@gmod/bbi 5.0.2 → 6.0.0

package/esm/block-view.js

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import QuickLRU from 'quick-lru';
 // locals
@@ -17,22 +16,18 @@ function coordFilter(s1, e1, s2, e2) {
  * @constructs
  */
 export class BlockView {
-    constructor(bbi, refsByName, cirTreeOffset, isBigEndian, isCompressed, blockType) {
+    constructor(bbi, refsByName, cirTreeOffset, isCompressed, blockType) {
         this.bbi = bbi;
         this.refsByName = refsByName;
         this.cirTreeOffset = cirTreeOffset;
-        this.isBigEndian = isBigEndian;
         this.isCompressed = isCompressed;
         this.blockType = blockType;
         this.featureCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 1000 }),
             fill: async (requestData, signal) => {
-                const len = requestData.length;
-                const off = requestData.offset;
-                const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, off, {
+                return this.bbi.read(requestData.length, requestData.offset, {
                     signal,
                 });
-                return buffer;
             },
         });
         if (!(cirTreeOffset >= 0)) {
@@ -41,22 +36,20 @@ export class BlockView {
     }
     async readWigData(chrName, start, end, observer, opts) {
         try {
-            const { refsByName, bbi, cirTreeOffset, isBigEndian } = this;
+            const { refsByName, bbi, cirTreeOffset } = this;
             const chrId = refsByName[chrName];
             if (chrId === undefined) {
                 observer.complete();
             }
             const request = { chrId, start, end };
             if (!this.cirTreePromise) {
-                this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, cirTreeOffset, opts);
+                this.cirTreePromise = bbi.read(48, cirTreeOffset, opts);
             }
-            const { buffer } = await this.cirTreePromise;
-            const cirBlockSize = isBigEndian
-                ? buffer.readUInt32BE(4)
-                : buffer.readUInt32LE(4);
+            const buffer = await this.cirTreePromise;
+            const dataView = new DataView(buffer.buffer);
+            const cirBlockSize = dataView.getUint32(4, true);
             let blocksToFetch = [];
             let outstanding = 0;
-            const le = true;
             const cirFobRecur2 = (cirBlockData, offset2, level) => {
                 try {
                     const data = cirBlockData.subarray(offset2);
@@ -65,22 +58,22 @@ export class BlockView {
                     let offset = 0;
                     const isLeaf = dataView.getUint8(offset);
                     offset += 2; // 1 skip
-                    const cnt = dataView.getUint16(offset, le);
+                    const cnt = dataView.getUint16(offset, true);
                     offset += 2;
                     if (isLeaf === 1) {
                         const blocksToFetch2 = [];
                         for (let i = 0; i < cnt; i++) {
-                            const startChrom = dataView.getUint32(offset, le);
+                            const startChrom = dataView.getUint32(offset, true);
                             offset += 4;
-                            const startBase = dataView.getUint32(offset, le);
+                            const startBase = dataView.getUint32(offset, true);
                             offset += 4;
-                            const endChrom = dataView.getUint32(offset, le);
+                            const endChrom = dataView.getUint32(offset, true);
                             offset += 4;
-                            const endBase = dataView.getUint32(offset, le);
+                            const endBase = dataView.getUint32(offset, true);
                             offset += 4;
-                            const blockOffset = Number(dataView.getBigUint64(offset, le));
+                            const blockOffset = Number(dataView.getBigUint64(offset, true));
                             offset += 8;
-                            const blockSize = Number(dataView.getBigUint64(offset, le));
+                            const blockSize = Number(dataView.getBigUint64(offset, true));
                             offset += 8;
                             blocksToFetch2.push({
                                 startChrom,
@@ -102,15 +95,15 @@ export class BlockView {
                     else if (isLeaf === 0) {
                         const recurOffsets = [];
                         for (let i = 0; i < cnt; i++) {
-                            const startChrom = dataView.getUint32(offset, le);
+                            const startChrom = dataView.getUint32(offset, true);
                             offset += 4;
-                            const startBase = dataView.getUint32(offset, le);
+                            const startBase = dataView.getUint32(offset, true);
                             offset += 4;
-                            const endChrom = dataView.getUint32(offset, le);
+                            const endChrom = dataView.getUint32(offset, true);
                             offset += 4;
-                            const endBase = dataView.getUint32(offset, le);
+                            const endBase = dataView.getUint32(offset, true);
                             offset += 4;
-                            const blockOffset = Number(dataView.getBigUint64(offset, le));
+                            const blockOffset = Number(dataView.getBigUint64(offset, true));
                             offset += 8;
                             recurOffsets.push({
                                 startChrom,
@@ -142,7 +135,7 @@ export class BlockView {
                 try {
                     const length = fr.max - fr.min;
                     const offset = fr.min;
-                    const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts === null || opts === void 0 ? void 0 : opts.signal);
+                    const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts?.signal);
                     for (const element of off) {
                         if (fr.contains(element)) {
                             cirFobRecur2(resultBuffer, element - offset, level);
@@ -237,19 +230,17 @@ export class BlockView {
         return features;
     }
     parseBigBedBlock(data, startOffset, offset, request) {
-        var _a;
         const items = [];
         let currOffset = startOffset;
-        const le = true;
         const b = data;
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
         while (currOffset < data.byteLength) {
             const c2 = currOffset;
-            const chromId = dataView.getUint32(currOffset, le);
+            const chromId = dataView.getUint32(currOffset, true);
             currOffset += 4;
-            const start = dataView.getInt32(currOffset, le);
+            const start = dataView.getInt32(currOffset, true);
             currOffset += 4;
-            const end = dataView.getInt32(currOffset, le);
+            const end = dataView.getInt32(currOffset, true);
             currOffset += 4;
             let i = currOffset;
             for (; i < data.length; i++) {
@@ -258,7 +249,7 @@ export class BlockView {
                 }
             }
             const b = data.subarray(currOffset, i);
-            const rest = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
+            const rest = decoder?.decode(b) ?? b.toString();
             currOffset = i + 1;
             items.push({
                 chromId,
@@ -349,24 +340,22 @@ export class BlockView {
                 const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
                 for (const block of blockGroup.blocks) {
                     checkAbortSignal(signal);
-                    let blockOffset = Number(block.offset) - Number(blockGroup.offset);
-                    let resultData = data;
+                    let resultData = data.subarray(Number(block.offset) - Number(blockGroup.offset));
                     if (isCompressed) {
-                        resultData = unzip(data.subarray(blockOffset));
-                        blockOffset = 0;
+                        resultData = unzip(resultData);
                     }
                     checkAbortSignal(signal);
                     switch (blockType) {
                         case 'summary': {
-                            observer.next(this.parseSummaryBlock(resultData, blockOffset, request));
+                            observer.next(this.parseSummaryBlock(resultData, 0, request));
                             break;
                         }
                         case 'bigwig': {
-                            observer.next(this.parseBigWigBlock(resultData, blockOffset, request));
+                            observer.next(this.parseBigWigBlock(resultData, 0, request));
                             break;
                         }
                         case 'bigbed': {
-                            observer.next(this.parseBigBedBlock(resultData, blockOffset, Number(block.offset) * (1 << 8), request));
+                            observer.next(this.parseBigBedBlock(resultData, 0, Number(block.offset) * (1 << 8), request));
                             break;
                         }
                         default: {

package/esm/block-view.js.map

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package/esm/unzip-pako.d.ts

@@ -1,2 +1 @@
-import { Buffer } from 'buffer';
-export declare function unzip(input: Buffer): Uint8Array;
+export declare function unzip(input: Uint8Array): Uint8Array;

package/esm/unzip-pako.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AAEjC,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,UAAU,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}
+{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AAEjC,MAAM,UAAU,KAAK,CAAC,KAAiB;IACrC,OAAO,UAAU,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "5.0.2",
+  "version": "6.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -25,8 +25,8 @@
     "format": "prettier",
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean",
-    "build:esm": "tsc --target es2018 --outDir esm --module es2020",
-    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "build:esm": "tsc --outDir esm",
+    "build:es5": "tsc --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "preversion": "npm run lint && npm test run && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
@@ -42,22 +42,20 @@
   ],
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "buffer": "^6.0.3",
-    "generic-filehandle": "^3.0.0",
+    "generic-filehandle2": "^0.0.1",
     "pako": "^2.0.0",
     "quick-lru": "^4.0.0",
     "rxjs": "^7.8.0"
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
-    "@types/jest": "^29.5.12",
     "@types/node": "^20.11.16",
     "@types/pako": "^2.0.0",
     "@typescript-eslint/eslint-plugin": "^8.4.0",
     "@typescript-eslint/parser": "^8.4.0",
     "@vitest/coverage-v8": "^2.0.5",
     "eslint": "^9.9.1",
-    "eslint-plugin-unicorn": "^55.0.0",
+    "eslint-plugin-unicorn": "^56.0.0",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",

package/src/bbi.ts

@@ -1,5 +1,4 @@
-import { Buffer } from 'buffer'
-import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
+import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle2'
 import { firstValueFrom, Observable } from 'rxjs'
 import { toArray } from 'rxjs/operators'
 import { BlockView } from './block-view'
@@ -7,7 +6,7 @@ import { BlockView } from './block-view'
 const BIG_WIG_MAGIC = -2003829722
 const BIG_BED_MAGIC = -2021002517
 
-interface ZoomLevel {
+export interface ZoomLevel {
   reductionLevel: number
   reserved: number
   dataOffset: number
@@ -27,7 +26,7 @@ export interface Feature {
   uniqueId?: string // for bigbed contains uniqueId calculated from file offset
   field?: number // used in bigbed searching
 }
-interface Statistics {
+export interface Statistics {
   scoreSum: number
   basesCovered: number
   scoreSumSquares: number
@@ -35,7 +34,7 @@ interface Statistics {
   scoreMax: number
 }
 
-interface RefInfo {
+export interface RefInfo {
   name: string
   id: number
   length: number
@@ -57,7 +56,6 @@ export interface MainHeader {
   uncompressBufSize: number
   chromTreeOffset: number
   extHeaderOffset: number
-  isBigEndian: boolean
   fileType: string
 }
 export interface Header extends MainHeader {
@@ -71,6 +69,11 @@ export interface RequestOptions {
   [key: string]: unknown
 }
 
+export interface RequestOptions2 extends RequestOptions {
+  scale?: number
+  basesPerSpan?: number
+}
+
 export abstract class BBI {
   protected bbi: GenericFilehandle
 
@@ -89,8 +92,7 @@ export abstract class BBI {
   }
 
   /*
-   * @param filehandle - a filehandle from generic-filehandle or implementing
-   * something similar to the node10 fs.promises API
+   * @param filehandle - a filehandle from generic-filehandle2
    *
    * @param path - a Local file path as a string
    *
@@ -121,58 +123,57 @@ export abstract class BBI {
   private async _getHeader(opts?: RequestOptions) {
     const header = await this._getMainHeader(opts)
     const chroms = await this._readChromTree(header, opts)
-    return { ...header, ...chroms }
+    return {
+      ...header,
+      ...chroms,
+    }
   }
 
   private async _getMainHeader(
     opts?: RequestOptions,
     requestSize = 2000,
   ): Promise<MainHeader> {
-    const le = true
-    const { buffer } = await this.bbi.read(
-      Buffer.alloc(requestSize),
-      0,
-      requestSize,
-      0,
-      opts,
-    )
-    const isBigEndian = this._isBigEndian(buffer)
-    const b = buffer
+    const b = await this.bbi.read(requestSize, 0, opts)
     const dataView = new DataView(b.buffer, b.byteOffset, b.length)
+
+    const r1 = dataView.getInt32(0, true)
+    if (r1 !== BIG_WIG_MAGIC && r1 !== BIG_BED_MAGIC) {
+      throw new Error('not a BigWig/BigBed file')
+    }
     let offset = 0
-    const magic = dataView.getInt32(offset, le)
+    const magic = dataView.getInt32(offset, true)
     offset += 4
-    const version = dataView.getUint16(offset, le)
+    const version = dataView.getUint16(offset, true)
     offset += 2
-    const numZoomLevels = dataView.getUint16(offset, le)
+    const numZoomLevels = dataView.getUint16(offset, true)
     offset += 2
-    const chromTreeOffset = Number(dataView.getBigUint64(offset, le))
+    const chromTreeOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
-    const unzoomedDataOffset = Number(dataView.getBigUint64(offset, le))
+    const unzoomedDataOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
-    const unzoomedIndexOffset = Number(dataView.getBigUint64(offset, le))
+    const unzoomedIndexOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
-    const fieldCount = dataView.getUint16(offset, le)
+    const fieldCount = dataView.getUint16(offset, true)
     offset += 2
-    const definedFieldCount = dataView.getUint16(offset, le)
+    const definedFieldCount = dataView.getUint16(offset, true)
     offset += 2
-    const asOffset = Number(dataView.getBigUint64(offset, le))
+    const asOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
-    const totalSummaryOffset = Number(dataView.getBigUint64(offset, le))
+    const totalSummaryOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
-    const uncompressBufSize = dataView.getUint32(offset, le)
+    const uncompressBufSize = dataView.getUint32(offset, true)
     offset += 4
-    const extHeaderOffset = Number(dataView.getBigUint64(offset, le))
+    const extHeaderOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
     const zoomLevels = [] as ZoomLevel[]
     for (let i = 0; i < numZoomLevels; i++) {
-      const reductionLevel = dataView.getUint32(offset, le)
+      const reductionLevel = dataView.getUint32(offset, true)
       offset += 4
-      const reserved = dataView.getUint32(offset, le)
+      const reserved = dataView.getUint32(offset, true)
       offset += 4
-      const dataOffset = Number(dataView.getBigUint64(offset, le))
+      const dataOffset = Number(dataView.getBigUint64(offset, true))
       offset += 8
-      const indexOffset = Number(dataView.getBigUint64(offset, le))
+      const indexOffset = Number(dataView.getBigUint64(offset, true))
       offset += 8
       zoomLevels.push({ reductionLevel, reserved, dataOffset, indexOffset })
     }
@@ -187,18 +188,18 @@ export abstract class BBI {
 
     let totalSummary: Statistics
     if (totalSummaryOffset) {
-      const b = buffer.subarray(Number(totalSummaryOffset))
+      const b2 = b.subarray(Number(totalSummaryOffset))
       let offset = 0
-      const dataView = new DataView(b.buffer, b.byteOffset, b.length)
-      const basesCovered = Number(dataView.getBigUint64(offset, le))
+      const dataView = new DataView(b2.buffer, b2.byteOffset, b2.length)
+      const basesCovered = Number(dataView.getBigUint64(offset, true))
       offset += 8
-      const scoreMin = dataView.getFloat64(offset, le)
+      const scoreMin = dataView.getFloat64(offset, true)
       offset += 8
-      const scoreMax = dataView.getFloat64(offset, le)
+      const scoreMax = dataView.getFloat64(offset, true)
       offset += 8
-      const scoreSum = dataView.getFloat64(offset, le)
+      const scoreSum = dataView.getFloat64(offset, true)
       offset += 8
-      const scoreSumSquares = dataView.getFloat64(offset, le)
+      const scoreSumSquares = dataView.getFloat64(offset, true)
       offset += 8
 
       totalSummary = {
@@ -211,6 +212,7 @@ export abstract class BBI {
     } else {
       throw new Error('no stats')
     }
+    const decoder = new TextDecoder('utf8')
 
     return {
       zoomLevels,
@@ -228,36 +230,17 @@ export abstract class BBI {
       unzoomedIndexOffset,
       fileType,
       version,
-      isBigEndian,
       autoSql: asOffset
-        ? buffer.subarray(asOffset, buffer.indexOf(0, asOffset)).toString()
+        ? decoder.decode(b.subarray(asOffset, b.indexOf(0, asOffset)))
         : '',
     }
   }
 
-  private _isBigEndian(buffer: Buffer) {
-    let ret = buffer.readInt32LE(0)
-    if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
-      return false
-    }
-    ret = buffer.readInt32BE(0)
-    if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
-      return true
-    }
-    throw new Error('not a BigWig/BigBed file')
-  }
-
-  // todo: add progress if long running
   private async _readChromTree(
     header: MainHeader,
     opts?: { signal?: AbortSignal },
   ) {
-    const isBE = header.isBigEndian
-    const le = !isBE
-    const refsByNumber: Record<
-      number,
-      { name: string; id: number; length: number }
-    > = []
+    const refsByNumber: Record<number, RefInfo> = []
     const refsByName: Record<string, number> = {}
 
     let unzoomedDataOffset = header.unzoomedDataOffset
@@ -266,60 +249,56 @@ export abstract class BBI {
       unzoomedDataOffset += 1
     }
     const off = unzoomedDataOffset - chromTreeOffset
-    const { buffer } = await this.bbi.read(
-      Buffer.alloc(off),
-      0,
-      off,
-      Number(chromTreeOffset),
-      opts,
-    )
+    const b = await this.bbi.read(off, Number(chromTreeOffset), opts)
 
-    const b = buffer
     const dataView = new DataView(b.buffer, b.byteOffset, b.length)
     let offset = 0
-    //    const magic = dataView.getUint32(offset, le)
+    //    const magic = dataView.getUint32(offset, true)
     offset += 4
-    //   const blockSize = dataView.getUint32(offset, le)
+    //   const blockSize = dataView.getUint32(offset, true)
     offset += 4
-    const keySize = dataView.getUint32(offset, le)
+    const keySize = dataView.getUint32(offset, true)
     offset += 4
-    //  const valSize = dataView.getUint32(offset, le)
+    //  const valSize = dataView.getUint32(offset, true)
     offset += 4
-    // const itemCount = dataView.getBigUint64(offset, le)
+    // const itemCount = dataView.getBigUint64(offset, true)
     offset += 8
 
     const rootNodeOffset = 32
+    const decoder = new TextDecoder('utf8')
     const bptReadNode = async (currentOffset: number) => {
       let offset = currentOffset
-      if (offset >= buffer.length) {
+      if (offset >= b.length) {
         throw new Error('reading beyond end of buffer')
       }
       const isLeafNode = dataView.getUint8(offset)
       offset += 2 //skip 1
-      const cnt = dataView.getUint16(offset, le)
+      const cnt = dataView.getUint16(offset, true)
       offset += 2
       if (isLeafNode) {
         for (let n = 0; n < cnt; n++) {
-          const key = buffer
-            .subarray(offset, offset + keySize)
-            .toString()
+          const key = decoder
+            .decode(b.subarray(offset, offset + keySize))
             .replaceAll('\0', '')
           offset += keySize
-          const refId = dataView.getUint32(offset, le)
+          const refId = dataView.getUint32(offset, true)
           offset += 4
-          const refSize = dataView.getUint32(offset, le)
+          const refSize = dataView.getUint32(offset, true)
           offset += 4
 
-          const refRec = { name: key, id: refId, length: refSize }
           refsByName[this.renameRefSeqs(key)] = refId
-          refsByNumber[refId] = refRec
+          refsByNumber[refId] = {
+            name: key,
+            id: refId,
+            length: refSize,
+          }
         }
       } else {
         // parse index node
         const nextNodes = []
         for (let n = 0; n < cnt; n++) {
           offset += keySize
-          const childOffset = Number(dataView.getBigUint64(offset, le))
+          const childOffset = Number(dataView.getBigUint64(offset, true))
           offset += 8
           nextNodes.push(
             bptReadNode(Number(childOffset) - Number(chromTreeOffset)),
@@ -340,18 +319,12 @@ export abstract class BBI {
    * @param abortSignal - a signal to optionally abort this operation
    */
   protected async getUnzoomedView(opts?: RequestOptions) {
-    const {
-      unzoomedIndexOffset,
-      refsByName,
-      uncompressBufSize,
-      isBigEndian,
-      fileType,
-    } = await this.getHeader(opts)
+    const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } =
+      await this.getHeader(opts)
     return new BlockView(
       this.bbi,
       refsByName,
       unzoomedIndexOffset,
-      isBigEndian,
       uncompressBufSize > 0,
       fileType,
     )
@@ -369,15 +342,19 @@ export abstract class BBI {
    * Gets features from a BigWig file
    *
    * @param refName - The chromosome name
+   *
    * @param start - The start of a region
+   *
    * @param end - The end of a region
-   * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+   *
+   * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+   * or scale used to infer the zoomLevel to use
    */
   public async getFeatureStream(
     refName: string,
     start: number,
     end: number,
-    opts?: RequestOptions & { scale?: number; basesPerSpan?: number },
+    opts?: RequestOptions2,
   ) {
     await this.getHeader(opts)
     const chrName = this.renameRefSeqs(refName)
@@ -405,7 +382,7 @@ export abstract class BBI {
     refName: string,
     start: number,
     end: number,
-    opts?: RequestOptions & { scale?: number; basesPerSpan?: number },
+    opts?: RequestOptions2,
   ) {
     const ob = await this.getFeatureStream(refName, start, end, opts)