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Stevens","email":"stevens.garrett.j@gmail.com","url":"https://github.com/garrettjstevens"},"license":"MIT","homepage":"https://github.com/GMOD/ucsc-hub-js#readme","keywords":["trackDb","genomics","bionode","biojs"],"repository":{"type":"git","url":"git+https://github.com/GMOD/ucsc-hub-js.git"},"description":"Read and write UCSC track and assembly hub files in node or the browser","maintainers":[{"name":"rbuels","email":"rbuels@gmail.com"},{"name":"cmdcolin","email":"colin.diesh@gmail.com"},{"name":"garrettjstevens","email":"stevens.garrett.j@gmail.com"}],"readme":"# ucsc-hub-js\n\nRead and write UCSC track and assembly hub files in Node or the browser.\n\n[![NPM version](https://img.shields.io/npm/v/@gmod/ucsc-hub.svg?logo=npm&style=flat-square)](https://npmjs.org/package/@gmod/ucsc-hub)\n![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/ucsc-hub-js/publish.yml?branch=main)\n\n## Install\n\n```sh\nnpm install @gmod/ucsc-hub\n```\n\n## Usage\n\nSee the\n[UCSC track hub documentation](https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html)\nfor the hub.txt, genomes.txt, and trackDb.txt file formats.\n\n```js\nimport {\n  HubFile,\n  GenomesFile,\n  TrackDbFile,\n  SingleFileHub,\n} from '@gmod/ucsc-hub'\n\nconst hub = new HubFile(hubText)\nconsole.log(hub.data.shortLabel)\n\nconst genomes = new GenomesFile(genomesText)\nconsole.log(genomes.data['hg38'].data.trackDb)\n\nconst trackDb = new TrackDbFile(trackDbText)\nconsole.log(trackDb.settings('myTrack'))\n\nconst singleHub = new SingleFileHub(hubText)\nconsole.log(singleHub.hubData, singleHub.genome, singleHub.tracks)\n```\n\n## API\n\n<!-- Generated by documentation.js. Update this documentation by updating the source code. -->\n\n#### Table of Contents\n\n- [GenomesFile](#genomesfile)\n  - [Parameters](#parameters)\n- [HubFile](#hubfile)\n  - [Parameters](#parameters-1)\n- [RaFile](#rafile)\n  - [Parameters](#parameters-2)\n  - [Properties](#properties)\n- [RaStanza](#rastanza)\n  - [Parameters](#parameters-3)\n- [SingleFileHub](#singlefilehub)\n  - [Parameters](#parameters-4)\n- [TrackDbFile](#trackdbfile)\n  - [Parameters](#parameters-5)\n  - [settings](#settings)\n    - [Parameters](#parameters-6)\n\n### GenomesFile\n\n**Extends RaFile**\n\nClass representing a genomes.txt file.\n\n#### Parameters\n\n- `genomesFile`\n  **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)\n  |\n  [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)**\n  A genomes.txt file as a string (optional, default `[]`)\n\n<!---->\n\n- Throws\n  **[Error](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Error)**\n  Throws if the first line of the genomes.txt file doesn't start with \"genome\n  \\<genome_name>\" or if it has invalid entries\n\n### HubFile\n\n**Extends RaStanza**\n\nClass representing a hub.txt file.\n\n#### Parameters\n\n- `hubFile`\n  **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)\n  |\n  [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)**\n  A hub.txt file as a string (optional, default `[]`)\n\n<!---->\n\n- Throws\n  **[Error](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Error)**\n  Throws if the first line of the hub.txt file doesn't start with \"hub\n  \\<hub_name>\", if it has invalid entries, or is missing required entries\n\n### RaFile\n\nClass representing an ra file. Each file is composed of multiple stanzas, and\neach stanza is separated by one or more blank lines. Each stanza is stored in a\nMap with the key being the value of the first key-value pair in the stanza. The\nusual Map methods can be used on the file. An additional method `add()` is\navailable to take a raw line of text and break it up into a key and value and\nadd them to the class. This should be favored over `set()` when possible, as it\nperforms more validity checks than using `set()`.\n\n#### Parameters\n\n- `raFile`\n  **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)\n  |\n  [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)**\n  An ra file, either as a single string or an array of strings with one stanza\n  per entry. Supports both LF and CRLF line terminators. (optional, default\n  `[]`)\n- `options`\n  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;\n  - `options.checkIndent`\n    **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)**\n    \\[true] - Check if a the stanzas within the file are indented consistently\n    and keep track of the indentation\n\n#### Properties\n\n- `nameKey`\n  **([undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)\n  |\n  [string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String))**\n  The key of the first line of all the stanzas (`undefined` if the stanza has no\n  lines yet).\n\n<!---->\n\n- Throws\n  **[Error](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Error)**\n  Throws if an empty stanza is added, if the key in the first key-value pair of\n  each stanza isn't the same, or if two stanzas have the same value for the\n  key-value pair in their first lines.\n\n### RaStanza\n\nClass representing an ra file stanza. Each stanza line is split into its key and\nvalue and stored as a Map, so the usual Map methods can be used on the stanza.\n\n#### Parameters\n\n- `stanza`\n  **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)\n  |\n  [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)**\n  (optional, default `[]`)\n- `options` **{checkIndent:\n  [boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?,\n  skipValidation:\n  [boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?}?**&#x20;\n\n### SingleFileHub\n\nClass representing a \"single-file\" hub.txt file that contains all the sections\nof a hub in a single file.\n\n#### Parameters\n\n- `hubText`\n  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**&#x20;\n\n### TrackDbFile\n\n**Extends RaFile**\n\nClass representing a trackDb.txt file.\n\n#### Parameters\n\n- `trackDbFile`\n  **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)\n  |\n  [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)**\n  A trackDb.txt file as a string (optional, default `[]`)\n- `options` **any?**&#x20;\n\n<!---->\n\n- Throws\n  **[Error](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Error)**\n  Throws if \"track\" is not the first key in each track or if a track is missing\n  required keys\n\n#### settings\n\nGets all track entries including those of parent tracks, with closer entries\noverriding more distant ones\n\n##### Parameters\n\n- `trackName`\n  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**\n  The name of a track\n\n<!---->\n\n- Throws\n  **[Error](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Error)**\n  Throws if track name does not exist in the trackDb\n\n## License\n\nMIT © [Generic Model Organism Database Project](http://gmod.org/wiki/Main_Page)\n\n## Publishing\n\n[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub\nActions.\n\n```bash\npnpm version patch  # or minor/major\n```\n","readmeFilename":"README.md"}