@gmod/bbi 6.0.1 → 6.0.3

package/src/bbi.ts

@@ -1,83 +1,28 @@
-import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle2'
-import { firstValueFrom, Observable } from 'rxjs'
+import { LocalFile, RemoteFile } from 'generic-filehandle2'
+import { Observable, firstValueFrom } from 'rxjs'
 import { toArray } from 'rxjs/operators'
+
 import { BlockView } from './block-view'
 
+import type {
+  BigWigHeader,
+  BigWigHeaderWithRefNames,
+  Feature,
+  RefInfo,
+  RequestOptions2,
+  RequestOptions,
+  Statistics,
+  ZoomLevel,
+} from './types'
+import type { GenericFilehandle } from 'generic-filehandle2'
+
 const BIG_WIG_MAGIC = -2003829722
 const BIG_BED_MAGIC = -2021002517
 
-export interface ZoomLevel {
-  reductionLevel: number
-  reserved: number
-  dataOffset: number
-  indexOffset: number
-}
-
-export interface Feature {
-  offset?: number
-  chromId: number
-  start: number
-  end: number
-  score?: number
-  rest?: string // for bigbed line
-  minScore?: number // for summary line
-  maxScore?: number // for summary line
-  summary?: boolean // is summary line
-  uniqueId?: string // for bigbed contains uniqueId calculated from file offset
-  field?: number // used in bigbed searching
-}
-export interface Statistics {
-  scoreSum: number
-  basesCovered: number
-  scoreSumSquares: number
-  scoreMin: number
-  scoreMax: number
-}
-
-export interface RefInfo {
-  name: string
-  id: number
-  length: number
-}
-
-export interface MainHeader {
-  magic: number
-  version: number
-  autoSql: string
-  totalSummary: Statistics
-  asOffset: number
-  zoomLevels: ZoomLevel[]
-  fieldCount: number
-  numZoomLevels: number
-  unzoomedIndexOffset: number
-  totalSummaryOffset: number
-  unzoomedDataOffset: number
-  definedFieldCount: number
-  uncompressBufSize: number
-  chromTreeOffset: number
-  extHeaderOffset: number
-  fileType: string
-}
-export interface Header extends MainHeader {
-  refsByName: Record<string, number>
-  refsByNumber: Record<number, RefInfo>
-}
-
-export interface RequestOptions {
-  signal?: AbortSignal
-  headers?: Record<string, string>
-  [key: string]: unknown
-}
-
-export interface RequestOptions2 extends RequestOptions {
-  scale?: number
-  basesPerSpan?: number
-}
-
 export abstract class BBI {
   protected bbi: GenericFilehandle
 
-  private headerP?: Promise<Header>
+  private headerP?: Promise<BigWigHeaderWithRefNames>
 
   protected renameRefSeqs: (a: string) => string
 
@@ -132,7 +77,7 @@ export abstract class BBI {
   private async _getMainHeader(
     opts?: RequestOptions,
     requestSize = 2000,
-  ): Promise<MainHeader> {
+  ): Promise<BigWigHeader> {
     const b = await this.bbi.read(requestSize, 0, opts)
     const dataView = new DataView(b.buffer, b.byteOffset, b.length)
 
@@ -175,7 +120,12 @@ export abstract class BBI {
       offset += 8
       const indexOffset = Number(dataView.getBigUint64(offset, true))
       offset += 8
-      zoomLevels.push({ reductionLevel, reserved, dataOffset, indexOffset })
+      zoomLevels.push({
+        reductionLevel,
+        reserved,
+        dataOffset,
+        indexOffset,
+      })
     }
 
     const fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig'
@@ -237,7 +187,7 @@ export abstract class BBI {
   }
 
   private async _readChromTree(
-    header: MainHeader,
+    header: BigWigHeader,
     opts?: { signal?: AbortSignal },
   ) {
     const refsByNumber: Record<number, RefInfo> = []
@@ -253,14 +203,18 @@ export abstract class BBI {
 
     const dataView = new DataView(b.buffer, b.byteOffset, b.length)
     let offset = 0
+    // unused:
     //    const magic = dataView.getUint32(offset, true)
     offset += 4
+    // unused:
     //   const blockSize = dataView.getUint32(offset, true)
     offset += 4
     const keySize = dataView.getUint32(offset, true)
     offset += 4
+    // unused:
     //  const valSize = dataView.getUint32(offset, true)
     offset += 4
+    // unused:
     // const itemCount = dataView.getBigUint64(offset, true)
     offset += 8
 
@@ -273,6 +227,10 @@ export abstract class BBI {
       }
       const isLeafNode = dataView.getUint8(offset)
       offset += 2 //skip 1
+
+      if (offset >= b.length) {
+        return
+      }
       const cnt = dataView.getUint16(offset, true)
       offset += 2
       if (isLeafNode) {
@@ -294,7 +252,6 @@ export abstract class BBI {
           }
         }
       } else {
-        // parse index node
         const nextNodes = []
         for (let n = 0; n < cnt; n++) {
           offset += keySize

package/src/bigbed.ts

@@ -1,10 +1,11 @@
-import { Observable, merge, firstValueFrom } from 'rxjs'
-import { map, reduce } from 'rxjs/operators'
 import AbortablePromiseCache from '@gmod/abortable-promise-cache'
 import QuickLRU from 'quick-lru'
+import { Observable, firstValueFrom, merge } from 'rxjs'
+import { map, reduce } from 'rxjs/operators'
+
+import { BBI } from './bbi'
 
-// locals
-import { BBI, Feature, RequestOptions } from './bbi'
+import type { Feature, RequestOptions } from './types'
 
 interface Loc {
   key: string
@@ -109,7 +110,7 @@ export class BigBed extends BBI {
       return []
     }
     const decoder = new TextDecoder('utf8')
-    const locs = indices.map(async (index): Promise<Loc | undefined> => {
+    const locs = indices.map(async index => {
       const { offset: offset2, field } = index
       const b = await this.bbi.read(32, offset2, opts)
 
@@ -183,15 +184,17 @@ export class BigBed extends BBI {
 
           for (const n of keys) {
             if (n.key === name) {
-              return { ...n, field }
+              return {
+                ...n,
+                field,
+              }
             }
           }
 
           return undefined
         }
       }
-      const rootNodeOffset = 32
-      return bptReadNode(offset2 + rootNodeOffset)
+      return bptReadNode(offset2 + 32)
     })
     return filterUndef(await Promise.all(locs))
   }

package/src/bigint-polyfill/polyfill.ts

@@ -1,3 +1,6 @@
+// from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
+// license:MIT
+// needed for browsers including safari 14
 import { getBigInt64, getBigUint64 } from './pure'
 
 if (!('getBigInt64' in DataView)) {

package/src/bigint-polyfill/pure.ts

@@ -1,3 +1,7 @@
+// from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
+// license:MIT
+// needed for browsers including safari 14
+
 const BigInt32 = BigInt(32)
 
 export function getBigInt64(

package/src/bigwig.ts

@@ -1,5 +1,7 @@
+import { BBI } from './bbi'
 import { BlockView } from './block-view'
-import { BBI, RequestOptions } from './bbi'
+
+import type { RequestOptions } from './types'
 
 export class BigWig extends BBI {
   /**

package/src/block-view.ts

@@ -1,13 +1,13 @@
-import { Observer } from 'rxjs'
 import AbortablePromiseCache from '@gmod/abortable-promise-cache'
-import { GenericFilehandle } from 'generic-filehandle2'
 import QuickLRU from 'quick-lru'
 
-// locals
 import Range from './range'
 import { unzip } from './unzip'
-import { Feature } from './bbi'
-import { groupBlocks, checkAbortSignal } from './util'
+import { checkAbortSignal, groupBlocks } from './util'
+
+import type { Feature } from './types'
+import type { GenericFilehandle } from 'generic-filehandle2'
+import type { Observer } from 'rxjs'
 
 const decoder =
   typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined
@@ -37,7 +37,6 @@ function coordFilter(s1: number, e1: number, s2: number, e2: number): boolean {
  *
  * Adapted by Robert Buels and Colin Diesh from bigwig.js in the Dalliance
  * Genome Explorer by Thomas Down.
- * @constructs
  */
 
 export class BlockView {
@@ -46,11 +45,8 @@ export class BlockView {
   private featureCache = new AbortablePromiseCache<ReadData, Uint8Array>({
     cache: new QuickLRU({ maxSize: 1000 }),
 
-    fill: async (requestData, signal) => {
-      return this.bbi.read(requestData.length, requestData.offset, {
-        signal,
-      })
-    },
+    fill: async ({ length, offset }, signal) =>
+      this.bbi.read(length, offset, { signal }),
   })
 
   public constructor(
@@ -73,14 +69,13 @@ export class BlockView {
     opts?: Options,
   ) {
     try {
-      const { refsByName, bbi, cirTreeOffset } = this
-      const chrId = refsByName[chrName]
+      const chrId = this.refsByName[chrName]
       if (chrId === undefined) {
         observer.complete()
       }
       const request = { chrId, start, end }
       if (!this.cirTreePromise) {
-        this.cirTreePromise = bbi.read(48, cirTreeOffset, opts)
+        this.cirTreePromise = this.bbi.read(48, this.cirTreeOffset, opts)
       }
       const buffer = await this.cirTreePromise
       const dataView = new DataView(buffer.buffer)
@@ -243,7 +238,7 @@ export class BlockView {
         }
       }
 
-      cirFobRecur([Number(cirTreeOffset) + 48], 1)
+      cirFobRecur([Number(this.cirTreeOffset) + 48], 1)
       return
     } catch (e) {
       observer.error(e)

package/src/index.ts

@@ -1,7 +1,4 @@
-// from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
-// license:MIT
-// needed for browsers including safari 14
 import './bigint-polyfill/polyfill'
 export { BigWig } from './bigwig'
 export { BigBed } from './bigbed'
-export { Feature, Header, RequestOptions } from './bbi'
+export type { BigWigHeader, Feature, RequestOptions } from './types'

package/src/types.ts

@@ -0,0 +1,66 @@
+export interface ZoomLevel {
+  reductionLevel: number
+  reserved: number
+  dataOffset: number
+  indexOffset: number
+}
+
+export interface Feature {
+  offset?: number
+  chromId: number
+  start: number
+  end: number
+  score?: number
+  rest?: string // for bigbed line
+  minScore?: number // for summary line
+  maxScore?: number // for summary line
+  summary?: boolean // is summary line
+  uniqueId?: string // for bigbed contains uniqueId calculated from file offset
+  field?: number // used in bigbed searching
+}
+export interface Statistics {
+  scoreSum: number
+  basesCovered: number
+  scoreSumSquares: number
+  scoreMin: number
+  scoreMax: number
+}
+
+export interface RefInfo {
+  name: string
+  id: number
+  length: number
+}
+
+export interface BigWigHeader {
+  magic: number
+  version: number
+  autoSql: string
+  totalSummary: Statistics
+  asOffset: number
+  zoomLevels: ZoomLevel[]
+  fieldCount: number
+  numZoomLevels: number
+  unzoomedIndexOffset: number
+  totalSummaryOffset: number
+  unzoomedDataOffset: number
+  definedFieldCount: number
+  uncompressBufSize: number
+  chromTreeOffset: number
+  extHeaderOffset: number
+  fileType: string
+}
+export interface BigWigHeaderWithRefNames extends BigWigHeader {
+  refsByName: Record<string, number>
+  refsByNumber: Record<number, RefInfo>
+}
+
+export interface RequestOptions {
+  signal?: AbortSignal
+  headers?: Record<string, string>
+}
+
+export interface RequestOptions2 extends RequestOptions {
+  scale?: number
+  basesPerSpan?: number
+}