@gmod/vcf/esm/parseGenotypesOnly.js

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

export function parseGenotypesOnly(format, prerest, samples) {
    const rest = prerest.split('\t');
    const genotypes = {};
    let i = 0;
    if (format.includes('GT')) {
        const formatSplit = format.split(':');
        if (formatSplit.length === 1) {
            for (const sample of samples) {
                genotypes[sample] = rest[i++];
            }
        }
        else {
            const gtIndex = formatSplit.indexOf('GT');
            if (gtIndex === 0) {
                for (const sample of samples) {
                    const val = rest[i++];
                    const idx = val.indexOf(':');
                    genotypes[sample] = idx !== -1 ? val.slice(0, idx) : val;
                }
            }
            else {
                for (const sample of samples) {
                    const val = rest[i++].split(':');
                    genotypes[sample] = val[gtIndex];
                }
            }
        }
    }
    return genotypes;
}
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