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Capable of streaming. For use in the browser or on Node.js.","license":"MIT","readme":"# BigWig Reader\nA Typescript library for reading BigWig, BigBed, 2bit, and Bam files. Capable of streaming.\nFor use in the browser or on Node.js.\n\nBrought to you by UMass Medical School, Weng Lab.\n\n## Installation\n\nFor npm use: `npm install bigwig-reader --save`\n\nFor yarn use: `yarn add bigwig-reader`\n\n## Usage\n\n### Importing\n```typescript\nimport { AxiosDataLoader, BigWigReader } from \"bigwig-reader\";\n```\n\n### Creating readers\nYou will need to create a `DataLoader` and `BigWigReader` for each file you want to read. DataLoaders handle IO. Readers are top level objects that read and parse data.\n\n`AxiosDataLoader` is a provided `DataLoader` that handles loading data ranges for http requests. It's constructor allows you to optionally provide your own instance of Axios to add your own configurations. For example, if you want to add your own custom auth headers.\n\nCreate your own implementation of DataLoader for loading data other ways, \nie. from file system, ftp, cloud storage, etc...\n```typescript\nconst loader = new AxiosDataLoader(\"http://localhost/sample.bigwig\", /* Optional */ Axios.create());\nconst reader = new BigWigReader(loader);\n```\n\n### Reading BigWig / BigBed data\nTo read file header data do\n```typescript\nconst header: HeaderData = await reader.getHeader();\n```\n\nTo read data we have the following three functions. All read functions take the following arguments: `startChromosome`, `startBasePair`, `endChromosome`, `endBasePair`.\n```typescript\n// Get unzoomed wig data (from BigWig files)\nconst wigData: BigWigData[] = await reader.readBigWigData(\"chr14\", 19_485_000, \"chr14\", 20_000_100);\n\n// Get unzoomed bed data (from BigBed files)\nconst bedData: BigBedData[] = await reader.readBigBedData(\"chr21\", 10_000_000, \"chr21\", 20_000_000);\n\n// Get zoom data (from BigWig or BigBed files)\n// You can find Zoom Level Index in HeaderData.zoomLevelHeaders.index\nconst zoomData: BigZoomData[] = await reader.readZoomData(\"chr2\", 0, \"chr6\", 1000, /* Zoom Level Index */ 9);\n```\n\nTo stream \"Big\" data, just use the stream versions of these functions. For example:\n\n```typescript\n// Stream unzoomed wig data\nconst wigDataStream: Readable = await reader.streamBigWigData(\"chr14\", 19_485_000, \"chr14\", 20_000_100);\n\n// log bigwig data point objects as they are read in\nseqStream.on(\"data\", (wigData: BigWigData) => console.log(wigData));\n```\n\n### Reading 2bit data\n\nTo read 2bit file data do\n```typescript\n// Get sequence data from 2bit file for chr1:100000-200000\nconst sequence: string = await reader.readTwoBitData(\"chr1\", 100_000, 200_000);\n```\n\nTo stream the same data do\n```typescript\n// Get a readable stream of sequence data\nconst seqStream: Readable = await reader.streamTwoBitData(\"chr1\", 100_000, 200_000, 1024 /* Optional chunk size */);\n\n// log sequence as it is read\nseqStream.on(\"data\", (chunk: string) => console.log(chunk));\n```\n\n### Reading BAM data\nCurrently, only indexed reads using bai indexes are supported.\n\nUnlike \"big\" file indexes, the entire bam index needs to be read to be useful, so the \nBamReader will read and cache the entire index on the first read.\n\nThe BAM header is also automatically read and cached with the reader.\n\n```typescript\n// Create data loaders for bam and index\nconst bamLoader = new AxiosDataLoader(\"http://localhost/sample.bam\");\nconst bamIndexLoader = new AxiosDataLoader(\"http://localhost/sample.bam.bai\");\n\nconst reader = new BamReader(bamLoader, bamIndexLoader);\n// First read will load entire index and bam header into memory.\nconst alignments: BamAlignment[] = await reader.read(\"chr22\", 20_000_000, 20_010_000);\n// Subsequent reads will use cached index and header.\nconst otherAlignments: BamAlignment[] = await reader.read(\"chr22\", 20_010_000, 20_020_000);\n\n// This will fetch the parsed index. Uses cache.\nconst bamIndex: BamIndexData = await reader.getIndexData();\n// This will fetch the parsed header. Uses cache.\nconst bamHeader: BamHeader = await reader.getHeaderData();\n```\n\n## For contributers\n\n### Building\n* Run `yarn install` to install dependencies.\n* Run `yarn build` to build.\n\n### Testing\nYou must have Node.js and docker-compose installed. \n* `scripts/test.sh` to run automated tests.\n* `scripts/run-dependencies.sh` to stand up a web server to host static sample BigWig and BigBed files. `scripts/test.sh` runs this for you.\n* `scripts/stop-dependencies.sh` to stop bring down the server.","readmeFilename":"README.md","keywords":["bigwig","bigbed"],"repository":{"type":"git","url":"https://www.github.com/weng-lab/bigwig-reader"}}