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Stevens","email":"stevens.garrett.j@gmail.com","url":"https://github.com/garrettjstevens"},"license":"MIT","homepage":"https://github.com/GMOD/vcf-js#vcf-js","keywords":["vcf","genomics","bionode","biojs"],"repository":{"type":"git","url":"git+https://github.com/GMOD/vcf-js.git"},"description":"High performance streaming Variant Call Format (VCF) parser in pure JavaScript","maintainers":[{"name":"rbuels","email":"rbuels@gmail.com"},{"name":"cmdcolin","email":"colin.diesh@gmail.com"},{"name":"garrettjstevens","email":"stevens.garrett.j@gmail.com"}],"readme":"# vcf-js\n\nVCF (variant call format) parser\n\n[![NPM version](https://img.shields.io/npm/v/@gmod/vcf.svg?logo=npm&style=flat-square)](https://npmjs.org/package/@gmod/vcf)\n![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/vcf-js/publish.yml?branch=main)\n\n## Install\n\n```sh\nnpm install @gmod/vcf\n```\n\n## Usage\n\n```typescript\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport VCF, { type Variant } from '@gmod/vcf'\n\nconst tbiIndexed = new TabixIndexedFile({ path: '/path/to/my.vcf.gz' })\n\nconst headerText = await tbiIndexed.getHeader()\nconst parser = new VCF({ header: headerText })\n\nconst variants: Variant[] = []\nawait tbiIndexed.getLines('ctgA', 200, 300, line => {\n  variants.push(parser.parseLine(line))\n})\n```\n\nReuse one parser for all lines — the header is parsed once per `VCF`.\n\n`strict` (default `true`) makes `parseLine` throw on a line with no INFO column;\nthe VCF spec requires at least a `.` there.\n\n## Variant\n\n`parseLine(line)` returns a `Variant`:\n\n```typescript\n{\n  CHROM: 'contigA',\n  POS: 3000,\n  ID: ['rs17883296'],  // undefined if '.'\n  REF: 'G',\n  ALT: ['T', 'A'],     // undefined if '.'\n  QUAL: 100,           // undefined if '.'\n  FILTER: 'PASS',      // 'PASS' | string[] of filter names | undefined if '.'\n  FORMAT: 'GT:DP',     // undefined if the file has no samples\n  INFO: {\n    NS: [3],\n    DP: [14],\n    AF: [0.5],\n    DB: true,   // Type=Flag, a bare key, or KEY= with an empty value\n    XYZ: ['5'], // unknown fields default to Number=1, Type=String\n  },\n}\n```\n\nINFO and FORMAT values are typed using header metadata. Values are arrays unless\n`Type=Flag`, in which case they are `true`. Fields defined in the\n[VCF spec](https://samtools.github.io/hts-specs/VCFv4.3.pdf) are typed even\nwithout a header entry. `.` inside a value becomes `undefined`, and `%XX`\nescapes are percent-decoded.\n\n`JSON.stringify(variant)` serializes the columns above only — sample data is not\nincluded.\n\n### Sample methods\n\nSample data is not touched until one of these is called, so lines from a\nmany-sample file are cheap to parse if you only need the columns above.\n\n- `variant.SAMPLES()` — all FORMAT fields, keyed by sample name\n- `variant.GENOTYPES()` — GT strings only, keyed by sample name\n- `variant.processGenotypes(callback)` — GT positions only, no allocation\n\n```typescript\nlet homRef = 0\nvariant.processGenotypes((str, start, end, sampleIdx) => {\n  if (\n    end - start === 3 && // e.g. \"0|0\"\n    str.charCodeAt(start) === 48 && // 48 = '0'\n    str.charCodeAt(start + 2) === 48\n  ) {\n    homRef++\n  }\n})\n```\n\n## Performance\n\nFor files with many samples:\n\n| method               | allocates per sample                    |\n| -------------------- | --------------------------------------- |\n| `processGenotypes()` | nothing — indices into the line         |\n| `GENOTYPES()`        | one string                              |\n| `SAMPLES()`          | one object plus an array per FORMAT key |\n\n- `SAMPLES()` re-parses on every call. Call it once and keep the result.\n- `processGenotypes` ignores the callback's return value, so there is no early\n  exit — it always visits every sample.\n- `GENOTYPES()` returns a null-prototype object; use `Object.keys` / `in`, not\n  `hasOwnProperty`.\n- INFO is parsed eagerly for every line, unlike sample data. Files with large\n  INFO columns pay that cost even if you only read `CHROM`/`POS`.\n- A retained `Variant` holds a reference to its whole input line. Streaming is\n  fine, but collecting variants from a many-sample file keeps every line in\n  memory.\n\n## Metadata\n\n`parser.getMetadata(...keys)` returns header metadata, filtered by the keys\nprovided:\n\n```typescript\nparser.getMetadata('INFO', 'DP')\n// { Number: 1, Type: 'Integer', Description: 'combined depth across samples' }\n\nparser.getMetadata('INFO', 'DP', 'Number')\n// 1\n```\n\nCall with no arguments to get all metadata. `parser.samples` lists sample names.\n\n## Streaming\n\nWithout tabix, collect header lines until the first non-header line, then\nconstruct the parser:\n\n```typescript\nimport fs from 'node:fs'\nimport readline from 'node:readline'\nimport VCF from '@gmod/vcf'\n\nconst rl = readline.createInterface({\n  input: fs.createReadStream('file.vcf'),\n})\n\nconst header: string[] = []\nlet parser: VCF | undefined\n\nfor await (const line of rl) {\n  if (line.startsWith('#')) {\n    header.push(line)\n  } else {\n    parser ??= new VCF({ header: header.join('\\n') })\n    const variant = parser.parseLine(line)\n    console.log(variant.CHROM, variant.POS)\n  }\n}\n```\n\nFor `.vcf.gz`, pipe the read stream through `createGunzip()` from `node:zlib`.\n\n## Breakends\n\n`parseBreakend(alt)` parses a breakend ALT string, returning `undefined` for\nanything that isn't one:\n\n```typescript\nimport { parseBreakend } from '@gmod/vcf'\n\nparseBreakend('C[2:321682[')\n// { MateDirection: 'right', Replacement: 'C', MatePosition: '2:321682', Join: 'right' }\n```\n\nAll four bracket forms from the VCF spec:\n\n| ALT form | Join  | MateDirection |\n| -------- | ----- | ------------- |\n| `t[p[`   | right | right         |\n| `t]p]`   | right | left          |\n| `[p[t`   | left  | right         |\n| `]p]t`   | left  | left          |\n\n- `Join` — whether the replacement base appears before (`right`) or after\n  (`left`) the mate position\n- `MateDirection` — `[` means the mate sequence extends rightward; `]` means\n  leftward\n\n### Single breakends\n\nWhen the ALT starts or ends with `.`, the result has `SingleBreakend: true` and\nno `MatePosition`:\n\n```typescript\nparseBreakend('C.')\n// { Join: 'right', Replacement: 'C', SingleBreakend: true }\n\nparseBreakend('.ACGT')\n// { Join: 'left', Replacement: 'ACGT', SingleBreakend: true }\n```\n\n### Symbolic alleles\n\nAn ALT containing `<...>` uses the symbol as the mate contig:\n\n```typescript\nparseBreakend('<DUP>ACGT')\n// { Join: 'left', Replacement: 'ACGT', MateDirection: 'right', MatePosition: '<DUP>:1' }\n\nparseBreakend('ACGT<DUP>')\n// { Join: 'right', Replacement: 'ACGT', MateDirection: 'right', MatePosition: '<DUP>:1' }\n```\n\n## Exports\n\n`default` (the parser), `Variant`, `parseBreakend`, and the types `Breakend`,\n`Samples`, `SampleData`, `SampleValue`, `InfoValue`, `MetaMap`, `MetaField`,\n`GenotypeCallback`.\n\n## Contributing\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md).\n","readmeFilename":"README.md"}