@gmod/bam 8.3.1 → 8.4.1

package/README.md

@@ -120,8 +120,9 @@ whatever it reached and never lowers — and for a page that holds a `BamFile` f
 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 rather than from when it was parsed,
-so panning back and forth over one region never expires it. Measured on a pan
+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:

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;
@@ -42,7 +43,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     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;
@@ -91,10 +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;

package/dist/bamFile.js

@@ -110,12 +110,13 @@ 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, 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

package/dist/bamFile.js.map

@@ -1 +1 @@
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package/esm/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;
@@ -42,7 +43,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     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;
@@ -91,10 +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;

package/esm/bamFile.js

@@ -104,12 +104,13 @@ 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, cacheIdleTimeoutMs = DEFAULT_CACHE_IDLE_TIMEOUT_MS, }) {
+    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, cacheBudget, }) {
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? BAMFeature);
         this.chunkFeatureCache = new 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

package/esm/bamFile.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "8.3.1",
+  "version": "8.4.1",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
@@ -27,7 +27,7 @@
   ],
   "scripts": {
     "test": "vitest",
-    "test:coverage": "vitest run --coverage",
+    "coverage": "pnpm test --coverage",
     "clean": "rimraf dist esm",
     "format": "prettier --write .",
     "format:check": "prettier --check .",
@@ -37,7 +37,7 @@
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "preversion": "pnpm lint && pnpm test --run && pnpm build",
+    "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test --run && pnpm build",
     "postversion": "git push --follow-tags",
     "build": "pnpm build:esm && pnpm build:es5",
     "benchonly": "vitest bench",
@@ -52,7 +52,7 @@
   ],
   "dependencies": {
     "@gmod/bgzf-filehandle": "^6.3.2",
-    "@gmod/shared-read-cache": "^1.4.4",
+    "@gmod/shared-read-cache": "^1.5.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "crc": "^4.3.2",
     "generic-filehandle2": "^2.2.1"

package/src/bamFile.ts

@@ -17,6 +17,7 @@ import {
 
 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 {
@@ -183,6 +184,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     recordClass,
     maxCacheBytes = DEFAULT_MAX_CACHE_BYTES,
     cacheIdleTimeoutMs = DEFAULT_CACHE_IDLE_TIMEOUT_MS,
+    cacheBudget,
   }: {
     bamFilehandle?: GenericFilehandle
     bamPath?: string
@@ -232,16 +234,37 @@ 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
   }) {
     this.renameRefSeq = renameRefSeqs
     this.RecordClass = (recordClass ?? BAMFeature) as BamRecordClass<T>
     this.chunkFeatureCache = new SharedReadCache<Chunk, ChunkEntry<T>>({
       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