@gmod/bam 7.8.2 → 7.9.0

package/esm/record.js.map

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

@@ -25,6 +25,16 @@ export interface BaseOpts {
      */
     onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
+/**
+ * Merge and order the chunks a query resolved to.
+ *
+ * Takes ownership of `chunks`: with no `lowest` to pre-filter against it sorts
+ * the array IN PLACE rather than copying. Every caller builds a fresh array to
+ * hand over, which is what makes that safe — passing something you still hold,
+ * or anything reachable from the index's per-refId cache, would reorder it
+ * underneath you. (The Chunk objects themselves are never mutated; a merged
+ * span produces a new instance.)
+ */
 export declare function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords): Chunk[];
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;

package/esm/util.js

@@ -1,5 +1,15 @@
 import Chunk from "./chunk.js";
 import { VirtualOffset } from "./virtualOffset.js";
+/**
+ * Merge and order the chunks a query resolved to.
+ *
+ * Takes ownership of `chunks`: with no `lowest` to pre-filter against it sorts
+ * the array IN PLACE rather than copying. Every caller builds a fresh array to
+ * hand over, which is what makes that safe — passing something you still hold,
+ * or anything reachable from the index's per-refId cache, would reorder it
+ * underneath you. (The Chunk objects themselves are never mutated; a merged
+ * span produces a new instance.)
+ */
 export function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
     if (n === 0) {
@@ -134,19 +144,14 @@ export function clampChunkEnds(chunks, extraBoundaries = []) {
     if (chunks.length === 0) {
         return;
     }
-    // A plain array, sized once and filled by index. Not a Float64Array: this
-    // runs once per reference, and an assembly with tens of thousands of unplaced
-    // scaffolds (cho.bam.bai has 28751 references) pays the allocation that many
-    // times over, where each individual boundary list is a handful of entries.
-    // The small-allocation cost dominates the faster typed sort by a wide margin
-    // at that shape. Filling by index still avoids the intermediate array that
-    // mapping the linear index to block positions used to build.
-    // Pre-sized and filled by index. Measured against both alternatives on five
-    // real .bai shapes (min of 21, interleaved, sign-stable over 3 runs):
-    // building with push instead is 5-8% slower here, and a Float64Array is
-    // faster to sort but allocates per reference, which costs 1.7x on an
-    // assembly with 28751 scaffolds. Filling by index also avoids the
-    // intermediate array that mapping the linear index used to build.
+    // A plain array, pre-sized and filled by index. Measured against both
+    // alternatives on five real .bai shapes (min of 21, interleaved, sign-stable
+    // over 3 runs): building with push instead is 5-8% slower, and a
+    // Float64Array is faster to sort but allocates per reference, which costs
+    // 1.7x on an assembly with tens of thousands of unplaced scaffolds
+    // (cho.bam.bai has 28751 references, each with a handful of boundaries).
+    // Filling by index also avoids the intermediate array that mapping the
+    // linear index to block positions used to build.
     const boundaries = new Array(extraBoundaries.length + chunks.length * 2);
     let n = 0;
     for (let i = 0, l = extraBoundaries.length; i < l; i++) {

package/esm/util.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.8.2",
+  "version": "7.9.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
@@ -27,9 +27,12 @@
   ],
   "scripts": {
     "test": "vitest",
+    "test:coverage": "vitest run --coverage",
     "clean": "rimraf dist esm",
     "format": "prettier --write .",
+    "format:check": "prettier --check .",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "typecheck": "tsc --noEmit -p tsconfig.lint.json",
     "prebuild": "pnpm clean",
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",

package/src/bai.ts

@@ -33,12 +33,20 @@ const BAI_MAGIC = 21578050 // BAI\1
 // https://github.com/samtools/hts-specs/blob/master/SAMv1.pdf
 const BAI_LINEAR_SHIFT = 14
 const BAI_LINEAR_INTERVAL = 1 << BAI_LINEAR_SHIFT // 16384
+const BAI_DEPTH = 5
+// Highest coordinate the scheme addresses: the deepest level's bins are
+// BAI_LINEAR_INTERVAL wide and there are 8^BAI_DEPTH of them.
+const BAI_MAX_POS = 2 ** (BAI_LINEAR_SHIFT + BAI_DEPTH * 3) // 2^29
 
 function roundDown(n: number, multiple: number) {
   return n - (n % multiple)
 }
+// Note the `rem === 0` case: without it a coordinate already on a window
+// boundary rounds up a whole extra window, which is enough to push indexCov's
+// range past the end of the linear index.
 function roundUp(n: number, multiple: number) {
-  return n - (n % multiple) + multiple
+  const rem = n % multiple
+  return rem === 0 ? n : n - rem + multiple
 }
 
 export interface IndexCovEntry {
@@ -50,6 +58,19 @@ export interface IndexCovEntry {
 // Compute bin ranges that overlap [beg, end). Each level's first-bin offset
 // is (8^L - 1) / 7. See SAMv1.pdf §5.1.1 for the binning derivation.
 function reg2bins(beg: number, end: number) {
+  // Clamp to what the scheme can address, the way CSI's reg2bins clamps to
+  // its own. The shifts below are the `>>` operator, so a coordinate past
+  // 2^31 wraps to a negative bin number and every level yields an empty
+  // range: `getRecordsForRange(chr, 0, 2**32)` — a caller asking for a whole
+  // reference without knowing its length — came back with NO records at all
+  // rather than all of them. Clamping is also what keeps a merely-large end
+  // from walking ~130k absent bin numbers before finding the same chunks.
+  if (beg > BAI_MAX_POS) {
+    beg = BAI_MAX_POS
+  }
+  if (end > BAI_MAX_POS) {
+    end = BAI_MAX_POS
+  }
   end -= 1
   return [
     [0, 0],
@@ -76,8 +97,7 @@ export default class BAI extends IndexFile<BaiParsed> {
     }
 
     const refCount = dataView.getInt32(4, true)
-    const depth = 5
-    const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7
+    const binLimit = ((1 << ((BAI_DEPTH + 1) * 3)) - 1) / 7
 
     // read the indexes for each reference sequence
     let curr = 8
@@ -100,11 +120,9 @@ export default class BAI extends IndexFile<BaiParsed> {
           throw new Error('bai index contains too many bins, please use CSI')
         } else {
           const chunkCount = dataView.getInt32(curr, true)
-          curr += 4
-          for (let k = 0; k < chunkCount; k++) {
-            curr += 8
-            curr += 8
-          }
+          // 16 bytes per chunk (two virtual offsets); the first pass only
+          // needs to step over them. Same shape as csi.ts's first pass.
+          curr += 4 + 16 * chunkCount
         }
       }
 
@@ -199,7 +217,6 @@ export default class BAI extends IndexFile<BaiParsed> {
     opts?: BaseOpts,
   ): Promise<IndexCovEntry[]> {
     const v = BAI_LINEAR_INTERVAL
-    const range = start !== undefined
     const indexData = await this.parse(opts)
     const seqIdx = indexData.indices(seqId)
 
@@ -211,15 +228,24 @@ export default class BAI extends IndexFile<BaiParsed> {
     if (nintv === 0) {
       return []
     }
-    const e = end === undefined ? (nintv - 1) * v : roundUp(end, v)
-    const s = start === undefined ? 0 : roundDown(start, v)
-    const depths: IndexCovEntry[] = range
-      ? new Array((e - s) / v)
-      : new Array(nintv - 1)
-    const totalSize = linearBlockPositions[nintv - 1]!
-    if (e > (nintv - 1) * v) {
-      throw new Error('query outside of range of linear index')
+    // The linear index describes [0, indexEnd): each window's score is the gap
+    // to the NEXT entry, so the final entry is a boundary rather than a window
+    // of its own. Both ends are clamped to it instead of throwing, so a range
+    // query returns the part of the reference the index covers — asking for the
+    // whole reference by its length (`indexCov(ref, 0, ctgLength)`, the obvious
+    // call, and one where end lands in the last window) used to throw "query
+    // outside of range of linear index" while `indexCov(ref)` answered fine.
+    const indexEnd = (nintv - 1) * v
+    const s =
+      start === undefined
+        ? 0
+        : Math.min(Math.max(roundDown(start, v), 0), indexEnd)
+    const e = end === undefined ? indexEnd : Math.min(roundUp(end, v), indexEnd)
+    if (e <= s) {
+      return []
     }
+    const depths: IndexCovEntry[] = new Array((e - s) / v)
+    const totalSize = linearBlockPositions[nintv - 1]!
     // 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

package/src/bamFile.ts

@@ -37,10 +37,13 @@ export const BAM_MAGIC = 21840194
 
 const blockLen = 1 << 16
 
-// Ceiling on the header read. A million contigs is roughly 10MB of compressed
-// @SQ lines and ref-seq table, so anything past this is a corrupt header
-// claiming a huge n_ref rather than a real one, and growing the read further
-// just downloads the file.
+// Ceiling on GROWING the header read. A million contigs is roughly 10MB of
+// compressed @SQ lines and ref-seq table, so a read that has doubled past this
+// is chasing a corrupt header claiming a huge n_ref rather than a real one, and
+// growing further just downloads the file. It does not cap the FIRST read: that
+// length comes from the index's firstDataLine, which is a real offset rather
+// than a guess, so a header that genuinely runs past this still gets its one
+// exact read. See getHeaderPre.
 const maxHeaderReadLen = 32 * 1024 * 1024
 
 function resolveFilehandle(
@@ -118,12 +121,24 @@ export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024
 const MAX_CONCURRENT_CHUNK_READS = 6
 
 class ChunkFeatureCache<T> {
-  public maxBytes: number
+  private _maxBytes: number
   private entries = new Map<string, ChunkEntry<T>>()
   private bytes = 0
 
   constructor(maxBytes: number) {
-    this.maxBytes = maxBytes
+    this._maxBytes = maxBytes
+  }
+
+  get maxBytes() {
+    return this._maxBytes
+  }
+
+  // Accessor rather than a plain field so lowering the budget frees memory now.
+  // As a field, a caller trimming the cache under memory pressure got nothing
+  // back until the next chunk read happened to call set().
+  set maxBytes(maxBytes: number) {
+    this._maxBytes = maxBytes
+    this.evict()
   }
 
   get size() {
@@ -148,11 +163,15 @@ class ChunkFeatureCache<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.
+    this.evict()
+  }
+
+  // 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.
+  private evict() {
     const lru = this.entries.keys()
-    while (this.bytes > this.maxBytes && this.entries.size > 1) {
+    while (this.bytes > this._maxBytes && this.entries.size > 1) {
       this.delete(lru.next().value!)
     }
   }
@@ -285,16 +304,21 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         ? blockLen
         : indexData.firstDataLine.blockPosition + blockLen
 
+    // do/while, so the index-derived length is always read once and only the
+    // doubling is bounded. Testing readLen before the first read instead meant
+    // a BAM whose header genuinely exceeds maxHeaderReadLen — millions of
+    // contigs — was rejected without a single byte being fetched, and reported
+    // as 'Insufficient data for reference sequences' when the data was there.
     let samHeader
-    let atEof = false
-    while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen) {
+    let atEof: boolean
+    do {
       const buffer = await this.bam.read(readLen, 0, { signal: opts.signal })
       // a short read means readLen ran past the end of the file, so there are
       // no more bytes to grow into
       atEof = buffer.length < readLen
       samHeader = this.applyHeader(await unzip(buffer))
       readLen *= 2
-    }
+    } while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen)
     if (samHeader === undefined) {
       throw new Error('Insufficient data for reference sequences')
     }
@@ -499,9 +523,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       // unbarriered pool exactly as before. That caps the cost of being wrong
       // at 0.92x-0.95x, against 0.82x-0.88x for barriering every wave.
       const batch = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length)
-      await Promise.all(
-        Array.from({ length: batch }, (_, ci) => readOne(ci)),
-      )
+      await Promise.all(Array.from({ length: batch }, (_, ci) => readOne(ci)))
       let stopped = false
       for (let ci = 0; ci < batch; ci++) {
         if (isPastQuery(featureLists[ci], chrId, max)) {
@@ -615,9 +637,13 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         const mateRecs = [] as T[]
         for (let i = 0, l = features.length; i < l; i++) {
           const feature = features[i]!
+          // fileOffset first: it is a number already on the record, where
+          // `name` decodes a string per record. A mate chunk usually overlaps
+          // the query region, so this skips the decode for every record the
+          // caller is already holding.
           if (
-            readNameCounts.get(feature.name) === 1 &&
-            !readIds.has(feature.fileOffset)
+            !readIds.has(feature.fileOffset) &&
+            readNameCounts.get(feature.name) === 1
           ) {
             mateRecs.push(feature)
           }
@@ -691,9 +717,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
           blockEnd,
           hasCpositions
             ? cpositions[pos]! * (1 << 8) +
-              (blockStart - dpositions[pos]!) +
-              chunk.minv.dataPosition +
-              1
+                (blockStart - dpositions[pos]!) +
+                chunk.minv.dataPosition +
+                1
             : crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
           dataView,
         )

package/src/csi.ts

@@ -96,6 +96,20 @@ export default class CSI extends IndexFile {
     this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7
     const maxBinNumber = this.maxBinNumber
     const auxLength = dataView.getInt32(12, true)
+    // A tabix-only branch, which is why parseAuxData and the parseNameBytes it
+    // calls show as uncovered. CSI is shared between `samtools index -c` and
+    // `tabix -C`, and the aux block is how a tabix index carries what a reader
+    // of bgzipped TEXT needs: which columns hold ref/start/end, the comment
+    // character, lines to skip, and the reference names — which a BAM takes
+    // from its own header instead. So a BAM .csi sets l_aux to 0 and never
+    // reaches here (checked: 0 of the 19 .csi fixtures carry one).
+    //
+    // Kept rather than deleted for two reasons. CSI is exported from
+    // index.ts, so pointing it at a tabix index is reachable (@gmod/tabix is
+    // the right tool, but this would half-work and then silently not).
+    // More importantly parseNameBytes is marked SYNC: with its tabix-js
+    // counterpart, and dropping one side of a deliberately-paired pair of
+    // implementations is exactly what that marker exists to prevent.
     const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined
     const refCount = dataView.getInt32(16 + auxLength, true)
 
@@ -200,6 +214,12 @@ export default class CSI extends IndexFile {
     for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
       const b = t + rshift(beg, s)
       const e = t + rshift(end, s)
+      // Unreachable as long as the clamp above stands, which is why it shows
+      // as uncovered: with end bounded to 2^(minShift + depth*3), level l
+      // spans at most 8^l - 1 bins, so the worst case is 8^depth - 1 + depth
+      // against a maxBinNumber of (8^(depth+1) - 1)/7, i.e. about 1.14 * 8^depth.
+      // Kept as a guard on the arithmetic rather than deleted — reg2bins is
+      // shared with tabix-js, whose callers reach it by other routes.
       if (e - b + bins.length > this.maxBinNumber) {
         throw new Error(
           `query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`,

package/src/index.ts

@@ -4,7 +4,12 @@ export { default as CSI } from './csi.ts'
 export { default as BamRecord } from './record.ts'
 export { default as HtsgetFile } from './htsget.ts'
 
-export type { Bytes } from './record.ts'
+export type { NumericCigar } from './record.ts'
 export type { BamRecordClass, BamRecordLike } from './bamFile.ts'
+// the options every query method takes, and the shapes they hand back. The
+// package has no subpath exports, so a consumer typing a wrapper around
+// getRecordsForRange/indexCov can only name these if they come out of here.
+export type { BamOpts, BaseOpts } from './util.ts'
+export type { IndexCovEntry } from './bai.ts'
 // for typing the HtsgetFile `fetch` option
 export type { Fetcher } from 'generic-filehandle2'

package/src/indexFile.ts

@@ -33,8 +33,11 @@ export function memoizeByRefId<T>(
 ) {
   const cache = new QuickLRU<number, T>({ maxSize })
   return (refId: number) => {
-    if (cache.has(refId)) {
-      return cache.get(refId)
+    // one lookup, not has()+get(): only truthy results are ever cached, so a
+    // miss and a cached value are already distinguishable
+    const cached = cache.get(refId)
+    if (cached !== undefined) {
+      return cached
     }
     const result = getIndices(refId)
     if (result) {