@gmod/bam 8.3.0 → 8.4.0

package/README.md

@@ -80,21 +80,66 @@ in each url's own `headers` field, which is applied either way.
   longer than 2^29
 - `renameRefSeqs` - `(refName: string) => string` applied to header ref names
 - `recordClass` - custom class extending `BamRecord` (see below)
-- `maxCacheBytes` - budget for the parsed-chunk cache, in decompressed bytes.
-  default: 1GB. A retention bound rather than a bound on peak memory — reads in
-  flight and the last settled entry are never evicted. Size it to hold several
-  queries: below one query's working set the hit rate drops to zero while the
-  memory is retained anyway, so a number between the two is the worst choice
+- `maxCacheBytes` - ceiling for the parsed-chunk cache, in decompressed bytes.
+  default: 1GB, `Infinity` for none. See [Caching](#caching)
 - `cacheIdleTimeoutMs` - drop a cached chunk once nothing has read it for this
-  long. default: 3 minutes; `0` disables it. This is what makes the budget above
-  a peak under panning rather than a level a parked page holds indefinitely, and
-  it is the only thing that lowers the cache while nothing is happening. The
-  clock runs from the last read of a chunk, so panning back and forth over one
-  region never expires it
+  long. default: 3 minutes; `0` disables it. See [Caching](#caching)
 
 The `path`/`url` forms are convenience wrappers for generic-filehandle2's
 `LocalFile` and `RemoteFile`.
 
+### Caching
+
+Parsed chunks — the unit the BAM index hands out — are cached, so overlapping
+and adjacent queries reuse decompressed records instead of re-fetching them. Two
+options bound that cache, and they answer different questions.
+
+**`maxCacheBytes` is a ceiling under load, not a limit on what you can ask
+for.** Nothing is ever refused for being too large: a chunk bigger than the
+whole budget is still cached, reads in flight are never evicted, and eviction
+only drops a value that has already been returned once. The worst a budget can
+cost you is a re-read. It can make a query slower; it can never make one fail or
+come back short.
+
+**It binds less often than its size suggests.** On the deepest data we measure —
+1000x coverage long reads, 240 windows over six laps — the cache settles at
+573MB across 60 entries and eviction never runs at the 1GB default. Treat it as
+a backstop against a session that pans forever, not as an operating constraint.
+
+**Don't pick a number between one query and several.** Below one query's working
+set the cache inverts: each chunk is evicted before the next pan can reuse it,
+so the hit rate is zero, the full re-decompress is paid every time, and the
+unevictable entries retain the memory anyway. At a 200MB budget on that same
+file the cache holds exactly one entry, because one chunk there decompresses to
+181MB. Either size it above the working set or pass `Infinity` and bound memory
+some other way.
+
+**`cacheIdleTimeoutMs` is the only thing that gives memory back.**
+`maxCacheBytes` is enforced when a read settles, so an idle cache sits at
+whatever it reached and never lowers — and for a page that holds a `BamFile` for
+the life of a track, that resting level is the number that actually matters. The
+idle sweep is what makes a generous ceiling affordable, by turning it into a
+peak under panning rather than a level a parked tab holds indefinitely. The
+clock runs from the last _read_ of a chunk, or from its parse landing if nothing
+has read it since, so panning back and forth over one region never expires it
+and a slow chunk still gets the full timeout to be reused in. Measured on a pan
+that held 331MB: 0MB once idle.
+
+**Neither bounds peak memory**, and on deep data the gap is not small:
+
+- Up to six chunk reads run at once and an in-flight read is never evicted. At
+  181MB a chunk, that is ~476MB in flight before retention holds anything.
+- A query holds every chunk it parsed until it returns, whether or not the cache
+  still does.
+- An entry is weighed once, when its read settles, and records grow after that.
+  `end`, `CIGAR` and `tags` each memoize onto the record the first time they are
+  read, which is what a renderer does to every visible read — measured at +38%
+  over the weighed size.
+
+So these are bounds on retained decompressed bytes, not on the heap. Size
+against what you want to keep, and bound total memory at a level that can see
+the whole process.
+
 ### HtsgetFile constructor
 
 - `baseUrl` - htsget reads endpoint, e.g. `https://htsget.example.com/reads`
@@ -156,7 +201,8 @@ warning before a large query.
 
 ### clearFeatureCache()
 
-Drops the parsed-chunk cache.
+Drops the parsed-chunk cache immediately, rather than waiting for
+`maxCacheBytes` or `cacheIdleTimeoutMs` to reclaim it. See [Caching](#caching).
 
 ### BamRecord
 

package/dist/bai.d.ts

@@ -21,5 +21,6 @@ export default class BAI extends IndexFile<BaiParsed> {
         blockPosition: number;
         dataPosition: number;
     } | undefined;
+    protected getHighestChunk(refIndex: BaiRefIndex, max: number): number | undefined;
 }
 export {};

package/dist/bai.js

@@ -261,6 +261,21 @@ class BAI extends indexFile_ts_1.default {
                 dataPosition: linearDataPositions[i],
             };
     }
+    // The linear-index entry one window PAST the query: the smallest file offset
+    // of any record overlapping the window after it. Records the query wants are
+    // overwhelmingly below it, which is what makes it a usable forecast — but not
+    // a bound, because a long read reaching into that next window pins the entry
+    // at ITS offset, and records starting later (still before the query end) sit
+    // above it. chunksLikelyRead says why an estimate may use it and a fetch may
+    // not.
+    //
+    // undefined past the end of the linear index, i.e. for a query running to the
+    // end of the reference, where there is no next window to bound anything with.
+    getHighestChunk(refIndex, max) {
+        const { linearBlockPositions } = refIndex;
+        const i = (max >> BAI_LINEAR_SHIFT) + 1;
+        return i < linearBlockPositions.length ? linearBlockPositions[i] : undefined;
+    }
 }
 exports.default = BAI;
 //# sourceMappingURL=bai.js.map

package/dist/bai.js.map

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

@@ -4,6 +4,7 @@ import CSI from './csi.ts';
 import BAMFeature from './record.ts';
 import type Chunk from './chunk.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
+import type { SharedBudget } from '@gmod/shared-read-cache';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface BamRecordLike {
     ref_id: number;
@@ -35,17 +36,14 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     }[];
     index?: BAI | CSI;
     htsget: boolean;
-    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}.
+     * The parsed header, as a shared read — see {@link getHeader}. One entry,
+     * never evicted, which is what a memo is.
      */
-    private headerSignal?;
+    private headerCache;
     chunkFeatureCache: SharedReadCache<Chunk, ChunkEntry<T>>;
     private RecordClass;
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, cacheBudget, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -63,13 +61,21 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
          * {@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
+         * not small on deep data. Four 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.
          *
+         * The fourth is that an entry is weighed ONCE, when its read settles, and
+         * records grow after that: `end`, `CIGAR` and `tags` each memoize onto the
+         * record the first time they are read, which is what a renderer does to
+         * every visible read. Measured on `chr22_nanopore_subset.bam`, a chunk
+         * weighed at 20.4MB retained a further 7.8MB — +38% — once its 383 records
+         * had been consumed. So a budget of N bytes can hold appreciably more than
+         * N; the number is a bound on decompressed bytes, not on the heap.
+         *
          * 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
@@ -86,10 +92,30 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
          * This is the only thing that lowers the cache while a consumer sits still,
          * and the reason `maxCacheBytes` can afford to be generous — it makes the
          * budget a peak under panning rather than a resting level. The clock runs
-         * from the last read of a chunk, not from when it was parsed, so panning
-         * back and forth over the same region never expires it (ADR 0015).
+         * from the last read of a chunk, or from its parse landing if nothing has
+         * read it since, so panning back and forth over the same region never
+         * expires it and a slow chunk still gets the full timeout to be reused in
+         * (ADR 0015).
          */
         cacheIdleTimeoutMs?: number;
+        /**
+         * A budget shared with other `BamFile`s — and with any other
+         * `@gmod/shared-read-cache` consumer — so that the ceiling applies to
+         * their sum rather than to each of them.
+         *
+         * {@link maxCacheBytes} is per file, which is not a bound on a consumer
+         * that opens one file per track. Three moderately deep alignments tracks
+         * browsing eight windows measured 1109MB retained with no cache anywhere
+         * near its own 1GB ceiling, so the ceiling was not doing anything at all;
+         * the sum is what a tab runs out of memory on.
+         *
+         * Pass one budget per worker and hand it to every file. Dividing
+         * `maxCacheBytes` by the track count instead reintroduces the cliff it
+         * exists to avoid — at 128MB a track re-reads every chunk on every pan —
+         * whereas a shared budget lets tracks nobody is looking at yield their
+         * space to the one being panned.
+         */
+        cacheBudget?: SharedBudget;
     });
     getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;
@@ -119,20 +145,31 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
      * 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.
+     * BAM read, 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 even though its own signal is
+     * untouched.
+     *
+     * The cache is what avoids that, on the same terms as the chunk reads: the
+     * parse runs under a signal of its own and is cancelled only once every
+     * caller waiting on it has given up, so an owner's abort is reported to the
+     * owner alone and the bystanders get the header from the read 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.
      *
-     * 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.
+     * The fill is per call rather than on the cache so that the caller who
+     * starts the parse has its `onProgress` reach the index download inside it.
      *
-     * SYNC: ~/src/gmod/tabix-js/src/tabixIndexedFile.ts getParsedHeader — same
-     * shape for the same reason.
+     * SYNC: ~/src/gmod/tabix-js/src/tabixIndexedFile.ts getParsedHeader,
+     * ~/src/gmod/bbi-js/src/bbi.ts getHeader — same shape for the same reason.
      */
-    getHeader(opts?: BaseOpts, retried?: boolean): Promise<Awaited<ReturnType<BamFile<T>['getHeaderPre']>>>;
-    private startHeaderParse;
+    getHeader(opts?: BaseOpts): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[]>;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     private getSeqId;
     /**

package/dist/bamFile.js

@@ -92,10 +92,6 @@ exports.DEFAULT_MAX_CACHE_BYTES = 1024 * 1024 * 1024;
 // gone away, not one who is reading the screen in front of them. A pan back to a
 // region a minute later should still hit (ADR 0015).
 exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = 3 * 60 * 1000;
-// 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 BamFile {
     renameRefSeq;
     bam;
@@ -104,25 +100,23 @@ class BamFile {
     indexToChr;
     index;
     htsget = false;
-    headerP;
     /**
-     * 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}.
+     * The parsed header, as a shared read — see {@link getHeader}. One entry,
+     * never evicted, which is what a memo is.
      */
-    headerSignal;
+    headerCache = new shared_read_cache_1.SharedReadCache({});
     // 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.
     chunkFeatureCache;
     RecordClass;
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, cacheIdleTimeoutMs = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS, }) {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, cacheIdleTimeoutMs = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS, cacheBudget, }) {
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? record_ts_1.default);
         this.chunkFeatureCache = new shared_read_cache_1.SharedReadCache({
             maxSize: maxCacheBytes,
             idleTimeoutMs: cacheIdleTimeoutMs,
+            budget: cacheBudget,
             // 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
@@ -225,55 +219,26 @@ class BamFile {
      * 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.
+     * BAM read, 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 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.
+     * The cache is what avoids that, on the same terms as the chunk reads: the
+     * parse runs under a signal of its own and is cancelled only once every
+     * caller waiting on it has given up, so an owner's abort is reported to the
+     * owner alone and the bystanders get the header from the read 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.
      *
-     * SYNC: ~/src/gmod/tabix-js/src/tabixIndexedFile.ts getParsedHeader — same
-     * shape 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 the index download inside it.
+     *
+     * SYNC: ~/src/gmod/tabix-js/src/tabixIndexedFile.ts getParsedHeader,
+     * ~/src/gmod/bbi-js/src/bbi.ts getHeader — same shape for the same reason.
      */
-    async getHeader(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.getHeader(opts, true);
-        }
-    }
-    startHeaderParse(opts) {
-        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;
+    getHeader(opts) {
+        return this.headerCache.get('header', opts?.signal, signal => this.getHeaderPre({ ...opts, signal }));
     }
     async getHeaderText(opts = {}) {
         await this.getHeader(opts);
@@ -368,7 +333,7 @@ class BamFile {
             // without stopping is one that needs its chunks, so it runs the
             // unbarriered pool exactly as before. That caps the cost of being wrong
             // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
-            const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
+            const batch = Math.min(util_ts_1.MAX_CONCURRENT_CHUNK_READS, chunks.length);
             await Promise.all(Array.from({ length: batch }, (_, ci) => readOne(ci)));
             let stopped = false;
             for (let ci = 0; ci < batch; ci++) {
@@ -384,7 +349,7 @@ class BamFile {
                         await readOne(next++);
                     }
                 };
-                const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length - batch);
+                const workers = Math.min(util_ts_1.MAX_CONCURRENT_CHUNK_READS, chunks.length - batch);
                 await Promise.all(Array.from({ length: workers }, () => readNext()));
             }
             // A determinate bar must still reach its total after an early stop.
@@ -474,7 +439,7 @@ class BamFile {
                 mateFeatLists[ci] = mateRecs;
             }
         };
-        const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, mateChunks.length);
+        const workers = Math.min(util_ts_1.MAX_CONCURRENT_CHUNK_READS, mateChunks.length);
         await Promise.all(Array.from({ length: workers }, () => readNext()));
         return mateFeatLists.flat();
     }

package/dist/bamFile.js.map

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package/dist/csi.d.ts

@@ -47,6 +47,7 @@ export default class CSI extends IndexFile {
         csi: boolean;
     }>;
     protected getLowestChunk(): VirtualOffset;
+    protected getHighestChunk(): undefined;
     /**
      * calculate the list of bins that may overlap with region [beg,end)
      * (zero-based half-open). Follows the reference implementation in hts-specs

package/dist/csi.js

@@ -197,6 +197,11 @@ class CSI extends indexFile_ts_1.default {
     getLowestChunk() {
         return ZERO_OFFSET;
     }
+    // ...and so there is nothing to bound the far end of a query with either, so
+    // estimatedBytesForRegions keeps summing every chunk on a CSI-indexed file.
+    getHighestChunk() {
+        return undefined;
+    }
     /**
      * calculate the list of bins that may overlap with region [beg,end)
      * (zero-based half-open). Follows the reference implementation in hts-specs

package/dist/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAE3C,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEpB,uEAAuE;IACvE,iEAAiE;IACjE,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC3D,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,wBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,yEAAyE;QACzE,sEAAsE;QACtE,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,UAAU,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACjD,oDAAoD;YACpD,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;QAC5C,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,2EAA2E;QAC3E,yEAAyE;QACzE,2EAA2E;QAC3E,wEAAwE;QACxE,wEAAwE;QACxE,uEAAuE;QACvE,+DAA+D;QAC/D,EAAE;QACF,iEAAiE;QACjE,yEAAyE;QACzE,mEAAmE;QACnE,oEAAoE;QACpE,sEAAsE;QACtE,iEAAiE;QACjE,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,mEAAmE;QACnE,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,sEAAsE;oBACtE,qEAAqE;oBACrE,sEAAsE;oBACtE,kDAAkD;oBAClD,aAAa,GAAG,IAAA,0BAAgB,EAAC,KAAK,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,CAAC,CAAA;oBAC/D,IAAI,IAAI,CAAC,CAAA,CAAC,UAAU;oBACpB,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA,CAAC,6DAA6D;oBACvE,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,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package/dist/htsget.d.ts

@@ -20,9 +20,18 @@ export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends Bam
          * `headers` field, which is applied either way.
          */
         fetch?: Fetcher;
-        /** see {@link BamFile}; htsget caches parsed chunks the same way */
+        /**
+         * Passed on to {@link BamFile}, where it bounds `chunkFeatureCache` —
+         * which htsget mode never fills. `getRecordsForRange` below reads whole
+         * ticket blocks rather than index chunks, so nothing here reaches that
+         * cache and neither of these options changes anything today. Accepted
+         * rather than rejected because the inherited cache is the thing that
+         * should eventually hold ticket responses (there is no read sharing or
+         * reuse in htsget mode at all right now), and that is when they start to
+         * bite.
+         */
         maxCacheBytes?: number;
-        /** see {@link BamFile}; htsget caches parsed chunks the same way */
+        /** see {@link maxCacheBytes}: inherited, and inert in htsget mode */
         cacheIdleTimeoutMs?: number;
     });
     /**

package/dist/htsget.js.map

@@ -1 +1 @@
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