@gmod/bam 7.9.1 → 8.1.0

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": "8.1.0",
   "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.
@@ -114,93 +101,31 @@ function chunkCacheKey(chunk: Chunk) {
 }
 
 // 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.
-export const 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.
+export const 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<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 +135,18 @@ 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>
 
@@ -248,12 +177,38 @@ 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
   }) {
     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 +317,70 @@ 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 +419,6 @@ 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 +433,11 @@ 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(

package/src/indexFile.ts

@@ -53,14 +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 `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?: AbortSignal
+  private parseSignal?: AbortSignal
 
   constructor({
     filehandle,
@@ -128,6 +128,8 @@ export default abstract 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.
    *
@@ -153,13 +155,13 @@ export default abstract class IndexFile<
    */
   async parse(opts: BaseOpts = {}, retried = false): Promise<TParsed> {
     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
     } catch (e) {
@@ -172,22 +174,22 @@ export default abstract class IndexFile<
 
   private startParse(opts: BaseOpts) {
     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
         }
       },
     )

package/src/util.ts

@@ -39,33 +39,10 @@ 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 function throwIfAborted(signal?: AbortSignal) {
-  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: Chunk[], lowest?: OffsetCoords) {
   const n = chunks.length