@gmod/cram/esm/cramFile/codecs/subexp.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 SubexpCodec extends CramCodec {
    constructor(parameters, dataType) {
        super(parameters, dataType);
        if (this.dataType !== 'int') {
            throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by SUBEXP codec`);
        }
    }
    decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
        let numLeadingOnes = 0;
        while (getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
            numLeadingOnes = numLeadingOnes + 1;
        }
        let b;
        let n;
        if (numLeadingOnes === 0) {
            b = this.parameters.K;
            n = getBits(coreDataBlock.content, cursors.coreBlock, b);
        }
        else {
            b = numLeadingOnes + this.parameters.K - 1;
            const bits = getBits(coreDataBlock.content, cursors.coreBlock, b);
            n = (1 << b) | bits;
        }
        return n - this.parameters.offset;
    }
}
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