@gmod/bam 7.5.0 → 7.6.1

package/esm/record.js.map

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

@@ -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[];

package/esm/util.js

@@ -1,5 +1,6 @@
 import Chunk from "./chunk.js";
 import { longFromBytesToUnsigned } from "./long.js";
+import { VirtualOffset } from "./virtualOffset.js";
 export function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
     if (n === 0) {
@@ -127,12 +128,35 @@ export function parseRefSeqs(uncba, start, renameRefSeq) {
     }
     return { chrToIndex, indexToChr };
 }
-export function findFirstData(firstDataLine, virtualOffset) {
-    return firstDataLine
-        ? firstDataLine.compareTo(virtualOffset) > 0
-            ? virtualOffset
-            : firstDataLine
-        : virtualOffset;
+// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset
+/**
+ * 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 function minVirtualOffset(bytes, offset, count, current) {
+    let minBlock = current ? current.blockPosition : Infinity;
+    let minData = current ? current.dataPosition : 0;
+    let found = false;
+    for (let i = 0; i < count; i++) {
+        const p = offset + i * 8;
+        const block = bytes[p + 7] * 0x10000000000 +
+            bytes[p + 6] * 0x100000000 +
+            bytes[p + 5] * 0x1000000 +
+            bytes[p + 4] * 0x10000 +
+            bytes[p + 3] * 0x100 +
+            bytes[p + 2];
+        const data = (bytes[p + 1] << 8) | bytes[p];
+        if (block < minBlock || (block === minBlock && data < minData)) {
+            minBlock = block;
+            minData = data;
+            found = true;
+        }
+    }
+    return found ? new VirtualOffset(minBlock, minData) : current;
 }
 // SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
 export function parseNameBytes(namesBytes, renameRefSeq = s => s) {

package/esm/util.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.5.0",
+  "version": "7.6.1",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",

package/src/bai.ts

@@ -1,6 +1,6 @@
 import Chunk from './chunk.ts'
 import IndexFile, { memoizeByRefId } from './indexFile.ts'
-import { clampChunkEnds, findFirstData, parsePseudoBin } from './util.ts'
+import { clampChunkEnds, minVirtualOffset, parsePseudoBin } from './util.ts'
 import { fromBytes } from './virtualOffset.ts'
 
 import type { ParsedIndexBase, RefIndex } from './indexFile.ts'
@@ -101,10 +101,8 @@ export default class BAI extends IndexFile<BaiParsed> {
       // 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 = findFirstData(firstDataLine, fromBytes(bytes, curr))
-        curr += 8
-      }
+      firstDataLine = minVirtualOffset(bytes, curr, linearCount, firstDataLine)
+      curr += 8 * linearCount
     }
 
     function getIndices(refId: number) {

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/csi.ts

@@ -4,7 +4,7 @@ import Chunk from './chunk.ts'
 import IndexFile, { memoizeByRefId } from './indexFile.ts'
 import {
   clampChunkEnds,
-  findFirstData,
+  minVirtualOffset,
   parseNameBytes,
   parsePseudoBin,
 } from './util.ts'
@@ -118,15 +118,14 @@ export default class CSI extends IndexFile {
         if (bin > this.maxBinNumber) {
           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 = 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 = fromBytes(bytes, curr)
-            curr += 8
-            curr += 8
-            firstDataLine = findFirstData(firstDataLine, u)
-          }
+          curr += 4 + 16 * chunkCount
         }
       }
     }

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() {

package/src/util.ts

@@ -1,7 +1,8 @@
 import Chunk from './chunk.ts'
 import { longFromBytesToUnsigned } from './long.ts'
+import { VirtualOffset } from './virtualOffset.ts'
 
-import type { Offset, VirtualOffset } from './virtualOffset.ts'
+import type { Offset } from './virtualOffset.ts'
 
 export interface BamOpts {
   viewAsPairs?: boolean
@@ -186,15 +187,41 @@ export function parseRefSeqs(
   return { chrToIndex, indexToChr }
 }
 
-export function findFirstData(
-  firstDataLine: VirtualOffset | undefined,
-  virtualOffset: VirtualOffset,
+// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset
+/**
+ * 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 function minVirtualOffset(
+  bytes: Uint8Array,
+  offset: number,
+  count: number,
+  current: VirtualOffset | undefined,
 ) {
-  return firstDataLine
-    ? firstDataLine.compareTo(virtualOffset) > 0
-      ? virtualOffset
-      : firstDataLine
-    : virtualOffset
+  let minBlock = current ? current.blockPosition : Infinity
+  let minData = current ? current.dataPosition : 0
+  let found = false
+  for (let i = 0; i < count; i++) {
+    const p = offset + i * 8
+    const block =
+      bytes[p + 7]! * 0x10000000000 +
+      bytes[p + 6]! * 0x100000000 +
+      bytes[p + 5]! * 0x1000000 +
+      bytes[p + 4]! * 0x10000 +
+      bytes[p + 3]! * 0x100 +
+      bytes[p + 2]!
+    const data = (bytes[p + 1]! << 8) | bytes[p]!
+    if (block < minBlock || (block === minBlock && data < minData)) {
+      minBlock = block
+      minData = data
+      found = true
+    }
+  }
+  return found ? new VirtualOffset(minBlock, minData) : current
 }
 
 // SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan