@gmod/indexedfasta/dist/bgzipIndexedFasta.js

read indexed fasta and bgzipped fasta formats

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
const generic_filehandle2_1 = require("generic-filehandle2");
const indexedFasta_ts_1 = __importDefault(require("./indexedFasta.js"));
class BgzipIndexedFasta extends indexedFasta_ts_1.default {
    constructor({ fasta, path, fai, faiPath, gzi, gziPath, }) {
        super({ fasta, path, fai, faiPath });
        if (fasta && gzi) {
            // @ts-expect-error
            this.fasta = new bgzf_filehandle_1.BgzfFilehandle({
                filehandle: fasta,
                gziFilehandle: gzi,
            });
        }
        else if (path && gziPath) {
            // @ts-expect-error
            this.fasta = new bgzf_filehandle_1.BgzfFilehandle({
                filehandle: new generic_filehandle2_1.LocalFile(path),
                gziFilehandle: new generic_filehandle2_1.LocalFile(gziPath),
            });
        }
    }
}
exports.default = BgzipIndexedFasta;
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