@gmod/indexedfasta/esm/bgzipIndexedFasta.js

read indexed fasta and bgzipped fasta formats

import { BgzfFilehandle } from '@gmod/bgzf-filehandle';
import { LocalFile } from 'generic-filehandle2';
import IndexedFasta from "./indexedFasta.js";
export default class BgzipIndexedFasta extends IndexedFasta {
    constructor({ fasta, path, fai, faiPath, gzi, gziPath, }) {
        super({ fasta, path, fai, faiPath });
        if (fasta && gzi) {
            // @ts-expect-error
            this.fasta = new BgzfFilehandle({
                filehandle: fasta,
                gziFilehandle: gzi,
            });
        }
        else if (path && gziPath) {
            // @ts-expect-error
            this.fasta = new BgzfFilehandle({
                filehandle: new LocalFile(path),
                gziFilehandle: new LocalFile(gziPath),
            });
        }
    }
}
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