@gmod/bam 6.0.4 → 6.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (17) hide show
  1. package/CHANGELOG.md +6 -2
  2. package/dist/bamFile.d.ts +5 -0
  3. package/dist/bamFile.js +8 -4
  4. package/dist/bamFile.js.map +1 -1
  5. package/dist/record.d.ts +1 -0
  6. package/dist/record.js +12 -0
  7. package/dist/record.js.map +1 -1
  8. package/esm/bamFile.d.ts +5 -0
  9. package/esm/bamFile.js +8 -4
  10. package/esm/bamFile.js.map +1 -1
  11. package/esm/record.d.ts +1 -0
  12. package/esm/record.js +12 -0
  13. package/esm/record.js.map +1 -1
  14. package/package.json +3 -2
  15. package/src/bamFile.ts +8 -4
  16. package/src/record.ts +16 -0
  17. package/dist/package.json +0 -1
package/CHANGELOG.md CHANGED
@@ -1,10 +1,14 @@
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- ## [6.0.4](https://github.com/GMOD/bam-js/compare/v6.0.3...v6.0.4) (2025-05-26)
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+ ## [6.1.1](https://github.com/GMOD/bam-js/compare/v6.1.0...v6.1.1) (2025-10-02)
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- ## [6.0.3](https://github.com/GMOD/bam-js/compare/v6.0.2...v6.0.3) (2025-05-13)
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+ # [6.1.0](https://github.com/GMOD/bam-js/compare/v6.0.4...v6.1.0) (2025-10-01)
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+
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+ ## [6.0.4](https://github.com/GMOD/bam-js/compare/v6.0.3...v6.0.4) (2025-05-26)
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+
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+ ## [6.0.3](https://github.com/GMOD/bam-js/compare/v6.0.2...v6.0.3) (2025-05-13)
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  ## [6.0.2](https://github.com/GMOD/bam-js/compare/v6.0.1...v6.0.2) (2025-04-30)
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package/dist/bamFile.d.ts CHANGED
@@ -1,3 +1,4 @@
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+ import QuickLRU from 'quick-lru';
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  import BAI from './bai.ts';
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  import Chunk from './chunk.ts';
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  import CSI from './csi.ts';
@@ -18,6 +19,10 @@ export default class BamFile {
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  index?: BAI | CSI;
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  htsget: boolean;
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  headerP?: ReturnType<BamFile['getHeaderPre']>;
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+ cache: QuickLRU<string, {
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+ buffer: Uint8Array;
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+ nextIn: number;
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+ }>;
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  constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
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  bamFilehandle?: GenericFilehandle;
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  bamPath?: string;
package/dist/bamFile.js CHANGED
@@ -7,6 +7,7 @@ exports.BAM_MAGIC = void 0;
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  const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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  const crc32_1 = __importDefault(require("crc/calculators/crc32"));
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  const generic_filehandle2_1 = require("generic-filehandle2");
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+ const quick_lru_1 = __importDefault(require("quick-lru"));
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  const bai_ts_1 = __importDefault(require("./bai.js"));
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  const csi_ts_1 = __importDefault(require("./csi.js"));
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  const nullFilehandle_ts_1 = __importDefault(require("./nullFilehandle.js"));
@@ -18,6 +19,9 @@ const blockLen = 1 << 16;
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  class BamFile {
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  constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
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  this.htsget = false;
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+ this.cache = new quick_lru_1.default({
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+ maxSize: 1000,
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+ });
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  this.renameRefSeq = renameRefSeqs;
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  if (bamFilehandle) {
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  this.bam = bamFilehandle;
@@ -250,14 +254,14 @@ class BamFile {
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  }
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  async _readChunk({ chunk, opts }) {
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  const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
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- const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
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+ const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk, this.cache);
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  return { data, cpositions, dpositions, chunk };
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  }
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  async readBamFeatures(ba, cpositions, dpositions, chunk) {
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  let blockStart = 0;
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  const sink = [];
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  let pos = 0;
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- let last = +Date.now();
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+ let last = Date.now();
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  const dataView = new DataView(ba.buffer);
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  while (blockStart + 4 < ba.length) {
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  const blockSize = dataView.getInt32(blockStart, true);
@@ -307,9 +311,9 @@ class BamFile {
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  (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0,
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  });
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  sink.push(feature);
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- if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
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+ if (this.yieldThreadTime && Date.now() - last > this.yieldThreadTime) {
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  await (0, util_ts_1.timeout)(1);
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- last = +Date.now();
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+ last = Date.now();
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  }
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  }
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  blockStart = blockEnd + 1;
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/record.d.ts CHANGED
@@ -68,6 +68,7 @@ export default class BamRecord {
68
68
  get next_refid(): number;
69
69
  get next_pos(): number;
70
70
  get template_length(): number;
71
+ seqAt(idx: number): string | undefined;
71
72
  toJSON(): Record<string, any>;
72
73
  }
73
74
  export {};
package/dist/record.js CHANGED
@@ -411,6 +411,18 @@ class BamRecord {
411
411
  get template_length() {
412
412
  return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 32, true);
413
413
  }
414
+ seqAt(idx) {
415
+ if (idx < this.seq_length) {
416
+ const byteIndex = idx >> 1;
417
+ const sb = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_ops * 4 + byteIndex];
418
+ return idx % 2 === 0
419
+ ? SEQRET_DECODER[(sb & 0xf0) >> 4]
420
+ : SEQRET_DECODER[sb & 0x0f];
421
+ }
422
+ else {
423
+ return undefined;
424
+ }
425
+ }
414
426
  toJSON() {
415
427
  const data = {};
416
428
  for (const k of Object.keys(this)) {
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bamFile.d.ts CHANGED
@@ -1,3 +1,4 @@
1
+ import QuickLRU from 'quick-lru';
1
2
  import BAI from './bai.ts';
2
3
  import Chunk from './chunk.ts';
3
4
  import CSI from './csi.ts';
@@ -18,6 +19,10 @@ export default class BamFile {
18
19
  index?: BAI | CSI;
19
20
  htsget: boolean;
20
21
  headerP?: ReturnType<BamFile['getHeaderPre']>;
22
+ cache: QuickLRU<string, {
23
+ buffer: Uint8Array;
24
+ nextIn: number;
25
+ }>;
21
26
  constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
22
27
  bamFilehandle?: GenericFilehandle;
23
28
  bamPath?: string;
package/esm/bamFile.js CHANGED
@@ -1,6 +1,7 @@
1
1
  import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
2
2
  import crc32 from 'crc/calculators/crc32';
3
3
  import { LocalFile, RemoteFile } from 'generic-filehandle2';
4
+ import QuickLRU from 'quick-lru';
4
5
  import BAI from "./bai.js";
5
6
  import CSI from "./csi.js";
6
7
  import NullFilehandle from "./nullFilehandle.js";
@@ -12,6 +13,9 @@ const blockLen = 1 << 16;
12
13
  export default class BamFile {
13
14
  constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
14
15
  this.htsget = false;
16
+ this.cache = new QuickLRU({
17
+ maxSize: 1000,
18
+ });
15
19
  this.renameRefSeq = renameRefSeqs;
16
20
  if (bamFilehandle) {
17
21
  this.bam = bamFilehandle;
@@ -244,14 +248,14 @@ export default class BamFile {
244
248
  }
245
249
  async _readChunk({ chunk, opts }) {
246
250
  const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
247
- const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
251
+ const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk, this.cache);
248
252
  return { data, cpositions, dpositions, chunk };
249
253
  }
250
254
  async readBamFeatures(ba, cpositions, dpositions, chunk) {
251
255
  let blockStart = 0;
252
256
  const sink = [];
253
257
  let pos = 0;
254
- let last = +Date.now();
258
+ let last = Date.now();
255
259
  const dataView = new DataView(ba.buffer);
256
260
  while (blockStart + 4 < ba.length) {
257
261
  const blockSize = dataView.getInt32(blockStart, true);
@@ -301,9 +305,9 @@ export default class BamFile {
301
305
  crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
302
306
  });
303
307
  sink.push(feature);
304
- if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
308
+ if (this.yieldThreadTime && Date.now() - last > this.yieldThreadTime) {
305
309
  await timeout(1);
306
- last = +Date.now();
310
+ last = Date.now();
307
311
  }
308
312
  }
309
313
  blockStart = blockEnd + 1;
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/record.d.ts CHANGED
@@ -68,6 +68,7 @@ export default class BamRecord {
68
68
  get next_refid(): number;
69
69
  get next_pos(): number;
70
70
  get template_length(): number;
71
+ seqAt(idx: number): string | undefined;
71
72
  toJSON(): Record<string, any>;
72
73
  }
73
74
  export {};
package/esm/record.js CHANGED
@@ -406,6 +406,18 @@ class BamRecord {
406
406
  get template_length() {
407
407
  return __classPrivateFieldGet(this, _BamRecord_dataView, "f").getInt32(this.bytes.start + 32, true);
408
408
  }
409
+ seqAt(idx) {
410
+ if (idx < this.seq_length) {
411
+ const byteIndex = idx >> 1;
412
+ const sb = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_ops * 4 + byteIndex];
413
+ return idx % 2 === 0
414
+ ? SEQRET_DECODER[(sb & 0xf0) >> 4]
415
+ : SEQRET_DECODER[sb & 0x0f];
416
+ }
417
+ else {
418
+ return undefined;
419
+ }
420
+ }
409
421
  toJSON() {
410
422
  const data = {};
411
423
  for (const k of Object.keys(this)) {
package/esm/record.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": "6.0.4",
3
+ "version": "6.1.1",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
@@ -31,6 +31,7 @@
31
31
  "test": "vitest",
32
32
  "lint": "eslint --report-unused-disable-directives --max-warnings 0",
33
33
  "clean": "rimraf dist esm",
34
+ "format": "prettier --write .",
34
35
  "build:esm": "tsc --outDir esm",
35
36
  "build:es5": "tsc --module commonjs --outDir dist",
36
37
  "build": "npm run build:esm && npm run build:es5",
@@ -58,7 +59,7 @@
58
59
  "@vitest/coverage-v8": "^3.0.9",
59
60
  "eslint": "^9.9.0",
60
61
  "eslint-plugin-import": "^2.31.0",
61
- "eslint-plugin-unicorn": "^59.0.0",
62
+ "eslint-plugin-unicorn": "^61.0.2",
62
63
  "prettier": "^3.3.3",
63
64
  "rimraf": "^6.0.1",
64
65
  "standard-changelog": "^7.0.1",
package/src/bamFile.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
2
2
  import crc32 from 'crc/calculators/crc32'
3
3
  import { LocalFile, RemoteFile } from 'generic-filehandle2'
4
+ import QuickLRU from 'quick-lru'
4
5
 
5
6
  import BAI from './bai.ts'
6
7
  import Chunk from './chunk.ts'
@@ -27,6 +28,9 @@ export default class BamFile {
27
28
  public index?: BAI | CSI
28
29
  public htsget = false
29
30
  public headerP?: ReturnType<BamFile['getHeaderPre']>
31
+ public cache = new QuickLRU<string, { buffer: Uint8Array; nextIn: number }>({
32
+ maxSize: 1000,
33
+ })
30
34
 
31
35
  constructor({
32
36
  bamFilehandle,
@@ -349,7 +353,7 @@ export default class BamFile {
349
353
  buffer: data,
350
354
  cpositions,
351
355
  dpositions,
352
- } = await unzipChunkSlice(buf, chunk)
356
+ } = await unzipChunkSlice(buf, chunk, this.cache)
353
357
  return { data, cpositions, dpositions, chunk }
354
358
  }
355
359
 
@@ -362,7 +366,7 @@ export default class BamFile {
362
366
  let blockStart = 0
363
367
  const sink = [] as BAMFeature[]
364
368
  let pos = 0
365
- let last = +Date.now()
369
+ let last = Date.now()
366
370
 
367
371
  const dataView = new DataView(ba.buffer)
368
372
  while (blockStart + 4 < ba.length) {
@@ -417,9 +421,9 @@ export default class BamFile {
417
421
  })
418
422
 
419
423
  sink.push(feature)
420
- if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
424
+ if (this.yieldThreadTime && Date.now() - last > this.yieldThreadTime) {
421
425
  await timeout(1)
422
- last = +Date.now()
426
+ last = Date.now()
423
427
  }
424
428
  }
425
429
 
package/src/record.ts CHANGED
@@ -438,6 +438,22 @@ export default class BamRecord {
438
438
  return this.#dataView.getInt32(this.bytes.start + 32, true)
439
439
  }
440
440
 
441
+ seqAt(idx: number): string | undefined {
442
+ if (idx < this.seq_length) {
443
+ const byteIndex = idx >> 1
444
+ const sb =
445
+ this.byteArray[
446
+ this.b0 + this.read_name_length + this.num_cigar_ops * 4 + byteIndex
447
+ ]!
448
+
449
+ return idx % 2 === 0
450
+ ? SEQRET_DECODER[(sb & 0xf0) >> 4]
451
+ : SEQRET_DECODER[sb & 0x0f]
452
+ } else {
453
+ return undefined
454
+ }
455
+ }
456
+
441
457
  toJSON() {
442
458
  const data: Record<string, any> = {}
443
459
  for (const k of Object.keys(this)) {
package/dist/package.json DELETED
@@ -1 +0,0 @@
1
- {"type": "commonjs"}