npm - @gmod/tabix - Versions diffs - 3.8.0 → 3.8.2 - Mend

@gmod/tabix 3.8.0 → 3.8.2

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.

Files changed (8) hide show

package/README.md +84 -83
package/dist/tabix-bundle.js +1 -1
package/dist/tabixIndexedFile.d.ts +24 -14
package/dist/tabixIndexedFile.js.map +1 -1
package/esm/tabixIndexedFile.d.ts +24 -14
package/esm/tabixIndexedFile.js.map +1 -1
package/package.json +3 -3
package/src/tabixIndexedFile.ts +24 -14

package/dist/tabixIndexedFile.d.ts CHANGED Viewed

@@ -9,11 +9,12 @@ interface GetLinesOpts {
     signal?: AbortSignal;
     lineCallback: GetLinesCallback;
     /**
-     * Called as the compressed data blocks covering the query are fetched, with
-     * cumulative downloaded bytes and the total bytes to fetch. Reported at block
-     * granularity (one tick per chunk, including instant ticks for cache hits),
-     * which is the natural unit since chunk byte sizes are known up front from
-     * the index. Lets callers render a determinate download progress bar.
+     * Called as the chunks covering the query are fetched, with cumulative
+     * downloaded bytes and the total bytes to fetch. One tick per chunk — the run
+     * of BGZF blocks the index resolves a query to — including instant ticks for
+     * chunks already cached. That is the natural unit here, since chunk byte
+     * sizes are known up front from the index, which is what lets a caller render
+     * a determinate progress bar rather than a spinner.
      */
     onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
@@ -49,12 +50,18 @@ export default class TabixIndexedFile {
          * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
          * asking for 800 whole decompressed chunks — unbounded in practice. It now
          * means 50MB, twenty times under the default, and the name did not change
-         * so nothing warns. jbrowse still passes exactly that in nine adapters:
-         * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
-         * 47 refills out of 47 on the warm pass against 0 at the default, holding
-         * 82.7MB in a single entry — over the budget it was given, because the last
-         * settled entry is kept whatever the budget. If you pinned a value here
-         * before v3.5.2, it does not mean what it did.
+         * so nothing warns. If you pinned a value here before v3.5.2, it does not
+         * mean what it did.
+         *
+         * What that costs is worth keeping, because it is the reason to check a
+         * pinned value rather than assume it is harmless: jbrowse passed exactly
+         * `50 * 2**20` in nine adapters, and measured on
+         * `test/data/1kg.chr1.subset.vcf.gz` that was a **total miss** — 47 refills
+         * out of 47 on the warm pass against 0 at the default, holding 82.7MB in a
+         * single entry, over the budget it was given because the last settled entry
+         * is kept whatever the budget. Those nine adapters now pass
+         * `chunkCacheBudget` and no `chunkCacheSize` at all, so that particular
+         * instance is gone; the trap it demonstrates is not.
          *
          * A retention bound, not a bound on peak memory: reads in flight are never
          * evicted and the last settled entry is kept whatever the budget. Size it
@@ -72,9 +79,12 @@ export default class TabixIndexedFile {
          */
         chunkCacheIdleTimeoutMs?: number;
         /**
-         * A budget shared with other files — any `@gmod/shared-read-cache`
-         * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
-         * that the ceiling applies to their sum rather than to each of them.
+         * A budget shared with other files, so that the ceiling applies to their
+         * sum rather than to each of them. Any `@gmod/shared-read-cache` consumer
+         * that weighs in the same unit can join it: `@gmod/bam` also weighs
+         * decompressed bytes, while `@gmod/cram` weighs decoded records and
+         * `@gmod/bbi` weighs entries, and a budget mixing those adds bytes to
+         * records and bounds neither.
          *
          * {@link chunkCacheSize} is per file, which is not a bound on a consumer
          * that opens one file per track. @gmod/bam measured the shape: six tracks

package/dist/tabixIndexedFile.js.map CHANGED Viewed

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package/esm/tabixIndexedFile.d.ts CHANGED Viewed

@@ -9,11 +9,12 @@ interface GetLinesOpts {
     signal?: AbortSignal;
     lineCallback: GetLinesCallback;
     /**
-     * Called as the compressed data blocks covering the query are fetched, with
-     * cumulative downloaded bytes and the total bytes to fetch. Reported at block
-     * granularity (one tick per chunk, including instant ticks for cache hits),
-     * which is the natural unit since chunk byte sizes are known up front from
-     * the index. Lets callers render a determinate download progress bar.
+     * Called as the chunks covering the query are fetched, with cumulative
+     * downloaded bytes and the total bytes to fetch. One tick per chunk — the run
+     * of BGZF blocks the index resolves a query to — including instant ticks for
+     * chunks already cached. That is the natural unit here, since chunk byte
+     * sizes are known up front from the index, which is what lets a caller render
+     * a determinate progress bar rather than a spinner.
      */
     onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
@@ -49,12 +50,18 @@ export default class TabixIndexedFile {
          * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
          * asking for 800 whole decompressed chunks — unbounded in practice. It now
          * means 50MB, twenty times under the default, and the name did not change
-         * so nothing warns. jbrowse still passes exactly that in nine adapters:
-         * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
-         * 47 refills out of 47 on the warm pass against 0 at the default, holding
-         * 82.7MB in a single entry — over the budget it was given, because the last
-         * settled entry is kept whatever the budget. If you pinned a value here
-         * before v3.5.2, it does not mean what it did.
+         * so nothing warns. If you pinned a value here before v3.5.2, it does not
+         * mean what it did.
+         *
+         * What that costs is worth keeping, because it is the reason to check a
+         * pinned value rather than assume it is harmless: jbrowse passed exactly
+         * `50 * 2**20` in nine adapters, and measured on
+         * `test/data/1kg.chr1.subset.vcf.gz` that was a **total miss** — 47 refills
+         * out of 47 on the warm pass against 0 at the default, holding 82.7MB in a
+         * single entry, over the budget it was given because the last settled entry
+         * is kept whatever the budget. Those nine adapters now pass
+         * `chunkCacheBudget` and no `chunkCacheSize` at all, so that particular
+         * instance is gone; the trap it demonstrates is not.
          *
          * A retention bound, not a bound on peak memory: reads in flight are never
          * evicted and the last settled entry is kept whatever the budget. Size it
@@ -72,9 +79,12 @@ export default class TabixIndexedFile {
          */
         chunkCacheIdleTimeoutMs?: number;
         /**
-         * A budget shared with other files — any `@gmod/shared-read-cache`
-         * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
-         * that the ceiling applies to their sum rather than to each of them.
+         * A budget shared with other files, so that the ceiling applies to their
+         * sum rather than to each of them. Any `@gmod/shared-read-cache` consumer
+         * that weighs in the same unit can join it: `@gmod/bam` also weighs
+         * decompressed bytes, while `@gmod/cram` weighs decoded records and
+         * `@gmod/bbi` weighs entries, and a budget mixing those adds bytes to
+         * records and bounds neither.
          *
          * {@link chunkCacheSize} is per file, which is not a bound on a consumer
          * that opens one file per track. @gmod/bam measured the shape: six tracks

package/esm/tabixIndexedFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.8.0",
+  "version": "3.8.2",
   "packageManager": "pnpm@11.15.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
@@ -51,8 +51,8 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.4.0",
-    "@gmod/shared-read-cache": "^1.5.1",
+    "@gmod/bgzf-filehandle": "^6.6.0",
+    "@gmod/shared-read-cache": "^1.7.2",
     "@jbrowse/quick-lru": "^7.3.5",
     "generic-filehandle2": "^2.2.1"
   },

package/src/tabixIndexedFile.ts CHANGED Viewed

@@ -64,11 +64,12 @@ interface GetLinesOpts {
   signal?: AbortSignal
   lineCallback: GetLinesCallback
   /**
-   * Called as the compressed data blocks covering the query are fetched, with
-   * cumulative downloaded bytes and the total bytes to fetch. Reported at block
-   * granularity (one tick per chunk, including instant ticks for cache hits),
-   * which is the natural unit since chunk byte sizes are known up front from
-   * the index. Lets callers render a determinate download progress bar.
+   * Called as the chunks covering the query are fetched, with cumulative
+   * downloaded bytes and the total bytes to fetch. One tick per chunk — the run
+   * of BGZF blocks the index resolves a query to — including instant ticks for
+   * chunks already cached. That is the natural unit here, since chunk byte
+   * sizes are known up front from the index, which is what lets a caller render
+   * a determinate progress bar rather than a spinner.
    */
   onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
 }
@@ -322,12 +323,18 @@ export default class TabixIndexedFile {
      * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
      * asking for 800 whole decompressed chunks — unbounded in practice. It now
      * means 50MB, twenty times under the default, and the name did not change
-     * so nothing warns. jbrowse still passes exactly that in nine adapters:
-     * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
-     * 47 refills out of 47 on the warm pass against 0 at the default, holding
-     * 82.7MB in a single entry — over the budget it was given, because the last
-     * settled entry is kept whatever the budget. If you pinned a value here
-     * before v3.5.2, it does not mean what it did.
+     * so nothing warns. If you pinned a value here before v3.5.2, it does not
+     * mean what it did.
+     *
+     * What that costs is worth keeping, because it is the reason to check a
+     * pinned value rather than assume it is harmless: jbrowse passed exactly
+     * `50 * 2**20` in nine adapters, and measured on
+     * `test/data/1kg.chr1.subset.vcf.gz` that was a **total miss** — 47 refills
+     * out of 47 on the warm pass against 0 at the default, holding 82.7MB in a
+     * single entry, over the budget it was given because the last settled entry
+     * is kept whatever the budget. Those nine adapters now pass
+     * `chunkCacheBudget` and no `chunkCacheSize` at all, so that particular
+     * instance is gone; the trap it demonstrates is not.
      *
      * A retention bound, not a bound on peak memory: reads in flight are never
      * evicted and the last settled entry is kept whatever the budget. Size it
@@ -345,9 +352,12 @@ export default class TabixIndexedFile {
      */
     chunkCacheIdleTimeoutMs?: number
     /**
-     * A budget shared with other files — any `@gmod/shared-read-cache`
-     * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
-     * that the ceiling applies to their sum rather than to each of them.
+     * A budget shared with other files, so that the ceiling applies to their
+     * sum rather than to each of them. Any `@gmod/shared-read-cache` consumer
+     * that weighs in the same unit can join it: `@gmod/bam` also weighs
+     * decompressed bytes, while `@gmod/cram` weighs decoded records and
+     * `@gmod/bbi` weighs entries, and a budget mixing those adds bytes to
+     * records and bounds neither.
      *
      * {@link chunkCacheSize} is per file, which is not a bound on a consumer
      * that opens one file per track. @gmod/bam measured the shape: six tracks