@gmod/bam 7.9.1 → 8.1.0

package/README.md

@@ -81,7 +81,11 @@ in each url's own `headers` field, which is applied either way.
 - `renameRefSeqs` - `(refName: string) => string` applied to header ref names
 - `recordClass` - custom class extending `BamRecord` (see below)
 - `maxCacheBytes` - budget for the parsed-chunk cache, in decompressed bytes.
-  default: 100MB
+  default: 512MB. A retention bound rather than a bound on peak memory — reads
+  in flight and the last settled entry are never evicted. 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
+  choice
 
 The `path`/`url` forms are convenience wrappers for generic-filehandle2's
 `LocalFile` and `RemoteFile`.

package/dist/bamFile.d.ts

@@ -1,3 +1,4 @@
+import { SharedReadCache } from '@gmod/shared-read-cache';
 import BAI from './bai.ts';
 import CSI from './csi.ts';
 import BAMFeature from './record.ts';
@@ -22,22 +23,6 @@ interface ChunkEntry<T> {
     features: T[];
 }
 export declare const DEFAULT_MAX_CACHE_BYTES: number;
-declare class ChunkFeatureCache<T> {
-    private _maxBytes;
-    private entries;
-    private bytes;
-    constructor(maxBytes: number);
-    get maxBytes(): number;
-    set maxBytes(maxBytes: number);
-    get size(): number;
-    get byteSize(): number;
-    get(key: string): ChunkEntry<T> | undefined;
-    set(key: string, entry: ChunkEntry<T>): void;
-    private evict;
-    delete(key: string): void;
-    clear(): void;
-    [Symbol.iterator](): MapIterator<[string, ChunkEntry<T>]>;
-}
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeq: (a: string) => string;
     bam: GenericFilehandle;
@@ -50,8 +35,14 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     index?: BAI | CSI;
     htsget: boolean;
     headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
-    chunkFeatureCache: ChunkFeatureCache<T>;
-    private inFlightChunks;
+    /**
+     * The signal `headerP` was started under, while it is still in flight. The
+     * header is parsed once and every query awaits it, so without this the first
+     * query to arrive would own a read all the others depend on — see
+     * {@link getHeader}.
+     */
+    private headerSignal?;
+    chunkFeatureCache: SharedReadCache<Chunk, ChunkEntry<T>>;
     private RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
         bamFilehandle?: GenericFilehandle;
@@ -66,7 +57,25 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         renameRefSeqs?: (a: string) => string;
         htsget?: boolean;
         recordClass?: BamRecordClass<T>;
-        /** budget for the parsed-chunk cache, in decompressed bytes */
+        /**
+         * Budget for the parsed-chunk cache, in decompressed bytes. Defaults to
+         * {@link DEFAULT_MAX_CACHE_BYTES}.
+         *
+         * A **retention** bound, not a bound on peak memory, and the difference is
+         * not small on deep data. Three things sit outside it: a read still in
+         * flight is never evicted, and up to `MAX_CONCURRENT_CHUNK_READS` of those
+         * run at once; the last settled entry is kept whatever the budget; and a
+         * query holds every chunk it parsed until it returns, whether or not the
+         * cache still does. On 1000x long-read data a single chunk decompresses to
+         * 180MB and six in flight is 476MB, neither of which this number can bound.
+         *
+         * Set it too low and the cache does not degrade gracefully — it inverts. A
+         * budget under one query's working set evicts each chunk before the next pan
+         * reuses it, so the hit rate is zero, the full re-decompress is paid on every
+         * pan, and the memory is retained anyway. Size it to hold several queries or
+         * pass `Infinity` and bound memory some other way; do not pick a number
+         * between the two (ADR 0014).
+         */
         maxCacheBytes?: number;
     });
     getHeaderPre(opts?: BaseOpts): Promise<{
@@ -89,13 +98,28 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
             value: string;
         }[];
     }[] | undefined;
-    getHeader(opts?: BaseOpts): Promise<{
-        tag: string;
-        data: {
-            tag: string;
-            value: string;
-        }[];
-    }[]>;
+    /**
+     * Parse the header, or join the parse already running.
+     *
+     * The header is parsed once for the life of this object and every query goes
+     * through it — `getSeqId` awaits it before anything else — so it is a read
+     * shared between queries, and the third place in this file where a
+     * cancellation could leak from the query that asked for it to a query that
+     * did not. `getHeaderPre` threads `opts` into both the index parse and the
+     * BAM read, 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 even though its own signal is untouched.
+     *
+     * Same bounded retry as `IndexFile.parse`, for the same reason — the header
+     * is parsed once, so there is no repeated waste to recover — and bounded at
+     * one attempt so the pathological case is a duplicate parse rather than a
+     * recursion whose depth depends on how the aborts interleave.
+     *
+     * SYNC: ~/src/gmod/tabix-js/src/tabixIndexedFile.ts getParsedHeader — same
+     * shape for the same reason.
+     */
+    getHeader(opts?: BaseOpts, retried?: boolean): Promise<Awaited<ReturnType<BamFile<T>['getHeaderPre']>>>;
+    private startHeaderParse;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     private getSeqId;
     /**
@@ -108,8 +132,6 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
      * it for every other query still holding that read. See ADR 0006.
      */
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
-    private _startChunkRead;
-    private joinChunkRead;
     private _cachedChunkFeatures;
     private _fetchChunkFeatures;
     fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;

package/dist/bamFile.js

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DEFAULT_MAX_CACHE_BYTES = exports.BAM_MAGIC = void 0;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const shared_read_cache_1 = require("@gmod/shared-read-cache");
 const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const generic_filehandle2_1 = require("generic-filehandle2");
 const bai_ts_1 = __importDefault(require("./bai.js"));
@@ -56,79 +57,29 @@ function chunkCacheKey(chunk) {
     return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
 }
 // Every record in an entry is a view into its chunk's decompressed buffer, so
-// caching one entry pins that whole buffer — 8MB apiece on the nanopore and
-// 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
-// so tens of MB is possible. A count-based LRU therefore gives no bound on
-// memory at all, which is why this budgets by decompressed bytes instead. It is
-// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
-// here costs a re-download and re-decompress the next time the view moves.
-exports.DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
+// caching one entry pins that whole buffer. A count-based LRU therefore gives no
+// bound on memory at all, which is why this budgets by decompressed bytes.
+//
+// Sized to hold SEVERAL of the largest query a consumer will issue, not one. A
+// budget below a single query's working set does not merely cache less — it
+// evicts each chunk before the next pan can reuse it, so the hit rate is zero
+// and the re-decompress is paid every time (ADR 0014).
+//
+// What sets that scale is the caller's own byte gate, not how deep data can get.
+// jbrowse compares `estimatedBytesForRegions` — COMPRESSED bytes, from the index
+// — against its `fetchSizeLimit` and refuses to query above it. Default 5MB
+// compressed; its own SV demo raises that to 30MB for PacBio HiFi. At the 2.1-7.3x
+// BGZF ratios measured across the jb2bench corpus, that is 10-37MB decompressed
+// per query at the stock gate and 63-219MB at the raised one, so six pan windows
+// want ~219MB and ~378MB respectively. 512MB clears both.
+//
+// It costs a consumer on ordinary data nothing, being a ceiling rather than an
+// allocation: 20x short-read data holds 7MB here whatever this is set to.
+exports.DEFAULT_MAX_CACHE_BYTES = 512 * 1024 * 1024;
 // How many of a query's chunks to read at once. Six is the HTTP/1.1
 // per-host connection cap browsers enforce, so going much above it buys
 // nothing on the transport that matters and only widens peak memory.
 const MAX_CONCURRENT_CHUNK_READS = 6;
-class ChunkFeatureCache {
-    _maxBytes;
-    entries = new Map();
-    bytes = 0;
-    constructor(maxBytes) {
-        this._maxBytes = maxBytes;
-    }
-    get maxBytes() {
-        return this._maxBytes;
-    }
-    // Accessor rather than a plain field so lowering the budget frees memory now.
-    // As a field, a caller trimming the cache under memory pressure got nothing
-    // back until the next chunk read happened to call set().
-    set maxBytes(maxBytes) {
-        this._maxBytes = maxBytes;
-        this.evict();
-    }
-    get size() {
-        return this.entries.size;
-    }
-    get byteSize() {
-        return this.bytes;
-    }
-    get(key) {
-        const entry = this.entries.get(key);
-        if (entry) {
-            // re-insert so Map iteration order stays least-recently-used first
-            this.entries.delete(key);
-            this.entries.set(key, entry);
-        }
-        return entry;
-    }
-    set(key, entry) {
-        this.delete(key);
-        this.entries.set(key, entry);
-        this.bytes += entry.bytes;
-        this.evict();
-    }
-    // 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);
-        }
-    }
-    delete(key) {
-        const entry = this.entries.get(key);
-        if (entry) {
-            this.entries.delete(key);
-            this.bytes -= entry.bytes;
-        }
-    }
-    clear() {
-        this.entries.clear();
-        this.bytes = 0;
-    }
-    [Symbol.iterator]() {
-        return this.entries[Symbol.iterator]();
-    }
-}
 class BamFile {
     renameRefSeq;
     bam;
@@ -138,17 +89,30 @@ class BamFile {
     index;
     htsget = false;
     headerP;
-    // Cache for parsed features by chunk, bounded by decompressed bytes
+    /**
+     * The signal `headerP` was started under, while it is still in flight. The
+     * header is parsed once and every query awaits it, so without this the first
+     * query to arrive would own a read all the others depend on — see
+     * {@link getHeader}.
+     */
+    headerSignal;
+    // Parsed features by chunk, bounded by decompressed bytes. Also the
+    // in-flight map: concurrent queries for the same chunk share one read rather
+    // than racing to decompress it twice.
     chunkFeatureCache;
-    // Chunks currently being read, so concurrent queries share one decompress
-    // instead of racing. Entries live only until the read settles; the resolved
-    // features land in chunkFeatureCache.
-    inFlightChunks = new Map();
     RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, }) {
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? record_ts_1.default);
-        this.chunkFeatureCache = new ChunkFeatureCache(maxCacheBytes);
+        this.chunkFeatureCache = new shared_read_cache_1.SharedReadCache({
+            maxSize: maxCacheBytes,
+            // decompressed bytes, not entry count: parsed records are views into
+            // their chunk's decompressed buffer, so a cached entry pins that whole
+            // buffer and entry count says nothing about memory
+            sizeOf: entry => entry.bytes,
+            cacheKey: chunkCacheKey,
+            fill: (chunk, signal) => this._readChunkFeatures(chunk, { signal }),
+        });
         const bamFh = resolveFilehandle(bamFilehandle, bamPath, bamUrl);
         if (bamFh) {
             this.bam = bamFh;
@@ -236,14 +200,63 @@ class BamFile {
         }
         return samHeader;
     }
-    getHeader(opts) {
-        if (!this.headerP) {
-            this.headerP = this.getHeaderPre(opts).catch((e) => {
-                this.headerP = undefined;
+    /**
+     * Parse the header, or join the parse already running.
+     *
+     * The header is parsed once for the life of this object and every query goes
+     * through it — `getSeqId` awaits it before anything else — so it is a read
+     * shared between queries, and the third place in this file where a
+     * cancellation could leak from the query that asked for it to a query that
+     * did not. `getHeaderPre` threads `opts` into both the index parse and the
+     * BAM read, 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 even though its own signal is untouched.
+     *
+     * Same bounded retry as `IndexFile.parse`, for the same reason — the header
+     * is parsed once, so there is no repeated waste to recover — and bounded at
+     * one attempt so the pathological case is a duplicate parse rather than a
+     * recursion whose depth depends on how the aborts interleave.
+     *
+     * SYNC: ~/src/gmod/tabix-js/src/tabixIndexedFile.ts getParsedHeader — same
+     * shape for the same reason.
+     */
+    async getHeader(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.getHeader(opts, true);
         }
-        return this.headerP;
+    }
+    startHeaderParse(opts) {
+        const pending = this.getHeaderPre(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;
     }
     async getHeaderText(opts = {}) {
         await this.getHeader(opts);
@@ -273,86 +286,6 @@ class BamFile {
         const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
         return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
-    // Read a chunk, publish it to the cache, and keep the in-flight promise
-    // discoverable while it runs.
-    //
-    // The read runs under this entry's own controller rather than any one
-    // caller's signal, because the read is shared: it must survive until every
-    // caller waiting on it has given up. joinChunkRead is what registers them.
-    _startChunkRead(cacheKey, chunk) {
-        const controller = new AbortController();
-        const promise = this._readChunkFeatures(chunk, {
-            signal: controller.signal,
-        }).then(entry => {
-            this.chunkFeatureCache.set(cacheKey, entry);
-            return entry;
-        });
-        const inFlight = {
-            promise,
-            signals: new Set(),
-            pinned: false,
-            controller,
-            dispose: new AbortController(),
-            settled: false,
-        };
-        this.inFlightChunks.set(cacheKey, inFlight);
-        // `.then(f, f)` rather than `.finally(f)` so the handler's own promise never
-        // carries an unhandled rejection.
-        const clear = () => {
-            inFlight.settled = true;
-            // nothing reads these once the read has settled, and holding them would
-            // pin each caller's AbortController behind this entry
-            inFlight.dispose.abort();
-            inFlight.signals.clear();
-            // only clear our own entry: a later read for this chunk may have replaced it
-            if (this.inFlightChunks.get(cacheKey) === inFlight) {
-                this.inFlightChunks.delete(cacheKey);
-            }
-        };
-        promise.then(clear, clear);
-        return inFlight;
-    }
-    // Register a caller's interest, so the read survives until that caller has
-    // given up too.
-    //
-    // A caller with no signal cannot give up, so it pins the read: there is no
-    // longer any set of aborts that should stop it. That is the honest reading of
-    // a caller that never asked to be cancellable, and it means one signal-free
-    // query makes that chunk's read uncancellable for everyone joined to it.
-    joinChunkRead(inFlight, signal) {
-        if (signal === undefined) {
-            inFlight.pinned = true;
-        }
-        else if (signal.aborted) {
-            // A caller that has already given up is not a waiter, and must not be
-            // counted as one: an `abort` listener never fires on a signal that
-            // aborted before it was added, so nothing would ever take this signal
-            // back out of the set. The count would never reach zero and the read
-            // would be uncancellable for everyone joined to it, silently.
-            //
-            // `_cachedChunkFeatures` rejects such a caller before it reaches here,
-            // with no `await` in between, so this is unreachable today. It is here
-            // because this is the bug that shipped, and an invariant that fails this
-            // quietly should not rest on a check twenty lines away. `@gmod/cram`
-            // guards the same spot for the same reason; see its ADR 0003.
-            if (!inFlight.pinned && inFlight.signals.size === 0) {
-                inFlight.controller.abort(signal.reason);
-            }
-        }
-        else if (!inFlight.signals.has(signal)) {
-            // guarded so one signal joining twice — a viewAsPairs query reaching the
-            // same chunk for a read and for its mate — does not add two listeners
-            inFlight.signals.add(signal);
-            signal.addEventListener('abort', () => {
-                inFlight.signals.delete(signal);
-                if (!inFlight.pinned && inFlight.signals.size === 0) {
-                    inFlight.controller.abort(signal.reason);
-                }
-            }, 
-            // `once` covers the abort firing; `dispose` covers it never firing
-            { once: true, signal: inFlight.dispose.signal });
-        }
-    }
     // Parsed records for a chunk, reading and decompressing it only on a miss.
     // Every path that wants a chunk's features goes through here — mate lookups
     // included, since a viewAsPairs query revisits the same mate chunks each time
@@ -364,54 +297,11 @@ class BamFile {
     // each caller its own objects, but roughly doubles a warm query on dense data
     // — measured, and rejected, in that ADR.
     async _cachedChunkFeatures(chunk, opts) {
-        // Before anything else, including the cache hit. A caller reaches here with
-        // a signal that has already fired on the ordinary pan — the abort lands
-        // while blocksForRange is still reading the index, and nothing between
-        // there and here looks at it, since bai.ts and csi.ts never read the
-        // signal. Such a caller must not start a read it has no interest in, and
-        // must not be registered as a waiter on someone else's: see joinChunkRead.
-        // @gmod/cram checks in exactly this position, in SliceRecordCache.getOrFill.
-        (0, util_ts_1.throwIfAborted)(opts.signal);
-        const cacheKey = chunkCacheKey(chunk);
-        const cached = this.chunkFeatureCache.get(cacheKey);
-        if (cached) {
-            return cached.features;
-        }
-        // Join a read already running for this chunk rather than decompressing it a
-        // second time. jbrowse fetches a row of adjacent blocks concurrently and
-        // they collapse onto very few chunk keys, so without this a query pays for
-        // the same inflate several times over — the dominant cost of a cold query
-        // (ADR 0003).
-        let pending = this.inFlightChunks.get(cacheKey);
-        // A read every caller has abandoned is on its way out but may not have
-        // noticed yet. Start a fresh one rather than joining one already doomed.
-        if (pending?.controller.signal.aborted && !pending.settled) {
-            if (this.inFlightChunks.get(cacheKey) === pending) {
-                this.inFlightChunks.delete(cacheKey);
-            }
-            pending = undefined;
-        }
-        pending ??= this._startChunkRead(cacheKey, chunk);
-        // Only a read still running has anything to cancel. Joining a settled one
-        // would add this caller to a set nothing will ever take it out of, since
-        // the entry drops its abort listeners when it settles.
-        if (!pending.settled) {
-            this.joinChunkRead(pending, opts.signal);
-        }
-        try {
-            const entry = await pending.promise;
-            // the read finished, but this caller gave up while waiting for it
-            (0, util_ts_1.throwIfAborted)(opts.signal);
-            return entry.features;
-        }
-        catch (e) {
-            // Prefer this caller's own cancellation to whatever the shared read
-            // reported. If we asked to stop, that is the answer we want — and when
-            // the read itself was cancelled it is because we, and everyone else,
-            // asked it to.
-            (0, util_ts_1.throwIfAborted)(opts.signal);
-            throw e;
-        }
+        // The cache does the rest: one read per chunk shared by every caller that
+        // asks for it while it is in flight, cancelled only once every one of them
+        // has given up (ADR 0007), and bounded by decompressed bytes.
+        const entry = await this.chunkFeatureCache.get(chunk, opts.signal);
+        return entry.features;
     }
     async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
         const { viewAsPairs, onProgress } = opts;

package/dist/bamFile.js.map

@@ -1 +1 @@
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package/dist/indexFile.d.ts

@@ -22,14 +22,14 @@ export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | und
 export default abstract class IndexFile<TParsed extends ParsedIndexBase = ParsedIndexBase> {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
-    private setupP?;
+    private parseP?;
     /**
-     * The signal `setupP` was started under, while it is still in flight. The
+     * 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 setupSignal?;
+    private parseSignal?;
     constructor({ filehandle, renameRefSeq, }: {
         filehandle: GenericFilehandle;
         renameRefSeq?: (a: string) => string;