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ctgA:1-50000`\nconst records = await bam.getRecordsForRange('ctgA', 0, 50000)\n```\n\nCoordinates are 0-based half-open, where `samtools view` takes 1-based closed —\n`ctgA:1-50000` there is `('ctgA', 0, 50000)` here. `bamPath` reads a local file,\nso it is node-only; in the browser pass a URL or a generic-filehandle2\nfilehandle instead:\n\n```typescript\nconst bam = new BamFile({\n  bamUrl: 'https://example.com/yourfile.bam',\n  baiUrl: 'https://example.com/yourfile.bam.bai',\n})\n```\n\nOver HTTP it is worth putting\n[`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)\nunderneath the filehandle. A query fetches the index once, then reads the\nrecords as a handful of byte ranges spread through the BAM —\n[this visualizer](https://cmdcolin.github.io/bam_index_visualizer) draws that\npattern for a file of your choosing. The cache serves those ranges out of 256\nKiB chunks, so neighboring ranges share a request and later queries reuse what\nis already fetched. `bamFilehandle` and `baiFilehandle` accept any\ngeneric-filehandle2 object, so it drops straight in:\n\n```typescript\nimport { RemoteFileWithRangeCache } from '@gmod/range-cache-filehandle'\n\nconst bam = new BamFile({\n  bamFilehandle: new RemoteFileWithRangeCache(url),\n  baiFilehandle: new RemoteFileWithRangeCache(`${url}.bai`),\n})\n```\n\nRecords come back unfiltered, and overlapping queries share them — treat them as\nread-only. Filter them yourself with the flag helpers and `getTag`, which\ndecodes one tag instead of all of them:\n\n```typescript\nconst records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(\n  r => r.isProperlyPaired() && !r.isSecondary() && r.getTag('RG') === 'rg1',\n)\n```\n\n## Unsorted BAM\n\nA BAM that is unsorted, or still name-sorted as it came off the sequencer, has\nno index to query and so no `chr:start-end` to query it with. `streamBamRecords`\nwalks one end to end instead, a batch of records at a time:\n\n```typescript\nimport { streamBamRecords } from '@gmod/bam'\n\nfor await (const records of streamBamRecords({ bamUrl: 'unsorted.bam' })) {\n  for (const record of records) {\n    // ...\n  }\n}\n```\n\n`streamBamRecords` reads the file a window at a time rather than all at once, so\na 1GB BAM streams through in bounded memory. It is a standalone function rather\nthan a `BamFile` method, so that streaming alone leaves `BAI`/`CSI` and the\nchunk cache out of your bundle. See [docs/api.md](docs/api.md) for `onHeader`\nand the window size.\n\n## Mismatches\n\n`record.getMismatches()` gives every difference between a read and the reference\n— substitutions, insertions, deletions, reference skips and clips — without you\ninterpreting `CIGAR` and `MD` yourself:\n\n```typescript\nconst bam = new BamFile({\n  bamPath: 'test.bam',\n  // reference bases for reads with no MD tag, at most one call per query\n  fetchReferenceSequence: (refName, start, end) =>\n    myGenome.getSequence(refName, start, end),\n})\n\nfor (const record of await bam.getRecordsForRange('ctgA', 0, 50000)) {\n  // for a read at 100 with CIGAR 5M1I4M2D3M, SEQ ACGGTCAACGTTA, MD 3A5^GG3\n  for (const { code, refPos, length, bases } of record.getMismatches()) {\n    console.log(String.fromCharCode(code), refPos, length, bases)\n  }\n}\n// X 103 1 G   substitution to G, over a reference A\n// I 105 0 C   one base inserted before 105\n// D 109 2     two reference bases deleted from 109\n```\n\n`code` is a CIGAR char code, to compare against the exported `MISMATCH_SUBST`,\n`MISMATCH_INSERTION`, … constants, and `record.forEachMismatch(cb, opts?)`\nreports the same set while allocating nothing per difference. What the two\nfields mean, with that read walked through them:\n[docs/cigar-and-md.md](docs/cigar-and-md.md).\n\nSubstitutions need either an `MD` tag on the read or the reference bases, which\n`fetchReferenceSequence` supplies above — most aligners leave `MD` off, and a\nquery calls it only when one of its reads needs it. Without it, `getMismatches`\nstill returns indels and clips for a read lacking `MD`, but no substitutions —\nthe record does not contain their positions.\n[docs/api.md](docs/api.md#mismatches) has the field meanings, and what to do\nabout reads that run past the region you are looking at.\n\n## How a query flows\n\nA query turns the region into BGZF chunks through the index and decompresses\neach one in wasm. With nothing cached yet, decompression takes 70-90% of the\ntime that query needs. The rest is ordinary JS: records are views into their\nchunk's decompressed buffer, and their fields decode on access, so a query costs\nwhat you read off it. [docs/dataflow.md](docs/dataflow.md) has the diagram and\nwalks it through.\n\nThe file then holds on to those decompressed chunks, so overlapping and adjacent\nqueries reuse them instead of inflating again — up to 1GB per file, dropped\nafter three idle minutes. A consumer holding one file per track should bound\nthem together with a shared `cacheBudget` rather than shrinking each file's own\nceiling: [docs/caching.md](docs/caching.md).\n\n## Decompressing on a worker pool\n\nBGZF blocks inflate independently, so that decompression can spread across\nthreads — measured 2.7-4.1x on the pool's own fixtures.\n\n```typescript\nimport { getSharedWorkerPool } from '@gmod/bgzf-filehandle'\n\nconst bam = new BamFile({\n  bamUrl: 'https://example.com/yourfile.bam',\n  // the pending promise is fine — it is awaited at the point of use\n  bgzfWorkerPool: getSharedWorkerPool(),\n})\n```\n\nSafe to pass unconditionally: `getSharedWorkerPool()` returns `undefined` under\nnode, or anywhere the host forbids Workers, which keeps the in-process path. No\ncross-origin isolation needed. bam-js never creates a pool on its own — the\nconsumer controls the thread budget. Worker counts, lifecycle and benchmarks:\n[bgzf-filehandle's worker pool docs](https://github.com/GMOD/bgzf-filehandle/blob/main/docs/worker-pool.md).\n\n## Usage with htsget\n\n```typescript\nimport { HtsgetFile } from '@gmod/bam'\n\nconst bam = new HtsgetFile({\n  baseUrl: 'http://htsnexus.rnd.dnanex.us/v1/reads',\n  trackId: 'BroadHiSeqX_b37/NA12878',\n})\nconst records = await bam.getRecordsForRange('1', 2000000, 2000001)\n```\n\nhtsget fetches the server's range as-is, so it ignores the mate-pairing options.\nPass a `fetch` to add auth:\n\n```typescript\nconst bam = new HtsgetFile({\n  baseUrl: 'https://htsget.example.com/reads',\n  trackId: 'NA12878',\n  fetch: (url, init) => {\n    const headers = new Headers(init?.headers)\n    headers.set('authorization', `Bearer ${token}`)\n    return fetch(url, { ...init, headers })\n  },\n})\n```\n\nThe `fetch` you pass makes both the ticket request and the data-block requests\nthe ticket points at, and those data-block URLs may be on a third-party host —\nso only attach credentials to hosts you trust.\n\n## Docs\n\n- [docs/api.md](docs/api.md) — every constructor option, method and `BamRecord`\n  field, plus custom record classes\n- [docs/cigar-and-md.md](docs/cigar-and-md.md) — what `CIGAR` and `MD` mean, and\n  how the walk reads mismatches out of them\n- [docs/dataflow.md](docs/dataflow.md) — how a query flows, and where wasm sits\n- [docs/optimizations.md](docs/optimizations.md) — why each step of that path\n  looks the way it does, and what measured it\n- [docs/caching.md](docs/caching.md) — sizing the parsed-chunk cache\n- [agent-docs/adr/](agent-docs/adr/) — the measurements behind the performance\n  and caching decisions\n- [CONTRIBUTING.md](CONTRIBUTING.md) — development and release steps\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"}