@gmod/bbi/esm/bbi.d.ts

Parser for BigWig/BigBed files

import { Observable } from 'rxjs';
import { BlockView } from './block-view.ts';
import type { BigWigFeatureArrays, BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions, SummaryFeatureArrays } from './types.ts';
import type { GenericFilehandle } from 'generic-filehandle2';
export declare abstract class BBI {
    protected bbi: GenericFilehandle;
    private headerP?;
    protected renameRefSeqs: (a: string) => string;
    getHeader(opts?: RequestOptions): Promise<BigWigHeaderWithRefNames>;
    constructor(args: {
        filehandle?: GenericFilehandle;
        path?: string;
        url?: string;
        renameRefSeqs?: (a: string) => string;
    });
    private _getHeader;
    private _getMainHeader;
    private _readChromosomeTree;
    protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
    protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
    /**
     * Gets features from a BigWig file
     *
     * @param refName - The chromosome name
     *
     * @param start - The start of a region
     *
     * @param end - The end of a region
     *
     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
     * or scale used to infer the zoomLevel to use
     */
    getFeatureStream(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Observable<Feature[]>>;
    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<any[]>;
    /**
     * Gets features from a BigWig file as typed arrays (more efficient than getFeatures)
     *
     * @param refName - The chromosome name
     * @param start - The start of a region
     * @param end - The end of a region
     * @param opts - Options including basesPerSpan or scale
     * @returns Promise with typed arrays: starts, ends, scores (and minScores/maxScores for summary data)
     */
    getFeaturesAsArrays(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<BigWigFeatureArrays | SummaryFeatureArrays>;
}