@jbrowse/plugin-bed 3.0.1 → 3.0.3
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/BedAdapter/BedAdapter.js +6 -3
- package/dist/BedTabixAdapter/BedTabixAdapter.d.ts +25 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.js +27 -10
- package/dist/BigBedAdapter/BigBedAdapter.js +13 -6
- package/esm/BedAdapter/BedAdapter.js +6 -3
- package/esm/BedTabixAdapter/BedTabixAdapter.d.ts +25 -1
- package/esm/BedTabixAdapter/BedTabixAdapter.js +28 -11
- package/esm/BigBedAdapter/BigBedAdapter.js +14 -7
- package/package.json +3 -3
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@@ -127,9 +127,12 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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return (0, rxjs_1.ObservableCreate)(async (observer) => {
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const { start, end, refName } = query;
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const intervalTree = await this.loadFeatureIntervalTree(refName);
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intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])
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-
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-
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const features = intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]);
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if (features) {
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for (const f of features) {
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observer.next(f);
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}
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}
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observer.complete();
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}, opts.stopToken);
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}
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@@ -11,9 +11,33 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
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protected columnNames: string[];
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protected scoreColumn: string;
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static capabilities: string[];
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setupP?: Promise<{
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meta: Awaited<ReturnType<TabixIndexedFile['getMetadata']>>;
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}>;
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constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
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getRefNames(opts?: BaseOptions): Promise<string[]>;
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-
getHeader(): Promise<string>;
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getHeader(opts?: BaseOptions): Promise<string>;
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getMetadataPre2(_opts?: BaseOptions): Promise<{
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meta: Awaited<ReturnType<TabixIndexedFile["getMetadata"]>>;
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}>;
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getMetadataPre(): Promise<{
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meta: {
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[key: string]: any;
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refNameToId: Record<string, number>;
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refIdToName: string[];
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metaChar: string | null;
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columnNumbers: {
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ref: number;
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start: number;
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end: number;
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};
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coordinateType: string;
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format: string;
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};
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}>;
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getMetadata(opts?: BaseOptions): Promise<{
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meta: Awaited<ReturnType<TabixIndexedFile["getMetadata"]>>;
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}>;
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getNames(): Promise<string[] | undefined>;
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getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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freeResources(): void;
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@@ -32,14 +32,31 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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async getRefNames(opts = {}) {
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return this.bed.getReferenceSequenceNames(opts);
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}
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async getHeader() {
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return this.bed.getHeader();
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async getHeader(opts) {
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return this.bed.getHeader(opts);
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}
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async getMetadataPre2(_opts) {
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if (!this.setupP) {
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this.setupP = this.getMetadataPre().catch((e) => {
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this.setupP = undefined;
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throw e;
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});
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}
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return this.setupP;
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}
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async getMetadataPre() {
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const meta = await this.bed.getMetadata();
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return { meta };
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}
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async getMetadata(opts) {
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const { statusCallback = () => { } } = opts || {};
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return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.getMetadataPre2(opts));
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}
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async getNames() {
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if (this.columnNames.length) {
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return this.columnNames;
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}
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const header = await this.
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const header = await this.getHeader();
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const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
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const defline = defs.at(-1);
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return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
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@@ -49,10 +66,10 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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.map(f => f.trim())
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: undefined;
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}
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getFeatures(query, opts
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const { stopToken } = opts;
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getFeatures(query, opts) {
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const { stopToken, statusCallback = () => { } } = opts || {};
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return (0, rxjs_1.ObservableCreate)(async (observer) => {
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const meta = await this.
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const { meta } = await this.getMetadata();
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const { columnNumbers } = meta;
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const colRef = columnNumbers.ref - 1;
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const colStart = columnNumbers.start - 1;
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@@ -60,7 +77,7 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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const names = await this.getNames();
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let start = performance.now();
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(0, stopToken_1.checkStopToken)(stopToken);
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await this.bed.getLines(query.refName, query.start, query.end, {
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await (0, util_1.updateStatus)('Downloading features', statusCallback, () => this.bed.getLines(query.refName, query.start, query.end, {
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lineCallback: (line, fileOffset) => {
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if (performance.now() - start > 200) {
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(0, stopToken_1.checkStopToken)(stopToken);
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@@ -77,10 +94,10 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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names,
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})));
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},
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stopToken
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});
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stopToken,
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}));
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observer.complete();
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},
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}, stopToken);
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}
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freeResources() { }
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}
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@@ -67,17 +67,18 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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}
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async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
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var _a;
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const { stopToken } = opts;
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const { stopToken, statusCallback = () => { } } = 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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const { parser, bigbed } = await (0, util_1.updateStatus)('Downloading header', statusCallback, () => this.configure(opts));
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const feats = await (0, util_1.updateStatus)('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
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stopToken,
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basesPerSpan: query.end - query.start,
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});
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}));
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if (allowRedispatch && feats.length) {
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let minStart = Number.POSITIVE_INFINITY;
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let maxEnd = Number.NEGATIVE_INFINITY;
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let hasAnyAggregationField = false;
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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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@@ -85,8 +86,12 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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if (feat.end > maxEnd) {
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maxEnd = feat.end;
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}
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if (feat[aggregateField]) {
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hasAnyAggregationField = true;
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}
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}
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if (
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if (hasAnyAggregationField &&
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(maxEnd > query.end || minStart < query.start)) {
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await this.getFeaturesHelper({
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query: {
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...query,
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@@ -112,7 +117,9 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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`${feat.end}`,
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...(((_a = feat.rest) === null || _a === void 0 ? void 0 : _a.split('\t')) || []),
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];
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const data = parser.parseLine(splitLine, {
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const data = parser.parseLine(splitLine, {
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uniqueId: feat.uniqueId,
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});
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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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@@ -122,9 +122,12 @@ class BedAdapter extends BaseFeatureDataAdapter {
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return ObservableCreate(async (observer) => {
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const { start, end, refName } = query;
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const intervalTree = await this.loadFeatureIntervalTree(refName);
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intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])
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const features = intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]);
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if (features) {
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for (const f of features) {
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observer.next(f);
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}
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}
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observer.complete();
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}, opts.stopToken);
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}
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protected columnNames: string[];
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protected scoreColumn: string;
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static capabilities: string[];
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setupP?: Promise<{
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meta: Awaited<ReturnType<TabixIndexedFile['getMetadata']>>;
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}>;
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constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
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getRefNames(opts?: BaseOptions): Promise<string[]>;
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getHeader(): Promise<string>;
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getHeader(opts?: BaseOptions): Promise<string>;
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getMetadataPre2(_opts?: BaseOptions): Promise<{
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meta: Awaited<ReturnType<TabixIndexedFile["getMetadata"]>>;
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}>;
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getMetadataPre(): Promise<{
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meta: {
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[key: string]: any;
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refNameToId: Record<string, number>;
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refIdToName: string[];
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metaChar: string | null;
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columnNumbers: {
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ref: number;
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start: number;
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end: number;
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};
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coordinateType: string;
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format: string;
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};
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}>;
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getMetadata(opts?: BaseOptions): Promise<{
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meta: Awaited<ReturnType<TabixIndexedFile["getMetadata"]>>;
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}>;
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getNames(): Promise<string[] | undefined>;
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getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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freeResources(): void;
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@@ -1,7 +1,7 @@
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import BED from '@gmod/bed';
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import { TabixIndexedFile } from '@gmod/tabix';
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import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { SimpleFeature } from '@jbrowse/core/util';
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import { SimpleFeature, updateStatus } from '@jbrowse/core/util';
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import { openLocation } from '@jbrowse/core/util/io';
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import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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import { checkStopToken } from '@jbrowse/core/util/stopToken';
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@@ -27,14 +27,31 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
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async getRefNames(opts = {}) {
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return this.bed.getReferenceSequenceNames(opts);
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}
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async getHeader() {
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return this.bed.getHeader();
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async getHeader(opts) {
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return this.bed.getHeader(opts);
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}
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async getMetadataPre2(_opts) {
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if (!this.setupP) {
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this.setupP = this.getMetadataPre().catch((e) => {
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this.setupP = undefined;
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throw e;
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});
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}
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return this.setupP;
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}
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async getMetadataPre() {
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const meta = await this.bed.getMetadata();
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return { meta };
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}
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async getMetadata(opts) {
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const { statusCallback = () => { } } = opts || {};
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return updateStatus('Downloading index', statusCallback, () => this.getMetadataPre2(opts));
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}
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async getNames() {
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if (this.columnNames.length) {
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return this.columnNames;
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}
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const header = await this.
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const header = await this.getHeader();
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const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
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const defline = defs.at(-1);
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return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
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.map(f => f.trim())
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: undefined;
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}
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getFeatures(query, opts
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const { stopToken } = opts;
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getFeatures(query, opts) {
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const { stopToken, statusCallback = () => { } } = opts || {};
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return ObservableCreate(async (observer) => {
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const meta = await this.
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const { meta } = await this.getMetadata();
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const { columnNumbers } = meta;
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const colRef = columnNumbers.ref - 1;
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const colStart = columnNumbers.start - 1;
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@@ -55,7 +72,7 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
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const names = await this.getNames();
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let start = performance.now();
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checkStopToken(stopToken);
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await this.bed.getLines(query.refName, query.start, query.end, {
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await updateStatus('Downloading features', statusCallback, () => this.bed.getLines(query.refName, query.start, query.end, {
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lineCallback: (line, fileOffset) => {
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if (performance.now() - start > 200) {
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checkStopToken(stopToken);
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@@ -72,10 +89,10 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
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names,
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})));
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},
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stopToken
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});
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stopToken,
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}));
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observer.complete();
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},
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}, stopToken);
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}
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freeResources() { }
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}
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@@ -1,7 +1,7 @@
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1
1
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import { BigBed } from '@gmod/bbi';
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|
2
2
|
import BED from '@gmod/bed';
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3
3
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import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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|
4
|
-
import { SimpleFeature, doesIntersect2, max, min } from '@jbrowse/core/util';
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|
4
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+
import { SimpleFeature, doesIntersect2, max, min, updateStatus, } from '@jbrowse/core/util';
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5
5
|
import { openLocation } from '@jbrowse/core/util/io';
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|
6
6
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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|
7
7
|
import { firstValueFrom, toArray } from 'rxjs';
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@@ -62,17 +62,18 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
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|
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62
62
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}
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|
63
63
|
async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
|
|
64
64
|
var _a;
|
|
65
|
-
const { stopToken } = opts;
|
|
65
|
+
const { stopToken, statusCallback = () => { } } = opts;
|
|
66
66
|
const scoreColumn = this.getConf('scoreColumn');
|
|
67
67
|
const aggregateField = this.getConf('aggregateField');
|
|
68
|
-
const { parser, bigbed } = await this.configure(opts);
|
|
69
|
-
const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
|
|
68
|
+
const { parser, bigbed } = await updateStatus('Downloading header', statusCallback, () => this.configure(opts));
|
|
69
|
+
const feats = await updateStatus('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
|
|
70
70
|
stopToken,
|
|
71
71
|
basesPerSpan: query.end - query.start,
|
|
72
|
-
});
|
|
72
|
+
}));
|
|
73
73
|
if (allowRedispatch && feats.length) {
|
|
74
74
|
let minStart = Number.POSITIVE_INFINITY;
|
|
75
75
|
let maxEnd = Number.NEGATIVE_INFINITY;
|
|
76
|
+
let hasAnyAggregationField = false;
|
|
76
77
|
for (const feat of feats) {
|
|
77
78
|
if (feat.start < minStart) {
|
|
78
79
|
minStart = feat.start;
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|
@@ -80,8 +81,12 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
|
80
81
|
if (feat.end > maxEnd) {
|
|
81
82
|
maxEnd = feat.end;
|
|
82
83
|
}
|
|
84
|
+
if (feat[aggregateField]) {
|
|
85
|
+
hasAnyAggregationField = true;
|
|
86
|
+
}
|
|
83
87
|
}
|
|
84
|
-
if (
|
|
88
|
+
if (hasAnyAggregationField &&
|
|
89
|
+
(maxEnd > query.end || minStart < query.start)) {
|
|
85
90
|
await this.getFeaturesHelper({
|
|
86
91
|
query: {
|
|
87
92
|
...query,
|
|
@@ -107,7 +112,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
|
|
|
107
112
|
`${feat.end}`,
|
|
108
113
|
...(((_a = feat.rest) === null || _a === void 0 ? void 0 : _a.split('\t')) || []),
|
|
109
114
|
];
|
|
110
|
-
const data = parser.parseLine(splitLine, {
|
|
115
|
+
const data = parser.parseLine(splitLine, {
|
|
116
|
+
uniqueId: feat.uniqueId,
|
|
117
|
+
});
|
|
111
118
|
const aggr = data[aggregateField];
|
|
112
119
|
if (!parentAggregation[aggr]) {
|
|
113
120
|
parentAggregation[aggr] = [];
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-bed",
|
|
3
|
-
"version": "3.0.
|
|
3
|
+
"version": "3.0.3",
|
|
4
4
|
"description": "JBrowse 2 bed adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -41,7 +41,7 @@
|
|
|
41
41
|
"@gmod/bed": "^2.1.2",
|
|
42
42
|
"@gmod/bgzf-filehandle": "^2.0.1",
|
|
43
43
|
"@gmod/tabix": "^2.0.0",
|
|
44
|
-
"@jbrowse/core": "^3.0.
|
|
44
|
+
"@jbrowse/core": "^3.0.3",
|
|
45
45
|
"mobx": "^6.0.0",
|
|
46
46
|
"mobx-react": "^9.0.0",
|
|
47
47
|
"mobx-state-tree": "^5.0.0",
|
|
@@ -53,5 +53,5 @@
|
|
|
53
53
|
"distModule": "esm/index.js",
|
|
54
54
|
"srcModule": "src/index.ts",
|
|
55
55
|
"module": "esm/index.js",
|
|
56
|
-
"gitHead": "
|
|
56
|
+
"gitHead": "f516540428282351d26e46743e69a724651bfb2c"
|
|
57
57
|
}
|