@gmod/bam 8.9.0 → 8.10.0

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Files changed (12) hide show
  1. package/README.md +66 -33
  2. package/dist/bamFile.d.ts +4 -3
  3. package/dist/bamFile.js +2 -2
  4. package/dist/bamFile.js.map +1 -1
  5. package/dist/index.d.ts +2 -0
  6. package/esm/bamFile.d.ts +4 -3
  7. package/esm/bamFile.js +2 -2
  8. package/esm/bamFile.js.map +1 -1
  9. package/esm/index.d.ts +2 -0
  10. package/package.json +1 -1
  11. package/src/bamFile.ts +6 -5
  12. package/src/index.ts +5 -0
package/README.md CHANGED
@@ -1,3 +1,5 @@
1
+ # @gmod/bam
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+
1
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  [![NPM version](https://img.shields.io/npm/v/@gmod/bam.svg?style=flat-square)](https://npmjs.org/package/@gmod/bam)
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  ![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bam-js/publish.yml?branch=main)
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@@ -20,9 +22,10 @@ const bam = new BamFile({ bamPath: 'test.bam' })
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  const records = await bam.getRecordsForRange('ctgA', 0, 50000)
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  ```
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- Coordinates are 0-based half-open (not the same as `samtools view` inputs).
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- `bamPath` reads a local file, so it is node-only; in the browser pass a URL or a
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- generic-filehandle2 filehandle instead:
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+ Coordinates are 0-based half-open, where `samtools view` takes 1-based closed —
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+ `ctgA:1-50000` there is `('ctgA', 0, 50000)` here. `bamPath` reads a local file,
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+ so it is node-only; in the browser pass a URL or a generic-filehandle2
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+ filehandle instead:
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  ```typescript
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  const bam = new BamFile({
@@ -45,39 +48,60 @@ const records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(
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  `record.getMismatches()` gives every difference between a read and the reference
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  — substitutions, insertions, deletions, reference skips and clips — without you
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- having to interpret `CIGAR` and `MD` yourself. There is a callback form,
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- `record.forEachMismatch(cb, opts?)`, which allocates nothing per difference and
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- takes a reference window to report within.
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-
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- Substitutions need either an `MD` tag on the read or the reference bases, and
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- most aligners leave `MD` off. `fetchReferenceSequence` is how you supply them:
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+ interpreting `CIGAR` and `MD` yourself:
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52
 
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  ```typescript
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  const bam = new BamFile({
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  bamPath: 'test.bam',
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- fetchReferenceSequence: async (refName, start, end) =>
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+ // reference bases for reads with no MD tag, at most one call per query
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+ fetchReferenceSequence: (refName, start, end) =>
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  myGenome.getSequence(refName, start, end),
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  })
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- // one sequence fetch for the whole query, and only if some read needs it
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- const records = await bam.getRecordsForRange('ctgA', 0, 50000)
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- records[0].getMismatches()
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- // [{ code: 88 /* 'X' */, refPos: 188, length: 1, bases: 'A', qual: 17,
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- // refBaseCode: 84 /* 'T' */, clipLength: 0 }, ...]
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+ for (const record of await bam.getRecordsForRange('ctgA', 0, 50000)) {
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+ // for a read at 100 with CIGAR 5M1I4M2D3M, SEQ ACGGTCAACGTTA, MD 3A5^GG3
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+ for (const { code, refPos, length, bases } of record.getMismatches()) {
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+ console.log(String.fromCharCode(code), refPos, length, bases)
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+ }
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+ }
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+ // X 103 1 G substitution to G, over a reference A
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+ // I 105 0 C one base inserted before 105
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+ // D 109 2 two reference bases deleted from 109
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  ```
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71
 
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- Without it, a read lacking `MD` still reports its indels and clips, but no
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- substitutions — nothing in the record says where they are. See
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- [docs/api.md](docs/api.md#mismatches) for the field meanings and for reads
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- longer than the region you are looking at.
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+ `code` is a CIGAR char code, to compare against the exported `MISMATCH_SUBST`,
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+ `MISMATCH_INSERTION`, … constants, and `record.forEachMismatch(cb, opts?)`
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+ reports the same set while allocating nothing per difference. What those two
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+ fields say, with that read walked through them:
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+ [docs/cigar-and-md.md](docs/cigar-and-md.md).
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+
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+ Substitutions need either an `MD` tag on the read or the reference bases, which
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+ is what `fetchReferenceSequence` is doing above — most aligners leave `MD` off,
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+ and it is called only if some read in the query needs it. Without it, a read
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+ lacking `MD` still reports its indels and clips but no substitutions — nothing
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+ in the record says where they are. [docs/api.md](docs/api.md#mismatches) has the
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+ field meanings, and what to do about reads that run past the region you are
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+ looking at.
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+
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+ ## How a query flows
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+
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+ A query turns the region into BGZF chunks through the index and decompresses
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+ each one in wasm. When nothing is cached yet, 70-90% of the time it takes to
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+ answer that query is spent decompressing. The rest is ordinary JS: records are
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+ views into their chunk's decompressed buffer, and their fields decode on access,
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+ so a query costs what you read off it. [docs/dataflow.md](docs/dataflow.md) has
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+ the diagram and walks it through.
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+
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+ Those decompressed chunks are then kept, so overlapping and adjacent queries
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+ reuse them instead of inflating again — up to 1GB per file, dropped after three
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+ idle minutes. A consumer holding one file per track should bound them together
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+ with a shared `cacheBudget` rather than shrinking each file's own ceiling:
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+ [docs/caching.md](docs/caching.md).
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  ## Decompressing on a worker pool
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- BGZF decompression is 70-90% of a cold query, and BGZF blocks are independently
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- inflatable. Hand `BamFile` a
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- [`@gmod/bgzf-filehandle`](https://github.com/GMOD/bgzf-filehandle) worker pool
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- and it inflates chunks there instead of on the calling thread — measured
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- 2.7-4.1x on the pool's own fixtures.
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+ BGZF blocks are independently inflatable, so that decompression can be spread
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+ across threads — measured 2.7-4.1x on the pool's own fixtures.
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  ```typescript
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  import { getSharedWorkerPool } from '@gmod/bgzf-filehandle'
@@ -89,11 +113,10 @@ const bam = new BamFile({
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  })
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  ```
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- No cross-origin isolation is needed. `getSharedWorkerPool()` gives back
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- `undefined` under node, or anywhere Workers cannot be created, which keeps the
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- in-process path — so this is safe to pass unconditionally. bam-js never creates
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- a pool on its own: the thread budget belongs to the consumer. For worker counts,
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- lifecycle and the pool's own benchmarks, see
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+ Safe to pass unconditionally: `getSharedWorkerPool()` is `undefined` under node,
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+ or anywhere Workers cannot be created, which keeps the in-process path. No
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+ cross-origin isolation needed. bam-js never creates a pool on its own — the
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+ thread budget belongs to the consumer. Worker counts, lifecycle and benchmarks:
97
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  [bgzf-filehandle's worker pool docs](https://github.com/GMOD/bgzf-filehandle/blob/main/docs/worker-pool.md).
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  ## Usage with htsget
@@ -108,9 +131,8 @@ const bam = new HtsgetFile({
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  const records = await bam.getRecordsForRange('1', 2000000, 2000001)
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132
  ```
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133
 
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- htsget fetches the server's range as-is, so `viewAsPairs`, `pairAcrossChr` and
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- `maxInsertSize` are ignored. For a server that requires authentication, pass a
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- `fetch` that adds the bearer token:
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+ htsget fetches the server's range as-is, so the mate-pairing options are
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+ ignored. Pass a `fetch` to add auth:
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136
 
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  ```typescript
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  const bam = new HtsgetFile({
@@ -124,7 +146,7 @@ const bam = new HtsgetFile({
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146
  })
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  ```
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148
 
127
- Your `fetch` is called for the ticket request _and_ for the data-block urls the
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+ That `fetch` is called for the ticket request _and_ for the data-block urls the
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  ticket points at, which may live on a third-party host — so only attach
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  credentials to hosts you trust.
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@@ -132,11 +154,22 @@ credentials to hosts you trust.
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154
 
133
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  - [docs/api.md](docs/api.md) — every constructor option, method and `BamRecord`
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156
  field, plus custom record classes
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+ - [docs/cigar-and-md.md](docs/cigar-and-md.md) — what `CIGAR` and `MD` say, and
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+ how mismatches are decoded from them
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+ - [docs/dataflow.md](docs/dataflow.md) — how a query flows, and where wasm sits
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+ - [docs/optimizations.md](docs/optimizations.md) — why each step of that path
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+ looks the way it does, and what measured it
135
162
  - [docs/caching.md](docs/caching.md) — sizing the parsed-chunk cache
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163
  - [agent-docs/adr/](agent-docs/adr/) — the measurements behind the performance
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164
  and caching decisions
138
165
  - [CONTRIBUTING.md](CONTRIBUTING.md) — development and release steps
139
166
 
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+ ## Academic Use
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+
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+ Written with [NHGRI](http://genome.gov) funding as part of
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+ [JBrowse](http://jbrowse.org). If you use this in a publication, please cite the
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+ most recent JBrowse paper at [jbrowse.org](http://jbrowse.org).
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+
140
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  ## License
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174
 
142
175
  MIT © [Colin Diesh](https://github.com/cmdcolin)
package/dist/bamFile.d.ts CHANGED
@@ -154,9 +154,10 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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  * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
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  * instead of inflating them on the calling thread.
156
156
  *
157
- * BGZF decompression is 70-90% of a cold query (ADR 0003), and BGZF blocks
158
- * are independently inflatable, so this is the one remaining lever of that
159
- * size. Measured 2.7-4.1x on the pool's own fixtures.
157
+ * Inflating the BGZF blocks is 70-90% of the wall clock of a query that
158
+ * finds nothing cached (ADR 0003), and BGZF blocks are independently
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+ * inflatable, so this is the one remaining lever of that size. Measured
160
+ * 2.7-4.1x on the pool's own fixtures.
160
161
  *
161
162
  * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
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163
  * so a caller whose own construction is synchronous can hand the pending
package/dist/bamFile.js CHANGED
@@ -584,8 +584,8 @@ class BamFile {
584
584
  // does not even take an options argument, so every read under it runs to
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  // completion and arrives here with the cancellation unnoticed. Without this
586
586
  // a fully abandoned chunk still gets inflated and decoded — measured at 6
587
- // chunks for one 20kb query on out.bam — which is the dominant cost of a
588
- // cold query (ADR 0003), spent on records nobody will ever look at.
587
+ // chunks for one 20kb query on out.bam — which is where an uncached query
588
+ // spends most of its time (ADR 0003), on records nobody will ever look at.
589
589
  //
590
590
  // Safe precisely because this is the SHARED signal, not a caller's: it
591
591
  // fires only once every waiter has given up, so there is never a live
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/index.d.ts CHANGED
@@ -11,4 +11,6 @@ export type { Mismatch, MismatchCallback, MismatchOptions, } from './mismatches.
11
11
  export type { PackedReference } from './reference.ts';
12
12
  export type { BamOpts, BaseOpts } from './util.ts';
13
13
  export type { IndexCovEntry } from './bai.ts';
14
+ export type { default as Chunk } from './chunk.ts';
15
+ export type { Offset, OffsetCoords } from './virtualOffset.ts';
14
16
  export type { Fetcher } from 'generic-filehandle2';
package/esm/bamFile.d.ts CHANGED
@@ -154,9 +154,10 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
154
154
  * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
155
155
  * instead of inflating them on the calling thread.
156
156
  *
157
- * BGZF decompression is 70-90% of a cold query (ADR 0003), and BGZF blocks
158
- * are independently inflatable, so this is the one remaining lever of that
159
- * size. Measured 2.7-4.1x on the pool's own fixtures.
157
+ * Inflating the BGZF blocks is 70-90% of the wall clock of a query that
158
+ * finds nothing cached (ADR 0003), and BGZF blocks are independently
159
+ * inflatable, so this is the one remaining lever of that size. Measured
160
+ * 2.7-4.1x on the pool's own fixtures.
160
161
  *
161
162
  * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
162
163
  * so a caller whose own construction is synchronous can hand the pending
package/esm/bamFile.js CHANGED
@@ -578,8 +578,8 @@ export default class BamFile {
578
578
  // does not even take an options argument, so every read under it runs to
579
579
  // completion and arrives here with the cancellation unnoticed. Without this
580
580
  // a fully abandoned chunk still gets inflated and decoded — measured at 6
581
- // chunks for one 20kb query on out.bam — which is the dominant cost of a
582
- // cold query (ADR 0003), spent on records nobody will ever look at.
581
+ // chunks for one 20kb query on out.bam — which is where an uncached query
582
+ // spends most of its time (ADR 0003), on records nobody will ever look at.
583
583
  //
584
584
  // Safe precisely because this is the SHARED signal, not a caller's: it
585
585
  // fires only once every waiter has given up, so there is never a live
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/index.d.ts CHANGED
@@ -11,4 +11,6 @@ export type { Mismatch, MismatchCallback, MismatchOptions, } from './mismatches.
11
11
  export type { PackedReference } from './reference.ts';
12
12
  export type { BamOpts, BaseOpts } from './util.ts';
13
13
  export type { IndexCovEntry } from './bai.ts';
14
+ export type { default as Chunk } from './chunk.ts';
15
+ export type { Offset, OffsetCoords } from './virtualOffset.ts';
14
16
  export type { Fetcher } from 'generic-filehandle2';
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "8.9.0",
3
+ "version": "8.10.0",
4
4
  "packageManager": "pnpm@11.15.1",
5
5
  "description": "Parser for BAM and BAM index (bai) files",
6
6
  "license": "MIT",
package/src/bamFile.ts CHANGED
@@ -308,9 +308,10 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
308
308
  * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
309
309
  * instead of inflating them on the calling thread.
310
310
  *
311
- * BGZF decompression is 70-90% of a cold query (ADR 0003), and BGZF blocks
312
- * are independently inflatable, so this is the one remaining lever of that
313
- * size. Measured 2.7-4.1x on the pool's own fixtures.
311
+ * Inflating the BGZF blocks is 70-90% of the wall clock of a query that
312
+ * finds nothing cached (ADR 0003), and BGZF blocks are independently
313
+ * inflatable, so this is the one remaining lever of that size. Measured
314
+ * 2.7-4.1x on the pool's own fixtures.
314
315
  *
315
316
  * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
316
317
  * so a caller whose own construction is synchronous can hand the pending
@@ -926,8 +927,8 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
926
927
  // does not even take an options argument, so every read under it runs to
927
928
  // completion and arrives here with the cancellation unnoticed. Without this
928
929
  // a fully abandoned chunk still gets inflated and decoded — measured at 6
929
- // chunks for one 20kb query on out.bam — which is the dominant cost of a
930
- // cold query (ADR 0003), spent on records nobody will ever look at.
930
+ // chunks for one 20kb query on out.bam — which is where an uncached query
931
+ // spends most of its time (ADR 0003), on records nobody will ever look at.
931
932
  //
932
933
  // Safe precisely because this is the SHARED signal, not a caller's: it
933
934
  // fires only once every waiter has given up, so there is never a live
package/src/index.ts CHANGED
@@ -47,5 +47,10 @@ export type { PackedReference } from './reference.ts'
47
47
  // getRecordsForRange/indexCov can only name these if they come out of here.
48
48
  export type { BamOpts, BaseOpts } from './util.ts'
49
49
  export type { IndexCovEntry } from './bai.ts'
50
+ // `blocksForRange` hands these back, so a caller sizing or describing a query
51
+ // off them needs to be able to name them. Type-only: chunks come out of the
52
+ // index, and nothing outside builds one.
53
+ export type { default as Chunk } from './chunk.ts'
54
+ export type { Offset, OffsetCoords } from './virtualOffset.ts'
50
55
  // for typing the HtsgetFile `fetch` option
51
56
  export type { Fetcher } from 'generic-filehandle2'