@gmod/bam 7.1.18 → 7.1.19

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 (9) hide show
  1. package/CHANGELOG.md +3 -5
  2. package/dist/bamFile.d.ts +1 -0
  3. package/dist/bamFile.js +41 -17
  4. package/dist/bamFile.js.map +1 -1
  5. package/esm/bamFile.d.ts +1 -0
  6. package/esm/bamFile.js +41 -17
  7. package/esm/bamFile.js.map +1 -1
  8. package/package.json +1 -1
  9. package/src/bamFile.ts +52 -24
package/CHANGELOG.md CHANGED
@@ -1,15 +1,13 @@
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- ## [7.1.18](https://github.com/GMOD/bam-js/compare/v7.1.17...v7.1.18) (2026-03-04)
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-
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+ ## [7.1.19](https://github.com/GMOD/bam-js/compare/v7.1.18...v7.1.19) (2026-03-04)
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- ## [7.1.17](https://github.com/GMOD/bam-js/compare/v7.1.16...v7.1.17) (2026-02-14)
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+ ## [7.1.18](https://github.com/GMOD/bam-js/compare/v7.1.17...v7.1.18) (2026-03-04)
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+ ## [7.1.17](https://github.com/GMOD/bam-js/compare/v7.1.16...v7.1.17) (2026-02-14)
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  ## [7.1.16](https://github.com/GMOD/bam-js/compare/v7.1.15...v7.1.16) (2026-02-14)
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-
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-
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  ## [7.1.15](https://github.com/GMOD/bam-js/compare/v7.1.14...v7.1.15) (2025-12-17)
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  ## [7.1.14](https://github.com/GMOD/bam-js/compare/v7.1.13...v7.1.14) (2025-12-17)
package/dist/bamFile.d.ts CHANGED
@@ -70,6 +70,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
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  }[];
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  }[] | undefined>;
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  getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
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+ _hasEnoughRefSeqData(uncba: Uint8Array, start: number): boolean;
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  _parseRefSeqs(uncba: Uint8Array, start: number): {
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  chrToIndex: Record<string, number>;
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  indexToChr: {
package/dist/bamFile.js CHANGED
@@ -81,26 +81,37 @@ class BamFile {
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  const indexData = await this.index.parse(opts);
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  // firstDataLine is not defined in cases where there is no data in the file
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  // (just bam header and nothing else)
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- const buffer = indexData.firstDataLine === undefined
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+ let readLen = indexData.firstDataLine === undefined
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+ ? undefined
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+ : indexData.firstDataLine.blockPosition + blockLen;
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+ const buffer = readLen === undefined
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  ? await this.bam.readFile()
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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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+ : await this.bam.read(readLen, 0);
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+ let 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) {
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  throw new Error('Not a BAM file');
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  }
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  const headLen = dataView.getInt32(4, true);
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- const decoder = new TextDecoder('utf8');
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- this.header = decoder.decode(uncba.subarray(8, 8 + headLen));
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- const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, headLen + 8);
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- this.chrToIndex = chrToIndex;
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- this.indexToChr = indexToChr;
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- return (0, sam_ts_1.parseHeaderText)(this.header);
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+ this.header = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
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+ // BAM files with many reference sequences may need more data than the
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+ // initial read provides, so re-fetch with doubled size until it fits
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+ const refSeqStart = headLen + 8;
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+ const maxRetries = 5;
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+ for (let attempt = 0; attempt < maxRetries; attempt++) {
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+ if (this._hasEnoughRefSeqData(uncba, refSeqStart)) {
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+ const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, refSeqStart);
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+ this.chrToIndex = chrToIndex;
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+ this.indexToChr = indexToChr;
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+ return (0, sam_ts_1.parseHeaderText)(this.header);
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+ }
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+ if (readLen === undefined) {
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+ throw new Error(`Insufficient data for reference sequences in ${uncba.length} bytes`);
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+ }
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+ readLen *= 2;
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+ uncba = await (0, bgzf_filehandle_1.unzip)(await this.bam.read(readLen, 0));
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+ }
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+ throw new Error(`Insufficient data for reference sequences after ${maxRetries} retries`);
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  }
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  getHeader(opts) {
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  if (!this.headerP) {
@@ -115,6 +126,22 @@ class BamFile {
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  await this.getHeader(opts);
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  return this.header;
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  }
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+ _hasEnoughRefSeqData(uncba, start) {
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+ if (start + 4 > uncba.length) {
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+ return false;
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+ }
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+ const dataView = new DataView(uncba.buffer);
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+ const nRef = dataView.getInt32(start, true);
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+ let p = start + 4;
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+ for (let i = 0; i < nRef; i += 1) {
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+ if (p + 8 > uncba.length) {
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+ return false;
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+ }
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+ const lName = dataView.getInt32(p, true);
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+ p = p + 8 + lName;
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+ }
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+ return true;
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+ }
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  _parseRefSeqs(uncba, start) {
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  const dataView = new DataView(uncba.buffer);
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  const nRef = dataView.getInt32(start, true);
@@ -123,9 +150,6 @@ class BamFile {
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  const indexToChr = [];
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  const decoder = new TextDecoder('utf8');
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  for (let i = 0; i < nRef; i += 1) {
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- if (p + 8 > uncba.length) {
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- throw new Error(`Insufficient data for reference sequences: need more than ${uncba.length} bytes`);
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- }
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  const lName = dataView.getInt32(p, true);
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  const refName = this.renameRefSeq(decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)));
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  const lRef = dataView.getInt32(p + lName + 4, true);
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
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package/esm/bamFile.d.ts CHANGED
@@ -70,6 +70,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
70
70
  }[];
71
71
  }[] | undefined>;
72
72
  getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
73
+ _hasEnoughRefSeqData(uncba: Uint8Array, start: number): boolean;
73
74
  _parseRefSeqs(uncba: Uint8Array, start: number): {
74
75
  chrToIndex: Record<string, number>;
75
76
  indexToChr: {
package/esm/bamFile.js CHANGED
@@ -75,26 +75,37 @@ export default class BamFile {
75
75
  const indexData = await this.index.parse(opts);
76
76
  // firstDataLine is not defined in cases where there is no data in the file
77
77
  // (just bam header and nothing else)
78
- const buffer = indexData.firstDataLine === undefined
78
+ let readLen = indexData.firstDataLine === undefined
79
+ ? undefined
80
+ : indexData.firstDataLine.blockPosition + blockLen;
81
+ const buffer = readLen === undefined
79
82
  ? await this.bam.readFile()
80
- : // the logic indexData.firstDataLine is a virtualOffset telling us
81
- // where the data is. It is in the middle of a virtualOffset
82
- // (provided by the bgzip block offset at blockPosition + the
83
- // virtualOffset dataPosition, so we add one extra blockLen to make
84
- // sure we consume the full header)
85
- await this.bam.read(indexData.firstDataLine.blockPosition + blockLen, 0);
86
- const uncba = await unzip(buffer);
83
+ : await this.bam.read(readLen, 0);
84
+ let uncba = await unzip(buffer);
87
85
  const dataView = new DataView(uncba.buffer);
88
86
  if (dataView.getInt32(0, true) !== BAM_MAGIC) {
89
87
  throw new Error('Not a BAM file');
90
88
  }
91
89
  const headLen = dataView.getInt32(4, true);
92
- const decoder = new TextDecoder('utf8');
93
- this.header = decoder.decode(uncba.subarray(8, 8 + headLen));
94
- const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, headLen + 8);
95
- this.chrToIndex = chrToIndex;
96
- this.indexToChr = indexToChr;
97
- return parseHeaderText(this.header);
90
+ this.header = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
91
+ // BAM files with many reference sequences may need more data than the
92
+ // initial read provides, so re-fetch with doubled size until it fits
93
+ const refSeqStart = headLen + 8;
94
+ const maxRetries = 5;
95
+ for (let attempt = 0; attempt < maxRetries; attempt++) {
96
+ if (this._hasEnoughRefSeqData(uncba, refSeqStart)) {
97
+ const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, refSeqStart);
98
+ this.chrToIndex = chrToIndex;
99
+ this.indexToChr = indexToChr;
100
+ return parseHeaderText(this.header);
101
+ }
102
+ if (readLen === undefined) {
103
+ throw new Error(`Insufficient data for reference sequences in ${uncba.length} bytes`);
104
+ }
105
+ readLen *= 2;
106
+ uncba = await unzip(await this.bam.read(readLen, 0));
107
+ }
108
+ throw new Error(`Insufficient data for reference sequences after ${maxRetries} retries`);
98
109
  }
99
110
  getHeader(opts) {
100
111
  if (!this.headerP) {
@@ -109,6 +120,22 @@ export default class BamFile {
109
120
  await this.getHeader(opts);
110
121
  return this.header;
111
122
  }
123
+ _hasEnoughRefSeqData(uncba, start) {
124
+ if (start + 4 > uncba.length) {
125
+ return false;
126
+ }
127
+ const dataView = new DataView(uncba.buffer);
128
+ const nRef = dataView.getInt32(start, true);
129
+ let p = start + 4;
130
+ for (let i = 0; i < nRef; i += 1) {
131
+ if (p + 8 > uncba.length) {
132
+ return false;
133
+ }
134
+ const lName = dataView.getInt32(p, true);
135
+ p = p + 8 + lName;
136
+ }
137
+ return true;
138
+ }
112
139
  _parseRefSeqs(uncba, start) {
113
140
  const dataView = new DataView(uncba.buffer);
114
141
  const nRef = dataView.getInt32(start, true);
@@ -117,9 +144,6 @@ export default class BamFile {
117
144
  const indexToChr = [];
118
145
  const decoder = new TextDecoder('utf8');
119
146
  for (let i = 0; i < nRef; i += 1) {
120
- if (p + 8 > uncba.length) {
121
- throw new Error(`Insufficient data for reference sequences: need more than ${uncba.length} bytes`);
122
- }
123
147
  const lName = dataView.getInt32(p, true);
124
148
  const refName = this.renameRefSeq(decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)));
125
149
  const lRef = dataView.getInt32(p + lName + 4, true);
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "7.1.18",
3
+ "version": "7.1.19",
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
@@ -139,32 +139,49 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
139
139
 
140
140
  // firstDataLine is not defined in cases where there is no data in the file
141
141
  // (just bam header and nothing else)
142
- const buffer =
142
+ let readLen =
143
143
  indexData.firstDataLine === undefined
144
+ ? undefined
145
+ : indexData.firstDataLine.blockPosition + blockLen
146
+
147
+ const buffer =
148
+ readLen === undefined
144
149
  ? await this.bam.readFile()
145
- : // the logic indexData.firstDataLine is a virtualOffset telling us
146
- // where the data is. It is in the middle of a virtualOffset
147
- // (provided by the bgzip block offset at blockPosition + the
148
- // virtualOffset dataPosition, so we add one extra blockLen to make
149
- // sure we consume the full header)
150
- await this.bam.read(
151
- indexData.firstDataLine.blockPosition + blockLen,
152
- 0,
153
- )
154
- const uncba = await unzip(buffer)
150
+ : await this.bam.read(readLen, 0)
151
+ let uncba = await unzip(buffer)
155
152
  const dataView = new DataView(uncba.buffer)
156
153
 
157
154
  if (dataView.getInt32(0, true) !== BAM_MAGIC) {
158
155
  throw new Error('Not a BAM file')
159
156
  }
160
157
  const headLen = dataView.getInt32(4, true)
161
- const decoder = new TextDecoder('utf8')
162
- this.header = decoder.decode(uncba.subarray(8, 8 + headLen))
163
-
164
- const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, headLen + 8)
165
- this.chrToIndex = chrToIndex
166
- this.indexToChr = indexToChr
167
- return parseHeaderText(this.header)
158
+ this.header = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen))
159
+
160
+ // BAM files with many reference sequences may need more data than the
161
+ // initial read provides, so re-fetch with doubled size until it fits
162
+ const refSeqStart = headLen + 8
163
+ const maxRetries = 5
164
+ for (let attempt = 0; attempt < maxRetries; attempt++) {
165
+ if (this._hasEnoughRefSeqData(uncba, refSeqStart)) {
166
+ const { chrToIndex, indexToChr } = this._parseRefSeqs(
167
+ uncba,
168
+ refSeqStart,
169
+ )
170
+ this.chrToIndex = chrToIndex
171
+ this.indexToChr = indexToChr
172
+ return parseHeaderText(this.header)
173
+ }
174
+ if (readLen === undefined) {
175
+ throw new Error(
176
+ `Insufficient data for reference sequences in ${uncba.length} bytes`,
177
+ )
178
+ }
179
+ readLen *= 2
180
+ uncba = await unzip(await this.bam.read(readLen, 0))
181
+ }
182
+ throw new Error(
183
+ `Insufficient data for reference sequences after ${maxRetries} retries`,
184
+ )
168
185
  }
169
186
 
170
187
  getHeader(opts?: BaseOpts) {
@@ -182,6 +199,23 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
182
199
  return this.header
183
200
  }
184
201
 
202
+ _hasEnoughRefSeqData(uncba: Uint8Array, start: number) {
203
+ if (start + 4 > uncba.length) {
204
+ return false
205
+ }
206
+ const dataView = new DataView(uncba.buffer)
207
+ const nRef = dataView.getInt32(start, true)
208
+ let p = start + 4
209
+ for (let i = 0; i < nRef; i += 1) {
210
+ if (p + 8 > uncba.length) {
211
+ return false
212
+ }
213
+ const lName = dataView.getInt32(p, true)
214
+ p = p + 8 + lName
215
+ }
216
+ return true
217
+ }
218
+
185
219
  _parseRefSeqs(
186
220
  uncba: Uint8Array,
187
221
  start: number,
@@ -198,12 +232,6 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
198
232
  const decoder = new TextDecoder('utf8')
199
233
 
200
234
  for (let i = 0; i < nRef; i += 1) {
201
- if (p + 8 > uncba.length) {
202
- throw new Error(
203
- `Insufficient data for reference sequences: need more than ${uncba.length} bytes`,
204
- )
205
- }
206
-
207
235
  const lName = dataView.getInt32(p, true)
208
236
  const refName = this.renameRefSeq(
209
237
  decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)),