genomic-reader/dist/bam/Bgzf.js

A Typescript library for reading BigWig, BigBed, 2bit, and Bam files. Capable of streaming. For use in the browser or on Node.js.

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.bgzfUnzip = void 0;
const pako_1 = require("pako");
function bgzfUnzip(inputData, chunk) {
    let pos = 0;
    const decompressedBlocks = [];
    const fileStartingOffset = chunk !== undefined ? chunk.start.blockPosition : undefined;
    let stream;
    do {
        const remainingInput = inputData.slice(pos);
        const inflator = new pako_1.Inflate();
        stream = inflator.strm;
        inflator.push(remainingInput, 2);
        if (inflator.err)
            throw new Error(inflator.msg);
        decompressedBlocks.push(inflator.result);
        if (chunk !== undefined) {
            if (decompressedBlocks.length === 1 && chunk.start.dataPosition) {
                decompressedBlocks[0] = decompressedBlocks[0].slice(chunk.start.dataPosition);
            }
            if (fileStartingOffset + pos >= chunk.end.blockPosition) {
                const newEnd = chunk.end.blockPosition === chunk.start.blockPosition ?
                    chunk.end.dataPosition - chunk.start.dataPosition + 1 : chunk.end.dataPosition + 1;
                const lastIndex = decompressedBlocks.length - 1;
                decompressedBlocks[lastIndex] = decompressedBlocks[lastIndex].slice(0, newEnd);
                break;
            }
        }
        pos += stream.next_in;
    } while (stream.avail_in);
    const result = mergedTypedArrays(decompressedBlocks, Uint8Array);
    return result.buffer;
}
exports.bgzfUnzip = bgzfUnzip;
function mergedTypedArrays(arrays, type = Uint8Array) {
    const ret = new (type)(arrays.reduce((acc, arr) => acc + arr.byteLength, 0));
    let off = 0;
    arrays.forEach((arr) => {
        ret.set(arr, off);
        off += arr.byteLength;
    });
    return ret;
}
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