genomic-reader/dist/bam/BamReader.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.

import { DataLoader } from "../loader/DataLoader";
import { BamHeader } from "./BamHeaderReader";
import { Chunk, BamIndexData } from "./BamIndexReader";
export interface CigarOp {
    opLen: number;
    op: string;
    seqOffset: number;
}
export interface BamAlignmentMate {
    chr: string;
    position: number;
    strand: boolean;
}
export interface BamAlignment {
    chr: string;
    start: number;
    flags: number;
    strand: boolean;
    readName: string;
    cigarOps: Array<CigarOp>;
    templateLength: number;
    mappingQuality: number;
    seq: string;
    phredQualities: Array<number>;
    lengthOnRef: number;
}
export declare function isFlagged(bitwiseFlags: number, flag: BamAlignmentFlag): boolean;
export declare enum BamAlignmentFlag {
    READ_PAIRED = 1,
    PROPER_PAIR = 2,
    READ_UNMAPPED = 4,
    MATE_UNMAPPED = 8,
    READ_STRAND = 16,
    MATE_STRAND = 32,
    FIRST_OF_PAIR = 64,
    SECOND_OF_PAIR = 128,
    SECONDARY_ALIGNMNET = 256,
    READ_FAILS_VENDOR_QUALITY_CHECK = 512,
    DUPLICATE_READ = 1024,
    SUPPLEMENTARY_ALIGNMENT = 2048
}
export declare class BamReader {
    private bamDataLoader;
    private bamIndexDataLoader;
    constructor(bamDataLoader: DataLoader, bamIndexDataLoader: DataLoader);
    private indexData?;
    getIndexData(): Promise<BamIndexData>;
    private headerData?;
    getHeaderData(): Promise<BamHeader>;
    read(chr: string, start: number, end: number): Promise<Array<BamAlignment>>;
}
export declare function readBam(bamDataLoader: DataLoader, chunks: Array<Chunk>, refId: number, chr: string, start: number, end: number): Promise<Array<BamAlignment>>;