@gmod/bam 7.3.4 → 7.4.0

package/esm/record.js.map

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

@@ -54,10 +54,10 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
 export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
 export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
-export declare function filterCacheKey(filterBy?: FilterBy): string;
 interface Filterable {
     flags: number;
     tags: Record<string, unknown>;
+    getTag?(tag: string): unknown;
 }
 export declare function applyFilters<T extends Filterable>(records: T[], filterBy: FilterBy): T[];
 interface Positioned {

package/esm/util.js

@@ -103,9 +103,11 @@ export function parseRefSeqs(uncba, start, renameRefSeq) {
     if (start + 4 > uncba.length) {
         return undefined;
     }
-    const dataView = new DataView(uncba.buffer);
+    const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
     const nRef = dataView.getInt32(start, true);
-    const chrToIndex = {};
+    // null prototype: ref names come from the file, so a contig named
+    // "constructor" must not resolve to Object.prototype's
+    const chrToIndex = Object.create(null);
     const indexToChr = [];
     const decoder = new TextDecoder('utf8');
     let p = start + 4;
@@ -138,7 +140,7 @@ export function parseNameBytes(namesBytes, renameRefSeq = s => s) {
     let currRefId = 0;
     let currNameStart = 0;
     const refIdToName = [];
-    const refNameToId = {};
+    const refNameToId = Object.create(null);
     for (let i = 0; i < namesBytes.length; i++) {
         if (!namesBytes[i]) {
             if (currNameStart < i) {
@@ -173,13 +175,11 @@ export function filterTagValue(readVal, filterVal) {
         ? readVal === undefined
         : `${readVal}` !== `${filterVal}`;
 }
-export function filterCacheKey(filterBy) {
-    if (!filterBy) {
-        return '';
-    }
-    const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy;
-    const tagPart = tagFilter ? `:${tagFilter.tag}=${tagFilter.value ?? '*'}` : '';
-    return `:f${flagInclude}x${flagExclude}${tagPart}`;
+// Read a single tag, preferring the targeted accessor. Reaching for `tags`
+// instead would decode every unrelated tag on the record (NM/AS/ms/de/… — often
+// ~10 per read) just to test one, which measured 2.6x the cost of getTag.
+function readTag(record, tag) {
+    return record.getTag ? record.getTag(tag) : record.tags[tag];
 }
 // Apply flagInclude/flagExclude/tagFilter to a list of records.
 export function applyFilters(records, filterBy) {
@@ -188,7 +188,7 @@ export function applyFilters(records, filterBy) {
     for (let i = 0, l = records.length; i < l; i++) {
         const r = records[i];
         if (!filterReadFlag(r.flags, flagInclude, flagExclude) &&
-            !(tagFilter && filterTagValue(r.tags[tagFilter.tag], tagFilter.value))) {
+            !(tagFilter && filterTagValue(readTag(r, tagFilter.tag), tagFilter.value))) {
             out.push(r);
         }
     }

package/esm/util.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.3.4",
+  "version": "7.4.0",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": {
@@ -8,6 +8,7 @@
     "url": "https://github.com/GMOD/bam-js.git"
   },
   "type": "module",
+  "sideEffects": false,
   "main": "dist/index.js",
   "exports": {
     "import": "./esm/index.js",

package/src/bai.ts

@@ -53,7 +53,11 @@ function reg2bins(beg: number, end: number) {
 export default class BAI extends IndexFile<BaiParsed> {
   async _parse(opts: BaseOpts): Promise<BaiParsed> {
     const bytes = await this.filehandle.readFile(opts)
-    const dataView = new DataView(bytes.buffer)
+    const dataView = new DataView(
+      bytes.buffer,
+      bytes.byteOffset,
+      bytes.byteLength,
+    )
 
     // check BAI magic numbers
     if (dataView.getUint32(0, true) !== BAI_MAGIC) {
@@ -186,26 +190,29 @@ export default class BAI extends IndexFile<BaiParsed> {
     }
     const e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v)
     const s = start === undefined ? 0 : roundDown(start, v)
-    const depths = range
+    const depths: IndexCovEntry[] = range
       ? new Array((e - s) / v)
       : new Array(linearIndex.length - 1)
     const totalSize = linearIndex[linearIndex.length - 1]!.blockPosition
     if (e > (linearIndex.length - 1) * v) {
       throw new Error('query outside of range of linear index')
     }
+    // Scale the block-delta into a read count as we go, rather than building the
+    // entries and then rebuilding every one of them to apply the scale. Keep the
+    // multiply-then-divide order: hoisting lineCount/totalSize into a factor
+    // reassociates the arithmetic and shifts scores by an ulp.
+    const lineCount = stats?.lineCount ?? 0
     let currentPos = linearIndex[s / v]!.blockPosition
     for (let i = s / v, j = 0; i < e / v; i++, j++) {
+      const nextPos = linearIndex[i + 1]!.blockPosition
       depths[j] = {
-        score: linearIndex[i + 1]!.blockPosition - currentPos,
+        score: ((nextPos - currentPos) * lineCount) / totalSize,
         start: i * v,
         end: i * v + v,
       }
-      currentPos = linearIndex[i + 1]!.blockPosition
+      currentPos = nextPos
     }
-    return depths.map(d => ({
-      ...d,
-      score: (d.score * (stats?.lineCount ?? 0)) / totalSize,
-    }))
+    return depths
   }
 
   protected reg2bins(min: number, max: number) {

package/src/bamFile.ts

@@ -1,5 +1,4 @@
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
-import QuickLRU from '@jbrowse/quick-lru'
 import crc32 from 'crc/calculators/crc32'
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
 
@@ -8,16 +7,11 @@ import CSI from './csi.ts'
 import NullFilehandle from './nullFilehandle.ts'
 import BAMFeature from './record.ts'
 import { parseHeaderText } from './sam.ts'
-import {
-  appendInRange,
-  applyFilters,
-  filterCacheKey,
-  parseRefSeqs,
-} from './util.ts'
+import { appendInRange, applyFilters, parseRefSeqs } from './util.ts'
 
 import type Chunk from './chunk.ts'
 import type { Bytes } from './record.ts'
-import type { BamOpts, BaseOpts, FilterBy } from './util.ts'
+import type { BamOpts, BaseOpts } from './util.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
 export interface BamRecordLike {
@@ -56,12 +50,83 @@ function resolveFilehandle(
 interface ChunkEntry<T> {
   minBlock: number
   maxBlock: number
+  // decompressed size of the chunk these features are views into
+  bytes: number
   features: T[]
 }
 
-function chunkCacheKey(chunk: Chunk, filterBy?: FilterBy) {
+// Keyed on the chunk's byte span only, not on filterBy: the cached value is the
+// unfiltered parsed records (decompression + parse is the expensive part).
+// Filters are applied cheaply on retrieval so toggling a filter over the same
+// region is a cache hit rather than a re-decompress.
+function chunkCacheKey(chunk: Chunk) {
   const { minv, maxv } = chunk
-  return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}${filterCacheKey(filterBy)}`
+  return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`
+}
+
+// Every record in an entry is a view into its chunk's decompressed buffer, so
+// caching one entry pins that whole buffer — 8MB apiece on the nanopore and
+// 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
+// so tens of MB is possible. A count-based LRU therefore gives no bound on
+// memory at all, which is why this budgets by decompressed bytes instead.
+export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024
+
+class ChunkFeatureCache<T> {
+  public maxBytes: number
+  private entries = new Map<string, ChunkEntry<T>>()
+  private bytes = 0
+
+  constructor(maxBytes: number) {
+    this.maxBytes = maxBytes
+  }
+
+  get size() {
+    return this.entries.size
+  }
+
+  get byteSize() {
+    return this.bytes
+  }
+
+  get(key: string) {
+    const entry = this.entries.get(key)
+    if (entry) {
+      // re-insert so Map iteration order stays least-recently-used first
+      this.entries.delete(key)
+      this.entries.set(key, entry)
+    }
+    return entry
+  }
+
+  set(key: string, entry: ChunkEntry<T>) {
+    this.delete(key)
+    this.entries.set(key, entry)
+    this.bytes += entry.bytes
+    // Evict from the least-recently-used end. The size > 1 guard means a single
+    // chunk larger than the whole budget is still kept: the caller needs it for
+    // the query in flight, and dropping it would only force a re-decompress.
+    const lru = this.entries.keys()
+    while (this.bytes > this.maxBytes && this.entries.size > 1) {
+      this.delete(lru.next().value!)
+    }
+  }
+
+  delete(key: string) {
+    const entry = this.entries.get(key)
+    if (entry) {
+      this.entries.delete(key)
+      this.bytes -= entry.bytes
+    }
+  }
+
+  clear() {
+    this.entries.clear()
+    this.bytes = 0
+  }
+
+  [Symbol.iterator]() {
+    return this.entries[Symbol.iterator]()
+  }
 }
 
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
@@ -76,9 +141,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
 
   // Cache for parsed features by chunk
   // When a new chunk overlaps a cached chunk, we evict the cached one
-  public chunkFeatureCache = new QuickLRU<string, ChunkEntry<T>>({
-    maxSize: 100,
-  })
+  public chunkFeatureCache: ChunkFeatureCache<T>
 
   private RecordClass: BamRecordClass<T>
 
@@ -95,6 +158,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     htsget,
     renameRefSeqs = n => n,
     recordClass,
+    maxCacheBytes = DEFAULT_MAX_CACHE_BYTES,
   }: {
     bamFilehandle?: GenericFilehandle
     bamPath?: string
@@ -108,9 +172,12 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeqs?: (a: string) => string
     htsget?: boolean
     recordClass?: BamRecordClass<T>
+    /** budget for the parsed-chunk cache, in decompressed bytes */
+    maxCacheBytes?: number
   }) {
     this.renameRefSeq = renameRefSeqs
     this.RecordClass = (recordClass ?? BAMFeature) as BamRecordClass<T>
+    this.chunkFeatureCache = new ChunkFeatureCache<T>(maxCacheBytes)
 
     const bamFh = resolveFilehandle(bamFilehandle, bamPath, bamUrl)
     if (bamFh) {
@@ -162,7 +229,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         ? await this.bam.readFile()
         : await this.bam.read(readLen, 0)
     let uncba = await unzip(buffer)
-    const dataView = new DataView(uncba.buffer)
+    const dataView = new DataView(
+      uncba.buffer,
+      uncba.byteOffset,
+      uncba.byteLength,
+    )
 
     if (dataView.getInt32(0, true) !== BAM_MAGIC) {
       throw new Error('Not a BAM file')
@@ -221,7 +292,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       return []
     }
     const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts)
-    return this._fetchChunkFeaturesDirect(chunks, chrId, min, max, opts)
+    return this._fetchChunkFeatures(chunks, chrId, min, max, opts)
   }
 
   // Evict any cached chunks whose block range overlaps [minBlock, maxBlock]
@@ -233,7 +304,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     }
   }
 
-  private async _fetchChunkFeaturesDirect(
+  private async _fetchChunkFeatures(
     chunks: Chunk[],
     chrId: number,
     min: number,
@@ -252,24 +323,20 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
 
     for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
       const chunk = chunks[ci]!
-      const cacheKey = chunkCacheKey(chunk, filterBy)
+      const cacheKey = chunkCacheKey(chunk)
       const minBlock = chunk.minv.blockPosition
       const maxBlock = chunk.maxv.blockPosition
 
-      let records: T[]
-      const cached = this.chunkFeatureCache.get(cacheKey)
-      if (cached) {
-        records = cached.features
-      } else {
+      let cached = this.chunkFeatureCache.get(cacheKey)
+      if (!cached) {
         this.evictOverlappingChunks(minBlock, maxBlock)
-        const allRecords = await this._readChunkFeatures(chunk, opts)
-        records = filterBy ? applyFilters(allRecords, filterBy) : allRecords
-        this.chunkFeatureCache.set(cacheKey, {
-          minBlock,
-          maxBlock,
-          features: records,
-        })
+        const { features, bytes } = await this._readChunkFeatures(chunk, opts)
+        cached = { minBlock, maxBlock, bytes, features }
+        this.chunkFeatureCache.set(cacheKey, cached)
       }
+      const records = filterBy
+        ? applyFilters(cached.features, filterBy)
+        : cached.features
 
       downloadedBytes += chunk.fetchedSize()
       onProgress?.(downloadedBytes, totalBytes)
@@ -288,13 +355,16 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
 
   async fetchPairs(chrId: number, records: T[], opts: BamOpts) {
     const { pairAcrossChr, maxInsertSize = 200000 } = opts
-    const readNameCounts: Record<string, number> = {}
+    // Map, not a plain object: read names come from the file, and on a plain
+    // object a read named "constructor" would read back Object.prototype's and
+    // make the count NaN.
+    const readNameCounts = new Map<string, number>()
     const readIds = new Set<number>()
 
     for (let i = 0, l = records.length; i < l; i++) {
       const r = records[i]!
       const name = r.name
-      readNameCounts[name] = (readNameCounts[name] ?? 0) + 1
+      readNameCounts.set(name, (readNameCounts.get(name) ?? 0) + 1)
       readIds.add(r.fileOffset)
     }
 
@@ -304,7 +374,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       const name = f.name
       if (
         this.index &&
-        readNameCounts[name] === 1 &&
+        readNameCounts.get(name) === 1 &&
         (pairAcrossChr ||
           (f.next_refid === chrId &&
             Math.abs(f.start - f.next_pos) < maxInsertSize))
@@ -332,12 +402,12 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
 
     const mateFeatLists = await Promise.all(
       [...map.values()].map(async c => {
-        const features = await this._readChunkFeatures(c, opts)
+        const { features } = await this._readChunkFeatures(c, opts)
         const mateRecs = [] as T[]
         for (let i = 0, l = features.length; i < l; i++) {
           const feature = features[i]!
           if (
-            readNameCounts[feature.name] === 1 &&
+            readNameCounts.get(feature.name) === 1 &&
             !readIds.has(feature.fileOffset)
           ) {
             mateRecs.push(feature)
@@ -355,18 +425,25 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     // filehandle's own streaming onProgress also fired this callback it would
     // report a different `total` (this chunk's size, not the whole query),
     // making the determinate bar jump around.
-    const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, {
-      signal: opts.signal,
-    })
+    const buf = await this.bam.read(
+      chunk.fetchedSize(),
+      chunk.minv.blockPosition,
+      {
+        signal: opts.signal,
+      },
+    )
     const {
       buffer: data,
       cpositions,
       dpositions,
     } = await unzipChunkSlice(buf, chunk)
-    return this.readBamFeatures(data, cpositions, dpositions, chunk)
+    return {
+      features: this.readBamFeatures(data, cpositions, dpositions, chunk),
+      bytes: data.byteLength,
+    }
   }
 
-  async readBamFeatures(
+  readBamFeatures(
     ba: Uint8Array,
     cpositions: number[],
     dpositions: number[],
@@ -376,7 +453,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     const sink = [] as T[]
     let pos = 0
 
-    const dataView = new DataView(ba.buffer)
+    const dataView = new DataView(ba.buffer, ba.byteOffset, ba.byteLength)
     const hasDpositions = dpositions.length > 0
     const hasCpositions = cpositions.length > 0
 

package/src/csi.ts

@@ -36,7 +36,11 @@ export default class CSI extends IndexFile {
   }
 
   parseAuxData(bytes: Uint8Array, offset: number) {
-    const dataView = new DataView(bytes.buffer)
+    const dataView = new DataView(
+      bytes.buffer,
+      bytes.byteOffset,
+      bytes.byteLength,
+    )
     const formatFlags = dataView.getUint32(offset, true)
     const coordinateType =
       formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
@@ -74,7 +78,11 @@ export default class CSI extends IndexFile {
     const buffer = await this.filehandle.readFile(opts)
     const bytes = await unzip(buffer)
 
-    const dataView = new DataView(bytes.buffer)
+    const dataView = new DataView(
+      bytes.buffer,
+      bytes.byteOffset,
+      bytes.byteLength,
+    )
     let csiVersion
     const magic = dataView.getUint32(0, true)
 

package/src/htsget.ts

@@ -78,7 +78,7 @@ export default class HtsgetFile<
     })
 
     const zero = new VirtualOffset(0, 0)
-    const allRecords = await this.readBamFeatures(
+    const allRecords = this.readBamFeatures(
       uncba,
       [],
       [],
@@ -95,7 +95,11 @@ export default class HtsgetFile<
     const uncba = await fetchAndConcat(data.htsget.urls, {
       signal: opts.signal,
     })
-    const dataView = new DataView(uncba.buffer)
+    const dataView = new DataView(
+      uncba.buffer,
+      uncba.byteOffset,
+      uncba.byteLength,
+    )
 
     if (dataView.getInt32(0, true) !== BAM_MAGIC) {
       throw new Error('Not a BAM file')

package/src/index.ts

@@ -1,5 +1,5 @@
 export { default as BAI } from './bai.ts'
-export { default as BamFile } from './bamFile.ts'
+export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts'
 export { default as CSI } from './csi.ts'
 export { default as BamRecord } from './record.ts'
 export { default as HtsgetFile } from './htsget.ts'