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

read CRAM files with pure Javascript

import CramCodec from "./_base.js";
import { getBits } from "./getBits.js";
import { CramUnimplementedError } from "../../errors.js";
export default class GammaCodec extends CramCodec {
    constructor(parameters, dataType) {
        super(parameters, dataType);
        if (this.dataType !== 'int') {
            throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`);
        }
    }
    decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
        let length = 1;
        while (getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
            length = length + 1;
        }
        const readBits = getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
        const value = readBits | (1 << (length - 1));
        return value - this.parameters.offset;
    }
}
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