@gmod/bam 7.5.0 → 7.6.0

package/dist/bamFile.d.ts

@@ -2,7 +2,6 @@ import BAI from './bai.ts';
 import CSI from './csi.ts';
 import BAMFeature from './record.ts';
 import type Chunk from './chunk.ts';
-import type { Bytes } from './record.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface BamRecordLike {
@@ -16,11 +15,7 @@ export interface BamRecordLike {
     flags: number;
     tags: Record<string, unknown>;
 }
-export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
-    bytes: Bytes;
-    fileOffset: number;
-    dataView: DataView;
-}) => T;
+export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView) => T;
 export declare const BAM_MAGIC = 21840194;
 interface ChunkEntry<T> {
     bytes: number;
@@ -53,6 +48,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     htsget: boolean;
     headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
     chunkFeatureCache: ChunkFeatureCache<T>;
+    private inFlightChunks;
     private RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
         bamFilehandle?: GenericFilehandle;
@@ -86,7 +82,17 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     }[] | undefined>;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     private getSeqId;
+    /**
+     * Records overlapping `chr:min-max`.
+     *
+     * The returned records are CACHED AND SHARED — two queries resolving to the
+     * same chunk span get the same objects back, so treat them as read-only.
+     * Anything you want to attach for the duration of one query belongs on a
+     * wrapper you own, never on the record; writing a field here silently rebinds
+     * it for every other query still holding that read. See ADR 0006.
+     */
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
+    private _startChunkRead;
     private _cachedChunkFeatures;
     private _fetchChunkFeatures;
     fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;

package/dist/bamFile.js

@@ -31,6 +31,10 @@ function chunkCacheKey(chunk) {
 // 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;
+// 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 ChunkFeatureCache {
     maxBytes;
     entries = new Map();
@@ -91,6 +95,10 @@ class BamFile {
     headerP;
     // Cache for parsed features by chunk, bounded by decompressed bytes
     chunkFeatureCache;
+    // Chunks currently being read, so concurrent queries share one decompress
+    // instead of racing. Entries live only until the read settles; the resolved
+    // features land in chunkFeatureCache.
+    inFlightChunks = new Map();
     RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, }) {
         this.renameRefSeq = renameRefSeqs;
@@ -177,6 +185,15 @@ class BamFile {
         await this.getHeader(opts);
         return this.chrToIndex?.[seqName];
     }
+    /**
+     * Records overlapping `chr:min-max`.
+     *
+     * The returned records are CACHED AND SHARED — two queries resolving to the
+     * same chunk span get the same objects back, so treat them as read-only.
+     * Anything you want to attach for the duration of one query belongs on a
+     * wrapper you own, never on the record; writing a field here silently rebinds
+     * it for every other query still holding that read. See ADR 0006.
+     */
     async getRecordsForRange(chr, min, max, opts) {
         const chrId = await this.getSeqId(chr, opts);
         if (chrId === undefined || !this.index) {
@@ -185,18 +202,65 @@ class BamFile {
         const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
         return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
+    // Read a chunk, publish it to the cache, and keep the in-flight promise
+    // discoverable while it runs.
+    _startChunkRead(cacheKey, chunk, opts) {
+        const promise = this._readChunkFeatures(chunk, opts).then(entry => {
+            this.chunkFeatureCache.set(cacheKey, entry);
+            return entry;
+        });
+        const inFlight = { promise, signal: opts.signal };
+        this.inFlightChunks.set(cacheKey, inFlight);
+        // Only clear our own entry: a retry may already have replaced it. `.then(f,
+        // f)` rather than `.finally(f)` so the handler's own promise never carries
+        // an unhandled rejection.
+        const clear = () => {
+            if (this.inFlightChunks.get(cacheKey) === inFlight) {
+                this.inFlightChunks.delete(cacheKey);
+            }
+        };
+        promise.then(clear, clear);
+        return promise;
+    }
     // Parsed records for a chunk, reading and decompressing it only on a miss.
     // Every path that wants a chunk's features goes through here — mate lookups
     // included, since a viewAsPairs query revisits the same mate chunks each time
     // the view moves.
+    //
+    // This hands the SAME record objects to every query that hits the key, which
+    // is what makes callers' per-query writes onto a record leak across queries
+    // (ADR 0006). Caching the inflated buffer and re-scanning per query would give
+    // each caller its own objects, but roughly doubles a warm query on dense data
+    // — measured, and rejected, in that ADR.
     async _cachedChunkFeatures(chunk, opts) {
         const cacheKey = chunkCacheKey(chunk);
-        let entry = this.chunkFeatureCache.get(cacheKey);
-        if (!entry) {
-            entry = await this._readChunkFeatures(chunk, opts);
-            this.chunkFeatureCache.set(cacheKey, entry);
+        const cached = this.chunkFeatureCache.get(cacheKey);
+        if (cached) {
+            return cached.features;
+        }
+        // Join a read already running for this chunk rather than decompressing it a
+        // second time. jbrowse fetches a row of adjacent blocks concurrently and
+        // they collapse onto very few chunk keys, so without this a query pays for
+        // the same inflate several times over — the dominant cost of a cold query
+        // (ADR 0003).
+        const pending = this.inFlightChunks.get(cacheKey);
+        if (!pending) {
+            return (await this._startChunkRead(cacheKey, chunk, opts)).features;
+        }
+        try {
+            return (await pending.promise).features;
+        }
+        catch (e) {
+            // The read we joined was started by another caller. If that caller
+            // aborted and we did not, the failure is theirs and says nothing about
+            // our query, so start over — which picks up the cache, joins a sibling's
+            // retry, or reads under our own signal. Any other failure (and our own
+            // abort) propagates as it would have without sharing.
+            if (!pending.signal?.aborted || opts.signal?.aborted) {
+                throw e;
+            }
+            return this._cachedChunkFeatures(chunk, opts);
         }
-        return entry.features;
     }
     async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
         const { viewAsPairs, onProgress } = opts;
@@ -207,12 +271,42 @@ class BamFile {
         }
         let downloadedBytes = 0;
         onProgress?.(0, totalBytes);
+        const featureLists = new Array(chunks.length);
+        if (chunks.length === 1) {
+            // Very common — most small files, and any query landing inside one bin.
+            // Worth its own path: the pool below allocates a closure, a worker array
+            // and a Promise.all, all of which is pure overhead for one chunk and
+            // measurable on queries that take ~0.2ms.
+            featureLists[0] = await this._cachedChunkFeatures(chunks[0], opts);
+            onProgress?.(totalBytes, totalBytes);
+        }
+        else {
+            // Fetch the chunks concurrently. A query routinely spans a dozen or more
+            // chunks (14.8 on average for a 20kb window on the test 18MB file) and
+            // each is its own range request, so reading them one after another costs
+            // a network round trip apiece — the dominant cost of a remote query, well
+            // ahead of decompression. Bounded because browsers cap concurrent
+            // connections per host anyway, and an unbounded fan-out would inflate
+            // every chunk of a whole-chromosome query at once.
+            let next = 0;
+            const readNext = async () => {
+                while (next < chunks.length) {
+                    const ci = next++;
+                    const chunk = chunks[ci];
+                    featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
+                    downloadedBytes += chunk.fetchedSize();
+                    onProgress?.(downloadedBytes, totalBytes);
+                }
+            };
+            const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
+            await Promise.all(Array.from({ length: workers }, () => readNext()));
+        }
+        // Append in chunk order, not completion order, so the result is the same
+        // sequence a sequential walk produced. (That is not coordinate order — bins
+        // at different levels cover overlapping spans — but it is what every caller
+        // has always been handed.)
         for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
-            const chunk = chunks[ci];
-            const features = await this._cachedChunkFeatures(chunk, opts);
-            downloadedBytes += chunk.fetchedSize();
-            onProgress?.(downloadedBytes, totalBytes);
-            (0, util_ts_1.appendInRange)(features, chrId, min, max, result);
+            (0, util_ts_1.appendInRange)(featureLists[ci], chrId, min, max, result);
         }
         if (viewAsPairs) {
             const pairs = await this.fetchPairs(chrId, result, opts);
@@ -302,20 +396,12 @@ class BamFile {
                 }
             }
             if (blockEnd < ba.length) {
-                const feature = new this.RecordClass({
-                    bytes: {
-                        byteArray: ba,
-                        start: blockStart,
-                        end: blockEnd,
-                    },
-                    fileOffset: hasCpositions
-                        ? cpositions[pos] * (1 << 8) +
-                            (blockStart - dpositions[pos]) +
-                            chunk.minv.dataPosition +
-                            1
-                        : (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0,
-                    dataView,
-                });
+                const feature = new this.RecordClass(ba, blockStart, blockEnd, hasCpositions
+                    ? cpositions[pos] * (1 << 8) +
+                        (blockStart - dpositions[pos]) +
+                        chunk.minv.dataPosition +
+                        1
+                    : (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0, dataView);
                 sink.push(feature);
             }
             blockStart = blockEnd + 1;

package/dist/bamFile.js.map

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

@@ -16,11 +16,7 @@ export default class BamRecord {
     private _cachedNumericCigar?;
     private _cachedNUMERIC_MD?;
     private _cachedSeqStart?;
-    constructor(args: {
-        bytes: Bytes;
-        fileOffset: number;
-        dataView: DataView;
-    });
+    constructor(byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView);
     get byteArray(): Uint8Array<ArrayBufferLike>;
     get flags(): number;
     get ref_id(): number;

package/dist/record.js

@@ -263,12 +263,18 @@ class BamRecord {
     _cachedNumericCigar;
     _cachedNUMERIC_MD;
     _cachedSeqStart;
-    constructor(args) {
-        this._byteArray = args.bytes.byteArray;
-        this._start = args.bytes.start;
-        this._end = args.bytes.end;
-        this.fileOffset = args.fileOffset;
-        this._dataView = args.dataView;
+    // Positional rather than an options object, because every argument is
+    // unpacked into a field immediately and nothing keeps the wrapper. The
+    // options form allocated two throwaway objects for each of the ~200k records
+    // a deep pileup decodes — the `{byteArray, start, end}` literal and the
+    // `{bytes, fileOffset, dataView}` around it — purely to be taken apart again
+    // one line later.
+    constructor(byteArray, start, end, fileOffset, dataView) {
+        this._byteArray = byteArray;
+        this._start = start;
+        this._end = end;
+        this.fileOffset = fileOffset;
+        this._dataView = dataView;
     }
     get byteArray() {
         return this._byteArray;

package/dist/record.js.map

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

@@ -2,7 +2,6 @@ import BAI from './bai.ts';
 import CSI from './csi.ts';
 import BAMFeature from './record.ts';
 import type Chunk from './chunk.ts';
-import type { Bytes } from './record.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface BamRecordLike {
@@ -16,11 +15,7 @@ export interface BamRecordLike {
     flags: number;
     tags: Record<string, unknown>;
 }
-export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
-    bytes: Bytes;
-    fileOffset: number;
-    dataView: DataView;
-}) => T;
+export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView) => T;
 export declare const BAM_MAGIC = 21840194;
 interface ChunkEntry<T> {
     bytes: number;
@@ -53,6 +48,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     htsget: boolean;
     headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
     chunkFeatureCache: ChunkFeatureCache<T>;
+    private inFlightChunks;
     private RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
         bamFilehandle?: GenericFilehandle;
@@ -86,7 +82,17 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     }[] | undefined>;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     private getSeqId;
+    /**
+     * Records overlapping `chr:min-max`.
+     *
+     * The returned records are CACHED AND SHARED — two queries resolving to the
+     * same chunk span get the same objects back, so treat them as read-only.
+     * Anything you want to attach for the duration of one query belongs on a
+     * wrapper you own, never on the record; writing a field here silently rebinds
+     * it for every other query still holding that read. See ADR 0006.
+     */
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
+    private _startChunkRead;
     private _cachedChunkFeatures;
     private _fetchChunkFeatures;
     fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;

package/esm/bamFile.js

@@ -25,6 +25,10 @@ function chunkCacheKey(chunk) {
 // 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;
+// 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 ChunkFeatureCache {
     maxBytes;
     entries = new Map();
@@ -85,6 +89,10 @@ export default class BamFile {
     headerP;
     // Cache for parsed features by chunk, bounded by decompressed bytes
     chunkFeatureCache;
+    // Chunks currently being read, so concurrent queries share one decompress
+    // instead of racing. Entries live only until the read settles; the resolved
+    // features land in chunkFeatureCache.
+    inFlightChunks = new Map();
     RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, }) {
         this.renameRefSeq = renameRefSeqs;
@@ -171,6 +179,15 @@ export default class BamFile {
         await this.getHeader(opts);
         return this.chrToIndex?.[seqName];
     }
+    /**
+     * Records overlapping `chr:min-max`.
+     *
+     * The returned records are CACHED AND SHARED — two queries resolving to the
+     * same chunk span get the same objects back, so treat them as read-only.
+     * Anything you want to attach for the duration of one query belongs on a
+     * wrapper you own, never on the record; writing a field here silently rebinds
+     * it for every other query still holding that read. See ADR 0006.
+     */
     async getRecordsForRange(chr, min, max, opts) {
         const chrId = await this.getSeqId(chr, opts);
         if (chrId === undefined || !this.index) {
@@ -179,18 +196,65 @@ export default class BamFile {
         const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
         return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
+    // Read a chunk, publish it to the cache, and keep the in-flight promise
+    // discoverable while it runs.
+    _startChunkRead(cacheKey, chunk, opts) {
+        const promise = this._readChunkFeatures(chunk, opts).then(entry => {
+            this.chunkFeatureCache.set(cacheKey, entry);
+            return entry;
+        });
+        const inFlight = { promise, signal: opts.signal };
+        this.inFlightChunks.set(cacheKey, inFlight);
+        // Only clear our own entry: a retry may already have replaced it. `.then(f,
+        // f)` rather than `.finally(f)` so the handler's own promise never carries
+        // an unhandled rejection.
+        const clear = () => {
+            if (this.inFlightChunks.get(cacheKey) === inFlight) {
+                this.inFlightChunks.delete(cacheKey);
+            }
+        };
+        promise.then(clear, clear);
+        return promise;
+    }
     // Parsed records for a chunk, reading and decompressing it only on a miss.
     // Every path that wants a chunk's features goes through here — mate lookups
     // included, since a viewAsPairs query revisits the same mate chunks each time
     // the view moves.
+    //
+    // This hands the SAME record objects to every query that hits the key, which
+    // is what makes callers' per-query writes onto a record leak across queries
+    // (ADR 0006). Caching the inflated buffer and re-scanning per query would give
+    // each caller its own objects, but roughly doubles a warm query on dense data
+    // — measured, and rejected, in that ADR.
     async _cachedChunkFeatures(chunk, opts) {
         const cacheKey = chunkCacheKey(chunk);
-        let entry = this.chunkFeatureCache.get(cacheKey);
-        if (!entry) {
-            entry = await this._readChunkFeatures(chunk, opts);
-            this.chunkFeatureCache.set(cacheKey, entry);
+        const cached = this.chunkFeatureCache.get(cacheKey);
+        if (cached) {
+            return cached.features;
+        }
+        // Join a read already running for this chunk rather than decompressing it a
+        // second time. jbrowse fetches a row of adjacent blocks concurrently and
+        // they collapse onto very few chunk keys, so without this a query pays for
+        // the same inflate several times over — the dominant cost of a cold query
+        // (ADR 0003).
+        const pending = this.inFlightChunks.get(cacheKey);
+        if (!pending) {
+            return (await this._startChunkRead(cacheKey, chunk, opts)).features;
+        }
+        try {
+            return (await pending.promise).features;
+        }
+        catch (e) {
+            // The read we joined was started by another caller. If that caller
+            // aborted and we did not, the failure is theirs and says nothing about
+            // our query, so start over — which picks up the cache, joins a sibling's
+            // retry, or reads under our own signal. Any other failure (and our own
+            // abort) propagates as it would have without sharing.
+            if (!pending.signal?.aborted || opts.signal?.aborted) {
+                throw e;
+            }
+            return this._cachedChunkFeatures(chunk, opts);
         }
-        return entry.features;
     }
     async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
         const { viewAsPairs, onProgress } = opts;
@@ -201,12 +265,42 @@ export default class BamFile {
         }
         let downloadedBytes = 0;
         onProgress?.(0, totalBytes);
+        const featureLists = new Array(chunks.length);
+        if (chunks.length === 1) {
+            // Very common — most small files, and any query landing inside one bin.
+            // Worth its own path: the pool below allocates a closure, a worker array
+            // and a Promise.all, all of which is pure overhead for one chunk and
+            // measurable on queries that take ~0.2ms.
+            featureLists[0] = await this._cachedChunkFeatures(chunks[0], opts);
+            onProgress?.(totalBytes, totalBytes);
+        }
+        else {
+            // Fetch the chunks concurrently. A query routinely spans a dozen or more
+            // chunks (14.8 on average for a 20kb window on the test 18MB file) and
+            // each is its own range request, so reading them one after another costs
+            // a network round trip apiece — the dominant cost of a remote query, well
+            // ahead of decompression. Bounded because browsers cap concurrent
+            // connections per host anyway, and an unbounded fan-out would inflate
+            // every chunk of a whole-chromosome query at once.
+            let next = 0;
+            const readNext = async () => {
+                while (next < chunks.length) {
+                    const ci = next++;
+                    const chunk = chunks[ci];
+                    featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
+                    downloadedBytes += chunk.fetchedSize();
+                    onProgress?.(downloadedBytes, totalBytes);
+                }
+            };
+            const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
+            await Promise.all(Array.from({ length: workers }, () => readNext()));
+        }
+        // Append in chunk order, not completion order, so the result is the same
+        // sequence a sequential walk produced. (That is not coordinate order — bins
+        // at different levels cover overlapping spans — but it is what every caller
+        // has always been handed.)
         for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
-            const chunk = chunks[ci];
-            const features = await this._cachedChunkFeatures(chunk, opts);
-            downloadedBytes += chunk.fetchedSize();
-            onProgress?.(downloadedBytes, totalBytes);
-            appendInRange(features, chrId, min, max, result);
+            appendInRange(featureLists[ci], chrId, min, max, result);
         }
         if (viewAsPairs) {
             const pairs = await this.fetchPairs(chrId, result, opts);
@@ -296,20 +390,12 @@ export default class BamFile {
                 }
             }
             if (blockEnd < ba.length) {
-                const feature = new this.RecordClass({
-                    bytes: {
-                        byteArray: ba,
-                        start: blockStart,
-                        end: blockEnd,
-                    },
-                    fileOffset: hasCpositions
-                        ? cpositions[pos] * (1 << 8) +
-                            (blockStart - dpositions[pos]) +
-                            chunk.minv.dataPosition +
-                            1
-                        : crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
-                    dataView,
-                });
+                const feature = new this.RecordClass(ba, blockStart, blockEnd, hasCpositions
+                    ? cpositions[pos] * (1 << 8) +
+                        (blockStart - dpositions[pos]) +
+                        chunk.minv.dataPosition +
+                        1
+                    : crc32(ba.subarray(blockStart, blockEnd)) >>> 0, dataView);
                 sink.push(feature);
             }
             blockStart = blockEnd + 1;

package/esm/bamFile.js.map

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

@@ -16,11 +16,7 @@ export default class BamRecord {
     private _cachedNumericCigar?;
     private _cachedNUMERIC_MD?;
     private _cachedSeqStart?;
-    constructor(args: {
-        bytes: Bytes;
-        fileOffset: number;
-        dataView: DataView;
-    });
+    constructor(byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView);
     get byteArray(): Uint8Array<ArrayBufferLike>;
     get flags(): number;
     get ref_id(): number;

package/esm/record.js

@@ -258,12 +258,18 @@ export default class BamRecord {
     _cachedNumericCigar;
     _cachedNUMERIC_MD;
     _cachedSeqStart;
-    constructor(args) {
-        this._byteArray = args.bytes.byteArray;
-        this._start = args.bytes.start;
-        this._end = args.bytes.end;
-        this.fileOffset = args.fileOffset;
-        this._dataView = args.dataView;
+    // Positional rather than an options object, because every argument is
+    // unpacked into a field immediately and nothing keeps the wrapper. The
+    // options form allocated two throwaway objects for each of the ~200k records
+    // a deep pileup decodes — the `{byteArray, start, end}` literal and the
+    // `{bytes, fileOffset, dataView}` around it — purely to be taken apart again
+    // one line later.
+    constructor(byteArray, start, end, fileOffset, dataView) {
+        this._byteArray = byteArray;
+        this._start = start;
+        this._end = end;
+        this.fileOffset = fileOffset;
+        this._dataView = dataView;
     }
     get byteArray() {
         return this._byteArray;

package/esm/record.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.5.0",
+  "version": "7.6.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",

package/src/bamFile.ts

@@ -10,7 +10,6 @@ import { parseHeaderText } from './sam.ts'
 import { appendInRange, parseRefSeqs } from './util.ts'
 
 import type Chunk from './chunk.ts'
-import type { Bytes } from './record.ts'
 import type { BamOpts, BaseOpts } from './util.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
@@ -26,11 +25,13 @@ export interface BamRecordLike {
   tags: Record<string, unknown>
 }
 
-export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
-  bytes: Bytes
-  fileOffset: number
-  dataView: DataView
-}) => T
+export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (
+  byteArray: Uint8Array,
+  start: number,
+  end: number,
+  fileOffset: number,
+  dataView: DataView,
+) => T
 
 export const BAM_MAGIC = 21840194
 
@@ -53,6 +54,13 @@ interface ChunkEntry<T> {
   features: T[]
 }
 
+interface InFlightChunk<T> {
+  promise: Promise<ChunkEntry<T>>
+  // the signal the read was started with, so a waiter can tell "the owner
+  // aborted" apart from "the read genuinely failed"
+  signal?: AbortSignal
+}
+
 function chunkCacheKey(chunk: Chunk) {
   const { minv, maxv } = chunk
   return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`
@@ -67,6 +75,11 @@ function chunkCacheKey(chunk: Chunk) {
 // here costs a re-download and re-decompress the next time the view moves.
 export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024
 
+// 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 ChunkFeatureCache<T> {
   public maxBytes: number
   private entries = new Map<string, ChunkEntry<T>>()
@@ -138,6 +151,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
   // Cache for parsed features by chunk, bounded by decompressed bytes
   public chunkFeatureCache: ChunkFeatureCache<T>
 
+  // Chunks currently being read, so concurrent queries share one decompress
+  // instead of racing. Entries live only until the read settles; the resolved
+  // features land in chunkFeatureCache.
+  private inFlightChunks = new Map<string, InFlightChunk<T>>()
+
   private RecordClass: BamRecordClass<T>
 
   constructor({
@@ -276,6 +294,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     return this.chrToIndex?.[seqName]
   }
 
+  /**
+   * Records overlapping `chr:min-max`.
+   *
+   * The returned records are CACHED AND SHARED — two queries resolving to the
+   * same chunk span get the same objects back, so treat them as read-only.
+   * Anything you want to attach for the duration of one query belongs on a
+   * wrapper you own, never on the record; writing a field here silently rebinds
+   * it for every other query still holding that read. See ADR 0006.
+   */
   async getRecordsForRange(
     chr: string,
     min: number,
@@ -290,18 +317,70 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     return this._fetchChunkFeatures(chunks, chrId, min, max, opts)
   }
 
+  // Read a chunk, publish it to the cache, and keep the in-flight promise
+  // discoverable while it runs.
+  private _startChunkRead(cacheKey: string, chunk: Chunk, opts: BaseOpts) {
+    const promise = this._readChunkFeatures(chunk, opts).then(entry => {
+      this.chunkFeatureCache.set(cacheKey, entry)
+      return entry
+    })
+    const inFlight: InFlightChunk<T> = { promise, signal: opts.signal }
+    this.inFlightChunks.set(cacheKey, inFlight)
+    // Only clear our own entry: a retry may already have replaced it. `.then(f,
+    // f)` rather than `.finally(f)` so the handler's own promise never carries
+    // an unhandled rejection.
+    const clear = () => {
+      if (this.inFlightChunks.get(cacheKey) === inFlight) {
+        this.inFlightChunks.delete(cacheKey)
+      }
+    }
+    promise.then(clear, clear)
+    return promise
+  }
+
   // Parsed records for a chunk, reading and decompressing it only on a miss.
   // Every path that wants a chunk's features goes through here — mate lookups
   // included, since a viewAsPairs query revisits the same mate chunks each time
   // the view moves.
-  private async _cachedChunkFeatures(chunk: Chunk, opts: BaseOpts) {
+  //
+  // This hands the SAME record objects to every query that hits the key, which
+  // is what makes callers' per-query writes onto a record leak across queries
+  // (ADR 0006). Caching the inflated buffer and re-scanning per query would give
+  // each caller its own objects, but roughly doubles a warm query on dense data
+  // — measured, and rejected, in that ADR.
+  private async _cachedChunkFeatures(
+    chunk: Chunk,
+    opts: BaseOpts,
+  ): Promise<T[]> {
     const cacheKey = chunkCacheKey(chunk)
-    let entry = this.chunkFeatureCache.get(cacheKey)
-    if (!entry) {
-      entry = await this._readChunkFeatures(chunk, opts)
-      this.chunkFeatureCache.set(cacheKey, entry)
+    const cached = this.chunkFeatureCache.get(cacheKey)
+    if (cached) {
+      return cached.features
+    }
+
+    // Join a read already running for this chunk rather than decompressing it a
+    // second time. jbrowse fetches a row of adjacent blocks concurrently and
+    // they collapse onto very few chunk keys, so without this a query pays for
+    // the same inflate several times over — the dominant cost of a cold query
+    // (ADR 0003).
+    const pending = this.inFlightChunks.get(cacheKey)
+    if (!pending) {
+      return (await this._startChunkRead(cacheKey, chunk, opts)).features
+    }
+
+    try {
+      return (await pending.promise).features
+    } catch (e) {
+      // The read we joined was started by another caller. If that caller
+      // aborted and we did not, the failure is theirs and says nothing about
+      // our query, so start over — which picks up the cache, joins a sibling's
+      // retry, or reads under our own signal. Any other failure (and our own
+      // abort) propagates as it would have without sharing.
+      if (!pending.signal?.aborted || opts.signal?.aborted) {
+        throw e
+      }
+      return this._cachedChunkFeatures(chunk, opts)
     }
-    return entry.features
   }
 
   private async _fetchChunkFeatures(
@@ -321,13 +400,42 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     let downloadedBytes = 0
     onProgress?.(0, totalBytes)
 
-    for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
-      const chunk = chunks[ci]!
-      const features = await this._cachedChunkFeatures(chunk, opts)
+    const featureLists = new Array<T[]>(chunks.length)
+    if (chunks.length === 1) {
+      // Very common — most small files, and any query landing inside one bin.
+      // Worth its own path: the pool below allocates a closure, a worker array
+      // and a Promise.all, all of which is pure overhead for one chunk and
+      // measurable on queries that take ~0.2ms.
+      featureLists[0] = await this._cachedChunkFeatures(chunks[0]!, opts)
+      onProgress?.(totalBytes, totalBytes)
+    } else {
+      // Fetch the chunks concurrently. A query routinely spans a dozen or more
+      // chunks (14.8 on average for a 20kb window on the test 18MB file) and
+      // each is its own range request, so reading them one after another costs
+      // a network round trip apiece — the dominant cost of a remote query, well
+      // ahead of decompression. Bounded because browsers cap concurrent
+      // connections per host anyway, and an unbounded fan-out would inflate
+      // every chunk of a whole-chromosome query at once.
+      let next = 0
+      const readNext = async () => {
+        while (next < chunks.length) {
+          const ci = next++
+          const chunk = chunks[ci]!
+          featureLists[ci] = await this._cachedChunkFeatures(chunk, opts)
+          downloadedBytes += chunk.fetchedSize()
+          onProgress?.(downloadedBytes, totalBytes)
+        }
+      }
+      const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length)
+      await Promise.all(Array.from({ length: workers }, () => readNext()))
+    }
 
-      downloadedBytes += chunk.fetchedSize()
-      onProgress?.(downloadedBytes, totalBytes)
-      appendInRange(features, chrId, min, max, result)
+    // Append in chunk order, not completion order, so the result is the same
+    // sequence a sequential walk produced. (That is not coordinate order — bins
+    // at different levels cover overlapping spans — but it is what every caller
+    // has always been handed.)
+    for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
+      appendInRange(featureLists[ci]!, chrId, min, max, result)
     }
 
     if (viewAsPairs) {
@@ -456,20 +564,18 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       }
 
       if (blockEnd < ba.length) {
-        const feature = new this.RecordClass({
-          bytes: {
-            byteArray: ba,
-            start: blockStart,
-            end: blockEnd,
-          },
-          fileOffset: hasCpositions
+        const feature = new this.RecordClass(
+          ba,
+          blockStart,
+          blockEnd,
+          hasCpositions
             ? cpositions[pos]! * (1 << 8) +
               (blockStart - dpositions[pos]!) +
               chunk.minv.dataPosition +
               1
             : crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
           dataView,
-        })
+        )
 
         sink.push(feature)
       }

package/src/record.ts

@@ -315,12 +315,24 @@ export default class BamRecord {
   private _cachedNUMERIC_MD?: Uint8Array | null
   private _cachedSeqStart?: number
 
-  constructor(args: { bytes: Bytes; fileOffset: number; dataView: DataView }) {
-    this._byteArray = args.bytes.byteArray
-    this._start = args.bytes.start
-    this._end = args.bytes.end
-    this.fileOffset = args.fileOffset
-    this._dataView = args.dataView
+  // Positional rather than an options object, because every argument is
+  // unpacked into a field immediately and nothing keeps the wrapper. The
+  // options form allocated two throwaway objects for each of the ~200k records
+  // a deep pileup decodes — the `{byteArray, start, end}` literal and the
+  // `{bytes, fileOffset, dataView}` around it — purely to be taken apart again
+  // one line later.
+  constructor(
+    byteArray: Uint8Array,
+    start: number,
+    end: number,
+    fileOffset: number,
+    dataView: DataView,
+  ) {
+    this._byteArray = byteArray
+    this._start = start
+    this._end = end
+    this.fileOffset = fileOffset
+    this._dataView = dataView
   }
 
   get byteArray() {