@gmod/tabix 3.5.5 → 3.6.0

package/esm/tabixIndexedFile.d.ts

@@ -1,3 +1,4 @@
+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';
@@ -15,15 +16,23 @@ interface GetLinesOpts {
      */
     onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
+type ReadChunk = ChunkSlice;
 /**
  * Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
  */
 export default class TabixIndexedFile {
     private filehandle;
     private index;
-    private chunkCache;
+    chunkCache: SharedReadCache<Chunk, ReadChunk>;
     private headerP?;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, }: {
+    /**
+     * 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}.
+     */
+    private headerSignal?;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         url?: string;
@@ -33,9 +42,34 @@ export default class TabixIndexedFile {
         csiPath?: string;
         csiUrl?: string;
         csiFilehandle?: GenericFilehandle;
-        /** budget for the decompressed chunk cache, in bytes */
+        /**
+         * Budget for the decompressed chunk cache, in bytes. Default 1GB.
+         *
+         * 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
+         * drops to zero while the memory is retained anyway, so a number between
+         * the two is the worst available choice.
+         */
         chunkCacheSize?: number;
+        /**
+         * Drop a cached chunk once nothing has read it for this many milliseconds.
+         * Default 3 minutes; `0` keeps chunks until `chunkCacheSize` evicts them.
+         *
+         * The only thing that lowers the cache while nothing is happening, and what
+         * makes the budget above a peak rather than a resting level.
+         */
+        chunkCacheIdleTimeoutMs?: number;
     });
+    /**
+     * Drops every decompressed chunk held by the cache, and stops the idle sweep
+     * until something is cached again.
+     *
+     * `chunkCacheIdleTimeoutMs` reclaims a view the user has wandered away from;
+     * this is for a consumer that knows it is finished — a closed track, a
+     * changed assembly — and should not have to wait it out.
+     */
+    clearChunkCache(): void;
     /**
      * Estimates the compressed byte size of the index chunks covering the given
      * regions. Useful for byte budgeting before issuing a `getLines` call to
@@ -92,7 +126,24 @@ export default class TabixIndexedFile {
      * which matters for a VCF header that can run to megabytes.
      */
     private parseHeader;
+    /**
+     * Parse the header, or join the parse already running.
+     *
+     * `parseHeader` threads `opts` into both `getMetadata` and the header read,
+     * so memoizing it on the first caller's opts put that caller's signal in
+     * 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`.
+     *
+     * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
+     * reason, on the header rather than the index.
+     */
     private getParsedHeader;
+    private startHeaderParse;
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the
      * string form: this hands back the buffer, and holding one for the lifetime

package/esm/tabixIndexedFile.js

@@ -1,9 +1,9 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
+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 } from "./util.js";
+import { optimizeChunks, throwIfAborted } from "./util.js";
 const TAB = 9;
 const NEWLINE = 10;
 const CARRIAGE_RETURN = 13;
@@ -19,78 +19,27 @@ const MAX_READ_AHEAD_CHUNKS = 6;
 // a dense VCF (test/data/1kg.chr1.subset.vcf.gz — 213MB over 600kb of chr1)
 // has single index bins of 17MB compressed, 120MB decompressed. Panning it
 // under the old 80-entry cache peaked at 2GB RSS.
-const DEFAULT_CHUNK_CACHE_BYTES = 100 * 2 ** 20;
-/**
- * Backing store for the chunk cache, bounded by the decompressed size of the
- * chunks it holds rather than by entry count.
- *
- * A chunk's size is only known once its read settles, so `set` records the
- * entry immediately and charges it to the budget later. Unsettled entries are
- * therefore free, which is what we want: they are reads a query is waiting on.
- */
-class ByteBoundedChunkCache {
-    entries = new Map();
-    bytes = 0;
-    maxBytes;
-    constructor(maxBytes) {
-        this.maxBytes = maxBytes;
-    }
-    get byteSize() {
-        return this.bytes;
-    }
-    get size() {
-        return this.entries.size;
-    }
-    has(key) {
-        return this.entries.has(key);
-    }
-    get(key) {
-        const cached = this.entries.get(key);
-        if (cached) {
-            // re-insert so Map iteration order stays least-recently-used first
-            this.entries.delete(key);
-            this.entries.set(key, cached);
-        }
-        return cached?.entry;
-    }
-    set(key, entry) {
-        this.delete(key);
-        const cached = { entry, bytes: 0 };
-        this.entries.set(key, cached);
-        void entry.promise
-            .then(chunk => {
-            // a later set() may have replaced this key while the read was in
-            // flight; charging these bytes to it would then double-count
-            if (this.entries.get(key) === cached) {
-                cached.bytes = chunk.buffer.byteLength;
-                this.bytes += cached.bytes;
-                this.evict();
-            }
-        })
-            .catch(() => {
-            // a failed or aborted read caches nothing and costs nothing
-        });
-    }
-    delete(key) {
-        const cached = this.entries.get(key);
-        if (cached) {
-            this.entries.delete(key);
-            this.bytes -= cached.bytes;
-        }
-    }
-    keys() {
-        return this.entries.keys();
-    }
-    // Evict from the least-recently-used end. The size > 1 guard means a single
-    // chunk larger than the whole budget is still kept: the caller needs it for
-    // the query in flight, and dropping it would only force a re-decompress.
-    evict() {
-        const lru = this.entries.keys();
-        while (this.bytes > this.maxBytes && this.entries.size > 1) {
-            this.delete(lru.next().value);
-        }
-    }
-}
+//
+// That 120MB figure is also why this is no longer 100MB. A budget below one
+// query's working set does not cache less, it caches NOTHING: each entry is
+// evicted before the next pan can reuse it, so the hit rate is zero and the
+// decompress is paid again every time. On that same fixture, a six-window 50kb
+// pan measured 17 refills out of 17 — a total miss — at 100MB, against 0 at
+// 800MB, and 2596ms against 600ms. The working set plateaus at 497MB held, so
+// 1GB clears it with headroom and nothing above 800MB buys anything.
+//
+// Affordable as a ceiling only because of the idle timeout below: it is a peak
+// under panning, not a level a parked consumer holds. A small file is
+// unaffected either way, this being a ceiling and not an allocation.
+const DEFAULT_CHUNK_CACHE_BYTES = 1024 * 2 ** 20;
+// SYNC: ~/src/gmod/bam-js/src/bamFile.ts DEFAULT_CACHE_IDLE_TIMEOUT_MS
+//
+// Drop a chunk nothing has looked at for three minutes. The budget above is
+// only applied when a read settles, so it does nothing at all for a consumer
+// sitting still — and a genome browser holds one of these per track for as long
+// as the track is open. Timed from the last read, not the fetch, so panning
+// back and forth over one region never expires it.
+const DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS = 3 * 60 * 1000;
 function resolveFilehandle(filehandle, path, url) {
     if (filehandle) {
         return filehandle;
@@ -240,7 +189,14 @@ export default class TabixIndexedFile {
     index;
     chunkCache;
     headerP;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, }) {
+    /**
+     * 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}.
+     */
+    headerSignal;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
             tbiFilehandle,
@@ -252,11 +208,27 @@ export default class TabixIndexedFile {
             path,
             url,
         });
-        this.chunkCache = new AbortablePromiseCache({
-            cache: new ByteBoundedChunkCache(chunkCacheSize),
-            fill: (args, signal) => this.readChunk(args, { signal }),
+        this.chunkCache = new SharedReadCache({
+            maxSize: chunkCacheSize,
+            // decompressed bytes, not entry count: we fetch compressed and cache
+            // decompressed, and an entry is a whole chunk
+            sizeOf: read => read.buffer.byteLength,
+            cacheKey: chunk => chunk.toString(),
+            idleTimeoutMs: chunkCacheIdleTimeoutMs,
+            fill: (chunk, signal) => this.readChunk(chunk, { signal }),
         });
     }
+    /**
+     * Drops every decompressed chunk held by the cache, and stops the idle sweep
+     * until something is cached again.
+     *
+     * `chunkCacheIdleTimeoutMs` reclaims a view the user has wandered away from;
+     * this is for a consumer that knows it is finished — a closed track, a
+     * changed assembly — and should not have to wait it out.
+     */
+    clearChunkCache() {
+        this.chunkCache.clear();
+    }
     /**
      * Estimates the compressed byte size of the index chunks covering the given
      * regions. Useful for byte budgeting before issuing a `getLines` call to
@@ -345,7 +317,7 @@ export default class TabixIndexedFile {
         const ensureReadsStarted = (count) => {
             while (reads.length < Math.min(count, chunks.length)) {
                 const c = chunks[reads.length];
-                const read = this.chunkCache.get(c.toString(), c, signal);
+                const read = this.chunkCache.get(c, signal);
                 void read.catch(() => {
                     // a prefetch the early return skips is never awaited, so swallow its
                     // rejection here rather than let it surface unhandled
@@ -469,12 +441,59 @@ export default class TabixIndexedFile {
             skippedLines: skipLines > 0 ? firstLines(bytes, skipLines) : [],
         };
     }
-    async getParsedHeader(opts = {}) {
-        this.headerP ??= this.parseHeader(opts).catch((error) => {
-            this.headerP = undefined;
-            throw error;
+    /**
+     * Parse the header, or join the parse already running.
+     *
+     * `parseHeader` threads `opts` into both `getMetadata` and the header read,
+     * so memoizing it on the first caller's opts put that caller's signal in
+     * 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`.
+     *
+     * 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 this.headerP;
+        return pending;
     }
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the

package/esm/tabixIndexedFile.js.map

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package/esm/util.d.ts

@@ -1,5 +1,6 @@
 import Chunk from './chunk.ts';
 import VirtualOffset from './virtualOffset.ts';
+export { throwIfAborted } from '@gmod/shared-read-cache';
 export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
 export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
 /**

package/esm/util.js

@@ -3,6 +3,10 @@ import Chunk from "./chunk.js";
 import { longFromBytesToUnsigned } from "./long.js";
 import VirtualOffset from "./virtualOffset.js";
 // SYNC: ~/src/gmod/bam-js/src/util.ts optimizeChunks
+// Re-exported so the internal import path stays './util.ts'. The
+// implementation moved to @gmod/shared-read-cache, which needs it anyway --
+// every consumer of that package was carrying an identical copy.
+export { throwIfAborted } from '@gmod/shared-read-cache';
 export function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
     if (n === 0) {

package/esm/util.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.5.5",
+  "version": "3.6.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
@@ -13,7 +13,7 @@
   "license": "MIT",
   "repository": {
     "type": "git",
-    "url": "https://github.com/GMOD/tabix-js.git"
+    "url": "git+https://github.com/GMOD/tabix-js.git"
   },
   "author": {
     "name": "Robert Buels",
@@ -29,7 +29,9 @@
     "test": "vitest",
     "clean": "rimraf dist esm",
     "format": "prettier --write .",
+    "format:check": "prettier --check .",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "typecheck": "tsc --noEmit -p tsconfig.lint.json",
     "prebuild": "pnpm clean",
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
@@ -49,26 +51,25 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/abortable-promise-cache": "^3.0.4",
     "@gmod/bgzf-filehandle": "^6.3.2",
+    "@gmod/shared-read-cache": "^1.4.1",
     "@jbrowse/quick-lru": "^7.3.5",
-    "generic-filehandle2": "^2.2.0"
+    "generic-filehandle2": "^2.2.1"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
-    "@types/node": "^26.1.1",
+    "@types/node": "^26.1.2",
     "@vitest/coverage-v8": "^4.1.10",
-    "eslint": "^10.7.0",
+    "eslint": "^10.8.0",
     "eslint-plugin-import-x": "^4.17.1",
-    "eslint-plugin-unicorn": "^72.0.0",
     "git-cliff": "^2.13.1",
     "prettier": "^3.9.6",
     "rimraf": "^6.1.3",
-    "typescript": "^6.0.0",
+    "typescript": "^6.0.3",
     "typescript-eslint": "^8.65.0",
     "vitest": "^4.1.10",
-    "webpack": "^5.108.4",
-    "webpack-cli": "^7.2.1"
+    "webpack": "^5.109.2",
+    "webpack-cli": "^7.2.2"
   },
   "publishConfig": {
     "access": "public"

package/src/indexFile.ts

@@ -1,6 +1,6 @@
 import { unzip } from '@gmod/bgzf-filehandle'
 
-import { optimizeChunks } from './util.ts'
+import { optimizeChunks, throwIfAborted } from './util.ts'
 
 import type Chunk from './chunk.ts'
 import type VirtualOffset from './virtualOffset.ts'
@@ -52,6 +52,13 @@ 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}.
+   */
+  private parseSignal?: AbortSignal
 
   constructor({ filehandle }: { filehandle: GenericFilehandle }) {
     this.filehandle = filehandle
@@ -151,13 +158,75 @@ export default abstract class IndexFile {
     return optimizeChunks(chunks, this.lowestOffset(ba, min, indexData))
   }
 
-  /** @internal */
-  async parse(opts: Options = {}) {
-    this.parseP ??= this._parse(opts).catch((error: unknown) => {
-      this.parseP = undefined
-      throw error
-    })
-    return this.parseP
+  // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same owner-signal
+  // tracking and one-attempt retry, 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.
+   *
+   * 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.
+   *
+   * 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.
+   *
+   * @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
+        }
+      },
+    )
+    return pending
   }
 
   /** @internal */