@gmod/bam 8.0.0 → 8.2.0

package/README.md

@@ -81,7 +81,16 @@ in each url's own `headers` field, which is applied either way.
 - `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: 100MB
+  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
+- `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
 
 The `path`/`url` forms are convenience wrappers for generic-filehandle2's
 `LocalFile` and `RemoteFile`.

package/dist/bamFile.d.ts

@@ -23,6 +23,7 @@ interface ChunkEntry<T> {
     features: T[];
 }
 export declare const DEFAULT_MAX_CACHE_BYTES: number;
+export declare const DEFAULT_CACHE_IDLE_TIMEOUT_MS: number;
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeq: (a: string) => string;
     bam: GenericFilehandle;
@@ -44,7 +45,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     private headerSignal?;
     chunkFeatureCache: SharedReadCache<Chunk, ChunkEntry<T>>;
     private RecordClass;
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -57,8 +58,38 @@ 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;
+        /**
+         * Drop a cached chunk once nothing has asked for it for this many
+         * milliseconds. Defaults to {@link DEFAULT_CACHE_IDLE_TIMEOUT_MS}; pass
+         * `0` to keep chunks until `maxCacheBytes` evicts them.
+         *
+         * 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).
+         */
+        cacheIdleTimeoutMs?: number;
     });
     getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;

package/dist/bamFile.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.DEFAULT_MAX_CACHE_BYTES = exports.BAM_MAGIC = void 0;
+exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.DEFAULT_MAX_CACHE_BYTES = exports.BAM_MAGIC = void 0;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const shared_read_cache_1 = require("@gmod/shared-read-cache");
 const crc32_1 = __importDefault(require("crc/calculators/crc32"));
@@ -57,13 +57,41 @@ function chunkCacheKey(chunk) {
     return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
 }
 // 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.
-exports.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.
+//
+// 1GB clears both with room for the deepest data measured — a six-window pan on
+// 1000x long-read peaks at 569MB — and is affordable only because of
+// DEFAULT_CACHE_IDLE_TIMEOUT_MS below. It is a ceiling under active panning, not
+// a resting level, and it costs a consumer on ordinary data nothing either way:
+// 20x short-read holds 7MB here whatever this is set to.
+exports.DEFAULT_MAX_CACHE_BYTES = 1024 * 1024 * 1024;
+// Drop a chunk nothing has looked at for three minutes.
+//
+// This is what makes the ceiling above affordable rather than alarming. jbrowse
+// memoizes one BamFile per adapter for the life of the track and passes no
+// budget, so without this a tab parked on a deep region holds its whole last
+// view until the track is closed, times every track open. The budget alone
+// cannot lower that: it is enforced when a read settles, so an idle cache stays
+// wherever it got to.
+//
+// Three minutes rather than seconds because the point is to catch a user who has
+// 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.
@@ -89,11 +117,12 @@ class BamFile {
     // 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, }) {
+    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, }) {
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? record_ts_1.default);
         this.chunkFeatureCache = new shared_read_cache_1.SharedReadCache({
             maxSize: maxCacheBytes,
+            idleTimeoutMs: cacheIdleTimeoutMs,
             // 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

package/dist/bamFile.js.map

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

@@ -1,5 +1,5 @@
 export { default as BAI } from './bai.ts';
-export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts';
+export { DEFAULT_CACHE_IDLE_TIMEOUT_MS, DEFAULT_MAX_CACHE_BYTES, default as BamFile, } from './bamFile.ts';
 export { default as CSI } from './csi.ts';
 export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';

package/dist/index.js

@@ -3,10 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.BAI = void 0;
+exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
 var bai_ts_1 = require("./bai.js");
 Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_ts_1).default; } });
 var bamFile_ts_1 = require("./bamFile.js");
+Object.defineProperty(exports, "DEFAULT_CACHE_IDLE_TIMEOUT_MS", { enumerable: true, get: function () { return bamFile_ts_1.DEFAULT_CACHE_IDLE_TIMEOUT_MS; } });
 Object.defineProperty(exports, "DEFAULT_MAX_CACHE_BYTES", { enumerable: true, get: function () { return bamFile_ts_1.DEFAULT_MAX_CACHE_BYTES; } });
 Object.defineProperty(exports, "BamFile", { enumerable: true, get: function () { return __importDefault(bamFile_ts_1).default; } });
 var csi_ts_1 = require("./csi.js");

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAA0E;AAAjE,qHAAA,uBAAuB,OAAA;AAAE,sHAAA,OAAO,OAAW;AACpD,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc"}

package/esm/bamFile.d.ts

@@ -23,6 +23,7 @@ interface ChunkEntry<T> {
     features: T[];
 }
 export declare const DEFAULT_MAX_CACHE_BYTES: number;
+export declare const DEFAULT_CACHE_IDLE_TIMEOUT_MS: number;
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeq: (a: string) => string;
     bam: GenericFilehandle;
@@ -44,7 +45,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     private headerSignal?;
     chunkFeatureCache: SharedReadCache<Chunk, ChunkEntry<T>>;
     private RecordClass;
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, cacheIdleTimeoutMs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -57,8 +58,38 @@ 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;
+        /**
+         * Drop a cached chunk once nothing has asked for it for this many
+         * milliseconds. Defaults to {@link DEFAULT_CACHE_IDLE_TIMEOUT_MS}; pass
+         * `0` to keep chunks until `maxCacheBytes` evicts them.
+         *
+         * 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).
+         */
+        cacheIdleTimeoutMs?: number;
     });
     getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;

package/esm/bamFile.js

@@ -51,13 +51,41 @@ function chunkCacheKey(chunk) {
     return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
 }
 // 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.
+//
+// 1GB clears both with room for the deepest data measured — a six-window pan on
+// 1000x long-read peaks at 569MB — and is affordable only because of
+// DEFAULT_CACHE_IDLE_TIMEOUT_MS below. It is a ceiling under active panning, not
+// a resting level, and it costs a consumer on ordinary data nothing either way:
+// 20x short-read holds 7MB here whatever this is set to.
+export const DEFAULT_MAX_CACHE_BYTES = 1024 * 1024 * 1024;
+// Drop a chunk nothing has looked at for three minutes.
+//
+// This is what makes the ceiling above affordable rather than alarming. jbrowse
+// memoizes one BamFile per adapter for the life of the track and passes no
+// budget, so without this a tab parked on a deep region holds its whole last
+// view until the track is closed, times every track open. The budget alone
+// cannot lower that: it is enforced when a read settles, so an idle cache stays
+// wherever it got to.
+//
+// Three minutes rather than seconds because the point is to catch a user who has
+// 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).
+export const 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.
@@ -83,11 +111,12 @@ export default class BamFile {
     // than racing to decompress it twice.
     chunkFeatureCache;
     RecordClass;
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, }) {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, cacheIdleTimeoutMs = DEFAULT_CACHE_IDLE_TIMEOUT_MS, }) {
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? BAMFeature);
         this.chunkFeatureCache = new SharedReadCache({
             maxSize: maxCacheBytes,
+            idleTimeoutMs: cacheIdleTimeoutMs,
             // 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

package/esm/bamFile.js.map

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

@@ -1,5 +1,5 @@
 export { default as BAI } from './bai.ts';
-export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts';
+export { DEFAULT_CACHE_IDLE_TIMEOUT_MS, DEFAULT_MAX_CACHE_BYTES, default as BamFile, } from './bamFile.ts';
 export { default as CSI } from './csi.ts';
 export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';

package/esm/index.js

@@ -1,5 +1,5 @@
 export { default as BAI } from "./bai.js";
-export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from "./bamFile.js";
+export { DEFAULT_CACHE_IDLE_TIMEOUT_MS, DEFAULT_MAX_CACHE_BYTES, default as BamFile, } from "./bamFile.js";
 export { default as CSI } from "./csi.js";
 export { default as BamRecord } from "./record.js";
 export { default as HtsgetFile } from "./htsget.js";

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,uBAAuB,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAA;AAC1E,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EACL,6BAA6B,EAC7B,uBAAuB,EACvB,OAAO,IAAI,OAAO,GACnB,MAAM,cAAc,CAAA;AACrB,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "8.0.0",
+  "version": "8.2.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
@@ -52,7 +52,7 @@
   ],
   "dependencies": {
     "@gmod/bgzf-filehandle": "^6.3.2",
-    "@gmod/shared-read-cache": "^1.3.0",
+    "@gmod/shared-read-cache": "^1.4.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "crc": "^4.3.2",
     "generic-filehandle2": "^2.2.1"

package/src/bamFile.ts

@@ -101,13 +101,42 @@ 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.
+//
+// 1GB clears both with room for the deepest data measured — a six-window pan on
+// 1000x long-read peaks at 569MB — and is affordable only because of
+// DEFAULT_CACHE_IDLE_TIMEOUT_MS below. It is a ceiling under active panning, not
+// a resting level, and it costs a consumer on ordinary data nothing either way:
+// 20x short-read holds 7MB here whatever this is set to.
+export const DEFAULT_MAX_CACHE_BYTES = 1024 * 1024 * 1024
+
+// Drop a chunk nothing has looked at for three minutes.
+//
+// This is what makes the ceiling above affordable rather than alarming. jbrowse
+// memoizes one BamFile per adapter for the life of the track and passes no
+// budget, so without this a tab parked on a deep region holds its whole last
+// view until the track is closed, times every track open. The budget alone
+// cannot lower that: it is enforced when a read settles, so an idle cache stays
+// wherever it got to.
+//
+// Three minutes rather than seconds because the point is to catch a user who has
+// 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).
+export const 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
@@ -152,6 +181,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeqs = n => n,
     recordClass,
     maxCacheBytes = DEFAULT_MAX_CACHE_BYTES,
+    cacheIdleTimeoutMs = DEFAULT_CACHE_IDLE_TIMEOUT_MS,
   }: {
     bamFilehandle?: GenericFilehandle
     bamPath?: string
@@ -165,13 +195,44 @@ 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
+    /**
+     * Drop a cached chunk once nothing has asked for it for this many
+     * milliseconds. Defaults to {@link DEFAULT_CACHE_IDLE_TIMEOUT_MS}; pass
+     * `0` to keep chunks until `maxCacheBytes` evicts them.
+     *
+     * 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).
+     */
+    cacheIdleTimeoutMs?: number
   }) {
     this.renameRefSeq = renameRefSeqs
     this.RecordClass = (recordClass ?? BAMFeature) as BamRecordClass<T>
     this.chunkFeatureCache = new SharedReadCache<Chunk, ChunkEntry<T>>({
       maxSize: maxCacheBytes,
+      idleTimeoutMs: cacheIdleTimeoutMs,
       // 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

package/src/index.ts

@@ -1,5 +1,9 @@
 export { default as BAI } from './bai.ts'
-export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts'
+export {
+  DEFAULT_CACHE_IDLE_TIMEOUT_MS,
+  DEFAULT_MAX_CACHE_BYTES,
+  default as BamFile,
+} from './bamFile.ts'
 export { default as CSI } from './csi.ts'
 export { default as BamRecord } from './record.ts'
 export { default as HtsgetFile } from './htsget.ts'