@gmod/bbi 8.1.1 → 9.0.0

package/dist/wasm/inflate_wasm_bg.js

@@ -1,6 +1,5 @@
 "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;
@@ -8,89 +7,8 @@ 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;
+exports.__wbg_Error_83742b46f01ce22d = __wbg_Error_83742b46f01ce22d;
+exports.__wbg_set_wasm = __wbg_set_wasm;
 /**
  * Combined decompress + parse for BigWig blocks
  * Returns same format as parse_bigwig_block but handles multiple compressed blocks
@@ -299,9 +217,90 @@ function parse_summary_block(data, req_chr_id, req_start, req_end) {
         wasm.__wbindgen_add_to_stack_pointer(16);
     }
 }
-function __wbg_Error_52673b7de5a0ca89(arg0, arg1) {
+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;
+function __wbg_set_wasm(val) {
+    wasm = val;
+}
 //# sourceMappingURL=inflate_wasm_bg.js.map

package/dist/wasm/inflate_wasm_bg.js.map

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package/esm/array-feature-view.d.ts

@@ -18,5 +18,8 @@ export declare class ArrayFeatureView {
     minScore(i: number): number | undefined;
     maxScore(i: number): number | undefined;
     id(i: number): string;
-    get(i: number, key: string): string | number | boolean | undefined;
+    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;
 }

package/esm/array-feature-view.js.map

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

@@ -1,6 +1,5 @@
-import { Observable } from 'rxjs';
 import { BlockView } from './block-view.ts';
-import type { BigWigFeatureArrays, BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions, SummaryFeatureArrays } from './types.ts';
+import type { BigWigFeatureArrays, BigWigHeaderWithRefNames, RequestOptions2, RequestOptions, SummaryFeatureArrays } from './types.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export declare abstract class BBI {
     protected bbi: GenericFilehandle;
@@ -16,30 +15,11 @@ export declare abstract class BBI {
     private _getHeader;
     private _getMainHeader;
     private _readChromosomeTree;
+    private viewCache;
+    protected getOrCreateBlockView(refsByName: Record<string, number>, rTreeOffset: number, uncompressBufSize: number, blockType: string): BlockView;
     protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
     protected abstract getView(scale: number, 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
-     */
-    getFeatureStream(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Observable<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)
-     */
+    private _getView;
+    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<import("./types.ts").Feature[]>;
     getFeaturesAsArrays(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<BigWigFeatureArrays | SummaryFeatureArrays>;
 }

package/esm/bbi.js

@@ -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.js";
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
@@ -58,13 +56,12 @@ export class BBI {
     async _getMainHeader(opts, requestSize = 2000) {
         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);
@@ -125,7 +122,6 @@ export class BBI {
             const scoreSum = dataView.getFloat64(offset, true);
             offset += 8;
             const scoreSumSquares = dataView.getFloat64(offset, true);
-            offset += 8;
             totalSummary = {
                 scoreMin,
                 scoreMax,
@@ -166,33 +162,18 @@ export class BBI {
         const refsByName = {};
         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;
-        // 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) => {
-            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);
+                const b = await this.bbi.read(count * (keySize + valSize), 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 = keyEnd !== -1 && keyEnd < offset + keySize
@@ -205,18 +186,14 @@ export class BBI {
                     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 dataView = getDataView(await this.bbi.read(count * (keySize + 8), currentOffset + 4));
                 const nextNodes = [];
-                const dataView = getDataView(await this.bbi.read(count * (keySize + 8), currentOffset + offset));
-                offset = 0;
+                let offset = 0;
                 for (let n = 0; n < count; n++) {
                     offset += keySize;
                     const childOffset = Number(dataView.getBigUint64(offset, true));
@@ -232,115 +209,36 @@ export class BBI {
             refsByNumber,
         };
     }
+    viewCache = new Map();
+    getOrCreateBlockView(refsByName, rTreeOffset, uncompressBufSize, blockType) {
+        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
      */
     async getUnzoomedView(opts) {
         const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } = await this.getHeader(opts);
-        return new BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize, fileType);
+        return this.getOrCreateBlockView(refsByName, unzoomedIndexOffset, uncompressBufSize, fileType);
     }
-    /**
-     * 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
-     */
-    async getFeatureStream(refName, start, end, opts) {
-        await this.getHeader(opts);
-        const chrName = this.renameRefSeqs(refName);
-        let view;
+    async _getView(opts) {
         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(observer => {
-            view
-                .readWigData(chrName, start, end, observer, opts)
-                .catch((e) => {
-                observer.error(e);
-            });
-        });
+        const viewScale = basesPerSpan ? 1 / basesPerSpan : (scale ?? 1);
+        return this.getView(viewScale, opts);
     }
     async getFeatures(refName, start, end, opts) {
-        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)
-     */
     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),
-                isSummary: false,
-            };
-        }
-        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,
-            };
-        }
-        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 };
+        const view = await this._getView(opts);
+        return view.readWigDataAsArrays(this.renameRefSeqs(refName), start, end, opts);
     }
 }
 //# sourceMappingURL=bbi.js.map

package/esm/bbi.js.map

@@ -1 +1 @@
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package/esm/bigbed.d.ts

@@ -7,7 +7,6 @@ interface Index {
     offset: number;
     field: number;
 }
-export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
 export declare class BigBed extends BBI {
     readIndicesCache: AbortablePromiseCache<RequestOptions, Index[], string>;
     readIndices(opts?: RequestOptions): Promise<Index[]>;