@gmod/bbi 8.1.1 → 9.0.0

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 = [];
@@ -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

@@ -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 {};