@gmod/bam 7.1.3 → 7.1.4

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Files changed (7) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/record.js +25 -22
  3. package/dist/record.js.map +1 -1
  4. package/esm/record.js +25 -22
  5. package/esm/record.js.map +1 -1
  6. package/package.json +1 -1
  7. package/src/record.ts +25 -23
package/CHANGELOG.md CHANGED
@@ -1,3 +1,7 @@
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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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+
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+
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+
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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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package/dist/record.js CHANGED
@@ -78,50 +78,52 @@ class BamRecord {
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  this.num_seq_bytes +
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  this.seq_length;
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  const blockEnd = this.bytes.end;
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+ const ba = this.byteArray;
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  while (p < blockEnd) {
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- const tag = String.fromCharCode(this.byteArray[p]) +
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- String.fromCharCode(this.byteArray[p + 1]);
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- const type = String.fromCharCode(this.byteArray[p + 2]);
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+ const tag1 = ba[p];
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+ const tag2 = ba[p + 1];
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+ const type = ba[p + 2];
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  p += 3;
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- if (tag === 'MD' && type === 'Z') {
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+ // 'M' = 0x4D, 'D' = 0x44, 'Z' = 0x5A
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+ if (tag1 === 0x4d && tag2 === 0x44 && type === 0x5a) {
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  const start = p;
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- while (p < blockEnd && this.byteArray[p] !== 0) {
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+ while (p < blockEnd && ba[p] !== 0) {
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  p++;
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  }
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- return this.byteArray.subarray(start, p);
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+ return ba.subarray(start, p);
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  }
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  switch (type) {
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- case 'A':
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+ case 0x41: // 'A'
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  p += 1;
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  break;
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- case 'i':
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- case 'I':
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- case 'f':
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+ case 0x69: // 'i'
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+ case 0x49: // 'I'
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+ case 0x66: // 'f'
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  p += 4;
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  break;
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- case 'c':
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- case 'C':
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+ case 0x63: // 'c'
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+ case 0x43: // 'C'
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  p += 1;
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  break;
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- case 's':
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- case 'S':
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+ case 0x73: // 's'
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+ case 0x53: // 'S'
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  p += 2;
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  break;
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- case 'Z':
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- case 'H':
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- while (p <= blockEnd && this.byteArray[p++] !== 0) { }
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+ case 0x5a: // 'Z'
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+ case 0x48: // 'H'
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+ while (p <= blockEnd && ba[p++] !== 0) { }
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  break;
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- case 'B': {
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- const Btype = String.fromCharCode(this.byteArray[p++]);
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+ case 0x42: { // 'B'
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+ const Btype = ba[p++];
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  const limit = this._dataView.getInt32(p, true);
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  p += 4;
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- if (Btype === 'i' || Btype === 'I' || Btype === 'f') {
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+ if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
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  p += limit << 2;
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  }
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- else if (Btype === 's' || Btype === 'S') {
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+ else if (Btype === 0x73 || Btype === 0x53) {
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  p += limit << 1;
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  }
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- else if (Btype === 'c' || Btype === 'C') {
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+ else if (Btype === 0x63 || Btype === 0x43) {
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  p += limit;
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  }
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  break;
@@ -516,4 +518,5 @@ cacheGetter(BamRecord, 'cigarAndLength');
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  cacheGetter(BamRecord, 'seq');
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  cacheGetter(BamRecord, 'qual');
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  cacheGetter(BamRecord, 'end');
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+ cacheGetter(BamRecord, 'NUMERIC_MD');
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  //# sourceMappingURL=record.js.map
package/dist/record.js.map CHANGED
@@ -1 +1 @@
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- 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package/esm/record.js CHANGED
@@ -73,50 +73,52 @@ export default class BamRecord {
73
73
  this.num_seq_bytes +
74
74
  this.seq_length;
75
75
  const blockEnd = this.bytes.end;
76
+ const ba = this.byteArray;
76
77
  while (p < blockEnd) {
77
- const tag = String.fromCharCode(this.byteArray[p]) +
78
- String.fromCharCode(this.byteArray[p + 1]);
79
- const type = String.fromCharCode(this.byteArray[p + 2]);
78
+ const tag1 = ba[p];
79
+ const tag2 = ba[p + 1];
80
+ const type = ba[p + 2];
80
81
  p += 3;
81
- if (tag === 'MD' && type === 'Z') {
82
+ // 'M' = 0x4D, 'D' = 0x44, 'Z' = 0x5A
83
+ if (tag1 === 0x4d && tag2 === 0x44 && type === 0x5a) {
82
84
  const start = p;
83
- while (p < blockEnd && this.byteArray[p] !== 0) {
85
+ while (p < blockEnd && ba[p] !== 0) {
84
86
  p++;
85
87
  }
86
- return this.byteArray.subarray(start, p);
88
+ return ba.subarray(start, p);
87
89
  }
88
90
  switch (type) {
89
- case 'A':
91
+ case 0x41: // 'A'
90
92
  p += 1;
91
93
  break;
92
- case 'i':
93
- case 'I':
94
- case 'f':
94
+ case 0x69: // 'i'
95
+ case 0x49: // 'I'
96
+ case 0x66: // 'f'
95
97
  p += 4;
96
98
  break;
97
- case 'c':
98
- case 'C':
99
+ case 0x63: // 'c'
100
+ case 0x43: // 'C'
99
101
  p += 1;
100
102
  break;
101
- case 's':
102
- case 'S':
103
+ case 0x73: // 's'
104
+ case 0x53: // 'S'
103
105
  p += 2;
104
106
  break;
105
- case 'Z':
106
- case 'H':
107
- while (p <= blockEnd && this.byteArray[p++] !== 0) { }
107
+ case 0x5a: // 'Z'
108
+ case 0x48: // 'H'
109
+ while (p <= blockEnd && ba[p++] !== 0) { }
108
110
  break;
109
- case 'B': {
110
- const Btype = String.fromCharCode(this.byteArray[p++]);
111
+ case 0x42: { // 'B'
112
+ const Btype = ba[p++];
111
113
  const limit = this._dataView.getInt32(p, true);
112
114
  p += 4;
113
- if (Btype === 'i' || Btype === 'I' || Btype === 'f') {
115
+ if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
114
116
  p += limit << 2;
115
117
  }
116
- else if (Btype === 's' || Btype === 'S') {
118
+ else if (Btype === 0x73 || Btype === 0x53) {
117
119
  p += limit << 1;
118
120
  }
119
- else if (Btype === 'c' || Btype === 'C') {
121
+ else if (Btype === 0x63 || Btype === 0x43) {
120
122
  p += limit;
121
123
  }
122
124
  break;
@@ -510,4 +512,5 @@ cacheGetter(BamRecord, 'cigarAndLength');
510
512
  cacheGetter(BamRecord, 'seq');
511
513
  cacheGetter(BamRecord, 'qual');
512
514
  cacheGetter(BamRecord, 'end');
515
+ cacheGetter(BamRecord, 'NUMERIC_MD');
513
516
  //# sourceMappingURL=record.js.map
package/esm/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "7.1.3",
3
+ "version": "7.1.4",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
package/src/record.ts CHANGED
@@ -107,51 +107,52 @@ export default class BamRecord {
107
107
  this.seq_length
108
108
 
109
109
  const blockEnd = this.bytes.end
110
+ const ba = this.byteArray
110
111
  while (p < blockEnd) {
111
- const tag =
112
- String.fromCharCode(this.byteArray[p]!) +
113
- String.fromCharCode(this.byteArray[p + 1]!)
114
- const type = String.fromCharCode(this.byteArray[p + 2]!)
112
+ const tag1 = ba[p]!
113
+ const tag2 = ba[p + 1]!
114
+ const type = ba[p + 2]!
115
115
  p += 3
116
116
 
117
- if (tag === 'MD' && type === 'Z') {
117
+ // 'M' = 0x4D, 'D' = 0x44, 'Z' = 0x5A
118
+ if (tag1 === 0x4d && tag2 === 0x44 && type === 0x5a) {
118
119
  const start = p
119
- while (p < blockEnd && this.byteArray[p] !== 0) {
120
+ while (p < blockEnd && ba[p] !== 0) {
120
121
  p++
121
122
  }
122
- return this.byteArray.subarray(start, p)
123
+ return ba.subarray(start, p)
123
124
  }
124
125
 
125
126
  switch (type) {
126
- case 'A':
127
+ case 0x41: // 'A'
127
128
  p += 1
128
129
  break
129
- case 'i':
130
- case 'I':
131
- case 'f':
130
+ case 0x69: // 'i'
131
+ case 0x49: // 'I'
132
+ case 0x66: // 'f'
132
133
  p += 4
133
134
  break
134
- case 'c':
135
- case 'C':
135
+ case 0x63: // 'c'
136
+ case 0x43: // 'C'
136
137
  p += 1
137
138
  break
138
- case 's':
139
- case 'S':
139
+ case 0x73: // 's'
140
+ case 0x53: // 'S'
140
141
  p += 2
141
142
  break
142
- case 'Z':
143
- case 'H':
144
- while (p <= blockEnd && this.byteArray[p++] !== 0) {}
143
+ case 0x5a: // 'Z'
144
+ case 0x48: // 'H'
145
+ while (p <= blockEnd && ba[p++] !== 0) {}
145
146
  break
146
- case 'B': {
147
- const Btype = String.fromCharCode(this.byteArray[p++]!)
147
+ case 0x42: { // 'B'
148
+ const Btype = ba[p++]!
148
149
  const limit = this._dataView.getInt32(p, true)
149
150
  p += 4
150
- if (Btype === 'i' || Btype === 'I' || Btype === 'f') {
151
+ if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
151
152
  p += limit << 2
152
- } else if (Btype === 's' || Btype === 'S') {
153
+ } else if (Btype === 0x73 || Btype === 0x53) {
153
154
  p += limit << 1
154
- } else if (Btype === 'c' || Btype === 'C') {
155
+ } else if (Btype === 0x63 || Btype === 0x43) {
155
156
  p += limit
156
157
  }
157
158
  break
@@ -613,3 +614,4 @@ cacheGetter(BamRecord, 'cigarAndLength')
613
614
  cacheGetter(BamRecord, 'seq')
614
615
  cacheGetter(BamRecord, 'qual')
615
616
  cacheGetter(BamRecord, 'end')
617
+ cacheGetter(BamRecord, 'NUMERIC_MD')