@gmod/bbi 8.1.2 → 9.0.3

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

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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[]>;

package/esm/bigbed.js

@@ -1,12 +1,7 @@
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import QuickLRU from '@jbrowse/quick-lru';
-import { Observable, firstValueFrom, merge } from 'rxjs';
-import { map, reduce } from 'rxjs/operators';
 import { BBI } from "./bbi.js";
 const decoder = new TextDecoder('utf8');
-export function filterUndef(ts) {
-    return ts.filter((t) => !!t);
-}
 function getTabField(str, fieldIndex) {
     if (fieldIndex < 0) {
         return undefined;
@@ -34,11 +29,9 @@ async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, n
     const len = 4 + blockSize * (keySize + valSize);
     const buffer = await bbi.read(len, nodeOffset, opts);
     const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
-    let offset = 0;
-    const nodeType = dataView.getInt8(offset);
-    offset += 2; // skip nodeType byte + 1 reserved byte
-    const cnt = dataView.getInt16(offset, true);
-    offset += 2;
+    const nodeType = dataView.getInt8(0);
+    const cnt = dataView.getInt16(2, true);
+    let offset = 4;
     // Non-leaf node (nodeType === 0): contains keys and child node pointers for navigation
     if (nodeType === 0) {
         const leafkeys = [];
@@ -105,6 +98,7 @@ async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, n
         }
         return undefined;
     }
+    return undefined;
 }
 export class BigBed extends BBI {
     readIndicesCache = new AbortablePromiseCache({
@@ -132,13 +126,8 @@ export class BigBed extends BBI {
         const { extHeaderOffset } = await this.getHeader(opts);
         const b = await this.bbi.read(64, extHeaderOffset);
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-        let offset = 0;
-        // const _size = dataView.getUint16(offset, true)
-        offset += 2;
-        const count = dataView.getUint16(offset, true);
-        offset += 2;
-        const dataOffset = Number(dataView.getBigUint64(offset, true));
-        offset += 8;
+        const count = dataView.getUint16(2, true);
+        const dataOffset = Number(dataView.getBigUint64(4, true));
         // no extra index is defined if count==0
         if (count === 0) {
             return [];
@@ -150,14 +139,10 @@ export class BigBed extends BBI {
         for (let i = 0; i < count; i += 1) {
             const b = buffer.subarray(i * blocklen);
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-            let offset = 0;
-            const type = dataView.getInt16(offset, true);
-            offset += 2;
-            const fieldcount = dataView.getInt16(offset, true);
-            offset += 2;
-            const dataOffset = Number(dataView.getBigUint64(offset, true));
-            offset += 8 + 4; // skip 8-byte offset + 4 reserved bytes
-            const field = dataView.getInt16(offset, true);
+            const type = dataView.getInt16(0, true);
+            const fieldcount = dataView.getInt16(2, true);
+            const dataOffset = Number(dataView.getBigUint64(4, true));
+            const field = dataView.getInt16(16, true);
             indices.push({
                 type,
                 fieldcount,
@@ -186,20 +171,13 @@ export class BigBed extends BBI {
             const { offset: offset2, field } = index;
             const b = await this.bbi.read(32, offset2, opts);
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-            let offset = 0;
-            // const _magic = dataView.getInt32(offset, true)
-            offset += 4;
-            const blockSize = dataView.getInt32(offset, true);
-            offset += 4;
-            const keySize = dataView.getInt32(offset, true);
-            offset += 4;
-            const valSize = dataView.getInt32(offset, true);
-            offset += 4;
-            // const _itemCount = Number(dataView.getBigUint64(offset, true))
-            offset += 8;
+            const blockSize = dataView.getInt32(4, true);
+            const keySize = dataView.getInt32(8, true);
+            const valSize = dataView.getInt32(12, true);
             return readBPlusTreeNode(this.bbi, offset2 + 32, blockSize, keySize, valSize, name, field, opts);
         });
-        return filterUndef(await Promise.all(locs));
+        const results = await Promise.all(locs);
+        return results.filter((l) => l !== undefined);
     }
     /*
      * retrieve the features from the bigbed data that were found through the
@@ -218,20 +196,12 @@ export class BigBed extends BBI {
             return [];
         }
         const view = await this.getUnzoomedView(opts);
-        const res = blocks.map(block => {
-            return new Observable(observer => {
-                view.readFeatures(observer, [block], opts).catch((e) => {
-                    observer.error(e);
-                });
-            }).pipe(reduce((acc, curr) => {
-                acc.push(...curr);
-                return acc;
-            }, []), map(features => features.map(f => ({ ...f, field: block.field }))));
-        });
-        const ret = await firstValueFrom(merge(...res));
-        // Filter to features where the indexed field matches the search name
+        const results = await Promise.all(blocks.map(async (block) => {
+            const features = await view.readFeatures([block], opts);
+            return features.map(f => ({ ...f, field: block.field }));
+        }));
         // field offset is adjusted by -3 to account for chrom, chromStart, chromEnd columns
-        return ret.filter(f => {
+        return results.flat().filter(f => {
             if (!f.rest) {
                 return false;
             }

package/esm/bigbed.js.map

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

@@ -1,5 +1,4 @@
 import { BBI } from './bbi.ts';
-import { BlockView } from './block-view.ts';
 import type { RequestOptions } from './types.ts';
 export declare class BigWig extends BBI {
     /**
@@ -10,5 +9,5 @@ export declare class BigWig extends BBI {
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
      * or scale used to infer the zoomLevel to use
      */
-    protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
+    protected getView(scale: number, opts: RequestOptions): Promise<import("./block-view.ts").BlockView>;
 }

package/esm/bigwig.js

@@ -1,5 +1,4 @@
 import { BBI } from "./bbi.js";
-import { BlockView } from "./block-view.js";
 export class BigWig extends BBI {
     /**
      * Retrieves a BlockView of a specific zoomLevel
@@ -16,7 +15,7 @@ export class BigWig extends BBI {
         for (let i = maxLevel; i >= 0; i -= 1) {
             const zh = zoomLevels[i];
             if (zh && zh.reductionLevel <= 2 * basesPerPx) {
-                return new BlockView(this.bbi, refsByName, zh.indexOffset, uncompressBufSize, 'summary');
+                return this.getOrCreateBlockView(refsByName, zh.indexOffset, uncompressBufSize, 'summary');
             }
         }
         return this.getUnzoomedView(opts);

package/esm/bigwig.js.map

@@ -1 +1 @@
-{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAC9B,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAI3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,EACjB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}
+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAI9B,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,CAAC,oBAAoB,CAC9B,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,EACjB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}

package/esm/block-view.d.ts

@@ -1,7 +1,6 @@
 import type { Feature } from './types.ts';
 import type { BigWigFeatureArrays, SummaryFeatureArrays } from './unzip.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
-import type { Observer } from 'rxjs';
 interface CoordRequest {
     chrId: number;
     start: number;
@@ -26,22 +25,14 @@ export declare class BlockView {
     private rTreePromise?;
     private featureCache;
     constructor(bbi: GenericFilehandle, refsByName: Record<string, number>, rTreeOffset: number, uncompressBufSize: number, blockType: string);
-    readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts?: Options): Promise<void>;
-    private parseSummaryBlock;
-    private parseBigBedBlock;
-    private parseBigWigBlock;
-    private parseBigWigBlockAsArrays;
-    readFeatures(observer: Observer<Feature[]>, blocks: {
+    private _collectBlocks;
+    readWigData(chrName: string, start: number, end: number, opts?: Options): Promise<Feature[]>;
+    readWigDataAsArrays(chrName: string, start: number, end: number, opts?: Options): Promise<BigWigFeatureArrays | SummaryFeatureArrays>;
+    readFeatures(blocks: {
         offset: number;
         length: number;
-    }[], opts?: Options): Promise<void>;
-    readBigWigFeaturesAsArrays(blocks: {
-        offset: number;
-        length: number;
-    }[], opts?: Options): Promise<BigWigFeatureArrays>;
-    readSummaryFeaturesAsArrays(blocks: {
-        offset: number;
-        length: number;
-    }[], opts?: Options): Promise<SummaryFeatureArrays>;
+    }[], opts?: Options): Promise<Feature[]>;
+    private _readBigWigFeaturesAsArrays;
+    private _readSummaryFeaturesAsArrays;
 }
 export {};