@gmod/bam 7.6.2 → 7.7.1

package/esm/sam.js.map

@@ -1 +1 @@
-{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAC5B,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,qEAAqE;oBACrE,mEAAmE;oBACnE,uEAAuE;oBACvE,kEAAkE;oBAClE,gEAAgE;oBAChE,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE;wBACvB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAA;gBACnD,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/esm/util.d.ts

@@ -1,6 +1,6 @@
 import Chunk from './chunk.ts';
 import { VirtualOffset } from './virtualOffset.ts';
-import type { Offset } from './virtualOffset.ts';
+import type { OffsetCoords } from './virtualOffset.ts';
 export interface BamOpts {
     viewAsPairs?: boolean;
     pairAcrossChr?: boolean;
@@ -25,11 +25,11 @@ export interface BaseOpts {
      */
     onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
 }
-export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[];
+export declare function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords): Chunk[];
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;
 };
-export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
+export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: ArrayLike<number>): void;
 export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRefSeq: (s: string) => string): {
     chrToIndex: Record<string, number>;
     indexToChr: {

package/esm/util.js

@@ -1,5 +1,4 @@
 import Chunk from "./chunk.js";
-import { longFromBytesToUnsigned } from "./long.js";
 import { VirtualOffset } from "./virtualOffset.js";
 export function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
@@ -60,9 +59,20 @@ export function optimizeChunks(chunks, lowest) {
     }
     return mergedChunks;
 }
+// The pseudo-bin's mapped-record count, a little-endian uint64. Read as two
+// 32-bit halves rather than via BigInt: exact up to Number.MAX_SAFE_INTEGER,
+// which is far past any real record count, and allocates nothing.
 export function parsePseudoBin(bytes, offset) {
+    const low = bytes[offset] |
+        (bytes[offset + 1] << 8) |
+        (bytes[offset + 2] << 16) |
+        (bytes[offset + 3] << 24);
+    const high = bytes[offset + 4] |
+        (bytes[offset + 5] << 8) |
+        (bytes[offset + 6] << 16) |
+        (bytes[offset + 7] << 24);
     return {
-        lineCount: longFromBytesToUnsigned(bytes, offset),
+        lineCount: (high >>> 0) * 2 ** 32 + (low >>> 0),
     };
 }
 // Tighten each chunk's endPosition (default: a full max-size BGZF block past
@@ -73,9 +83,30 @@ export function parsePseudoBin(bytes, offset) {
 // least the true block end, so the clamped fetch still contains the whole block.
 // Shrinks both the byte estimate and the actual fetch with no extra I/O.
 export function clampChunkEnds(chunks, extraBoundaries = []) {
-    const boundaries = [...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.
+    const boundaries = new Array(extraBoundaries.length + chunks.length * 2);
+    let n = 0;
+    for (let i = 0, l = extraBoundaries.length; i < l; i++) {
+        boundaries[n++] = extraBoundaries[i];
+    }
     for (const c of chunks) {
-        boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
+        boundaries[n++] = c.minv.blockPosition;
+        boundaries[n++] = c.maxv.blockPosition;
     }
     boundaries.sort((a, b) => a - b);
     for (const c of chunks) {

package/esm/util.js.map

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

@@ -1,14 +1,19 @@
-export interface Offset {
+/**
+ * The two coordinates a virtual offset packs, without the `blockPos:dataPos`
+ * string form. What every consumer that only compares positions needs — the
+ * BAI linear index stores these as raw numbers and materializes no object.
+ */
+export interface OffsetCoords {
     blockPosition: number;
     dataPosition: number;
+}
+export interface Offset extends OffsetCoords {
     toString(): string;
-    compareTo(arg: Offset): number;
 }
 export declare class VirtualOffset {
     blockPosition: number;
     dataPosition: number;
     constructor(blockPosition: number, dataPosition: number);
     toString(): string;
-    compareTo(b: VirtualOffset): number;
 }
 export declare function fromBytes(bytes: Uint8Array, offset?: number): VirtualOffset;

package/esm/virtualOffset.js

@@ -8,9 +8,6 @@ export class VirtualOffset {
     toString() {
         return `${this.blockPosition}:${this.dataPosition}`;
     }
-    compareTo(b) {
-        return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
-    }
 }
 export function fromBytes(bytes, offset = 0) {
     return new VirtualOffset(bytes[offset + 7] * 0x10000000000 +

package/esm/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC;IACrD,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAcA,MAAM,OAAO,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC;IACrD,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.6.2",
+  "version": "7.7.1",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",

package/src/bai.ts

@@ -7,10 +7,21 @@ import type { ParsedIndexBase, RefIndex } from './indexFile.ts'
 import type { BaseOpts } from './util.ts'
 import type { VirtualOffset } from './virtualOffset.ts'
 
+// The linear index as two parallel Float64Arrays rather than an array of
+// VirtualOffset objects. A human-sized reference has one entry per 16kb window
+// — ~15k for chr1 — and an object apiece costs roughly an order of magnitude
+// more memory than the packed form, retained for as long as memoizeByRefId
+// holds the reference. Both consumers want the raw numbers anyway: indexCov and
+// clampChunkEnds read blockPosition only, and getLowestChunk builds the one
+// VirtualOffset a query actually needs. Same shape as bgzf-filehandle's
+// GziIndex, for the same reason.
 interface BaiRefIndex extends RefIndex {
-  linearIndex: VirtualOffset[]
+  linearBlockPositions: Float64Array
+  linearDataPositions: Float64Array
 }
 
+const EMPTY_POSITIONS = new Float64Array(0)
+
 interface BaiParsed extends ParsedIndexBase<BaiRefIndex> {
   bai: true
 }
@@ -142,19 +153,33 @@ export default class BAI extends IndexFile<BaiParsed> {
 
       const linearCount = dataView.getInt32(curr, true)
       curr += 4
-      const linearIndex = new Array<VirtualOffset>(linearCount)
+      // Share one empty array rather than allocating a pair per reference. An
+      // assembly with tens of thousands of unplaced scaffolds (cho.bam.bai:
+      // 28751 references, 205 linear entries between them) reaches here once
+      // per reference, and almost every one of those has an empty linear index.
+      const linearBlockPositions =
+        linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount)
+      const linearDataPositions =
+        linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount)
       for (let j = 0; j < linearCount; j++) {
-        linearIndex[j] = fromBytes(bytes, curr)
+        // a virtual offset is a 48-bit block position in the high bytes and a
+        // 16-bit data position in the low two
+        linearBlockPositions[j] =
+          bytes[curr + 7]! * 0x10000000000 +
+          bytes[curr + 6]! * 0x100000000 +
+          bytes[curr + 5]! * 0x1000000 +
+          bytes[curr + 4]! * 0x10000 +
+          bytes[curr + 3]! * 0x100 +
+          bytes[curr + 2]!
+        linearDataPositions[j] = (bytes[curr + 1]! << 8) | bytes[curr]!
         curr += 8
       }
 
-      clampChunkEnds(
-        Object.values(binIndex).flat(),
-        linearIndex.map(v => v.blockPosition),
-      )
+      clampChunkEnds(Object.values(binIndex).flat(), linearBlockPositions)
       return {
         binIndex,
-        linearIndex,
+        linearBlockPositions,
+        linearDataPositions,
         stats,
       }
     }
@@ -162,7 +187,6 @@ export default class BAI extends IndexFile<BaiParsed> {
     return {
       bai: true,
       firstDataLine,
-      maxBlockSize: 1 << 16,
       indices: memoizeByRefId(getIndices),
       refCount,
     }
@@ -182,17 +206,18 @@ export default class BAI extends IndexFile<BaiParsed> {
     if (!seqIdx) {
       return []
     }
-    const { linearIndex, stats } = seqIdx
-    if (linearIndex.length === 0) {
+    const { linearBlockPositions, stats } = seqIdx
+    const nintv = linearBlockPositions.length
+    if (nintv === 0) {
       return []
     }
-    const e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v)
+    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(linearIndex.length - 1)
-    const totalSize = linearIndex[linearIndex.length - 1]!.blockPosition
-    if (e > (linearIndex.length - 1) * 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')
     }
     // Scale the block-delta into a read count as we go, rather than building the
@@ -200,9 +225,9 @@ export default class BAI extends IndexFile<BaiParsed> {
     // 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
+    let currentPos = linearBlockPositions[s / v]!
     for (let i = s / v, j = 0; i < e / v; i++, j++) {
-      const nextPos = linearIndex[i + 1]!.blockPosition
+      const nextPos = linearBlockPositions[i + 1]!
       depths[j] = {
         score: ((nextPos - currentPos) * lineCount) / totalSize,
         start: i * v,
@@ -221,8 +246,13 @@ export default class BAI extends IndexFile<BaiParsed> {
   // contain alignments in the region. Linear index entries are monotonically
   // non-decreasing, so the first entry at minLin is the minimum.
   protected getLowestChunk(refIndex: BaiRefIndex, min: number) {
-    const { linearIndex } = refIndex
-    const nintv = linearIndex.length
-    return linearIndex[Math.min(min >> BAI_LINEAR_SHIFT, nintv - 1)]
+    const { linearBlockPositions, linearDataPositions } = refIndex
+    const i = Math.min(min >> BAI_LINEAR_SHIFT, linearBlockPositions.length - 1)
+    return i < 0
+      ? undefined
+      : {
+          blockPosition: linearBlockPositions[i]!,
+          dataPosition: linearDataPositions[i]!,
+        }
   }
 }

package/src/bamFile.ts

@@ -232,7 +232,14 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
 
   async getHeaderPre(opts: BaseOpts = {}) {
     if (!this.index) {
-      return undefined
+      // Only reachable via `new BamFile({htsget: true})` used directly rather
+      // than through HtsgetFile, which overrides this. Throwing rather than
+      // returning undefined keeps `| undefined` off getHeader()'s public type,
+      // and makes that misuse loud instead of silently answering every query
+      // with zero records (getSeqId would find no chrToIndex).
+      throw new Error(
+        'no index to read a header from: use HtsgetFile for htsget sources',
+      )
     }
     const indexData = await this.index.parse(opts)
 
@@ -512,13 +519,26 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       const chunks = res[i]!
       for (let j = 0, jl = chunks.length; j < jl; j++) {
         const m = chunks[j]!
-        map.set(m.toString(), m)
+        // Key on the virtual-offset span — the same key _cachedChunkFeatures
+        // uses. Chunk.toString() also folds in `bin` and fetchedSize(), which
+        // keeps two chunks covering an identical span apart here even though
+        // the cache below collapses them, so their records came back twice.
+        map.set(chunkCacheKey(m), m)
       }
     }
-
-    const mateFeatLists = await Promise.all(
-      [...map.values()].map(async c => {
-        const features = await this._cachedChunkFeatures(c, opts)
+    const mateChunks = [...map.values()]
+
+    // Bounded for the reason ADR 0008 bounds the main query path: a viewAsPairs
+    // query over a busy region resolves to many distinct mate chunks, and an
+    // unbounded fan-out inflates every one of them at once. Same inline pool
+    // shape as _fetchChunkFeatures — ADR 0009 measured extracting a shared
+    // mapConcurrent helper at ~11% on the hot path, so it stays inline.
+    const mateFeatLists = new Array<T[]>(mateChunks.length)
+    let next = 0
+    const readNext = async () => {
+      while (next < mateChunks.length) {
+        const ci = next++
+        const features = await this._cachedChunkFeatures(mateChunks[ci]!, opts)
         const mateRecs = [] as T[]
         for (let i = 0, l = features.length; i < l; i++) {
           const feature = features[i]!
@@ -529,9 +549,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
             mateRecs.push(feature)
           }
         }
-        return mateRecs
-      }),
-    )
+        mateFeatLists[ci] = mateRecs
+      }
+    }
+    const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, mateChunks.length)
+    await Promise.all(Array.from({ length: workers }, () => readNext()))
     return mateFeatLists.flat()
   }
 
@@ -559,10 +581,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     }
   }
 
+  // cpositions/dpositions are `ArrayLike`, not `number[]`, because the wasm
+  // decompressor produces them as Float64Arrays — @gmod/bgzf-filehandle spreads
+  // them into plain arrays on the way out, and this signature is what lets that
+  // copy be dropped there without a change here. Only indexed reads and
+  // `.length` are used below either way.
   readBamFeatures(
     ba: Uint8Array,
-    cpositions: number[],
-    dpositions: number[],
+    cpositions: ArrayLike<number>,
+    dpositions: ArrayLike<number>,
     chunk: Chunk,
   ) {
     let blockStart = 0

package/src/chunk.ts

@@ -29,14 +29,6 @@ export default class Chunk {
     }, fetchedSize ${this.fetchedSize()})`
   }
 
-  compareTo(b: Chunk) {
-    return (
-      this.minv.compareTo(b.minv) ||
-      this.maxv.compareTo(b.maxv) ||
-      this.bin - b.bin
-    )
-  }
-
   fetchedSize() {
     return this.endPosition - this.minv.blockPosition
   }

package/src/csi.ts

@@ -83,16 +83,12 @@ export default class CSI extends IndexFile {
       bytes.byteOffset,
       bytes.byteLength,
     )
-    let csiVersion
+    // CSI\1 and CSI\2 are parsed identically here — v2 only adds fields this
+    // reader doesn't consume — so the version is validated, not retained.
     const magic = dataView.getUint32(0, true)
-
-    if (magic === CSI1_MAGIC) {
-      csiVersion = 1
-    } else if (magic === CSI2_MAGIC) {
-      csiVersion = 2
-    } else {
-      throw new Error(`Not a CSI file ${magic}`)
+    if (magic !== CSI1_MAGIC && magic !== CSI2_MAGIC) {
       // TODO: do we need to support big-endian CSI files?
+      throw new Error(`Not a CSI file ${magic}`)
     }
 
     this.minShift = dataView.getInt32(4, true)
@@ -170,12 +166,10 @@ export default class CSI extends IndexFile {
     }
 
     return {
-      csiVersion,
       firstDataLine,
       indices: memoizeByRefId(getIndices),
       refCount,
       csi: true,
-      maxBlockSize: 1 << 16,
       ...aux,
     }
   }

package/src/indexFile.ts

@@ -4,7 +4,7 @@ import { optimizeChunks } from './util.ts'
 
 import type Chunk from './chunk.ts'
 import type { BaseOpts } from './util.ts'
-import type { Offset, VirtualOffset } from './virtualOffset.ts'
+import type { OffsetCoords, VirtualOffset } from './virtualOffset.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
 export interface Region {
@@ -21,7 +21,6 @@ export interface RefIndex {
 export interface ParsedIndexBase<R extends RefIndex = RefIndex> {
   firstDataLine: VirtualOffset | undefined
   refCount: number
-  maxBlockSize: number
   indices: (refId: number) => R | undefined
 }
 
@@ -84,7 +83,7 @@ export default abstract class IndexFile<
   protected abstract getLowestChunk(
     refIndex: RefIndex,
     min: number,
-  ): Offset | undefined
+  ): OffsetCoords | undefined
 
   async blocksForRange(
     refId: number,

package/src/sam.ts

@@ -8,9 +8,14 @@ export function parseHeaderText(text: string) {
         tag: tag.slice(1),
         data: fields.map(f => {
           const r = f.indexOf(':')
-          const fieldTag = f.slice(0, r)
-          const value = f.slice(r + 1)
-          return { tag: fieldTag, value }
+          // A field with no colon is not a TAG:VALUE pair — @CO lines are free
+          // text, one comment per line (`samtools view -H c2#pad.3.0.cram`).
+          // Without this branch `slice(0, -1)` silently drops the comment's last
+          // character into the tag. Same shape @gmod/cram's parseHeaderText
+          // returns, so both feed a consumer's header parser identically.
+          return r === -1
+            ? { tag: f, value: '' }
+            : { tag: f.slice(0, r), value: f.slice(r + 1) }
         }),
       })
     }

package/src/util.ts

@@ -1,8 +1,7 @@
 import Chunk from './chunk.ts'
-import { longFromBytesToUnsigned } from './long.ts'
 import { VirtualOffset } from './virtualOffset.ts'
 
-import type { Offset } from './virtualOffset.ts'
+import type { OffsetCoords } from './virtualOffset.ts'
 
 export interface BamOpts {
   viewAsPairs?: boolean
@@ -30,7 +29,7 @@ export interface BaseOpts {
   onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
 }
 
-export function optimizeChunks(chunks: Chunk[], lowest?: Offset) {
+export function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords) {
   const n = chunks.length
   if (n === 0) {
     return chunks
@@ -102,9 +101,22 @@ export function optimizeChunks(chunks: Chunk[], lowest?: Offset) {
   return mergedChunks
 }
 
+// The pseudo-bin's mapped-record count, a little-endian uint64. Read as two
+// 32-bit halves rather than via BigInt: exact up to Number.MAX_SAFE_INTEGER,
+// which is far past any real record count, and allocates nothing.
 export function parsePseudoBin(bytes: Uint8Array, offset: number) {
+  const low =
+    bytes[offset]! |
+    (bytes[offset + 1]! << 8) |
+    (bytes[offset + 2]! << 16) |
+    (bytes[offset + 3]! << 24)
+  const high =
+    bytes[offset + 4]! |
+    (bytes[offset + 5]! << 8) |
+    (bytes[offset + 6]! << 16) |
+    (bytes[offset + 7]! << 24)
   return {
-    lineCount: longFromBytesToUnsigned(bytes, offset),
+    lineCount: (high >>> 0) * 2 ** 32 + (low >>> 0),
   }
 }
 
@@ -117,11 +129,34 @@ export function parsePseudoBin(bytes: Uint8Array, offset: number) {
 // Shrinks both the byte estimate and the actual fetch with no extra I/O.
 export function clampChunkEnds(
   chunks: Chunk[],
-  extraBoundaries: number[] = [],
+  extraBoundaries: ArrayLike<number> = [],
 ) {
-  const boundaries = [...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.
+  const boundaries = new Array<number>(
+    extraBoundaries.length + chunks.length * 2,
+  )
+  let n = 0
+  for (let i = 0, l = extraBoundaries.length; i < l; i++) {
+    boundaries[n++] = extraBoundaries[i]!
+  }
   for (const c of chunks) {
-    boundaries.push(c.minv.blockPosition, c.maxv.blockPosition)
+    boundaries[n++] = c.minv.blockPosition
+    boundaries[n++] = c.maxv.blockPosition
   }
   boundaries.sort((a, b) => a - b)
 

package/src/virtualOffset.ts

@@ -1,8 +1,15 @@
-export interface Offset {
+/**
+ * The two coordinates a virtual offset packs, without the `blockPos:dataPos`
+ * string form. What every consumer that only compares positions needs — the
+ * BAI linear index stores these as raw numbers and materializes no object.
+ */
+export interface OffsetCoords {
   blockPosition: number
   dataPosition: number
+}
+
+export interface Offset extends OffsetCoords {
   toString(): string
-  compareTo(arg: Offset): number
 }
 
 export class VirtualOffset {
@@ -16,12 +23,6 @@ export class VirtualOffset {
   toString() {
     return `${this.blockPosition}:${this.dataPosition}`
   }
-
-  compareTo(b: VirtualOffset) {
-    return (
-      this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition
-    )
-  }
 }
 export function fromBytes(bytes: Uint8Array, offset = 0) {
   return new VirtualOffset(

package/dist/long.d.ts

@@ -1 +0,0 @@
-export declare function longFromBytesToUnsigned(source: Uint8Array, i?: number): number;

package/dist/long.js

@@ -1,17 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.longFromBytesToUnsigned = longFromBytesToUnsigned;
-const TWO_PWR_32_DBL = 2 ** 32;
-// avoids dependency on long.js
-function longFromBytesToUnsigned(source, i = 0) {
-    const low = source[i] |
-        (source[i + 1] << 8) |
-        (source[i + 2] << 16) |
-        (source[i + 3] << 24);
-    const high = source[i + 4] |
-        (source[i + 5] << 8) |
-        (source[i + 6] << 16) |
-        (source[i + 7] << 24);
-    return (high >>> 0) * TWO_PWR_32_DBL + (low >>> 0);
-}
-//# sourceMappingURL=long.js.map

package/dist/long.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;AAGA,0DAYC;AAfD,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AAE9B,+BAA+B;AAC/B,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}

package/esm/long.d.ts

@@ -1 +0,0 @@
-export declare function longFromBytesToUnsigned(source: Uint8Array, i?: number): number;

package/esm/long.js

@@ -1,14 +0,0 @@
-const TWO_PWR_32_DBL = 2 ** 32;
-// avoids dependency on long.js
-export function longFromBytesToUnsigned(source, i = 0) {
-    const low = source[i] |
-        (source[i + 1] << 8) |
-        (source[i + 2] << 16) |
-        (source[i + 3] << 24);
-    const high = source[i + 4] |
-        (source[i + 5] << 8) |
-        (source[i + 6] << 16) |
-        (source[i + 7] << 24);
-    return (high >>> 0) * TWO_PWR_32_DBL + (low >>> 0);
-}
-//# sourceMappingURL=long.js.map

package/esm/long.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AAE9B,+BAA+B;AAC/B,MAAM,UAAU,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}