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'@gmod/indexedfasta'\n\nconst fasta = new IndexedFasta({\n  path: 'test.fa',\n  faiPath: 'test.fa.fai',\n})\n// or\nconst bgzipFasta = new BgzipIndexedFasta({\n  path: 'test.fa.gz',\n  faiPath: 'test.fa.gz.fai',\n  gziPath: 'test.fa.gz.gzi',\n})\n\n// coordinates are UCSC standard 0-based half-open\n// returns a string of bases, or undefined if the sequence is not in the index\nconst bases = await fasta.getSequence('chr1', 0, 10)\n\nconst seqNames = await fasta.getSequenceNames() // ['chr1', ...]\nconst sizes = await fasta.getSequenceSizes() // { chr1: 100100, ... }\nconst chr1Size = await fasta.getSequenceSize('chr1')\n```\n\nTo read remote files in the browser or in Node, pass filehandles instead of\npaths:\n\n```typescript\nimport { RemoteFile } from 'generic-filehandle2'\n\nconst fasta = new IndexedFasta({\n  fasta: new RemoteFile('https://example.com/test.fa'),\n  fai: new RemoteFile('https://example.com/test.fa.fai'),\n})\n```\n\nWhen the files are remote,\n[`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)\ncan be used in place of `RemoteFile`. It caches the byte ranges it reads in 256\nKiB chunks, so returning to a region you have already fetched costs no request\nat all, and neighboring regions are fetched together.\n\nSee [docs/api.md](docs/api.md) for the full API, including abort signals and\n`FetchableSmallFasta` for small unindexed files.\n\n## Academic Use\n\nThis package was written with funding from the [NHGRI](http://genome.gov) as\npart of the [JBrowse](http://jbrowse.org) project. If you use it in an academic\nproject that you publish, please cite the most recent JBrowse paper, which will\nbe linked from [jbrowse.org](http://jbrowse.org).\n\n## Contributing\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for development and release steps.\n\n## License\n\nMIT © [Colin Diesh](https://github.com/cmdcolin)\n","readmeFilename":"README.md"}