@gmod/bam 7.9.0 → 8.0.0

package/esm/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,oBAAoB,CAAA;AAEzC,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAwB1D,uDAAuD;AACvD,6EAA6E;AAC7E,2CAA2C;AAC3C,MAAM,UAAU,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,KAAK,GAAG,IAAI,QAAQ,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAClD,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,yEAAyE;QACzE,sDAAsD;QACtD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC/B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,EAAE,CAAC;YACX,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1B,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAgB,SAAS;IAG9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAElC,MAAM,CAAmB;IACjC;;;;;OAKG;IACK,WAAW,CAAc;IAEjC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAwBD,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAY,EAAE,CAAA;QAC1B,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,uEAAuE;IACvE,gEAAgE;IAChE;;;;;;;;;;;;;;;;;;;;;;OAsBG;IACH,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE,EAAE,OAAO,GAAG,KAAK;QAC9C,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAC3B,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QAC3B,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC;QAED,4EAA4E;QAC5E,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACpC,IAAI,CAAC;YACH,OAAO,MAAM,OAAO,CAAA;QACtB,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,IAAI,OAAO,IAAI,CAAC,WAAW,EAAE,OAAO,IAAI,IAAI,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC;gBAC7D,MAAM,CAAC,CAAA;YACT,CAAC;YACD,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAC/B,CAAC;IACH,CAAC;IAEO,UAAU,CAAC,IAAc;QAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QACjC,IAAI,CAAC,MAAM,GAAG,OAAO,CAAA;QACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,CAAA;QAC9B,6EAA6E;QAC7E,mEAAmE;QACnE,2EAA2E;QAC3E,mCAAmC;QACnC,OAAO,CAAC,IAAI,CACV,GAAG,EAAE;YACH,IAAI,IAAI,CAAC,MAAM,KAAK,OAAO,EAAE,CAAC;gBAC5B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC9B,CAAC;QACH,CAAC,EACD,GAAG,EAAE;YACH,IAAI,IAAI,CAAC,MAAM,KAAK,OAAO,EAAE,CAAC;gBAC5B,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC9B,CAAC;QACH,CAAC,CACF,CAAA;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IACnC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,cAAc,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF"}

package/esm/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/esm/util.js

@@ -10,6 +10,10 @@ import { VirtualOffset } from "./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.
+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

@@ -1,12 +1,12 @@
 {
   "name": "@gmod/bam",
-  "version": "7.9.0",
+  "version": "8.0.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": {
     "type": "git",
-    "url": "https://github.com/GMOD/bam-js.git"
+    "url": "git+https://github.com/GMOD/bam-js.git"
   },
   "type": "module",
   "sideEffects": false,
@@ -51,24 +51,24 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.2.0",
+    "@gmod/bgzf-filehandle": "^6.3.2",
+    "@gmod/shared-read-cache": "^1.3.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.2.0"
+    "generic-filehandle2": "^2.2.1"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
-    "@types/node": "^25.9.2",
-    "@vitest/coverage-v8": "^4.1.8",
-    "eslint": "^10.4.1",
-    "eslint-plugin-import-x": "^4.16.2",
-    "eslint-plugin-unicorn": "^65.0.0",
+    "@types/node": "^25.9.5",
+    "@vitest/coverage-v8": "^4.1.10",
+    "eslint": "^10.8.0",
+    "eslint-plugin-import-x": "^4.17.1",
     "git-cliff": "^2.13.1",
-    "prettier": "^3.8.3",
+    "prettier": "^3.9.6",
     "rimraf": "^6.1.3",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.61.0",
-    "vitest": "^4.1.8"
+    "typescript-eslint": "^8.65.0",
+    "vitest": "^4.1.10"
   },
   "publishConfig": {
     "access": "public"

package/src/bamFile.ts

@@ -1,4 +1,5 @@
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
+import { SharedReadCache } from '@gmod/shared-read-cache'
 import crc32 from 'crc/calculators/crc32'
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
 
@@ -7,7 +8,7 @@ import CSI from './csi.ts'
 import NullFilehandle from './nullFilehandle.ts'
 import BAMFeature from './record.ts'
 import { parseHeaderText } from './sam.ts'
-import { appendInRange, parseRefSeqs } from './util.ts'
+import { appendInRange, parseRefSeqs, throwIfAborted } from './util.ts'
 
 import type Chunk from './chunk.ts'
 import type { BamOpts, BaseOpts } from './util.ts'
@@ -63,13 +64,6 @@ interface ChunkEntry<T> {
   features: T[]
 }
 
-interface InFlightChunk<T> {
-  promise: Promise<ChunkEntry<T>>
-  // the signal the read was started with, so a waiter can tell "the owner
-  // aborted" apart from "the read genuinely failed"
-  signal?: AbortSignal
-}
-
 /**
  * Whether a chunk's first record already lies past `chrId:..-max`, which means
  * every later chunk does too and none of them need to be read.
@@ -120,80 +114,6 @@ export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024
 // nothing on the transport that matters and only widens peak memory.
 const MAX_CONCURRENT_CHUNK_READS = 6
 
-class ChunkFeatureCache<T> {
-  private _maxBytes: number
-  private entries = new Map<string, ChunkEntry<T>>()
-  private bytes = 0
-
-  constructor(maxBytes: number) {
-    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: number) {
-    this._maxBytes = maxBytes
-    this.evict()
-  }
-
-  get size() {
-    return this.entries.size
-  }
-
-  get byteSize() {
-    return this.bytes
-  }
-
-  get(key: string) {
-    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: string, entry: ChunkEntry<T>) {
-    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.
-  private evict() {
-    const lru = this.entries.keys()
-    while (this.bytes > this._maxBytes && this.entries.size > 1) {
-      this.delete(lru.next().value!)
-    }
-  }
-
-  delete(key: string) {
-    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]()
-  }
-}
-
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
   public renameRefSeq: (a: string) => string
   public bam: GenericFilehandle
@@ -203,14 +123,18 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
   public index?: BAI | CSI
   public htsget = false
   public headerP?: ReturnType<BamFile<T>['getHeaderPre']>
+  /**
+   * 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?: AbortSignal
 
-  // Cache for parsed features by chunk, bounded by decompressed bytes
-  public chunkFeatureCache: ChunkFeatureCache<T>
-
-  // 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.
-  private inFlightChunks = new Map<string, InFlightChunk<T>>()
+  // 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.
+  public chunkFeatureCache: SharedReadCache<Chunk, ChunkEntry<T>>
 
   private RecordClass: BamRecordClass<T>
 
@@ -246,7 +170,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
   }) {
     this.renameRefSeq = renameRefSeqs
     this.RecordClass = (recordClass ?? BAMFeature) as BamRecordClass<T>
-    this.chunkFeatureCache = new ChunkFeatureCache<T>(maxCacheBytes)
+    this.chunkFeatureCache = new SharedReadCache<Chunk, ChunkEntry<T>>({
+      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) {
@@ -355,14 +287,70 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     return samHeader
   }
 
-  getHeader(opts?: BaseOpts) {
-    if (!this.headerP) {
-      this.headerP = this.getHeaderPre(opts).catch((e: unknown) => {
-        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?: BaseOpts,
+    retried = false,
+  ): Promise<Awaited<ReturnType<BamFile<T>['getHeaderPre']>>> {
+    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
+  }
+
+  private startHeaderParse(opts?: BaseOpts) {
+    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: BaseOpts = {}) {
@@ -392,6 +380,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     max: number,
     opts?: BamOpts,
   ) {
+    throwIfAborted(opts?.signal)
     const chrId = await this.getSeqId(chr, opts)
     if (chrId === undefined || !this.index) {
       return []
@@ -400,27 +389,6 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     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.
-  private _startChunkRead(cacheKey: string, chunk: Chunk, opts: BaseOpts) {
-    const promise = this._readChunkFeatures(chunk, opts).then(entry => {
-      this.chunkFeatureCache.set(cacheKey, entry)
-      return entry
-    })
-    const inFlight: InFlightChunk<T> = { 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
@@ -435,35 +403,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     chunk: Chunk,
     opts: BaseOpts,
   ): Promise<T[]> {
-    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
   }
 
   private async _fetchChunkFeatures(
@@ -669,6 +613,21 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         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`.
+    throwIfAborted(opts.signal)
+
     const {
       buffer: data,
       cpositions,

package/src/indexFile.ts

@@ -1,6 +1,6 @@
 import QuickLRU from '@jbrowse/quick-lru'
 
-import { optimizeChunks } from './util.ts'
+import { optimizeChunks, throwIfAborted } from './util.ts'
 
 import type Chunk from './chunk.ts'
 import type { BaseOpts } from './util.ts'
@@ -53,7 +53,14 @@ export default abstract class IndexFile<
   public filehandle: GenericFilehandle
   public renameRefSeq: (s: string) => string
 
-  private setupP?: Promise<TParsed>
+  private parseP?: Promise<TParsed>
+  /**
+   * 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,
@@ -121,14 +128,72 @@ export default abstract class IndexFile<
     return optimizeChunks(chunks, this.getLowestChunk(ba, min))
   }
 
-  parse(opts: BaseOpts = {}): Promise<TParsed> {
-    if (!this.setupP) {
-      this.setupP = this._parse(opts).catch((e: unknown) => {
-        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: BaseOpts = {}, retried = false): Promise<TParsed> {
+    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
+  }
+
+  private startParse(opts: BaseOpts) {
+    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: number, opts?: BaseOpts) {

package/src/util.ts

@@ -39,6 +39,11 @@ export interface BaseOpts {
  * 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.
+export { throwIfAborted } from '@gmod/shared-read-cache'
+
 export function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords) {
   const n = chunks.length
   if (n === 0) {