@gmod/bam 8.8.1 → 8.9.0

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Files changed (6) hide show
  1. package/dist/bamFile.js +39 -7
  2. package/dist/bamFile.js.map +1 -1
  3. package/esm/bamFile.js +39 -7
  4. package/esm/bamFile.js.map +1 -1
  5. package/package.json +1 -1
  6. package/src/bamFile.ts +40 -7
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 @@
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- 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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": "8.8.1",
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",
package/src/bamFile.ts CHANGED
@@ -737,19 +737,52 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
737
737
  // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
738
738
  const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length)
739
739
  await Promise.all(Array.from({ length: batch }, (_, ci) => readOne(ci)))
740
- let stopped = false
741
- for (let ci = 0; ci < batch; ci++) {
742
- if (isPastQuery(featureLists[ci], chrId, max)) {
743
- stopped = true
744
- 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
745
772
  }
746
773
  }
774
+ for (let ci = 0; ci < batch; ci++) {
775
+ noteStop(ci)
776
+ }
777
+ const stopped = stopIndex < chunks.length
747
778
 
748
779
  if (!stopped && chunks.length > batch) {
749
780
  let next = batch
750
781
  const readNext = async () => {
751
- while (next < chunks.length) {
752
- await readOne(next++)
782
+ while (next < stopIndex) {
783
+ const ci = next++
784
+ await readOne(ci)
785
+ noteStop(ci)
753
786
  }
754
787
  }
755
788
  const workers = Math.min(