@gmod/bbi 4.0.5 → 5.0.0

package/esm/unzip.d.ts

@@ -1,2 +1 @@
-/// <reference types="node" />
 export { inflateSync as unzip } from 'zlib';

package/esm/util.d.ts

@@ -2,22 +2,19 @@ export declare class AbortError extends Error {
     code: string;
     constructor(message: string);
 }
-export declare function groupBlocks(blocks: {
-    offset: bigint;
-    length: bigint;
-}[]): {
-    blocks: {
-        offset: bigint;
-        length: bigint;
-    }[];
-    length: bigint;
-    offset: bigint;
+interface Block {
+    offset: number;
+    length: number;
+}
+export declare function groupBlocks(blocks: Block[]): {
+    blocks: Block[];
+    length: number;
+    offset: number;
 }[];
 /**
- * Properly check if the given AbortSignal is aborted.
- * Per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
+ * Properly check if the given AbortSignal is aborted. Per the standard, if the
+ * signal reads as aborted, this function throws either a DOMException
+ * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
  *
  * For convenience, passing `undefined` is a no-op
  *
@@ -32,3 +29,4 @@ export declare function checkAbortSignal(signal?: AbortSignal): void;
  * @param {AbortSignal} signal
  */
 export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
+export {};

package/esm/util.js

@@ -7,18 +7,14 @@ export class AbortError extends Error {
 // sort blocks by file offset and
 // group blocks that are within 2KB of eachother
 export function groupBlocks(blocks) {
-    blocks.sort((b0, b1) => Number(b0.offset) - Number(b1.offset));
+    blocks.sort((b0, b1) => b0.offset - b1.offset);
     const blockGroups = [];
     let lastBlock;
     let lastBlockEnd;
     for (const block of blocks) {
-        if (lastBlock &&
-            lastBlockEnd &&
-            Number(block.offset) - lastBlockEnd <= 2000) {
-            lastBlock.length = BigInt(Number(lastBlock.length) +
-                Number(block.length) -
-                lastBlockEnd +
-                Number(block.offset));
+        if (lastBlock && lastBlockEnd && block.offset - lastBlockEnd <= 2000) {
+            lastBlock.length =
+                lastBlock.length + block.length - lastBlockEnd + block.offset;
             lastBlock.blocks.push(block);
         }
         else {
@@ -28,15 +24,14 @@ export function groupBlocks(blocks) {
                 offset: block.offset,
             }));
         }
-        lastBlockEnd = Number(lastBlock.offset) + Number(lastBlock.length);
+        lastBlockEnd = lastBlock.offset + lastBlock.length;
     }
     return blockGroups;
 }
 /**
- * Properly check if the given AbortSignal is aborted.
- * Per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
+ * Properly check if the given AbortSignal is aborted. Per the standard, if the
+ * signal reads as aborted, this function throws either a DOMException
+ * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
  *
  * For convenience, passing `undefined` is a no-op
  *
@@ -48,7 +43,6 @@ export function checkAbortSignal(signal) {
         return;
     }
     if (signal.aborted) {
-        // console.log('bam aborted!')
         if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';

package/esm/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,UAAW,SAAQ,KAAK;IAGnC,YAAmB,OAAe;QAChC,KAAK,CAAC,OAAO,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,GAAG,aAAa,CAAA;IAC3B,CAAC;CACF;AAMD,iCAAiC;AACjC,gDAAgD;AAChD,MAAM,UAAU,WAAW,CAAC,MAAe;IACzC,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,CAAA;IAE9C,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,IAAI,SAAoD,CAAA;IACxD,IAAI,YAAgC,CAAA;IACpC,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,SAAS,IAAI,YAAY,IAAI,KAAK,CAAC,MAAM,GAAG,YAAY,IAAI,IAAI,EAAE,CAAC;YACrE,SAAS,CAAC,MAAM;gBACd,SAAS,CAAC,MAAM,GAAG,KAAK,CAAC,MAAM,GAAG,YAAY,GAAG,KAAK,CAAC,MAAM,CAAA;YAC/D,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC9B,CAAC;aAAM,CAAC;YACN,WAAW,CAAC,IAAI,CACd,CAAC,SAAS,GAAG;gBACX,MAAM,EAAE,CAAC,KAAK,CAAC;gBACf,MAAM,EAAE,KAAK,CAAC,MAAM;gBACpB,MAAM,EAAE,KAAK,CAAC,MAAM;aACrB,CAAC,CACH,CAAA;QACH,CAAC;QACD,YAAY,GAAG,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACpD,CAAC;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "4.0.5",
+  "version": "5.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -42,8 +42,7 @@
     "genomics"
   ],
   "dependencies": {
-    "abortable-promise-cache": "^1.4.1",
-    "binary-parser": "^2.1.0",
+    "@gmod/abortable-promise-cache": "^2.0.0",
     "generic-filehandle": "^3.0.0",
     "pako": "^2.0.0",
     "quick-lru": "^4.0.0",
@@ -54,16 +53,16 @@
     "@types/jest": "^29.5.12",
     "@types/node": "^20.11.16",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^7.3.1",
-    "@typescript-eslint/parser": "^7.3.1",
+    "@typescript-eslint/eslint-plugin": "^8.0.1",
+    "@typescript-eslint/parser": "^8.0.1",
     "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^54.0.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "jest": "^29.6.2",
     "jest-environment-jsdom": "^29.6.2",
     "prettier": "^3.2.5",
-    "rimraf": "^5.0.1",
+    "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",
     "ts-jest": "^29.1.2",
     "typescript": "^5.1.6"

package/src/bbi.ts

@@ -1,5 +1,4 @@
 import { Buffer } from 'buffer'
-import { Parser } from 'binary-parser'
 import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
 import { firstValueFrom, Observable } from 'rxjs'
 import { toArray } from 'rxjs/operators'
@@ -8,14 +7,22 @@ import { BlockView } from './block-view'
 const BIG_WIG_MAGIC = -2003829722
 const BIG_BED_MAGIC = -2021002517
 
-function toString(arr: Uint8Array) {
+function myToString(arr: Uint8Array) {
   return new TextDecoder().decode(arr)
 }
+interface ZoomLevel {
+  reductionLevel: number
+  reserved: number
+  dataOffset: number
+  indexOffset: number
+}
 
 export interface Feature {
+  offset?: number
+  chromId: number
   start: number
   end: number
-  score: number
+  score?: number
   rest?: string // for bigbed line
   minScore?: number // for summary line
   maxScore?: number // for summary line
@@ -27,6 +34,8 @@ interface Statistics {
   scoreSum: number
   basesCovered: number
   scoreSumSquares: number
+  scoreMin: number
+  scoreMax: number
 }
 
 interface RefInfo {
@@ -34,87 +43,31 @@ interface RefInfo {
   id: number
   length: number
 }
-export interface Header {
+
+export interface MainHeader {
+  magic: number
   version: number
   autoSql: string
   totalSummary: Statistics
-  zoomLevels: any
+  asOffset: number
+  zoomLevels: ZoomLevel[]
+  fieldCount: number
+  numZoomLevels: number
   unzoomedIndexOffset: number
+  totalSummaryOffset: number
   unzoomedDataOffset: number
   definedFieldCount: number
   uncompressBufSize: number
   chromTreeOffset: number
-  fileSize: number
   extHeaderOffset: number
   isBigEndian: boolean
   fileType: string
+}
+export interface Header extends MainHeader {
   refsByName: Record<string, number>
   refsByNumber: Record<number, RefInfo>
 }
 
-/**
- * get the compiled parsers for different sections of the bigwig file
- *
- * @param isBE - is big endian, typically false
- * @return an object with compiled parsers
- */
-function getParsers(isBE: boolean) {
-  const le = isBE ? 'big' : 'little'
-  const headerParser = new Parser()
-    .endianess(le)
-    .int32('magic')
-    .uint16('version')
-    .uint16('numZoomLevels')
-    .uint64('chromTreeOffset')
-    .uint64('unzoomedDataOffset')
-    .uint64('unzoomedIndexOffset')
-    .uint16('fieldCount')
-    .uint16('definedFieldCount')
-    .uint64('asOffset') // autoSql offset, used in bigbed
-    .uint64('totalSummaryOffset')
-    .uint32('uncompressBufSize')
-    .uint64('extHeaderOffset') // name index offset, used in bigbed
-    .array('zoomLevels', {
-      length: 'numZoomLevels',
-      type: new Parser()
-        .endianess(le)
-        .uint32('reductionLevel')
-        .uint32('reserved')
-        .uint64('dataOffset')
-        .uint64('indexOffset'),
-    })
-
-  const totalSummaryParser = new Parser()
-    .endianess(le)
-    .uint64('basesCovered')
-    .doublele('scoreMin')
-    .doublele('scoreMax')
-    .doublele('scoreSum')
-    .doublele('scoreSumSquares')
-
-  const chromTreeParser = new Parser()
-    .endianess(le)
-    .uint32('magic')
-    .uint32('blockSize')
-    .uint32('keySize')
-    .uint32('valSize')
-    .uint64('itemCount')
-
-  const isLeafNode = new Parser()
-    .endianess(le)
-    .uint8('isLeafNode')
-    .skip(1)
-    .uint16('cnt')
-    .saveOffset('offset')
-
-  return {
-    chromTreeParser,
-    totalSummaryParser,
-    headerParser,
-    isLeafNode,
-  }
-}
-
 export interface RequestOptions {
   signal?: AbortSignal
   headers?: Record<string, string>
@@ -139,7 +92,8 @@ 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-filehandle or implementing
+   * something similar to the node10 fs.promises API
    *
    * @param path - a Local file path as a string
    *
@@ -176,7 +130,8 @@ export abstract class BBI {
   private async _getMainHeader(
     opts?: RequestOptions,
     requestSize = 2000,
-  ): Promise<Header> {
+  ): Promise<MainHeader> {
+    const le = true
     const { buffer } = await this.bbi.read(
       Buffer.alloc(requestSize),
       0,
@@ -185,30 +140,102 @@ export abstract class BBI {
       opts,
     )
     const isBigEndian = this._isBigEndian(buffer)
-    const ret = getParsers(isBigEndian)
-    const header = ret.headerParser.parse(buffer)
-    const { magic, asOffset, totalSummaryOffset } = header
-    header.fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig'
-    if (asOffset > requestSize || totalSummaryOffset > requestSize) {
-      return this._getMainHeader(opts, requestSize * 2)
-    }
-    if (asOffset) {
-      const off = Number(header.asOffset)
-      header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)))
+    const b = buffer
+    const dataView = new DataView(b.buffer, b.byteOffset, b.length)
+    let offset = 0
+    const magic = dataView.getInt32(offset, le)
+    offset += 4
+    const version = dataView.getUint16(offset, le)
+    offset += 2
+    const numZoomLevels = dataView.getUint16(offset, le)
+    offset += 2
+    const chromTreeOffset = Number(dataView.getBigUint64(offset, le))
+    offset += 8
+    const unzoomedDataOffset = Number(dataView.getBigUint64(offset, le))
+    offset += 8
+    const unzoomedIndexOffset = Number(dataView.getBigUint64(offset, le))
+    offset += 8
+    const fieldCount = dataView.getUint16(offset, le)
+    offset += 2
+    const definedFieldCount = dataView.getUint16(offset, le)
+    offset += 2
+    const asOffset = Number(dataView.getBigUint64(offset, le))
+    offset += 8
+    const totalSummaryOffset = Number(dataView.getBigUint64(offset, le))
+    offset += 8
+    const uncompressBufSize = dataView.getUint32(offset, le)
+    offset += 4
+    const extHeaderOffset = Number(dataView.getBigUint64(offset, le))
+    offset += 8
+    const zoomLevels = [] as ZoomLevel[]
+    for (let i = 0; i < numZoomLevels; i++) {
+      const reductionLevel = dataView.getUint32(offset, le)
+      offset += 4
+      const reserved = dataView.getUint32(offset, le)
+      offset += 4
+      const dataOffset = Number(dataView.getBigUint64(offset, le))
+      offset += 8
+      const indexOffset = Number(dataView.getBigUint64(offset, le))
+      offset += 8
+      zoomLevels.push({ reductionLevel, reserved, dataOffset, indexOffset })
     }
 
+    const fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig'
+
     // refetch header if it is too large on first pass,
     // 8*5 is the sizeof the totalSummary struct
-    if (header.totalSummaryOffset > requestSize - 8 * 5) {
+    if (asOffset > requestSize || totalSummaryOffset > requestSize - 8 * 5) {
       return this._getMainHeader(opts, requestSize * 2)
     }
 
-    if (header.totalSummaryOffset) {
-      const tail = buffer.subarray(Number(header.totalSummaryOffset))
-      const sum = ret.totalSummaryParser.parse(tail)
-      header.totalSummary = { ...sum, basesCovered: Number(sum.basesCovered) }
+    let totalSummary: Statistics
+    if (totalSummaryOffset) {
+      const b = buffer.subarray(Number(totalSummaryOffset))
+      let offset = 0
+      const dataView = new DataView(b.buffer, b.byteOffset, b.length)
+      const basesCovered = Number(dataView.getBigUint64(offset, le))
+      offset += 8
+      const scoreMin = dataView.getFloat64(offset, le)
+      offset += 8
+      const scoreMax = dataView.getFloat64(offset, le)
+      offset += 8
+      const scoreSum = dataView.getFloat64(offset, le)
+      offset += 8
+      const scoreSumSquares = dataView.getFloat64(offset, le)
+      offset += 8
+
+      totalSummary = {
+        scoreMin,
+        scoreMax,
+        scoreSum,
+        scoreSumSquares,
+        basesCovered,
+      }
+    } else {
+      throw new Error('no stats')
+    }
+
+    return {
+      zoomLevels,
+      magic,
+      extHeaderOffset,
+      numZoomLevels,
+      fieldCount,
+      totalSummary,
+      definedFieldCount,
+      uncompressBufSize,
+      asOffset,
+      chromTreeOffset,
+      totalSummaryOffset,
+      unzoomedDataOffset,
+      unzoomedIndexOffset,
+      fileType,
+      version,
+      isBigEndian,
+      autoSql: asOffset
+        ? myToString(buffer.subarray(asOffset, buffer.indexOf(0, asOffset)))
+        : '',
     }
-    return { ...header, isBigEndian }
   }
 
   private _isBigEndian(buffer: Buffer) {
@@ -225,19 +252,19 @@ export abstract class BBI {
 
   // todo: add progress if long running
   private async _readChromTree(
-    header: Header,
+    header: MainHeader,
     opts?: { signal?: AbortSignal },
   ) {
     const isBE = header.isBigEndian
-    const le = isBE ? 'big' : 'little'
+    const le = !isBE
     const refsByNumber: Record<
       number,
       { name: string; id: number; length: number }
     > = []
     const refsByName: Record<string, number> = {}
 
-    let unzoomedDataOffset = Number(header.unzoomedDataOffset)
-    const chromTreeOffset = Number(header.chromTreeOffset)
+    let unzoomedDataOffset = header.unzoomedDataOffset
+    const chromTreeOffset = header.chromTreeOffset
     while (unzoomedDataOffset % 4 !== 0) {
       unzoomedDataOffset += 1
     }
@@ -250,33 +277,42 @@ export abstract class BBI {
       opts,
     )
 
-    const p = getParsers(isBE)
-    const { keySize } = p.chromTreeParser.parse(buffer)
-    const leafNodeParser = new Parser()
-      .endianess(le)
-      .string('key', { stripNull: true, length: keySize })
-      .uint32('refId')
-      .uint32('refSize')
-      .saveOffset('offset')
-    const nonleafNodeParser = new Parser()
-      .endianess(le)
-      .skip(keySize)
-      .uint64('childOffset')
-      .saveOffset('offset')
+    const b = buffer
+    const dataView = new DataView(b.buffer, b.byteOffset, b.length)
+    let offset = 0
+    //    const magic = dataView.getUint32(offset, le)
+    offset += 4
+    //   const blockSize = dataView.getUint32(offset, le)
+    offset += 4
+    const keySize = dataView.getUint32(offset, le)
+    offset += 4
+    //  const valSize = dataView.getUint32(offset, le)
+    offset += 4
+    // const itemCount = dataView.getBigUint64(offset, le)
+    offset += 8
+
     const rootNodeOffset = 32
     const bptReadNode = async (currentOffset: number) => {
       let offset = currentOffset
       if (offset >= buffer.length) {
         throw new Error('reading beyond end of buffer')
       }
-      const ret = p.isLeafNode.parse(buffer.subarray(offset))
-      const { isLeafNode, cnt } = ret
-      offset += ret.offset
+      const isLeafNode = dataView.getUint8(offset)
+      offset += 2 //skip 1
+      const cnt = dataView.getUint16(offset, le)
+      offset += 2
       if (isLeafNode) {
-        for (let n = 0; n < cnt; n += 1) {
-          const leafRet = leafNodeParser.parse(buffer.subarray(offset))
-          offset += leafRet.offset
-          const { key, refId, refSize } = leafRet
+        for (let n = 0; n < cnt; n++) {
+          const key = buffer
+            .subarray(offset, offset + keySize)
+            .toString()
+            .replaceAll('\0', '')
+          offset += keySize
+          const refId = dataView.getUint32(offset, le)
+          offset += 4
+          const refSize = dataView.getUint32(offset, le)
+          offset += 4
+
           const refRec = { name: key, id: refId, length: refSize }
           refsByName[this.renameRefSeqs(key)] = refId
           refsByNumber[refId] = refRec
@@ -284,10 +320,10 @@ export abstract class BBI {
       } else {
         // parse index node
         const nextNodes = []
-        for (let n = 0; n < cnt; n += 1) {
-          const nonleafRet = nonleafNodeParser.parse(buffer.subarray(offset))
-          const { childOffset } = nonleafRet
-          offset += nonleafRet.offset
+        for (let n = 0; n < cnt; n++) {
+          offset += keySize
+          const childOffset = Number(dataView.getBigUint64(offset, le))
+          offset += 8
           nextNodes.push(
             bptReadNode(Number(childOffset) - Number(chromTreeOffset)),
           )