@gmod/tabix 3.7.3 → 3.8.1

package/dist/tabixIndexedFile.d.ts

@@ -1,7 +1,7 @@
 import { SharedReadCache } from '@gmod/shared-read-cache';
 import type Chunk from './chunk.ts';
 import type { Options } from './indexFile.ts';
-import type { ChunkSlice } from '@gmod/bgzf-filehandle';
+import type { BgzfWorkerPool, ChunkSlice } from '@gmod/bgzf-filehandle';
 import type { SharedBudget } from '@gmod/shared-read-cache';
 import type { GenericFilehandle } from 'generic-filehandle2';
 type GetLinesCallback = (line: string, fileOffset: number, start: number, end: number) => void;
@@ -30,7 +30,9 @@ export default class TabixIndexedFile {
      * entry, never evicted, which is what a memo is.
      */
     private headerCache;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, chunkCacheBudget, }: {
+    /** see the constructor option of the same name */
+    private bgzfWorkerPool?;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, chunkCacheBudget, bgzfWorkerPool, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         url?: string;
@@ -47,12 +49,18 @@ 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
@@ -87,6 +95,23 @@ export default class TabixIndexedFile {
          * reading hand their space to the one being panned.
          */
         chunkCacheBudget?: SharedBudget;
+        /**
+         * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
+         * instead of inflating them on the calling thread.
+         *
+         * BGZF decompression dominates a cold query and BGZF blocks are
+         * independently inflatable, so this is the one remaining lever of that
+         * size. @gmod/bam measured 1.95x end to end wiring the same pool into a
+         * genome browser's read path.
+         *
+         * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
+         * so a caller whose own construction is synchronous can hand the pending
+         * pool straight over — it is awaited at the point of use, by which time it
+         * has long since resolved. `undefined` (which is what that helper gives
+         * back under node, or anywhere Workers cannot be created) keeps the
+         * in-process path, so this is safe to pass unconditionally.
+         */
+        bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
     });
     /**
      * Drops every decompressed chunk held by the cache, and stops the idle sweep

package/dist/tabixIndexedFile.js

@@ -198,7 +198,10 @@ class TabixIndexedFile {
      * entry, never evicted, which is what a memo is.
      */
     headerCache = new shared_read_cache_1.SharedReadCache({});
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, chunkCacheBudget, }) {
+    /** see the constructor option of the same name */
+    bgzfWorkerPool;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, chunkCacheBudget, bgzfWorkerPool, }) {
+        this.bgzfWorkerPool = bgzfWorkerPool;
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
             tbiFilehandle,
@@ -533,7 +536,11 @@ class TabixIndexedFile {
     /** @internal */
     async readChunk(c, opts = {}) {
         const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
-        return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c);
+        // Awaited rather than stored resolved: the pool is commonly handed over as
+        // the pending promise from getSharedWorkerPool(), and awaiting an
+        // already-settled promise costs a microtask.
+        const pool = await this.bgzfWorkerPool;
+        return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c, pool);
     }
 }
 exports.default = TabixIndexedFile;

package/dist/tabixIndexedFile.js.map

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package/esm/tabixIndexedFile.d.ts

@@ -1,7 +1,7 @@
 import { SharedReadCache } from '@gmod/shared-read-cache';
 import type Chunk from './chunk.ts';
 import type { Options } from './indexFile.ts';
-import type { ChunkSlice } from '@gmod/bgzf-filehandle';
+import type { BgzfWorkerPool, ChunkSlice } from '@gmod/bgzf-filehandle';
 import type { SharedBudget } from '@gmod/shared-read-cache';
 import type { GenericFilehandle } from 'generic-filehandle2';
 type GetLinesCallback = (line: string, fileOffset: number, start: number, end: number) => void;
@@ -30,7 +30,9 @@ export default class TabixIndexedFile {
      * entry, never evicted, which is what a memo is.
      */
     private headerCache;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, chunkCacheBudget, }: {
+    /** see the constructor option of the same name */
+    private bgzfWorkerPool?;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, chunkCacheBudget, bgzfWorkerPool, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         url?: string;
@@ -47,12 +49,18 @@ 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
@@ -87,6 +95,23 @@ export default class TabixIndexedFile {
          * reading hand their space to the one being panned.
          */
         chunkCacheBudget?: SharedBudget;
+        /**
+         * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
+         * instead of inflating them on the calling thread.
+         *
+         * BGZF decompression dominates a cold query and BGZF blocks are
+         * independently inflatable, so this is the one remaining lever of that
+         * size. @gmod/bam measured 1.95x end to end wiring the same pool into a
+         * genome browser's read path.
+         *
+         * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
+         * so a caller whose own construction is synchronous can hand the pending
+         * pool straight over — it is awaited at the point of use, by which time it
+         * has long since resolved. `undefined` (which is what that helper gives
+         * back under node, or anywhere Workers cannot be created) keeps the
+         * in-process path, so this is safe to pass unconditionally.
+         */
+        bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined;
     });
     /**
      * Drops every decompressed chunk held by the cache, and stops the idle sweep

package/esm/tabixIndexedFile.js

@@ -193,7 +193,10 @@ export default class TabixIndexedFile {
      * entry, never evicted, which is what a memo is.
      */
     headerCache = new SharedReadCache({});
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, chunkCacheBudget, }) {
+    /** see the constructor option of the same name */
+    bgzfWorkerPool;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, chunkCacheBudget, bgzfWorkerPool, }) {
+        this.bgzfWorkerPool = bgzfWorkerPool;
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
             tbiFilehandle,
@@ -528,7 +531,11 @@ export default class TabixIndexedFile {
     /** @internal */
     async readChunk(c, opts = {}) {
         const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
-        return unzipChunkSlice(ret, c);
+        // Awaited rather than stored resolved: the pool is commonly handed over as
+        // the pending promise from getSharedWorkerPool(), and awaiting an
+        // already-settled promise costs a microtask.
+        const pool = await this.bgzfWorkerPool;
+        return unzipChunkSlice(ret, c, pool);
     }
 }
 //# sourceMappingURL=tabixIndexedFile.js.map

package/esm/tabixIndexedFile.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.7.3",
+  "version": "3.8.1",
   "packageManager": "pnpm@11.15.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
@@ -51,7 +51,7 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.3.2",
+    "@gmod/bgzf-filehandle": "^6.6.0",
     "@gmod/shared-read-cache": "^1.5.1",
     "@jbrowse/quick-lru": "^7.3.5",
     "generic-filehandle2": "^2.2.1"

package/src/tabixIndexedFile.ts

@@ -9,7 +9,7 @@ import { optimizeChunks } from './util.ts'
 import type Chunk from './chunk.ts'
 import type IndexFile from './indexFile.ts'
 import type { Options } from './indexFile.ts'
-import type { ChunkSlice } from '@gmod/bgzf-filehandle'
+import type { BgzfWorkerPool, ChunkSlice } from '@gmod/bgzf-filehandle'
 import type { SharedBudget } from '@gmod/shared-read-cache'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
@@ -287,6 +287,10 @@ export default class TabixIndexedFile {
     { header: string; skippedLines: string[] }
   >({})
 
+  /** see the constructor option of the same name */
+  private bgzfWorkerPool?:
+    BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined
+
   constructor({
     path,
     filehandle,
@@ -300,6 +304,7 @@ export default class TabixIndexedFile {
     chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES,
     chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS,
     chunkCacheBudget,
+    bgzfWorkerPool,
   }: {
     path?: string
     filehandle?: GenericFilehandle
@@ -317,12 +322,18 @@ 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
@@ -357,7 +368,26 @@ export default class TabixIndexedFile {
      * reading hand their space to the one being panned.
      */
     chunkCacheBudget?: SharedBudget
+    /**
+     * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
+     * instead of inflating them on the calling thread.
+     *
+     * BGZF decompression dominates a cold query and BGZF blocks are
+     * independently inflatable, so this is the one remaining lever of that
+     * size. @gmod/bam measured 1.95x end to end wiring the same pool into a
+     * genome browser's read path.
+     *
+     * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
+     * so a caller whose own construction is synchronous can hand the pending
+     * pool straight over — it is awaited at the point of use, by which time it
+     * has long since resolved. `undefined` (which is what that helper gives
+     * back under node, or anywhere Workers cannot be created) keeps the
+     * in-process path, so this is safe to pass unconditionally.
+     */
+    bgzfWorkerPool?:
+      BgzfWorkerPool | Promise<BgzfWorkerPool | undefined> | undefined
   }) {
+    this.bgzfWorkerPool = bgzfWorkerPool
     this.filehandle = resolveFilehandle(filehandle, path, url)
     this.index = resolveIndex({
       tbiFilehandle,
@@ -767,6 +797,10 @@ export default class TabixIndexedFile {
       c.minv.blockPosition,
       opts,
     )
-    return unzipChunkSlice(ret, c)
+    // Awaited rather than stored resolved: the pool is commonly handed over as
+    // the pending promise from getSharedWorkerPool(), and awaiting an
+    // already-settled promise costs a microtask.
+    const pool = await this.bgzfWorkerPool
+    return unzipChunkSlice(ret, c, pool)
   }
 }