@gmod/bam 7.0.5 → 7.1.0

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Files changed (9) hide show
  1. package/CHANGELOG.md +5 -1
  2. package/dist/bamFile.d.ts +3 -2
  3. package/dist/bamFile.js +2 -9
  4. package/dist/bamFile.js.map +1 -1
  5. package/esm/bamFile.d.ts +3 -2
  6. package/esm/bamFile.js +2 -9
  7. package/esm/bamFile.js.map +1 -1
  8. package/package.json +6 -6
  9. package/src/bamFile.ts +4 -18
package/CHANGELOG.md CHANGED
@@ -1,6 +1,10 @@
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- ## [7.0.5](https://github.com/GMOD/bam-js/compare/v7.0.4...v7.0.5) (2025-11-27)
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+ # [7.1.0](https://github.com/GMOD/bam-js/compare/v7.0.6...v7.1.0) (2025-12-11)
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+
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+ ## [7.0.6](https://github.com/GMOD/bam-js/compare/v7.0.5...v7.0.6) (2025-11-28)
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+
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+ ## [7.0.5](https://github.com/GMOD/bam-js/compare/v7.0.4...v7.0.5) (2025-11-27)
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  ## [7.0.4](https://github.com/GMOD/bam-js/compare/v7.0.3...v7.0.4) (2025-11-24)
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package/dist/bamFile.d.ts CHANGED
@@ -19,6 +19,7 @@ export default class BamFile {
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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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+ bytesRead: number;
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  buffer: Uint8Array;
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  nextIn: number;
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  }>;
@@ -65,12 +66,12 @@ export default class BamFile {
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  chunk: Chunk;
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  opts: BaseOpts;
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  }): Promise<{
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- data: Uint8Array<ArrayBuffer>;
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+ data: Uint8Array<ArrayBufferLike>;
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  cpositions: number[];
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  dpositions: number[];
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  chunk: Chunk;
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  }>;
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- readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk, chrId?: number, min?: number, max?: number): Promise<BAMFeature[]>;
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+ readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
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  _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
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  hasRefSeq(seqName: string): Promise<boolean | undefined>;
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  lineCount(seqName: string): Promise<number>;
package/dist/bamFile.js CHANGED
@@ -153,7 +153,7 @@ class BamFile {
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  chunk,
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  opts,
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  });
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- const records = await this.readBamFeatures(data, cpositions, dpositions, chunk, chrId, min, max);
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+ const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
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  const recs = [];
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  for (const feature of records) {
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  if (feature.ref_id === chrId) {
@@ -243,14 +243,13 @@ class BamFile {
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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, chrId, min, max) {
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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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  const dataView = new DataView(ba.buffer);
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  const hasDpositions = dpositions.length > 0;
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  const hasCpositions = cpositions.length > 0;
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- const hasFilter = chrId !== undefined && min !== undefined && max !== undefined;
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  while (blockStart + 4 < ba.length) {
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  const blockSize = dataView.getInt32(blockStart, true);
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  const blockEnd = blockStart + 4 + blockSize - 1;
@@ -259,12 +258,6 @@ class BamFile {
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  pos--;
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  }
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  if (blockEnd < ba.length) {
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- if (hasFilter &&
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- blockStart + 12 < ba.length &&
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- !this._shouldIncludeFeature(dataView, blockStart, chrId, max)) {
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- blockStart = blockEnd + 1;
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- continue;
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- }
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  const feature = new record_ts_1.default({
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  bytes: {
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  byteArray: ba,
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bamFile.d.ts CHANGED
@@ -19,6 +19,7 @@ export default class BamFile {
19
19
  htsget: boolean;
20
20
  headerP?: ReturnType<BamFile['getHeaderPre']>;
21
21
  cache: QuickLRU<string, {
22
+ bytesRead: number;
22
23
  buffer: Uint8Array;
23
24
  nextIn: number;
24
25
  }>;
@@ -65,12 +66,12 @@ export default class BamFile {
65
66
  chunk: Chunk;
66
67
  opts: BaseOpts;
67
68
  }): Promise<{
68
- data: Uint8Array<ArrayBuffer>;
69
+ data: Uint8Array<ArrayBufferLike>;
69
70
  cpositions: number[];
70
71
  dpositions: number[];
71
72
  chunk: Chunk;
72
73
  }>;
73
- readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk, chrId?: number, min?: number, max?: number): Promise<BAMFeature[]>;
74
+ readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
74
75
  _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
75
76
  hasRefSeq(seqName: string): Promise<boolean | undefined>;
76
77
  lineCount(seqName: string): Promise<number>;
package/esm/bamFile.js CHANGED
@@ -147,7 +147,7 @@ export default class BamFile {
147
147
  chunk,
148
148
  opts,
149
149
  });
150
- const records = await this.readBamFeatures(data, cpositions, dpositions, chunk, chrId, min, max);
150
+ const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
151
151
  const recs = [];
152
152
  for (const feature of records) {
153
153
  if (feature.ref_id === chrId) {
@@ -237,14 +237,13 @@ export default class BamFile {
237
237
  const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk, this.cache);
238
238
  return { data, cpositions, dpositions, chunk };
239
239
  }
240
- async readBamFeatures(ba, cpositions, dpositions, chunk, chrId, min, max) {
240
+ async readBamFeatures(ba, cpositions, dpositions, chunk) {
241
241
  let blockStart = 0;
242
242
  const sink = [];
243
243
  let pos = 0;
244
244
  const dataView = new DataView(ba.buffer);
245
245
  const hasDpositions = dpositions.length > 0;
246
246
  const hasCpositions = cpositions.length > 0;
247
- const hasFilter = chrId !== undefined && min !== undefined && max !== undefined;
248
247
  while (blockStart + 4 < ba.length) {
249
248
  const blockSize = dataView.getInt32(blockStart, true);
250
249
  const blockEnd = blockStart + 4 + blockSize - 1;
@@ -253,12 +252,6 @@ export default class BamFile {
253
252
  pos--;
254
253
  }
255
254
  if (blockEnd < ba.length) {
256
- if (hasFilter &&
257
- blockStart + 12 < ba.length &&
258
- !this._shouldIncludeFeature(dataView, blockStart, chrId, max)) {
259
- blockStart = blockEnd + 1;
260
- continue;
261
- }
262
255
  const feature = new BAMFeature({
263
256
  bytes: {
264
257
  byteArray: ba,
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": "7.0.5",
3
+ "version": "7.1.0",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
@@ -50,23 +50,23 @@
50
50
  "genomics"
51
51
  ],
52
52
  "dependencies": {
53
- "@gmod/bgzf-filehandle": "^5.0.2",
53
+ "@gmod/bgzf-filehandle": "^6.0.3",
54
54
  "crc": "^4.3.2",
55
55
  "generic-filehandle2": "^2.0.1",
56
56
  "quick-lru": "^4.0.0"
57
57
  },
58
58
  "devDependencies": {
59
59
  "@types/node": "^24.10.0",
60
- "@vitest/coverage-v8": "^4.0.14",
60
+ "@vitest/coverage-v8": "^4.0.15",
61
61
  "eslint": "^9.9.0",
62
62
  "eslint-plugin-import": "^2.31.0",
63
63
  "eslint-plugin-unicorn": "^62.0.0",
64
- "prettier": "^3.3.3",
64
+ "prettier": "^3.7.4",
65
65
  "rimraf": "^6.1.2",
66
66
  "standard-changelog": "^7.0.1",
67
67
  "typescript": "^5.0.4",
68
- "typescript-eslint": "^8.48.0",
69
- "vitest": "^4.0.14"
68
+ "typescript-eslint": "^8.49.0",
69
+ "vitest": "^4.0.15"
70
70
  },
71
71
  "publishConfig": {
72
72
  "access": "public"
package/src/bamFile.ts CHANGED
@@ -27,7 +27,10 @@ export default class BamFile {
27
27
  public index?: BAI | CSI
28
28
  public htsget = false
29
29
  public headerP?: ReturnType<BamFile['getHeaderPre']>
30
- public cache = new QuickLRU<string, { buffer: Uint8Array; nextIn: number }>({
30
+ public cache = new QuickLRU<
31
+ string,
32
+ { bytesRead: number; buffer: Uint8Array; nextIn: number }
33
+ >({
31
34
  maxSize: 1000,
32
35
  })
33
36
 
@@ -227,9 +230,6 @@ export default class BamFile {
227
230
  cpositions,
228
231
  dpositions,
229
232
  chunk,
230
- chrId,
231
- min,
232
- max,
233
233
  )
234
234
 
235
235
  const recs = [] as BAMFeature[]
@@ -352,9 +352,6 @@ export default class BamFile {
352
352
  cpositions: number[],
353
353
  dpositions: number[],
354
354
  chunk: Chunk,
355
- chrId?: number,
356
- min?: number,
357
- max?: number,
358
355
  ) {
359
356
  let blockStart = 0
360
357
  const sink = [] as BAMFeature[]
@@ -363,8 +360,6 @@ export default class BamFile {
363
360
  const dataView = new DataView(ba.buffer)
364
361
  const hasDpositions = dpositions.length > 0
365
362
  const hasCpositions = cpositions.length > 0
366
- const hasFilter =
367
- chrId !== undefined && min !== undefined && max !== undefined
368
363
 
369
364
  while (blockStart + 4 < ba.length) {
370
365
  const blockSize = dataView.getInt32(blockStart, true)
@@ -376,15 +371,6 @@ export default class BamFile {
376
371
  }
377
372
 
378
373
  if (blockEnd < ba.length) {
379
- if (
380
- hasFilter &&
381
- blockStart + 12 < ba.length &&
382
- !this._shouldIncludeFeature(dataView, blockStart, chrId, max)
383
- ) {
384
- blockStart = blockEnd + 1
385
- continue
386
- }
387
-
388
374
  const feature = new BAMFeature({
389
375
  bytes: {
390
376
  byteArray: ba,