@gmod/vcf
Version:
High performance streaming Variant Call Format (VCF) parser in pure JavaScript
96 lines • 3.25 kB
JavaScript
;
Object.defineProperty(exports, "__esModule", { value: true });
exports.processGenotypes = processGenotypes;
/**
* 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;
}
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;
}
}
//# sourceMappingURL=processGenotypes.js.map