@gmod/bam 8.8.0 → 8.9.0

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Files changed (8) hide show
  1. package/dist/bamFile.d.ts +14 -0
  2. package/dist/bamFile.js +39 -7
  3. package/dist/bamFile.js.map +1 -1
  4. package/esm/bamFile.d.ts +14 -0
  5. package/esm/bamFile.js +39 -7
  6. package/esm/bamFile.js.map +1 -1
  7. package/package.json +2 -2
  8. package/src/bamFile.ts +54 -7
package/dist/bamFile.d.ts CHANGED
@@ -164,6 +164,20 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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  * has long since resolved. `undefined` (which is what that helper gives
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  * back under node, or anywhere Workers cannot be created) keeps the
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  * in-process path, so this is safe to pass unconditionally.
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+ *
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+ * **Holding a pool for the life of this object is fine, and deliberately
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+ * so.** It is stored here and awaited once per chunk read, which used to
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+ * mean four workers and their grow-only wasm heaps stayed up from the first
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+ * query until the page went away. As of `@gmod/bgzf-filehandle` 6.6.0 a
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+ * pool reaps its own workers after 3 minutes idle and spawns a fresh set on
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+ * the next call, and that is invisible from here — the pool object stays
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+ * valid throughout.
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+ *
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+ * Which is also why a caller must NOT try to reclaim it by calling
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+ * `destroySharedWorkerPool()` on an idle timer of its own: a destroyed pool
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+ * throws out of `decompressBlocks`, so every open `BamFile` still holding
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+ * one would fail its next read rather than fall back to inflating in
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+ * process. Reclaiming is the pool's job, not the consumer's.
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  */
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  bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
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  /**
package/dist/bamFile.js CHANGED
@@ -425,18 +425,50 @@ class BamFile {
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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(util_ts_1.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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+ // The stop, re-tested as each chunk lands rather than only once after the
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+ // first batch.
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+ //
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+ // WHAT MAKES THIS DETERMINISTIC is that past-ness is MONOTONE in chunk
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+ // index. `optimizeChunks` returns chunks sorted by `minv`, and a sorted
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+ // BAM's file order is its coordinate order, so if chunk i's first record
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+ // is past the query then every chunk after it is too. `stopIndex` is
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+ // therefore the smallest such index whatever order the reads finish in,
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+ // and no chunk below it is ever skipped — which is the property ADR 0010
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+ // requires. What timing still varies is the OVERSHOOT: a worker that had
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+ // already taken an index keeps it, so up to the pool width is fetched past
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+ // the stop. Those chunks contribute nothing to the result either way.
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+ //
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+ // Checking once was calibrated on fixtures where the stop, when there was
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+ // one, always fired inside the first batch. That holds while a query's own
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+ // data is 1-3 chunks and breaks when it is more than
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+ // MAX_CONCURRENT_CHUNK_READS of them: on a 300x BAM a 100kb window's data
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+ // is SEVEN chunks, so nothing in the first six is past the query and the
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+ // stop never fires. The query then reads 21 further chunks the BAI bin
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+ // hierarchy hands back from beyond it — 131-349 records each, not one of
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+ // them in range, 2.0MB and 21 round trips for nothing.
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+ //
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+ // A completed-PREFIX check was tried first and does not work here, for a
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+ // reason worth keeping: chunk 6 is 3.5MB and slow, so while it is in
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+ // flight the other five workers consume all 21 tiny tail chunks, and the
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+ // prefix is blocked at exactly the boundary that would have stopped it.
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+ // Measured: 28 requests, unchanged.
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+ let stopIndex = chunks.length;
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+ const noteStop = (ci) => {
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+ if (ci < stopIndex && isPastQuery(featureLists[ci], chrId, max)) {
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+ stopIndex = ci;
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  }
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+ };
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+ for (let ci = 0; ci < batch; ci++) {
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+ noteStop(ci);
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  }
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+ const stopped = stopIndex < chunks.length;
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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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+ while (next < stopIndex) {
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+ const ci = next++;
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+ await readOne(ci);
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+ noteStop(ci);
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  }
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  };
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  const workers = Math.min(util_ts_1.MAX_CONCURRENT_CHUNK_READS, chunks.length - batch);
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/bamFile.d.ts CHANGED
@@ -164,6 +164,20 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
164
164
  * has long since resolved. `undefined` (which is what that helper gives
165
165
  * back under node, or anywhere Workers cannot be created) keeps the
166
166
  * in-process path, so this is safe to pass unconditionally.
167
+ *
168
+ * **Holding a pool for the life of this object is fine, and deliberately
169
+ * so.** It is stored here and awaited once per chunk read, which used to
170
+ * mean four workers and their grow-only wasm heaps stayed up from the first
171
+ * query until the page went away. As of `@gmod/bgzf-filehandle` 6.6.0 a
172
+ * pool reaps its own workers after 3 minutes idle and spawns a fresh set on
173
+ * the next call, and that is invisible from here — the pool object stays
174
+ * valid throughout.
175
+ *
176
+ * Which is also why a caller must NOT try to reclaim it by calling
177
+ * `destroySharedWorkerPool()` on an idle timer of its own: a destroyed pool
178
+ * throws out of `decompressBlocks`, so every open `BamFile` still holding
179
+ * one would fail its next read rather than fall back to inflating in
180
+ * process. Reclaiming is the pool's job, not the consumer's.
167
181
  */
168
182
  bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
169
183
  /**
package/esm/bamFile.js CHANGED
@@ -419,18 +419,50 @@ export default class BamFile {
419
419
  // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
420
420
  const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
421
421
  await Promise.all(Array.from({ length: batch }, (_, ci) => readOne(ci)));
422
- let stopped = false;
423
- for (let ci = 0; ci < batch; ci++) {
424
- if (isPastQuery(featureLists[ci], chrId, max)) {
425
- stopped = true;
426
- break;
422
+ // The stop, re-tested as each chunk lands rather than only once after the
423
+ // first batch.
424
+ //
425
+ // WHAT MAKES THIS DETERMINISTIC is that past-ness is MONOTONE in chunk
426
+ // index. `optimizeChunks` returns chunks sorted by `minv`, and a sorted
427
+ // BAM's file order is its coordinate order, so if chunk i's first record
428
+ // is past the query then every chunk after it is too. `stopIndex` is
429
+ // therefore the smallest such index whatever order the reads finish in,
430
+ // and no chunk below it is ever skipped — which is the property ADR 0010
431
+ // requires. What timing still varies is the OVERSHOOT: a worker that had
432
+ // already taken an index keeps it, so up to the pool width is fetched past
433
+ // the stop. Those chunks contribute nothing to the result either way.
434
+ //
435
+ // Checking once was calibrated on fixtures where the stop, when there was
436
+ // one, always fired inside the first batch. That holds while a query's own
437
+ // data is 1-3 chunks and breaks when it is more than
438
+ // MAX_CONCURRENT_CHUNK_READS of them: on a 300x BAM a 100kb window's data
439
+ // is SEVEN chunks, so nothing in the first six is past the query and the
440
+ // stop never fires. The query then reads 21 further chunks the BAI bin
441
+ // hierarchy hands back from beyond it — 131-349 records each, not one of
442
+ // them in range, 2.0MB and 21 round trips for nothing.
443
+ //
444
+ // A completed-PREFIX check was tried first and does not work here, for a
445
+ // reason worth keeping: chunk 6 is 3.5MB and slow, so while it is in
446
+ // flight the other five workers consume all 21 tiny tail chunks, and the
447
+ // prefix is blocked at exactly the boundary that would have stopped it.
448
+ // Measured: 28 requests, unchanged.
449
+ let stopIndex = chunks.length;
450
+ const noteStop = (ci) => {
451
+ if (ci < stopIndex && isPastQuery(featureLists[ci], chrId, max)) {
452
+ stopIndex = ci;
427
453
  }
454
+ };
455
+ for (let ci = 0; ci < batch; ci++) {
456
+ noteStop(ci);
428
457
  }
458
+ const stopped = stopIndex < chunks.length;
429
459
  if (!stopped && chunks.length > batch) {
430
460
  let next = batch;
431
461
  const readNext = async () => {
432
- while (next < chunks.length) {
433
- await readOne(next++);
462
+ while (next < stopIndex) {
463
+ const ci = next++;
464
+ await readOne(ci);
465
+ noteStop(ci);
434
466
  }
435
467
  };
436
468
  const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length - batch);
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": "8.8.0",
3
+ "version": "8.9.0",
4
4
  "packageManager": "pnpm@11.15.1",
5
5
  "description": "Parser for BAM and BAM index (bai) files",
6
6
  "license": "MIT",
@@ -51,7 +51,7 @@
51
51
  "genomics"
52
52
  ],
53
53
  "dependencies": {
54
- "@gmod/bgzf-filehandle": "^6.4.0",
54
+ "@gmod/bgzf-filehandle": "^6.6.0",
55
55
  "@gmod/shared-read-cache": "^1.5.1",
56
56
  "@jbrowse/quick-lru": "^7.3.5",
57
57
  "crc": "^4.3.2",
package/src/bamFile.ts CHANGED
@@ -318,6 +318,20 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
318
318
  * has long since resolved. `undefined` (which is what that helper gives
319
319
  * back under node, or anywhere Workers cannot be created) keeps the
320
320
  * in-process path, so this is safe to pass unconditionally.
321
+ *
322
+ * **Holding a pool for the life of this object is fine, and deliberately
323
+ * so.** It is stored here and awaited once per chunk read, which used to
324
+ * mean four workers and their grow-only wasm heaps stayed up from the first
325
+ * query until the page went away. As of `@gmod/bgzf-filehandle` 6.6.0 a
326
+ * pool reaps its own workers after 3 minutes idle and spawns a fresh set on
327
+ * the next call, and that is invisible from here — the pool object stays
328
+ * valid throughout.
329
+ *
330
+ * Which is also why a caller must NOT try to reclaim it by calling
331
+ * `destroySharedWorkerPool()` on an idle timer of its own: a destroyed pool
332
+ * throws out of `decompressBlocks`, so every open `BamFile` still holding
333
+ * one would fail its next read rather than fall back to inflating in
334
+ * process. Reclaiming is the pool's job, not the consumer's.
321
335
  */
322
336
  bgzfWorkerPool?:
323
337
  BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined
@@ -723,19 +737,52 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
723
737
  // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
724
738
  const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length)
725
739
  await Promise.all(Array.from({ length: batch }, (_, ci) => readOne(ci)))
726
- let stopped = false
727
- for (let ci = 0; ci < batch; ci++) {
728
- if (isPastQuery(featureLists[ci], chrId, max)) {
729
- stopped = true
730
- break
740
+
741
+ // The stop, re-tested as each chunk lands rather than only once after the
742
+ // first batch.
743
+ //
744
+ // WHAT MAKES THIS DETERMINISTIC is that past-ness is MONOTONE in chunk
745
+ // index. `optimizeChunks` returns chunks sorted by `minv`, and a sorted
746
+ // BAM's file order is its coordinate order, so if chunk i's first record
747
+ // is past the query then every chunk after it is too. `stopIndex` is
748
+ // therefore the smallest such index whatever order the reads finish in,
749
+ // and no chunk below it is ever skipped — which is the property ADR 0010
750
+ // requires. What timing still varies is the OVERSHOOT: a worker that had
751
+ // already taken an index keeps it, so up to the pool width is fetched past
752
+ // the stop. Those chunks contribute nothing to the result either way.
753
+ //
754
+ // Checking once was calibrated on fixtures where the stop, when there was
755
+ // one, always fired inside the first batch. That holds while a query's own
756
+ // data is 1-3 chunks and breaks when it is more than
757
+ // MAX_CONCURRENT_CHUNK_READS of them: on a 300x BAM a 100kb window's data
758
+ // is SEVEN chunks, so nothing in the first six is past the query and the
759
+ // stop never fires. The query then reads 21 further chunks the BAI bin
760
+ // hierarchy hands back from beyond it — 131-349 records each, not one of
761
+ // them in range, 2.0MB and 21 round trips for nothing.
762
+ //
763
+ // A completed-PREFIX check was tried first and does not work here, for a
764
+ // reason worth keeping: chunk 6 is 3.5MB and slow, so while it is in
765
+ // flight the other five workers consume all 21 tiny tail chunks, and the
766
+ // prefix is blocked at exactly the boundary that would have stopped it.
767
+ // Measured: 28 requests, unchanged.
768
+ let stopIndex = chunks.length
769
+ const noteStop = (ci: number) => {
770
+ if (ci < stopIndex && isPastQuery(featureLists[ci], chrId, max)) {
771
+ stopIndex = ci
731
772
  }
732
773
  }
774
+ for (let ci = 0; ci < batch; ci++) {
775
+ noteStop(ci)
776
+ }
777
+ const stopped = stopIndex < chunks.length
733
778
 
734
779
  if (!stopped && chunks.length > batch) {
735
780
  let next = batch
736
781
  const readNext = async () => {
737
- while (next < chunks.length) {
738
- await readOne(next++)
782
+ while (next < stopIndex) {
783
+ const ci = next++
784
+ await readOne(ci)
785
+ noteStop(ci)
739
786
  }
740
787
  }
741
788
  const workers = Math.min(