@gmod/bam 7.0.4 → 7.0.6

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 (31) hide show
  1. package/CHANGELOG.md +5 -3
  2. package/dist/bamFile.d.ts +1 -1
  3. package/dist/bamFile.js +8 -10
  4. package/dist/bamFile.js.map +1 -1
  5. package/dist/chunk.d.ts +1 -1
  6. package/dist/htsget.d.ts +1 -1
  7. package/dist/htsget.js +0 -1
  8. package/dist/htsget.js.map +1 -1
  9. package/dist/long.js +1 -0
  10. package/dist/long.js.map +1 -1
  11. package/dist/record.d.ts +1 -0
  12. package/dist/record.js +22 -20
  13. package/dist/record.js.map +1 -1
  14. package/esm/bamFile.d.ts +1 -1
  15. package/esm/bamFile.js +8 -10
  16. package/esm/bamFile.js.map +1 -1
  17. package/esm/chunk.d.ts +1 -1
  18. package/esm/htsget.d.ts +1 -1
  19. package/esm/htsget.js +0 -1
  20. package/esm/htsget.js.map +1 -1
  21. package/esm/long.js +1 -0
  22. package/esm/long.js.map +1 -1
  23. package/esm/record.d.ts +1 -0
  24. package/esm/record.js +22 -20
  25. package/esm/record.js.map +1 -1
  26. package/package.json +6 -6
  27. package/src/bamFile.ts +6 -19
  28. package/src/chunk.ts +1 -1
  29. package/src/htsget.ts +0 -1
  30. package/src/long.ts +1 -0
  31. package/src/record.ts +24 -22
package/CHANGELOG.md CHANGED
@@ -1,14 +1,16 @@
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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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+ ## [7.0.6](https://github.com/GMOD/bam-js/compare/v7.0.5...v7.0.6) (2025-11-28)
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- ## [7.0.3](https://github.com/GMOD/bam-js/compare/v7.0.2...v7.0.3) (2025-11-24)
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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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- ## [7.0.2](https://github.com/GMOD/bam-js/compare/v7.0.1...v7.0.2) (2025-11-24)
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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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+ ## [7.0.3](https://github.com/GMOD/bam-js/compare/v7.0.2...v7.0.3) (2025-11-24)
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+ ## [7.0.2](https://github.com/GMOD/bam-js/compare/v7.0.1...v7.0.2) (2025-11-24)
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  ## [7.0.1](https://github.com/GMOD/bam-js/compare/v7.0.0...v7.0.1) (2025-11-24)
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package/dist/bamFile.d.ts CHANGED
@@ -70,7 +70,7 @@ 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, 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
@@ -80,7 +80,12 @@ class BamFile {
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  // (just bam header and nothing else)
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  const buffer = indexData.firstDataLine === undefined
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  ? await this.bam.readFile()
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- : await this.bam.read(indexData.firstDataLine.blockPosition + blockLen, 0);
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+ : // the logic indexData.firstDataLine is a virtualOffset telling us
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+ // where the data is. It is in the middle of a virtualOffset
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+ // (provided by the bgzip block offset at blockPosition + the
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+ // virtualOffset dataPosition, so we add one extra blockLen to make
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+ // sure we consume the full header)
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+ await this.bam.read(indexData.firstDataLine.blockPosition + blockLen, 0);
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  const uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
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  const dataView = new DataView(uncba.buffer);
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  if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
@@ -148,7 +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) {
@@ -238,14 +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;
@@ -254,12 +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/dist/chunk.d.ts CHANGED
@@ -4,7 +4,7 @@ export default class Chunk {
4
4
  maxv: Offset;
5
5
  bin: number;
6
6
  _fetchedSize?: number | undefined;
7
- buffer?: Uint8Array;
7
+ buffer?: Uint8Array<ArrayBuffer>;
8
8
  constructor(minv: Offset, maxv: Offset, bin: number, _fetchedSize?: number | undefined);
9
9
  toUniqueString(): string;
10
10
  toString(): string;
package/dist/htsget.d.ts CHANGED
@@ -13,7 +13,7 @@ export default class HtsgetFile extends BamFile {
13
13
  chunk: Chunk;
14
14
  opts: BaseOpts;
15
15
  }): Promise<{
16
- data: Uint8Array<ArrayBufferLike>;
16
+ data: Uint8Array<ArrayBuffer>;
17
17
  cpositions: never[];
18
18
  dpositions: never[];
19
19
  chunk: Chunk;
package/dist/htsget.js CHANGED
@@ -118,7 +118,6 @@ class HtsgetFile extends bamFile_ts_1.default {
118
118
  ], chrId, min, max, opts);
119
119
  }
120
120
  }
121
- // @ts-expect-error
122
121
  async _readChunk({ chunk }) {
123
122
  if (!chunk.buffer) {
124
123
  throw new Error('expected chunk.buffer in htsget');
package/dist/htsget.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/long.js CHANGED
@@ -4,6 +4,7 @@ exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL = void 0;
4
4
  exports.longFromBytesToUnsigned = longFromBytesToUnsigned;
5
5
  exports.TWO_PWR_16_DBL = 1 << 16;
6
6
  exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL * exports.TWO_PWR_16_DBL;
7
+ // avoids dependency on long.js
7
8
  function longFromBytesToUnsigned(source, i = 0) {
8
9
  const low = source[i] |
9
10
  (source[i + 1] << 8) |
package/dist/long.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;;AAGA,0DAYC;AAfY,QAAA,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACxB,QAAA,cAAc,GAAG,sBAAc,GAAG,sBAAc,CAAA;AAE7D,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,sBAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
1
+ {"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;;AAIA,0DAYC;AAhBY,QAAA,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACxB,QAAA,cAAc,GAAG,sBAAc,GAAG,sBAAc,CAAA;AAE7D,+BAA+B;AAC/B,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,sBAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
package/dist/record.d.ts CHANGED
@@ -59,6 +59,7 @@ export default class BamRecord {
59
59
  get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
60
60
  get CIGAR(): string;
61
61
  get num_cigar_ops(): number;
62
+ get num_cigar_bytes(): number;
62
63
  get read_name_length(): number;
63
64
  get num_seq_bytes(): number;
64
65
  get NUMERIC_SEQ(): Uint8Array<ArrayBufferLike>;
package/dist/record.js CHANGED
@@ -14,6 +14,9 @@ const CIGAR_INS = 1;
14
14
  const CIGAR_REF_SKIP = 3;
15
15
  const CIGAR_SOFT_CLIP = 4;
16
16
  const CIGAR_HARD_CLIP = 5;
17
+ // const CIGAR_PAD = 6
18
+ // ops that don't consume reference: INS, SOFT_CLIP, HARD_CLIP
19
+ const CIGAR_SKIP_MASK = (1 << CIGAR_INS) | (1 << CIGAR_SOFT_CLIP) | (1 << CIGAR_HARD_CLIP);
17
20
  class BamRecord {
18
21
  constructor(args) {
19
22
  this.bytes = args.bytes;
@@ -51,7 +54,7 @@ class BamRecord {
51
54
  }
52
55
  const p = this.b0 +
53
56
  this.read_name_length +
54
- this.num_cigar_ops * 4 +
57
+ this.num_cigar_bytes +
55
58
  this.num_seq_bytes;
56
59
  return this.byteArray.subarray(p, p + this.seq_length);
57
60
  }
@@ -71,7 +74,7 @@ class BamRecord {
71
74
  get tags() {
72
75
  let p = this.b0 +
73
76
  this.read_name_length +
74
- this.num_cigar_ops * 4 +
77
+ this.num_cigar_bytes +
75
78
  this.num_seq_bytes +
76
79
  this.seq_length;
77
80
  const blockEnd = this.bytes.end;
@@ -140,40 +143,40 @@ class BamRecord {
140
143
  tags[tag] = new Int32Array(this.byteArray.buffer, absOffset, limit);
141
144
  }
142
145
  else {
143
- const bytes = this.byteArray.slice(p, p + limit * 4);
146
+ const bytes = this.byteArray.slice(p, p + (limit << 2));
144
147
  tags[tag] = new Int32Array(bytes.buffer, bytes.byteOffset, limit);
145
148
  }
146
- p += limit * 4;
149
+ p += limit << 2;
147
150
  }
148
151
  else if (Btype === 'I') {
149
152
  if (absOffset % 4 === 0) {
150
153
  tags[tag] = new Uint32Array(this.byteArray.buffer, absOffset, limit);
151
154
  }
152
155
  else {
153
- const bytes = this.byteArray.slice(p, p + limit * 4);
156
+ const bytes = this.byteArray.slice(p, p + (limit << 2));
154
157
  tags[tag] = new Uint32Array(bytes.buffer, bytes.byteOffset, limit);
155
158
  }
156
- p += limit * 4;
159
+ p += limit << 2;
157
160
  }
158
161
  else if (Btype === 's') {
159
162
  if (absOffset % 2 === 0) {
160
163
  tags[tag] = new Int16Array(this.byteArray.buffer, absOffset, limit);
161
164
  }
162
165
  else {
163
- const bytes = this.byteArray.slice(p, p + limit * 2);
166
+ const bytes = this.byteArray.slice(p, p + (limit << 1));
164
167
  tags[tag] = new Int16Array(bytes.buffer, bytes.byteOffset, limit);
165
168
  }
166
- p += limit * 2;
169
+ p += limit << 1;
167
170
  }
168
171
  else if (Btype === 'S') {
169
172
  if (absOffset % 2 === 0) {
170
173
  tags[tag] = new Uint16Array(this.byteArray.buffer, absOffset, limit);
171
174
  }
172
175
  else {
173
- const bytes = this.byteArray.slice(p, p + limit * 2);
176
+ const bytes = this.byteArray.slice(p, p + (limit << 1));
174
177
  tags[tag] = new Uint16Array(bytes.buffer, bytes.byteOffset, limit);
175
178
  }
176
- p += limit * 2;
179
+ p += limit << 1;
177
180
  }
178
181
  else if (Btype === 'c') {
179
182
  tags[tag] = new Int8Array(this.byteArray.buffer, absOffset, limit);
@@ -188,10 +191,10 @@ class BamRecord {
188
191
  tags[tag] = new Float32Array(this.byteArray.buffer, absOffset, limit);
189
192
  }
190
193
  else {
191
- const bytes = this.byteArray.slice(p, p + limit * 4);
194
+ const bytes = this.byteArray.slice(p, p + (limit << 2));
192
195
  tags[tag] = new Float32Array(bytes.buffer, bytes.byteOffset, limit);
193
196
  }
194
- p += limit * 4;
197
+ p += limit << 2;
195
198
  }
196
199
  break;
197
200
  }
@@ -287,16 +290,12 @@ class BamRecord {
287
290
  const absOffset = this.byteArray.byteOffset + p;
288
291
  const cigarView = absOffset % 4 === 0
289
292
  ? new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps)
290
- : new Uint32Array(this.byteArray.slice(p, p + numCigarOps * 4).buffer, 0, numCigarOps);
293
+ : new Uint32Array(this.byteArray.slice(p, p + (numCigarOps << 2)).buffer, 0, numCigarOps);
291
294
  let lref = 0;
292
295
  for (let c = 0; c < numCigarOps; ++c) {
293
296
  const cigop = cigarView[c];
294
297
  const op = cigop & 0xf;
295
- // soft clip, hard clip, and insertion don't count toward the length on
296
- // the reference
297
- if (op !== CIGAR_HARD_CLIP &&
298
- op !== CIGAR_SOFT_CLIP &&
299
- op !== CIGAR_INS) {
298
+ if (!((1 << op) & CIGAR_SKIP_MASK)) {
300
299
  lref += cigop >> 4;
301
300
  }
302
301
  }
@@ -326,6 +325,9 @@ class BamRecord {
326
325
  get num_cigar_ops() {
327
326
  return this.flag_nc & 0xffff;
328
327
  }
328
+ get num_cigar_bytes() {
329
+ return this.num_cigar_ops << 2;
330
+ }
329
331
  get read_name_length() {
330
332
  return this.bin_mq_nl & 0xff;
331
333
  }
@@ -333,7 +335,7 @@ class BamRecord {
333
335
  return (this.seq_length + 1) >> 1;
334
336
  }
335
337
  get NUMERIC_SEQ() {
336
- const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
338
+ const p = this.b0 + this.read_name_length + this.num_cigar_bytes;
337
339
  const seqBytes = this.byteArray.subarray(p, p + this.num_seq_bytes);
338
340
  return new Uint8Array(seqBytes.buffer, seqBytes.byteOffset, this.num_seq_bytes);
339
341
  }
@@ -410,7 +412,7 @@ class BamRecord {
410
412
  seqAt(idx) {
411
413
  if (idx < this.seq_length) {
412
414
  const byteIndex = idx >> 1;
413
- const sb = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_ops * 4 + byteIndex];
415
+ const sb = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_bytes + byteIndex];
414
416
  return idx % 2 === 0
415
417
  ? SEQRET_DECODER[(sb & 0xf0) >> 4]
416
418
  : SEQRET_DECODER[sb & 0x0f];
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/bamFile.d.ts CHANGED
@@ -70,7 +70,7 @@ export default class BamFile {
70
70
  dpositions: number[];
71
71
  chunk: Chunk;
72
72
  }>;
73
- readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk, chrId?: number, min?: number, max?: number): Promise<BAMFeature[]>;
73
+ readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
74
74
  _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
75
75
  hasRefSeq(seqName: string): Promise<boolean | undefined>;
76
76
  lineCount(seqName: string): Promise<number>;
package/esm/bamFile.js CHANGED
@@ -74,7 +74,12 @@ export default class BamFile {
74
74
  // (just bam header and nothing else)
75
75
  const buffer = indexData.firstDataLine === undefined
76
76
  ? await this.bam.readFile()
77
- : await this.bam.read(indexData.firstDataLine.blockPosition + blockLen, 0);
77
+ : // the logic indexData.firstDataLine is a virtualOffset telling us
78
+ // where the data is. It is in the middle of a virtualOffset
79
+ // (provided by the bgzip block offset at blockPosition + the
80
+ // virtualOffset dataPosition, so we add one extra blockLen to make
81
+ // sure we consume the full header)
82
+ await this.bam.read(indexData.firstDataLine.blockPosition + blockLen, 0);
78
83
  const uncba = await unzip(buffer);
79
84
  const dataView = new DataView(uncba.buffer);
80
85
  if (dataView.getInt32(0, true) !== BAM_MAGIC) {
@@ -142,7 +147,7 @@ export default class BamFile {
142
147
  chunk,
143
148
  opts,
144
149
  });
145
- const records = await this.readBamFeatures(data, cpositions, dpositions, chunk, chrId, min, max);
150
+ const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
146
151
  const recs = [];
147
152
  for (const feature of records) {
148
153
  if (feature.ref_id === chrId) {
@@ -232,14 +237,13 @@ export default class BamFile {
232
237
  const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk, this.cache);
233
238
  return { data, cpositions, dpositions, chunk };
234
239
  }
235
- async readBamFeatures(ba, cpositions, dpositions, chunk, chrId, min, max) {
240
+ async readBamFeatures(ba, cpositions, dpositions, chunk) {
236
241
  let blockStart = 0;
237
242
  const sink = [];
238
243
  let pos = 0;
239
244
  const dataView = new DataView(ba.buffer);
240
245
  const hasDpositions = dpositions.length > 0;
241
246
  const hasCpositions = cpositions.length > 0;
242
- const hasFilter = chrId !== undefined && min !== undefined && max !== undefined;
243
247
  while (blockStart + 4 < ba.length) {
244
248
  const blockSize = dataView.getInt32(blockStart, true);
245
249
  const blockEnd = blockStart + 4 + blockSize - 1;
@@ -248,12 +252,6 @@ export default class BamFile {
248
252
  pos--;
249
253
  }
250
254
  if (blockEnd < ba.length) {
251
- if (hasFilter &&
252
- blockStart + 12 < ba.length &&
253
- !this._shouldIncludeFeature(dataView, blockStart, chrId, max)) {
254
- blockStart = blockEnd + 1;
255
- continue;
256
- }
257
255
  const feature = new BAMFeature({
258
256
  bytes: {
259
257
  byteArray: ba,
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/esm/chunk.d.ts CHANGED
@@ -4,7 +4,7 @@ export default class Chunk {
4
4
  maxv: Offset;
5
5
  bin: number;
6
6
  _fetchedSize?: number | undefined;
7
- buffer?: Uint8Array;
7
+ buffer?: Uint8Array<ArrayBuffer>;
8
8
  constructor(minv: Offset, maxv: Offset, bin: number, _fetchedSize?: number | undefined);
9
9
  toUniqueString(): string;
10
10
  toString(): string;
package/esm/htsget.d.ts CHANGED
@@ -13,7 +13,7 @@ export default class HtsgetFile extends BamFile {
13
13
  chunk: Chunk;
14
14
  opts: BaseOpts;
15
15
  }): Promise<{
16
- data: Uint8Array<ArrayBufferLike>;
16
+ data: Uint8Array<ArrayBuffer>;
17
17
  cpositions: never[];
18
18
  dpositions: never[];
19
19
  chunk: Chunk;
package/esm/htsget.js CHANGED
@@ -83,7 +83,6 @@ export default class HtsgetFile extends BamFile {
83
83
  ], chrId, min, max, opts);
84
84
  }
85
85
  }
86
- // @ts-expect-error
87
86
  async _readChunk({ chunk }) {
88
87
  if (!chunk.buffer) {
89
88
  throw new Error('expected chunk.buffer in htsget');
package/esm/htsget.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/long.js CHANGED
@@ -1,5 +1,6 @@
1
1
  export const TWO_PWR_16_DBL = 1 << 16;
2
2
  export const TWO_PWR_32_DBL = TWO_PWR_16_DBL * TWO_PWR_16_DBL;
3
+ // avoids dependency on long.js
3
4
  export function longFromBytesToUnsigned(source, i = 0) {
4
5
  const low = source[i] |
5
6
  (source[i + 1] << 8) |
package/esm/long.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACrC,MAAM,CAAC,MAAM,cAAc,GAAG,cAAc,GAAG,cAAc,CAAA;AAE7D,MAAM,UAAU,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
1
+ {"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACrC,MAAM,CAAC,MAAM,cAAc,GAAG,cAAc,GAAG,cAAc,CAAA;AAE7D,+BAA+B;AAC/B,MAAM,UAAU,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
package/esm/record.d.ts CHANGED
@@ -59,6 +59,7 @@ export default class BamRecord {
59
59
  get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
60
60
  get CIGAR(): string;
61
61
  get num_cigar_ops(): number;
62
+ get num_cigar_bytes(): number;
62
63
  get read_name_length(): number;
63
64
  get num_seq_bytes(): number;
64
65
  get NUMERIC_SEQ(): Uint8Array<ArrayBufferLike>;
package/esm/record.js CHANGED
@@ -9,6 +9,9 @@ const CIGAR_INS = 1;
9
9
  const CIGAR_REF_SKIP = 3;
10
10
  const CIGAR_SOFT_CLIP = 4;
11
11
  const CIGAR_HARD_CLIP = 5;
12
+ // const CIGAR_PAD = 6
13
+ // ops that don't consume reference: INS, SOFT_CLIP, HARD_CLIP
14
+ const CIGAR_SKIP_MASK = (1 << CIGAR_INS) | (1 << CIGAR_SOFT_CLIP) | (1 << CIGAR_HARD_CLIP);
12
15
  export default class BamRecord {
13
16
  constructor(args) {
14
17
  this.bytes = args.bytes;
@@ -46,7 +49,7 @@ export default class BamRecord {
46
49
  }
47
50
  const p = this.b0 +
48
51
  this.read_name_length +
49
- this.num_cigar_ops * 4 +
52
+ this.num_cigar_bytes +
50
53
  this.num_seq_bytes;
51
54
  return this.byteArray.subarray(p, p + this.seq_length);
52
55
  }
@@ -66,7 +69,7 @@ export default class BamRecord {
66
69
  get tags() {
67
70
  let p = this.b0 +
68
71
  this.read_name_length +
69
- this.num_cigar_ops * 4 +
72
+ this.num_cigar_bytes +
70
73
  this.num_seq_bytes +
71
74
  this.seq_length;
72
75
  const blockEnd = this.bytes.end;
@@ -135,40 +138,40 @@ export default class BamRecord {
135
138
  tags[tag] = new Int32Array(this.byteArray.buffer, absOffset, limit);
136
139
  }
137
140
  else {
138
- const bytes = this.byteArray.slice(p, p + limit * 4);
141
+ const bytes = this.byteArray.slice(p, p + (limit << 2));
139
142
  tags[tag] = new Int32Array(bytes.buffer, bytes.byteOffset, limit);
140
143
  }
141
- p += limit * 4;
144
+ p += limit << 2;
142
145
  }
143
146
  else if (Btype === 'I') {
144
147
  if (absOffset % 4 === 0) {
145
148
  tags[tag] = new Uint32Array(this.byteArray.buffer, absOffset, limit);
146
149
  }
147
150
  else {
148
- const bytes = this.byteArray.slice(p, p + limit * 4);
151
+ const bytes = this.byteArray.slice(p, p + (limit << 2));
149
152
  tags[tag] = new Uint32Array(bytes.buffer, bytes.byteOffset, limit);
150
153
  }
151
- p += limit * 4;
154
+ p += limit << 2;
152
155
  }
153
156
  else if (Btype === 's') {
154
157
  if (absOffset % 2 === 0) {
155
158
  tags[tag] = new Int16Array(this.byteArray.buffer, absOffset, limit);
156
159
  }
157
160
  else {
158
- const bytes = this.byteArray.slice(p, p + limit * 2);
161
+ const bytes = this.byteArray.slice(p, p + (limit << 1));
159
162
  tags[tag] = new Int16Array(bytes.buffer, bytes.byteOffset, limit);
160
163
  }
161
- p += limit * 2;
164
+ p += limit << 1;
162
165
  }
163
166
  else if (Btype === 'S') {
164
167
  if (absOffset % 2 === 0) {
165
168
  tags[tag] = new Uint16Array(this.byteArray.buffer, absOffset, limit);
166
169
  }
167
170
  else {
168
- const bytes = this.byteArray.slice(p, p + limit * 2);
171
+ const bytes = this.byteArray.slice(p, p + (limit << 1));
169
172
  tags[tag] = new Uint16Array(bytes.buffer, bytes.byteOffset, limit);
170
173
  }
171
- p += limit * 2;
174
+ p += limit << 1;
172
175
  }
173
176
  else if (Btype === 'c') {
174
177
  tags[tag] = new Int8Array(this.byteArray.buffer, absOffset, limit);
@@ -183,10 +186,10 @@ export default class BamRecord {
183
186
  tags[tag] = new Float32Array(this.byteArray.buffer, absOffset, limit);
184
187
  }
185
188
  else {
186
- const bytes = this.byteArray.slice(p, p + limit * 4);
189
+ const bytes = this.byteArray.slice(p, p + (limit << 2));
187
190
  tags[tag] = new Float32Array(bytes.buffer, bytes.byteOffset, limit);
188
191
  }
189
- p += limit * 4;
192
+ p += limit << 2;
190
193
  }
191
194
  break;
192
195
  }
@@ -282,16 +285,12 @@ export default class BamRecord {
282
285
  const absOffset = this.byteArray.byteOffset + p;
283
286
  const cigarView = absOffset % 4 === 0
284
287
  ? new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps)
285
- : new Uint32Array(this.byteArray.slice(p, p + numCigarOps * 4).buffer, 0, numCigarOps);
288
+ : new Uint32Array(this.byteArray.slice(p, p + (numCigarOps << 2)).buffer, 0, numCigarOps);
286
289
  let lref = 0;
287
290
  for (let c = 0; c < numCigarOps; ++c) {
288
291
  const cigop = cigarView[c];
289
292
  const op = cigop & 0xf;
290
- // soft clip, hard clip, and insertion don't count toward the length on
291
- // the reference
292
- if (op !== CIGAR_HARD_CLIP &&
293
- op !== CIGAR_SOFT_CLIP &&
294
- op !== CIGAR_INS) {
293
+ if (!((1 << op) & CIGAR_SKIP_MASK)) {
295
294
  lref += cigop >> 4;
296
295
  }
297
296
  }
@@ -321,6 +320,9 @@ export default class BamRecord {
321
320
  get num_cigar_ops() {
322
321
  return this.flag_nc & 0xffff;
323
322
  }
323
+ get num_cigar_bytes() {
324
+ return this.num_cigar_ops << 2;
325
+ }
324
326
  get read_name_length() {
325
327
  return this.bin_mq_nl & 0xff;
326
328
  }
@@ -328,7 +330,7 @@ export default class BamRecord {
328
330
  return (this.seq_length + 1) >> 1;
329
331
  }
330
332
  get NUMERIC_SEQ() {
331
- const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
333
+ const p = this.b0 + this.read_name_length + this.num_cigar_bytes;
332
334
  const seqBytes = this.byteArray.subarray(p, p + this.num_seq_bytes);
333
335
  return new Uint8Array(seqBytes.buffer, seqBytes.byteOffset, this.num_seq_bytes);
334
336
  }
@@ -405,7 +407,7 @@ export default class BamRecord {
405
407
  seqAt(idx) {
406
408
  if (idx < this.seq_length) {
407
409
  const byteIndex = idx >> 1;
408
- const sb = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_ops * 4 + byteIndex];
410
+ const sb = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_bytes + byteIndex];
409
411
  return idx % 2 === 0
410
412
  ? SEQRET_DECODER[(sb & 0xf0) >> 4]
411
413
  : SEQRET_DECODER[sb & 0x0f];
package/esm/record.js.map CHANGED
@@ -1 +1 @@
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "7.0.4",
3
+ "version": "7.0.6",
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": "^5.0.1",
53
+ "@gmod/bgzf-filehandle": "^5.0.2",
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": "^4.0.3",
60
+ "@vitest/coverage-v8": "^4.0.14",
61
61
  "eslint": "^9.9.0",
62
62
  "eslint-plugin-import": "^2.31.0",
63
63
  "eslint-plugin-unicorn": "^62.0.0",
64
64
  "prettier": "^3.3.3",
65
- "rimraf": "^6.0.1",
65
+ "rimraf": "^6.1.2",
66
66
  "standard-changelog": "^7.0.1",
67
67
  "typescript": "^5.0.4",
68
- "typescript-eslint": "^8.27.0",
69
- "vitest": "^4.0.3"
68
+ "typescript-eslint": "^8.48.0",
69
+ "vitest": "^4.0.14"
70
70
  },
71
71
  "publishConfig": {
72
72
  "access": "public"
package/src/bamFile.ts CHANGED
@@ -105,7 +105,12 @@ export default class BamFile {
105
105
  const buffer =
106
106
  indexData.firstDataLine === undefined
107
107
  ? await this.bam.readFile()
108
- : await this.bam.read(
108
+ : // the logic indexData.firstDataLine is a virtualOffset telling us
109
+ // where the data is. It is in the middle of a virtualOffset
110
+ // (provided by the bgzip block offset at blockPosition + the
111
+ // virtualOffset dataPosition, so we add one extra blockLen to make
112
+ // sure we consume the full header)
113
+ await this.bam.read(
109
114
  indexData.firstDataLine.blockPosition + blockLen,
110
115
  0,
111
116
  )
@@ -122,7 +127,6 @@ export default class BamFile {
122
127
  const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, headLen + 8)
123
128
  this.chrToIndex = chrToIndex
124
129
  this.indexToChr = indexToChr
125
-
126
130
  return parseHeaderText(this.header)
127
131
  }
128
132
 
@@ -223,9 +227,6 @@ export default class BamFile {
223
227
  cpositions,
224
228
  dpositions,
225
229
  chunk,
226
- chrId,
227
- min,
228
- max,
229
230
  )
230
231
 
231
232
  const recs = [] as BAMFeature[]
@@ -348,9 +349,6 @@ export default class BamFile {
348
349
  cpositions: number[],
349
350
  dpositions: number[],
350
351
  chunk: Chunk,
351
- chrId?: number,
352
- min?: number,
353
- max?: number,
354
352
  ) {
355
353
  let blockStart = 0
356
354
  const sink = [] as BAMFeature[]
@@ -359,8 +357,6 @@ export default class BamFile {
359
357
  const dataView = new DataView(ba.buffer)
360
358
  const hasDpositions = dpositions.length > 0
361
359
  const hasCpositions = cpositions.length > 0
362
- const hasFilter =
363
- chrId !== undefined && min !== undefined && max !== undefined
364
360
 
365
361
  while (blockStart + 4 < ba.length) {
366
362
  const blockSize = dataView.getInt32(blockStart, true)
@@ -372,15 +368,6 @@ export default class BamFile {
372
368
  }
373
369
 
374
370
  if (blockEnd < ba.length) {
375
- if (
376
- hasFilter &&
377
- blockStart + 12 < ba.length &&
378
- !this._shouldIncludeFeature(dataView, blockStart, chrId, max)
379
- ) {
380
- blockStart = blockEnd + 1
381
- continue
382
- }
383
-
384
371
  const feature = new BAMFeature({
385
372
  bytes: {
386
373
  byteArray: ba,
package/src/chunk.ts CHANGED
@@ -2,7 +2,7 @@ import { Offset } from './virtualOffset.ts'
2
2
 
3
3
  // little class representing a chunk in the index
4
4
  export default class Chunk {
5
- public buffer?: Uint8Array
5
+ public buffer?: Uint8Array<ArrayBuffer>
6
6
 
7
7
  constructor(
8
8
  public minv: Offset,
package/src/htsget.ts CHANGED
@@ -118,7 +118,6 @@ export default class HtsgetFile extends BamFile {
118
118
  }
119
119
  }
120
120
 
121
- // @ts-expect-error
122
121
  async _readChunk({ chunk }: { chunk: Chunk; opts: BaseOpts }) {
123
122
  if (!chunk.buffer) {
124
123
  throw new Error('expected chunk.buffer in htsget')
package/src/long.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  export const TWO_PWR_16_DBL = 1 << 16
2
2
  export const TWO_PWR_32_DBL = TWO_PWR_16_DBL * TWO_PWR_16_DBL
3
3
 
4
+ // avoids dependency on long.js
4
5
  export function longFromBytesToUnsigned(source: Uint8Array, i = 0) {
5
6
  const low =
6
7
  source[i]! |
package/src/record.ts CHANGED
@@ -12,6 +12,10 @@ const CIGAR_REF_SKIP = 3
12
12
  const CIGAR_SOFT_CLIP = 4
13
13
  const CIGAR_HARD_CLIP = 5
14
14
  // const CIGAR_PAD = 6
15
+
16
+ // ops that don't consume reference: INS, SOFT_CLIP, HARD_CLIP
17
+ const CIGAR_SKIP_MASK =
18
+ (1 << CIGAR_INS) | (1 << CIGAR_SOFT_CLIP) | (1 << CIGAR_HARD_CLIP)
15
19
  // const CIGAR_EQUAL = 7
16
20
  // const CIGAR_DIFF = 8
17
21
 
@@ -74,7 +78,7 @@ export default class BamRecord {
74
78
  const p =
75
79
  this.b0 +
76
80
  this.read_name_length +
77
- this.num_cigar_ops * 4 +
81
+ this.num_cigar_bytes +
78
82
  this.num_seq_bytes
79
83
  return this.byteArray.subarray(p, p + this.seq_length)
80
84
  }
@@ -98,7 +102,7 @@ export default class BamRecord {
98
102
  let p =
99
103
  this.b0 +
100
104
  this.read_name_length +
101
- this.num_cigar_ops * 4 +
105
+ this.num_cigar_bytes +
102
106
  this.num_seq_bytes +
103
107
  this.seq_length
104
108
 
@@ -172,10 +176,10 @@ export default class BamRecord {
172
176
  limit,
173
177
  )
174
178
  } else {
175
- const bytes = this.byteArray.slice(p, p + limit * 4)
179
+ const bytes = this.byteArray.slice(p, p + (limit << 2))
176
180
  tags[tag] = new Int32Array(bytes.buffer, bytes.byteOffset, limit)
177
181
  }
178
- p += limit * 4
182
+ p += limit << 2
179
183
  } else if (Btype === 'I') {
180
184
  if (absOffset % 4 === 0) {
181
185
  tags[tag] = new Uint32Array(
@@ -184,10 +188,10 @@ export default class BamRecord {
184
188
  limit,
185
189
  )
186
190
  } else {
187
- const bytes = this.byteArray.slice(p, p + limit * 4)
191
+ const bytes = this.byteArray.slice(p, p + (limit << 2))
188
192
  tags[tag] = new Uint32Array(bytes.buffer, bytes.byteOffset, limit)
189
193
  }
190
- p += limit * 4
194
+ p += limit << 2
191
195
  } else if (Btype === 's') {
192
196
  if (absOffset % 2 === 0) {
193
197
  tags[tag] = new Int16Array(
@@ -196,10 +200,10 @@ export default class BamRecord {
196
200
  limit,
197
201
  )
198
202
  } else {
199
- const bytes = this.byteArray.slice(p, p + limit * 2)
203
+ const bytes = this.byteArray.slice(p, p + (limit << 1))
200
204
  tags[tag] = new Int16Array(bytes.buffer, bytes.byteOffset, limit)
201
205
  }
202
- p += limit * 2
206
+ p += limit << 1
203
207
  } else if (Btype === 'S') {
204
208
  if (absOffset % 2 === 0) {
205
209
  tags[tag] = new Uint16Array(
@@ -208,10 +212,10 @@ export default class BamRecord {
208
212
  limit,
209
213
  )
210
214
  } else {
211
- const bytes = this.byteArray.slice(p, p + limit * 2)
215
+ const bytes = this.byteArray.slice(p, p + (limit << 1))
212
216
  tags[tag] = new Uint16Array(bytes.buffer, bytes.byteOffset, limit)
213
217
  }
214
- p += limit * 2
218
+ p += limit << 1
215
219
  } else if (Btype === 'c') {
216
220
  tags[tag] = new Int8Array(this.byteArray.buffer, absOffset, limit)
217
221
  p += limit
@@ -226,14 +230,14 @@ export default class BamRecord {
226
230
  limit,
227
231
  )
228
232
  } else {
229
- const bytes = this.byteArray.slice(p, p + limit * 4)
233
+ const bytes = this.byteArray.slice(p, p + (limit << 2))
230
234
  tags[tag] = new Float32Array(
231
235
  bytes.buffer,
232
236
  bytes.byteOffset,
233
237
  limit,
234
238
  )
235
239
  }
236
- p += limit * 4
240
+ p += limit << 2
237
241
  }
238
242
  break
239
243
  }
@@ -345,7 +349,7 @@ export default class BamRecord {
345
349
  absOffset % 4 === 0
346
350
  ? new Uint32Array(this.byteArray.buffer, absOffset, numCigarOps)
347
351
  : new Uint32Array(
348
- this.byteArray.slice(p, p + numCigarOps * 4).buffer,
352
+ this.byteArray.slice(p, p + (numCigarOps << 2)).buffer,
349
353
  0,
350
354
  numCigarOps,
351
355
  )
@@ -353,13 +357,7 @@ export default class BamRecord {
353
357
  for (let c = 0; c < numCigarOps; ++c) {
354
358
  const cigop = cigarView[c]!
355
359
  const op = cigop & 0xf
356
- // soft clip, hard clip, and insertion don't count toward the length on
357
- // the reference
358
- if (
359
- op !== CIGAR_HARD_CLIP &&
360
- op !== CIGAR_SOFT_CLIP &&
361
- op !== CIGAR_INS
362
- ) {
360
+ if (!((1 << op) & CIGAR_SKIP_MASK)) {
363
361
  lref += cigop >> 4
364
362
  }
365
363
  }
@@ -395,6 +393,10 @@ export default class BamRecord {
395
393
  return this.flag_nc & 0xffff
396
394
  }
397
395
 
396
+ get num_cigar_bytes() {
397
+ return this.num_cigar_ops << 2
398
+ }
399
+
398
400
  get read_name_length() {
399
401
  return this.bin_mq_nl & 0xff
400
402
  }
@@ -404,7 +406,7 @@ export default class BamRecord {
404
406
  }
405
407
 
406
408
  get NUMERIC_SEQ() {
407
- const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4
409
+ const p = this.b0 + this.read_name_length + this.num_cigar_bytes
408
410
  const seqBytes = this.byteArray.subarray(p, p + this.num_seq_bytes)
409
411
  return new Uint8Array(
410
412
  seqBytes.buffer,
@@ -500,7 +502,7 @@ export default class BamRecord {
500
502
  const byteIndex = idx >> 1
501
503
  const sb =
502
504
  this.byteArray[
503
- this.b0 + this.read_name_length + this.num_cigar_ops * 4 + byteIndex
505
+ this.b0 + this.read_name_length + this.num_cigar_bytes + byteIndex
504
506
  ]!
505
507
 
506
508
  return idx % 2 === 0