@gmod/bam 7.9.0 → 8.0.0

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;
@@ -89,13 +80,28 @@ 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;
     /**
@@ -108,7 +114,6 @@ 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 _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"));
@@ -67,68 +68,6 @@ exports.DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
 // 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 +77,30 @@ 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 +188,63 @@ 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);
@@ -265,6 +266,7 @@ class BamFile {
      * it for every other query still holding that read. See ADR 0006.
      */
     async getRecordsForRange(chr, min, max, opts) {
+        (0, util_ts_1.throwIfAborted)(opts?.signal);
         const chrId = await this.getSeqId(chr, opts);
         if (chrId === undefined || !this.index) {
             return [];
@@ -272,26 +274,6 @@ 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.
-    _startChunkRead(cacheKey, chunk, opts) {
-        const promise = this._readChunkFeatures(chunk, opts).then(entry => {
-            this.chunkFeatureCache.set(cacheKey, entry);
-            return entry;
-        });
-        const inFlight = { promise, signal: opts.signal };
-        this.inFlightChunks.set(cacheKey, inFlight);
-        // Only clear our own entry: a retry may already have replaced it. `.then(f,
-        // f)` rather than `.finally(f)` so the handler's own promise never carries
-        // an unhandled rejection.
-        const clear = () => {
-            if (this.inFlightChunks.get(cacheKey) === inFlight) {
-                this.inFlightChunks.delete(cacheKey);
-            }
-        };
-        promise.then(clear, clear);
-        return promise;
-    }
     // 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
@@ -303,34 +285,11 @@ 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) {
-        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).
-        const pending = this.inFlightChunks.get(cacheKey);
-        if (!pending) {
-            return (await this._startChunkRead(cacheKey, chunk, opts)).features;
-        }
-        try {
-            return (await pending.promise).features;
-        }
-        catch (e) {
-            // The read we joined was started by another caller. If that caller
-            // aborted and we did not, the failure is theirs and says nothing about
-            // our query, so start over — which picks up the cache, joins a sibling's
-            // retry, or reads under our own signal. Any other failure (and our own
-            // abort) propagates as it would have without sharing.
-            if (!pending.signal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this._cachedChunkFeatures(chunk, opts);
-        }
+        // 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;
@@ -499,6 +458,20 @@ class BamFile {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, {
             signal: opts.signal,
         });
+        // The last chance to bail before the expensive part, and the reason it is
+        // worth having: honouring the signal is optional in the filehandle.
+        // `RemoteFile` hands it to `fetch`, but `LocalFile.read(length, position)`
+        // does not even take an options argument, so every read under it runs to
+        // completion and arrives here with the cancellation unnoticed. Without this
+        // a fully abandoned chunk still gets inflated and decoded — measured at 6
+        // chunks for one 20kb query on out.bam — which is the dominant cost of a
+        // cold query (ADR 0003), spent on records nobody will ever look at.
+        //
+        // Safe precisely because this is the SHARED signal, not a caller's: it
+        // fires only once every waiter has given up, so there is never a live
+        // caller left to be denied the result. @gmod/cram checks in the same place
+        // and for the same reason, before the decode loop in `_fetchRecords`.
+        (0, util_ts_1.throwIfAborted)(opts.signal);
         const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
         return {
             features: this.readBamFeatures(data, cpositions, dpositions, chunk),

package/dist/bamFile.js.map

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

@@ -22,7 +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 `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?;
     constructor({ filehandle, renameRefSeq, }: {
         filehandle: GenericFilehandle;
         renameRefSeq?: (a: string) => string;
@@ -36,7 +43,31 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
     protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
     protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
-    parse(opts?: BaseOpts): Promise<TParsed>;
+    /**
+     * 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 `filehandle.readFile`, 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 `_cachedChunkFeatures` uses, for
+     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
+     * is parsed once for the life of the object, so there is no repeated waste to
+     * recover, and this is a dozen lines against restructuring the memo.
+     */
+    parse(opts?: BaseOpts, retried?: boolean): Promise<TParsed>;
+    private startParse;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
     estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;

package/dist/indexFile.js

@@ -28,7 +28,14 @@ function memoizeByRefId(getIndices, maxSize = 5) {
 class IndexFile {
     filehandle;
     renameRefSeq;
-    setupP;
+    parseP;
+    /**
+     * 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}.
+     */
+    parseSignal;
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
@@ -60,14 +67,68 @@ class IndexFile {
         }
         return (0, util_ts_1.optimizeChunks)(chunks, this.getLowestChunk(ba, min));
     }
-    parse(opts = {}) {
-        if (!this.setupP) {
-            this.setupP = this._parse(opts).catch((e) => {
-                this.setupP = undefined;
+    // SYNC: ~/src/gmod/tabix-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 `filehandle.readFile`, 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 `_cachedChunkFeatures` uses, for
+     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
+     * is parsed once for the life of the object, so there is no repeated waste to
+     * recover, and this is a dozen lines against restructuring the memo.
+     */
+    async parse(opts = {}, retried = false) {
+        (0, util_ts_1.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);
         }
-        return this.setupP;
+    }
+    startParse(opts) {
+        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;
     }
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);

package/dist/indexFile.js.map

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

@@ -35,6 +35,7 @@ export interface BaseOpts {
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
+export { throwIfAborted } from '@gmod/shared-read-cache';
 export declare function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords): Chunk[];
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;
@@ -75,4 +76,3 @@ interface Positioned {
     end: number;
 }
 export declare function appendInRange<T extends Positioned>(records: T[], chrId: number, min: number, max: number, out?: T[]): T[];
-export {};

package/dist/util.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.throwIfAborted = void 0;
 exports.optimizeChunks = optimizeChunks;
 exports.parsePseudoBin = parsePseudoBin;
 exports.clampChunkEnds = clampChunkEnds;
@@ -23,6 +24,11 @@ const virtualOffset_ts_1 = require("./virtualOffset.js");
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
+// 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) {