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

read CRAM files with pure Javascript

import CramCodec from "./_base.js";
import { CramUnimplementedError } from "../../errors.js";
export default class BetaCodec extends CramCodec {
    constructor(parameters, dataType) {
        super(parameters, dataType);
        if (this.dataType !== 'int') {
            throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`);
        }
    }
    decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
        return decodeBetaInline(coreDataBlock.content, cursors.coreBlock, this.parameters.length, this.parameters.offset);
    }
}
/**
 * Optimized beta decoder with inlined bit reading.
 */
function decodeBetaInline(data, cursor, numBits, offset) {
    let { bytePosition, bitPosition } = cursor;
    // Fast path: reading exactly 8 bits when byte-aligned
    if (numBits === 8 && bitPosition === 7) {
        const val = data[bytePosition];
        cursor.bytePosition = bytePosition + 1;
        return val - offset;
    }
    // General case
    let val = 0;
    for (let i = 0; i < numBits; i++) {
        val <<= 1;
        val |= (data[bytePosition] >> bitPosition) & 1;
        bitPosition -= 1;
        if (bitPosition < 0) {
            bytePosition += 1;
            bitPosition = 7;
        }
    }
    cursor.bytePosition = bytePosition;
    cursor.bitPosition = bitPosition;
    return val - offset;
}
//# sourceMappingURL=beta.js.map