@gmod/bam 8.4.1 → 8.5.0

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Files changed (8) hide show
  1. package/dist/bamFile.d.ts +20 -1
  2. package/dist/bamFile.js +9 -2
  3. package/dist/bamFile.js.map +1 -1
  4. package/esm/bamFile.d.ts +20 -1
  5. package/esm/bamFile.js +9 -2
  6. package/esm/bamFile.js.map +1 -1
  7. package/package.json +3 -3
  8. package/src/bamFile.ts +29 -1
package/dist/bamFile.d.ts CHANGED
@@ -4,6 +4,7 @@ import CSI from './csi.ts';
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  import BAMFeature from './record.ts';
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  import type Chunk from './chunk.ts';
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  import type { BamOpts, BaseOpts } from './util.ts';
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+ import type { BgzfWorkerPool } from '@gmod/bgzf-filehandle';
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  import type { SharedBudget } from '@gmod/shared-read-cache';
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  import type { GenericFilehandle } from 'generic-filehandle2';
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  export interface BamRecordLike {
@@ -43,7 +44,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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  private headerCache;
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  chunkFeatureCache: SharedReadCache<Chunk, ChunkEntry<T>>;
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  private RecordClass;
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- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, cacheBudget, }: {
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+ /** see the constructor option of the same name */
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+ private bgzfWorkerPool?;
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+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, cacheBudget, bgzfWorkerPool, }: {
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  bamFilehandle?: GenericFilehandle;
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  bamPath?: string;
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  bamUrl?: string;
@@ -116,6 +119,22 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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  * space to the one being panned.
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  */
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  cacheBudget?: SharedBudget;
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+ /**
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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.
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+ *
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+ * BGZF decompression is 70-90% of a cold query (ADR 0003), and BGZF blocks
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+ * are independently inflatable, so this is the one remaining lever of that
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+ * size. Measured 2.7-4.1x on the pool's own fixtures.
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+ *
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+ * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
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+ * so a caller whose own construction is synchronous can hand the pending
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+ * pool straight over — it is awaited at the point of use, by which time it
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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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+ bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
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  });
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  getHeaderPre(opts?: BaseOpts): Promise<{
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  tag: string;
package/dist/bamFile.js CHANGED
@@ -110,8 +110,11 @@ class BamFile {
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  // than racing to decompress it twice.
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  chunkFeatureCache;
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  RecordClass;
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- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, cacheIdleTimeoutMs = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS, cacheBudget, }) {
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+ /** see the constructor option of the same name */
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+ bgzfWorkerPool;
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+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, cacheIdleTimeoutMs = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS, cacheBudget, bgzfWorkerPool, }) {
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  this.renameRefSeq = renameRefSeqs;
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+ this.bgzfWorkerPool = bgzfWorkerPool;
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  this.RecordClass = (recordClass ?? record_ts_1.default);
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  this.chunkFeatureCache = new shared_read_cache_1.SharedReadCache({
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  maxSize: maxCacheBytes,
@@ -466,7 +469,11 @@ class BamFile {
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  // caller left to be denied the result. @gmod/cram checks in the same place
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  // and for the same reason, before the decode loop in `_fetchRecords`.
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  (0, util_ts_1.throwIfAborted)(opts.signal);
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- const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
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+ // Awaited rather than stored resolved: the pool is commonly handed over
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+ // as the pending promise from getSharedWorkerPool(), and awaiting an
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+ // already-settled promise costs a microtask.
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+ const pool = await this.bgzfWorkerPool;
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+ const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk, pool);
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  return {
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  features: this.readBamFeatures(data, cpositions, dpositions, chunk),
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  bytes: data.byteLength,
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
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1
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package/esm/bamFile.d.ts CHANGED
@@ -4,6 +4,7 @@ import CSI from './csi.ts';
4
4
  import BAMFeature from './record.ts';
5
5
  import type Chunk from './chunk.ts';
6
6
  import type { BamOpts, BaseOpts } from './util.ts';
7
+ import type { BgzfWorkerPool } from '@gmod/bgzf-filehandle';
7
8
  import type { SharedBudget } from '@gmod/shared-read-cache';
8
9
  import type { GenericFilehandle } from 'generic-filehandle2';
9
10
  export interface BamRecordLike {
@@ -43,7 +44,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
43
44
  private headerCache;
44
45
  chunkFeatureCache: SharedReadCache<Chunk, ChunkEntry<T>>;
45
46
  private RecordClass;
46
- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, cacheBudget, }: {
47
+ /** see the constructor option of the same name */
48
+ private bgzfWorkerPool?;
49
+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, cacheBudget, bgzfWorkerPool, }: {
47
50
  bamFilehandle?: GenericFilehandle;
48
51
  bamPath?: string;
49
52
  bamUrl?: string;
@@ -116,6 +119,22 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
116
119
  * space to the one being panned.
117
120
  */
118
121
  cacheBudget?: SharedBudget;
122
+ /**
123
+ * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
124
+ * instead of inflating them on the calling thread.
125
+ *
126
+ * BGZF decompression is 70-90% of a cold query (ADR 0003), and BGZF blocks
127
+ * are independently inflatable, so this is the one remaining lever of that
128
+ * size. Measured 2.7-4.1x on the pool's own fixtures.
129
+ *
130
+ * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
131
+ * so a caller whose own construction is synchronous can hand the pending
132
+ * pool straight over — it is awaited at the point of use, by which time it
133
+ * has long since resolved. `undefined` (which is what that helper gives
134
+ * back under node, or anywhere Workers cannot be created) keeps the
135
+ * in-process path, so this is safe to pass unconditionally.
136
+ */
137
+ bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
119
138
  });
120
139
  getHeaderPre(opts?: BaseOpts): Promise<{
121
140
  tag: string;
package/esm/bamFile.js CHANGED
@@ -104,8 +104,11 @@ export default class BamFile {
104
104
  // than racing to decompress it twice.
105
105
  chunkFeatureCache;
106
106
  RecordClass;
107
- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, cacheIdleTimeoutMs = DEFAULT_CACHE_IDLE_TIMEOUT_MS, cacheBudget, }) {
107
+ /** see the constructor option of the same name */
108
+ bgzfWorkerPool;
109
+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, cacheIdleTimeoutMs = DEFAULT_CACHE_IDLE_TIMEOUT_MS, cacheBudget, bgzfWorkerPool, }) {
108
110
  this.renameRefSeq = renameRefSeqs;
111
+ this.bgzfWorkerPool = bgzfWorkerPool;
109
112
  this.RecordClass = (recordClass ?? BAMFeature);
110
113
  this.chunkFeatureCache = new SharedReadCache({
111
114
  maxSize: maxCacheBytes,
@@ -460,7 +463,11 @@ export default class BamFile {
460
463
  // caller left to be denied the result. @gmod/cram checks in the same place
461
464
  // and for the same reason, before the decode loop in `_fetchRecords`.
462
465
  throwIfAborted(opts.signal);
463
- const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
466
+ // Awaited rather than stored resolved: the pool is commonly handed over
467
+ // as the pending promise from getSharedWorkerPool(), and awaiting an
468
+ // already-settled promise costs a microtask.
469
+ const pool = await this.bgzfWorkerPool;
470
+ const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk, pool);
464
471
  return {
465
472
  features: this.readBamFeatures(data, cpositions, dpositions, chunk),
466
473
  bytes: data.byteLength,
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": "8.4.1",
3
+ "version": "8.5.0",
4
4
  "packageManager": "pnpm@11.15.1",
5
5
  "description": "Parser for BAM and BAM index (bai) files",
6
6
  "license": "MIT",
@@ -51,8 +51,8 @@
51
51
  "genomics"
52
52
  ],
53
53
  "dependencies": {
54
- "@gmod/bgzf-filehandle": "^6.3.2",
55
- "@gmod/shared-read-cache": "^1.5.0",
54
+ "@gmod/bgzf-filehandle": "^6.4.0",
55
+ "@gmod/shared-read-cache": "^1.5.1",
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
@@ -17,6 +17,7 @@ import {
17
17
 
18
18
  import type Chunk from './chunk.ts'
19
19
  import type { BamOpts, BaseOpts } from './util.ts'
20
+ import type { BgzfWorkerPool } from '@gmod/bgzf-filehandle'
20
21
  import type { SharedBudget } from '@gmod/shared-read-cache'
21
22
  import type { GenericFilehandle } from 'generic-filehandle2'
22
23
 
@@ -169,6 +170,10 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
169
170
 
170
171
  private RecordClass: BamRecordClass<T>
171
172
 
173
+ /** see the constructor option of the same name */
174
+ private bgzfWorkerPool?:
175
+ BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined
176
+
172
177
  constructor({
173
178
  bamFilehandle,
174
179
  bamPath,
@@ -185,6 +190,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
185
190
  maxCacheBytes = DEFAULT_MAX_CACHE_BYTES,
186
191
  cacheIdleTimeoutMs = DEFAULT_CACHE_IDLE_TIMEOUT_MS,
187
192
  cacheBudget,
193
+ bgzfWorkerPool,
188
194
  }: {
189
195
  bamFilehandle?: GenericFilehandle
190
196
  bamPath?: string
@@ -258,8 +264,26 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
258
264
  * space to the one being panned.
259
265
  */
260
266
  cacheBudget?: SharedBudget
267
+ /**
268
+ * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
269
+ * instead of inflating them on the calling thread.
270
+ *
271
+ * BGZF decompression is 70-90% of a cold query (ADR 0003), and BGZF blocks
272
+ * are independently inflatable, so this is the one remaining lever of that
273
+ * size. Measured 2.7-4.1x on the pool's own fixtures.
274
+ *
275
+ * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
276
+ * so a caller whose own construction is synchronous can hand the pending
277
+ * pool straight over — it is awaited at the point of use, by which time it
278
+ * has long since resolved. `undefined` (which is what that helper gives
279
+ * back under node, or anywhere Workers cannot be created) keeps the
280
+ * in-process path, so this is safe to pass unconditionally.
281
+ */
282
+ bgzfWorkerPool?:
283
+ BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined
261
284
  }) {
262
285
  this.renameRefSeq = renameRefSeqs
286
+ this.bgzfWorkerPool = bgzfWorkerPool
263
287
  this.RecordClass = (recordClass ?? BAMFeature) as BamRecordClass<T>
264
288
  this.chunkFeatureCache = new SharedReadCache<Chunk, ChunkEntry<T>>({
265
289
  maxSize: maxCacheBytes,
@@ -687,11 +711,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
687
711
  // and for the same reason, before the decode loop in `_fetchRecords`.
688
712
  throwIfAborted(opts.signal)
689
713
 
714
+ // Awaited rather than stored resolved: the pool is commonly handed over
715
+ // as the pending promise from getSharedWorkerPool(), and awaiting an
716
+ // already-settled promise costs a microtask.
717
+ const pool = await this.bgzfWorkerPool
690
718
  const {
691
719
  buffer: data,
692
720
  cpositions,
693
721
  dpositions,
694
- } = await unzipChunkSlice(buf, chunk)
722
+ } = await unzipChunkSlice(buf, chunk, pool)
695
723
  return {
696
724
  features: this.readBamFeatures(data, cpositions, dpositions, chunk),
697
725
  bytes: data.byteLength,