@gmod/cram/esm/cramFile/codecs/byteArrayLength.js

read CRAM files with pure Javascript

import CramCodec from "./_base.js";
export default class ByteArrayLengthCodec extends CramCodec {
    instantiateCodec;
    _lengthCodecCache;
    _dataCodecCache;
    constructor(parameters, dataType, instantiateCodec) {
        super(parameters, dataType);
        this.instantiateCodec = instantiateCodec;
    }
    decode(slice, coreDataBlock, blocksByContentId, cursors) {
        const lengthCodec = this._getLengthCodec();
        const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
        if (arrayLength > 0) {
            const dataCodec = this._getDataCodec();
            const subarray = dataCodec.getBytesSubarray(blocksByContentId, cursors, arrayLength);
            if (subarray) {
                return subarray;
            }
            else {
                const data = new Uint8Array(arrayLength);
                for (let i = 0; i < arrayLength; i += 1) {
                    data[i] = dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
                }
                return data;
            }
        }
        else {
            return new Uint8Array(0);
        }
    }
    _getLengthCodec() {
        this._lengthCodecCache ??= this.instantiateCodec(this.parameters.lengthsEncoding, 'int');
        return this._lengthCodecCache;
    }
    _getDataCodec() {
        this._dataCodecCache ??= this.instantiateCodec(this.parameters.valuesEncoding, 'byte');
        return this._dataCodecCache;
    }
}
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