@gmod/tabix 3.8.0 → 3.8.1

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Files changed (7) hide show
  1. package/dist/tabix-bundle.js +1 -1
  2. package/dist/tabixIndexedFile.d.ts +12 -6
  3. package/dist/tabixIndexedFile.js.map +1 -1
  4. package/esm/tabixIndexedFile.d.ts +12 -6
  5. package/esm/tabixIndexedFile.js.map +1 -1
  6. package/package.json +2 -2
  7. package/src/tabixIndexedFile.ts +12 -6
package/dist/tabixIndexedFile.d.ts CHANGED
@@ -49,12 +49,18 @@ export default class TabixIndexedFile {
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  * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
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  * asking for 800 whole decompressed chunks — unbounded in practice. It now
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  * means 50MB, twenty times under the default, and the name did not change
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- * so nothing warns. jbrowse still passes exactly that in nine adapters:
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- * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
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- * 47 refills out of 47 on the warm pass against 0 at the default, holding
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- * 82.7MB in a single entry — over the budget it was given, because the last
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- * settled entry is kept whatever the budget. If you pinned a value here
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- * before v3.5.2, it does not mean what it did.
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+ * so nothing warns. If you pinned a value here before v3.5.2, it does not
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+ * mean what it did.
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+ *
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+ * What that costs is worth keeping, because it is the reason to check a
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+ * pinned value rather than assume it is harmless: jbrowse passed exactly
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+ * `50 * 2**20` in nine adapters, and measured on
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+ * `test/data/1kg.chr1.subset.vcf.gz` that was a **total miss** — 47 refills
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+ * out of 47 on the warm pass against 0 at the default, holding 82.7MB in a
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+ * single entry, over the budget it was given because the last settled entry
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+ * is kept whatever the budget. Those nine adapters now pass
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+ * `chunkCacheBudget` and no `chunkCacheSize` at all, so that particular
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+ * instance is gone; the trap it demonstrates is not.
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  *
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  * A retention bound, not a bound on peak memory: reads in flight are never
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  * evicted and the last settled entry is kept whatever the budget. Size it
package/dist/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/tabixIndexedFile.d.ts CHANGED
@@ -49,12 +49,18 @@ export default class TabixIndexedFile {
49
49
  * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
50
50
  * asking for 800 whole decompressed chunks — unbounded in practice. It now
51
51
  * means 50MB, twenty times under the default, and the name did not change
52
- * so nothing warns. jbrowse still passes exactly that in nine adapters:
53
- * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
54
- * 47 refills out of 47 on the warm pass against 0 at the default, holding
55
- * 82.7MB in a single entry — over the budget it was given, because the last
56
- * settled entry is kept whatever the budget. If you pinned a value here
57
- * before v3.5.2, it does not mean what it did.
52
+ * so nothing warns. If you pinned a value here before v3.5.2, it does not
53
+ * mean what it did.
54
+ *
55
+ * What that costs is worth keeping, because it is the reason to check a
56
+ * pinned value rather than assume it is harmless: jbrowse passed exactly
57
+ * `50 * 2**20` in nine adapters, and measured on
58
+ * `test/data/1kg.chr1.subset.vcf.gz` that was a **total miss** — 47 refills
59
+ * out of 47 on the warm pass against 0 at the default, holding 82.7MB in a
60
+ * single entry, over the budget it was given because the last settled entry
61
+ * is kept whatever the budget. Those nine adapters now pass
62
+ * `chunkCacheBudget` and no `chunkCacheSize` at all, so that particular
63
+ * instance is gone; the trap it demonstrates is not.
58
64
  *
59
65
  * A retention bound, not a bound on peak memory: reads in flight are never
60
66
  * evicted and the last settled entry is kept whatever the budget. Size it
package/esm/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/tabix",
3
- "version": "3.8.0",
3
+ "version": "3.8.1",
4
4
  "packageManager": "pnpm@11.15.1",
5
5
  "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
6
6
  "type": "module",
@@ -51,7 +51,7 @@
51
51
  "genomics"
52
52
  ],
53
53
  "dependencies": {
54
- "@gmod/bgzf-filehandle": "^6.4.0",
54
+ "@gmod/bgzf-filehandle": "^6.6.0",
55
55
  "@gmod/shared-read-cache": "^1.5.1",
56
56
  "@jbrowse/quick-lru": "^7.3.5",
57
57
  "generic-filehandle2": "^2.2.1"
package/src/tabixIndexedFile.ts CHANGED
@@ -322,12 +322,18 @@ export default class TabixIndexedFile {
322
322
  * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
323
323
  * asking for 800 whole decompressed chunks — unbounded in practice. It now
324
324
  * means 50MB, twenty times under the default, and the name did not change
325
- * so nothing warns. jbrowse still passes exactly that in nine adapters:
326
- * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
327
- * 47 refills out of 47 on the warm pass against 0 at the default, holding
328
- * 82.7MB in a single entry — over the budget it was given, because the last
329
- * settled entry is kept whatever the budget. If you pinned a value here
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- * before v3.5.2, it does not mean what it did.
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+ * so nothing warns. If you pinned a value here before v3.5.2, it does not
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+ * mean what it did.
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+ *
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+ * What that costs is worth keeping, because it is the reason to check a
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+ * pinned value rather than assume it is harmless: jbrowse passed exactly
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+ * `50 * 2**20` in nine adapters, and measured on
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+ * `test/data/1kg.chr1.subset.vcf.gz` that was a **total miss** — 47 refills
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+ * out of 47 on the warm pass against 0 at the default, holding 82.7MB in a
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+ * single entry, over the budget it was given because the last settled entry
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+ * is kept whatever the budget. Those nine adapters now pass
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+ * `chunkCacheBudget` and no `chunkCacheSize` at all, so that particular
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+ * instance is gone; the trap it demonstrates is not.
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  *
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  * A retention bound, not a bound on peak memory: reads in flight are never
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  * evicted and the last settled entry is kept whatever the budget. Size it