@gmod/bam 7.7.1 → 7.8.0

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Files changed (6) hide show
  1. package/dist/bamFile.js +71 -12
  2. package/dist/bamFile.js.map +1 -1
  3. package/esm/bamFile.js +71 -12
  4. package/esm/bamFile.js.map +1 -1
  5. package/package.json +1 -1
  6. package/src/bamFile.ts +85 -12
package/dist/bamFile.js CHANGED
@@ -24,6 +24,30 @@ function resolveFilehandle(filehandle, path, url) {
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  return (filehandle ??
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  (path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.RemoteFile(url) : undefined));
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  }
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+ /**
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+ * Whether a chunk's first record already lies past `chrId:..-max`, which means
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+ * every later chunk does too and none of them need to be read.
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+ *
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+ * Sound because of two orderings that already hold. `optimizeChunks` returns
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+ * chunks sorted by `minv.blockPosition`, and a coordinate-sorted BAM stores
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+ * records in (ref_id, start) order — so chunk i's first record is at or before
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+ * chunk i+1's, and a chunk whose first record is past the query has only
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+ * past-the-query records behind it.
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+ *
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+ * That coordinate-sorted assumption is not new: `appendInRange` already breaks
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+ * out of a chunk on exactly it. This applies the same rule one level up, so a
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+ * BAM that violates it was already returning short results before this existed.
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+ *
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+ * `first.ref_id > chrId` matters as much as the position: `optimizeChunks`
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+ * merges spans up to 5MB, which can carry a chunk across a reference boundary.
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+ *
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+ * An empty chunk says nothing about position, so it never stops the walk.
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+ */
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+ function isPastQuery(features, chrId, max) {
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+ const first = features?.[0];
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+ return (!!first &&
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+ (first.ref_id > chrId || (first.ref_id === chrId && first.start >= max)));
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+ }
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  function chunkCacheKey(chunk) {
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  const { minv, maxv } = chunk;
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  return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
@@ -313,25 +337,60 @@ class BamFile {
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  // ahead of decompression. Bounded because browsers cap concurrent
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  // connections per host anyway, and an unbounded fan-out would inflate
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  // every chunk of a whole-chromosome query at once.
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- let next = 0;
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- const readNext = async () => {
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- while (next < chunks.length) {
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- const ci = next++;
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- const chunk = chunks[ci];
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- featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
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- downloadedBytes += chunk.fetchedSize();
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- onProgress?.(downloadedBytes, totalBytes);
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- }
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+ const readOne = async (ci) => {
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+ const chunk = chunks[ci];
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+ featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
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+ downloadedBytes += chunk.fetchedSize();
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+ onProgress?.(downloadedBytes, totalBytes);
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  };
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- const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
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- await Promise.all(Array.from({ length: workers }, () => readNext()));
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+ // One barrier, after the first batch, then the pool for the rest.
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+ //
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+ // The barrier is what makes the early stop DETERMINISTIC: the batch is
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+ // chunks [0, MAX_CONCURRENT_CHUNK_READS), fixed by index rather than by
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+ // which read happens to finish first, so the decision cannot depend on
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+ // timing or on what the chunk cache already holds. An earlier attempt
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+ // checked the stop inside the pool instead, and a warm cache raced past
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+ // it — the same query read 6 chunks cold and 9 warm, so a repeat query
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+ // did MORE I/O than the first (ADR 0010).
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+ //
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+ // Only ONE barrier, rather than one per wave, because the stop — when
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+ // there is one — always fired inside the first batch on every fixture
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+ // measured (the first 1-3 chunks). A query that gets through the batch
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+ // without stopping is one that needs its chunks, so it runs the
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+ // unbarriered pool exactly as before. That caps the cost of being wrong
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+ // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
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+ const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
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+ await Promise.all(Array.from({ length: batch }, (_, ci) => readOne(ci)));
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+ let stopped = false;
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+ for (let ci = 0; ci < batch; ci++) {
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+ if (isPastQuery(featureLists[ci], chrId, max)) {
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+ stopped = true;
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+ break;
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+ }
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+ }
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+ if (!stopped && chunks.length > batch) {
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+ let next = batch;
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+ const readNext = async () => {
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+ while (next < chunks.length) {
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+ await readOne(next++);
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+ }
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+ };
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+ const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length - batch);
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+ await Promise.all(Array.from({ length: workers }, () => readNext()));
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+ }
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+ // A determinate bar must still reach its total after an early stop.
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+ onProgress?.(totalBytes, totalBytes);
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  }
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  // Append in chunk order, not completion order, so the result is the same
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  // sequence a sequential walk produced. (That is not coordinate order — bins
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  // at different levels cover overlapping spans — but it is what every caller
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  // has always been handed.)
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  for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
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- (0, util_ts_1.appendInRange)(featureLists[ci], chrId, min, max, result);
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+ // undefined for chunks the early stop skipped
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+ const features = featureLists[ci];
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+ if (features) {
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+ (0, util_ts_1.appendInRange)(features, chrId, min, max, result);
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+ }
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  }
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  if (viewAsPairs) {
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  const pairs = await this.fetchPairs(chrId, result, opts);
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/bamFile.js CHANGED
@@ -18,6 +18,30 @@ function resolveFilehandle(filehandle, path, url) {
18
18
  return (filehandle ??
19
19
  (path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));
20
20
  }
21
+ /**
22
+ * Whether a chunk's first record already lies past `chrId:..-max`, which means
23
+ * every later chunk does too and none of them need to be read.
24
+ *
25
+ * Sound because of two orderings that already hold. `optimizeChunks` returns
26
+ * chunks sorted by `minv.blockPosition`, and a coordinate-sorted BAM stores
27
+ * records in (ref_id, start) order — so chunk i's first record is at or before
28
+ * chunk i+1's, and a chunk whose first record is past the query has only
29
+ * past-the-query records behind it.
30
+ *
31
+ * That coordinate-sorted assumption is not new: `appendInRange` already breaks
32
+ * out of a chunk on exactly it. This applies the same rule one level up, so a
33
+ * BAM that violates it was already returning short results before this existed.
34
+ *
35
+ * `first.ref_id > chrId` matters as much as the position: `optimizeChunks`
36
+ * merges spans up to 5MB, which can carry a chunk across a reference boundary.
37
+ *
38
+ * An empty chunk says nothing about position, so it never stops the walk.
39
+ */
40
+ function isPastQuery(features, chrId, max) {
41
+ const first = features?.[0];
42
+ return (!!first &&
43
+ (first.ref_id > chrId || (first.ref_id === chrId && first.start >= max)));
44
+ }
21
45
  function chunkCacheKey(chunk) {
22
46
  const { minv, maxv } = chunk;
23
47
  return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
@@ -307,25 +331,60 @@ export default class BamFile {
307
331
  // ahead of decompression. Bounded because browsers cap concurrent
308
332
  // connections per host anyway, and an unbounded fan-out would inflate
309
333
  // every chunk of a whole-chromosome query at once.
310
- let next = 0;
311
- const readNext = async () => {
312
- while (next < chunks.length) {
313
- const ci = next++;
314
- const chunk = chunks[ci];
315
- featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
316
- downloadedBytes += chunk.fetchedSize();
317
- onProgress?.(downloadedBytes, totalBytes);
318
- }
334
+ const readOne = async (ci) => {
335
+ const chunk = chunks[ci];
336
+ featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
337
+ downloadedBytes += chunk.fetchedSize();
338
+ onProgress?.(downloadedBytes, totalBytes);
319
339
  };
320
- const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
321
- await Promise.all(Array.from({ length: workers }, () => readNext()));
340
+ // One barrier, after the first batch, then the pool for the rest.
341
+ //
342
+ // The barrier is what makes the early stop DETERMINISTIC: the batch is
343
+ // chunks [0, MAX_CONCURRENT_CHUNK_READS), fixed by index rather than by
344
+ // which read happens to finish first, so the decision cannot depend on
345
+ // timing or on what the chunk cache already holds. An earlier attempt
346
+ // checked the stop inside the pool instead, and a warm cache raced past
347
+ // it — the same query read 6 chunks cold and 9 warm, so a repeat query
348
+ // did MORE I/O than the first (ADR 0010).
349
+ //
350
+ // Only ONE barrier, rather than one per wave, because the stop — when
351
+ // there is one — always fired inside the first batch on every fixture
352
+ // measured (the first 1-3 chunks). A query that gets through the batch
353
+ // without stopping is one that needs its chunks, so it runs the
354
+ // unbarriered pool exactly as before. That caps the cost of being wrong
355
+ // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
356
+ const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
357
+ await Promise.all(Array.from({ length: batch }, (_, ci) => readOne(ci)));
358
+ let stopped = false;
359
+ for (let ci = 0; ci < batch; ci++) {
360
+ if (isPastQuery(featureLists[ci], chrId, max)) {
361
+ stopped = true;
362
+ break;
363
+ }
364
+ }
365
+ if (!stopped && chunks.length > batch) {
366
+ let next = batch;
367
+ const readNext = async () => {
368
+ while (next < chunks.length) {
369
+ await readOne(next++);
370
+ }
371
+ };
372
+ const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length - batch);
373
+ await Promise.all(Array.from({ length: workers }, () => readNext()));
374
+ }
375
+ // A determinate bar must still reach its total after an early stop.
376
+ onProgress?.(totalBytes, totalBytes);
322
377
  }
323
378
  // Append in chunk order, not completion order, so the result is the same
324
379
  // sequence a sequential walk produced. (That is not coordinate order — bins
325
380
  // at different levels cover overlapping spans — but it is what every caller
326
381
  // has always been handed.)
327
382
  for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
328
- appendInRange(featureLists[ci], chrId, min, max, result);
383
+ // undefined for chunks the early stop skipped
384
+ const features = featureLists[ci];
385
+ if (features) {
386
+ appendInRange(features, chrId, min, max, result);
387
+ }
329
388
  }
330
389
  if (viewAsPairs) {
331
390
  const pairs = await this.fetchPairs(chrId, result, opts);
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "7.7.1",
3
+ "version": "7.8.0",
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
@@ -67,6 +67,37 @@ interface InFlightChunk<T> {
67
67
  signal?: AbortSignal
68
68
  }
69
69
 
70
+ /**
71
+ * Whether a chunk's first record already lies past `chrId:..-max`, which means
72
+ * every later chunk does too and none of them need to be read.
73
+ *
74
+ * Sound because of two orderings that already hold. `optimizeChunks` returns
75
+ * chunks sorted by `minv.blockPosition`, and a coordinate-sorted BAM stores
76
+ * records in (ref_id, start) order — so chunk i's first record is at or before
77
+ * chunk i+1's, and a chunk whose first record is past the query has only
78
+ * past-the-query records behind it.
79
+ *
80
+ * That coordinate-sorted assumption is not new: `appendInRange` already breaks
81
+ * out of a chunk on exactly it. This applies the same rule one level up, so a
82
+ * BAM that violates it was already returning short results before this existed.
83
+ *
84
+ * `first.ref_id > chrId` matters as much as the position: `optimizeChunks`
85
+ * merges spans up to 5MB, which can carry a chunk across a reference boundary.
86
+ *
87
+ * An empty chunk says nothing about position, so it never stops the walk.
88
+ */
89
+ function isPastQuery(
90
+ features: { ref_id: number; start: number }[] | undefined,
91
+ chrId: number,
92
+ max: number,
93
+ ) {
94
+ const first = features?.[0]
95
+ return (
96
+ !!first &&
97
+ (first.ref_id > chrId || (first.ref_id === chrId && first.start >= max))
98
+ )
99
+ }
100
+
70
101
  function chunkCacheKey(chunk: Chunk) {
71
102
  const { minv, maxv } = chunk
72
103
  return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`
@@ -428,7 +459,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
428
459
  let downloadedBytes = 0
429
460
  onProgress?.(0, totalBytes)
430
461
 
431
- const featureLists = new Array<T[]>(chunks.length)
462
+ const featureLists = new Array<T[] | undefined>(chunks.length)
432
463
  if (chunks.length === 1) {
433
464
  // Very common — most small files, and any query landing inside one bin.
434
465
  // Worth its own path: the pool below allocates a closure, a worker array
@@ -444,18 +475,56 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
444
475
  // ahead of decompression. Bounded because browsers cap concurrent
445
476
  // connections per host anyway, and an unbounded fan-out would inflate
446
477
  // every chunk of a whole-chromosome query at once.
447
- let next = 0
448
- const readNext = async () => {
449
- while (next < chunks.length) {
450
- const ci = next++
451
- const chunk = chunks[ci]!
452
- featureLists[ci] = await this._cachedChunkFeatures(chunk, opts)
453
- downloadedBytes += chunk.fetchedSize()
454
- onProgress?.(downloadedBytes, totalBytes)
478
+ const readOne = async (ci: number) => {
479
+ const chunk = chunks[ci]!
480
+ featureLists[ci] = await this._cachedChunkFeatures(chunk, opts)
481
+ downloadedBytes += chunk.fetchedSize()
482
+ onProgress?.(downloadedBytes, totalBytes)
483
+ }
484
+
485
+ // One barrier, after the first batch, then the pool for the rest.
486
+ //
487
+ // The barrier is what makes the early stop DETERMINISTIC: the batch is
488
+ // chunks [0, MAX_CONCURRENT_CHUNK_READS), fixed by index rather than by
489
+ // which read happens to finish first, so the decision cannot depend on
490
+ // timing or on what the chunk cache already holds. An earlier attempt
491
+ // checked the stop inside the pool instead, and a warm cache raced past
492
+ // it — the same query read 6 chunks cold and 9 warm, so a repeat query
493
+ // did MORE I/O than the first (ADR 0010).
494
+ //
495
+ // Only ONE barrier, rather than one per wave, because the stop — when
496
+ // there is one — always fired inside the first batch on every fixture
497
+ // measured (the first 1-3 chunks). A query that gets through the batch
498
+ // without stopping is one that needs its chunks, so it runs the
499
+ // unbarriered pool exactly as before. That caps the cost of being wrong
500
+ // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
501
+ const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length)
502
+ await Promise.all(
503
+ Array.from({ length: batch }, (_, ci) => readOne(ci)),
504
+ )
505
+ let stopped = false
506
+ for (let ci = 0; ci < batch; ci++) {
507
+ if (isPastQuery(featureLists[ci], chrId, max)) {
508
+ stopped = true
509
+ break
455
510
  }
456
511
  }
457
- const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length)
458
- await Promise.all(Array.from({ length: workers }, () => readNext()))
512
+
513
+ if (!stopped && chunks.length > batch) {
514
+ let next = batch
515
+ const readNext = async () => {
516
+ while (next < chunks.length) {
517
+ await readOne(next++)
518
+ }
519
+ }
520
+ const workers = Math.min(
521
+ MAX_CONCURRENT_CHUNK_READS,
522
+ chunks.length - batch,
523
+ )
524
+ await Promise.all(Array.from({ length: workers }, () => readNext()))
525
+ }
526
+ // A determinate bar must still reach its total after an early stop.
527
+ onProgress?.(totalBytes, totalBytes)
459
528
  }
460
529
 
461
530
  // Append in chunk order, not completion order, so the result is the same
@@ -463,7 +532,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
463
532
  // at different levels cover overlapping spans — but it is what every caller
464
533
  // has always been handed.)
465
534
  for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
466
- appendInRange(featureLists[ci]!, chrId, min, max, result)
535
+ // undefined for chunks the early stop skipped
536
+ const features = featureLists[ci]
537
+ if (features) {
538
+ appendInRange(features, chrId, min, max, result)
539
+ }
467
540
  }
468
541
 
469
542
  if (viewAsPairs) {