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Diesh","email":"colin.diesh@gmail.com"},"license":"MIT","homepage":"https://github.com/GMOD/bgzf-filehandle#readme","keywords":["bionode","biojs"],"repository":{"url":"git+https://github.com/GMOD/bgzf-filehandle.git","type":"git"},"description":"read from a compressed bgzip file (with .gzi) as if it were uncompressed","maintainers":[{"name":"rbuels","email":"rbuels@gmail.com"},{"name":"cmdcolin","email":"colin.diesh@gmail.com"},{"name":"garrettjstevens","email":"stevens.garrett.j@gmail.com"}],"readme":"# @gmod/bgzf-filehandle\n\n[![NPM version](https://img.shields.io/npm/v/@gmod/bgzf-filehandle.svg?style=flat-square)](https://npmjs.org/package/@gmod/bgzf-filehandle)\n[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bgzf-filehandle/publish.yml?branch=main)](https://github.com/GMOD/bgzf-filehandle/actions/workflows/publish.yml)\n\nReads [block-gzipped (BGZF)](http://www.htslib.org/doc/bgzip.html) files, such\nas those created by bgzip, using coordinates from the uncompressed file.\n[@gmod/indexedfasta](https://github.com/GMOD/indexedfasta),\n[@gmod/bam](https://github.com/GMOD/bam-js) and\n[@gmod/tabix](https://github.com/GMOD/tabix-js) all read their BGZF through it.\n\nDecompression runs on [libdeflate](https://github.com/ebiggers/libdeflate),\ncompiled to WebAssembly and inlined in the bundle as base64, so there is no\n`.wasm` file to serve. On this repo's fixtures it inflates two to three times\nfaster than pako, and about twice as fast as the browser's own\n`DecompressionStream` — tables and reasoning, including\n[why not just use `DecompressionStream`](docs/optimizations.md#why-not-decompressionstream-for-everything),\nin [docs/optimizations.md](docs/optimizations.md).\n\n## Terms\n\nThe docs here lean on three words, and two of them mean something narrower than\nthey sound:\n\n- **BGZF block** — bgzip files are so called 'multi-member gzip files',\n  basically indepently compressed gzip blocks that are concatenated together.\n  https://www.htslib.org/doc/bgzip.html they are at most 64KB compressed, its\n  trailer recording its own uncompressed length. Blocks decode independently of\n  each other, enabling both random access and the worker pool. A bare \"block\"\n  always means this one, never a deflate block.\n- **Virtual offset** — `{blockPosition, dataPosition}`: which BGZF block, and\n  how far into that block's decompressed bytes.\n- **Chunk** — a range between two virtual offsets, `{minv, maxv}`; a BAM or\n  tabix index resolves a query to one or more chunks. A chunk covers a run of\n  consecutive BGZF blocks and usually starts and ends partway through the first\n  and last of them.\n\n## Install\n\n```sh\nnpm install @gmod/bgzf-filehandle\n```\n\n## BgzfFilehandle\n\nRead a bgzip-compressed file with a `.gzi` index as though it never was:\n\n```typescript\nimport { BgzfFilehandle } from '@gmod/bgzf-filehandle'\nimport { LocalFile } from 'generic-filehandle2'\n\nconst f = new BgzfFilehandle({\n  filehandle: new LocalFile('path/to/my_file.gz'),\n  gziFilehandle: new LocalFile('path/to/my_file.gz.gzi'),\n  blockConcurrency: 10, // concurrent range requests per read, default 10\n})\n\n// read(length, position) — matches generic-filehandle2\nconst data: Uint8Array = await f.read(300, 0)\n```\n\nCreate the index with `bgzip -i my_file`, or `bgzip -r my_file.gz` for an\nalready-compressed one. Everything a read touches arrives as one contiguous\nrange and inflates in one call.\n\nWhen the file is remote, pass\n[`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)\nas the filehandle. Each of those contiguous ranges is then cached in 256 KiB\nchunks, so a later read that overlaps one already fetched is served from memory\ninstead of the network.\n\n## unzip\n\nDecompress a BGZF or plain gzip buffer, falling back to plain gzip if the input\nis not BGZF:\n\n```typescript\nimport { unzip } from '@gmod/bgzf-filehandle'\n\nconst decompressed: Uint8Array = await unzip(compressedData)\n```\n\n## unzipChunkSlice\n\nDecompress a range of BGZF blocks and slice out a virtual offset range — what\nBAM and tabix readers do with a chunk from a BAI/TBI:\n\n```typescript\nimport { MAX_BGZF_BLOCK_SIZE, unzipChunkSlice } from '@gmod/bgzf-filehandle'\n\nconst minv = { blockPosition: 1234, dataPosition: 56 }\nconst maxv = { blockPosition: 9876, dataPosition: 78 }\n\n// input starts at minv.blockPosition and must run through the END of the block\n// at maxv.blockPosition. That block's compressed length is recorded nowhere, so\n// over-read by one maximum-size block to cover it\nconst compressedData = await filehandle.read(\n  maxv.blockPosition + MAX_BGZF_BLOCK_SIZE - minv.blockPosition,\n  minv.blockPosition,\n)\n\nconst { buffer, cpositions, dpositions } = await unzipChunkSlice(\n  compressedData,\n  { minv, maxv },\n)\n```\n\n`buffer` holds the decompressed bytes between the two offsets. `cpositions` and\n`dpositions` are `Float64Array` block boundaries in compressed and decompressed\ncoordinates, for generating stable feature IDs across chunk boundaries.\n\n## Worker pool\n\n`unzipChunkSlice` takes an optional pool that spreads a chunk's blocks across\nWeb Workers — close to linear to about four workers. Bytes cross as\n[transferable objects](https://developer.mozilla.org/en-US/docs/Web/API/Web_Workers_API/Transferable_objects)\nrather than copies, so the handoff costs the same whatever the size and needs no\ncross-origin isolation:\n\n```typescript\nimport { getSharedWorkerPool, unzipChunkSlice } from '@gmod/bgzf-filehandle'\n\nconst pool = await getSharedWorkerPool() // undefined if Workers are unavailable\nconst result = await unzipChunkSlice(compressedData, chunk, pool)\n```\n\nA chunk under 0.4MB inflated stays on the calling thread, where a worker costs\nmore than it returns, so a shared pool starts its workers only once a larger one\narrives. No read waits on them: a pool inflates on the calling thread while its\nworkers boot, and for good if one of them fails.\n\nSafe to pass unconditionally — `undefined` keeps the sequential wasm path, and\nreaders that take a pool of their own (`@gmod/bam`'s `bgzfWorkerPool`) accept\nthe same value. Worker counts, cross-thread sharing, lifecycle and driving a\npool directly: [docs/worker-pool.md](docs/worker-pool.md).\n\n## Docs\n\n- [docs/optimizations.md](docs/optimizations.md) — benchmark numbers, and what\n  we measured, kept and rejected\n- [docs/worker-pool.md](docs/worker-pool.md) — pool lifecycle, sizing, sharing,\n  and `scanBgzfBlocks`\n- [CONTRIBUTING.md](CONTRIBUTING.md) — development and release steps\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## License\n\nMIT © [Robert Buels](https://github.com/rbuels),\n[Colin Diesh](https://github.com/cmdcolin)\n","readmeFilename":"README.md"}