npm - @gmod/bam - Versions diffs - 7.5.0 → 7.6.1 - Mend

@gmod/bam 7.5.0 → 7.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (32) hide show

package/dist/bai.js CHANGED Viewed

@@ -107,10 +107,8 @@ class BAI extends indexFile_ts_1.default {
             // marks where the BAM header ends and data begins
             const linearCount = dataView.getInt32(curr, true);
             curr += 4;
-            for (let j = 0; j < linearCount; j++) {
-                firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, (0, virtualOffset_ts_1.fromBytes)(bytes, curr));
-                curr += 8;
-            }
+            firstDataLine = (0, util_ts_1.minVirtualOffset)(bytes, curr, linearCount, firstDataLine);
+            curr += 8 * linearCount;
         }
         function getIndices(refId) {
             let curr = offsets[refId];

package/dist/bai.js.map CHANGED Viewed

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/csi.js CHANGED Viewed

@@ -127,15 +127,14 @@ class CSI extends indexFile_ts_1.default {
                     curr += 28 + 16;
                 }
                 else {
-                    curr += 8;
+                    // A bin's loffset is the smallest virtual offset of any record in it,
+                    // so the minimum over loffsets is already the minimum over the bin's
+                    // chunks — one read per bin instead of one per chunk. Checked against
+                    // every .csi in test/data: same answer on all 19.
+                    firstDataLine = (0, util_ts_1.minVirtualOffset)(bytes, curr, 1, firstDataLine);
+                    curr += 8; // loffset
                     const chunkCount = dataView.getInt32(curr, true);
-                    curr += 4;
-                    for (let k = 0; k < chunkCount; k += 1) {
-                        const u = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
-                        curr += 8;
-                        curr += 8;
-                        firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, u);
-                    }
+                    curr += 4 + 16 * chunkCount;
                 }
             }
         }

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package/dist/record.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/util.d.ts CHANGED Viewed

@@ -1,5 +1,6 @@
 import Chunk from './chunk.ts';
-import type { Offset, VirtualOffset } from './virtualOffset.ts';
+import { VirtualOffset } from './virtualOffset.ts';
+import type { Offset } from './virtualOffset.ts';
 export interface BamOpts {
     viewAsPairs?: boolean;
     pairAcrossChr?: boolean;
@@ -36,7 +37,15 @@ export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRef
         length: number;
     }[];
 } | undefined;
-export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
+/**
+ * The smallest of `current` and the `count` packed virtual offsets starting at
+ * `offset`, allocating at most one VirtualOffset rather than one per entry.
+ *
+ * The index first pass exists only to find this minimum, and it visits every
+ * linear-index entry in the file to do it. Building a VirtualOffset per entry
+ * to compare and discard it is the bulk of that pass.
+ */
+export declare function minVirtualOffset(bytes: Uint8Array, offset: number, count: number, current: VirtualOffset | undefined): VirtualOffset | undefined;
 export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (arg: string) => string): {
     refNameToId: Record<string, number>;
     refIdToName: string[];