@gmod/vcf/esm/processGenotypes.js

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

/**
 * Process genotypes by calling a callback for each one, avoiding intermediate
 * object/string allocation. This is useful for operations like counting alleles
 * where you don't need to build the full genotypes object.
 *
 * @param format - The FORMAT field from the VCF line
 * @param prerest - The sample data portion of the VCF line (after FORMAT)
 * @param samplesLen - Number of samples
 * @param callback - Called for each genotype with (string, startIndex, endIndex)
 */
const TAB = 9;
const COLON = 58;
const G = 71;
const T = 84;
// Column index of the exact "GT" field among the colon-separated FORMAT
// keys, or -1 if absent. Matches the field exactly so keys that merely
// contain "GT" (e.g. GATK's PGT) are not mistaken for it.
function gtColumnIndex(format) {
    let col = 0;
    let start = 0;
    const len = format.length;
    for (let j = 0; j <= len; j++) {
        if (j === len || format.charCodeAt(j) === COLON) {
            if (j - start === 2 &&
                format.charCodeAt(start) === G &&
                format.charCodeAt(start + 1) === T) {
                return col;
            }
            col++;
            start = j + 1;
        }
    }
    return -1;
}
export function processGenotypes(format, prerest, samplesLen, callback) {
    const prerestLen = prerest.length;
    let pos = 0;
    // Fast path: format is exactly "GT"
    if (format === 'GT') {
        for (let idx = 0; idx < samplesLen; idx++) {
            const start = pos;
            while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
                pos++;
            }
            callback(prerest, start, pos, idx);
            pos++;
        }
        return;
    }
    const colonCount = gtColumnIndex(format);
    if (colonCount === -1) {
        return;
    }
    // GT is first field but not only field
    if (colonCount === 0) {
        for (let idx = 0; idx < samplesLen; idx++) {
            const start = pos;
            while (pos < prerestLen &&
                prerest.charCodeAt(pos) !== COLON &&
                prerest.charCodeAt(pos) !== TAB) {
                pos++;
            }
            callback(prerest, start, pos, idx);
            while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
                pos++;
            }
            pos++;
        }
        return;
    }
    // GT is not first field - skip to its column (colonCount fields precede it)
    for (let idx = 0; idx < samplesLen; idx++) {
        const sampleStart = pos;
        let tabIdx = pos;
        while (tabIdx < prerestLen && prerest.charCodeAt(tabIdx) !== TAB) {
            tabIdx++;
        }
        let colons = 0;
        let fieldStart = sampleStart;
        for (let j = sampleStart; j <= tabIdx; j++) {
            if (j === tabIdx || prerest.charCodeAt(j) === COLON) {
                if (colons === colonCount) {
                    callback(prerest, fieldStart, j, idx);
                    break;
                }
                colons++;
                fieldStart = j + 1;
            }
        }
        pos = tabIdx + 1;
    }
}
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