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Buels","email":"rbuels@gmail.com"},"license":"MIT","homepage":"https://github.com/GMOD/tabix-js#readme","keywords":["bionode","biojs","genomics"],"repository":{"url":"git+https://github.com/GMOD/tabix-js.git","type":"git"},"description":"Read Tabix-indexed files, supports both .tbi and .csi indexes","maintainers":[{"name":"rbuels","email":"rbuels@gmail.com"},{"name":"cmdcolin","email":"colin.diesh@gmail.com"},{"name":"garrettjstevens","email":"stevens.garrett.j@gmail.com"}],"readme":"# @gmod/tabix\n\n[![NPM version](https://img.shields.io/npm/v/@gmod/tabix.svg?style=flat-square)](https://npmjs.org/package/@gmod/tabix)\n![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/tabix-js/publish.yml?branch=main)\n\nRead Tabix-indexed files using either .tbi or .csi indexes.\n\n## Install\n\n```bash\nnpm install @gmod/tabix\n```\n\n## Usage\n\n```typescript\nimport { TabixIndexedFile } from '@gmod/tabix'\n\n// Local file — TBI index assumed at path + '.tbi'\nconst file = new TabixIndexedFile({ path: 'file.vcf.gz' })\n\n// CSI index\nconst csi = new TabixIndexedFile({\n  path: 'file.vcf.gz',\n  csiPath: 'file.vcf.gz.csi',\n})\n\n// Remote files: one HTTP request per read\nconst remote = new TabixIndexedFile({\n  url: 'https://example.com/file.vcf.gz',\n  tbiUrl: 'https://example.com/file.vcf.gz.tbi',\n})\n\n// Remote files through a range cache (recommended)\nimport { RemoteFileWithRangeCache } from '@gmod/range-cache-filehandle'\n\nconst cached = new TabixIndexedFile({\n  filehandle: new RemoteFileWithRangeCache('https://example.com/file.vcf.gz'),\n  tbiFilehandle: new RemoteFileWithRangeCache(\n    'https://example.com/file.vcf.gz.tbi',\n  ),\n})\n```\n\nA bare `url` sends one request per read and caches nothing.\n[`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)\nmerges neighboring blocks into one request and fetches each byte once. Without\nit, twenty half-overlapping windows panned across the 3.4 MB test BED file read\n11 MB.\n\n### getLines\n\nFetches lines overlapping a region. `start`/`end` are 0-based half-open\ncoordinates (unlike the tabix CLI which uses 1-based closed).\n\n```typescript\nconst lines: string[] = []\nawait file.getLines('chr1', 200, 300, line => lines.push(line))\n```\n\nThe callback also receives the virtual file offset and parsed coordinates for\nthe line:\n\n```typescript\nawait file.getLines('chr1', 200, 300, (line, fileOffset, start, end) => {\n  lines.push(line)\n})\n```\n\nPass an options object instead of a bare callback to abort the query or track\ndownload progress:\n\n```typescript\nconst aborter = new AbortController()\nawait file.getLines('chr1', 200, 300, {\n  lineCallback: (line, fileOffset, start, end) => lines.push(line),\n  signal: aborter.signal,\n  onProgress: (bytesDownloaded, totalBytes) => {\n    console.log(`${bytesDownloaded}/${totalBytes}`)\n  },\n})\n```\n\n`onProgress` ticks once per chunk, the run of BGZF blocks the index resolves a\nquery to. `totalBytes` comes from the index and is known up front.\n\nNotes:\n\n- The scan skips meta/comment lines\n- Line strings have no trailing whitespace\n- Pass `undefined` for `end` to read to the end of the contig\n- A `refName` that is not in the index yields no lines and no error, so a\n  `chr1`/`1` naming mismatch looks like an empty region. Check against\n  [`getReferenceSequenceNames`](docs/api.md#getreferencesequencenamesopts-promisestring)\n  if a query comes back unexpectedly empty\n- `start > end` throws a `TypeError`; `start === end` returns without reading\n\n### GAF\n\ntabix-js reads `tabix -p gaf` indexes of sorted GAF (e.g. from `vg gamsort`):\n\n- `refName` is ignored; `getReferenceSequenceNames()` returns `[]`\n- `start`/`end` are node ids: a read matches when its lowest-to-highest node\n  range `[min, max]` touches any of `start..end-1`, the same reads as\n  `tabix file.gaf.gz \"{x}:start-end\"` (no `+1`)\n- The callback gets `min` and `max + 1`\n- `getLines` skips reads whose path is a stable sequence name (no `>`/`<`)\n\n### Without NPM (CDN)\n\n```html\n<script src=\"https://unpkg.com/@gmod/tabix/dist/tabix-bundle.js\"></script>\n```\n\nSee [example/index.html](example/index.html) for a demo; serve the directory\n(e.g. `npx serve example`) rather than opening the file directly.\n\n## How a query flows\n\n`getLines` looks up a region's BGZF chunks in the index, decompresses each chunk\nin wasm, and scans the bytes for matching lines in JS; see\n[docs/dataflow.md](docs/dataflow.md).\n\n`TabixIndexedFile` caches decompressed chunks, up to 1GB per file, and drops\nthem after three idle minutes. A consumer holding one file per track should\nbound them together with a shared `chunkCacheBudget` rather than shrinking each\nfile's ceiling; see [docs/caching.md](docs/caching.md).\n\n## Decompressing on a worker pool\n\nBGZF blocks inflate independently, so a worker pool can spread decompression\nacross threads.\n\n```typescript\nimport { getSharedWorkerPool } from '@gmod/bgzf-filehandle'\n\nconst file = new TabixIndexedFile({\n  url: 'https://example.com/yourfile.vcf.gz',\n  // the pending promise is fine — it is awaited at the point of use\n  bgzfWorkerPool: getSharedWorkerPool(),\n})\n```\n\nYou can pass the pool unconditionally: `getSharedWorkerPool()` returns\n`undefined` under node, or anywhere the host forbids Workers, and tabix-js then\ndecompresses in-process. The pool needs no cross-origin isolation, and tabix-js\nnever creates one itself, so the consumer controls the thread budget.\n\nOn a multi-sample VCF the pool speeds up end-to-end queries by about 1.4x; see\n[docs/optimizations.md](docs/optimizations.md) and\n[bgzf-filehandle's worker pool docs](https://github.com/GMOD/bgzf-filehandle/blob/main/docs/worker-pool.md).\n\n## Docs\n\n- [docs/api.md](docs/api.md) — every constructor arg and method\n- [docs/dataflow.md](docs/dataflow.md) — a query end to end, diagrammed\n- [docs/optimizations.md](docs/optimizations.md) — why each step looks the way\n  it does\n- [docs/caching.md](docs/caching.md) — sizing the decompressed-chunk cache\n- [agent-docs/architecture-decision-records/](agent-docs/architecture-decision-records/)\n  — the measurements behind those decisions\n- [agent-docs/TODO.md](agent-docs/TODO.md) — what is worth doing next\n- [CONTRIBUTING.md](CONTRIBUTING.md) — development and release steps\n\n## Academic Use\n\nWritten with [NHGRI](http://genome.gov) funding as part of\n[JBrowse](http://jbrowse.org). If you use this in a publication, please cite the\nmost recent JBrowse paper at [jbrowse.org](http://jbrowse.org).\n\n## License\n\nMIT\n","readmeFilename":"README.md"}