@gmod/bam/esm/record.d.ts

Parser for BAM and BAM index (bai) files

interface Bytes {
    start: number;
    end: number;
    byteArray: Uint8Array;
}
export default class BamRecord {
    #private;
    fileOffset: number;
    private bytes;
    constructor(args: {
        bytes: Bytes;
        fileOffset: number;
    });
    get byteArray(): Uint8Array<ArrayBufferLike>;
    get flags(): number;
    get ref_id(): number;
    get start(): number;
    get end(): number;
    get id(): number;
    get mq(): number | undefined;
    get score(): number | undefined;
    get qual(): Uint8Array<ArrayBufferLike> | undefined;
    get strand(): 1 | -1;
    get b0(): number;
    get name(): string;
    get tags(): Record<string, unknown>;
    /**
     * @returns {boolean} true if the read is paired, regardless of whether both
     * segments are mapped
     */
    isPaired(): boolean;
    /** @returns {boolean} true if the read is paired, and both segments are mapped */
    isProperlyPaired(): boolean;
    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
    isSegmentUnmapped(): boolean;
    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
    isMateUnmapped(): boolean;
    /** @returns {boolean} true if the read is mapped to the reverse strand */
    isReverseComplemented(): boolean;
    /** @returns {boolean} true if the mate is mapped to the reverse strand */
    isMateReverseComplemented(): boolean;
    /** @returns {boolean} true if this is read number 1 in a pair */
    isRead1(): boolean;
    /** @returns {boolean} true if this is read number 2 in a pair */
    isRead2(): boolean;
    /** @returns {boolean} true if this is a secondary alignment */
    isSecondary(): boolean;
    /** @returns {boolean} true if this read has failed QC checks */
    isFailedQc(): boolean;
    /** @returns {boolean} true if the read is an optical or PCR duplicate */
    isDuplicate(): boolean;
    /** @returns {boolean} true if this is a supplementary alignment */
    isSupplementary(): boolean;
    get cigarAndLength(): {
        length_on_ref: number;
        CIGAR: string;
    };
    get length_on_ref(): number;
    get CIGAR(): string;
    get num_cigar_ops(): number;
    get read_name_length(): number;
    get num_seq_bytes(): number;
    get seq(): string;
    get pair_orientation(): string | undefined;
    get bin_mq_nl(): number;
    get flag_nc(): number;
    get seq_length(): number;
    get next_refid(): number;
    get next_pos(): number;
    get template_length(): number;
    toJSON(): Record<string, any>;
}
export {};