@gmod/tabix 3.6.0 → 3.7.1

package/esm/tabixIndexedFile.js

@@ -3,7 +3,7 @@ import { SharedReadCache } from '@gmod/shared-read-cache';
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import CSI from "./csi.js";
 import TBI from "./tbi.js";
-import { optimizeChunks, throwIfAborted } from "./util.js";
+import { optimizeChunks } from "./util.js";
 const TAB = 9;
 const NEWLINE = 10;
 const CARRIAGE_RETURN = 13;
@@ -188,15 +188,12 @@ export default class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
-    headerP;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    headerSignal;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, }) {
+    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, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
             tbiFilehandle,
@@ -215,6 +212,7 @@ export default class TabixIndexedFile {
             sizeOf: read => read.buffer.byteLength,
             cacheKey: chunk => chunk.toString(),
             idleTimeoutMs: chunkCacheIdleTimeoutMs,
+            budget: chunkCacheBudget,
             fill: (chunk, signal) => this.readChunk(chunk, { signal }),
         });
     }
@@ -449,51 +447,22 @@ export default class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * A caller that joined someone else's parse and saw it fail because *they*
-     * aborted starts over rather than inheriting the failure — once, then
-     * propagates. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and the same rule: the parse runs under
+     * a signal of its own and is cancelled only once every caller waiting on it
+     * has given up, so one caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
-    async getParsedHeader(opts = {}, retried = false) {
-        throwIfAborted(opts.signal);
-        const pending = this.headerP;
-        if (!pending) {
-            return this.startHeaderParse(opts);
-        }
-        // read before awaiting: the owner is forgotten as soon as the parse settles
-        const ownerSignal = this.headerSignal;
-        try {
-            return await pending;
-        }
-        catch (e) {
-            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this.getParsedHeader(opts, true);
-        }
-    }
-    startHeaderParse(opts) {
-        const pending = this.parseHeader(opts);
-        this.headerP = pending;
-        this.headerSignal = opts.signal;
-        // Drop a rejection rather than keeping it, so one transient failure does not
-        // poison the header for the lifetime of the file. Both branches are
-        // identity-checked so a retry started after this settles is not cleared by
-        // the attempt it already replaced.
-        pending.then(() => {
-            if (this.headerP === pending) {
-                this.headerSignal = undefined;
-            }
-        }, () => {
-            if (this.headerP === pending) {
-                this.headerP = undefined;
-                this.headerSignal = undefined;
-            }
-        });
-        return pending;
+    getParsedHeader(opts = {}) {
+        return this.headerCache.get('header', opts.signal, signal => this.parseHeader({ ...opts, signal }));
     }
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the

package/esm/tabixIndexedFile.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.6.0",
+  "version": "3.7.1",
   "packageManager": "pnpm@11.15.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
@@ -52,7 +52,7 @@
   ],
   "dependencies": {
     "@gmod/bgzf-filehandle": "^6.3.2",
-    "@gmod/shared-read-cache": "^1.4.1",
+    "@gmod/shared-read-cache": "^1.5.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "generic-filehandle2": "^2.2.1"
   },

package/src/indexFile.ts

@@ -1,6 +1,7 @@
 import { unzip } from '@gmod/bgzf-filehandle'
+import { SharedReadCache } from '@gmod/shared-read-cache'
 
-import { optimizeChunks, throwIfAborted } from './util.ts'
+import { optimizeChunks } from './util.ts'
 
 import type Chunk from './chunk.ts'
 import type VirtualOffset from './virtualOffset.ts'
@@ -51,14 +52,11 @@ export interface IndexData {
 
 export default abstract class IndexFile {
   public filehandle: GenericFilehandle
-  private parseP?: Promise<IndexData>
   /**
-   * The signal `parseP` was started under, while it is still in flight. The
-   * index is parsed once and shared by every query against the file, so without
-   * this the first query to arrive would own a read all the others depend on —
-   * see {@link parse}.
+   * The parsed index, as a shared read — see {@link parse}. One entry, never
+   * evicted, which is what a memo is.
    */
-  private parseSignal?: AbortSignal
+  private parseCache = new SharedReadCache<string, IndexData>({})
 
   constructor({ filehandle }: { filehandle: GenericFilehandle }) {
     this.filehandle = filehandle
@@ -158,75 +156,38 @@ export default abstract class IndexFile {
     return optimizeChunks(chunks, this.lowestOffset(ba, min, indexData))
   }
 
-  // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same owner-signal
-  // tracking and one-attempt retry, and the same reasoning below.
+  // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same shape and the same
+  // reasoning below.
   /**
    * Parse the index, or join the parse already running.
    *
    * The index is downloaded and parsed once for the life of this object, so it
    * is the one read here that is shared between queries — and therefore the one
    * place a cancellation can leak from the query that asked for it to a query
-   * that did not. `_parse` hands `opts` straight to `readIndexBytes`, so
-   * without this the first query to arrive owns a read every other query
-   * depends on: when it pans away, every concurrent query fails with its abort.
+   * that did not. `_parse` hands `opts` straight to `readIndexBytes`, so a bare
+   * memoized promise makes the first query to arrive the owner of a read every
+   * other query depends on: when it pans away, every concurrent query fails
+   * with its abort.
    *
-   * A caller that joined someone else's parse and saw it fail because *they*
-   * aborted starts over rather than inheriting the failure — once, then
-   * propagates. Bounding it at one attempt is what jbrowse's
-   * `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
-   * down, and for the reason it gives: the pathological case becomes one
-   * duplicate parse rather than a recursion whose depth depends on how the
-   * aborts interleave.
+   * The same cache `ChunkCache` uses, for the same reason and with the same
+   * rule: the parse runs under a signal of its own and is cancelled only once
+   * every caller waiting on it has given up, so one query's abort is reported
+   * to that query alone and a bystander gets the parse already in flight rather
+   * than having to re-read the index. A rejection is dropped rather than
+   * cached, so a transient failure does not poison the index for the life of
+   * the file.
    *
-   * A retry rather than the reference count `ChunkCache` uses, because the
-   * index is parsed once for the life of the object: there is no repeated waste
-   * to recover, and this is a dozen lines against restructuring the memo.
-   * `@gmod/bam`'s `IndexFile` and `@gmod/cram`'s `CraiIndex` make the same
-   * split for the same reason.
+   * The fill is per call rather than on the cache so that the caller who starts
+   * the parse has its `onProgress` reach `readIndexBytes` — the index is a
+   * whole-file read, and a determinate "downloading index" bar is what that
+   * callback exists for.
    *
    * @internal
    */
-  async parse(opts: Options = {}, retried = false): Promise<IndexData> {
-    throwIfAborted(opts.signal)
-    const pending = this.parseP
-    if (!pending) {
-      return this.startParse(opts)
-    }
-
-    // read before awaiting: the owner is forgotten as soon as the parse settles
-    const ownerSignal = this.parseSignal
-    try {
-      return await pending
-    } catch (e) {
-      if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-        throw e
-      }
-      return this.parse(opts, true)
-    }
-  }
-
-  private startParse(opts: Options) {
-    const pending = this._parse(opts)
-    this.parseP = pending
-    this.parseSignal = opts.signal
-    // Drop a rejection rather than keeping it, so one transient failure does not
-    // poison the index for the lifetime of the file. Both branches are
-    // identity-checked so a retry started after this settles is not cleared by
-    // the attempt it already replaced.
-    pending.then(
-      () => {
-        if (this.parseP === pending) {
-          this.parseSignal = undefined
-        }
-      },
-      () => {
-        if (this.parseP === pending) {
-          this.parseP = undefined
-          this.parseSignal = undefined
-        }
-      },
+  parse(opts: Options = {}): Promise<IndexData> {
+    return this.parseCache.get('index', opts.signal, signal =>
+      this._parse({ ...opts, signal }),
     )
-    return pending
   }
 
   /** @internal */

package/src/tabixIndexedFile.ts

@@ -4,12 +4,13 @@ import { LocalFile, RemoteFile } from 'generic-filehandle2'
 
 import CSI from './csi.ts'
 import TBI from './tbi.ts'
-import { optimizeChunks, throwIfAborted } from './util.ts'
+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 { SharedBudget } from '@gmod/shared-read-cache'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
 const TAB = 9
@@ -277,14 +278,14 @@ export default class TabixIndexedFile {
   private filehandle: GenericFilehandle
   private index: IndexFile
   public chunkCache: SharedReadCache<Chunk, ReadChunk>
-  private headerP?: Promise<{ header: string; skippedLines: string[] }>
   /**
-   * The signal `headerP` was started under, while it is still in flight. The
-   * header is parsed once and shared by every caller, so without this the first
-   * one to arrive would own a read all the others depend on — see
-   * {@link getParsedHeader}.
+   * The parsed header, as a shared read — see {@link getParsedHeader}. One
+   * entry, never evicted, which is what a memo is.
    */
-  private headerSignal?: AbortSignal
+  private headerCache = new SharedReadCache<
+    string,
+    { header: string; skippedLines: string[] }
+  >({})
 
   constructor({
     path,
@@ -298,6 +299,7 @@ export default class TabixIndexedFile {
     csiFilehandle,
     chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES,
     chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS,
+    chunkCacheBudget,
   }: {
     path?: string
     filehandle?: GenericFilehandle
@@ -311,6 +313,17 @@ export default class TabixIndexedFile {
     /**
      * Budget for the decompressed chunk cache, in bytes. Default 1GB.
      *
+     * **The unit changed in v3.5.2** (ADR 0001). Before that this was divided
+     * 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.
+     *
      * 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
      * to hold several queries — below one query's working set the hit rate
@@ -326,6 +339,24 @@ export default class TabixIndexedFile {
      * makes the budget above a peak rather than a resting level.
      */
     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.
+     *
+     * {@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
+     * browsing six windows retained 1442 MB with every cache still under its
+     * own ceiling, so the ceiling was not holding the line and nothing else
+     * was. The idle timeout cannot help there — it does nothing while the
+     * reader is browsing, which is the whole case.
+     *
+     * Dividing {@link chunkCacheSize} by the track count instead reintroduces
+     * the cliff it exists to avoid. A shared budget does not, because a member
+     * yields only what is globally least-recently-used: files nobody is
+     * reading hand their space to the one being panned.
+     */
+    chunkCacheBudget?: SharedBudget
   }) {
     this.filehandle = resolveFilehandle(filehandle, path, url)
     this.index = resolveIndex({
@@ -346,6 +377,7 @@ export default class TabixIndexedFile {
       sizeOf: read => read.buffer.byteLength,
       cacheKey: chunk => chunk.toString(),
       idleTimeoutMs: chunkCacheIdleTimeoutMs,
+      budget: chunkCacheBudget,
       fill: (chunk, signal) => this.readChunk(chunk, { signal }),
     })
   }
@@ -641,58 +673,24 @@ export default class TabixIndexedFile {
    * charge of a read every later caller joins: when it aborted, they failed
    * with its cancellation, their own signals untouched.
    *
-   * A caller that joined someone else's parse and saw it fail because *they*
-   * aborted starts over rather than inheriting the failure — once, then
-   * propagates. Same bounded retry, and the same reasoning, as
-   * `IndexFile.parse`.
+   * The same cache the chunk reads use, and the same rule: the parse runs under
+   * a signal of its own and is cancelled only once every caller waiting on it
+   * has given up, so one caller's abort is reported to that caller alone and a
+   * bystander gets the parse already in flight. There is no retry here because
+   * there is nothing to retry — the parse a bystander joined is not cancelled by
+   * someone else's abort. A rejection is dropped rather than cached, so a
+   * transient failure does not poison the header for the life of the file.
+   *
+   * The fill is per call rather than on the cache, so the caller that starts the
+   * parse has its `onProgress` reach the index download inside `getMetadata`.
    *
    * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
    * reason, on the header rather than the index.
    */
-  private async getParsedHeader(
-    opts: Options = {},
-    retried = false,
-  ): Promise<{ header: string; skippedLines: string[] }> {
-    throwIfAborted(opts.signal)
-    const pending = this.headerP
-    if (!pending) {
-      return this.startHeaderParse(opts)
-    }
-
-    // read before awaiting: the owner is forgotten as soon as the parse settles
-    const ownerSignal = this.headerSignal
-    try {
-      return await pending
-    } catch (e) {
-      if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-        throw e
-      }
-      return this.getParsedHeader(opts, true)
-    }
-  }
-
-  private startHeaderParse(opts: Options) {
-    const pending = this.parseHeader(opts)
-    this.headerP = pending
-    this.headerSignal = opts.signal
-    // Drop a rejection rather than keeping it, so one transient failure does not
-    // poison the header for the lifetime of the file. Both branches are
-    // identity-checked so a retry started after this settles is not cleared by
-    // the attempt it already replaced.
-    pending.then(
-      () => {
-        if (this.headerP === pending) {
-          this.headerSignal = undefined
-        }
-      },
-      () => {
-        if (this.headerP === pending) {
-          this.headerP = undefined
-          this.headerSignal = undefined
-        }
-      },
+  private getParsedHeader(opts: Options = {}) {
+    return this.headerCache.get('header', opts.signal, signal =>
+      this.parseHeader({ ...opts, signal }),
     )
-    return pending
   }
 
   /**