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@gmod/bam

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Parser for BAM and BAM index (bai) files

github.com/GMOD/bam-js

GMOD/bam-js

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export interface Bytes { start: number; end: number; byteArray: Uint8Array; } export default class BamRecord { fileOffset: number; private _byteArray; private _start; private _end; private _dataView; private _cachedEnd?; private _cachedTags?; private _cachedLengthOnRef?; private _cachedNumericCigar?; private _cachedNUMERIC_MD?; private _cachedSeqStart?; constructor(args: { bytes: Bytes; fileOffset: number; dataView: DataView; }); get byteArray(): Uint8Array<ArrayBufferLike>; get flags(): number; get ref_id(): number; get start(): number; get end(): number; get mq(): number | undefined; get score(): number | undefined; get qual(): Uint8Array<ArrayBufferLike> | null; get strand(): 1 | -1; get b0(): number; get seqStart(): number; get tagsStart(): number; get name(): string; get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined; get tags(): Record<string, unknown>; getTag(tagName: string): unknown; getTagRaw(tagName: string): string | number | Uint8Array<ArrayBufferLike> | number[] | Uint32Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int8Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined; private _findTag; private _computeTags; isPaired(): boolean; isProperlyPaired(): boolean; isSegmentUnmapped(): boolean; isMateUnmapped(): boolean; isReverseComplemented(): boolean; isMateReverseComplemented(): boolean; isRead1(): boolean; isRead2(): boolean; isSecondary(): boolean; isFailedQc(): boolean; isDuplicate(): boolean; isSupplementary(): boolean; private _isCGTagPattern; private _computeLengthOnRef; private _computeNumericCigar; get length_on_ref(): number; get NUMERIC_CIGAR(): number[] | Uint32Array<ArrayBufferLike>; get CIGAR(): string; get num_cigar_ops(): number; get num_cigar_bytes(): number; get read_name_length(): number; get num_seq_bytes(): number; get NUMERIC_SEQ(): Uint8Array<ArrayBufferLike>; 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; seqAt(idx: number): string | undefined; toJSON(): Record<string, unknown>; }