@gmod/bam 7.1.4 → 7.1.6

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Files changed (30) hide show
  1. package/CHANGELOG.md +4 -8
  2. package/README.md +41 -13
  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/cigar.d.ts +9 -0
  7. package/dist/cigar.js +13 -0
  8. package/dist/cigar.js.map +1 -0
  9. package/dist/index.d.ts +2 -2
  10. package/dist/index.js.map +1 -1
  11. package/dist/record.d.ts +13 -21
  12. package/dist/record.js +148 -166
  13. package/dist/record.js.map +1 -1
  14. package/esm/bamFile.d.ts +25 -9
  15. package/esm/bamFile.js +3 -2
  16. package/esm/bamFile.js.map +1 -1
  17. package/esm/cigar.d.ts +9 -0
  18. package/esm/cigar.js +10 -0
  19. package/esm/cigar.js.map +1 -0
  20. package/esm/index.d.ts +2 -2
  21. package/esm/index.js +1 -1
  22. package/esm/index.js.map +1 -1
  23. package/esm/record.d.ts +13 -21
  24. package/esm/record.js +145 -163
  25. package/esm/record.js.map +1 -1
  26. package/package.json +1 -1
  27. package/src/bamFile.ts +31 -10
  28. package/src/cigar.ts +9 -0
  29. package/src/index.ts +6 -2
  30. package/src/record.ts +171 -204
package/CHANGELOG.md CHANGED
@@ -1,23 +1,19 @@
1
- ## [7.1.4](https://github.com/GMOD/bam-js/compare/v7.1.3...v7.1.4) (2025-12-13)
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+ ## [7.1.6](https://github.com/GMOD/bam-js/compare/v7.1.5...v7.1.6) (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)
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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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+ ## [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)
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  ## [7.1.2](https://github.com/GMOD/bam-js/compare/v7.1.1...v7.1.2) (2025-12-12)
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-
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-
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  ## [7.1.1](https://github.com/GMOD/bam-js/compare/v7.1.0...v7.1.1) (2025-12-12)
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-
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-
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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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-
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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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  ## [7.0.5](https://github.com/GMOD/bam-js/compare/v7.0.4...v7.0.5) (2025-11-27)
package/README.md CHANGED
@@ -141,21 +141,49 @@ 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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-
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- Example
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+ ### BamRecord properties
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  ```typescript
149
- 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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+ // 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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  ## 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: number;
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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[];
30
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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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  }[];
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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 {
79
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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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  _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
@@ -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;
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  class BamFile {
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- constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, }) {
20
+ constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
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  this.htsget = false;
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  this.cache = new quick_lru_1.default({
23
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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
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  pos--;
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  }
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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/cigar.d.ts ADDED
@@ -0,0 +1,9 @@
1
+ export declare const CIGAR_MATCH = 0;
2
+ export declare const CIGAR_INS = 1;
3
+ export declare const CIGAR_DEL = 2;
4
+ export declare const CIGAR_REF_SKIP = 3;
5
+ export declare const CIGAR_SOFT_CLIP = 4;
6
+ export declare const CIGAR_HARD_CLIP = 5;
7
+ export declare const CIGAR_PAD = 6;
8
+ export declare const CIGAR_EQUAL = 7;
9
+ export declare const CIGAR_DIFF = 8;
package/dist/cigar.js ADDED
@@ -0,0 +1,13 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.CIGAR_DIFF = exports.CIGAR_EQUAL = exports.CIGAR_PAD = exports.CIGAR_HARD_CLIP = exports.CIGAR_SOFT_CLIP = exports.CIGAR_REF_SKIP = exports.CIGAR_DEL = exports.CIGAR_INS = exports.CIGAR_MATCH = void 0;
4
+ exports.CIGAR_MATCH = 0;
5
+ exports.CIGAR_INS = 1;
6
+ exports.CIGAR_DEL = 2;
7
+ exports.CIGAR_REF_SKIP = 3;
8
+ exports.CIGAR_SOFT_CLIP = 4;
9
+ exports.CIGAR_HARD_CLIP = 5;
10
+ exports.CIGAR_PAD = 6;
11
+ exports.CIGAR_EQUAL = 7;
12
+ exports.CIGAR_DIFF = 8;
13
+ //# sourceMappingURL=cigar.js.map
package/dist/cigar.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"cigar.js","sourceRoot":"","sources":["../src/cigar.ts"],"names":[],"mappings":";;;AAAa,QAAA,WAAW,GAAG,CAAC,CAAA;AACf,QAAA,SAAS,GAAG,CAAC,CAAA;AACb,QAAA,SAAS,GAAG,CAAC,CAAA;AACb,QAAA,cAAc,GAAG,CAAC,CAAA;AAClB,QAAA,eAAe,GAAG,CAAC,CAAA;AACnB,QAAA,eAAe,GAAG,CAAC,CAAA;AACnB,QAAA,SAAS,GAAG,CAAC,CAAA;AACb,QAAA,WAAW,GAAG,CAAC,CAAA;AACf,QAAA,UAAU,GAAG,CAAC,CAAA"}
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
@@ -1,12 +1,20 @@
1
- interface Bytes {
1
+ export interface Bytes {
2
2
  start: number;
3
3
  end: number;
4
4
  byteArray: Uint8Array;
5
5
  }
6
+ interface CIGAR_AND_LENGTH {
7
+ length_on_ref: number;
8
+ NUMERIC_CIGAR: Uint32Array;
9
+ }
6
10
  export default class BamRecord {
7
11
  fileOffset: number;
8
12
  private bytes;
9
13
  private _dataView;
14
+ private _cachedFlags?;
15
+ private _cachedTags?;
16
+ private _cachedCigarAndLength?;
17
+ private _cachedNUMERIC_MD?;
10
18
  constructor(args: {
11
19
  bytes: Bytes;
12
20
  fileOffset: number;
@@ -19,43 +27,27 @@ export default class BamRecord {
19
27
  get id(): number;
20
28
  get mq(): number | undefined;
21
29
  get score(): number | undefined;
22
- get qual(): Uint8Array<ArrayBufferLike> | undefined;
30
+ get qual(): Uint8Array<ArrayBufferLike> | null;
23
31
  get strand(): 1 | -1;
24
32
  get b0(): number;
25
33
  get name(): string;
26
34
  get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
27
35
  get tags(): Record<string, unknown>;
28
- /**
29
- * @returns {boolean} true if the read is paired, regardless of whether both
30
- * segments are mapped
31
- */
36
+ private _computeTags;
32
37
  isPaired(): boolean;
33
- /** @returns {boolean} true if the read is paired, and both segments are mapped */
34
38
  isProperlyPaired(): boolean;
35
- /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
36
39
  isSegmentUnmapped(): boolean;
37
- /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
38
40
  isMateUnmapped(): boolean;
39
- /** @returns {boolean} true if the read is mapped to the reverse strand */
40
41
  isReverseComplemented(): boolean;
41
- /** @returns {boolean} true if the mate is mapped to the reverse strand */
42
42
  isMateReverseComplemented(): boolean;
43
- /** @returns {boolean} true if this is read number 1 in a pair */
44
43
  isRead1(): boolean;
45
- /** @returns {boolean} true if this is read number 2 in a pair */
46
44
  isRead2(): boolean;
47
- /** @returns {boolean} true if this is a secondary alignment */
48
45
  isSecondary(): boolean;
49
- /** @returns {boolean} true if this read has failed QC checks */
50
46
  isFailedQc(): boolean;
51
- /** @returns {boolean} true if the read is an optical or PCR duplicate */
52
47
  isDuplicate(): boolean;
53
- /** @returns {boolean} true if this is a supplementary alignment */
54
48
  isSupplementary(): boolean;
55
- get cigarAndLength(): {
56
- NUMERIC_CIGAR: Uint32Array<ArrayBufferLike>;
57
- length_on_ref: number;
58
- };
49
+ get cigarAndLength(): CIGAR_AND_LENGTH;
50
+ private _computeCigarAndLength;
59
51
  get length_on_ref(): number;
60
52
  get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
61
53
  get CIGAR(): string;