@gmod/bam 7.2.4 → 7.3.1

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 (28) hide show
  1. package/README.md +28 -1
  2. package/dist/bamFile.d.ts +3 -2
  3. package/dist/bamFile.js +32 -19
  4. package/dist/bamFile.js.map +1 -1
  5. package/dist/htsget.js +1 -0
  6. package/dist/htsget.js.map +1 -1
  7. package/dist/record.d.ts +1 -1
  8. package/dist/record.js +111 -162
  9. package/dist/record.js.map +1 -1
  10. package/dist/util.d.ts +8 -0
  11. package/dist/util.js +6 -2
  12. package/dist/util.js.map +1 -1
  13. package/esm/bamFile.d.ts +3 -2
  14. package/esm/bamFile.js +32 -19
  15. package/esm/bamFile.js.map +1 -1
  16. package/esm/htsget.js +1 -0
  17. package/esm/htsget.js.map +1 -1
  18. package/esm/record.d.ts +1 -1
  19. package/esm/record.js +111 -162
  20. package/esm/record.js.map +1 -1
  21. package/esm/util.d.ts +8 -0
  22. package/esm/util.js +6 -2
  23. package/esm/util.js.map +1 -1
  24. package/package.json +9 -9
  25. package/src/bamFile.ts +34 -23
  26. package/src/htsget.ts +1 -0
  27. package/src/record.ts +128 -145
  28. package/src/util.ts +13 -2
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/util.d.ts CHANGED
@@ -15,6 +15,14 @@ export interface BamOpts {
15
15
  maxInsertSize?: number;
16
16
  signal?: AbortSignal;
17
17
  filterBy?: FilterBy;
18
+ /**
19
+ * Called as the BGZF blocks covering the query are fetched, with cumulative
20
+ * downloaded bytes and the total to fetch. Reported at block granularity (one
21
+ * tick per chunk, including instant ticks for cache hits) since chunk byte
22
+ * sizes are known up front from the index. Lets callers render a determinate
23
+ * download progress bar.
24
+ */
25
+ onProgress?: (bytesDownloaded: number, totalBytes: number) => void;
18
26
  }
19
27
  export interface BaseOpts {
20
28
  signal?: AbortSignal;
package/dist/util.js CHANGED
@@ -179,8 +179,9 @@ function applyFilters(records, filterBy) {
179
179
  return out;
180
180
  }
181
181
  // Append records overlapping [min, max) on `chrId` into `out` (or a fresh
182
- // array if omitted). Records are assumed sorted by start, so we stop scanning
183
- // at the first record past `max`. Returns the populated array.
182
+ // array if omitted). Records are assumed coordinate-sorted (by ref_id, then
183
+ // start), so we stop scanning once we pass `max` within `chrId` or move past
184
+ // `chrId` entirely. Returns the populated array.
184
185
  function appendInRange(records, chrId, min, max, out = []) {
185
186
  for (let i = 0, l = records.length; i < l; i++) {
186
187
  const r = records[i];
@@ -192,6 +193,9 @@ function appendInRange(records, chrId, min, max, out = []) {
192
193
  out.push(r);
193
194
  }
194
195
  }
196
+ else if (r.ref_id > chrId) {
197
+ break;
198
+ }
195
199
  }
196
200
  return out;
197
201
  }
package/dist/util.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/bamFile.d.ts CHANGED
@@ -71,14 +71,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
71
71
  }[];
72
72
  }[] | undefined>;
73
73
  getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
74
+ private getSeqId;
74
75
  getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
75
76
  private evictOverlappingChunks;
76
77
  private _fetchChunkFeaturesDirect;
77
78
  fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
78
79
  _readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<T[]>;
79
80
  readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<T[]>;
80
- hasRefSeq(seqName: string): Promise<boolean>;
81
- lineCount(seqName: string): Promise<number>;
81
+ hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
82
+ lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
82
83
  indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;
83
84
  blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[] | never[]>;
84
85
  clearFeatureCache(): void;
package/esm/bamFile.js CHANGED
@@ -111,9 +111,14 @@ export default class BamFile {
111
111
  await this.getHeader(opts);
112
112
  return this.header;
113
113
  }
114
- async getRecordsForRange(chr, min, max, opts) {
114
+ // Resolve a reference name to its numeric id, ensuring the header (which
115
+ // populates chrToIndex) has been parsed first.
116
+ async getSeqId(seqName, opts) {
115
117
  await this.getHeader(opts);
116
- const chrId = this.chrToIndex?.[chr];
118
+ return this.chrToIndex?.[seqName];
119
+ }
120
+ async getRecordsForRange(chr, min, max, opts) {
121
+ const chrId = await this.getSeqId(chr, opts);
117
122
  if (chrId === undefined || !this.index) {
118
123
  return [];
119
124
  }
@@ -129,8 +134,14 @@ export default class BamFile {
129
134
  }
130
135
  }
131
136
  async _fetchChunkFeaturesDirect(chunks, chrId, min, max, opts = {}) {
132
- const { viewAsPairs, filterBy } = opts;
137
+ const { viewAsPairs, filterBy, onProgress } = opts;
133
138
  const result = [];
139
+ let totalBytes = 0;
140
+ for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
141
+ totalBytes += chunks[ci].fetchedSize();
142
+ }
143
+ let downloadedBytes = 0;
144
+ onProgress?.(0, totalBytes);
134
145
  for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
135
146
  const chunk = chunks[ci];
136
147
  const cacheKey = chunkCacheKey(chunk, filterBy);
@@ -151,6 +162,8 @@ export default class BamFile {
151
162
  features: records,
152
163
  });
153
164
  }
165
+ downloadedBytes += chunk.fetchedSize();
166
+ onProgress?.(downloadedBytes, totalBytes);
154
167
  appendInRange(records, chrId, min, max, result);
155
168
  }
156
169
  if (viewAsPairs) {
@@ -207,7 +220,14 @@ export default class BamFile {
207
220
  return mateFeatLists.flat();
208
221
  }
209
222
  async _readChunkFeatures(chunk, opts) {
210
- const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
223
+ // Don't forward onProgress to the inner read: getRecordsForRange already
224
+ // reports progress at chunk granularity (downloadedBytes/totalBytes). If the
225
+ // filehandle's own streaming onProgress also fired this callback it would
226
+ // report a different `total` (this chunk's size, not the whole query),
227
+ // making the determinate bar jump around.
228
+ const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, {
229
+ signal: opts.signal,
230
+ });
211
231
  const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
212
232
  return this.readBamFeatures(data, cpositions, dpositions, chunk);
213
233
  }
@@ -248,24 +268,24 @@ export default class BamFile {
248
268
  }
249
269
  return sink;
250
270
  }
251
- async hasRefSeq(seqName) {
252
- const seqId = this.chrToIndex?.[seqName];
271
+ async hasRefSeq(seqName, opts) {
272
+ const seqId = await this.getSeqId(seqName, opts);
253
273
  return !this.index || seqId === undefined
254
274
  ? false
255
275
  : this.index.hasRefSeq(seqId);
256
276
  }
257
- async lineCount(seqName) {
258
- const seqId = this.chrToIndex?.[seqName];
277
+ async lineCount(seqName, opts) {
278
+ const seqId = await this.getSeqId(seqName, opts);
259
279
  return !this.index || seqId === undefined ? 0 : this.index.lineCount(seqId);
260
280
  }
261
281
  async indexCov(seqName, start, end) {
262
- const seqId = this.chrToIndex?.[seqName];
282
+ const seqId = await this.getSeqId(seqName);
263
283
  return !this.index || seqId === undefined
264
284
  ? []
265
285
  : this.index.indexCov(seqId, start, end);
266
286
  }
267
287
  async blocksForRange(seqName, start, end, opts) {
268
- const seqId = this.chrToIndex?.[seqName];
288
+ const seqId = await this.getSeqId(seqName, opts);
269
289
  return !this.index || seqId === undefined
270
290
  ? []
271
291
  : this.index.blocksForRange(seqId, start, end, opts);
@@ -278,16 +298,9 @@ export default class BamFile {
278
298
  return 0;
279
299
  }
280
300
  await this.getHeader(opts);
281
- const chrToIndex = this.chrToIndex;
282
- if (!chrToIndex) {
283
- throw new Error('Header not yet parsed');
284
- }
285
301
  const mapped = regions.flatMap(r => {
286
- const refId = chrToIndex[r.refName];
287
- if (refId === undefined) {
288
- return [];
289
- }
290
- return [{ refId, start: r.start, end: r.end }];
302
+ const refId = this.chrToIndex?.[r.refName];
303
+ return refId === undefined ? [] : [{ refId, start: r.start, end: r.end }];
291
304
  });
292
305
  return this.index.estimatedBytesForRegions(mapped, opts);
293
306
  }
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/esm/htsget.js CHANGED
@@ -34,6 +34,7 @@ export default class HtsgetFile extends BamFile {
34
34
  this.trackId = args.trackId;
35
35
  }
36
36
  async getRecordsForRange(chr, min, max, opts) {
37
+ await this.getHeader(opts);
37
38
  const base = `${this.baseUrl}/${this.trackId}`;
38
39
  const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
39
40
  const chrId = this.chrToIndex?.[chr];
package/esm/htsget.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,eAAe,EAAE,MAAM,UAAU,CAAA;AAC1C,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAC3D,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAWlD,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IACpD,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAClC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IAC5E,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,EAAE,GAAG,EAAE,OAAO,EAAe,EAAE,IAAkB;IACzE,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC;QACpB,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAClD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAAC,GAAkB,EAAE,IAAkB;IAClE,2EAA2E;IAC3E,OAAO,gBAAgB,CACrB,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,KAAK,CAAC,MAAM,UAAU,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CACxE,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAEnB,SAAQ,OAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEvB,YAAY,IAIX;QACC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;YAC5D,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;QAEF,MAAM,IAAI,GAAG,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,eAAe,CAC3C,KAAK,EACL,EAAE,EACF,EAAE,EACF,IAAI,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QAED,OAAO,aAAa,CAAC,UAAU,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IACnD,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE;YACnD,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC,CAAA;QACF,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAE1C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAC,CAAA;QACjE,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
package/esm/record.d.ts CHANGED
@@ -36,7 +36,7 @@ export default class BamRecord {
36
36
  get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
37
37
  get tags(): Record<string, unknown>;
38
38
  getTag(tagName: string): unknown;
39
- getTagRaw(tagName: string): string | number | Uint8Array<ArrayBufferLike> | number[] | Uint32Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int8Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
39
+ getTagRaw(tagName: string): string | number | Uint8Array<ArrayBufferLike> | number[] | Int8Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Uint32Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
40
40
  private _findTag;
41
41
  private _computeTags;
42
42
  isPaired(): boolean;