@gmod/tabix 3.6.0 → 3.7.1

package/dist/tabixIndexedFile.d.ts

@@ -2,6 +2,7 @@ import { SharedReadCache } from '@gmod/shared-read-cache';
 import type Chunk from './chunk.ts';
 import type { Options } from './indexFile.ts';
 import type { ChunkSlice } from '@gmod/bgzf-filehandle';
+import type { SharedBudget } from '@gmod/shared-read-cache';
 import type { GenericFilehandle } from 'generic-filehandle2';
 type GetLinesCallback = (line: string, fileOffset: number, start: number, end: number) => void;
 interface GetLinesOpts {
@@ -24,15 +25,12 @@ export default class TabixIndexedFile {
     private filehandle;
     private index;
     chunkCache: SharedReadCache<Chunk, ReadChunk>;
-    private headerP?;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    private headerSignal?;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, }: {
+    private headerCache;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, chunkCacheBudget, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         url?: string;
@@ -45,6 +43,17 @@ export default class TabixIndexedFile {
         /**
          * Budget for the decompressed chunk cache, in bytes. Default 1GB.
          *
+         * **The unit changed in v3.5.2** (ADR 0001). Before that this was divided
+         * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
+         * asking for 800 whole decompressed chunks — unbounded in practice. It now
+         * means 50MB, twenty times under the default, and the name did not change
+         * so nothing warns. jbrowse still passes exactly that in nine adapters:
+         * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
+         * 47 refills out of 47 on the warm pass against 0 at the default, holding
+         * 82.7MB in a single entry — over the budget it was given, because the last
+         * settled entry is kept whatever the budget. If you pinned a value here
+         * before v3.5.2, it does not mean what it did.
+         *
          * A retention bound, not a bound on peak memory: reads in flight are never
          * evicted and the last settled entry is kept whatever the budget. Size it
          * to hold several queries — below one query's working set the hit rate
@@ -60,6 +69,24 @@ export default class TabixIndexedFile {
          * makes the budget above a peak rather than a resting level.
          */
         chunkCacheIdleTimeoutMs?: number;
+        /**
+         * A budget shared with other files — any `@gmod/shared-read-cache`
+         * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
+         * that the ceiling applies to their sum rather than to each of them.
+         *
+         * {@link chunkCacheSize} is per file, which is not a bound on a consumer
+         * that opens one file per track. @gmod/bam measured the shape: six tracks
+         * browsing six windows retained 1442 MB with every cache still under its
+         * own ceiling, so the ceiling was not holding the line and nothing else
+         * was. The idle timeout cannot help there — it does nothing while the
+         * reader is browsing, which is the whole case.
+         *
+         * Dividing {@link chunkCacheSize} by the track count instead reintroduces
+         * the cliff it exists to avoid. A shared budget does not, because a member
+         * yields only what is globally least-recently-used: files nobody is
+         * reading hand their space to the one being panned.
+         */
+        chunkCacheBudget?: SharedBudget;
     });
     /**
      * Drops every decompressed chunk held by the cache, and stops the idle sweep
@@ -134,16 +161,21 @@ export default class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * 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. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and the same rule: the parse runs under
+     * a signal of its own and is cancelled only once every caller waiting on it
+     * has given up, so one caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
     private getParsedHeader;
-    private startHeaderParse;
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the
      * string form: this hands back the buffer, and holding one for the lifetime

package/dist/tabixIndexedFile.js

@@ -193,15 +193,12 @@ class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
-    headerP;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    headerSignal;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, }) {
+    headerCache = new shared_read_cache_1.SharedReadCache({});
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, chunkCacheBudget, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
             tbiFilehandle,
@@ -220,6 +217,7 @@ class TabixIndexedFile {
             sizeOf: read => read.buffer.byteLength,
             cacheKey: chunk => chunk.toString(),
             idleTimeoutMs: chunkCacheIdleTimeoutMs,
+            budget: chunkCacheBudget,
             fill: (chunk, signal) => this.readChunk(chunk, { signal }),
         });
     }
@@ -454,51 +452,22 @@ class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * 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. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and the same rule: the parse runs under
+     * a signal of its own and is cancelled only once every caller waiting on it
+     * has given up, so one caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
-    async getParsedHeader(opts = {}, retried = false) {
-        (0, util_ts_1.throwIfAborted)(opts.signal);
-        const pending = this.headerP;
-        if (!pending) {
-            return this.startHeaderParse(opts);
-        }
-        // read before awaiting: the owner is forgotten as soon as the parse settles
-        const ownerSignal = this.headerSignal;
-        try {
-            return await pending;
-        }
-        catch (e) {
-            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this.getParsedHeader(opts, true);
-        }
-    }
-    startHeaderParse(opts) {
-        const pending = this.parseHeader(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;
+    getParsedHeader(opts = {}) {
+        return this.headerCache.get('header', opts.signal, signal => this.parseHeader({ ...opts, signal }));
     }
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the

package/dist/tabixIndexedFile.js.map

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package/esm/indexFile.d.ts

@@ -49,14 +49,11 @@ export interface IndexData {
 }
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
-    private parseP?;
     /**
-     * The signal `parseP` was started under, while it is still in flight. The
-     * index is parsed once and shared by every query against the file, so without
-     * this the first query to arrive would own a read all the others depend on —
-     * see {@link parse}.
+     * The parsed index, as a shared read — see {@link parse}. One entry, never
+     * evicted, which is what a memo is.
      */
-    private parseSignal?;
+    private parseCache;
     constructor({ filehandle }: {
         filehandle: GenericFilehandle;
     });
@@ -124,28 +121,27 @@ export default abstract class IndexFile {
      * 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 `readIndexBytes`, 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.
+     * that did not. `_parse` hands `opts` straight to `readIndexBytes`, so a bare
+     * memoized promise makes the first query to arrive the owner of 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.
+     * The same cache `ChunkCache` uses, for the same reason and with the same
+     * rule: the parse runs under a signal of its own and is cancelled only once
+     * every caller waiting on it has given up, so one query's abort is reported
+     * to that query alone and a bystander gets the parse already in flight rather
+     * than having to re-read the index. A rejection is dropped rather than
+     * cached, so a transient failure does not poison the index for the life of
+     * the file.
      *
-     * A retry rather than the reference count `ChunkCache` uses, because the
-     * index is parsed once for the life of the object: there is no repeated waste
-     * to recover, and this is a dozen lines against restructuring the memo.
-     * `@gmod/bam`'s `IndexFile` and `@gmod/cram`'s `CraiIndex` make the same
-     * split for the same reason.
+     * The fill is per call rather than on the cache so that the caller who starts
+     * the parse has its `onProgress` reach `readIndexBytes` — the index is a
+     * whole-file read, and a determinate "downloading index" bar is what that
+     * callback exists for.
      *
      * @internal
      */
-    parse(opts?: Options, retried?: boolean): Promise<IndexData>;
-    private startParse;
+    parse(opts?: Options): Promise<IndexData>;
     /** @internal */
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
 }

package/esm/indexFile.js

@@ -1,15 +1,13 @@
 import { unzip } from '@gmod/bgzf-filehandle';
-import { optimizeChunks, throwIfAborted } from "./util.js";
+import { SharedReadCache } from '@gmod/shared-read-cache';
+import { optimizeChunks } from "./util.js";
 export default class IndexFile {
     filehandle;
-    parseP;
     /**
-     * The signal `parseP` was started under, while it is still in flight. The
-     * index is parsed once and shared by every query against the file, so without
-     * this the first query to arrive would own a read all the others depend on —
-     * see {@link parse}.
+     * The parsed index, as a shared read — see {@link parse}. One entry, never
+     * evicted, which is what a memo is.
      */
-    parseSignal;
+    parseCache = new SharedReadCache({});
     constructor({ filehandle }) {
         this.filehandle = filehandle;
     }
@@ -73,71 +71,36 @@ export default class IndexFile {
         }
         return optimizeChunks(chunks, this.lowestOffset(ba, min, indexData));
     }
-    // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same owner-signal
-    // tracking and one-attempt retry, and the same reasoning below.
+    // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same shape 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 `readIndexBytes`, 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.
+     * that did not. `_parse` hands `opts` straight to `readIndexBytes`, so a bare
+     * memoized promise makes the first query to arrive the owner of 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.
+     * The same cache `ChunkCache` uses, for the same reason and with the same
+     * rule: the parse runs under a signal of its own and is cancelled only once
+     * every caller waiting on it has given up, so one query's abort is reported
+     * to that query alone and a bystander gets the parse already in flight rather
+     * than having to re-read the index. A rejection is dropped rather than
+     * cached, so a transient failure does not poison the index for the life of
+     * the file.
      *
-     * A retry rather than the reference count `ChunkCache` uses, because the
-     * index is parsed once for the life of the object: there is no repeated waste
-     * to recover, and this is a dozen lines against restructuring the memo.
-     * `@gmod/bam`'s `IndexFile` and `@gmod/cram`'s `CraiIndex` make the same
-     * split for the same reason.
+     * The fill is per call rather than on the cache so that the caller who starts
+     * the parse has its `onProgress` reach `readIndexBytes` — the index is a
+     * whole-file read, and a determinate "downloading index" bar is what that
+     * callback exists for.
      *
      * @internal
      */
-    async parse(opts = {}, retried = false) {
-        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);
-        }
-    }
-    startParse(opts) {
-        const pending = this._parse(opts);
-        this.parseP = pending;
-        this.parseSignal = opts.signal;
-        // Drop a rejection rather than keeping it, so one transient failure does not
-        // poison the index for the lifetime of the file. Both branches are
-        // identity-checked so a retry started after this settles is not cleared by
-        // the attempt it already replaced.
-        pending.then(() => {
-            if (this.parseP === pending) {
-                this.parseSignal = undefined;
-            }
-        }, () => {
-            if (this.parseP === pending) {
-                this.parseP = undefined;
-                this.parseSignal = undefined;
-            }
-        });
-        return pending;
+    parse(opts = {}) {
+        return this.parseCache.get('index', opts.signal, signal => this._parse({ ...opts, signal }));
     }
     /** @internal */
     async hasRefSeq(seqId, opts = {}) {

package/esm/indexFile.js.map

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package/esm/tabixIndexedFile.d.ts

@@ -2,6 +2,7 @@ import { SharedReadCache } from '@gmod/shared-read-cache';
 import type Chunk from './chunk.ts';
 import type { Options } from './indexFile.ts';
 import type { ChunkSlice } from '@gmod/bgzf-filehandle';
+import type { SharedBudget } from '@gmod/shared-read-cache';
 import type { GenericFilehandle } from 'generic-filehandle2';
 type GetLinesCallback = (line: string, fileOffset: number, start: number, end: number) => void;
 interface GetLinesOpts {
@@ -24,15 +25,12 @@ export default class TabixIndexedFile {
     private filehandle;
     private index;
     chunkCache: SharedReadCache<Chunk, ReadChunk>;
-    private headerP?;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    private headerSignal?;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, }: {
+    private headerCache;
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, chunkCacheBudget, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         url?: string;
@@ -45,6 +43,17 @@ export default class TabixIndexedFile {
         /**
          * Budget for the decompressed chunk cache, in bytes. Default 1GB.
          *
+         * **The unit changed in v3.5.2** (ADR 0001). Before that this was divided
+         * by 64KB to get an entry count, so a caller passing `50 * 2**20` was
+         * asking for 800 whole decompressed chunks — unbounded in practice. It now
+         * means 50MB, twenty times under the default, and the name did not change
+         * so nothing warns. jbrowse still passes exactly that in nine adapters:
+         * measured on `test/data/1kg.chr1.subset.vcf.gz` it is a **total miss**,
+         * 47 refills out of 47 on the warm pass against 0 at the default, holding
+         * 82.7MB in a single entry — over the budget it was given, because the last
+         * settled entry is kept whatever the budget. If you pinned a value here
+         * before v3.5.2, it does not mean what it did.
+         *
          * A retention bound, not a bound on peak memory: reads in flight are never
          * evicted and the last settled entry is kept whatever the budget. Size it
          * to hold several queries — below one query's working set the hit rate
@@ -60,6 +69,24 @@ export default class TabixIndexedFile {
          * makes the budget above a peak rather than a resting level.
          */
         chunkCacheIdleTimeoutMs?: number;
+        /**
+         * A budget shared with other files — any `@gmod/shared-read-cache`
+         * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
+         * that the ceiling applies to their sum rather than to each of them.
+         *
+         * {@link chunkCacheSize} is per file, which is not a bound on a consumer
+         * that opens one file per track. @gmod/bam measured the shape: six tracks
+         * browsing six windows retained 1442 MB with every cache still under its
+         * own ceiling, so the ceiling was not holding the line and nothing else
+         * was. The idle timeout cannot help there — it does nothing while the
+         * reader is browsing, which is the whole case.
+         *
+         * Dividing {@link chunkCacheSize} by the track count instead reintroduces
+         * the cliff it exists to avoid. A shared budget does not, because a member
+         * yields only what is globally least-recently-used: files nobody is
+         * reading hand their space to the one being panned.
+         */
+        chunkCacheBudget?: SharedBudget;
     });
     /**
      * Drops every decompressed chunk held by the cache, and stops the idle sweep
@@ -134,16 +161,21 @@ export default class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * 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. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and the same rule: the parse runs under
+     * a signal of its own and is cancelled only once every caller waiting on it
+     * has given up, so one caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
     private getParsedHeader;
-    private startHeaderParse;
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the
      * string form: this hands back the buffer, and holding one for the lifetime