@gmod/bam 7.9.1 → 8.0.0

package/esm/indexFile.js

@@ -22,14 +22,14 @@ export function memoizeByRefId(getIndices, maxSize = 5) {
 export default class IndexFile {
     filehandle;
     renameRefSeq;
-    setupP;
+    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}.
      */
-    setupSignal;
+    parseSignal;
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
@@ -61,6 +61,8 @@ export default class IndexFile {
         }
         return optimizeChunks(chunks, this.getLowestChunk(ba, min));
     }
+    // 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.
      *
@@ -86,12 +88,12 @@ export default class IndexFile {
      */
     async parse(opts = {}, retried = false) {
         throwIfAborted(opts.signal);
-        const pending = this.setupP;
+        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.setupSignal;
+        const ownerSignal = this.parseSignal;
         try {
             return await pending;
         }
@@ -104,20 +106,20 @@ export default class IndexFile {
     }
     startParse(opts) {
         const pending = this._parse(opts);
-        this.setupP = pending;
-        this.setupSignal = opts.signal;
+        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.setupP === pending) {
-                this.setupSignal = undefined;
+            if (this.parseP === pending) {
+                this.parseSignal = undefined;
             }
         }, () => {
-            if (this.setupP === pending) {
-                this.setupP = undefined;
-                this.setupSignal = undefined;
+            if (this.parseP === pending) {
+                this.parseP = undefined;
+                this.parseSignal = undefined;
             }
         });
         return pending;

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

@@ -35,26 +35,7 @@ export interface BaseOpts {
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
-/**
- * `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 — `test/csi.test.ts` casts a
- * bare `{ aborted }` through `as AbortSignal`, which is a fair model of what
- * consumers do; calling a missing method there is a `TypeError` rather than the
- * cancellation the caller asked for, which is 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 in this dependency tree needs, since
- * `generic-filehandle2` only ever forwards a signal to `fetch`, and higher than
- * every sibling gmod library, which use plain `.aborted`. Three lines here
- * keeps that floor where it was.
- *
- * Faithful to the spec otherwise: an aborted signal throws its `reason`
- * whatever that is, and only synthesizes an `AbortError` when there is none.
- */
-export declare function throwIfAborted(signal?: AbortSignal): void;
+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;
@@ -95,4 +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

@@ -10,33 +10,10 @@ import { VirtualOffset } from "./virtualOffset.js";
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
-/**
- * `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 — `test/csi.test.ts` casts a
- * bare `{ aborted }` through `as AbortSignal`, which is a fair model of what
- * consumers do; calling a missing method there is a `TypeError` rather than the
- * cancellation the caller asked for, which is 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 in this dependency tree needs, since
- * `generic-filehandle2` only ever forwards a signal to `fetch`, and higher than
- * every sibling gmod library, which use plain `.aborted`. Three lines here
- * keeps that floor where it was.
- *
- * Faithful to the spec otherwise: an aborted signal throws its `reason`
- * whatever that is, and only synthesizes an `AbortError` when there is none.
- */
-export function throwIfAborted(signal) {
-    if (signal?.aborted) {
-        const { reason } = signal;
-        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.
+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": "7.9.1",
+  "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,
@@ -51,23 +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",
+    "@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'
 
@@ -63,20 +64,6 @@ interface ChunkEntry<T> {
   features: T[]
 }
 
-interface InFlightChunk<T> {
-  promise: Promise<ChunkEntry<T>>
-  // Signals of the callers still waiting on this read. The read is cancelled
-  // only once every one of them has given up — see joinChunkRead and ADR 0007.
-  signals: Set<AbortSignal>
-  // true once a caller joins without a signal, which pins the read
-  pinned: boolean
-  // aborts when every caller has given up. what the read actually runs under
-  controller: AbortController
-  // aborted to take this read's listeners back off its callers' signals
-  dispose: AbortController
-  settled: boolean
-}
-
 /**
  * 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.
@@ -127,80 +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
@@ -210,14 +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>
 
@@ -253,7 +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) {
@@ -362,14 +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 = {}) {
@@ -408,89 +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.
-  //
-  // 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.
-  private _startChunkRead(cacheKey: string, chunk: Chunk) {
-    const controller = new AbortController()
-    const promise = this._readChunkFeatures(chunk, {
-      signal: controller.signal,
-    }).then(entry => {
-      this.chunkFeatureCache.set(cacheKey, entry)
-      return entry
-    })
-    const inFlight: InFlightChunk<T> = {
-      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.
-  private joinChunkRead(inFlight: InFlightChunk<T>, signal?: AbortSignal) {
-    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
@@ -505,56 +403,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     chunk: Chunk,
     opts: BaseOpts,
   ): Promise<T[]> {
-    // 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.
-    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
-      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.
-      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
   }
 
   private async _fetchChunkFeatures(