@gmod/vcf/dist/parseBreakend.js

High performance streaming Variant Call Format (VCF) parser in pure JavaScript

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseBreakend = parseBreakend;
const ANGLE_BRACKET_START_REGEX = /<(.*)>(.*)/;
const ANGLE_BRACKET_END_REGEX = /(.*)<(.*)>/;
function parseBreakend(breakendString) {
    const firstChar = breakendString[0];
    const lastChar = breakendString.at(-1);
    if (firstChar === '[' ||
        firstChar === ']' ||
        lastChar === '[' ||
        lastChar === ']') {
        const tokens = breakendString.split(/[[\]]/);
        const MateDirection = breakendString.includes('[') ? 'right' : 'left';
        let Join;
        let Replacement;
        let MatePosition;
        for (const tok of tokens) {
            if (tok) {
                if (tok.includes(':')) {
                    MatePosition = tok;
                    Join = Replacement ? 'right' : 'left';
                }
                else {
                    Replacement = tok;
                }
            }
        }
        if (!(MatePosition && Join && Replacement)) {
            throw new Error(`Invalid breakend: ${breakendString}`);
        }
        return { MatePosition, Join, Replacement, MateDirection };
    }
    if (firstChar === '.') {
        return {
            Join: 'left',
            SingleBreakend: true,
            Replacement: breakendString.slice(1),
        };
    }
    if (lastChar === '.') {
        return {
            Join: 'right',
            SingleBreakend: true,
            Replacement: breakendString.slice(0, -1),
        };
    }
    if (firstChar === '<') {
        const res = ANGLE_BRACKET_START_REGEX.exec(breakendString);
        if (!res) {
            throw new Error(`failed to parse ${breakendString}`);
        }
        const Replacement = res[2];
        return Replacement
            ? {
                Join: 'left',
                Replacement,
                MateDirection: 'right',
                MatePosition: `<${res[1] ?? ''}>:1`,
            }
            : undefined;
    }
    if (breakendString.includes('<')) {
        const res = ANGLE_BRACKET_END_REGEX.exec(breakendString);
        if (!res) {
            throw new Error(`failed to parse ${breakendString}`);
        }
        const Replacement = res[1];
        return Replacement
            ? {
                Join: 'right',
                Replacement,
                MateDirection: 'right',
                MatePosition: `<${res[2] ?? ''}>:1`,
            }
            : undefined;
    }
    return undefined;
}
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