@gmod/bbi 8.1.1 → 9.0.0

package/esm/wasm/inflate_wasm_bg.js

@@ -1,85 +1,3 @@
-let wasm;
-export function __wbg_set_wasm(val) {
-    wasm = val;
-}
-function addHeapObject(obj) {
-    if (heap_next === heap.length)
-        heap.push(heap.length + 1);
-    const idx = heap_next;
-    heap_next = heap[idx];
-    heap[idx] = obj;
-    return idx;
-}
-function dropObject(idx) {
-    if (idx < 132)
-        return;
-    heap[idx] = heap_next;
-    heap_next = idx;
-}
-function getArrayU8FromWasm0(ptr, len) {
-    ptr = ptr >>> 0;
-    return getUint8ArrayMemory0().subarray(ptr / 1, ptr / 1 + len);
-}
-let cachedDataViewMemory0 = null;
-function getDataViewMemory0() {
-    if (cachedDataViewMemory0 === null || cachedDataViewMemory0.buffer.detached === true || (cachedDataViewMemory0.buffer.detached === undefined && cachedDataViewMemory0.buffer !== wasm.memory.buffer)) {
-        cachedDataViewMemory0 = new DataView(wasm.memory.buffer);
-    }
-    return cachedDataViewMemory0;
-}
-function getStringFromWasm0(ptr, len) {
-    ptr = ptr >>> 0;
-    return decodeText(ptr, len);
-}
-let cachedUint32ArrayMemory0 = null;
-function getUint32ArrayMemory0() {
-    if (cachedUint32ArrayMemory0 === null || cachedUint32ArrayMemory0.byteLength === 0) {
-        cachedUint32ArrayMemory0 = new Uint32Array(wasm.memory.buffer);
-    }
-    return cachedUint32ArrayMemory0;
-}
-let cachedUint8ArrayMemory0 = null;
-function getUint8ArrayMemory0() {
-    if (cachedUint8ArrayMemory0 === null || cachedUint8ArrayMemory0.byteLength === 0) {
-        cachedUint8ArrayMemory0 = new Uint8Array(wasm.memory.buffer);
-    }
-    return cachedUint8ArrayMemory0;
-}
-function getObject(idx) { return heap[idx]; }
-let heap = new Array(128).fill(undefined);
-heap.push(undefined, null, true, false);
-let heap_next = heap.length;
-function passArray32ToWasm0(arg, malloc) {
-    const ptr = malloc(arg.length * 4, 4) >>> 0;
-    getUint32ArrayMemory0().set(arg, ptr / 4);
-    WASM_VECTOR_LEN = arg.length;
-    return ptr;
-}
-function passArray8ToWasm0(arg, malloc) {
-    const ptr = malloc(arg.length * 1, 1) >>> 0;
-    getUint8ArrayMemory0().set(arg, ptr / 1);
-    WASM_VECTOR_LEN = arg.length;
-    return ptr;
-}
-function takeObject(idx) {
-    const ret = getObject(idx);
-    dropObject(idx);
-    return ret;
-}
-let cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
-cachedTextDecoder.decode();
-const MAX_SAFARI_DECODE_BYTES = 2146435072;
-let numBytesDecoded = 0;
-function decodeText(ptr, len) {
-    numBytesDecoded += len;
-    if (numBytesDecoded >= MAX_SAFARI_DECODE_BYTES) {
-        cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
-        cachedTextDecoder.decode();
-        numBytesDecoded = len;
-    }
-    return cachedTextDecoder.decode(getUint8ArrayMemory0().subarray(ptr, ptr + len));
-}
-let WASM_VECTOR_LEN = 0;
 /**
  * Combined decompress + parse for BigWig blocks
  * Returns same format as parse_bigwig_block but handles multiple compressed blocks
@@ -288,9 +206,90 @@ export function parse_summary_block(data, req_chr_id, req_start, req_end) {
         wasm.__wbindgen_add_to_stack_pointer(16);
     }
 }
-export function __wbg_Error_52673b7de5a0ca89(arg0, arg1) {
+export function __wbg_Error_83742b46f01ce22d(arg0, arg1) {
     const ret = Error(getStringFromWasm0(arg0, arg1));
     return addHeapObject(ret);
 }
-;
+function addHeapObject(obj) {
+    if (heap_next === heap.length)
+        heap.push(heap.length + 1);
+    const idx = heap_next;
+    heap_next = heap[idx];
+    heap[idx] = obj;
+    return idx;
+}
+function dropObject(idx) {
+    if (idx < 1028)
+        return;
+    heap[idx] = heap_next;
+    heap_next = idx;
+}
+function getArrayU8FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getUint8ArrayMemory0().subarray(ptr / 1, ptr / 1 + len);
+}
+let cachedDataViewMemory0 = null;
+function getDataViewMemory0() {
+    if (cachedDataViewMemory0 === null || cachedDataViewMemory0.buffer.detached === true || (cachedDataViewMemory0.buffer.detached === undefined && cachedDataViewMemory0.buffer !== wasm.memory.buffer)) {
+        cachedDataViewMemory0 = new DataView(wasm.memory.buffer);
+    }
+    return cachedDataViewMemory0;
+}
+function getStringFromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return decodeText(ptr, len);
+}
+let cachedUint32ArrayMemory0 = null;
+function getUint32ArrayMemory0() {
+    if (cachedUint32ArrayMemory0 === null || cachedUint32ArrayMemory0.byteLength === 0) {
+        cachedUint32ArrayMemory0 = new Uint32Array(wasm.memory.buffer);
+    }
+    return cachedUint32ArrayMemory0;
+}
+let cachedUint8ArrayMemory0 = null;
+function getUint8ArrayMemory0() {
+    if (cachedUint8ArrayMemory0 === null || cachedUint8ArrayMemory0.byteLength === 0) {
+        cachedUint8ArrayMemory0 = new Uint8Array(wasm.memory.buffer);
+    }
+    return cachedUint8ArrayMemory0;
+}
+function getObject(idx) { return heap[idx]; }
+let heap = new Array(1024).fill(undefined);
+heap.push(undefined, null, true, false);
+let heap_next = heap.length;
+function passArray32ToWasm0(arg, malloc) {
+    const ptr = malloc(arg.length * 4, 4) >>> 0;
+    getUint32ArrayMemory0().set(arg, ptr / 4);
+    WASM_VECTOR_LEN = arg.length;
+    return ptr;
+}
+function passArray8ToWasm0(arg, malloc) {
+    const ptr = malloc(arg.length * 1, 1) >>> 0;
+    getUint8ArrayMemory0().set(arg, ptr / 1);
+    WASM_VECTOR_LEN = arg.length;
+    return ptr;
+}
+function takeObject(idx) {
+    const ret = getObject(idx);
+    dropObject(idx);
+    return ret;
+}
+let cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+cachedTextDecoder.decode();
+const MAX_SAFARI_DECODE_BYTES = 2146435072;
+let numBytesDecoded = 0;
+function decodeText(ptr, len) {
+    numBytesDecoded += len;
+    if (numBytesDecoded >= MAX_SAFARI_DECODE_BYTES) {
+        cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+        cachedTextDecoder.decode();
+        numBytesDecoded = len;
+    }
+    return cachedTextDecoder.decode(getUint8ArrayMemory0().subarray(ptr, ptr + len));
+}
+let WASM_VECTOR_LEN = 0;
+let wasm;
+export function __wbg_set_wasm(val) {
+    wasm = val;
+}
 //# sourceMappingURL=inflate_wasm_bg.js.map

package/esm/wasm/inflate_wasm_bg.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "8.1.1",
+  "version": "9.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -51,28 +51,26 @@
   "dependencies": {
     "@gmod/abortable-promise-cache": "^3.0.1",
     "@jbrowse/quick-lru": "^7.0.0",
-    "generic-filehandle2": "^2.0.16",
-    "pako-esm2": "^2.0.2",
-    "rxjs": "^7.8.0"
+    "generic-filehandle2": "^2.0.16"
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
-    "@types/node": "^24.10.0",
-    "@typescript-eslint/eslint-plugin": "^8.50.0",
-    "@typescript-eslint/parser": "^8.50.0",
-    "@vitest/coverage-v8": "^4.0.16",
-    "canvas": "^3.2.0",
-    "eslint": "^9.39.2",
+    "@types/node": "^25.5.0",
+    "@typescript-eslint/eslint-plugin": "^8.57.1",
+    "@typescript-eslint/parser": "^8.57.1",
+    "@vitest/coverage-v8": "^4.1.0",
+    "canvas": "^3.2.1",
+    "eslint": "^9.0.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^62.0.0",
+    "eslint-plugin-unicorn": "^63.0.0",
     "prettier": "^3.7.4",
-    "rimraf": "^6.1.2",
+    "rimraf": "^6.1.3",
     "standard-changelog": "^7.0.1",
     "typescript": "^5.1.6",
-    "typescript-eslint": "^8.50.0",
-    "vitest": "^4.0.16",
-    "webpack": "^5.104.1",
-    "webpack-cli": "^6.0.1"
+    "typescript-eslint": "^8.57.1",
+    "vitest": "^4.1.0",
+    "webpack": "^5.105.4",
+    "webpack-cli": "^7.0.2"
   },
   "publishConfig": {
     "access": "public"

package/src/array-feature-view.ts

@@ -61,6 +61,14 @@ export class ArrayFeatureView {
     return `${this._source}:${this._refName}:${this.starts[i]}-${this.ends[i]}`
   }
 
+  get(i: number, key: 'refName' | 'source'): string
+  get(
+    i: number,
+    key: 'start' | 'end' | 'score' | 'minScore' | 'maxScore',
+  ): number | undefined
+  get(i: number, key: 'summary'): boolean
+
+  get(i: number, key: string): any
   get(i: number, key: string) {
     switch (key) {
       case 'start':

package/src/bbi.ts

@@ -1,6 +1,4 @@
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
-import { Observable, firstValueFrom } from 'rxjs'
-import { toArray } from 'rxjs/operators'
 
 import { BlockView } from './block-view.ts'
 
@@ -8,7 +6,6 @@ import type {
   BigWigFeatureArrays,
   BigWigHeader,
   BigWigHeaderWithRefNames,
-  Feature,
   RefInfo,
   RequestOptions2,
   RequestOptions,
@@ -89,13 +86,12 @@ export abstract class BBI {
     const b = await this.bbi.read(requestSize, 0, opts)
     const dataView = getDataView(b)
 
-    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, true)
     offset += 4
+    if (magic !== BIG_WIG_MAGIC && magic !== BIG_BED_MAGIC) {
+      throw new Error('not a BigWig/BigBed file')
+    }
     const version = dataView.getUint16(offset, true)
     offset += 2
     const numZoomLevels = dataView.getUint16(offset, true)
@@ -159,7 +155,6 @@ export abstract class BBI {
       const scoreSum = dataView.getFloat64(offset, true)
       offset += 8
       const scoreSumSquares = dataView.getFloat64(offset, true)
-      offset += 8
 
       totalSummary = {
         scoreMin,
@@ -209,39 +204,23 @@ export abstract class BBI {
     const dataView = getDataView(
       await this.bbi.read(32, chromosomeTreeOffset, opts),
     )
-    let offset = 0
-    // const magic = dataView.getUint32(offset, true) // unused
-    offset += 4
-    // const blockSize = dataView.getUint32(offset, true) // unused
-    offset += 4
-    const keySize = dataView.getUint32(offset, true)
-    offset += 4
-    const valSize = dataView.getUint32(offset, true)
-    offset += 4
-    // const itemCount = dataView.getBigUint64(offset, true) // unused
-    offset += 8
+    const keySize = dataView.getUint32(8, true)
+    const valSize = dataView.getUint32(12, true)
 
     // Recursively traverses the B+ tree to populate chromosome name-to-ID mappings
     const readBPlusTreeNode = async (currentOffset: number) => {
-      const b = await this.bbi.read(4, currentOffset)
-      const dataView = getDataView(b)
-      let offset = 0
-      const isLeafNode = dataView.getUint8(offset)
-      offset += 1
-      // const reserved = dataView.getUint8(offset) // unused
-      offset += 1
-      const count = dataView.getUint16(offset, true)
-      offset += 2
+      const header = getDataView(await this.bbi.read(4, currentOffset))
+      const isLeafNode = header.getUint8(0)
+      const count = header.getUint16(2, true)
 
       // Leaf nodes contain the actual chromosome name-to-ID mappings
       if (isLeafNode) {
         const b = await this.bbi.read(
           count * (keySize + valSize),
-          currentOffset + offset,
+          currentOffset + 4,
         )
         const dataView = getDataView(b)
-        offset = 0
-
+        let offset = 0
         for (let n = 0; n < count; n++) {
           const keyEnd = b.indexOf(0, offset)
           const effectiveKeyEnd =
@@ -254,22 +233,16 @@ export abstract class BBI {
           offset += 4
           const refSize = dataView.getUint32(offset, true)
           offset += 4
-
           refsByName[this.renameRefSeqs(key)] = refId
-          refsByNumber[refId] = {
-            name: key,
-            id: refId,
-            length: refSize,
-          }
+          refsByNumber[refId] = { name: key, id: refId, length: refSize }
         }
       } else {
         // Non-leaf nodes contain pointers to child nodes
-        const nextNodes = []
         const dataView = getDataView(
-          await this.bbi.read(count * (keySize + 8), currentOffset + offset),
+          await this.bbi.read(count * (keySize + 8), currentOffset + 4),
         )
-        offset = 0
-
+        const nextNodes = []
+        let offset = 0
         for (let n = 0; n < count; n++) {
           offset += keySize
           const childOffset = Number(dataView.getBigUint64(offset, true))
@@ -286,6 +259,29 @@ export abstract class BBI {
     }
   }
 
+  private viewCache = new Map<string, BlockView>()
+
+  protected getOrCreateBlockView(
+    refsByName: Record<string, number>,
+    rTreeOffset: number,
+    uncompressBufSize: number,
+    blockType: string,
+  ) {
+    const key = `${rTreeOffset}_${blockType}`
+    let view = this.viewCache.get(key)
+    if (!view) {
+      view = new BlockView(
+        this.bbi,
+        refsByName,
+        rTreeOffset,
+        uncompressBufSize,
+        blockType,
+      )
+      this.viewCache.set(key, view)
+    }
+    return view
+  }
+
   /*
    * fetches the "unzoomed" view of the bigwig data. this is the default for bigbed
    * @param abortSignal - a signal to optionally abort this operation
@@ -293,8 +289,7 @@ export abstract class BBI {
   protected async getUnzoomedView(opts?: RequestOptions) {
     const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } =
       await this.getHeader(opts)
-    return new BlockView(
-      this.bbi,
+    return this.getOrCreateBlockView(
       refsByName,
       unzoomedIndexOffset,
       uncompressBufSize,
@@ -310,44 +305,10 @@ export abstract class BBI {
     opts?: RequestOptions,
   ): Promise<BlockView>
 
-  /**
-   * 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
-   */
-  public async getFeatureStream(
-    refName: string,
-    start: number,
-    end: number,
-    opts?: RequestOptions2,
-  ) {
-    await this.getHeader(opts)
-    const chrName = this.renameRefSeqs(refName)
-    let view: BlockView
+  private async _getView(opts?: RequestOptions2) {
     const { basesPerSpan, 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)
-    }
-
-    return new Observable<Feature[]>(observer => {
-      view
-        .readWigData(chrName, start, end, observer, opts)
-        .catch((e: unknown) => {
-          observer.error(e)
-        })
-    })
+    const viewScale = basesPerSpan ? 1 / basesPerSpan : (scale ?? 1)
+    return this.getView(viewScale, opts)
   }
 
   public async getFeatures(
@@ -356,86 +317,22 @@ export abstract class BBI {
     end: number,
     opts?: RequestOptions2,
   ) {
-    const ob = await this.getFeatureStream(refName, start, end, opts)
-
-    const arrays = await firstValueFrom(ob.pipe(toArray()))
-    const totalLength = arrays.reduce((sum, arr) => sum + arr.length, 0)
-    const result = new Array(totalLength)
-    let index = 0
-    for (const arr of arrays) {
-      for (const item of arr) {
-        result[index++] = item
-      }
-    }
-    return result
+    const view = await this._getView(opts)
+    return view.readWigData(this.renameRefSeqs(refName), start, end, opts)
   }
 
-  /**
-   * Gets features from a BigWig file as typed arrays (more efficient than getFeatures)
-   *
-   * @param refName - The chromosome name
-   * @param start - The start of a region
-   * @param end - The end of a region
-   * @param opts - Options including basesPerSpan or scale
-   * @returns Promise with typed arrays: starts, ends, scores (and minScores/maxScores for summary data)
-   */
   public async getFeaturesAsArrays(
     refName: string,
     start: number,
     end: number,
     opts?: RequestOptions2,
   ): Promise<BigWigFeatureArrays | SummaryFeatureArrays> {
-    const features = await this.getFeatures(refName, start, end, opts)
-    const count = features.length
-
-    if (count === 0) {
-      return {
-        starts: new Int32Array(0),
-        ends: new Int32Array(0),
-        scores: new Float32Array(0),
-        isSummary: false as const,
-      }
-    }
-
-    const hasSummary = features[0]?.summary === true
-
-    if (hasSummary) {
-      const starts = new Int32Array(count)
-      const ends = new Int32Array(count)
-      const scores = new Float32Array(count)
-      const minScores = new Float32Array(count)
-      const maxScores = new Float32Array(count)
-
-      for (let i = 0; i < count; i++) {
-        const f = features[i]!
-        starts[i] = f.start
-        ends[i] = f.end
-        scores[i] = f.score ?? 0
-        minScores[i] = f.minScore ?? 0
-        maxScores[i] = f.maxScore ?? 0
-      }
-
-      return {
-        starts,
-        ends,
-        scores,
-        minScores,
-        maxScores,
-        isSummary: true as const,
-      }
-    }
-
-    const starts = new Int32Array(count)
-    const ends = new Int32Array(count)
-    const scores = new Float32Array(count)
-
-    for (let i = 0; i < count; i++) {
-      const f = features[i]!
-      starts[i] = f.start
-      ends[i] = f.end
-      scores[i] = f.score ?? 0
-    }
-
-    return { starts, ends, scores, isSummary: false as const }
+    const view = await this._getView(opts)
+    return view.readWigDataAsArrays(
+      this.renameRefSeqs(refName),
+      start,
+      end,
+      opts,
+    )
   }
 }