@gmod/bam 7.3.0 → 7.3.2
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.
- package/dist/bamFile.js +8 -1
- package/dist/bamFile.js.map +1 -1
- package/dist/util.d.ts +8 -1
- package/dist/util.js.map +1 -1
- package/esm/bamFile.js +8 -1
- package/esm/bamFile.js.map +1 -1
- package/esm/util.d.ts +8 -1
- package/esm/util.js.map +1 -1
- package/package.json +2 -2
- package/src/bamFile.ts +8 -5
- package/src/util.ts +8 -1
package/dist/bamFile.js
CHANGED
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@@ -226,7 +226,14 @@ class BamFile {
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226
226
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return mateFeatLists.flat();
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227
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}
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228
228
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async _readChunkFeatures(chunk, opts) {
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229
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-
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229
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+
// Don't forward onProgress to the inner read: getRecordsForRange already
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230
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+
// reports progress at chunk granularity (downloadedBytes/totalBytes). If the
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231
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+
// filehandle's own streaming onProgress also fired this callback it would
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232
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+
// report a different `total` (this chunk's size, not the whole query),
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233
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+
// making the determinate bar jump around.
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234
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+
const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, {
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235
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+
signal: opts.signal,
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236
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+
});
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const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
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231
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return this.readBamFeatures(data, cpositions, dpositions, chunk);
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232
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}
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package/dist/bamFile.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
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|
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1
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+
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|
package/dist/util.d.ts
CHANGED
|
@@ -22,10 +22,17 @@ export interface BamOpts {
|
|
|
22
22
|
* sizes are known up front from the index. Lets callers render a determinate
|
|
23
23
|
* download progress bar.
|
|
24
24
|
*/
|
|
25
|
-
onProgress?: (bytesDownloaded: number, totalBytes
|
|
25
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
26
26
|
}
|
|
27
27
|
export interface BaseOpts {
|
|
28
28
|
signal?: AbortSignal;
|
|
29
|
+
/**
|
|
30
|
+
* Called as the index (.bai/.csi) is downloaded, with cumulative downloaded
|
|
31
|
+
* bytes and the total. The index is a whole-file read, so this streams real
|
|
32
|
+
* byte progress. Lets callers show a determinate "downloading index" bar.
|
|
33
|
+
* (total is optional to match generic-filehandle2's streaming callback.)
|
|
34
|
+
*/
|
|
35
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
29
36
|
}
|
|
30
37
|
export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[];
|
|
31
38
|
export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
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|
package/esm/bamFile.js
CHANGED
|
@@ -220,7 +220,14 @@ export default class BamFile {
|
|
|
220
220
|
return mateFeatLists.flat();
|
|
221
221
|
}
|
|
222
222
|
async _readChunkFeatures(chunk, opts) {
|
|
223
|
-
|
|
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
|
+
});
|
|
224
231
|
const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
|
|
225
232
|
return this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
226
233
|
}
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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+
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|
package/esm/util.d.ts
CHANGED
|
@@ -22,10 +22,17 @@ export interface BamOpts {
|
|
|
22
22
|
* sizes are known up front from the index. Lets callers render a determinate
|
|
23
23
|
* download progress bar.
|
|
24
24
|
*/
|
|
25
|
-
onProgress?: (bytesDownloaded: number, totalBytes
|
|
25
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
26
26
|
}
|
|
27
27
|
export interface BaseOpts {
|
|
28
28
|
signal?: AbortSignal;
|
|
29
|
+
/**
|
|
30
|
+
* Called as the index (.bai/.csi) is downloaded, with cumulative downloaded
|
|
31
|
+
* bytes and the total. The index is a whole-file read, so this streams real
|
|
32
|
+
* byte progress. Lets callers show a determinate "downloading index" bar.
|
|
33
|
+
* (total is optional to match generic-filehandle2's streaming callback.)
|
|
34
|
+
*/
|
|
35
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
29
36
|
}
|
|
30
37
|
export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[];
|
|
31
38
|
export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bam",
|
|
3
|
-
"version": "7.3.
|
|
3
|
+
"version": "7.3.2",
|
|
4
4
|
"description": "Parser for BAM and BAM index (bai) files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": {
|
|
@@ -49,7 +49,7 @@
|
|
|
49
49
|
"@gmod/bgzf-filehandle": "^6.2.0",
|
|
50
50
|
"@jbrowse/quick-lru": "^7.3.5",
|
|
51
51
|
"crc": "^4.3.2",
|
|
52
|
-
"generic-filehandle2": "^2.
|
|
52
|
+
"generic-filehandle2": "^2.2.0"
|
|
53
53
|
},
|
|
54
54
|
"devDependencies": {
|
|
55
55
|
"@eslint/js": "^10.0.1",
|
package/src/bamFile.ts
CHANGED
|
@@ -350,11 +350,14 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
350
350
|
}
|
|
351
351
|
|
|
352
352
|
async _readChunkFeatures(chunk: Chunk, opts: BaseOpts) {
|
|
353
|
-
|
|
354
|
-
|
|
355
|
-
|
|
356
|
-
|
|
357
|
-
|
|
353
|
+
// Don't forward onProgress to the inner read: getRecordsForRange already
|
|
354
|
+
// reports progress at chunk granularity (downloadedBytes/totalBytes). If the
|
|
355
|
+
// filehandle's own streaming onProgress also fired this callback it would
|
|
356
|
+
// report a different `total` (this chunk's size, not the whole query),
|
|
357
|
+
// making the determinate bar jump around.
|
|
358
|
+
const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, {
|
|
359
|
+
signal: opts.signal,
|
|
360
|
+
})
|
|
358
361
|
const {
|
|
359
362
|
buffer: data,
|
|
360
363
|
cpositions,
|
package/src/util.ts
CHANGED
|
@@ -27,11 +27,18 @@ export interface BamOpts {
|
|
|
27
27
|
* sizes are known up front from the index. Lets callers render a determinate
|
|
28
28
|
* download progress bar.
|
|
29
29
|
*/
|
|
30
|
-
onProgress?: (bytesDownloaded: number, totalBytes
|
|
30
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
|
|
31
31
|
}
|
|
32
32
|
|
|
33
33
|
export interface BaseOpts {
|
|
34
34
|
signal?: AbortSignal
|
|
35
|
+
/**
|
|
36
|
+
* Called as the index (.bai/.csi) is downloaded, with cumulative downloaded
|
|
37
|
+
* bytes and the total. The index is a whole-file read, so this streams real
|
|
38
|
+
* byte progress. Lets callers show a determinate "downloading index" bar.
|
|
39
|
+
* (total is optional to match generic-filehandle2's streaming callback.)
|
|
40
|
+
*/
|
|
41
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
|
|
35
42
|
}
|
|
36
43
|
|
|
37
44
|
export function optimizeChunks(chunks: Chunk[], lowest?: Offset) {
|