@gmod/bbi 7.1.0 → 8.0.1

package/esm/wasm/inflate_wasm_bg.d.ts

@@ -0,0 +1,68 @@
+export function __wbg_set_wasm(val: any): void;
+/**
+ * Combined decompress + parse for BigWig blocks
+ * Returns same format as parse_bigwig_block but handles multiple compressed blocks
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_bigwig(inputs: Uint8Array, input_offsets: Uint32Array, input_lengths: Uint32Array, max_block_size: number, req_start: number, req_end: number): Uint8Array;
+/**
+ * Combined decompress + parse for summary blocks
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_summary(inputs: Uint8Array, input_offsets: Uint32Array, input_lengths: Uint32Array, max_block_size: number, req_chr_id: number, req_start: number, req_end: number): Uint8Array;
+/**
+ * @param {Uint8Array} input
+ * @param {number} output_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw(input: Uint8Array, output_size: number): Uint8Array;
+/**
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_batch(inputs: Uint8Array, input_offsets: Uint32Array, input_lengths: Uint32Array, max_block_size: number): Uint8Array;
+/**
+ * @param {Uint8Array} input
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_unknown_size(input: Uint8Array): Uint8Array;
+/**
+ * Parse a BigWig data block and return packed typed arrays
+ * Block types: 1 = bedGraph, 2 = varstep, 3 = fixedstep
+ *
+ * Returns packed binary: [count: u32][starts: i32*count][ends: i32*count][scores: f32*count]
+ * @param {Uint8Array} data
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_bigwig_block(data: Uint8Array, req_start: number, req_end: number): Uint8Array;
+/**
+ * Parse a BigWig summary block and return packed typed arrays
+ * Summary blocks contain: chromId, start, end, validCnt, minScore, maxScore, sumData, sumSqData
+ *
+ * Returns: [count: u32][starts: i32*n][ends: i32*n][scores: f32*n][minScores: f32*n][maxScores: f32*n]
+ * @param {Uint8Array} data
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_summary_block(data: Uint8Array, req_chr_id: number, req_start: number, req_end: number): Uint8Array;
+export function __wbg_Error_52673b7de5a0ca89(arg0: any, arg1: any): number;

package/esm/wasm/inflate_wasm_bg.js

@@ -0,0 +1,296 @@
+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
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_bigwig(inputs, input_offsets, input_lengths, max_block_size, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(inputs, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(input_offsets, wasm.__wbindgen_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passArray32ToWasm0(input_lengths, wasm.__wbindgen_export);
+        const len2 = WASM_VECTOR_LEN;
+        wasm.decompress_and_parse_bigwig(retptr, ptr0, len0, ptr1, len1, ptr2, len2, max_block_size, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v4 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v4;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * Combined decompress + parse for summary blocks
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_summary(inputs, input_offsets, input_lengths, max_block_size, req_chr_id, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(inputs, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(input_offsets, wasm.__wbindgen_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passArray32ToWasm0(input_lengths, wasm.__wbindgen_export);
+        const len2 = WASM_VECTOR_LEN;
+        wasm.decompress_and_parse_summary(retptr, ptr0, len0, ptr1, len1, ptr2, len2, max_block_size, req_chr_id, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v4 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v4;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * @param {Uint8Array} input
+ * @param {number} output_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw(input, output_size) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(input, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.inflate_raw(retptr, ptr0, len0, output_size);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_batch(inputs, input_offsets, input_lengths, max_block_size) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(inputs, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(input_offsets, wasm.__wbindgen_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passArray32ToWasm0(input_lengths, wasm.__wbindgen_export);
+        const len2 = WASM_VECTOR_LEN;
+        wasm.inflate_raw_batch(retptr, ptr0, len0, ptr1, len1, ptr2, len2, max_block_size);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v4 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v4;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * @param {Uint8Array} input
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_unknown_size(input) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(input, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.inflate_raw_unknown_size(retptr, ptr0, len0);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * Parse a BigWig data block and return packed typed arrays
+ * Block types: 1 = bedGraph, 2 = varstep, 3 = fixedstep
+ *
+ * Returns packed binary: [count: u32][starts: i32*count][ends: i32*count][scores: f32*count]
+ * @param {Uint8Array} data
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_bigwig_block(data, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(data, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.parse_bigwig_block(retptr, ptr0, len0, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * Parse a BigWig summary block and return packed typed arrays
+ * Summary blocks contain: chromId, start, end, validCnt, minScore, maxScore, sumData, sumSqData
+ *
+ * Returns: [count: u32][starts: i32*n][ends: i32*n][scores: f32*n][minScores: f32*n][maxScores: f32*n]
+ * @param {Uint8Array} data
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_summary_block(data, req_chr_id, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(data, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.parse_summary_block(retptr, ptr0, len0, req_chr_id, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+export function __wbg_Error_52673b7de5a0ca89(arg0, arg1) {
+    const ret = Error(getStringFromWasm0(arg0, arg1));
+    return addHeapObject(ret);
+}
+;
+//# sourceMappingURL=inflate_wasm_bg.js.map

package/esm/wasm/inflate_wasm_bg.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "7.1.0",
+  "version": "8.0.1",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -25,14 +25,17 @@
   ],
   "scripts": {
     "test": "vitest",
+    "benchonly": "vitest bench",
+    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "format": "prettier --write .",
     "clean": "rimraf dist esm",
     "prebuild": "yarn clean",
+    "build:wasm": "./scripts/build-wasm.sh",
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "build": "yarn build:esm && yarn build:es5",
+    "build": "yarn build:wasm && yarn build:esm && yarn build:es5",
     "preversion": "yarn lint && yarn test --run && yarn build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push origin master --follow-tags"
@@ -47,26 +50,28 @@
   ],
   "dependencies": {
     "@gmod/abortable-promise-cache": "^3.0.1",
-    "generic-filehandle2": "^2.0.10",
-    "pako-esm2": "^1.0.13",
+    "generic-filehandle2": "^2.0.16",
+    "pako-esm2": "^2.0.2",
     "quick-lru": "^4.0.0",
     "rxjs": "^7.8.0"
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
     "@types/node": "^24.10.0",
-    "@typescript-eslint/eslint-plugin": "^8.4.0",
-    "@typescript-eslint/parser": "^8.4.0",
-    "@vitest/coverage-v8": "^4.0.6",
-    "eslint": "^9.9.1",
+    "@typescript-eslint/eslint-plugin": "^8.50.0",
+    "@typescript-eslint/parser": "^8.50.0",
+    "@vitest/coverage-v8": "^4.0.15",
+    "eslint": "^9.39.2",
     "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-unicorn": "^62.0.0",
-    "prettier": "^3.2.5",
-    "rimraf": "^6.0.1",
+    "prettier": "^3.7.4",
+    "rimraf": "^6.1.2",
     "standard-changelog": "^7.0.1",
     "typescript": "^5.1.6",
-    "typescript-eslint": "^8.4.0",
-    "vitest": "^4.0.6"
+    "typescript-eslint": "^8.50.0",
+    "vitest": "^4.0.15",
+    "webpack": "^5.104.0",
+    "webpack-cli": "^6.0.1"
   },
   "publishConfig": {
     "access": "public"

package/src/bbi.ts

@@ -5,6 +5,7 @@ import { toArray } from 'rxjs/operators'
 import { BlockView } from './block-view.ts'
 
 import type {
+  BigWigFeatureArrays,
   BigWigHeader,
   BigWigHeaderWithRefNames,
   Feature,
@@ -12,6 +13,7 @@ import type {
   RequestOptions2,
   RequestOptions,
   Statistics,
+  SummaryFeatureArrays,
   ZoomLevel,
 } from './types.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
@@ -19,6 +21,8 @@ import type { GenericFilehandle } from 'generic-filehandle2'
 const BIG_WIG_MAGIC = -2003829722
 const BIG_BED_MAGIC = -2021002517
 
+const decoder = new TextDecoder('utf8')
+
 function getDataView(buffer: Uint8Array) {
   return new DataView(buffer.buffer, buffer.byteOffset, buffer.length)
 }
@@ -71,7 +75,7 @@ export abstract class BBI {
 
   private async _getHeader(opts?: RequestOptions) {
     const header = await this._getMainHeader(opts)
-    const chroms = await this._readChromTree(header, opts)
+    const chroms = await this._readChromosomeTree(header, opts)
     return {
       ...header,
       ...chroms,
@@ -96,7 +100,8 @@ export abstract class BBI {
     offset += 2
     const numZoomLevels = dataView.getUint16(offset, true)
     offset += 2
-    const chromTreeOffset = Number(dataView.getBigUint64(offset, true))
+    // Offset to the B+ tree that maps chromosome names to integer IDs
+    const chromosomeTreeOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
     const unzoomedDataOffset = Number(dataView.getBigUint64(offset, true))
     offset += 8
@@ -166,7 +171,6 @@ export abstract class BBI {
     } else {
       throw new Error('no stats')
     }
-    const decoder = new TextDecoder('utf8')
 
     return {
       zoomLevels,
@@ -178,7 +182,7 @@ export abstract class BBI {
       definedFieldCount,
       uncompressBufSize,
       asOffset,
-      chromTreeOffset,
+      chromosomeTreeOffset,
       totalSummaryOffset,
       unzoomedDataOffset,
       unzoomedIndexOffset,
@@ -190,16 +194,21 @@ export abstract class BBI {
     }
   }
 
-  private async _readChromTree(
+  // Reads the B+ tree that maps chromosome names to integer IDs
+  // This is part of the "cirTree" (combined ID R-tree) structure, which uses
+  // integer chromosome IDs instead of strings for more efficient spatial indexing
+  private async _readChromosomeTree(
     header: BigWigHeader,
     opts?: { signal?: AbortSignal },
   ) {
-    const refsByNumber: Record<number, RefInfo> = []
-    const refsByName: Record<string, number> = {}
+    const refsByNumber: RefInfo[] = []
+    const refsByName = {} as Record<string, number>
 
-    const chromTreeOffset = header.chromTreeOffset
+    const chromosomeTreeOffset = header.chromosomeTreeOffset
 
-    const dataView = getDataView(await this.bbi.read(32, chromTreeOffset, opts))
+    const dataView = getDataView(
+      await this.bbi.read(32, chromosomeTreeOffset, opts),
+    )
     let offset = 0
     // const magic = dataView.getUint32(offset, true) // unused
     offset += 4
@@ -212,9 +221,8 @@ export abstract class BBI {
     // const itemCount = dataView.getBigUint64(offset, true) // unused
     offset += 8
 
-    const decoder = new TextDecoder('utf8')
-
-    const bptReadNode = async (currentOffset: number) => {
+    // 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
@@ -225,6 +233,7 @@ export abstract class BBI {
       const count = dataView.getUint16(offset, true)
       offset += 2
 
+      // Leaf nodes contain the actual chromosome name-to-ID mappings
       if (isLeafNode) {
         const b = await this.bbi.read(
           count * (keySize + valSize),
@@ -234,9 +243,12 @@ export abstract class BBI {
         offset = 0
 
         for (let n = 0; n < count; n++) {
-          const key = decoder
-            .decode(b.subarray(offset, offset + keySize))
-            .replaceAll('\0', '')
+          const keyEnd = b.indexOf(0, offset)
+          const effectiveKeyEnd =
+            keyEnd !== -1 && keyEnd < offset + keySize
+              ? keyEnd
+              : offset + keySize
+          const key = decoder.decode(b.subarray(offset, effectiveKeyEnd))
           offset += keySize
           const refId = dataView.getUint32(offset, true)
           offset += 4
@@ -251,6 +263,7 @@ export abstract class BBI {
           }
         }
       } else {
+        // Non-leaf nodes contain pointers to child nodes
         const nextNodes = []
         const dataView = getDataView(
           await this.bbi.read(count * (keySize + 8), currentOffset + offset),
@@ -261,12 +274,12 @@ export abstract class BBI {
           offset += keySize
           const childOffset = Number(dataView.getBigUint64(offset, true))
           offset += 8
-          nextNodes.push(bptReadNode(childOffset))
+          nextNodes.push(readBPlusTreeNode(childOffset))
         }
         await Promise.all(nextNodes)
       }
     }
-    await bptReadNode(chromTreeOffset + 32)
+    await readBPlusTreeNode(chromosomeTreeOffset + 32)
     return {
       refsByName,
       refsByNumber,
@@ -284,7 +297,7 @@ export abstract class BBI {
       this.bbi,
       refsByName,
       unzoomedIndexOffset,
-      uncompressBufSize > 0,
+      uncompressBufSize,
       fileType,
     )
   }
@@ -345,7 +358,76 @@ export abstract class BBI {
   ) {
     const ob = await this.getFeatureStream(refName, start, end, opts)
 
-    const ret = await firstValueFrom(ob.pipe(toArray()))
-    return ret.flat()
+    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
+  }
+
+  /**
+   * 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),
+      }
+    }
+
+    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 }
+    }
+
+    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 }
   }
 }