@gmod/bbi 3.0.1 → 4.0.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "3.0.1",
+  "version": "4.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -43,6 +43,7 @@
   "dependencies": {
     "abortable-promise-cache": "^1.4.1",
     "binary-parser": "^2.1.0",
+    "eslint-plugin-unicorn": "^46.0.0",
     "generic-filehandle": "^3.0.0",
     "pako": "^2.0.0",
     "quick-lru": "^4.0.0",
@@ -50,24 +51,23 @@
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
-    "@types/jest": "^29.2.4",
+    "@types/jest": "^29.5.0",
     "@types/long": "^5.0.0",
-    "@types/node": "^18.11.15",
+    "@types/node": "^18.15.7",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.46.1",
-    "@typescript-eslint/parser": "^5.46.1",
-    "cross-fetch": "^3.0.2",
-    "eslint": "^8.29.0",
-    "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-import": "^2.25.3",
+    "@typescript-eslint/eslint-plugin": "^5.56.0",
+    "@typescript-eslint/parser": "^5.56.0",
+    "eslint": "^8.36.0",
+    "eslint-config-prettier": "^8.8.0",
+    "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^29.3.1",
-    "jest-environment-jsdom": "^29.3.1",
-    "prettier": "^2.8.1",
-    "rimraf": "^3.0.2",
+    "jest": "^29.5.0",
+    "jest-environment-jsdom": "^29.5.0",
+    "prettier": "^2.8.7",
+    "rimraf": "^5.0.0",
     "standard-changelog": "^2.0.11",
-    "ts-jest": "^29.0.3",
-    "typescript": "^4.9.4"
+    "ts-jest": "^29.0.5",
+    "typescript": "^5.0.2"
   },
   "publishConfig": {
     "access": "public"

package/src/bbi.ts

@@ -1,9 +1,9 @@
 import { Buffer } from 'buffer'
 import { Parser } from 'binary-parser'
 import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
-import { firstValueFrom, Observable, Observer } from 'rxjs'
+import { firstValueFrom, Observable } from 'rxjs'
 import { toArray } from 'rxjs/operators'
-import { BlockView } from './blockView'
+import { BlockView } from './block-view'
 
 const BIG_WIG_MAGIC = -2003829722
 const BIG_BED_MAGIC = -2021002517
@@ -130,10 +130,9 @@ export abstract class BBI {
    * @param abortSignal - abort the operation, can be null
    * @return a Header object
    */
-  public getHeader(opts: RequestOptions | AbortSignal = {}) {
-    const options = 'aborted' in opts ? { signal: opts as AbortSignal } : opts
+  public getHeader(opts?: RequestOptions) {
     if (!this.headerP) {
-      this.headerP = this._getHeader(options).catch(e => {
+      this.headerP = this._getHeader(opts).catch(e => {
         this.headerP = undefined
         throw e
       })
@@ -147,15 +146,13 @@ export abstract class BBI {
    * @param url - a URL string
    * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
    */
-  public constructor(
-    options: {
-      filehandle?: GenericFilehandle
-      path?: string
-      url?: string
-      renameRefSeqs?: (a: string) => string
-    } = {},
-  ) {
-    const { filehandle, renameRefSeqs = s => s, path, url } = options
+  public constructor(args: {
+    filehandle?: GenericFilehandle
+    path?: string
+    url?: string
+    renameRefSeqs?: (a: string) => string
+  }) {
+    const { filehandle, renameRefSeqs = s => s, path, url } = args
     this.renameRefSeqs = renameRefSeqs
     if (filehandle) {
       this.bbi = filehandle
@@ -168,14 +165,14 @@ export abstract class BBI {
     }
   }
 
-  private async _getHeader(opts: RequestOptions) {
+  private async _getHeader(opts?: RequestOptions) {
     const header = await this._getMainHeader(opts)
     const chroms = await this._readChromTree(header, opts)
     return { ...header, ...chroms }
   }
 
   private async _getMainHeader(
-    opts: RequestOptions,
+    opts?: RequestOptions,
     requestSize = 2000,
   ): Promise<Header> {
     const { buffer } = await this.bbi.read(
@@ -208,7 +205,7 @@ export abstract class BBI {
     return { ...header, isBigEndian }
   }
 
-  private _isBigEndian(buffer: Buffer): boolean {
+  private _isBigEndian(buffer: Buffer) {
     let ret = buffer.readInt32LE(0)
     if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
       return false
@@ -221,7 +218,10 @@ export abstract class BBI {
   }
 
   // todo: add progress if long running
-  private async _readChromTree(header: Header, opts: { signal?: AbortSignal }) {
+  private async _readChromTree(
+    header: Header,
+    opts?: { signal?: AbortSignal },
+  ) {
     const isBE = header.isBigEndian
     const le = isBE ? 'big' : 'little'
     const refsByNumber: {
@@ -299,7 +299,7 @@ export abstract class BBI {
    * fetches the "unzoomed" view of the bigwig data. this is the default for bigbed
    * @param abortSignal - a signal to optionally abort this operation
    */
-  protected async getUnzoomedView(opts: RequestOptions): Promise<BlockView> {
+  protected async getUnzoomedView(opts?: RequestOptions) {
     const {
       unzoomedIndexOffset,
       refsByName,
@@ -322,7 +322,7 @@ export abstract class BBI {
    */
   protected abstract getView(
     scale: number,
-    opts: RequestOptions,
+    opts?: RequestOptions,
   ): Promise<BlockView>
 
   /**
@@ -337,26 +337,22 @@ export abstract class BBI {
     refName: string,
     start: number,
     end: number,
-    opts: RequestOptions & { scale?: number; basesPerSpan?: number } = {
-      scale: 1,
-    },
-  ): Promise<Observable<Feature[]>> {
+    opts?: RequestOptions & { scale?: number; basesPerSpan?: number },
+  ) {
     await this.getHeader(opts)
     const chrName = this.renameRefSeqs(refName)
     let view: BlockView
+    const { basesPerSpan, scale } = opts || {}
 
-    if (opts.basesPerSpan) {
-      view = await this.getView(1 / opts.basesPerSpan, opts)
-    } else if (opts.scale) {
-      view = await this.getView(opts.scale, opts)
+    if (basesPerSpan) {
+      view = await this.getView(1 / basesPerSpan, opts)
+    } else if (scale) {
+      view = await this.getView(scale, opts)
     } else {
       view = await this.getView(1, opts)
     }
 
-    if (!view) {
-      throw new Error('unable to get block view for data')
-    }
-    return new Observable((observer: Observer<Feature[]>): void => {
+    return new Observable<Feature[]>(observer => {
       view.readWigData(chrName, start, end, observer, opts)
     })
   }
@@ -365,9 +361,7 @@ export abstract class BBI {
     refName: string,
     start: number,
     end: number,
-    opts: RequestOptions & { scale?: number; basesPerSpan?: number } = {
-      scale: 1,
-    },
+    opts?: RequestOptions & { scale?: number; basesPerSpan?: number },
   ) {
     const ob = await this.getFeatureStream(refName, start, end, opts)
 

package/src/bigbed.ts

@@ -6,7 +6,6 @@ import AbortablePromiseCache from 'abortable-promise-cache'
 import QuickLRU from 'quick-lru'
 
 import { BBI, Feature, RequestOptions } from './bbi'
-import { BlockView } from './blockView'
 
 interface Loc {
   key: string
@@ -27,32 +26,21 @@ export function filterUndef<T>(ts: (T | undefined)[]): T[] {
 }
 
 export class BigBed extends BBI {
-  public readIndicesCache = new AbortablePromiseCache({
+  public readIndicesCache = new AbortablePromiseCache<RequestOptions, Index[]>({
     cache: new QuickLRU({ maxSize: 1 }),
-    fill: async (args: any, signal?: AbortSignal) => {
-      return this._readIndices({ ...args, signal })
-    },
+    fill: (args: RequestOptions, signal?: AbortSignal) =>
+      this._readIndices({ ...args, signal }),
   })
 
-  public readIndices(opts: AbortSignal | RequestOptions = {}) {
-    const options = 'aborted' in opts ? { signal: opts } : opts
-    return this.readIndicesCache.get(
-      JSON.stringify(options),
-      options,
-      options.signal,
-    )
+  public readIndices(opts: RequestOptions = {}) {
+    const { signal, ...rest } = opts
+    return this.readIndicesCache.get(JSON.stringify(rest), opts, signal)
   }
 
   /*
    * retrieve unzoomed view for any scale
-   * @param scale - unused
-   * @param abortSignal - an optional AbortSignal to kill operation
-   * @return promise for a BlockView
    */
-  protected async getView(
-    _scale: number,
-    opts: RequestOptions,
-  ): Promise<BlockView> {
+  protected async getView(_scale: number, opts?: RequestOptions) {
     return this.getUnzoomedView(opts)
   }
 
@@ -121,7 +109,7 @@ export class BigBed extends BBI {
   ): Promise<Loc[]> {
     const { isBigEndian } = await this.getHeader(opts)
     const indices = await this.readIndices(opts)
-    if (!indices.length) {
+    if (indices.length === 0) {
       return []
     }
     const locs = indices.map(async (index: any): Promise<Loc | undefined> => {
@@ -219,7 +207,7 @@ export class BigBed extends BBI {
    */
   public async searchExtraIndex(name: string, opts: RequestOptions = {}) {
     const blocks = await this.searchExtraIndexBlocks(name, opts)
-    if (!blocks.length) {
+    if (blocks.length === 0) {
       return []
     }
     const view = await this.getUnzoomedView(opts)
@@ -229,8 +217,8 @@ export class BigBed extends BBI {
       }).pipe(
         reduce((acc, curr) => acc.concat(curr)),
         map(x => {
-          for (let i = 0; i < x.length; i += 1) {
-            x[i].field = block.field
+          for (const element of x) {
+            element.field = block.field
           }
           return x
         }),

package/src/bigwig.ts

@@ -1,4 +1,4 @@
-import { BlockView } from './blockView'
+import { BlockView } from './block-view'
 import { BBI, RequestOptions } from './bbi'
 
 export class BigWig extends BBI {

package/src/{blockView.ts → block-view.ts}

@@ -29,9 +29,10 @@ interface DataBlock {
   sumData: number
   sumSqData: number
 }
+
 interface ReadData {
-  offset: number
-  length: number
+  offset: bigint | number
+  length: bigint | number
 }
 
 interface Options {
@@ -154,10 +155,10 @@ function getParsers(isBigEndian: boolean) {
 export class BlockView {
   private cirTreePromise?: Promise<{ bytesRead: number; buffer: Buffer }>
 
-  private featureCache = new AbortablePromiseCache({
+  private featureCache = new AbortablePromiseCache<ReadData, Buffer>({
     cache: new QuickLRU({ maxSize: 1000 }),
 
-    fill: async (requestData: ReadData, signal: AbortSignal) => {
+    fill: async (requestData, signal) => {
       const len = Number(requestData.length)
       const off = Number(requestData.offset)
       const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, off, {
@@ -193,7 +194,7 @@ export class BlockView {
     start: number,
     end: number,
     observer: Observer<Feature[]>,
-    opts: Options,
+    opts?: Options,
   ) {
     try {
       const { refsByName, bbi, cirTreeOffset, isBigEndian } = this
@@ -233,7 +234,7 @@ export class BlockView {
           if (p.blocksToFetch) {
             blocksToFetch = blocksToFetch.concat(
               p.blocksToFetch
-                .filter(filterFeats)
+                .filter(f => filterFeats(f))
                 .map((l: { blockOffset: bigint; blockSize: bigint }) => ({
                   offset: l.blockOffset,
                   length: l.blockSize,
@@ -242,7 +243,7 @@ export class BlockView {
           }
           if (p.recurOffsets) {
             const recurOffsets = p.recurOffsets
-              .filter(filterFeats)
+              .filter(f => filterFeats(f))
               .map(l => Number(l.blockOffset))
             if (recurOffsets.length > 0) {
               cirFobRecur(recurOffsets, level + 1)
@@ -272,11 +273,11 @@ export class BlockView {
           const resultBuffer: Buffer = await this.featureCache.get(
             `${length}_${offset}`,
             { length, offset },
-            opts.signal,
+            opts?.signal,
           )
-          for (let i = 0; i < off.length; i += 1) {
-            if (fr.contains(off[i])) {
-              cirFobRecur2(resultBuffer, off[i] - offset, level)
+          for (const element of off) {
+            if (fr.contains(element)) {
+              cirFobRecur2(resultBuffer, element - offset, level)
               outstanding -= 1
               if (outstanding === 0) {
                 this.readFeatures(observer, blocksToFetch, { ...opts, request })
@@ -291,7 +292,8 @@ export class BlockView {
         try {
           outstanding += offset.length
 
-          const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32 // Upper bound on size, based on a completely full leaf node.
+          // Upper bound on size, based on a completely full leaf node.
+          const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32
           let spans = new Range(offset[0], offset[0] + maxCirBlockSpan)
           for (let i = 1; i < offset.length; i += 1) {
             const blockSpan = new Range(offset[i], offset[i] + maxCirBlockSpan)
@@ -406,7 +408,7 @@ export class BlockView {
     offset += 2
     const items = new Array(itemCount)
     switch (blockType) {
-      case 1:
+      case 1: {
         for (let i = 0; i < itemCount; i++) {
           const start = dataView.getInt32(offset, true)
           offset += 4
@@ -417,7 +419,8 @@ export class BlockView {
           items[i] = { start, end, score }
         }
         break
-      case 2:
+      }
+      case 2: {
         for (let i = 0; i < itemCount; i++) {
           const start = dataView.getInt32(offset, true)
           offset += 4
@@ -426,7 +429,8 @@ export class BlockView {
           items[i] = { score, start, end: start + itemSpan }
         }
         break
-      case 3:
+      }
+      case 3: {
         for (let i = 0; i < itemCount; i++) {
           const score = dataView.getFloat32(offset, true)
           offset += 4
@@ -434,6 +438,7 @@ export class BlockView {
           items[i] = { score, start, end: start + itemSpan }
         }
         break
+      }
     }
 
     return request
@@ -462,7 +467,7 @@ export class BlockView {
             blockGroup,
             signal,
           )
-          blockGroup.blocks.forEach(block => {
+          for (const block of blockGroup.blocks) {
             checkAbortSignal(signal)
             let blockOffset = Number(block.offset) - Number(blockGroup.offset)
             let resultData = data
@@ -473,17 +478,19 @@ export class BlockView {
             checkAbortSignal(signal)
 
             switch (blockType) {
-              case 'summary':
+              case 'summary': {
                 observer.next(
                   this.parseSummaryBlock(resultData, blockOffset, request),
                 )
                 break
-              case 'bigwig':
+              }
+              case 'bigwig': {
                 observer.next(
                   this.parseBigWigBlock(resultData, blockOffset, request),
                 )
                 break
-              case 'bigbed':
+              }
+              case 'bigbed': {
                 observer.next(
                   this.parseBigBedBlock(
                     resultData,
@@ -493,10 +500,12 @@ export class BlockView {
                   ),
                 )
                 break
-              default:
+              }
+              default: {
                 console.warn(`Don't know what to do with ${blockType}`)
+              }
             }
-          })
+          }
         }),
       )
       observer.complete()

package/src/range.ts

@@ -69,7 +69,7 @@ export default class Range {
   }
 
   public intersection(arg: Range): Range {
-    // eslint-disable-next-line @typescript-eslint/no-this-alias
+    // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
     let s0 = this
     let s1 = arg
     const r0 = this.ranges()
@@ -109,8 +109,7 @@ export default class Range {
   public coverage(): number {
     let tot = 0
     const rl = this.ranges()
-    for (let ri = 0; ri < rl.length; ri += 1) {
-      const r = rl[ri]
+    for (const r of rl) {
       tot += r.max() - r.min() + 1
     }
     return tot
@@ -121,7 +120,7 @@ export default class Range {
     let b = tmpb
     if (arguments.length < 2) {
       b = a
-      // eslint-disable-next-line @typescript-eslint/no-this-alias
+      // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
       a = this
     }
 

package/src/unzip.ts

@@ -1,2 +1 @@
-import { inflateSync } from 'zlib'
-export { inflateSync as unzip }
+export { inflateSync as unzip } from 'zlib'

package/src/util.ts

@@ -15,25 +15,25 @@ export function groupBlocks(blocks: { offset: bigint; length: bigint }[]) {
   const blockGroups = []
   let lastBlock
   let lastBlockEnd
-  for (let i = 0; i < blocks.length; i += 1) {
+  for (const block of blocks) {
     if (
       lastBlock &&
       lastBlockEnd &&
-      Number(blocks[i].offset) - lastBlockEnd <= 2000
+      Number(block.offset) - lastBlockEnd <= 2000
     ) {
       lastBlock.length = BigInt(
         Number(lastBlock.length) +
-          Number(blocks[i].length) -
+          Number(block.length) -
           lastBlockEnd +
-          Number(blocks[i].offset),
+          Number(block.offset),
       )
-      lastBlock.blocks.push(blocks[i])
+      lastBlock.blocks.push(block)
     } else {
       blockGroups.push(
         (lastBlock = {
-          blocks: [blocks[i]],
-          length: blocks[i].length,
-          offset: blocks[i].offset,
+          blocks: [block],
+          length: block.length,
+          offset: block.offset,
         }),
       )
     }
@@ -61,12 +61,12 @@ export function checkAbortSignal(signal?: AbortSignal): void {
 
   if (signal.aborted) {
     // console.log('bam aborted!')
-    if (typeof DOMException !== 'undefined') {
-      throw new DOMException('aborted', 'AbortError')
-    } else {
+    if (typeof DOMException === 'undefined') {
       const e = new AbortError('aborted')
       e.code = 'ERR_ABORTED'
       throw e
+    } else {
+      throw new DOMException('aborted', 'AbortError')
     }
   }
 }

package/dist/blockView.js.map

@@ -1 +0,0 @@
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package/esm/blockView.js.map

@@ -1 +0,0 @@
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package/src/declare.d.ts

@@ -1,2 +0,0 @@
-declare module 'abortable-promise-cache'
-declare module '@gmod/bed'