npm - @gmod/bbi - Versions diffs - 8.1.2 → 9.0.0 - Mend

@gmod/bbi 8.1.2 → 9.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (61) hide show

package/CHANGELOG.md +2 -0
package/README.md +0 -24
package/dist/array-feature-view.js.map +1 -1
package/dist/bbi.d.ts +5 -25
package/dist/bbi.js +31 -133
package/dist/bbi.js.map +1 -1
package/dist/bigbed.d.ts +0 -1
package/dist/bigbed.js +19 -51
package/dist/bigbed.js.map +1 -1
package/dist/bigwig.d.ts +1 -2
package/dist/bigwig.js +1 -2
package/dist/bigwig.js.map +1 -1
package/dist/block-view.d.ts +7 -16
package/dist/block-view.js +369 -443
package/dist/block-view.js.map +1 -1
package/dist/parse-bigwig.d.ts +2 -2
package/dist/parse-bigwig.js +5 -5
package/dist/parse-bigwig.js.map +1 -1
package/dist/range.d.ts +1 -15
package/dist/range.js +16 -49
package/dist/range.js.map +1 -1
package/dist/util.d.ts +0 -22
package/dist/util.js +0 -46
package/dist/util.js.map +1 -1
package/dist/wasm/inflate-wasm-inlined.js +1 -1
package/dist/wasm/inflate-wasm-inlined.js.map +1 -1
package/esm/array-feature-view.js.map +1 -1
package/esm/bbi.d.ts +5 -25
package/esm/bbi.js +31 -133
package/esm/bbi.js.map +1 -1
package/esm/bigbed.d.ts +0 -1
package/esm/bigbed.js +19 -50
package/esm/bigbed.js.map +1 -1
package/esm/bigwig.d.ts +1 -2
package/esm/bigwig.js +1 -2
package/esm/bigwig.js.map +1 -1
package/esm/block-view.d.ts +7 -16
package/esm/block-view.js +369 -443
package/esm/block-view.js.map +1 -1
package/esm/parse-bigwig.d.ts +2 -2
package/esm/parse-bigwig.js +5 -5
package/esm/parse-bigwig.js.map +1 -1
package/esm/range.d.ts +1 -15
package/esm/range.js +15 -48
package/esm/range.js.map +1 -1
package/esm/util.d.ts +0 -22
package/esm/util.js +0 -42
package/esm/util.js.map +1 -1
package/esm/wasm/inflate-wasm-inlined.js +1 -1
package/esm/wasm/inflate-wasm-inlined.js.map +1 -1
package/package.json +3 -6
package/src/array-feature-view.ts +4 -1
package/src/bbi.ts +50 -153
package/src/bigbed.ts +22 -55
package/src/bigwig.ts +1 -3
package/src/block-view.ts +525 -639
package/src/parse-bigwig.ts +7 -9
package/src/range.ts +19 -58
package/src/util.ts +0 -46
package/src/wasm/inflate-wasm-inlined.js +1 -1
package/src/wasm/inflate_wasm_bg.wasm +0 -0

package/dist/wasm/inflate-wasm-inlined.js.map CHANGED Viewed

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

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

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package/esm/bigbed.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 = [];
@@ -132,13 +125,8 @@ 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 +138,10 @@ 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 +170,13 @@ 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 +195,12 @@ 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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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