@gmod/bbi 1.0.35 → 2.0.2

package/esm/bbi.js

@@ -1,9 +1,7 @@
-import { Parser } from '@gmod/binary-parser';
+import { Parser } from 'binary-parser';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
 import { Observable } from 'rxjs';
 import { reduce } from 'rxjs/operators';
-import AbortablePromiseCache from 'abortable-promise-cache';
-import QuickLRU from 'quick-lru';
 import { BlockView } from './blockView';
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
@@ -31,6 +29,7 @@ function getParsers(isBE) {
         .array('zoomLevels', {
         length: 'numZoomLevels',
         type: new Parser()
+            .endianess(le)
             .uint32('reductionLevel')
             .uint32('reserved')
             .uint64('dataOffset')
@@ -39,10 +38,10 @@ function getParsers(isBE) {
     const totalSummaryParser = new Parser()
         .endianess(le)
         .uint64('basesCovered')
-        .double('scoreMin')
-        .double('scoreMax')
-        .double('scoreSum')
-        .double('scoreSumSquares');
+        .doublele('scoreMin')
+        .doublele('scoreMax')
+        .doublele('scoreSum')
+        .doublele('scoreSumSquares');
     const chromTreeParser = new Parser()
         .endianess(le)
         .uint32('magic')
@@ -54,7 +53,8 @@ function getParsers(isBE) {
         .endianess(le)
         .uint8('isLeafNode')
         .skip(1)
-        .uint16('cnt');
+        .uint16('cnt')
+        .saveOffset('offset');
     return {
         chromTreeParser,
         totalSummaryParser,
@@ -70,14 +70,8 @@ export class BBI {
      * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
      */
     constructor(options = {}) {
-        this.headerCache = new AbortablePromiseCache({
-            cache: new QuickLRU({ maxSize: 1 }),
-            fill: async (params, signal) => {
-                return this._getHeader({ ...params, signal });
-            },
-        });
-        const { filehandle, renameRefSeqs, path, url } = options;
-        this.renameRefSeqs = renameRefSeqs || ((s) => s);
+        const { filehandle, renameRefSeqs = s => s, path, url } = options;
+        this.renameRefSeqs = renameRefSeqs;
         if (filehandle) {
             this.bbi = filehandle;
         }
@@ -97,7 +91,13 @@ export class BBI {
      */
     getHeader(opts = {}) {
         const options = 'aborted' in opts ? { signal: opts } : opts;
-        return this.headerCache.get(JSON.stringify(options), options, options.signal);
+        if (!this.headerP) {
+            this.headerP = this._getHeader(options).catch(e => {
+                this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
     }
     async _getHeader(opts) {
         const header = await this._getMainHeader(opts);
@@ -108,23 +108,25 @@ export class BBI {
         const { buffer } = await this.bbi.read(Buffer.alloc(requestSize), 0, requestSize, 0, opts);
         const isBigEndian = this._isBigEndian(buffer);
         const ret = getParsers(isBigEndian);
-        const header = ret.headerParser.parse(buffer).result;
-        header.fileType = header.magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig';
-        if (header.asOffset > requestSize ||
-            header.totalSummaryOffset > requestSize) {
+        const header = ret.headerParser.parse(buffer);
+        const { magic, asOffset, totalSummaryOffset } = header;
+        header.fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig';
+        if (asOffset > requestSize || totalSummaryOffset > requestSize) {
             return this._getMainHeader(opts, requestSize * 2);
         }
-        if (header.asOffset) {
+        if (asOffset) {
+            const off = Number(header.asOffset);
             header.autoSql = buffer
-                .slice(header.asOffset, buffer.indexOf(0, header.asOffset))
+                .subarray(off, buffer.indexOf(0, off))
                 .toString('utf8');
         }
         if (header.totalSummaryOffset > requestSize) {
             return this._getMainHeader(opts, requestSize * 2);
         }
         if (header.totalSummaryOffset) {
-            const tail = buffer.slice(header.totalSummaryOffset);
-            header.totalSummary = ret.totalSummaryParser.parse(tail).result;
+            const tail = buffer.subarray(Number(header.totalSummaryOffset));
+            const sum = ret.totalSummaryParser.parse(tail);
+            header.totalSummary = { ...sum, basesCovered: Number(sum.basesCovered) };
         }
         return { ...header, isBigEndian };
     }
@@ -145,37 +147,40 @@ export class BBI {
         const le = isBE ? 'big' : 'little';
         const refsByNumber = [];
         const refsByName = {};
-        const { chromTreeOffset } = header;
-        let { unzoomedDataOffset } = header;
+        let unzoomedDataOffset = Number(header.unzoomedDataOffset);
+        const chromTreeOffset = Number(header.chromTreeOffset);
         while (unzoomedDataOffset % 4 !== 0) {
             unzoomedDataOffset += 1;
         }
-        const { buffer: data } = await this.bbi.read(Buffer.alloc(unzoomedDataOffset - chromTreeOffset), 0, unzoomedDataOffset - chromTreeOffset, chromTreeOffset, opts);
+        const off = unzoomedDataOffset - chromTreeOffset;
+        const { buffer } = await this.bbi.read(Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts);
         const p = getParsers(isBE);
-        const { keySize } = p.chromTreeParser.parse(data).result;
+        const { keySize } = p.chromTreeParser.parse(buffer);
         const leafNodeParser = new Parser()
             .endianess(le)
             .string('key', { stripNull: true, length: keySize })
             .uint32('refId')
-            .uint32('refSize');
+            .uint32('refSize')
+            .saveOffset('offset');
         const nonleafNodeParser = new Parser()
             .endianess(le)
             .skip(keySize)
-            .uint64('childOffset');
+            .uint64('childOffset')
+            .saveOffset('offset');
         const rootNodeOffset = 32;
         const bptReadNode = async (currentOffset) => {
             let offset = currentOffset;
-            if (offset >= data.length) {
+            if (offset >= buffer.length) {
                 throw new Error('reading beyond end of buffer');
             }
-            const ret = p.isLeafNode.parse(data.slice(offset));
-            const { isLeafNode, cnt } = ret.result;
+            const ret = p.isLeafNode.parse(buffer.subarray(offset));
+            const { isLeafNode, cnt } = ret;
             offset += ret.offset;
             if (isLeafNode) {
                 for (let n = 0; n < cnt; n += 1) {
-                    const leafRet = leafNodeParser.parse(data.slice(offset));
+                    const leafRet = leafNodeParser.parse(buffer.subarray(offset));
                     offset += leafRet.offset;
-                    const { key, refId, refSize } = leafRet.result;
+                    const { key, refId, refSize } = leafRet;
                     const refRec = { name: key, id: refId, length: refSize };
                     refsByName[this.renameRefSeqs(key)] = refId;
                     refsByNumber[refId] = refRec;
@@ -185,11 +190,10 @@ export class BBI {
                 // parse index node
                 const nextNodes = [];
                 for (let n = 0; n < cnt; n += 1) {
-                    const nonleafRet = nonleafNodeParser.parse(data.slice(offset));
-                    let { childOffset } = nonleafRet.result;
+                    const nonleafRet = nonleafNodeParser.parse(buffer.subarray(offset));
+                    const { childOffset } = nonleafRet;
                     offset += nonleafRet.offset;
-                    childOffset -= chromTreeOffset;
-                    nextNodes.push(bptReadNode(childOffset));
+                    nextNodes.push(bptReadNode(Number(childOffset) - Number(chromTreeOffset)));
                 }
                 await Promise.all(nextNodes);
             }
@@ -205,10 +209,8 @@ export class BBI {
      * @param abortSignal - a signal to optionally abort this operation
      */
     async getUnzoomedView(opts) {
-        const { unzoomedIndexOffset, zoomLevels, refsByName, uncompressBufSize, isBigEndian, fileType, } = await this.getHeader(opts);
-        const nzl = zoomLevels[0];
-        const cirLen = nzl ? nzl.dataOffset - unzoomedIndexOffset : 4000;
-        return new BlockView(this.bbi, refsByName, unzoomedIndexOffset, cirLen, isBigEndian, uncompressBufSize > 0, fileType);
+        const { unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType, } = await this.getHeader(opts);
+        return new BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
     }
     /**
      * Gets features from a BigWig file

package/esm/bbi.js.map

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package/esm/bigbed.d.ts

@@ -3,9 +3,8 @@ import { BlockView } from './blockView';
 export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
 export declare class BigBed extends BBI {
     readIndicesCache: any;
-    constructor(opts?: any);
     readIndices(opts?: AbortSignal | RequestOptions): any;
-    protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
+    protected getView(_scale: number, opts: RequestOptions): Promise<BlockView>;
     private _readIndices;
     private searchExtraIndexBlocks;
     searchExtraIndex(name: string, opts?: RequestOptions): Promise<Feature[]>;

package/esm/bigbed.js

@@ -1,4 +1,4 @@
-import { Parser } from '@gmod/binary-parser';
+import { Parser } from 'binary-parser';
 import { Observable, merge } from 'rxjs';
 import { map, reduce } from 'rxjs/operators';
 import AbortablePromiseCache from 'abortable-promise-cache';
@@ -8,8 +8,8 @@ export function filterUndef(ts) {
     return ts.filter((t) => !!t);
 }
 export class BigBed extends BBI {
-    constructor(opts) {
-        super(opts);
+    constructor() {
+        super(...arguments);
         this.readIndicesCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 1 }),
             fill: async (args, signal) => {
@@ -27,7 +27,7 @@ export class BigBed extends BBI {
      * @param abortSignal - an optional AbortSignal to kill operation
      * @return promise for a BlockView
      */
-    async getView(scale, opts) {
+    async getView(_scale, opts) {
         return this.getUnzoomedView(opts);
     }
     /*
@@ -37,14 +37,14 @@ export class BigBed extends BBI {
      */
     async _readIndices(opts) {
         const { extHeaderOffset, isBigEndian } = await this.getHeader(opts);
-        const { buffer: data } = await this.bbi.read(Buffer.alloc(64), 0, 64, extHeaderOffset);
+        const { buffer: data } = await this.bbi.read(Buffer.alloc(64), 0, 64, Number(extHeaderOffset));
         const le = isBigEndian ? 'big' : 'little';
         const ret = new Parser()
             .endianess(le)
             .uint16('size')
             .uint16('count')
             .uint64('offset')
-            .parse(data).result;
+            .parse(data);
         const { count, offset } = ret;
         // no extra index is defined if count==0
         if (count === 0) {
@@ -52,7 +52,7 @@ export class BigBed extends BBI {
         }
         const blocklen = 20;
         const len = blocklen * count;
-        const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, offset);
+        const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, Number(offset));
         const extParser = new Parser()
             .endianess(le)
             .int16('type')
@@ -62,7 +62,7 @@ export class BigBed extends BBI {
             .int16('field');
         const indices = [];
         for (let i = 0; i < count; i += 1) {
-            indices.push(extParser.parse(buffer.slice(i * blocklen)).result);
+            indices.push(extParser.parse(buffer.subarray(i * blocklen)));
         }
         return indices;
     }
@@ -82,17 +82,19 @@ export class BigBed extends BBI {
         }
         const locs = indices.map(async (index) => {
             const { offset, field } = index;
-            const { buffer: data } = await this.bbi.read(Buffer.alloc(32), 0, 32, offset, opts);
+            const { buffer: data } = await this.bbi.read(Buffer.alloc(32), 0, 32, Number(offset), opts);
+            const le = isBigEndian ? 'big' : 'little';
             const p = new Parser()
-                .endianess(isBigEndian ? 'big' : 'little')
+                .endianess(le)
                 .int32('magic')
                 .int32('blockSize')
                 .int32('keySize')
                 .int32('valSize')
                 .uint64('itemCount');
-            const { blockSize, keySize, valSize } = p.parse(data).result;
+            const { blockSize, keySize, valSize } = p.parse(data);
+            // console.log({blockSize,keySize,valSize})
             const bpt = new Parser()
-                .endianess(isBigEndian ? 'big' : 'little')
+                .endianess(le)
                 .int8('nodeType')
                 .skip(1)
                 .int16('cnt')
@@ -102,12 +104,14 @@ export class BigBed extends BBI {
                     0: new Parser().array('leafkeys', {
                         length: 'cnt',
                         type: new Parser()
+                            .endianess(le)
                             .string('key', { length: keySize, stripNull: true })
                             .uint64('offset'),
                     }),
                     1: new Parser().array('keys', {
                         length: 'cnt',
                         type: new Parser()
+                            .endianess(le)
                             .string('key', { length: keySize, stripNull: true })
                             .uint64('offset')
                             .uint32('length')
@@ -116,9 +120,10 @@ export class BigBed extends BBI {
                 },
             });
             const bptReadNode = async (nodeOffset) => {
+                const val = Number(nodeOffset);
                 const len = 4 + blockSize * (keySize + valSize);
-                const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, nodeOffset, opts);
-                const node = bpt.parse(buffer).result;
+                const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, val, opts);
+                const node = bpt.parse(buffer);
                 if (node.leafkeys) {
                     let lastOffset;
                     for (let i = 0; i < node.leafkeys.length; i += 1) {
@@ -138,7 +143,7 @@ export class BigBed extends BBI {
                 return undefined;
             };
             const rootNodeOffset = 32;
-            return bptReadNode(offset + rootNodeOffset);
+            return bptReadNode(Number(offset) + rootNodeOffset);
         });
         return filterUndef(await Promise.all(locs));
     }
@@ -157,7 +162,7 @@ export class BigBed extends BBI {
         }
         const view = await this.getUnzoomedView(opts);
         const res = blocks.map(block => {
-            return new Observable((observer) => {
+            return new Observable(observer => {
                 view.readFeatures(observer, [block], opts);
             }).pipe(reduce((acc, curr) => acc.concat(curr)), map(x => {
                 for (let i = 0; i < x.length; i += 1) {
@@ -167,9 +172,7 @@ export class BigBed extends BBI {
             }));
         });
         const ret = await merge(...res).toPromise();
-        return ret.filter((f) => {
-            return f.rest.split('\t')[f.field - 3] === name;
-        });
+        return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
     }
 }
 //# sourceMappingURL=bigbed.js.map

package/esm/bigbed.js.map

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

@@ -4,9 +4,7 @@ export declare class BigWig extends BBI {
     /**
      * Retrieves a BlockView of a specific zoomLevel
      *
-     * @param refName - The chromosome name
-     * @param start - The start of a region
-     * @param end - The end of a region
+     * @param scale - number
      * @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>;

package/esm/bigwig.js

@@ -4,9 +4,7 @@ export class BigWig extends BBI {
     /**
      * Retrieves a BlockView of a specific zoomLevel
      *
-     * @param refName - The chromosome name
-     * @param start - The start of a region
-     * @param end - The end of a region
+     * @param scale - number
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
      */
     async getView(scale, opts) {
@@ -20,10 +18,8 @@ export class BigWig extends BBI {
         for (let i = maxLevel; i >= 0; i -= 1) {
             const zh = zoomLevels[i];
             if (zh && zh.reductionLevel <= 2 * basesPerPx) {
-                const indexLength = i < zoomLevels.length - 1
-                    ? zoomLevels[i + 1].dataOffset - zh.indexOffset
-                    : fileSize - 4 - zh.indexOffset;
-                return new BlockView(this.bbi, refsByName, zh.indexOffset, indexLength, isBigEndian, uncompressBufSize > 0, 'summary');
+                const indexOffset = Number(zh.indexOffset);
+                return new BlockView(this.bbi, refsByName, indexOffset, isBigEndian, uncompressBufSize > 0, '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,SAAS,EAAE,MAAM,aAAa,CAAA;AACvC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CACrB,KAAa,EACb,IAAoB;QAEpB,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;QAChC,IAAI,CAAC,QAAQ,EAAE;YACb,4EAA4E;YAC5E,QAAQ,IAAI,CAAC,CAAA;SACd;QAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;YACrC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;gBAC7C,MAAM,WAAW,GACf,CAAC,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC;oBACvB,CAAC,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,GAAG,EAAE,CAAC,WAAW;oBAC/C,CAAC,CAAC,QAAQ,GAAG,CAAC,GAAG,EAAE,CAAC,WAAW,CAAA;gBACnC,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;aACF;SACF;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,SAAS,EAAE,MAAM,aAAa,CAAA;AACvC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;OAKG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;QAChC,IAAI,CAAC,QAAQ,EAAE;YACb,4EAA4E;YAC5E,QAAQ,IAAI,CAAC,CAAA;SACd;QAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;YACrC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;gBAC7C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;gBAE1C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;aACF;SACF;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}

package/esm/blockView.d.ts

@@ -18,25 +18,24 @@ interface Options {
  * @constructs
  */
 export declare class BlockView {
-    private cirTreeOffset;
-    private cirTreeLength;
     private bbi;
-    private isCompressed;
-    private isBigEndian;
     private refsByName;
+    private cirTreeOffset;
+    private isBigEndian;
+    private isCompressed;
     private blockType;
     private cirTreePromise?;
     private featureCache;
     private leafParser;
-    private bigWigParser;
     private bigBedParser;
-    private summaryParser;
-    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, cirTreeLength: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
+    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
     readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts: Options): Promise<void>;
     private parseSummaryBlock;
     private parseBigBedBlock;
     private parseBigWigBlock;
-    private static coordFilter;
-    readFeatures(observer: Observer<Feature[]>, blocks: any, opts?: Options): Promise<void>;
+    readFeatures(observer: Observer<Feature[]>, blocks: {
+        offset: bigint;
+        length: bigint;
+    }[], opts?: Options): Promise<void>;
 }
 export {};