@gmod/bam 7.9.1 → 8.1.0

package/dist/indexFile.js

@@ -28,14 +28,14 @@ function memoizeByRefId(getIndices, maxSize = 5) {
 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;
@@ -67,6 +67,8 @@ class IndexFile {
         }
         return (0, util_ts_1.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.
      *
@@ -92,12 +94,12 @@ class IndexFile {
      */
     async parse(opts = {}, retried = false) {
         (0, util_ts_1.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;
         }
@@ -110,20 +112,20 @@ 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/dist/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;AA6BA,wCAkBC;AA/CD,mEAAyC;AAEzC,uCAA0D;AAwB1D,uDAAuD;AACvD,6EAA6E;AAC7E,2CAA2C;AAC3C,SAAgB,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,KAAK,GAAG,IAAI,mBAAQ,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,MAA8B,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,IAAA,wBAAc,EAAC,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,IAAA,wBAAc,EAAC,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,IAAA,wBAAc,EAAC,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;AA7KD,4BA6KC"}

package/dist/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/dist/util.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.throwIfAborted = throwIfAborted;
+exports.throwIfAborted = void 0;
 exports.optimizeChunks = optimizeChunks;
 exports.parsePseudoBin = parsePseudoBin;
 exports.clampChunkEnds = clampChunkEnds;
@@ -24,33 +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.)
  */
-/**
- * `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.
- */
-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.
+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) {

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/bamFile.d.ts

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