@gmod/bam 8.11.0 → 8.11.1

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Files changed (7) hide show
  1. package/README.md +17 -0
  2. package/dist/bamFile.js +9 -7
  3. package/dist/bamFile.js.map +1 -1
  4. package/esm/bamFile.js +9 -7
  5. package/esm/bamFile.js.map +1 -1
  6. package/package.json +2 -2
  7. package/src/bamFile.ts +9 -7
package/README.md CHANGED
@@ -34,6 +34,23 @@ const bam = new BamFile({
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  })
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  ```
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+ Over HTTP it is worth putting
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+ [`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)
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+ underneath the filehandle. It caches what it reads in 256 KiB chunks and turns
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+ the chunks a read is missing into one request per contiguous run, so the
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+ scattered index and data reads a query makes arrive as a couple of fetches
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+ rather than dozens. `bamFilehandle` and `baiFilehandle` accept any
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+ generic-filehandle2 object, so it drops straight in:
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+
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+ ```typescript
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+ import { RemoteFileWithRangeCache } from '@gmod/range-cache-filehandle'
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+
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+ const bam = new BamFile({
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+ bamFilehandle: new RemoteFileWithRangeCache(url),
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+ baiFilehandle: new RemoteFileWithRangeCache(`${url}.bai`),
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+ })
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+ ```
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+
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  Records come back unfiltered, and overlapping queries share them — treat them as
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  read-only. Filter them yourself with the flag helpers and `getTag`, which
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  decodes one tag instead of all of them:
package/dist/bamFile.js CHANGED
@@ -573,13 +573,15 @@ class BamFile {
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  signal: opts.signal,
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  });
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  // The last chance to bail before the expensive part, and the reason it is
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- // worth having: honouring the signal is optional in the filehandle.
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- // `RemoteFile` hands it to `fetch`, but `LocalFile.read(length, position)`
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- // 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
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- // a fully abandoned chunk still gets inflated and decoded — measured at 6
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- // chunks for one 20kb query on out.bam — which is where an uncached query
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- // spends most of its time (ADR 0003), on records nobody will ever look at.
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+ // worth having: a filehandle can only honour the signal as far as its
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+ // transport allows. `RemoteFile` hands it to `fetch` and is cancelled
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+ // outright; `LocalFile` takes the signal and checks it either side of the
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+ // read, but node's fs has no signal on `FileHandle.read`, so the read
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+ // itself runs to completion whatever happens and arrives here with the
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+ // cancellation unnoticed. Without this a fully abandoned chunk still gets
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+ // inflated and decoded — measured at 6 chunks for one 20kb query on
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+ // out.bam — which is where an uncached query spends most of its time
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+ // (ADR 0003), on records nobody will ever look at.
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  //
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  // Safe precisely because this is the SHARED signal, not a caller's: it
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  // fires only once every waiter has given up, so there is never a live
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
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- 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package/esm/bamFile.js CHANGED
@@ -567,13 +567,15 @@ export default class BamFile {
567
567
  signal: opts.signal,
568
568
  });
569
569
  // The last chance to bail before the expensive part, and the reason it is
570
- // worth having: honouring the signal is optional in the filehandle.
571
- // `RemoteFile` hands it to `fetch`, but `LocalFile.read(length, position)`
572
- // does not even take an options argument, so every read under it runs to
573
- // completion and arrives here with the cancellation unnoticed. Without this
574
- // a fully abandoned chunk still gets inflated and decoded — measured at 6
575
- // chunks for one 20kb query on out.bam — which is where an uncached query
576
- // spends most of its time (ADR 0003), on records nobody will ever look at.
570
+ // worth having: a filehandle can only honour the signal as far as its
571
+ // transport allows. `RemoteFile` hands it to `fetch` and is cancelled
572
+ // outright; `LocalFile` takes the signal and checks it either side of the
573
+ // read, but node's fs has no signal on `FileHandle.read`, so the read
574
+ // itself runs to completion whatever happens and arrives here with the
575
+ // cancellation unnoticed. Without this a fully abandoned chunk still gets
576
+ // inflated and decoded — measured at 6 chunks for one 20kb query on
577
+ // out.bam — which is where an uncached query spends most of its time
578
+ // (ADR 0003), on records nobody will ever look at.
577
579
  //
578
580
  // Safe precisely because this is the SHARED signal, not a caller's: it
579
581
  // 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/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "8.11.0",
3
+ "version": "8.11.1",
4
4
  "packageManager": "pnpm@11.15.1",
5
5
  "description": "Parser for BAM and BAM index (bai) files",
6
6
  "license": "MIT",
@@ -52,7 +52,7 @@
52
52
  ],
53
53
  "dependencies": {
54
54
  "@gmod/bgzf-filehandle": "^6.6.0",
55
- "@gmod/shared-read-cache": "^1.5.1",
55
+ "@gmod/shared-read-cache": "^1.7.2",
56
56
  "@jbrowse/quick-lru": "^7.3.5",
57
57
  "crc": "^4.3.2",
58
58
  "generic-filehandle2": "^2.2.1"
package/src/bamFile.ts CHANGED
@@ -910,13 +910,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
910
910
  },
911
911
  )
912
912
  // The last chance to bail before the expensive part, and the reason it is
913
- // worth having: honouring the signal is optional in the filehandle.
914
- // `RemoteFile` hands it to `fetch`, but `LocalFile.read(length, position)`
915
- // does not even take an options argument, so every read under it runs to
916
- // completion and arrives here with the cancellation unnoticed. Without this
917
- // a fully abandoned chunk still gets inflated and decoded — measured at 6
918
- // chunks for one 20kb query on out.bam — which is where an uncached query
919
- // spends most of its time (ADR 0003), on records nobody will ever look at.
913
+ // worth having: a filehandle can only honour the signal as far as its
914
+ // transport allows. `RemoteFile` hands it to `fetch` and is cancelled
915
+ // outright; `LocalFile` takes the signal and checks it either side of the
916
+ // read, but node's fs has no signal on `FileHandle.read`, so the read
917
+ // itself runs to completion whatever happens and arrives here with the
918
+ // cancellation unnoticed. Without this a fully abandoned chunk still gets
919
+ // inflated and decoded — measured at 6 chunks for one 20kb query on
920
+ // out.bam — which is where an uncached query spends most of its time
921
+ // (ADR 0003), on records nobody will ever look at.
920
922
  //
921
923
  // Safe precisely because this is the SHARED signal, not a caller's: it
922
924
  // fires only once every waiter has given up, so there is never a live