@gmod/bam 7.1.6 → 7.1.8

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Files changed (17) hide show
  1. package/CHANGELOG.md +8 -0
  2. package/README.md +32 -4
  3. package/dist/bamFile.d.ts +1 -2
  4. package/dist/bamFile.js +2 -7
  5. package/dist/bamFile.js.map +1 -1
  6. package/dist/record.d.ts +0 -1
  7. package/dist/record.js +0 -3
  8. package/dist/record.js.map +1 -1
  9. package/esm/bamFile.d.ts +1 -2
  10. package/esm/bamFile.js +2 -7
  11. package/esm/bamFile.js.map +1 -1
  12. package/esm/record.d.ts +0 -1
  13. package/esm/record.js +0 -3
  14. package/esm/record.js.map +1 -1
  15. package/package.json +1 -1
  16. package/src/bamFile.ts +3 -14
  17. package/src/record.ts +0 -4
package/CHANGELOG.md CHANGED
@@ -1,3 +1,11 @@
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+ ## [7.1.8](https://github.com/GMOD/bam-js/compare/v7.1.7...v7.1.8) (2025-12-13)
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+
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+
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+
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+ ## [7.1.7](https://github.com/GMOD/bam-js/compare/v7.1.6...v7.1.7) (2025-12-13)
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+
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+
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+
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  ## [7.1.6](https://github.com/GMOD/bam-js/compare/v7.1.5...v7.1.6) (2025-12-13)
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package/README.md CHANGED
@@ -70,10 +70,8 @@ The BAM class constructor accepts arguments
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  - `csiPath`/`csiUrl`/`csiFilehandle` - a CSI index for the BAM file, required
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  for long chromosomes greater than 2^29 in length
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  - `baiPath`/`baiUrl`/`baiFilehandle` - a BAI index for the BAM file
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- - `cacheSize` - limit on number of chunks to cache. default: 50
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- - `yieldThreadTime` - the interval at which the code yields to the main thread
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- when it is parsing a lot of data. default: 100ms. Set to 0 to performed no
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- yielding
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+ - `recordClass` - a custom class extending BamRecord to use for records (see
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+ Custom BamRecord class section below)
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  Note: filehandles implement the Filehandle interface from
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  https://www.npmjs.com/package/generic-filehandle2.
@@ -145,6 +143,7 @@ Returns whether we have this refName in the sample
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  ```typescript
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  // Core alignment fields
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+ record.fileOffset // "file offset" based id -- not a true file offset
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  record.ref_id // numerical sequence id from SAM header
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  record.start // 0-based start coordinate
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  record.end // 0-based end coordinate
@@ -186,6 +185,35 @@ record.seqAt(idx) // get single base at position
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  record.toJSON() // serialize record
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  ```
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+ ### Custom BamRecord class
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+
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+ You can provide your own BamRecord class to add custom properties or methods:
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+
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+ ```typescript
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+ import { BamFile, BamRecord } from '@gmod/bam'
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+
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+ class CustomBamRecord extends BamRecord {
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+ get customProperty() {
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+ return `custom-${this.name}`
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+ }
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+
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+ getDoubleStart() {
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+ return this.start * 2
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+ }
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+ }
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+
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+ const bam = new BamFile<CustomBamRecord>({
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+ bamPath: 'test.bam',
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+ recordClass: CustomBamRecord,
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+ })
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+
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+ await bam.getHeader()
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+ const records = await bam.getRecordsForRange('ctgA', 0, 50000)
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+ // records are typed as CustomBamRecord[]
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+ console.log(records[0].customProperty)
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+ console.log(records[0].getDoubleStart())
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+ ```
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+
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  ## License
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  MIT © [Colin Diesh](https://github.com/cmdcolin)
package/dist/bamFile.d.ts CHANGED
@@ -11,7 +11,7 @@ export interface BamRecordLike {
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  start: number;
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  end: number;
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  name: string;
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- id: number;
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+ fileOffset: number;
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  next_pos: number;
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  next_refid: number;
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  }
@@ -96,7 +96,6 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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  chunk: Chunk;
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  }>;
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  readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<T[]>;
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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>;
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  indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
package/dist/bamFile.js CHANGED
@@ -233,7 +233,7 @@ class BamFile {
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  const readNames = {};
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  for (const element of ret) {
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  const name = element.name;
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- const id = element.id;
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+ const id = element.fileOffset;
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  if (!readNames[name]) {
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  readNames[name] = 0;
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  }
@@ -277,7 +277,7 @@ class BamFile {
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  });
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  const mateRecs = [];
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  for (const feature of await this.readBamFeatures(data, cpositions, dpositions, chunk)) {
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- if (unmatedPairs[feature.name] && !readIds[feature.id]) {
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+ if (unmatedPairs[feature.name] && !readIds[feature.fileOffset]) {
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  mateRecs.push(feature);
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  }
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  }
@@ -324,11 +324,6 @@ class BamFile {
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  }
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  return sink;
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  }
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- _shouldIncludeFeature(dataView, blockStart, chrId, max) {
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- const ref_id = dataView.getInt32(blockStart + 4, true);
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- const start = dataView.getInt32(blockStart + 8, true);
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- return ref_id === chrId && start < max;
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- }
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  async hasRefSeq(seqName) {
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  const seqId = this.chrToIndex?.[seqName];
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  return seqId === undefined ? false : this.index?.hasRefSeq(seqId);
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
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package/dist/record.d.ts CHANGED
@@ -24,7 +24,6 @@ export default class BamRecord {
24
24
  get ref_id(): number;
25
25
  get start(): number;
26
26
  get end(): number;
27
- get id(): number;
28
27
  get mq(): number | undefined;
29
28
  get score(): number | undefined;
30
29
  get qual(): Uint8Array<ArrayBufferLike> | null;
package/dist/record.js CHANGED
@@ -37,9 +37,6 @@ class BamRecord {
37
37
  get end() {
38
38
  return this.start + this.length_on_ref;
39
39
  }
40
- get id() {
41
- return this.fileOffset;
42
- }
43
40
  get mq() {
44
41
  const mq = (this.bin_mq_nl & 0xff00) >> 8;
45
42
  return mq === 255 ? undefined : mq;
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bamFile.d.ts CHANGED
@@ -11,7 +11,7 @@ export interface BamRecordLike {
11
11
  start: number;
12
12
  end: number;
13
13
  name: string;
14
- id: number;
14
+ fileOffset: number;
15
15
  next_pos: number;
16
16
  next_refid: number;
17
17
  }
@@ -96,7 +96,6 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
96
96
  chunk: Chunk;
97
97
  }>;
98
98
  readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<T[]>;
99
- _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
100
99
  hasRefSeq(seqName: string): Promise<boolean | undefined>;
101
100
  lineCount(seqName: string): Promise<number>;
102
101
  indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
package/esm/bamFile.js CHANGED
@@ -227,7 +227,7 @@ export default class BamFile {
227
227
  const readNames = {};
228
228
  for (const element of ret) {
229
229
  const name = element.name;
230
- const id = element.id;
230
+ const id = element.fileOffset;
231
231
  if (!readNames[name]) {
232
232
  readNames[name] = 0;
233
233
  }
@@ -271,7 +271,7 @@ export default class BamFile {
271
271
  });
272
272
  const mateRecs = [];
273
273
  for (const feature of await this.readBamFeatures(data, cpositions, dpositions, chunk)) {
274
- if (unmatedPairs[feature.name] && !readIds[feature.id]) {
274
+ if (unmatedPairs[feature.name] && !readIds[feature.fileOffset]) {
275
275
  mateRecs.push(feature);
276
276
  }
277
277
  }
@@ -318,11 +318,6 @@ export default class BamFile {
318
318
  }
319
319
  return sink;
320
320
  }
321
- _shouldIncludeFeature(dataView, blockStart, chrId, max) {
322
- const ref_id = dataView.getInt32(blockStart + 4, true);
323
- const start = dataView.getInt32(blockStart + 8, true);
324
- return ref_id === chrId && start < max;
325
- }
326
321
  async hasRefSeq(seqName) {
327
322
  const seqId = this.chrToIndex?.[seqName];
328
323
  return seqId === undefined ? false : this.index?.hasRefSeq(seqId);
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/record.d.ts CHANGED
@@ -24,7 +24,6 @@ export default class BamRecord {
24
24
  get ref_id(): number;
25
25
  get start(): number;
26
26
  get end(): number;
27
- get id(): number;
28
27
  get mq(): number | undefined;
29
28
  get score(): number | undefined;
30
29
  get qual(): Uint8Array<ArrayBufferLike> | null;
package/esm/record.js CHANGED
@@ -32,9 +32,6 @@ export default class BamRecord {
32
32
  get end() {
33
33
  return this.start + this.length_on_ref;
34
34
  }
35
- get id() {
36
- return this.fileOffset;
37
- }
38
35
  get mq() {
39
36
  const mq = (this.bin_mq_nl & 0xff00) >> 8;
40
37
  return mq === 255 ? undefined : mq;
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": "7.1.6",
3
+ "version": "7.1.8",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
package/src/bamFile.ts CHANGED
@@ -20,7 +20,7 @@ export interface BamRecordLike {
20
20
  start: number
21
21
  end: number
22
22
  name: string
23
- id: number
23
+ fileOffset: number
24
24
  next_pos: number
25
25
  next_refid: number
26
26
  }
@@ -347,7 +347,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
347
347
  const readNames: Record<string, number> = {}
348
348
  for (const element of ret) {
349
349
  const name = element.name
350
- const id = element.id
350
+ const id = element.fileOffset
351
351
  if (!readNames[name]) {
352
352
  readNames[name] = 0
353
353
  }
@@ -404,7 +404,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
404
404
  dpositions,
405
405
  chunk,
406
406
  )) {
407
- if (unmatedPairs[feature.name] && !readIds[feature.id]) {
407
+ if (unmatedPairs[feature.name] && !readIds[feature.fileOffset]) {
408
408
  mateRecs.push(feature)
409
409
  }
410
410
  }
@@ -475,17 +475,6 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
475
475
  return sink
476
476
  }
477
477
 
478
- _shouldIncludeFeature(
479
- dataView: DataView,
480
- blockStart: number,
481
- chrId: number,
482
- max: number,
483
- ) {
484
- const ref_id = dataView.getInt32(blockStart + 4, true)
485
- const start = dataView.getInt32(blockStart + 8, true)
486
- return ref_id === chrId && start < max
487
- }
488
-
489
478
  async hasRefSeq(seqName: string) {
490
479
  const seqId = this.chrToIndex?.[seqName]
491
480
  return seqId === undefined ? false : this.index?.hasRefSeq(seqId)
package/src/record.ts CHANGED
@@ -66,10 +66,6 @@ export default class BamRecord {
66
66
  return this.start + this.length_on_ref
67
67
  }
68
68
 
69
- get id() {
70
- return this.fileOffset
71
- }
72
-
73
69
  get mq() {
74
70
  const mq = (this.bin_mq_nl & 0xff00) >> 8
75
71
  return mq === 255 ? undefined : mq