@gmod/tabix 3.5.7 → 3.6.0

package/dist/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/dist/tabixIndexedFile.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const shared_read_cache_1 = require("@gmod/shared-read-cache");
 const generic_filehandle2_1 = require("generic-filehandle2");
 const csi_ts_1 = __importDefault(require("./csi.js"));
 const tbi_ts_1 = __importDefault(require("./tbi.js"));
@@ -24,78 +24,27 @@ 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;
@@ -245,7 +194,14 @@ 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,
@@ -257,11 +213,27 @@ class TabixIndexedFile {
             path,
             url,
         });
-        this.chunkCache = new abortable_promise_cache_1.default({
-            cache: new ByteBoundedChunkCache(chunkCacheSize),
-            fill: (args, signal) => this.readChunk(args, { signal }),
+        this.chunkCache = new shared_read_cache_1.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
@@ -350,7 +322,7 @@ 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
@@ -474,12 +446,59 @@ 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) {
+        (0, util_ts_1.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/dist/tabixIndexedFile.js.map

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package/dist/util.d.ts

@@ -1,23 +1,6 @@
 import Chunk from './chunk.ts';
 import VirtualOffset from './virtualOffset.ts';
-/**
- * `signal.throwIfAborted()`, without requiring either that method or `reason`.
- *
- * Two reasons not to call the built-in directly. It assumes a *real*
- * `AbortSignal`, and callers pass duck-typed ones, where calling a missing
- * method is a `TypeError` rather than the cancellation the caller asked for —
- * a strictly worse failure.
- *
- * And it sets a browser floor. `AbortSignal.prototype.throwIfAborted` and
- * `AbortSignal.reason` are Safari 15.4 / Chrome 100 / Firefox 97 (March 2022),
- * higher than anything else here needs: this package otherwise touches only
- * `.aborted`, and `generic-filehandle2` only forwards a signal to `fetch`.
- *
- * Faithful to the spec otherwise: an aborted signal throws its `reason`
- * whatever that is, and only synthesizes an `AbortError` when there is none.
- * Kept in sync with the copy in `@gmod/bam`'s `src/util.ts`.
- */
-export declare function throwIfAborted(signal?: AbortSignal): void;
+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/dist/util.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.throwIfAborted = throwIfAborted;
+exports.throwIfAborted = void 0;
 exports.optimizeChunks = optimizeChunks;
 exports.clampChunkEnds = clampChunkEnds;
 exports.minVirtualOffset = minVirtualOffset;
@@ -16,36 +16,11 @@ const chunk_ts_1 = __importDefault(require("./chunk.js"));
 const long_ts_1 = require("./long.js");
 const virtualOffset_ts_1 = __importDefault(require("./virtualOffset.js"));
 // SYNC: ~/src/gmod/bam-js/src/util.ts optimizeChunks
-/**
- * `signal.throwIfAborted()`, without requiring either that method or `reason`.
- *
- * Two reasons not to call the built-in directly. It assumes a *real*
- * `AbortSignal`, and callers pass duck-typed ones, where calling a missing
- * method is a `TypeError` rather than the cancellation the caller asked for —
- * a strictly worse failure.
- *
- * And it sets a browser floor. `AbortSignal.prototype.throwIfAborted` and
- * `AbortSignal.reason` are Safari 15.4 / Chrome 100 / Firefox 97 (March 2022),
- * higher than anything else here needs: this package otherwise touches only
- * `.aborted`, and `generic-filehandle2` only forwards a signal to `fetch`.
- *
- * Faithful to the spec otherwise: an aborted signal throws its `reason`
- * whatever that is, and only synthesizes an `AbortError` when there is none.
- * Kept in sync with the copy in `@gmod/bam`'s `src/util.ts`.
- */
-function throwIfAborted(signal) {
-    if (signal?.aborted) {
-        const reason = signal.reason;
-        // Spec-faithful: throwIfAborted throws `reason` verbatim, and `reason` is
-        // whatever the caller passed to abort() — `controller.abort('too slow')`
-        // makes it a string. Coercing it to an Error here would hide that from a
-        // consumer who set it deliberately.
-        // eslint-disable-next-line @typescript-eslint/only-throw-error
-        throw reason === undefined
-            ? new DOMException('This operation was aborted', 'AbortError')
-            : reason;
-    }
-}
+// 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.
+var shared_read_cache_1 = require("@gmod/shared-read-cache");
+Object.defineProperty(exports, "throwIfAborted", { enumerable: true, get: function () { return shared_read_cache_1.throwIfAborted; } });
 function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
     if (n === 0) {

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package/esm/indexFile.d.ts

@@ -136,11 +136,11 @@ export default abstract class IndexFile {
      * duplicate parse rather than a recursion whose depth depends on how the
      * aborts interleave.
      *
-     * A retry rather than the reference count `chunkCache` gets from
-     * `@gmod/abortable-promise-cache`, 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.
+     * 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
      */

package/esm/indexFile.js

@@ -73,6 +73,8 @@ export default 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.
     /**
      * Parse the index, or join the parse already running.
      *
@@ -91,11 +93,11 @@ export default class IndexFile {
      * duplicate parse rather than a recursion whose depth depends on how the
      * aborts interleave.
      *
-     * A retry rather than the reference count `chunkCache` gets from
-     * `@gmod/abortable-promise-cache`, 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.
+     * 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
      */
@@ -122,28 +124,19 @@ export default class IndexFile {
         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. Identity-checked so a retry
-        // started after this settles is not cleared by the attempt it replaced.
-        //
-        // Written as one try/catch rather than `.then(onFulfilled, onRejected)`
-        // because `unicorn/prefer-then-catch` rewrites the two-argument form to
-        // `.then(...).catch(...)`, which is not the same thing — that catch would
-        // also swallow anything the fulfilment handler threw.
-        void (async () => {
-            let failed = false;
-            try {
-                await pending;
-            }
-            catch {
-                failed = true;
+        // 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) {
-                if (failed) {
-                    this.parseP = undefined;
-                }
+                this.parseP = undefined;
                 this.parseSignal = undefined;
             }
-        })();
+        });
         return pending;
     }
     /** @internal */

package/esm/indexFile.js.map

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