@gmod/bam 7.1.2 → 7.1.3

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Files changed (9) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/record.d.ts +1 -0
  3. package/dist/record.js +59 -0
  4. package/dist/record.js.map +1 -1
  5. package/esm/record.d.ts +1 -0
  6. package/esm/record.js +59 -0
  7. package/esm/record.js.map +1 -1
  8. package/package.json +1 -1
  9. package/src/record.ts +62 -0
package/CHANGELOG.md CHANGED
@@ -1,3 +1,7 @@
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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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+
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+
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+
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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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package/dist/record.d.ts CHANGED
@@ -23,6 +23,7 @@ export default class BamRecord {
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  get strand(): 1 | -1;
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  get b0(): number;
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  get name(): string;
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+ get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
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  get tags(): Record<string, unknown>;
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  /**
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  * @returns {boolean} true if the read is paired, regardless of whether both
package/dist/record.js CHANGED
@@ -71,6 +71,65 @@ class BamRecord {
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  }
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  return str;
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  }
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+ get NUMERIC_MD() {
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+ let p = this.b0 +
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+ this.read_name_length +
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+ this.num_cigar_bytes +
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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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+ 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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+ p += 3;
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+ if (tag === 'MD' && type === 'Z') {
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+ const start = p;
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+ while (p < blockEnd && this.byteArray[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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+ }
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+ switch (type) {
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+ case '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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+ p += 4;
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+ break;
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+ case 'c':
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+ case '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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+ 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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+ break;
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+ case 'B': {
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+ const Btype = String.fromCharCode(this.byteArray[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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+ p += limit << 2;
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+ }
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+ else if (Btype === 's' || Btype === 'S') {
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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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+ p += limit;
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+ }
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+ break;
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+ }
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+ }
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+ }
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+ return undefined;
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+ }
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  get tags() {
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  let p = this.b0 +
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  this.read_name_length +
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/record.d.ts CHANGED
@@ -23,6 +23,7 @@ export default class BamRecord {
23
23
  get strand(): 1 | -1;
24
24
  get b0(): number;
25
25
  get name(): string;
26
+ get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
26
27
  get tags(): Record<string, unknown>;
27
28
  /**
28
29
  * @returns {boolean} true if the read is paired, regardless of whether both
package/esm/record.js CHANGED
@@ -66,6 +66,65 @@ export default class BamRecord {
66
66
  }
67
67
  return str;
68
68
  }
69
+ get NUMERIC_MD() {
70
+ let p = this.b0 +
71
+ this.read_name_length +
72
+ this.num_cigar_bytes +
73
+ this.num_seq_bytes +
74
+ this.seq_length;
75
+ const blockEnd = this.bytes.end;
76
+ 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]);
80
+ p += 3;
81
+ if (tag === 'MD' && type === 'Z') {
82
+ const start = p;
83
+ while (p < blockEnd && this.byteArray[p] !== 0) {
84
+ p++;
85
+ }
86
+ return this.byteArray.subarray(start, p);
87
+ }
88
+ switch (type) {
89
+ case 'A':
90
+ p += 1;
91
+ break;
92
+ case 'i':
93
+ case 'I':
94
+ case 'f':
95
+ p += 4;
96
+ break;
97
+ case 'c':
98
+ case 'C':
99
+ p += 1;
100
+ break;
101
+ case 's':
102
+ case 'S':
103
+ p += 2;
104
+ break;
105
+ case 'Z':
106
+ case 'H':
107
+ while (p <= blockEnd && this.byteArray[p++] !== 0) { }
108
+ break;
109
+ case 'B': {
110
+ const Btype = String.fromCharCode(this.byteArray[p++]);
111
+ const limit = this._dataView.getInt32(p, true);
112
+ p += 4;
113
+ if (Btype === 'i' || Btype === 'I' || Btype === 'f') {
114
+ p += limit << 2;
115
+ }
116
+ else if (Btype === 's' || Btype === 'S') {
117
+ p += limit << 1;
118
+ }
119
+ else if (Btype === 'c' || Btype === 'C') {
120
+ p += limit;
121
+ }
122
+ break;
123
+ }
124
+ }
125
+ }
126
+ return undefined;
127
+ }
69
128
  get tags() {
70
129
  let p = this.b0 +
71
130
  this.read_name_length +
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": "7.1.2",
3
+ "version": "7.1.3",
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
@@ -98,6 +98,68 @@ export default class BamRecord {
98
98
  return str
99
99
  }
100
100
 
101
+ get NUMERIC_MD() {
102
+ let p =
103
+ this.b0 +
104
+ this.read_name_length +
105
+ this.num_cigar_bytes +
106
+ this.num_seq_bytes +
107
+ this.seq_length
108
+
109
+ const blockEnd = this.bytes.end
110
+ 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]!)
115
+ p += 3
116
+
117
+ if (tag === 'MD' && type === 'Z') {
118
+ const start = p
119
+ while (p < blockEnd && this.byteArray[p] !== 0) {
120
+ p++
121
+ }
122
+ return this.byteArray.subarray(start, p)
123
+ }
124
+
125
+ switch (type) {
126
+ case 'A':
127
+ p += 1
128
+ break
129
+ case 'i':
130
+ case 'I':
131
+ case 'f':
132
+ p += 4
133
+ break
134
+ case 'c':
135
+ case 'C':
136
+ p += 1
137
+ break
138
+ case 's':
139
+ case 'S':
140
+ p += 2
141
+ break
142
+ case 'Z':
143
+ case 'H':
144
+ while (p <= blockEnd && this.byteArray[p++] !== 0) {}
145
+ break
146
+ case 'B': {
147
+ const Btype = String.fromCharCode(this.byteArray[p++]!)
148
+ const limit = this._dataView.getInt32(p, true)
149
+ p += 4
150
+ if (Btype === 'i' || Btype === 'I' || Btype === 'f') {
151
+ p += limit << 2
152
+ } else if (Btype === 's' || Btype === 'S') {
153
+ p += limit << 1
154
+ } else if (Btype === 'c' || Btype === 'C') {
155
+ p += limit
156
+ }
157
+ break
158
+ }
159
+ }
160
+ }
161
+ return undefined
162
+ }
101
163
  get tags() {
102
164
  let p =
103
165
  this.b0 +