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

read CRAM files with pure Javascript

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const _base_ts_1 = __importDefault(require("./_base.js"));
const getBits_ts_1 = require("./getBits.js");
const errors_ts_1 = require("../../errors.js");
class GammaCodec extends _base_ts_1.default {
    constructor(parameters, dataType) {
        super(parameters, dataType);
        if (this.dataType !== 'int') {
            throw new errors_ts_1.CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`);
        }
    }
    decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
        let length = 1;
        while ((0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
            length = length + 1;
        }
        const readBits = (0, getBits_ts_1.getBits)(coreDataBlock.content, cursors.coreBlock, length - 1);
        const value = readBits | (1 << (length - 1));
        return value - this.parameters.offset;
    }
}
exports.default = GammaCodec;
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