@gmod/bgzf-filehandle/dist/bgzFilehandle.js

read from a compressed bgzip file (with .gzi) as if it were uncompressed

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const gziIndex_ts_1 = __importDefault(require("./gziIndex.js"));
const unzip_ts_1 = require("./unzip.js");
const util_ts_1 = require("./util.js");
class BgzFilehandle {
    constructor({ filehandle, gziFilehandle, }) {
        this.filehandle = filehandle;
        this.gzi = new gziIndex_ts_1.default({
            filehandle: gziFilehandle,
        });
    }
    async _readAndUncompressBlock(compressedPosition, nextCompressedPosition) {
        let next = nextCompressedPosition;
        if (!next) {
            next = (await this.filehandle.stat()).size;
        }
        // read the compressed data into the block buffer
        const blockCompressedLength = next - compressedPosition;
        const blockBuffer = await this.filehandle.read(blockCompressedLength, compressedPosition);
        // uncompress it
        return (0, unzip_ts_1.unzip)(blockBuffer);
    }
    async read(length, position) {
        const blockPositions = await this.gzi.getRelevantBlocksForRead(length, position);
        const blocks = [];
        for (let blockNum = 0; blockNum < blockPositions.length - 1; blockNum += 1) {
            const uncompressedBuffer = await this._readAndUncompressBlock(blockPositions[blockNum][0], blockPositions[blockNum + 1][0]);
            const [, uncompressedPosition] = blockPositions[blockNum];
            const sourceOffset = uncompressedPosition >= position ? 0 : position - uncompressedPosition;
            const sourceEnd = Math.min(position + length, uncompressedPosition + uncompressedBuffer.length) - uncompressedPosition;
            if (sourceOffset >= 0 && sourceOffset < uncompressedBuffer.length) {
                blocks.push(uncompressedBuffer.subarray(sourceOffset, sourceEnd));
            }
        }
        return (0, util_ts_1.concatUint8Array)(blocks);
    }
}
exports.default = BgzFilehandle;
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