@gmod/bam 8.3.0 → 8.4.0

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;
@@ -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/esm/bamFile.js

@@ -7,7 +7,7 @@ import CSI from "./csi.js";
 import NullFilehandle from "./nullFilehandle.js";
 import BAMFeature from "./record.js";
 import { parseHeaderText } from "./sam.js";
-import { appendInRange, parseRefSeqs, throwIfAborted } from "./util.js";
+import { MAX_CONCURRENT_CHUNK_READS, appendInRange, parseRefSeqs, throwIfAborted, } from "./util.js";
 export const BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
 // Ceiling on GROWING the header read. A million contigs is roughly 10MB of
@@ -86,10 +86,6 @@ export const 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).
 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.
-const MAX_CONCURRENT_CHUNK_READS = 6;
 export default class BamFile {
     renameRefSeq;
     bam;
@@ -98,25 +94,23 @@ export default 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 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 = 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
@@ -219,55 +213,26 @@ export default 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) {
-        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);

package/esm/bamFile.js.map

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package/esm/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/esm/csi.js

@@ -159,6 +159,11 @@ export default class CSI extends IndexFile {
     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/esm/csi.js.map

@@ -1 +1 @@
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package/esm/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/esm/htsget.js.map

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

@@ -22,14 +22,11 @@ export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | und
 export default abstract class IndexFile<TParsed extends ParsedIndexBase = ParsedIndexBase> {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
-    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, renameRefSeq, }: {
         filehandle: GenericFilehandle;
         renameRefSeq?: (a: string) => string;
@@ -42,6 +39,7 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
     }[]>;
     protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
     protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
+    protected abstract getHighestChunk(refIndex: RefIndex, max: number): number | undefined;
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
     /**
      * Parse the index, or join the parse already running.
@@ -49,26 +47,50 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
      * 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 `filehandle.readFile`, 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 `filehandle.readFile`, 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 the chunk reads use, 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. 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 `_cachedChunkFeatures` uses, for
-     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
-     * is parsed once for the life of the object, so there is no repeated waste to
-     * recover, and this is a dozen lines against restructuring the memo.
+     * The fill is per call rather than on the cache so that the caller who starts
+     * the parse has its `onProgress` reach `filehandle.readFile` — the index is a
+     * whole-file read, and a determinate "downloading index" bar is what that
+     * callback exists for.
      */
-    parse(opts?: BaseOpts, retried?: boolean): Promise<TParsed>;
-    private startParse;
+    parse(opts?: BaseOpts): Promise<TParsed>;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
+    /**
+     * Compressed bytes a `getRecordsForRange` over these regions is expected to
+     * download, from the index alone.
+     *
+     * Per region this is `chunksLikelyRead`, not every chunk `blocksForRange`
+     * returns: the difference is the whole point on a long-read file, where a
+     * narrow window inherits every chunk of every overlapping bin and reads a
+     * handful of them. Measured on a 40x ONT BAM (COLO829BL, chr3), summing all
+     * chunks against the bytes the same query really pulls:
+     *
+     * | window | all chunks | actually read | this estimate |
+     * | ------ | ---------- | ------------- | ------------- |
+     * | 380bp  | 43.5MB     | 7.8MB         | 7.8MB         |
+     * | 3.4kb  | 43.5MB     | 7.8MB         | 7.8MB         |
+     * | 100kb  | 46.6MB     | 10.4MB        | 10.4MB        |
+     * | 2Mb    | 155.9MB    | 155.9MB       | 123.8MB       |
+     *
+     * A caller gating on this — jbrowse's "too much data" banner is the one that
+     * exists — was being told 5.6x the truth on exactly the windows a reader
+     * spends their time in, and cannot answer it by zooming: every window narrower
+     * than a linear-index interval resolves to the same chunks and so to the same
+     * number.
+     *
+     * Still summed over merged chunks rather than per region, so two regions
+     * sharing a chunk are charged for it once.
+     */
     estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;
 }