@gmod/indexedfasta/dist/indexedFasta.d.ts

read indexed fasta and bgzipped fasta formats

import type { GenericFilehandle } from 'generic-filehandle2';
interface BaseOpts {
    signal?: AbortSignal;
}
interface IndexEntry {
    offset: number;
    lineBytes: number;
    lineLength: number;
    length: number;
}
declare function readFAI(fai: GenericFilehandle, opts?: BaseOpts): Promise<{
    [k: string]: {
        readonly name: string;
        readonly length: number;
        readonly start: 0;
        readonly end: number;
        readonly offset: number;
        readonly lineLength: number;
        readonly lineBytes: number;
    };
}>;
export default class IndexedFasta {
    fasta: GenericFilehandle;
    fai: GenericFilehandle;
    indexes?: ReturnType<typeof readFAI>;
    constructor({ fasta, fai, path, faiPath, }: {
        fasta?: GenericFilehandle;
        fai?: GenericFilehandle;
        path?: string;
        faiPath?: string;
    });
    _getIndexes(opts?: BaseOpts): Promise<{
        [k: string]: {
            readonly name: string;
            readonly length: number;
            readonly start: 0;
            readonly end: number;
            readonly offset: number;
            readonly lineLength: number;
            readonly lineBytes: number;
        };
    }>;
    /**
     * @returns array of string sequence names that are present in the index, in
     * which the array index indicates the sequence ID, and the value is the
     * sequence name
     */
    getSequenceNames(opts?: BaseOpts): Promise<string[]>;
    /**
     * @returns array of string sequence names that are present in the index, in
     * which the array index indicates the sequence ID, and the value is the
     * sequence name
     */
    getSequenceSizes(opts?: BaseOpts): Promise<Record<string, number>>;
    /**
     * @returns array of string sequence names that are present in the index, in
     * which the array index indicates the sequence ID, and the value is the
     * sequence name
     */
    getSequenceSize(seqName: string, opts?: BaseOpts): Promise<number | undefined>;
    /**
     * @param name
     *
     * @returns true if the file contains the given reference sequence name
     */
    hasReferenceSequence(name: string, opts?: BaseOpts): Promise<boolean>;
    /**
     * @param seqName
     * @param min
     * @param max
     */
    getResiduesByName(seqName: string, min: number, max: number, opts?: BaseOpts): Promise<string | undefined>;
    getSequence(seqName: string, min: number, max: number, opts?: BaseOpts): Promise<string | undefined>;
    _fetchFromIndexEntry(indexEntry: IndexEntry, min?: number, max?: number, opts?: BaseOpts): Promise<string>;
}
export {};