@gmod/bam 3.0.2 → 4.0.0

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 (14) hide show
  1. package/CHANGELOG.md +8 -0
  2. package/dist/bai.js +1 -1
  3. package/dist/bai.js.map +1 -1
  4. package/dist/record.d.ts +1 -2
  5. package/dist/record.js +128 -151
  6. package/dist/record.js.map +1 -1
  7. package/esm/bai.js +1 -1
  8. package/esm/bai.js.map +1 -1
  9. package/esm/record.d.ts +1 -2
  10. package/esm/record.js +128 -151
  11. package/esm/record.js.map +1 -1
  12. package/package.json +1 -1
  13. package/src/bai.ts +2 -1
  14. package/src/record.ts +112 -152
package/CHANGELOG.md CHANGED
@@ -1,3 +1,11 @@
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+ # [4.0.0](https://github.com/GMOD/bam-js/compare/v3.0.3...v4.0.0) (2024-11-12)
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+ ## [3.0.3](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.3) (2024-11-11)
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  ## [3.0.2](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.2) (2024-11-11)
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package/dist/bai.js CHANGED
@@ -172,7 +172,7 @@ class BAI extends indexFile_1.default {
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  if (ba.binIndex[bin]) {
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  const binChunks = ba.binIndex[bin];
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  for (const binChunk of binChunks) {
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- chunks.push(binChunk);
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+ chunks.push(new chunk_1.default(binChunk.minv, binChunk.maxv, bin));
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  }
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  }
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  }
package/dist/bai.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/record.d.ts CHANGED
@@ -19,8 +19,7 @@ export default class BamRecord {
19
19
  get id(): number;
20
20
  get mq(): number | undefined;
21
21
  get score(): number | undefined;
22
- get qual(): string | undefined;
23
- get qualRaw(): Buffer | undefined;
22
+ get qual(): Buffer | undefined;
24
23
  get strand(): 1 | -1;
25
24
  get b0(): number;
26
25
  get name(): string;
package/dist/record.js CHANGED
@@ -37,10 +37,6 @@ class BamRecord {
37
37
  return this.mq;
38
38
  }
39
39
  get qual() {
40
- var _a;
41
- return (_a = this.qualRaw) === null || _a === void 0 ? void 0 : _a.join(' ');
42
- }
43
- get qualRaw() {
44
40
  if (this.isSegmentUnmapped()) {
45
41
  return;
46
42
  }
@@ -72,162 +68,143 @@ class BamRecord {
72
68
  const tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
73
69
  const type = String.fromCharCode(byteArray[p + 2]);
74
70
  p += 3;
75
- let value;
76
- switch (type) {
77
- case 'A': {
78
- value = String.fromCharCode(byteArray[p]);
79
- p += 1;
80
- break;
81
- }
82
- case 'i': {
83
- value = byteArray.readInt32LE(p);
84
- p += 4;
85
- break;
86
- }
87
- case 'I': {
88
- value = byteArray.readUInt32LE(p);
89
- p += 4;
90
- break;
91
- }
92
- case 'c': {
93
- value = byteArray.readInt8(p);
94
- p += 1;
95
- break;
96
- }
97
- case 'C': {
98
- value = byteArray.readUInt8(p);
99
- p += 1;
100
- break;
101
- }
102
- case 's': {
103
- value = byteArray.readInt16LE(p);
104
- p += 2;
105
- break;
106
- }
107
- case 'S': {
108
- value = byteArray.readUInt16LE(p);
109
- p += 2;
110
- break;
111
- }
112
- case 'f': {
113
- value = byteArray.readFloatLE(p);
114
- p += 4;
115
- break;
116
- }
117
- case 'Z':
118
- case 'H': {
119
- value = '';
120
- while (p <= blockEnd) {
121
- const cc = byteArray[p++];
122
- if (cc === 0) {
123
- break;
124
- }
125
- else {
126
- value += String.fromCharCode(cc);
127
- }
128
- }
129
- break;
130
- }
131
- case 'B': {
132
- value = '';
71
+ if (type === 'A') {
72
+ tags[tag] = String.fromCharCode(byteArray[p]);
73
+ p += 1;
74
+ }
75
+ else if (type === 'i') {
76
+ tags[tag] = byteArray.readInt32LE(p);
77
+ p += 4;
78
+ }
79
+ else if (type === 'I') {
80
+ tags[tag] = byteArray.readUInt32LE(p);
81
+ p += 4;
82
+ }
83
+ else if (type === 'c') {
84
+ tags[tag] = byteArray.readInt8(p);
85
+ p += 1;
86
+ }
87
+ else if (type === 'C') {
88
+ tags[tag] = byteArray.readUInt8(p);
89
+ p += 1;
90
+ }
91
+ else if (type === 's') {
92
+ tags[tag] = byteArray.readInt16LE(p);
93
+ p += 2;
94
+ }
95
+ else if (type === 'S') {
96
+ tags[tag] = byteArray.readUInt16LE(p);
97
+ p += 2;
98
+ }
99
+ else if (type === 'f') {
100
+ tags[tag] = byteArray.readFloatLE(p);
101
+ p += 4;
102
+ }
103
+ else if (type === 'Z' || type === 'H') {
104
+ const value = [];
105
+ while (p <= blockEnd) {
133
106
  const cc = byteArray[p++];
134
- const Btype = String.fromCharCode(cc);
135
- const limit = byteArray.readInt32LE(p);
136
- p += 4;
137
- if (Btype === 'i') {
138
- if (tag === 'CG') {
139
- for (let k = 0; k < limit; k++) {
140
- const cigop = byteArray.readInt32LE(p);
141
- const lop = cigop >> 4;
142
- const op = CIGAR_DECODER[cigop & 0xf];
143
- value += lop + op;
144
- p += 4;
145
- }
146
- }
147
- else {
148
- for (let k = 0; k < limit; k++) {
149
- value += byteArray.readInt32LE(p);
150
- if (k + 1 < limit) {
151
- value += ',';
152
- }
153
- p += 4;
154
- }
155
- }
107
+ if (cc !== 0) {
108
+ value.push(String.fromCharCode(cc));
156
109
  }
157
- if (Btype === 'I') {
158
- if (tag === 'CG') {
159
- for (let k = 0; k < limit; k++) {
160
- const cigop = byteArray.readUInt32LE(p);
161
- const lop = cigop >> 4;
162
- const op = CIGAR_DECODER[cigop & 0xf];
163
- value += lop + op;
164
- p += 4;
165
- }
166
- }
167
- else {
168
- for (let k = 0; k < limit; k++) {
169
- value += byteArray.readUInt32LE(p);
170
- if (k + 1 < limit) {
171
- value += ',';
172
- }
173
- p += 4;
174
- }
175
- }
110
+ else {
111
+ break;
176
112
  }
177
- if (Btype === 's') {
178
- for (let k = 0; k < limit; k++) {
179
- value += byteArray.readInt16LE(p);
180
- if (k + 1 < limit) {
181
- value += ',';
182
- }
183
- p += 2;
184
- }
185
- }
186
- if (Btype === 'S') {
113
+ }
114
+ tags[tag] = value.join('');
115
+ }
116
+ else if (type === 'B') {
117
+ const cc = byteArray[p++];
118
+ const Btype = String.fromCharCode(cc);
119
+ const limit = byteArray.readInt32LE(p);
120
+ p += 4;
121
+ if (Btype === 'i') {
122
+ if (tag === 'CG') {
123
+ const value = [];
187
124
  for (let k = 0; k < limit; k++) {
188
- value += byteArray.readUInt16LE(p);
189
- if (k + 1 < limit) {
190
- value += ',';
191
- }
192
- p += 2;
125
+ const cigop = byteArray.readInt32LE(p);
126
+ const lop = cigop >> 4;
127
+ const op = CIGAR_DECODER[cigop & 0xf];
128
+ value.push(lop + op);
129
+ p += 4;
193
130
  }
131
+ tags[tag] = value.join('');
194
132
  }
195
- if (Btype === 'c') {
133
+ else {
134
+ const value = [];
196
135
  for (let k = 0; k < limit; k++) {
197
- value += byteArray.readInt8(p);
198
- if (k + 1 < limit) {
199
- value += ',';
200
- }
201
- p += 1;
136
+ value.push(byteArray.readInt32LE(p));
137
+ p += 4;
202
138
  }
139
+ tags[tag] = value;
203
140
  }
204
- if (Btype === 'C') {
141
+ }
142
+ else if (Btype === 'I') {
143
+ if (tag === 'CG') {
144
+ const value = [];
205
145
  for (let k = 0; k < limit; k++) {
206
- value += byteArray.readUInt8(p);
207
- if (k + 1 < limit) {
208
- value += ',';
209
- }
210
- p += 1;
146
+ const cigop = byteArray.readUInt32LE(p);
147
+ const lop = cigop >> 4;
148
+ const op = CIGAR_DECODER[cigop & 0xf];
149
+ value.push(lop + op);
150
+ p += 4;
211
151
  }
152
+ tags[tag] = value.join('');
212
153
  }
213
- if (Btype === 'f') {
154
+ else {
155
+ const value = [];
214
156
  for (let k = 0; k < limit; k++) {
215
- value += byteArray.readFloatLE(p);
216
- if (k + 1 < limit) {
217
- value += ',';
218
- }
157
+ value.push(byteArray.readUInt32LE(p));
219
158
  p += 4;
220
159
  }
160
+ tags[tag] = value;
221
161
  }
222
- break;
223
162
  }
224
- default: {
225
- console.warn(`Unknown BAM tag type '${type}', tags may be incomplete`);
226
- value = undefined;
227
- p = blockEnd;
228
- } // stop parsing tags
163
+ else if (Btype === 's') {
164
+ const value = [];
165
+ for (let k = 0; k < limit; k++) {
166
+ value.push(byteArray.readInt16LE(p));
167
+ p += 2;
168
+ }
169
+ tags[tag] = value;
170
+ }
171
+ else if (Btype === 'S') {
172
+ const value = [];
173
+ for (let k = 0; k < limit; k++) {
174
+ value.push(byteArray.readUInt16LE(p));
175
+ p += 2;
176
+ }
177
+ tags[tag] = value;
178
+ }
179
+ else if (Btype === 'c') {
180
+ const value = [];
181
+ for (let k = 0; k < limit; k++) {
182
+ value.push(byteArray.readInt8(p));
183
+ p += 1;
184
+ }
185
+ tags[tag] = value;
186
+ }
187
+ else if (Btype === 'C') {
188
+ const value = [];
189
+ for (let k = 0; k < limit; k++) {
190
+ value.push(byteArray.readUInt8(p));
191
+ p += 1;
192
+ }
193
+ tags[tag] = value;
194
+ }
195
+ else if (Btype === 'f') {
196
+ const value = [];
197
+ for (let k = 0; k < limit; k++) {
198
+ value.push(byteArray.readFloatLE(p));
199
+ p += 4;
200
+ }
201
+ tags[tag] = value;
202
+ }
203
+ }
204
+ else {
205
+ console.error('Unknown BAM tag type', type);
206
+ break;
229
207
  }
230
- tags[tag] = value;
231
208
  }
232
209
  return tags;
233
210
  }
@@ -291,7 +268,7 @@ class BamRecord {
291
268
  }
292
269
  const numCigarOps = this.num_cigar_ops;
293
270
  let p = this.b0 + this.read_name_length;
294
- let CIGAR = '';
271
+ const CIGAR = [];
295
272
  // check for CG tag by inspecting whether the CIGAR field contains a clip
296
273
  // that consumes entire seqLen
297
274
  let cigop = this.byteArray.readInt32LE(p);
@@ -318,16 +295,16 @@ class BamRecord {
318
295
  cigop = this.byteArray.readInt32LE(p);
319
296
  lop = cigop >> 4;
320
297
  op = CIGAR_DECODER[cigop & 0xf];
321
- CIGAR += lop + op;
322
- // soft clip, hard clip, and insertion don't count toward
323
- // the length on the reference
298
+ CIGAR.push(lop + op);
299
+ // soft clip, hard clip, and insertion don't count toward the length on
300
+ // the reference
324
301
  if (op !== 'H' && op !== 'S' && op !== 'I') {
325
302
  lref += lop;
326
303
  }
327
304
  p += 4;
328
305
  }
329
306
  return {
330
- CIGAR,
307
+ CIGAR: CIGAR.join(''),
331
308
  length_on_ref: lref,
332
309
  };
333
310
  }
@@ -352,18 +329,18 @@ class BamRecord {
352
329
  const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
353
330
  const seqBytes = this.num_seq_bytes;
354
331
  const len = this.seq_length;
355
- let buf = '';
332
+ const buf = [];
356
333
  let i = 0;
357
334
  for (let j = 0; j < seqBytes; ++j) {
358
335
  const sb = byteArray[p + j];
359
- buf += SEQRET_DECODER[(sb & 0xf0) >> 4];
336
+ buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
360
337
  i++;
361
338
  if (i < len) {
362
- buf += SEQRET_DECODER[sb & 0x0f];
339
+ buf.push(SEQRET_DECODER[sb & 0x0f]);
363
340
  i++;
364
341
  }
365
342
  }
366
- return buf;
343
+ return buf.join('');
367
344
  }
368
345
  // adapted from igv.js
369
346
  get pair_orientation() {
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/bai.js CHANGED
@@ -154,7 +154,7 @@ export default class BAI extends IndexFile {
154
154
  if (ba.binIndex[bin]) {
155
155
  const binChunks = ba.binIndex[bin];
156
156
  for (const binChunk of binChunks) {
157
- chunks.push(binChunk);
157
+ chunks.push(new Chunk(binChunk.minv, binChunk.maxv, bin));
158
158
  }
159
159
  }
160
160
  }
package/esm/bai.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/record.d.ts CHANGED
@@ -19,8 +19,7 @@ export default class BamRecord {
19
19
  get id(): number;
20
20
  get mq(): number | undefined;
21
21
  get score(): number | undefined;
22
- get qual(): string | undefined;
23
- get qualRaw(): Buffer | undefined;
22
+ get qual(): Buffer | undefined;
24
23
  get strand(): 1 | -1;
25
24
  get b0(): number;
26
25
  get name(): string;