@gmod/bam 7.1.5 → 7.1.7

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Files changed (23) hide show
  1. package/CHANGELOG.md +7 -1
  2. package/README.md +69 -12
  3. package/dist/bamFile.d.ts +25 -9
  4. package/dist/bamFile.js +3 -2
  5. package/dist/bamFile.js.map +1 -1
  6. package/dist/index.d.ts +2 -2
  7. package/dist/index.js.map +1 -1
  8. package/dist/record.d.ts +2 -2
  9. package/dist/record.js +1 -1
  10. package/dist/record.js.map +1 -1
  11. package/esm/bamFile.d.ts +25 -9
  12. package/esm/bamFile.js +3 -2
  13. package/esm/bamFile.js.map +1 -1
  14. package/esm/index.d.ts +2 -2
  15. package/esm/index.js +1 -1
  16. package/esm/index.js.map +1 -1
  17. package/esm/record.d.ts +2 -2
  18. package/esm/record.js +1 -1
  19. package/esm/record.js.map +1 -1
  20. package/package.json +1 -1
  21. package/src/bamFile.ts +31 -10
  22. package/src/index.ts +6 -2
  23. package/src/record.ts +2 -2
package/CHANGELOG.md CHANGED
@@ -1,7 +1,13 @@
1
- ## [7.1.5](https://github.com/GMOD/bam-js/compare/v7.1.4...v7.1.5) (2025-12-13)
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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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+ ## [7.1.6](https://github.com/GMOD/bam-js/compare/v7.1.5...v7.1.6) (2025-12-13)
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+
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+ ## [7.1.5](https://github.com/GMOD/bam-js/compare/v7.1.4...v7.1.5) (2025-12-13)
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+
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  ## [7.1.4](https://github.com/GMOD/bam-js/compare/v7.1.3...v7.1.4) (2025-12-13)
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  ## [7.1.3](https://github.com/GMOD/bam-js/compare/v7.1.2...v7.1.3) (2025-12-12)
package/README.md CHANGED
@@ -141,21 +141,78 @@ refName not exist in sample
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  Returns whether we have this refName in the sample
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- ### Returned features
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+ ### BamRecord properties
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- Example
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+ ```typescript
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+ // Core alignment fields
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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
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+ record.name // QNAME
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+ record.seq // sequence string
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+ record.qual // Uint8Array of quality scores (null if unmapped)
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+ record.CIGAR // CIGAR string e.g. "50M2I48M"
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+ record.flags // SAM flags integer
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+ record.mq // mapping quality (undefined if 255)
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+ record.strand // 1 or -1
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+ record.template_length // TLEN
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+
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+ // Auxiliary data
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+ record.tags // object with all aux tags e.g. {MD: "100", NM: 0}
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+ record.NUMERIC_MD // MD tag as Uint8Array (for fast mismatch rendering)
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+ record.NUMERIC_CIGAR // Uint32Array of packed CIGAR operations
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+ record.NUMERIC_SEQ // Uint8Array of packed sequence (4-bit encoded)
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+
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+ // Mate info
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+ record.next_refid // mate reference id
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+ record.next_pos // mate position
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+
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+ // Flag methods
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+ record.isPaired()
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+ record.isProperlyPaired()
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+ record.isSegmentUnmapped()
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+ record.isMateUnmapped()
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+ record.isReverseComplemented()
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+ record.isMateReverseComplemented()
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+ record.isRead1()
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+ record.isRead2()
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+ record.isSecondary()
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+ record.isFailedQc()
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+ record.isDuplicate()
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+ record.isSupplementary()
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+
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+ // Utility
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+ record.seqAt(idx) // get single base at position
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+ record.toJSON() // serialize record
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+ ```
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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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192
 
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  ```typescript
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- feature.ref_id // numerical sequence id corresponding to position in the sam header
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- feature.start // 0-based half open start coordinate
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- feature.end // 0-based half open end coordinate
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- feature.name // QNAME
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- feature.seq // feature sequence
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- feature.qual // qualities
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- feature.CIGAR // CIGAR string
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- feature.tags // tags
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- feature.flags // flags
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- feature.template_length // TLEN
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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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217
 
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  ## License
package/dist/bamFile.d.ts CHANGED
@@ -3,10 +3,24 @@ import BAI from './bai.ts';
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  import Chunk from './chunk.ts';
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  import CSI from './csi.ts';
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  import BAMFeature from './record.ts';
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+ import type { Bytes } from './record.ts';
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  import type { BamOpts, BaseOpts } from './util.ts';
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  import type { GenericFilehandle } from 'generic-filehandle2';
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+ export interface BamRecordLike {
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+ ref_id: number;
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+ start: number;
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+ end: number;
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+ name: string;
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+ id: string;
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+ next_pos: number;
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+ next_refid: number;
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+ }
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+ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
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+ bytes: Bytes;
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+ fileOffset: number;
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+ }) => T;
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  export declare const BAM_MAGIC = 21840194;
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- export default class BamFile {
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+ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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  renameRefSeq: (a: string) => string;
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  bam: GenericFilehandle;
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  header?: string;
@@ -17,7 +31,7 @@ export default class BamFile {
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  }[];
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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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+ headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
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  cache: QuickLRU<string, {
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  bytesRead: number;
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  buffer: Uint8Array;
@@ -26,9 +40,10 @@ export default class BamFile {
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  chunkFeatureCache: QuickLRU<string, {
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  minBlock: number;
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  maxBlock: number;
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- features: BAMFeature[];
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+ features: T[];
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  }>;
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- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, }: {
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+ private RecordClass;
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+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
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  bamFilehandle?: GenericFilehandle;
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  bamPath?: string;
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  bamUrl?: string;
@@ -40,6 +55,7 @@ export default class BamFile {
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  csiUrl?: string;
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  renameRefSeqs?: (a: string) => string;
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  htsget?: boolean;
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+ recordClass?: BamRecordClass<T>;
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  });
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  getHeaderPre(origOpts?: BaseOpts): Promise<{
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  tag: string;
@@ -63,13 +79,13 @@ export default class BamFile {
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  length: number;
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80
  }[];
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  };
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- getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
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- streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
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+ getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
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+ streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
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  private chunkCacheKey;
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  private blocksOverlap;
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  private evictOverlappingChunks;
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- _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
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- fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
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+ _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
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+ fetchPairs(chrId: number, feats: T[][], opts: BamOpts): Promise<T[]>;
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  _readChunk({ chunk, opts }: {
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  chunk: Chunk;
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  opts: BaseOpts;
@@ -79,7 +95,7 @@ export default class BamFile {
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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): Promise<BAMFeature[]>;
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+ readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<T[]>;
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99
  _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
84
100
  hasRefSeq(seqName: string): Promise<boolean | undefined>;
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101
  lineCount(seqName: string): Promise<number>;
package/dist/bamFile.js CHANGED
@@ -17,7 +17,7 @@ const util_ts_1 = require("./util.js");
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  exports.BAM_MAGIC = 21840194;
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  const blockLen = 1 << 16;
19
19
  class BamFile {
20
- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, }) {
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+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
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21
  this.htsget = false;
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  this.cache = new quick_lru_1.default({
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  maxSize: 1000,
@@ -26,6 +26,7 @@ class BamFile {
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  // When a new chunk overlaps a cached chunk, we evict the cached one
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  this.chunkFeatureCache = new quick_lru_1.default({ maxSize: 100 });
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  this.renameRefSeq = renameRefSeqs;
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+ this.RecordClass = (recordClass ?? record_ts_1.default);
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30
  if (bamFilehandle) {
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  this.bam = bamFilehandle;
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  }
@@ -304,7 +305,7 @@ class BamFile {
304
305
  pos--;
305
306
  }
306
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  if (blockEnd < ba.length) {
307
- const feature = new record_ts_1.default({
308
+ const feature = new this.RecordClass({
308
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  bytes: {
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  byteArray: ba,
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  start: blockStart,
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/index.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  export { default as BAI } from './bai.ts';
2
- export { default as BamFile } from './bamFile.ts';
2
+ export { type BamRecordClass, type BamRecordLike, default as BamFile, } from './bamFile.ts';
3
3
  export { default as CSI } from './csi.ts';
4
- export { default as BamRecord } from './record.ts';
4
+ export { type Bytes, default as BamRecord } from './record.ts';
5
5
  export { default as HtsgetFile } from './htsget.ts';
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAAiD;AAAxC,sHAAA,OAAO,OAAW;AAC3B,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AADnB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAA8D;AAAzC,uHAAA,OAAO,OAAa;AACzC,yCAAmD;AAA1C,wHAAA,OAAO,OAAc"}
package/dist/record.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- interface Bytes {
1
+ export interface Bytes {
2
2
  start: number;
3
3
  end: number;
4
4
  byteArray: Uint8Array;
@@ -24,7 +24,7 @@ export default class BamRecord {
24
24
  get ref_id(): number;
25
25
  get start(): number;
26
26
  get end(): number;
27
- get id(): number;
27
+ get id(): string;
28
28
  get mq(): number | undefined;
29
29
  get score(): number | undefined;
30
30
  get qual(): Uint8Array<ArrayBufferLike> | null;
package/dist/record.js CHANGED
@@ -38,7 +38,7 @@ class BamRecord {
38
38
  return this.start + this.length_on_ref;
39
39
  }
40
40
  get id() {
41
- return this.fileOffset;
41
+ return `${this.fileOffset}`;
42
42
  }
43
43
  get mq() {
44
44
  const mq = (this.bin_mq_nl & 0xff00) >> 8;
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/bamFile.d.ts CHANGED
@@ -3,10 +3,24 @@ import BAI from './bai.ts';
3
3
  import Chunk from './chunk.ts';
4
4
  import CSI from './csi.ts';
5
5
  import BAMFeature from './record.ts';
6
+ import type { Bytes } from './record.ts';
6
7
  import type { BamOpts, BaseOpts } from './util.ts';
7
8
  import type { GenericFilehandle } from 'generic-filehandle2';
9
+ export interface BamRecordLike {
10
+ ref_id: number;
11
+ start: number;
12
+ end: number;
13
+ name: string;
14
+ id: string;
15
+ next_pos: number;
16
+ next_refid: number;
17
+ }
18
+ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
19
+ bytes: Bytes;
20
+ fileOffset: number;
21
+ }) => T;
8
22
  export declare const BAM_MAGIC = 21840194;
9
- export default class BamFile {
23
+ export default class BamFile<T extends BamRecordLike = BAMFeature> {
10
24
  renameRefSeq: (a: string) => string;
11
25
  bam: GenericFilehandle;
12
26
  header?: string;
@@ -17,7 +31,7 @@ export default class BamFile {
17
31
  }[];
18
32
  index?: BAI | CSI;
19
33
  htsget: boolean;
20
- headerP?: ReturnType<BamFile['getHeaderPre']>;
34
+ headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
21
35
  cache: QuickLRU<string, {
22
36
  bytesRead: number;
23
37
  buffer: Uint8Array;
@@ -26,9 +40,10 @@ export default class BamFile {
26
40
  chunkFeatureCache: QuickLRU<string, {
27
41
  minBlock: number;
28
42
  maxBlock: number;
29
- features: BAMFeature[];
43
+ features: T[];
30
44
  }>;
31
- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, }: {
45
+ private RecordClass;
46
+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
32
47
  bamFilehandle?: GenericFilehandle;
33
48
  bamPath?: string;
34
49
  bamUrl?: string;
@@ -40,6 +55,7 @@ export default class BamFile {
40
55
  csiUrl?: string;
41
56
  renameRefSeqs?: (a: string) => string;
42
57
  htsget?: boolean;
58
+ recordClass?: BamRecordClass<T>;
43
59
  });
44
60
  getHeaderPre(origOpts?: BaseOpts): Promise<{
45
61
  tag: string;
@@ -63,13 +79,13 @@ export default class BamFile {
63
79
  length: number;
64
80
  }[];
65
81
  };
66
- getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
67
- streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
82
+ getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
83
+ streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
68
84
  private chunkCacheKey;
69
85
  private blocksOverlap;
70
86
  private evictOverlappingChunks;
71
- _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
72
- fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
87
+ _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
88
+ fetchPairs(chrId: number, feats: T[][], opts: BamOpts): Promise<T[]>;
73
89
  _readChunk({ chunk, opts }: {
74
90
  chunk: Chunk;
75
91
  opts: BaseOpts;
@@ -79,7 +95,7 @@ export default class BamFile {
79
95
  dpositions: number[];
80
96
  chunk: Chunk;
81
97
  }>;
82
- readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
98
+ readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<T[]>;
83
99
  _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
84
100
  hasRefSeq(seqName: string): Promise<boolean | undefined>;
85
101
  lineCount(seqName: string): Promise<number>;
package/esm/bamFile.js CHANGED
@@ -11,7 +11,7 @@ import { gen2array, makeOpts } from "./util.js";
11
11
  export const BAM_MAGIC = 21840194;
12
12
  const blockLen = 1 << 16;
13
13
  export default class BamFile {
14
- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, }) {
14
+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
15
15
  this.htsget = false;
16
16
  this.cache = new QuickLRU({
17
17
  maxSize: 1000,
@@ -20,6 +20,7 @@ export default class BamFile {
20
20
  // When a new chunk overlaps a cached chunk, we evict the cached one
21
21
  this.chunkFeatureCache = new QuickLRU({ maxSize: 100 });
22
22
  this.renameRefSeq = renameRefSeqs;
23
+ this.RecordClass = (recordClass ?? BAMFeature);
23
24
  if (bamFilehandle) {
24
25
  this.bam = bamFilehandle;
25
26
  }
@@ -298,7 +299,7 @@ export default class BamFile {
298
299
  pos--;
299
300
  }
300
301
  if (blockEnd < ba.length) {
301
- const feature = new BAMFeature({
302
+ const feature = new this.RecordClass({
302
303
  bytes: {
303
304
  byteArray: ba,
304
305
  start: blockStart,
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/index.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  export { default as BAI } from './bai.ts';
2
- export { default as BamFile } from './bamFile.ts';
2
+ export { type BamRecordClass, type BamRecordLike, default as BamFile, } from './bamFile.ts';
3
3
  export { default as CSI } from './csi.ts';
4
- export { default as BamRecord } from './record.ts';
4
+ export { type Bytes, default as BamRecord } from './record.ts';
5
5
  export { default as HtsgetFile } from './htsget.ts';
package/esm/index.js CHANGED
@@ -1,5 +1,5 @@
1
1
  export { default as BAI } from "./bai.js";
2
- export { default as BamFile } from "./bamFile.js";
2
+ export { default as BamFile, } from "./bamFile.js";
3
3
  export { default as CSI } from "./csi.js";
4
4
  export { default as BamRecord } from "./record.js";
5
5
  export { default as HtsgetFile } from "./htsget.js";
package/esm/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAGL,OAAO,IAAI,OAAO,GACnB,MAAM,cAAc,CAAA;AACrB,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAc,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAC9D,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}
package/esm/record.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- interface Bytes {
1
+ export interface Bytes {
2
2
  start: number;
3
3
  end: number;
4
4
  byteArray: Uint8Array;
@@ -24,7 +24,7 @@ export default class BamRecord {
24
24
  get ref_id(): number;
25
25
  get start(): number;
26
26
  get end(): number;
27
- get id(): number;
27
+ get id(): string;
28
28
  get mq(): number | undefined;
29
29
  get score(): number | undefined;
30
30
  get qual(): Uint8Array<ArrayBufferLike> | null;
package/esm/record.js CHANGED
@@ -33,7 +33,7 @@ export default class BamRecord {
33
33
  return this.start + this.length_on_ref;
34
34
  }
35
35
  get id() {
36
- return this.fileOffset;
36
+ return `${this.fileOffset}`;
37
37
  }
38
38
  get mq() {
39
39
  const mq = (this.bin_mq_nl & 0xff00) >> 8;
package/esm/record.js.map CHANGED
@@ -1 +1 @@
1
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C,CAAC,GAAG,CAAA;YACvD,IAAI,EAAE,GAAG,GAAG,CAAA;YACZ,IAAI,EAAE,GAAG,GAAG,CAAA;YACZ,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;gBACnB,EAAE,GAAG,GAAG,CAAA;gBACR,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;gBAC1B,EAAE,GAAG,GAAG,CAAA;gBACR,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;YAED,MAAM,GAAG,GAAG,EAAE,CAAA;YACd,MAAM,KAAK,GAAG,IAAI,CAAC,eAAe,CAAA;YAClC,IAAI,KAAK,GAAG,CAAC,EAAE,CAAC;gBACd,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACX,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACX,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACX,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;YACb,CAAC;iBAAM,CAAC;gBACN,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACX,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACX,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACX,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;YACb,CAAC;YACD,OAAO,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrB,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,SAAS;QACX,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,OAAO;QACT,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,UAAU;QACZ,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,UAAU;QACZ,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,QAAQ;QACV,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,IAAI,eAAe;QACjB,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,GAAW;QACf,IAAI,GAAG,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC;YAC1B,MAAM,SAAS,GAAG,GAAG,IAAI,CAAC,CAAA;YAC1B,MAAM,EAAE,GACN,IAAI,CAAC,SAAS,CACZ,IAAI,CAAC,EAAE,GAAG,IAAI,CAAC,gBAAgB,GAAG,IAAI,CAAC,eAAe,GAAG,SAAS,CAClE,CAAA;YAEJ,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC;gBAClB,CAAC,CAAC,cAAc,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC;gBAClC,CAAC,CAAC,cAAc,CAAC,EAAE,GAAG,IAAI,CAAC,CAAA;QAC/B,CAAC;aAAM,CAAC;YACN,OAAO,SAAS,CAAA;QAClB,CAAC;IACH,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAAwB,EAAE,CAAA;QACpC,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAClC,IAAI,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,OAAO,EAAE,CAAC;gBACvC,SAAQ;YACV,CAAC;YACD,aAAa;YACb,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACnB,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "7.1.5",
3
+ "version": "7.1.7",
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
@@ -11,14 +11,30 @@ import BAMFeature from './record.ts'
11
11
  import { parseHeaderText } from './sam.ts'
12
12
  import { gen2array, makeOpts } from './util.ts'
13
13
 
14
+ import type { Bytes } from './record.ts'
14
15
  import type { BamOpts, BaseOpts } from './util.ts'
15
16
  import type { GenericFilehandle } from 'generic-filehandle2'
16
17
 
18
+ export interface BamRecordLike {
19
+ ref_id: number
20
+ start: number
21
+ end: number
22
+ name: string
23
+ id: string
24
+ next_pos: number
25
+ next_refid: number
26
+ }
27
+
28
+ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
29
+ bytes: Bytes
30
+ fileOffset: number
31
+ }) => T
32
+
17
33
  export const BAM_MAGIC = 21840194
18
34
 
19
35
  const blockLen = 1 << 16
20
36
 
21
- export default class BamFile {
37
+ export default class BamFile<T extends BamRecordLike = BAMFeature> {
22
38
  public renameRefSeq: (a: string) => string
23
39
  public bam: GenericFilehandle
24
40
  public header?: string
@@ -26,7 +42,7 @@ export default class BamFile {
26
42
  public indexToChr?: { refName: string; length: number }[]
27
43
  public index?: BAI | CSI
28
44
  public htsget = false
29
- public headerP?: ReturnType<BamFile['getHeaderPre']>
45
+ public headerP?: ReturnType<BamFile<T>['getHeaderPre']>
30
46
  public cache = new QuickLRU<
31
47
  string,
32
48
  { bytesRead: number; buffer: Uint8Array; nextIn: number }
@@ -38,9 +54,11 @@ export default class BamFile {
38
54
  // When a new chunk overlaps a cached chunk, we evict the cached one
39
55
  public chunkFeatureCache = new QuickLRU<
40
56
  string,
41
- { minBlock: number; maxBlock: number; features: BAMFeature[] }
57
+ { minBlock: number; maxBlock: number; features: T[] }
42
58
  >({ maxSize: 100 })
43
59
 
60
+ private RecordClass: BamRecordClass<T>
61
+
44
62
  constructor({
45
63
  bamFilehandle,
46
64
  bamPath,
@@ -53,6 +71,7 @@ export default class BamFile {
53
71
  csiUrl,
54
72
  htsget,
55
73
  renameRefSeqs = n => n,
74
+ recordClass,
56
75
  }: {
57
76
  bamFilehandle?: GenericFilehandle
58
77
  bamPath?: string
@@ -65,8 +84,10 @@ export default class BamFile {
65
84
  csiUrl?: string
66
85
  renameRefSeqs?: (a: string) => string
67
86
  htsget?: boolean
87
+ recordClass?: BamRecordClass<T>
68
88
  }) {
69
89
  this.renameRefSeq = renameRefSeqs
90
+ this.RecordClass = (recordClass ?? BAMFeature) as BamRecordClass<T>
70
91
 
71
92
  if (bamFilehandle) {
72
93
  this.bam = bamFilehandle
@@ -252,7 +273,7 @@ export default class BamFile {
252
273
  opts: BamOpts = {},
253
274
  ) {
254
275
  const { viewAsPairs } = opts
255
- const feats = [] as BAMFeature[][]
276
+ const feats = [] as T[][]
256
277
  let done = false
257
278
  // let cacheHits = 0
258
279
  // let cacheMisses = 0
@@ -262,7 +283,7 @@ export default class BamFile {
262
283
  const minBlock = chunk.minv.blockPosition
263
284
  const maxBlock = chunk.maxv.blockPosition
264
285
 
265
- let records: BAMFeature[]
286
+ let records: T[]
266
287
  const cached = this.chunkFeatureCache.get(cacheKey)
267
288
  if (cached) {
268
289
  records = cached.features
@@ -287,7 +308,7 @@ export default class BamFile {
287
308
  // cacheMisses++
288
309
  }
289
310
 
290
- const recs = [] as BAMFeature[]
311
+ const recs = [] as T[]
291
312
  for (const feature of records) {
292
313
  if (feature.ref_id === chrId) {
293
314
  if (feature.start >= max) {
@@ -318,7 +339,7 @@ export default class BamFile {
318
339
  }
319
340
  }
320
341
 
321
- async fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts) {
342
+ async fetchPairs(chrId: number, feats: T[][], opts: BamOpts) {
322
343
  const { pairAcrossChr, maxInsertSize = 200000 } = opts
323
344
  const unmatedPairs: Record<string, boolean> = {}
324
345
  const readIds: Record<string, number> = {}
@@ -376,7 +397,7 @@ export default class BamFile {
376
397
  chunk: c,
377
398
  opts,
378
399
  })
379
- const mateRecs = [] as BAMFeature[]
400
+ const mateRecs = [] as T[]
380
401
  for (const feature of await this.readBamFeatures(
381
402
  data,
382
403
  cpositions,
@@ -415,7 +436,7 @@ export default class BamFile {
415
436
  chunk: Chunk,
416
437
  ) {
417
438
  let blockStart = 0
418
- const sink = [] as BAMFeature[]
439
+ const sink = [] as T[]
419
440
  let pos = 0
420
441
 
421
442
  const dataView = new DataView(ba.buffer)
@@ -432,7 +453,7 @@ export default class BamFile {
432
453
  }
433
454
 
434
455
  if (blockEnd < ba.length) {
435
- const feature = new BAMFeature({
456
+ const feature = new this.RecordClass({
436
457
  bytes: {
437
458
  byteArray: ba,
438
459
  start: blockStart,
package/src/index.ts CHANGED
@@ -1,5 +1,9 @@
1
1
  export { default as BAI } from './bai.ts'
2
- export { default as BamFile } from './bamFile.ts'
2
+ export {
3
+ type BamRecordClass,
4
+ type BamRecordLike,
5
+ default as BamFile,
6
+ } from './bamFile.ts'
3
7
  export { default as CSI } from './csi.ts'
4
- export { default as BamRecord } from './record.ts'
8
+ export { type Bytes, default as BamRecord } from './record.ts'
5
9
  export { default as HtsgetFile } from './htsget.ts'
package/src/record.ts CHANGED
@@ -15,7 +15,7 @@ const ASCII_CIGAR_CODES = [
15
15
  const CIGAR_SKIP_MASK =
16
16
  (1 << CIGAR_INS) | (1 << CIGAR_SOFT_CLIP) | (1 << CIGAR_HARD_CLIP)
17
17
 
18
- interface Bytes {
18
+ export interface Bytes {
19
19
  start: number
20
20
  end: number
21
21
  byteArray: Uint8Array
@@ -67,7 +67,7 @@ export default class BamRecord {
67
67
  }
68
68
 
69
69
  get id() {
70
- return this.fileOffset
70
+ return `${this.fileOffset}`
71
71
  }
72
72
 
73
73
  get mq() {