genomic-reader/dist/bigwig/BigWigReader.d.ts

A Typescript library for reading BigWig, BigBed, 2bit, and Bam files. Capable of streaming. For use in the browser or on Node.js.

/// <reference types="node" />
import { DataLoader } from "../loader/DataLoader";
import { HeaderData, FileType } from "./BigWigHeaderReader";
import { SequenceRecord } from "./TwoBitHeaderReader";
import { Readable } from "stream";
export interface BigWigData {
    chr: string;
    start: number;
    end: number;
    value: number;
}
export interface BigBedData {
    chr: string;
    start: number;
    end: number;
    name?: string;
    score?: number;
    strand?: string;
    cdStart?: number;
    cdEnd?: number;
    color?: string;
    exons?: Array<BigBedExon>;
}
export interface BigBedExon {
    start: number;
    end: number;
}
export interface BigZoomData {
    chr: string;
    start: number;
    end: number;
    validCount: number;
    minVal: number;
    maxVal: number;
    sumData: number;
    sumSquares: number;
}
export declare type ParseFunction<T> = (chrom: string, startBase: number, endBase: number, rest: string) => T;
export declare class BigWigReader {
    private dataLoader;
    private bufferSize;
    private cachedHeader?;
    private cachedSequenceRecords;
    constructor(dataLoader: DataLoader, bufferSize?: number);
    fileType(): Promise<FileType>;
    getHeader(): Promise<HeaderData>;
    getSequenceRecord(chrom: string): Promise<SequenceRecord>;
    readBigWigData(startChrom: string, startBase: number, endChrom: string, endBase: number): Promise<Array<BigWigData>>;
    streamBigWigData(startChrom: string, startBase: number, endChrom: string, endBase: number): Promise<Readable>;
    readBigBedData(startChrom: string, startBase: number, endChrom: string, endBase: number): Promise<Array<BigBedData>>;
    readBigBedData<T>(startChrom: string, startBase: number, endChrom: string, endBase: number, restParser: ParseFunction<T>): Promise<Array<T>>;
    streamBigBedData(startChrom: string, startBase: number, endChrom: string, endBase: number): Promise<Readable>;
    streamBigBedData<T>(startChrom: string, startBase: number, endChrom: string, endBase: number, restParser: ParseFunction<T>): Promise<Readable>;
    readTwoBitData(chrom: string, startBase: number, endBase: number): Promise<string>;
    readTwoBitDataMatrix(chrom: string, startBase: number, endBase: number): Promise<Array<Array<number>>>;
    streamTwoBitData(chrom: string, startBase: number, endBase: number, chunkSize?: number, oneHotEncodedData?: boolean): Promise<Readable>;
    readZoomData(startChrom: string, startBase: number, endChrom: string, endBase: number, zoomLevelIndex: number): Promise<Array<BigZoomData>>;
    streamZoomData(startChrom: string, startBase: number, endChrom: string, endBase: number, zoomLevelIndex: number): Promise<Readable>;
    private loadData;
    private readData;
    private streamData;
}
export declare function parseBigBed(chrom: string, startBase: number, endBase: number, rest: string): BigBedData;