@gmod/bbi 9.0.9 → 9.0.12

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "9.0.9",
+  "version": "9.0.12",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": {
@@ -8,7 +8,7 @@
     "url": "https://github.com/GMOD/bbi-js.git"
   },
   "type": "module",
-  "types": "./dist/index.d.ts",
+  "main": "dist/index.js",
   "exports": {
     "import": "./esm/index.js",
     "require": "./dist/index.js"
@@ -24,21 +24,23 @@
     "src"
   ],
   "scripts": {
-    "test": "vitest",
-    "benchonly": "vitest bench",
-    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
-    "format": "prettier --write .",
+    "test": "vitest --run",
+    "test:watch": "vitest",
+    "test:pack": "./scripts/test-pack.sh",
     "clean": "rimraf dist esm",
+    "format": "prettier --write .",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "prebuild": "pnpm clean",
-    "build:wasm": "pnpm --filter inflate-wasm-build build",
     "build:esm": "tsc --outDir esm",
+    "postbuild:esm": "mkdir -p esm/wasm && cp src/wasm/inflate-wasm-inlined.js src/wasm/inflate-wasm-inlined.d.ts esm/wasm/",
     "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
-    "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
+    "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json && mkdir -p dist/wasm && cp src/wasm/inflate-wasm-inlined.js src/wasm/inflate-wasm-inlined.d.ts dist/wasm/ && echo '{\"type\": \"module\"}' > dist/wasm/package.json",
+    "preversion": "pnpm lint && pnpm test && pnpm build && pnpm test:pack",
+    "postversion": "git push --follow-tags",
     "build": "pnpm build:wasm && pnpm build:esm && pnpm build:es5",
-    "preversion": "pnpm lint && pnpm test --run && pnpm build",
-    "version": "standard-changelog && git add CHANGELOG.md",
-    "postversion": "git push --follow-tags"
+    "benchonly": "vitest bench",
+    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
+    "build:wasm": "pnpm --filter inflate-wasm-build build"
   },
   "keywords": [
     "bionode",
@@ -56,18 +58,17 @@
   "devDependencies": {
     "@eslint/js": "^10.0.1",
     "@gmod/bed": "^2.1.10",
-    "@types/node": "^25.5.0",
-    "@vitest/coverage-v8": "^4.1.2",
-    "eslint": "^9.39.4",
-    "eslint-plugin-import": "^2.32.0",
+    "@types/node": "^25.6.0",
+    "@vitest/coverage-v8": "^4.1.5",
+    "eslint": "^10.2.1",
+    "eslint-plugin-import-x": "^4.16.2",
     "eslint-plugin-unicorn": "^64.0.0",
-    "prettier": "^3.8.1",
+    "prettier": "^3.8.3",
     "rimraf": "^6.1.3",
-    "standard-changelog": "^7.0.1",
-    "typescript": "^6.0.2",
-    "typescript-eslint": "^8.58.0",
-    "vitest": "^4.1.2",
-    "webpack": "^5.105.4",
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.0",
+    "vitest": "^4.1.5",
+    "webpack": "^5.106.2",
     "webpack-cli": "^7.0.2"
   },
   "publishConfig": {

package/src/array-feature-view.ts

@@ -10,8 +10,7 @@ export class BigWigFeature {
   get(key: 'start' | 'end' | 'score'): number
   get(key: 'minScore' | 'maxScore'): number | undefined
   get(key: 'summary'): boolean
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  get(key: string): any
+  get(key: string): string | number | boolean | undefined
   get(key: string) {
     return this.view.get(this.i, key)
   }
@@ -43,8 +42,8 @@ export class ArrayFeatureView {
   public readonly minScores: Float32Array | undefined
   public readonly maxScores: Float32Array | undefined
   public readonly isSummary: boolean
-  private _source: string
-  private _refName: string
+  public readonly source: string
+  public readonly refName: string
 
   constructor(
     arrays: BigWigFeatureArrays | SummaryFeatureArrays,
@@ -57,51 +56,41 @@ export class ArrayFeatureView {
     this.isSummary = arrays.isSummary
     this.minScores = arrays.isSummary ? arrays.minScores : undefined
     this.maxScores = arrays.isSummary ? arrays.maxScores : undefined
-    this._source = source
-    this._refName = refName
+    this.source = source
+    this.refName = refName
   }
 
   get length() {
     return this.starts.length
   }
 
-  get source() {
-    return this._source
-  }
-
-  get refName() {
-    return this._refName
-  }
-
-  start(i: number) {
+  start(i: number): number {
     return this.starts[i]!
   }
 
-  end(i: number) {
+  end(i: number): number {
     return this.ends[i]!
   }
 
-  score(i: number) {
+  score(i: number): number {
     return this.scores[i]!
   }
 
-  minScore(i: number) {
+  minScore(i: number): number | undefined {
     return this.minScores?.[i]
   }
 
-  maxScore(i: number) {
+  maxScore(i: number): number | undefined {
     return this.maxScores?.[i]
   }
 
   id(i: number) {
-    return `${this._source}:${this._refName}:${this.starts[i]}-${this.ends[i]}`
+    return `${this.source}:${this.refName}:${this.starts[i]}-${this.ends[i]}`
   }
 
   get(i: number, key: 'refName' | 'source'): string
-  get(
-    i: number,
-    key: 'start' | 'end' | 'score' | 'minScore' | 'maxScore',
-  ): number | undefined
+  get(i: number, key: 'start' | 'end' | 'score'): number
+  get(i: number, key: 'minScore' | 'maxScore'): number | undefined
   get(i: number, key: 'summary'): boolean
 
   get(i: number, key: string): string | number | boolean | undefined
@@ -114,9 +103,9 @@ export class ArrayFeatureView {
       case 'score':
         return this.scores[i]
       case 'refName':
-        return this._refName
+        return this.refName
       case 'source':
-        return this._source
+        return this.source
       case 'minScore':
         return this.minScores?.[i]
       case 'maxScore':

package/src/bbi.ts

@@ -1,6 +1,7 @@
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
 
 import { BlockView } from './block-view.ts'
+import { getDataView, parseKey } from './util.ts'
 
 import type {
   BigWigFeatureArrays,
@@ -20,10 +21,6 @@ const BIG_BED_MAGIC = -2021002517
 
 const decoder = new TextDecoder('utf8')
 
-function getDataView(buffer: Uint8Array) {
-  return new DataView(buffer.buffer, buffer.byteOffset, buffer.length)
-}
-
 export abstract class BBI {
   protected bbi: GenericFilehandle
 
@@ -119,15 +116,13 @@ export abstract class BBI {
     for (let i = 0; i < numZoomLevels; i++) {
       const reductionLevel = dataView.getUint32(offset, true)
       offset += 4
-      const reserved = dataView.getUint32(offset, true)
-      offset += 4
+      offset += 4 // reserved
       const dataOffset = Number(dataView.getBigUint64(offset, true))
       offset += 8
       const indexOffset = Number(dataView.getBigUint64(offset, true))
       offset += 8
       zoomLevels.push({
         reductionLevel,
-        reserved,
         dataOffset,
         indexOffset,
       })
@@ -143,30 +138,25 @@ export abstract class BBI {
 
     let totalSummary: Statistics
     if (totalSummaryOffset) {
-      const b2 = b.subarray(totalSummaryOffset)
-      let offset = 0
-      const dataView = getDataView(b2)
-      const basesCovered = Number(dataView.getBigUint64(offset, true))
-      offset += 8
-      const scoreMin = dataView.getFloat64(offset, true)
-      offset += 8
-      const scoreMax = dataView.getFloat64(offset, true)
-      offset += 8
-      const scoreSum = dataView.getFloat64(offset, true)
-      offset += 8
-      const scoreSumSquares = dataView.getFloat64(offset, true)
-
+      const summaryView = getDataView(b, totalSummaryOffset)
       totalSummary = {
-        scoreMin,
-        scoreMax,
-        scoreSum,
-        scoreSumSquares,
-        basesCovered,
+        basesCovered: Number(summaryView.getBigUint64(0, true)),
+        scoreMin: summaryView.getFloat64(8, true),
+        scoreMax: summaryView.getFloat64(16, true),
+        scoreSum: summaryView.getFloat64(24, true),
+        scoreSumSquares: summaryView.getFloat64(32, true),
       }
     } else {
       throw new Error('no stats')
     }
 
+    let autoSql = ''
+    if (asOffset) {
+      const nullPos = b.indexOf(0, asOffset)
+      const end = nullPos === -1 ? b.length : nullPos
+      autoSql = decoder.decode(b.subarray(asOffset, end))
+    }
+
     return {
       zoomLevels,
       magic,
@@ -183,9 +173,7 @@ export abstract class BBI {
       unzoomedIndexOffset,
       fileType,
       version,
-      autoSql: asOffset
-        ? decoder.decode(b.subarray(asOffset, b.indexOf(0, asOffset)))
-        : '',
+      autoSql,
     }
   }
 
@@ -209,7 +197,7 @@ export abstract class BBI {
 
     // Recursively traverses the B+ tree to populate chromosome name-to-ID mappings
     const readBPlusTreeNode = async (currentOffset: number) => {
-      const header = getDataView(await this.bbi.read(4, currentOffset))
+      const header = getDataView(await this.bbi.read(4, currentOffset, opts))
       const isLeafNode = header.getUint8(0)
       const count = header.getUint16(2, true)
 
@@ -218,16 +206,12 @@ export abstract class BBI {
         const b = await this.bbi.read(
           count * (keySize + valSize),
           currentOffset + 4,
+          opts,
         )
         const dataView = getDataView(b)
         let offset = 0
         for (let n = 0; n < count; n++) {
-          const keyEnd = b.indexOf(0, offset)
-          const effectiveKeyEnd =
-            keyEnd !== -1 && keyEnd < offset + keySize
-              ? keyEnd
-              : offset + keySize
-          const key = decoder.decode(b.subarray(offset, effectiveKeyEnd))
+          const key = parseKey(b, offset, keySize)
           offset += keySize
           const refId = dataView.getUint32(offset, true)
           offset += 4
@@ -239,7 +223,7 @@ export abstract class BBI {
       } else {
         // Non-leaf nodes contain pointers to child nodes
         const dataView = getDataView(
-          await this.bbi.read(count * (keySize + 8), currentOffset + 4),
+          await this.bbi.read(count * (keySize + 8), currentOffset + 4, opts),
         )
         const nextNodes = []
         let offset = 0

package/src/bigbed.ts

@@ -1,13 +1,9 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache'
-import QuickLRU from '@jbrowse/quick-lru'
-
 import { BBI } from './bbi.ts'
+import { getDataView, parseKey } from './util.ts'
 
 import type { RequestOptions } from './types.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
-const decoder = new TextDecoder('utf8')
-
 interface Loc {
   key: string
   offset: number
@@ -38,14 +34,6 @@ function getTabField(str: string, fieldIndex: number) {
   return end === -1 ? str.slice(start) : str.slice(start, end)
 }
 
-// Parses a null-terminated string key from a B+ tree node
-function parseKey(buffer: Uint8Array, offset: number, keySize: number) {
-  const keyEnd = buffer.indexOf(0, offset)
-  const effectiveKeyEnd =
-    keyEnd !== -1 && keyEnd < offset + keySize ? keyEnd : offset + keySize
-  return decoder.decode(buffer.subarray(offset, effectiveKeyEnd))
-}
-
 // Recursively traverses a B+ tree to search for a specific name in the BigBed extraIndex
 // B+ trees are balanced tree structures optimized for disk-based searches
 async function readBPlusTreeNode(
@@ -60,7 +48,7 @@ async function readBPlusTreeNode(
 ): Promise<Loc | undefined> {
   const len = 4 + blockSize * (keySize + valSize)
   const buffer = await bbi.read(len, nodeOffset, opts)
-  const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length)
+  const dataView = getDataView(buffer)
   const nodeType = dataView.getInt8(0)
   const cnt = dataView.getInt16(2, true)
   let offset = 4
@@ -79,25 +67,21 @@ async function readBPlusTreeNode(
       })
     }
 
-    // Binary search to find the appropriate child node
     let left = 0
     let right = leafkeys.length - 1
-    let targetIndex = leafkeys.length - 1
+    let targetIndex = -1
 
     while (left <= right) {
       const mid = Math.floor((left + right) / 2)
-      const cmp = name.localeCompare(leafkeys[mid]!.key)
-
-      if (cmp < 0) {
-        targetIndex = mid - 1
-        right = mid - 1
-      } else {
+      if (name.localeCompare(leafkeys[mid]!.key) >= 0) {
+        targetIndex = mid
         left = mid + 1
+      } else {
+        right = mid - 1
       }
     }
 
-    const childOffset =
-      targetIndex >= 0 ? leafkeys[targetIndex]!.offset : leafkeys[0]!.offset
+    const childOffset = leafkeys[Math.max(targetIndex, 0)]!.offset
     return readBPlusTreeNode(
       bbi,
       childOffset,
@@ -149,15 +133,16 @@ async function readBPlusTreeNode(
 }
 
 export class BigBed extends BBI {
-  public readIndicesCache = new AbortablePromiseCache<RequestOptions, Index[]>({
-    cache: new QuickLRU({ maxSize: 1 }),
-    fill: (args: RequestOptions, signal?: AbortSignal) =>
-      this._readIndices({ ...args, signal }),
-  })
+  private indicesP?: Promise<Index[]>
 
   public readIndices(opts: RequestOptions = {}) {
-    const { signal, ...rest } = opts
-    return this.readIndicesCache.get(JSON.stringify(rest), opts, signal)
+    if (!this.indicesP) {
+      this.indicesP = this._readIndices(opts).catch((e: unknown) => {
+        this.indicesP = undefined
+        throw e
+      })
+    }
+    return this.indicesP
   }
 
   /*
@@ -176,9 +161,9 @@ export class BigBed extends BBI {
    */
   private async _readIndices(opts: RequestOptions) {
     const { extHeaderOffset } = await this.getHeader(opts)
-    const b = await this.bbi.read(64, extHeaderOffset)
+    const b = await this.bbi.read(64, extHeaderOffset, opts)
 
-    const dataView = new DataView(b.buffer, b.byteOffset, b.length)
+    const dataView = getDataView(b)
     const count = dataView.getUint16(2, true)
     const dataOffset = Number(dataView.getBigUint64(4, true))
 
@@ -189,13 +174,12 @@ export class BigBed extends BBI {
 
     const blocklen = 20
     const len = blocklen * count
-    const buffer = await this.bbi.read(len, dataOffset)
+    const buffer = await this.bbi.read(len, dataOffset, opts)
 
     const indices: Index[] = []
 
     for (let i = 0; i < count; i += 1) {
-      const b = buffer.subarray(i * blocklen)
-      const dataView = new DataView(b.buffer, b.byteOffset, b.length)
+      const dataView = getDataView(buffer, i * blocklen)
       const type = dataView.getInt16(0, true)
       const fieldcount = dataView.getInt16(2, true)
       const dataOffset = Number(dataView.getBigUint64(4, true))
@@ -232,7 +216,7 @@ export class BigBed extends BBI {
       const { offset: offset2, field } = index
       const b = await this.bbi.read(32, offset2, opts)
 
-      const dataView = new DataView(b.buffer, b.byteOffset, b.length)
+      const dataView = getDataView(b)
       const blockSize = dataView.getInt32(4, true)
       const keySize = dataView.getInt32(8, true)
       const valSize = dataView.getInt32(12, true)
@@ -280,7 +264,7 @@ export class BigBed extends BBI {
       if (!f.rest) {
         return false
       }
-      const fieldIndex = (f.field || 0) - 3
+      const fieldIndex = (f.field ?? 0) - 3
       return getTabField(f.rest, fieldIndex) === name
     })
   }

package/src/bigwig.ts

@@ -18,8 +18,8 @@ export class BigWig extends BBI {
     const maxLevel = zoomLevels.length - 1
 
     for (let i = maxLevel; i >= 0; i -= 1) {
-      const zh = zoomLevels[i]
-      if (zh && zh.reductionLevel <= 2 * basesPerPx) {
+      const zh = zoomLevels[i]!
+      if (zh.reductionLevel <= 2 * basesPerPx) {
         return this.getOrCreateBlockView(
           refsByName,
           zh.indexOffset,