@gmod/vcf - npm Package Compare versions

+35

dist/Variant.d.ts

		import type { GenotypeCallback } from './processGenotypes.ts';
		export declare class Variant {
		CHROM: string \| undefined;
		POS: number;
		ID: string[] \| undefined;
		REF: string \| undefined;
		ALT: string[] \| undefined;
		QUAL: number \| undefined;
		FILTER: string \| string[] \| undefined;
		INFO: Record<string, unknown>;
		FORMAT: string \| undefined;
		private formatMeta;
		private rest;
		private sampleNames;
		constructor(line: string, infoMeta: Record<string, {
		Type?: string;
		}>, formatMeta: Record<string, {
		Type?: string;
		}>, sampleNames: string[], strict: boolean);
		private parseInfo;
		SAMPLES(): Record<string, Record<string, (string \| number \| undefined)[] \| undefined>>;
		GENOTYPES(): Record<string, string>;
		processGenotypes(callback: GenotypeCallback): void;
		toJSON(): {
		CHROM: string \| undefined;
		POS: number;
		ID: string[] \| undefined;
		REF: string \| undefined;
		ALT: string[] \| undefined;
		QUAL: number \| undefined;
		FILTER: string \| string[] \| undefined;
		INFO: Record<string, unknown>;
		FORMAT: string \| undefined;
		};
		}

+177

dist/Variant.js

		"use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.Variant = void 0;
		const parseGenotypesOnly_ts_1 = require("./parseGenotypesOnly.js");
		const processGenotypes_ts_1 = require("./processGenotypes.js");
		function decodeURIComponentNoThrow(uri) {
		try {
		return decodeURIComponent(uri);
		}
		catch (_e) {
		// avoid throwing exception on a failure to decode URI component
		return uri;
		}
		}
		class Variant {
		constructor(line, infoMeta, formatMeta, sampleNames, strict) {
		let currChar = 0;
		let tabCount = 0;
		while (currChar < line.length && tabCount < 9) {
		if (line[currChar] === '\t') {
		tabCount += 1;
		}
		currChar += 1;
		}
		const splitPos = tabCount === 9 ? currChar - 1 : currChar;
		const fields = line.slice(0, splitPos).split('\t');
		const rest = line.slice(splitPos + 1);
		const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields;
		const filter = FILTER === '.' ? undefined : FILTER.split(';');
		if (strict && !fields[7]) {
		throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
		}
		this.CHROM = CHROM;
		this.POS = +POS;
		this.ID = ID === '.' ? undefined : ID.split(';');
		this.REF = REF;
		this.ALT = ALT === '.' ? undefined : ALT.split(',');
		this.QUAL = QUAL === '.' ? undefined : +QUAL;
		this.FILTER = filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter;
		this.INFO =
		fields[7] === undefined \|\| fields[7] === '.'
		? {}
		: this.parseInfo(fields[7], infoMeta);
		this.FORMAT = fields[8];
		this.formatMeta = formatMeta;
		this.rest = rest;
		this.sampleNames = sampleNames;
		}
		parseInfo(infoStr, infoMeta) {
		const result = {};
		const hasDecode = infoStr.includes('%');
		const infoPairs = infoStr.split(';');
		const pairsLen = infoPairs.length;
		for (let i = 0; i < pairsLen; i++) {
		const pair = infoPairs[i];
		const eqIdx = pair.indexOf('=');
		const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx);
		const val = eqIdx === -1 ? undefined : pair.slice(eqIdx + 1);
		const itemType = infoMeta[key]?.Type;
		if (itemType === 'Flag') {
		result[key] = true;
		}
		else if (!val) {
		result[key] = true;
		}
		else {
		const isNumber = itemType === 'Integer' \|\| itemType === 'Float';
		const rawItems = val.split(',');
		const itemsLen = rawItems.length;
		if (hasDecode) {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		const decoded = decodeURIComponentNoThrow(v);
		items.push(isNumber ? Number(decoded) : decoded);
		}
		}
		result[key] = items;
		}
		else {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		items.push(isNumber ? Number(v) : v);
		}
		}
		result[key] = items;
		}
		}
		}
		return result;
		}
		SAMPLES() {
		const genotypes = {};
		const format = this.FORMAT;
		if (format) {
		const rest = this.rest.split('\t');
		const formatKeys = format.split(':');
		const isNumberType = [];
		for (let i = 0; i < formatKeys.length; i++) {
		const r = this.formatMeta[formatKeys[i]]?.Type;
		isNumberType.push(r === 'Integer' \|\| r === 'Float');
		}
		const numKeys = formatKeys.length;
		const samplesLen = this.sampleNames.length;
		for (let i = 0; i < samplesLen; i++) {
		const sample = this.sampleNames[i];
		const sampleData = {};
		const sampleStr = rest[i];
		const sampleStrLen = sampleStr.length;
		let colStart = 0;
		let colIdx = 0;
		for (let j = 0; j <= sampleStrLen; j++) {
		if (j === sampleStrLen \|\| sampleStr[j] === ':') {
		const val = sampleStr.slice(colStart, j);
		if (val === '' \|\| val === '.') {
		sampleData[formatKeys[colIdx]] = undefined;
		}
		else {
		const items = val.split(',');
		const result = [];
		if (isNumberType[colIdx]) {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : +ent);
		}
		}
		else {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : ent);
		}
		}
		sampleData[formatKeys[colIdx]] = result;
		}
		colStart = j + 1;
		colIdx += 1;
		if (colIdx >= numKeys) {
		break;
		}
		}
		}
		genotypes[sample] = sampleData;
		}
		}
		return genotypes;
		}
		GENOTYPES() {
		return (0, parseGenotypesOnly_ts_1.parseGenotypesOnly)(this.FORMAT ?? '', this.rest, this.sampleNames);
		}
		processGenotypes(callback) {
		(0, processGenotypes_ts_1.processGenotypes)(this.FORMAT ?? '', this.rest, this.sampleNames.length, callback);
		}
		toJSON() {
		return {
		CHROM: this.CHROM,
		POS: this.POS,
		ID: this.ID,
		REF: this.REF,
		ALT: this.ALT,
		QUAL: this.QUAL,
		FILTER: this.FILTER,
		INFO: this.INFO,
		FORMAT: this.FORMAT,
		};
		}
		}
		exports.Variant = Variant;
		//# sourceMappingURL=Variant.js.map

+1

dist/Variant.js.map

+35

esm/Variant.d.ts

		import type { GenotypeCallback } from './processGenotypes.ts';
		export declare class Variant {
		CHROM: string \| undefined;
		POS: number;
		ID: string[] \| undefined;
		REF: string \| undefined;
		ALT: string[] \| undefined;
		QUAL: number \| undefined;
		FILTER: string \| string[] \| undefined;
		INFO: Record<string, unknown>;
		FORMAT: string \| undefined;
		private formatMeta;
		private rest;
		private sampleNames;
		constructor(line: string, infoMeta: Record<string, {
		Type?: string;
		}>, formatMeta: Record<string, {
		Type?: string;
		}>, sampleNames: string[], strict: boolean);
		private parseInfo;
		SAMPLES(): Record<string, Record<string, (string \| number \| undefined)[] \| undefined>>;
		GENOTYPES(): Record<string, string>;
		processGenotypes(callback: GenotypeCallback): void;
		toJSON(): {
		CHROM: string \| undefined;
		POS: number;
		ID: string[] \| undefined;
		REF: string \| undefined;
		ALT: string[] \| undefined;
		QUAL: number \| undefined;
		FILTER: string \| string[] \| undefined;
		INFO: Record<string, unknown>;
		FORMAT: string \| undefined;
		};
		}

+173

esm/Variant.js

		import { parseGenotypesOnly } from "./parseGenotypesOnly.js";
		import { processGenotypes } from "./processGenotypes.js";
		function decodeURIComponentNoThrow(uri) {
		try {
		return decodeURIComponent(uri);
		}
		catch (_e) {
		// avoid throwing exception on a failure to decode URI component
		return uri;
		}
		}
		export class Variant {
		constructor(line, infoMeta, formatMeta, sampleNames, strict) {
		let currChar = 0;
		let tabCount = 0;
		while (currChar < line.length && tabCount < 9) {
		if (line[currChar] === '\t') {
		tabCount += 1;
		}
		currChar += 1;
		}
		const splitPos = tabCount === 9 ? currChar - 1 : currChar;
		const fields = line.slice(0, splitPos).split('\t');
		const rest = line.slice(splitPos + 1);
		const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields;
		const filter = FILTER === '.' ? undefined : FILTER.split(';');
		if (strict && !fields[7]) {
		throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
		}
		this.CHROM = CHROM;
		this.POS = +POS;
		this.ID = ID === '.' ? undefined : ID.split(';');
		this.REF = REF;
		this.ALT = ALT === '.' ? undefined : ALT.split(',');
		this.QUAL = QUAL === '.' ? undefined : +QUAL;
		this.FILTER = filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter;
		this.INFO =
		fields[7] === undefined \|\| fields[7] === '.'
		? {}
		: this.parseInfo(fields[7], infoMeta);
		this.FORMAT = fields[8];
		this.formatMeta = formatMeta;
		this.rest = rest;
		this.sampleNames = sampleNames;
		}
		parseInfo(infoStr, infoMeta) {
		const result = {};
		const hasDecode = infoStr.includes('%');
		const infoPairs = infoStr.split(';');
		const pairsLen = infoPairs.length;
		for (let i = 0; i < pairsLen; i++) {
		const pair = infoPairs[i];
		const eqIdx = pair.indexOf('=');
		const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx);
		const val = eqIdx === -1 ? undefined : pair.slice(eqIdx + 1);
		const itemType = infoMeta[key]?.Type;
		if (itemType === 'Flag') {
		result[key] = true;
		}
		else if (!val) {
		result[key] = true;
		}
		else {
		const isNumber = itemType === 'Integer' \|\| itemType === 'Float';
		const rawItems = val.split(',');
		const itemsLen = rawItems.length;
		if (hasDecode) {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		const decoded = decodeURIComponentNoThrow(v);
		items.push(isNumber ? Number(decoded) : decoded);
		}
		}
		result[key] = items;
		}
		else {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		items.push(isNumber ? Number(v) : v);
		}
		}
		result[key] = items;
		}
		}
		}
		return result;
		}
		SAMPLES() {
		const genotypes = {};
		const format = this.FORMAT;
		if (format) {
		const rest = this.rest.split('\t');
		const formatKeys = format.split(':');
		const isNumberType = [];
		for (let i = 0; i < formatKeys.length; i++) {
		const r = this.formatMeta[formatKeys[i]]?.Type;
		isNumberType.push(r === 'Integer' \|\| r === 'Float');
		}
		const numKeys = formatKeys.length;
		const samplesLen = this.sampleNames.length;
		for (let i = 0; i < samplesLen; i++) {
		const sample = this.sampleNames[i];
		const sampleData = {};
		const sampleStr = rest[i];
		const sampleStrLen = sampleStr.length;
		let colStart = 0;
		let colIdx = 0;
		for (let j = 0; j <= sampleStrLen; j++) {
		if (j === sampleStrLen \|\| sampleStr[j] === ':') {
		const val = sampleStr.slice(colStart, j);
		if (val === '' \|\| val === '.') {
		sampleData[formatKeys[colIdx]] = undefined;
		}
		else {
		const items = val.split(',');
		const result = [];
		if (isNumberType[colIdx]) {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : +ent);
		}
		}
		else {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : ent);
		}
		}
		sampleData[formatKeys[colIdx]] = result;
		}
		colStart = j + 1;
		colIdx += 1;
		if (colIdx >= numKeys) {
		break;
		}
		}
		}
		genotypes[sample] = sampleData;
		}
		}
		return genotypes;
		}
		GENOTYPES() {
		return parseGenotypesOnly(this.FORMAT ?? '', this.rest, this.sampleNames);
		}
		processGenotypes(callback) {
		processGenotypes(this.FORMAT ?? '', this.rest, this.sampleNames.length, callback);
		}
		toJSON() {
		return {
		CHROM: this.CHROM,
		POS: this.POS,
		ID: this.ID,
		REF: this.REF,
		ALT: this.ALT,
		QUAL: this.QUAL,
		FILTER: this.FILTER,
		INFO: this.INFO,
		FORMAT: this.FORMAT,
		};
		}
		}
		//# sourceMappingURL=Variant.js.map

+1

esm/Variant.js.map

+216

src/Variant.ts

		import { parseGenotypesOnly } from './parseGenotypesOnly.ts'
		import { processGenotypes } from './processGenotypes.ts'

		import type { GenotypeCallback } from './processGenotypes.ts'

		function decodeURIComponentNoThrow(uri: string) {
		try {
		return decodeURIComponent(uri)
		} catch (_e) {
		// avoid throwing exception on a failure to decode URI component
		return uri
		}
		}

		export class Variant {
		CHROM: string \| undefined
		POS: number
		ID: string[] \| undefined
		REF: string \| undefined
		ALT: string[] \| undefined
		QUAL: number \| undefined
		FILTER: string \| string[] \| undefined
		INFO: Record<string, unknown>
		FORMAT: string \| undefined

		private formatMeta: Record<string, { Type?: string }>
		private rest: string
		private sampleNames: string[]

		constructor(
		line: string,
		infoMeta: Record<string, { Type?: string }>,
		formatMeta: Record<string, { Type?: string }>,
		sampleNames: string[],
		strict: boolean,
		) {
		let currChar = 0
		let tabCount = 0
		while (currChar < line.length && tabCount < 9) {
		if (line[currChar] === '\t') {
		tabCount += 1
		}
		currChar += 1
		}
		const splitPos = tabCount === 9 ? currChar - 1 : currChar
		const fields = line.slice(0, splitPos).split('\t')
		const rest = line.slice(splitPos + 1)
		const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields
		const filter = FILTER === '.' ? undefined : FILTER!.split(';')

		if (strict && !fields[7]) {
		throw new Error(
		"no INFO field specified, must contain at least a '.' (turn off strict mode to allow)",
		)
		}

		this.CHROM = CHROM
		this.POS = +POS!
		this.ID = ID === '.' ? undefined : ID!.split(';')
		this.REF = REF
		this.ALT = ALT === '.' ? undefined : ALT!.split(',')
		this.QUAL = QUAL === '.' ? undefined : +QUAL!
		this.FILTER = filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter
		this.INFO =
		fields[7] === undefined \|\| fields[7] === '.'
		? {}
		: this.parseInfo(fields[7], infoMeta)
		this.FORMAT = fields[8]

		this.formatMeta = formatMeta
		this.rest = rest
		this.sampleNames = sampleNames
		}

		private parseInfo(
		infoStr: string,
		infoMeta: Record<string, { Type?: string }>,
		) {
		const result: Record<string, unknown> = {}
		const hasDecode = infoStr.includes('%')
		const infoPairs = infoStr.split(';')
		const pairsLen = infoPairs.length

		for (let i = 0; i < pairsLen; i++) {
		const pair = infoPairs[i]!
		const eqIdx = pair.indexOf('=')
		const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx)
		const val = eqIdx === -1 ? undefined : pair.slice(eqIdx + 1)
		const itemType = infoMeta[key]?.Type

		if (itemType === 'Flag') {
		result[key] = true
		} else if (!val) {
		result[key] = true
		} else {
		const isNumber = itemType === 'Integer' \|\| itemType === 'Float'
		const rawItems = val.split(',')
		const itemsLen = rawItems.length

		if (hasDecode) {
		const items: (string \| number \| undefined)[] = []
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j]!
		if (v === '.') {
		items.push(undefined)
		} else {
		const decoded = decodeURIComponentNoThrow(v)
		items.push(isNumber ? Number(decoded) : decoded)
		}
		}
		result[key] = items
		} else {
		const items: (string \| number \| undefined)[] = []
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j]!
		if (v === '.') {
		items.push(undefined)
		} else {
		items.push(isNumber ? Number(v) : v)
		}
		}
		result[key] = items
		}
		}
		}
		return result
		}

		SAMPLES() {
		const genotypes = {} as Record<
		string,
		Record<string, (string \| number \| undefined)[] \| undefined>
		>
		const format = this.FORMAT
		if (format) {
		const rest = this.rest.split('\t')
		const formatKeys = format.split(':')
		const isNumberType: boolean[] = []
		for (let i = 0; i < formatKeys.length; i++) {
		const r = this.formatMeta[formatKeys[i]!]?.Type
		isNumberType.push(r === 'Integer' \|\| r === 'Float')
		}
		const numKeys = formatKeys.length
		const samplesLen = this.sampleNames.length
		for (let i = 0; i < samplesLen; i++) {
		const sample = this.sampleNames[i]!
		const sampleData: Record<
		string,
		(string \| number \| undefined)[] \| undefined
		> = {}
		const sampleStr = rest[i]!
		const sampleStrLen = sampleStr.length
		let colStart = 0
		let colIdx = 0

		for (let j = 0; j <= sampleStrLen; j++) {
		if (j === sampleStrLen \|\| sampleStr[j] === ':') {
		const val = sampleStr.slice(colStart, j)
		if (val === '' \|\| val === '.') {
		sampleData[formatKeys[colIdx]!] = undefined
		} else {
		const items = val.split(',')
		const result: (string \| number \| undefined)[] = []
		if (isNumberType[colIdx]) {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k]!
		result.push(ent === '.' ? undefined : +ent)
		}
		} else {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k]!
		result.push(ent === '.' ? undefined : ent)
		}
		}
		sampleData[formatKeys[colIdx]!] = result
		}
		colStart = j + 1
		colIdx += 1
		if (colIdx >= numKeys) {
		break
		}
		}
		}
		genotypes[sample] = sampleData
		}
		}
		return genotypes
		}

		GENOTYPES() {
		return parseGenotypesOnly(this.FORMAT ?? '', this.rest, this.sampleNames)
		}

		processGenotypes(callback: GenotypeCallback) {
		processGenotypes(
		this.FORMAT ?? '',
		this.rest,
		this.sampleNames.length,
		callback,
		)
		}

		toJSON() {
		return {
		CHROM: this.CHROM,
		POS: this.POS,
		ID: this.ID,
		REF: this.REF,
		ALT: this.ALT,
		QUAL: this.QUAL,
		FILTER: this.FILTER,
		INFO: this.INFO,
		FORMAT: this.FORMAT,
		}
		}
		}

+3

-3

CHANGELOG.md

		@@ -1,9 +0,9 @@
		## [6.1.2](https://github.com/GMOD/vcf-js/compare/v6.1.1...v6.1.2) (2026-01-18)
		# [7.0.0](https://github.com/GMOD/vcf-js/compare/v6.1.2...v7.0.0) (2026-01-18)



		## [6.1.2](https://github.com/GMOD/vcf-js/compare/v6.1.1...v6.1.2) (2026-01-18)

		# [6.1.0](https://github.com/GMOD/vcf-js/compare/v6.0.9...v6.1.0) (2025-11-26)



		## [6.0.9](https://github.com/GMOD/vcf-js/compare/v6.0.8...v6.0.9) (2025-04-01)
		@@ -10,0 +10,0 @@

+2

-1

dist/index.d.ts

		@@ -1,3 +0,4 @@
		export type { Variant } from './parse.ts';
		export { Variant } from './Variant.ts';
		export type { GenotypeCallback } from './processGenotypes.ts';
		export { default } from './parse.ts';
		export * from './parseBreakend.ts';

+3

-1

dist/index.js

		@@ -20,3 +20,5 @@ "use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.default = void 0;
		exports.default = exports.Variant = void 0;
		var Variant_ts_1 = require("./Variant.js");
		Object.defineProperty(exports, "Variant", { enumerable: true, get: function () { return Variant_ts_1.Variant; } });
		var parse_ts_1 = require("./parse.js");
		@@ -23,0 +25,0 @@ Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(parse_ts_1).default; } });

+1

-1

dist/index.js.map

		@@ -1,1 +0,1 @@
		{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAEA,uCAAoC;AAA3B,oHAAA,OAAO,OAAA;AAChB,qDAAkC"}
		{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,2CAAsC;AAA7B,qGAAA,OAAO,OAAA;AAGhB,uCAAoC;AAA3B,oHAAA,OAAO,OAAA;AAChB,qDAAkC"}

+8

-54

dist/parse.d.ts

		@@ -0,1 +1,3 @@
		import { Variant } from './Variant.ts';
		export { Variant } from './Variant.ts';
		/**
		@@ -16,8 +18,6 @@ * Class representing a VCF parser, instantiated with the VCF header.
		samples: string[];
		constructor({ header, strict, }: {
		constructor({ header, strict }: {
		header: string;
		strict?: boolean;
		});
		private parseInfo;
		private parseSamples;
		/**
		@@ -52,57 +52,11 @@ * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
		/**
		* Parse a VCF line into an object like
		* Parse a VCF line into a Variant object.
		*
		* ```typescript
		* {
		* CHROM: 'contigA',
		* POS: 3000,
		* ID: ['rs17883296'],
		* REF: 'G',
		* ALT: ['T', 'A'],
		* QUAL: 100,
		* FILTER: 'PASS',
		* INFO: {
		* NS: [3],
		* DP: [14],
		* AF: [0.5],
		* DB: true,
		* XYZ: ['5'],
		* },
		* SAMPLES: () => ({
		* HG00096: {
		* GT: ['0\|0'],
		* AP: ['0.000', '0.000'],
		* }
		* }),
		* GENOTYPES: () => ({
		* HG00096: '0\|0'
		* })
		* }
		* ```
		* The returned Variant has SAMPLES() and GENOTYPES() methods which are
		* lazily evaluated to avoid parsing the potentially long list of samples from
		* e.g. 1000 genotypes data unless requested.
		*
		* SAMPLES and GENOTYPES methods are functions instead of static data fields
		* because it avoids parsing the potentially long list of samples from e.g.
		* 1000 genotypes data unless requested.
		*
		* The SAMPLES function gives all info about the samples
		*
		* The GENOTYPES function only extracts the raw GT string if it exists, for
		* potentially optimized parsing by programs that need it
		*
		* @param {string} line - A string of a line from a VCF
		*/
		parseLine(line: string): {
		CHROM: string \| undefined;
		POS: number;
		ALT: string[] \| undefined;
		INFO: Record<string, any>;
		REF: string \| undefined;
		FILTER: string \| string[] \| undefined;
		ID: string[] \| undefined;
		QUAL: number \| undefined;
		FORMAT: string \| undefined;
		SAMPLES: () => Record<string, Record<string, (string \| number \| undefined)[] \| undefined>>;
		GENOTYPES: () => Record<string, string>;
		};
		parseLine(line: string): Variant;
		}
		export type Variant = ReturnType<VCFParser['parseLine']>;

+10

-195

dist/parse.js

		@@ -6,14 +6,8 @@ "use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		const parseGenotypesOnly_ts_1 = require("./parseGenotypesOnly.js");
		exports.Variant = void 0;
		const Variant_ts_1 = require("./Variant.js");
		const parseMetaString_ts_1 = require("./parseMetaString.js");
		const vcfReserved_ts_1 = __importDefault(require("./vcfReserved.js"));
		function decodeURIComponentNoThrow(uri) {
		try {
		return decodeURIComponent(uri);
		}
		catch (_e) {
		// avoid throwing exception on a failure to decode URI component
		return uri;
		}
		}
		var Variant_ts_2 = require("./Variant.js");
		Object.defineProperty(exports, "Variant", { enumerable: true, get: function () { return Variant_ts_2.Variant; } });
		/**
		@@ -31,3 +25,3 @@ * Class representing a VCF parser, instantiated with the VCF header.
		class VCFParser {
		constructor({ header, strict = true, }) {
		constructor({ header, strict = true }) {
		if (!header.length) {
		@@ -84,110 +78,2 @@ throw new Error('empty header received');
		}
		parseInfo(infoStr) {
		const result = {};
		const hasDecode = infoStr.includes('%');
		const infoPairs = infoStr.split(';');
		const infoMeta = this.metadata.INFO;
		const pairsLen = infoPairs.length;
		for (let i = 0; i < pairsLen; i++) {
		const pair = infoPairs[i];
		const eqIdx = pair.indexOf('=');
		const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx);
		const val = eqIdx === -1 ? undefined : pair.slice(eqIdx + 1);
		const itemType = infoMeta[key]?.Type;
		if (itemType === 'Flag') {
		result[key] = true;
		}
		else if (!val) {
		result[key] = true;
		}
		else {
		const isNumber = itemType === 'Integer' \|\| itemType === 'Float';
		const rawItems = val.split(',');
		const itemsLen = rawItems.length;
		if (hasDecode) {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		const decoded = decodeURIComponentNoThrow(v);
		items.push(isNumber ? Number(decoded) : decoded);
		}
		}
		result[key] = items;
		}
		else {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		items.push(isNumber ? Number(v) : v);
		}
		}
		result[key] = items;
		}
		}
		}
		return result;
		}
		parseSamples(format, prerest) {
		const genotypes = {};
		if (format) {
		const rest = prerest.split('\t');
		const formatKeys = format.split(':');
		const formatMeta = this.metadata.FORMAT;
		const isNumberType = [];
		for (let i = 0; i < formatKeys.length; i++) {
		const r = formatMeta[formatKeys[i]]?.Type;
		isNumberType.push(r === 'Integer' \|\| r === 'Float');
		}
		const numKeys = formatKeys.length;
		const samplesLen = this.samples.length;
		for (let i = 0; i < samplesLen; i++) {
		const sample = this.samples[i];
		const sampleData = {};
		const sampleStr = rest[i];
		const sampleStrLen = sampleStr.length;
		let colStart = 0;
		let colIdx = 0;
		for (let j = 0; j <= sampleStrLen; j++) {
		if (j === sampleStrLen \|\| sampleStr[j] === ':') {
		const val = sampleStr.slice(colStart, j);
		if (val === '' \|\| val === '.') {
		sampleData[formatKeys[colIdx]] = undefined;
		}
		else {
		const items = val.split(',');
		const result = [];
		if (isNumberType[colIdx]) {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : +ent);
		}
		}
		else {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : ent);
		}
		}
		sampleData[formatKeys[colIdx]] = result;
		}
		colStart = j + 1;
		colIdx += 1;
		if (colIdx >= numKeys) {
		break;
		}
		}
		}
		genotypes[sample] = sampleData;
		}
		}
		return genotypes;
		}
		/**
		@@ -269,83 +155,12 @@ * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
		/**
		* Parse a VCF line into an object like
		* Parse a VCF line into a Variant object.
		*
		* ```typescript
		* {
		* CHROM: 'contigA',
		* POS: 3000,
		* ID: ['rs17883296'],
		* REF: 'G',
		* ALT: ['T', 'A'],
		* QUAL: 100,
		* FILTER: 'PASS',
		* INFO: {
		* NS: [3],
		* DP: [14],
		* AF: [0.5],
		* DB: true,
		* XYZ: ['5'],
		* },
		* SAMPLES: () => ({
		* HG00096: {
		* GT: ['0\|0'],
		* AP: ['0.000', '0.000'],
		* }
		* }),
		* GENOTYPES: () => ({
		* HG00096: '0\|0'
		* })
		* }
		* ```
		* The returned Variant has SAMPLES() and GENOTYPES() methods which are
		* lazily evaluated to avoid parsing the potentially long list of samples from
		* e.g. 1000 genotypes data unless requested.
		*
		* SAMPLES and GENOTYPES methods are functions instead of static data fields
		* because it avoids parsing the potentially long list of samples from e.g.
		* 1000 genotypes data unless requested.
		*
		* The SAMPLES function gives all info about the samples
		*
		* The GENOTYPES function only extracts the raw GT string if it exists, for
		* potentially optimized parsing by programs that need it
		*
		* @param {string} line - A string of a line from a VCF
		*/
		parseLine(line) {
		let currChar = 0;
		let tabCount = 0;
		while (currChar < line.length && tabCount < 9) {
		if (line[currChar] === '\t') {
		tabCount += 1;
		}
		currChar += 1;
		}
		const splitPos = tabCount === 9 ? currChar - 1 : currChar;
		const fields = line.slice(0, splitPos).split('\t');
		const rest = line.slice(splitPos + 1);
		const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields;
		const chrom = CHROM;
		const pos = +POS;
		const id = ID === '.' ? undefined : ID.split(';');
		const ref = REF;
		const alt = ALT === '.' ? undefined : ALT.split(',');
		const qual = QUAL === '.' ? undefined : +QUAL;
		const filter = FILTER === '.' ? undefined : FILTER.split(';');
		const format = fields[8];
		if (this.strict && !fields[7]) {
		throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
		}
		const info = fields[7] === undefined \|\| fields[7] === '.'
		? {}
		: this.parseInfo(fields[7]);
		return {
		CHROM: chrom,
		POS: pos,
		ALT: alt,
		INFO: info,
		REF: ref,
		FILTER: filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter,
		ID: id,
		QUAL: qual,
		FORMAT: format,
		SAMPLES: () => this.parseSamples(fields[8] ?? '', rest),
		GENOTYPES: () => (0, parseGenotypesOnly_ts_1.parseGenotypesOnly)(fields[8] ?? '', rest, this.samples),
		};
		return new Variant_ts_1.Variant(line, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);
		}
		@@ -352,0 +167,0 @@ }

+1

-1

dist/parse.js.map

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+2

-1

esm/index.d.ts

		@@ -1,3 +0,4 @@
		export type { Variant } from './parse.ts';
		export { Variant } from './Variant.ts';
		export type { GenotypeCallback } from './processGenotypes.ts';
		export { default } from './parse.ts';
		export * from './parseBreakend.ts';

+1

-0

esm/index.js

		@@ -0,3 +1,4 @@
		export { Variant } from "./Variant.js";
		export { default } from "./parse.js";
		export * from "./parseBreakend.js";
		//# sourceMappingURL=index.js.map

+1

-1

esm/index.js.map

		@@ -1,1 +0,1 @@
		{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,YAAY,CAAA;AACpC,cAAc,oBAAoB,CAAA"}
		{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,cAAc,CAAA;AAGtC,OAAO,EAAE,OAAO,EAAE,MAAM,YAAY,CAAA;AACpC,cAAc,oBAAoB,CAAA"}

+8

-54

esm/parse.d.ts

		@@ -0,1 +1,3 @@
		import { Variant } from './Variant.ts';
		export { Variant } from './Variant.ts';
		/**
		@@ -16,8 +18,6 @@ * Class representing a VCF parser, instantiated with the VCF header.
		samples: string[];
		constructor({ header, strict, }: {
		constructor({ header, strict }: {
		header: string;
		strict?: boolean;
		});
		private parseInfo;
		private parseSamples;
		/**
		@@ -52,57 +52,11 @@ * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
		/**
		* Parse a VCF line into an object like
		* Parse a VCF line into a Variant object.
		*
		* ```typescript
		* {
		* CHROM: 'contigA',
		* POS: 3000,
		* ID: ['rs17883296'],
		* REF: 'G',
		* ALT: ['T', 'A'],
		* QUAL: 100,
		* FILTER: 'PASS',
		* INFO: {
		* NS: [3],
		* DP: [14],
		* AF: [0.5],
		* DB: true,
		* XYZ: ['5'],
		* },
		* SAMPLES: () => ({
		* HG00096: {
		* GT: ['0\|0'],
		* AP: ['0.000', '0.000'],
		* }
		* }),
		* GENOTYPES: () => ({
		* HG00096: '0\|0'
		* })
		* }
		* ```
		* The returned Variant has SAMPLES() and GENOTYPES() methods which are
		* lazily evaluated to avoid parsing the potentially long list of samples from
		* e.g. 1000 genotypes data unless requested.
		*
		* SAMPLES and GENOTYPES methods are functions instead of static data fields
		* because it avoids parsing the potentially long list of samples from e.g.
		* 1000 genotypes data unless requested.
		*
		* The SAMPLES function gives all info about the samples
		*
		* The GENOTYPES function only extracts the raw GT string if it exists, for
		* potentially optimized parsing by programs that need it
		*
		* @param {string} line - A string of a line from a VCF
		*/
		parseLine(line: string): {
		CHROM: string \| undefined;
		POS: number;
		ALT: string[] \| undefined;
		INFO: Record<string, any>;
		REF: string \| undefined;
		FILTER: string \| string[] \| undefined;
		ID: string[] \| undefined;
		QUAL: number \| undefined;
		FORMAT: string \| undefined;
		SAMPLES: () => Record<string, Record<string, (string \| number \| undefined)[] \| undefined>>;
		GENOTYPES: () => Record<string, string>;
		};
		parseLine(line: string): Variant;
		}
		export type Variant = ReturnType<VCFParser['parseLine']>;

+8

-195

esm/parse.js

		@@ -1,13 +0,5 @@
		import { parseGenotypesOnly } from "./parseGenotypesOnly.js";
		import { Variant } from "./Variant.js";
		import { parseMetaString } from "./parseMetaString.js";
		import vcfReserved from "./vcfReserved.js";
		function decodeURIComponentNoThrow(uri) {
		try {
		return decodeURIComponent(uri);
		}
		catch (_e) {
		// avoid throwing exception on a failure to decode URI component
		return uri;
		}
		}
		export { Variant } from "./Variant.js";
		/**
		@@ -25,3 +17,3 @@ * Class representing a VCF parser, instantiated with the VCF header.
		export default class VCFParser {
		constructor({ header, strict = true, }) {
		constructor({ header, strict = true }) {
		if (!header.length) {
		@@ -78,110 +70,2 @@ throw new Error('empty header received');
		}
		parseInfo(infoStr) {
		const result = {};
		const hasDecode = infoStr.includes('%');
		const infoPairs = infoStr.split(';');
		const infoMeta = this.metadata.INFO;
		const pairsLen = infoPairs.length;
		for (let i = 0; i < pairsLen; i++) {
		const pair = infoPairs[i];
		const eqIdx = pair.indexOf('=');
		const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx);
		const val = eqIdx === -1 ? undefined : pair.slice(eqIdx + 1);
		const itemType = infoMeta[key]?.Type;
		if (itemType === 'Flag') {
		result[key] = true;
		}
		else if (!val) {
		result[key] = true;
		}
		else {
		const isNumber = itemType === 'Integer' \|\| itemType === 'Float';
		const rawItems = val.split(',');
		const itemsLen = rawItems.length;
		if (hasDecode) {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		const decoded = decodeURIComponentNoThrow(v);
		items.push(isNumber ? Number(decoded) : decoded);
		}
		}
		result[key] = items;
		}
		else {
		const items = [];
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j];
		if (v === '.') {
		items.push(undefined);
		}
		else {
		items.push(isNumber ? Number(v) : v);
		}
		}
		result[key] = items;
		}
		}
		}
		return result;
		}
		parseSamples(format, prerest) {
		const genotypes = {};
		if (format) {
		const rest = prerest.split('\t');
		const formatKeys = format.split(':');
		const formatMeta = this.metadata.FORMAT;
		const isNumberType = [];
		for (let i = 0; i < formatKeys.length; i++) {
		const r = formatMeta[formatKeys[i]]?.Type;
		isNumberType.push(r === 'Integer' \|\| r === 'Float');
		}
		const numKeys = formatKeys.length;
		const samplesLen = this.samples.length;
		for (let i = 0; i < samplesLen; i++) {
		const sample = this.samples[i];
		const sampleData = {};
		const sampleStr = rest[i];
		const sampleStrLen = sampleStr.length;
		let colStart = 0;
		let colIdx = 0;
		for (let j = 0; j <= sampleStrLen; j++) {
		if (j === sampleStrLen \|\| sampleStr[j] === ':') {
		const val = sampleStr.slice(colStart, j);
		if (val === '' \|\| val === '.') {
		sampleData[formatKeys[colIdx]] = undefined;
		}
		else {
		const items = val.split(',');
		const result = [];
		if (isNumberType[colIdx]) {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : +ent);
		}
		}
		else {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k];
		result.push(ent === '.' ? undefined : ent);
		}
		}
		sampleData[formatKeys[colIdx]] = result;
		}
		colStart = j + 1;
		colIdx += 1;
		if (colIdx >= numKeys) {
		break;
		}
		}
		}
		genotypes[sample] = sampleData;
		}
		}
		return genotypes;
		}
		/**
		@@ -263,85 +147,14 @@ * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
		/**
		* Parse a VCF line into an object like
		* Parse a VCF line into a Variant object.
		*
		* ```typescript
		* {
		* CHROM: 'contigA',
		* POS: 3000,
		* ID: ['rs17883296'],
		* REF: 'G',
		* ALT: ['T', 'A'],
		* QUAL: 100,
		* FILTER: 'PASS',
		* INFO: {
		* NS: [3],
		* DP: [14],
		* AF: [0.5],
		* DB: true,
		* XYZ: ['5'],
		* },
		* SAMPLES: () => ({
		* HG00096: {
		* GT: ['0\|0'],
		* AP: ['0.000', '0.000'],
		* }
		* }),
		* GENOTYPES: () => ({
		* HG00096: '0\|0'
		* })
		* }
		* ```
		* The returned Variant has SAMPLES() and GENOTYPES() methods which are
		* lazily evaluated to avoid parsing the potentially long list of samples from
		* e.g. 1000 genotypes data unless requested.
		*
		* SAMPLES and GENOTYPES methods are functions instead of static data fields
		* because it avoids parsing the potentially long list of samples from e.g.
		* 1000 genotypes data unless requested.
		*
		* The SAMPLES function gives all info about the samples
		*
		* The GENOTYPES function only extracts the raw GT string if it exists, for
		* potentially optimized parsing by programs that need it
		*
		* @param {string} line - A string of a line from a VCF
		*/
		parseLine(line) {
		let currChar = 0;
		let tabCount = 0;
		while (currChar < line.length && tabCount < 9) {
		if (line[currChar] === '\t') {
		tabCount += 1;
		}
		currChar += 1;
		}
		const splitPos = tabCount === 9 ? currChar - 1 : currChar;
		const fields = line.slice(0, splitPos).split('\t');
		const rest = line.slice(splitPos + 1);
		const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields;
		const chrom = CHROM;
		const pos = +POS;
		const id = ID === '.' ? undefined : ID.split(';');
		const ref = REF;
		const alt = ALT === '.' ? undefined : ALT.split(',');
		const qual = QUAL === '.' ? undefined : +QUAL;
		const filter = FILTER === '.' ? undefined : FILTER.split(';');
		const format = fields[8];
		if (this.strict && !fields[7]) {
		throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
		}
		const info = fields[7] === undefined \|\| fields[7] === '.'
		? {}
		: this.parseInfo(fields[7]);
		return {
		CHROM: chrom,
		POS: pos,
		ALT: alt,
		INFO: info,
		REF: ref,
		FILTER: filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter,
		ID: id,
		QUAL: qual,
		FORMAT: format,
		SAMPLES: () => this.parseSamples(fields[8] ?? '', rest),
		GENOTYPES: () => parseGenotypesOnly(fields[8] ?? '', rest, this.samples),
		};
		return new Variant(line, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);
		}
		}
		//# sourceMappingURL=parse.js.map

+1

-1

esm/parse.js.map

		@@ -1,1 +0,1 @@
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+1

-1

package.json

		{
		"name": "@gmod/vcf",
		"version": "6.1.2",
		"version": "7.0.0",
		"description": "High performance streaming Variant Call Format (VCF) parser in pure JavaScript",
		@@ -5,0 +5,0 @@ "type": "module",

+50

-71

README.md

		@@ -20,3 +20,3 @@ # vcf-js
		// with import
		import VCF, { parseBreakend } from '@gmod/vcf'
		import VCF, { parseBreakend, Variant } from '@gmod/vcf'

		@@ -82,3 +82,3 @@ // with require

		The `variant` object returned by `parseLine()` would be
		The `Variant` object returned by `parseLine()` has these properties:

		@@ -101,23 +101,16 @@ ```typescript
		},
		SAMPLES: () => ({
		HG00096: {
		GT: ['0\|0'],
		AP: ['0.000', '0.000'],
		},
		}),
		GENOTYPES: () => ({
		HG00096: '0\|0',
		}),
		}
		```

		The `variant.SAMPLES()` and `variant.GENOTYPES()` are functions because it does
		not try to eagerly parse all the genotype data, so will only do so when you call
		either of these which can save time especially if your VCF has a lot of samples
		in it.
		The `Variant` class also has methods for accessing sample data:

		The `variant.SAMPLES()` function parses out the FORMAT fields, while
		`variant.GENOTYPES()` returns just the genotypes string which can be faster if
		that is the only information you are interested in
		- `variant.SAMPLES()` - returns full sample data with all FORMAT fields parsed
		- `variant.GENOTYPES()` - returns just the GT strings (faster if that's all you
		need)
		- `variant.processGenotypes(callback)` - calls a callback for each genotype
		without allocating strings (fastest for counting/iteration)

		These methods lazily parse the genotype data, so they only do work when called.
		This saves time especially if your VCF has many samples (e.g. 1000 Genomes).

		The parser will try to convert the values in INFO and FORMAT to the proper types
		@@ -273,4 +266,2 @@ using the header metadata. For example, if there is a header line like

		<!-- Generated by documentation.js. Update this documentation by updating the source code. -->

		#### Table of Contents
		@@ -281,5 +272,7 @@
		- [getMetadata](#getmetadata)
		- [Parameters](#parameters-1)
		- [parseLine](#parseline)
		- [Parameters](#parameters-2)
		- [Variant](#variant)
		- [SAMPLES](#samples)
		- [GENOTYPES](#genotypes)
		- [processGenotypes](#processgenotypes)

		@@ -292,11 +285,5 @@ ### VCFParser

		- `args`
		[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)
		- `args.header`
		[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)
		The VCF header. Supports both LF and CRLF newlines. (optional, default `''`)
		- `args.strict`
		[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)
		Whether to parse in strict mode or not (default true) (optional, default
		`true`)
		- `args.header` string - The VCF header. Supports both LF and CRLF newlines.
		- `args.strict` boolean - Whether to parse in strict mode or not (default
		true)

		@@ -310,5 +297,3 @@ #### getMetadata

		- `args`
		...[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)
		List of metadata filter strings.
		- `...args` string[] - List of metadata filter strings.

		@@ -319,45 +304,39 @@ Returns any An object, string, or number, depending on the filtering

		Parse a VCF line into an object like
		Parse a VCF line into a `Variant` object.

		```typescript
		{
		CHROM: 'contigA',
		POS: 3000,
		ID: ['rs17883296'],
		REF: 'G',
		ALT: ['T', 'A'],
		QUAL: 100,
		FILTER: 'PASS',
		INFO: {
		NS: [3],
		DP: [14],
		AF: [0.5],
		DB: true,
		XYZ: ['5'],
		},
		SAMPLES: () => ({
		HG00096: {
		GT: ['0\|0'],
		AP: ['0.000', '0.000'],
		}
		}),
		GENOTYPES: () => ({
		HG00096: '0\|0'
		})
		}
		```
		##### Parameters

		SAMPLES and GENOTYPES methods are functions instead of static data fields
		because it avoids parsing the potentially long list of samples from e.g. 1000
		genotypes data unless requested.
		- `line` string - A string of a line from a VCF

		The SAMPLES function gives all info about the samples
		Returns Variant A Variant instance with the parsed data

		The GENOTYPES function only extracts the raw GT string if it exists, for
		potentially optimized parsing by programs that need it
		### Variant

		Class representing a parsed VCF variant line. Has data properties (CHROM, POS,
		ID, REF, ALT, QUAL, FILTER, INFO, FORMAT) and methods for accessing sample data.

		#### SAMPLES

		Returns full sample data with all FORMAT fields parsed.

		Returns **Record\<string, Record\<string, (string \| number \| undefined)[] \|
		undefined>>**

		#### GENOTYPES

		Returns just the GT strings for each sample (faster than SAMPLES if you only
		need genotypes).

		Returns Record\<string, string>

		#### processGenotypes

		Calls a callback for each genotype without allocating strings. Useful for
		counting or iterating over genotypes with minimal memory allocation.

		##### Parameters

		- `line`
		[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)
		A string of a line from a VCF
		- `callback` (str: string, start: number, end: number) => any - Called for
		each genotype with the raw string and indices. Use `str.slice(start, end)` to
		extract the genotype string, or `str.charCodeAt(start)` to read characters
		without allocation.

+2

-1

src/index.ts

		@@ -1,4 +0,5 @@
		export type { Variant } from './parse.ts'
		export { Variant } from './Variant.ts'
		export type { GenotypeCallback } from './processGenotypes.ts'

		export { default } from './parse.ts'
		export * from './parseBreakend.ts'

+14

-212

src/parse.ts

		@@ -1,13 +0,6 @@
		import { parseGenotypesOnly } from './parseGenotypesOnly.ts'
		import { Variant } from './Variant.ts'
		import { parseMetaString } from './parseMetaString.ts'
		import vcfReserved from './vcfReserved.ts'

		function decodeURIComponentNoThrow(uri: string) {
		try {
		return decodeURIComponent(uri)
		} catch (_e) {
		// avoid throwing exception on a failure to decode URI component
		return uri
		}
		}
		export { Variant } from './Variant.ts'

		@@ -30,9 +23,3 @@ /**

		constructor({
		header,
		strict = true,
		}: {
		header: string
		strict?: boolean
		}) {
		constructor({ header, strict = true }: { header: string; strict?: boolean }) {
		if (!header.length) {
		@@ -92,115 +79,2 @@ throw new Error('empty header received')

		private parseInfo(infoStr: string) {
		const result: Record<string, any> = {}
		const hasDecode = infoStr.includes('%')
		const infoPairs = infoStr.split(';')
		const infoMeta = this.metadata.INFO as Record<string, any>
		const pairsLen = infoPairs.length

		for (let i = 0; i < pairsLen; i++) {
		const pair = infoPairs[i]!
		const eqIdx = pair.indexOf('=')
		const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx)
		const val = eqIdx === -1 ? undefined : pair.slice(eqIdx + 1)
		const itemType = infoMeta[key]?.Type

		if (itemType === 'Flag') {
		result[key] = true
		} else if (!val) {
		result[key] = true
		} else {
		const isNumber = itemType === 'Integer' \|\| itemType === 'Float'
		const rawItems = val.split(',')
		const itemsLen = rawItems.length

		if (hasDecode) {
		const items: (string \| number \| undefined)[] = []
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j]!
		if (v === '.') {
		items.push(undefined)
		} else {
		const decoded = decodeURIComponentNoThrow(v)
		items.push(isNumber ? Number(decoded) : decoded)
		}
		}
		result[key] = items
		} else {
		const items: (string \| number \| undefined)[] = []
		for (let j = 0; j < itemsLen; j++) {
		const v = rawItems[j]!
		if (v === '.') {
		items.push(undefined)
		} else {
		items.push(isNumber ? Number(v) : v)
		}
		}
		result[key] = items
		}
		}
		}
		return result
		}

		private parseSamples(format: string, prerest: string) {
		const genotypes = {} as Record<
		string,
		Record<string, (string \| number \| undefined)[] \| undefined>
		>
		if (format) {
		const rest = prerest.split('\t')
		const formatKeys = format.split(':')
		const formatMeta = this.metadata.FORMAT as Record<string, any>
		const isNumberType: boolean[] = []
		for (let i = 0; i < formatKeys.length; i++) {
		const r = formatMeta[formatKeys[i]!]?.Type
		isNumberType.push(r === 'Integer' \|\| r === 'Float')
		}
		const numKeys = formatKeys.length
		const samplesLen = this.samples.length
		for (let i = 0; i < samplesLen; i++) {
		const sample = this.samples[i]!
		const sampleData: Record<
		string,
		(string \| number \| undefined)[] \| undefined
		> = {}
		const sampleStr = rest[i]!
		const sampleStrLen = sampleStr.length
		let colStart = 0
		let colIdx = 0

		for (let j = 0; j <= sampleStrLen; j++) {
		if (j === sampleStrLen \|\| sampleStr[j] === ':') {
		const val = sampleStr.slice(colStart, j)
		if (val === '' \|\| val === '.') {
		sampleData[formatKeys[colIdx]!] = undefined
		} else {
		const items = val.split(',')
		const result: (string \| number \| undefined)[] = []
		if (isNumberType[colIdx]) {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k]!
		result.push(ent === '.' ? undefined : +ent)
		}
		} else {
		for (let k = 0; k < items.length; k++) {
		const ent = items[k]!
		result.push(ent === '.' ? undefined : ent)
		}
		}
		sampleData[formatKeys[colIdx]!] = result
		}
		colStart = j + 1
		colIdx += 1
		if (colIdx >= numKeys) {
		break
		}
		}
		}
		genotypes[sample] = sampleData
		}
		}
		return genotypes
		}

		/**
		@@ -283,91 +157,19 @@ * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
		/**
		* Parse a VCF line into an object like
		* Parse a VCF line into a Variant object.
		*
		* ```typescript
		* {
		* CHROM: 'contigA',
		* POS: 3000,
		* ID: ['rs17883296'],
		* REF: 'G',
		* ALT: ['T', 'A'],
		* QUAL: 100,
		* FILTER: 'PASS',
		* INFO: {
		* NS: [3],
		* DP: [14],
		* AF: [0.5],
		* DB: true,
		* XYZ: ['5'],
		* },
		* SAMPLES: () => ({
		* HG00096: {
		* GT: ['0\|0'],
		* AP: ['0.000', '0.000'],
		* }
		* }),
		* GENOTYPES: () => ({
		* HG00096: '0\|0'
		* })
		* }
		* ```
		* The returned Variant has SAMPLES() and GENOTYPES() methods which are
		* lazily evaluated to avoid parsing the potentially long list of samples from
		* e.g. 1000 genotypes data unless requested.
		*
		* SAMPLES and GENOTYPES methods are functions instead of static data fields
		* because it avoids parsing the potentially long list of samples from e.g.
		* 1000 genotypes data unless requested.
		*
		* The SAMPLES function gives all info about the samples
		*
		* The GENOTYPES function only extracts the raw GT string if it exists, for
		* potentially optimized parsing by programs that need it
		*
		* @param {string} line - A string of a line from a VCF
		*/
		parseLine(line: string) {
		let currChar = 0
		let tabCount = 0
		while (currChar < line.length && tabCount < 9) {
		if (line[currChar] === '\t') {
		tabCount += 1
		}
		currChar += 1
		}
		const splitPos = tabCount === 9 ? currChar - 1 : currChar
		const fields = line.slice(0, splitPos).split('\t')
		const rest = line.slice(splitPos + 1)
		const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields
		const chrom = CHROM
		const pos = +POS!
		const id = ID === '.' ? undefined : ID!.split(';')
		const ref = REF
		const alt = ALT === '.' ? undefined : ALT!.split(',')
		const qual = QUAL === '.' ? undefined : +QUAL!
		const filter = FILTER === '.' ? undefined : FILTER!.split(';')
		const format = fields[8]

		if (this.strict && !fields[7]) {
		throw new Error(
		"no INFO field specified, must contain at least a '.' (turn off strict mode to allow)",
		)
		}
		const info =
		fields[7] === undefined \|\| fields[7] === '.'
		? {}
		: this.parseInfo(fields[7])

		return {
		CHROM: chrom,
		POS: pos,
		ALT: alt,
		INFO: info,
		REF: ref,
		FILTER: filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter,
		ID: id,
		QUAL: qual,
		FORMAT: format,
		SAMPLES: () => this.parseSamples(fields[8] ?? '', rest),
		GENOTYPES: () => parseGenotypesOnly(fields[8] ?? '', rest, this.samples),
		}
		return new Variant(
		line,
		this.metadata.INFO as Record<string, { Type?: string }>,
		this.metadata.FORMAT as Record<string, { Type?: string }>,
		this.samples,
		this.strict,
		)
		}
		}

		export type Variant = ReturnType<VCFParser['parseLine']>

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