod/bbi").Header;
|
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11
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|
parser: BED;
|
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}>;
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|
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configure(opts?: BaseOptions): Promise<{
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bigbed: BigBed;
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-
header: Header;
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+
header: import("@gmod/bbi").Header;
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parser: BED;
|
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|
}>;
|
|
18
19
|
getRefNames(opts?: BaseOptions): Promise<string[]>;
|
|
19
20
|
getHeader(opts?: BaseOptions): Promise<{
|
|
20
|
-
version:
|
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21
|
+
version: number;
|
|
21
22
|
fileType: string;
|
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22
23
|
autoSql: {};
|
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23
24
|
fields: {
|
|
24
25
|
[k: string]: string;
|
|
25
26
|
};
|
|
26
27
|
}>;
|
|
27
|
-
|
|
28
|
+
getFeaturesHelper(query: Region, opts: BaseOptions | undefined, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
|
|
29
|
+
getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
|
|
28
30
|
freeResources(): void;
|
|
29
31
|
}
|
|
@@ -3,10 +3,9 @@ import BED from '@gmod/bed';
|
|
|
3
3
|
import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
|
|
4
4
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import { openLocation } from '@jbrowse/core/util/io';
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5
5
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import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
6
|
-
import SimpleFeature from '@jbrowse/core/util
|
|
7
|
-
import { map, mergeAll } from 'rxjs/operators';
|
|
6
|
+
import { doesIntersect2, max, min, SimpleFeature, } from '@jbrowse/core/util';
|
|
8
7
|
// locals
|
|
9
|
-
import {
|
|
8
|
+
import { isUcscProcessedTranscript, makeBlocks, ucscProcessedTranscript, } from '../util';
|
|
10
9
|
export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
11
10
|
async configurePre(opts) {
|
|
12
11
|
const pm = this.pluginManager;
|
|
@@ -32,7 +31,6 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
|
32
31
|
}
|
|
33
32
|
async getHeader(opts) {
|
|
34
33
|
const { parser, header } = await this.configure(opts);
|
|
35
|
-
// @ts-expect-error
|
|
36
34
|
const { version, fileType } = header;
|
|
37
35
|
const { fields, ...rest } = parser.autoSql;
|
|
38
36
|
return {
|
|
@@ -42,68 +40,121 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
|
42
40
|
fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
|
|
43
41
|
};
|
|
44
42
|
}
|
|
45
|
-
|
|
43
|
+
async getFeaturesHelper(query, opts = {}, observer, allowRedispatch, originalQuery = query) {
|
|
46
44
|
const { signal } = opts;
|
|
47
45
|
const scoreColumn = this.getConf('scoreColumn');
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
46
|
+
const aggregateField = this.getConf('aggregateField');
|
|
47
|
+
const { parser, bigbed } = await this.configure(opts);
|
|
48
|
+
const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
|
|
49
|
+
signal,
|
|
50
|
+
basesPerSpan: query.end - query.start,
|
|
51
|
+
});
|
|
52
|
+
if (allowRedispatch && feats.length) {
|
|
53
|
+
let minStart = Infinity;
|
|
54
|
+
let maxEnd = -Infinity;
|
|
55
|
+
for (const feat of feats) {
|
|
56
|
+
if (feat.start < minStart) {
|
|
57
|
+
minStart = feat.start;
|
|
58
|
+
}
|
|
59
|
+
if (feat.end > maxEnd) {
|
|
60
|
+
maxEnd = feat.end;
|
|
61
|
+
}
|
|
62
|
+
}
|
|
63
|
+
if (maxEnd > query.end || minStart < query.start) {
|
|
64
|
+
await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, observer, false, query);
|
|
65
|
+
return;
|
|
66
|
+
}
|
|
67
|
+
}
|
|
68
|
+
const parentAggregation = {};
|
|
69
|
+
if (feats.some(f => f.uniqueId === undefined)) {
|
|
70
|
+
throw new Error('found uniqueId undefined');
|
|
71
|
+
}
|
|
72
|
+
for (const feat of feats) {
|
|
73
|
+
const data = parser.parseLine(`${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, { uniqueId: feat.uniqueId });
|
|
74
|
+
const aggr = data[aggregateField];
|
|
75
|
+
if (!parentAggregation[aggr]) {
|
|
76
|
+
parentAggregation[aggr] = [];
|
|
77
|
+
}
|
|
78
|
+
const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
|
|
79
|
+
const subfeatures = blockCount
|
|
80
|
+
? makeBlocks({
|
|
81
|
+
chromStarts,
|
|
82
|
+
blockStarts,
|
|
83
|
+
blockCount,
|
|
84
|
+
blockSizes,
|
|
85
|
+
uniqueId,
|
|
86
|
+
refName: query.refName,
|
|
87
|
+
start: feat.start,
|
|
88
|
+
})
|
|
89
|
+
: [];
|
|
90
|
+
if (isUcscProcessedTranscript(data)) {
|
|
91
|
+
const f = ucscProcessedTranscript({
|
|
92
|
+
...rest,
|
|
93
|
+
uniqueId,
|
|
94
|
+
type,
|
|
95
|
+
start: feat.start,
|
|
96
|
+
end: feat.end,
|
|
97
|
+
refName: query.refName,
|
|
98
|
+
score: scoreColumn ? +data[scoreColumn] : score,
|
|
99
|
+
chromStarts,
|
|
100
|
+
blockCount,
|
|
101
|
+
blockSizes,
|
|
102
|
+
thickStart,
|
|
103
|
+
thickEnd,
|
|
104
|
+
subfeatures,
|
|
54
105
|
});
|
|
55
|
-
|
|
56
|
-
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
if (
|
|
60
|
-
|
|
106
|
+
if (aggr) {
|
|
107
|
+
parentAggregation[aggr].push(f);
|
|
108
|
+
}
|
|
109
|
+
else {
|
|
110
|
+
if (doesIntersect2(f.start, f.end, originalQuery.start, originalQuery.end)) {
|
|
111
|
+
observer.next(new SimpleFeature({ id: `${this.id}-${uniqueId}`, data: f }));
|
|
61
112
|
}
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
113
|
+
}
|
|
114
|
+
}
|
|
115
|
+
else {
|
|
116
|
+
if (doesIntersect2(feat.start, feat.end, originalQuery.start, originalQuery.end)) {
|
|
117
|
+
observer.next(new SimpleFeature({
|
|
118
|
+
id: `${this.id}-${uniqueId}`,
|
|
119
|
+
data: {
|
|
120
|
+
...rest,
|
|
69
121
|
uniqueId,
|
|
70
|
-
|
|
122
|
+
type,
|
|
71
123
|
start: feat.start,
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
})).subscribe(observer);
|
|
124
|
+
score: scoreColumn ? +data[scoreColumn] : score,
|
|
125
|
+
end: feat.end,
|
|
126
|
+
refName: query.refName,
|
|
127
|
+
subfeatures,
|
|
128
|
+
},
|
|
129
|
+
}));
|
|
130
|
+
}
|
|
131
|
+
}
|
|
132
|
+
}
|
|
133
|
+
Object.entries(parentAggregation).map(([name, subfeatures]) => {
|
|
134
|
+
const s = min(subfeatures.map(f => f.start));
|
|
135
|
+
const e = max(subfeatures.map(f => f.end));
|
|
136
|
+
if (doesIntersect2(s, e, originalQuery.start, originalQuery.end)) {
|
|
137
|
+
const { uniqueId, strand } = subfeatures[0];
|
|
138
|
+
observer.next(new SimpleFeature({
|
|
139
|
+
id: `${this.id}-${uniqueId}-parent`,
|
|
140
|
+
data: {
|
|
141
|
+
type: 'gene',
|
|
142
|
+
subfeatures,
|
|
143
|
+
strand,
|
|
144
|
+
name,
|
|
145
|
+
start: s,
|
|
146
|
+
end: e,
|
|
147
|
+
refName: query.refName,
|
|
148
|
+
},
|
|
149
|
+
}));
|
|
150
|
+
}
|
|
151
|
+
});
|
|
152
|
+
observer.complete();
|
|
153
|
+
}
|
|
154
|
+
getFeatures(query, opts = {}) {
|
|
155
|
+
return ObservableCreate(async (observer) => {
|
|
156
|
+
try {
|
|
157
|
+
await this.getFeaturesHelper(query, opts, observer, true);
|
|
107
158
|
}
|
|
108
159
|
catch (e) {
|
|
109
160
|
observer.error(e);
|
|
@@ -17,5 +17,13 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
|
|
|
17
17
|
description: string;
|
|
18
18
|
defaultValue: string;
|
|
19
19
|
};
|
|
20
|
+
/**
|
|
21
|
+
* #slot
|
|
22
|
+
*/
|
|
23
|
+
aggregateField: {
|
|
24
|
+
type: string;
|
|
25
|
+
description: string;
|
|
26
|
+
defaultValue: string;
|
|
27
|
+
};
|
|
20
28
|
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
21
29
|
export default BigBedAdapter;
|
|
@@ -19,5 +19,13 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
|
|
|
19
19
|
description: 'The column to use as a "score" attribute',
|
|
20
20
|
defaultValue: '',
|
|
21
21
|
},
|
|
22
|
+
/**
|
|
23
|
+
* #slot
|
|
24
|
+
*/
|
|
25
|
+
aggregateField: {
|
|
26
|
+
type: 'string',
|
|
27
|
+
description: 'An attribute to aggregate features with',
|
|
28
|
+
defaultValue: 'geneName',
|
|
29
|
+
},
|
|
22
30
|
}, { explicitlyTyped: true });
|
|
23
31
|
export default BigBedAdapter;
|
package/esm/util.d.ts
CHANGED
|
@@ -1,12 +1,13 @@
|
|
|
1
1
|
import BED from '@gmod/bed';
|
|
2
2
|
import { SimpleFeature } from '@jbrowse/core/util';
|
|
3
|
-
interface MinimalFeature {
|
|
3
|
+
export interface MinimalFeature {
|
|
4
4
|
type: string;
|
|
5
5
|
start: number;
|
|
6
6
|
end: number;
|
|
7
7
|
refName: string;
|
|
8
|
+
[key: string]: unknown;
|
|
8
9
|
}
|
|
9
|
-
interface TranscriptFeat {
|
|
10
|
+
export interface TranscriptFeat extends MinimalFeature {
|
|
10
11
|
thickStart: number;
|
|
11
12
|
thickEnd: number;
|
|
12
13
|
blockCount: number;
|
|
@@ -15,13 +16,14 @@ interface TranscriptFeat {
|
|
|
15
16
|
refName: string;
|
|
16
17
|
strand?: number;
|
|
17
18
|
subfeatures: MinimalFeature[];
|
|
18
|
-
[key: string]: unknown;
|
|
19
19
|
}
|
|
20
20
|
export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
|
|
21
21
|
strand: number;
|
|
22
22
|
type: string;
|
|
23
23
|
refName: string;
|
|
24
24
|
subfeatures: MinimalFeature[];
|
|
25
|
+
start: number;
|
|
26
|
+
end: number;
|
|
25
27
|
};
|
|
26
28
|
export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
|
|
27
29
|
blockCount: number;
|
|
@@ -39,9 +41,8 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
|
|
|
39
41
|
type: string;
|
|
40
42
|
}[];
|
|
41
43
|
export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
|
|
42
|
-
export declare function
|
|
44
|
+
export declare function isUcscProcessedTranscript(f: {
|
|
43
45
|
thickStart?: number;
|
|
44
46
|
blockCount?: number;
|
|
45
47
|
strand?: number;
|
|
46
48
|
}): boolean | 0 | undefined;
|
|
47
|
-
export {};
|
package/esm/util.js
CHANGED
|
@@ -155,7 +155,7 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
|
|
|
155
155
|
};
|
|
156
156
|
return new SimpleFeature({
|
|
157
157
|
id: uniqueId,
|
|
158
|
-
data:
|
|
158
|
+
data: isUcscProcessedTranscript(data)
|
|
159
159
|
? ucscProcessedTranscript({
|
|
160
160
|
thickStart,
|
|
161
161
|
thickEnd,
|
|
@@ -167,6 +167,6 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
|
|
|
167
167
|
: f,
|
|
168
168
|
});
|
|
169
169
|
}
|
|
170
|
-
export function
|
|
170
|
+
export function isUcscProcessedTranscript(f) {
|
|
171
171
|
return f.thickStart && f.blockCount && f.strand !== 0;
|
|
172
172
|
}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-bed",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.12.0",
|
|
4
4
|
"description": "JBrowse 2 bed adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -55,5 +55,5 @@
|
|
|
55
55
|
"distModule": "esm/index.js",
|
|
56
56
|
"srcModule": "src/index.ts",
|
|
57
57
|
"module": "esm/index.js",
|
|
58
|
-
"gitHead": "
|
|
58
|
+
"gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
|
|
59
59
|
}
|