@gmod/bbi 6.0.0 → 6.0.2

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
+}