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Diesh","email":"colin.diesh@gmail.com"},"license":"MIT","homepage":"https://github.com/GMOD/bbi-js#readme","keywords":["bionode","biojs","bigwig","bigbed","ucsc","genomics"],"repository":{"url":"git+https://github.com/GMOD/bbi-js.git","type":"git"},"description":"Parser for BigWig/BigBed files","maintainers":[{"name":"rbuels","email":"rbuels@gmail.com"},{"name":"cmdcolin","email":"colin.diesh@gmail.com"},{"name":"garrettjstevens","email":"stevens.garrett.j@gmail.com"}],"readme":"# bbi-js\n\n[![NPM version](https://img.shields.io/npm/v/@gmod/bbi.svg?style=flat-square)](https://npmjs.org/package/@gmod/bbi)\n![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bbi-js/publish.yml?branch=main)\n\nParser for BigWig and BigBed file formats.\n\n## Install\n\n```bash\nnpm install @gmod/bbi\n```\n\n## Usage\n\n```typescript\nimport { BigWig } from '@gmod/bbi'\nimport { RemoteFileWithRangeCache } from '@gmod/range-cache-filehandle'\n\nconst local = new BigWig({ path: 'volvox.bw' }) // node only\n\nconst remote = new BigWig({\n  filehandle: new RemoteFileWithRangeCache('https://example.com/file.bw'),\n})\n\nconst header = await remote.getHeader()\nconst features = await remote.getFeatures('chr1', 0, 100_000)\n```\n\n[`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)\nmerges adjacent reads and answers repeat reads from memory.\n`new BigWig({ url })` also works, without that cache.\n\n### Browser (CDN)\n\n```html\n<script type=\"module\">\n  import { BigWig } from 'https://esm.sh/@gmod/bbi'\n\n  const file = new BigWig({ url: 'https://example.com/file.bw' })\n  const features = await file.getFeatures('chr1', 0, 100)\n  console.log(features)\n</script>\n```\n\nNote that such CDN usage makes you reliant on a third party service, esm.sh,\nstaying up, so it's not necessarily recommended for production usage, but it\ndoes work\n\nSee the [example](./example/) folder for a complete working demo.\n\n## Decompression\n\nA Rust/WebAssembly [libdeflater](https://github.com/ebiggers/libdeflate) module,\ninlined in the bundle as base64, inflates the blocks at ~2.5–3× a pure-JS\ninflate, so there is nothing extra to install or configure. See\n[docs/wasm.md](docs/wasm.md).\n\n## Docs\n\n- [docs/api.md](docs/api.md) — constructor, options, methods, types,\n  BigWig/BigBed and helpers\n- [docs/optimizations.md](docs/optimizations.md) — decisions we made to improve\n  performance\n- [docs/concurrency.md](docs/concurrency.md) — how many range requests a query\n  makes\n- [docs/parser-selection.md](docs/parser-selection.md) — decision tree showing\n  decoding workflow\n- [docs/wasm.md](docs/wasm.md) — description of the Rust/WebAssembly\n  decompressor\n- [CONTRIBUTING.md](CONTRIBUTING.md) — development, release and publishing\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 © [Colin Diesh](https://github.com/cmdcolin)\n","readmeFilename":"README.md"}