@gmod/bbi 7.1.0 → 8.0.1

package/dist/wasm/inflate_wasm.js

@@ -0,0 +1,43 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const wasm = __importStar(require("./inflate_wasm_bg.wasm"));
+__exportStar(require("./inflate_wasm_bg.js"), exports);
+const inflate_wasm_bg_js_1 = require("./inflate_wasm_bg.js");
+(0, inflate_wasm_bg_js_1.__wbg_set_wasm)(wasm);
+//# sourceMappingURL=inflate_wasm.js.map

package/dist/wasm/inflate_wasm.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"inflate_wasm.js","sourceRoot":"","sources":["../../src/wasm/inflate_wasm.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,6DAA+C;AAC/C,uDAAqC;AACrC,6DAAsD;AACtD,IAAA,mCAAc,EAAC,IAAI,CAAC,CAAC"}

package/dist/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/dist/wasm/inflate_wasm_bg.js

@@ -0,0 +1,307 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.__wbg_set_wasm = __wbg_set_wasm;
+exports.decompress_and_parse_bigwig = decompress_and_parse_bigwig;
+exports.decompress_and_parse_summary = decompress_and_parse_summary;
+exports.inflate_raw = inflate_raw;
+exports.inflate_raw_batch = inflate_raw_batch;
+exports.inflate_raw_unknown_size = inflate_raw_unknown_size;
+exports.parse_bigwig_block = parse_bigwig_block;
+exports.parse_summary_block = parse_summary_block;
+exports.__wbg_Error_52673b7de5a0ca89 = __wbg_Error_52673b7de5a0ca89;
+let wasm;
+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}
+ */
+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}
+ */
+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}
+ */
+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}
+ */
+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}
+ */
+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}
+ */
+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}
+ */
+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);
+    }
+}
+function __wbg_Error_52673b7de5a0ca89(arg0, arg1) {
+    const ret = Error(getStringFromWasm0(arg0, arg1));
+    return addHeapObject(ret);
+}
+;
+//# sourceMappingURL=inflate_wasm_bg.js.map

package/dist/wasm/inflate_wasm_bg.js.map

@@ -0,0 +1 @@
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package/esm/bbi.d.ts

@@ -1,6 +1,6 @@
 import { Observable } from 'rxjs';
 import { BlockView } from './block-view.ts';
-import type { BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions } from './types.ts';
+import type { BigWigFeatureArrays, BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions, SummaryFeatureArrays } from './types.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export declare abstract class BBI {
     protected bbi: GenericFilehandle;
@@ -15,7 +15,7 @@ export declare abstract class BBI {
     });
     private _getHeader;
     private _getMainHeader;
-    private _readChromTree;
+    private _readChromosomeTree;
     protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
     protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
     /**
@@ -31,5 +31,15 @@ export declare abstract class BBI {
      * or scale used to infer the zoomLevel to use
      */
     getFeatureStream(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Observable<Feature[]>>;
-    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Feature[]>;
+    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<any[]>;
+    /**
+     * 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)
+     */
+    getFeaturesAsArrays(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<BigWigFeatureArrays | SummaryFeatureArrays>;
 }

package/esm/bbi.js

@@ -4,6 +4,7 @@ import { toArray } from 'rxjs/operators';
 import { BlockView } from "./block-view.js";
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
+const decoder = new TextDecoder('utf8');
 function getDataView(buffer) {
     return new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
 }
@@ -48,7 +49,7 @@ export class BBI {
     }
     async _getHeader(opts) {
         const header = await this._getMainHeader(opts);
-        const chroms = await this._readChromTree(header, opts);
+        const chroms = await this._readChromosomeTree(header, opts);
         return {
             ...header,
             ...chroms,
@@ -68,7 +69,8 @@ export 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;
@@ -135,7 +137,6 @@ export class BBI {
         else {
             throw new Error('no stats');
         }
-        const decoder = new TextDecoder('utf8');
         return {
             zoomLevels,
             magic,
@@ -146,7 +147,7 @@ export class BBI {
             definedFieldCount,
             uncompressBufSize,
             asOffset,
-            chromTreeOffset,
+            chromosomeTreeOffset,
             totalSummaryOffset,
             unzoomedDataOffset,
             unzoomedIndexOffset,
@@ -157,11 +158,14 @@ export class BBI {
                 : '',
         };
     }
-    async _readChromTree(header, opts) {
+    // 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
+    async _readChromosomeTree(header, opts) {
         const refsByNumber = [];
         const refsByName = {};
-        const chromTreeOffset = header.chromTreeOffset;
-        const dataView = getDataView(await this.bbi.read(32, chromTreeOffset, opts));
+        const chromosomeTreeOffset = header.chromosomeTreeOffset;
+        const dataView = getDataView(await this.bbi.read(32, chromosomeTreeOffset, opts));
         let offset = 0;
         // const magic = dataView.getUint32(offset, true) // unused
         offset += 4;
@@ -173,8 +177,8 @@ export class BBI {
         offset += 4;
         // const itemCount = dataView.getBigUint64(offset, true) // unused
         offset += 8;
-        const decoder = new TextDecoder('utf8');
-        const bptReadNode = async (currentOffset) => {
+        // Recursively traverses the B+ tree to populate chromosome name-to-ID mappings
+        const readBPlusTreeNode = async (currentOffset) => {
             const b = await this.bbi.read(4, currentOffset);
             const dataView = getDataView(b);
             let offset = 0;
@@ -184,14 +188,17 @@ export class BBI {
             offset += 1;
             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), currentOffset + offset);
                 const dataView = getDataView(b);
                 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;
@@ -206,6 +213,7 @@ export 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));
                 offset = 0;
@@ -213,12 +221,12 @@ export 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,
@@ -230,7 +238,7 @@ export class BBI {
      */
     async getUnzoomedView(opts) {
         const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } = await this.getHeader(opts);
-        return new BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize > 0, fileType);
+        return new BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize, fileType);
     }
     /**
      * Gets features from a BigWig file
@@ -268,8 +276,63 @@ export class BBI {
     }
     async getFeatures(refName, start, end, opts) {
         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)
+     */
+    async getFeaturesAsArrays(refName, start, end, opts) {
+        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 };
     }
 }
 //# sourceMappingURL=bbi.js.map