@gmod/bbi 4.0.5 → 5.0.0

package/esm/bbi.d.ts

@@ -1,10 +1,18 @@
 import { GenericFilehandle } from 'generic-filehandle';
 import { Observable } from 'rxjs';
 import { BlockView } from './block-view';
+interface ZoomLevel {
+    reductionLevel: number;
+    reserved: number;
+    dataOffset: number;
+    indexOffset: number;
+}
 export interface Feature {
+    offset?: number;
+    chromId: number;
     start: number;
     end: number;
-    score: number;
+    score?: number;
     rest?: string;
     minScore?: number;
     maxScore?: number;
@@ -16,26 +24,34 @@ interface Statistics {
     scoreSum: number;
     basesCovered: number;
     scoreSumSquares: number;
+    scoreMin: number;
+    scoreMax: number;
 }
 interface RefInfo {
     name: string;
     id: number;
     length: number;
 }
-export interface Header {
+export interface MainHeader {
+    magic: number;
     version: number;
     autoSql: string;
     totalSummary: Statistics;
-    zoomLevels: any;
+    asOffset: number;
+    zoomLevels: ZoomLevel[];
+    fieldCount: number;
+    numZoomLevels: number;
     unzoomedIndexOffset: number;
+    totalSummaryOffset: number;
     unzoomedDataOffset: number;
     definedFieldCount: number;
     uncompressBufSize: number;
     chromTreeOffset: number;
-    fileSize: number;
     extHeaderOffset: number;
     isBigEndian: boolean;
     fileType: string;
+}
+export interface Header extends MainHeader {
     refsByName: Record<string, number>;
     refsByNumber: Record<number, RefInfo>;
 }

package/esm/bbi.js

@@ -1,72 +1,13 @@
 import { Buffer } from 'buffer';
-import { Parser } from 'binary-parser';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
 import { firstValueFrom, Observable } from 'rxjs';
 import { toArray } from 'rxjs/operators';
 import { BlockView } from './block-view';
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
-function toString(arr) {
+function myToString(arr) {
     return new TextDecoder().decode(arr);
 }
-/**
- * get the compiled parsers for different sections of the bigwig file
- *
- * @param isBE - is big endian, typically false
- * @return an object with compiled parsers
- */
-function getParsers(isBE) {
-    const le = isBE ? 'big' : 'little';
-    const headerParser = new Parser()
-        .endianess(le)
-        .int32('magic')
-        .uint16('version')
-        .uint16('numZoomLevels')
-        .uint64('chromTreeOffset')
-        .uint64('unzoomedDataOffset')
-        .uint64('unzoomedIndexOffset')
-        .uint16('fieldCount')
-        .uint16('definedFieldCount')
-        .uint64('asOffset') // autoSql offset, used in bigbed
-        .uint64('totalSummaryOffset')
-        .uint32('uncompressBufSize')
-        .uint64('extHeaderOffset') // name index offset, used in bigbed
-        .array('zoomLevels', {
-        length: 'numZoomLevels',
-        type: new Parser()
-            .endianess(le)
-            .uint32('reductionLevel')
-            .uint32('reserved')
-            .uint64('dataOffset')
-            .uint64('indexOffset'),
-    });
-    const totalSummaryParser = new Parser()
-        .endianess(le)
-        .uint64('basesCovered')
-        .doublele('scoreMin')
-        .doublele('scoreMax')
-        .doublele('scoreSum')
-        .doublele('scoreSumSquares');
-    const chromTreeParser = new Parser()
-        .endianess(le)
-        .uint32('magic')
-        .uint32('blockSize')
-        .uint32('keySize')
-        .uint32('valSize')
-        .uint64('itemCount');
-    const isLeafNode = new Parser()
-        .endianess(le)
-        .uint8('isLeafNode')
-        .skip(1)
-        .uint16('cnt')
-        .saveOffset('offset');
-    return {
-        chromTreeParser,
-        totalSummaryParser,
-        headerParser,
-        isLeafNode,
-    };
-}
 export class BBI {
     getHeader(opts) {
         if (!this.headerP) {
@@ -78,7 +19,8 @@ export class BBI {
         return this.headerP;
     }
     /*
-     * @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
+     * @param filehandle - a filehandle from generic-filehandle or implementing
+     * something similar to the node10 fs.promises API
      *
      * @param path - a Local file path as a string
      *
@@ -109,30 +51,101 @@ export class BBI {
         return { ...header, ...chroms };
     }
     async _getMainHeader(opts, requestSize = 2000) {
+        const le = true;
         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);
-        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 (asOffset) {
-            const off = Number(header.asOffset);
-            header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
+        const b = buffer;
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        let offset = 0;
+        const magic = dataView.getInt32(offset, le);
+        offset += 4;
+        const version = dataView.getUint16(offset, le);
+        offset += 2;
+        const numZoomLevels = dataView.getUint16(offset, le);
+        offset += 2;
+        const chromTreeOffset = Number(dataView.getBigUint64(offset, le));
+        offset += 8;
+        const unzoomedDataOffset = Number(dataView.getBigUint64(offset, le));
+        offset += 8;
+        const unzoomedIndexOffset = Number(dataView.getBigUint64(offset, le));
+        offset += 8;
+        const fieldCount = dataView.getUint16(offset, le);
+        offset += 2;
+        const definedFieldCount = dataView.getUint16(offset, le);
+        offset += 2;
+        const asOffset = Number(dataView.getBigUint64(offset, le));
+        offset += 8;
+        const totalSummaryOffset = Number(dataView.getBigUint64(offset, le));
+        offset += 8;
+        const uncompressBufSize = dataView.getUint32(offset, le);
+        offset += 4;
+        const extHeaderOffset = Number(dataView.getBigUint64(offset, le));
+        offset += 8;
+        const zoomLevels = [];
+        for (let i = 0; i < numZoomLevels; i++) {
+            const reductionLevel = dataView.getUint32(offset, le);
+            offset += 4;
+            const reserved = dataView.getUint32(offset, le);
+            offset += 4;
+            const dataOffset = Number(dataView.getBigUint64(offset, le));
+            offset += 8;
+            const indexOffset = Number(dataView.getBigUint64(offset, le));
+            offset += 8;
+            zoomLevels.push({ reductionLevel, reserved, dataOffset, indexOffset });
         }
+        const fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig';
         // refetch header if it is too large on first pass,
         // 8*5 is the sizeof the totalSummary struct
-        if (header.totalSummaryOffset > requestSize - 8 * 5) {
+        if (asOffset > requestSize || totalSummaryOffset > requestSize - 8 * 5) {
             return this._getMainHeader(opts, requestSize * 2);
         }
-        if (header.totalSummaryOffset) {
-            const tail = buffer.subarray(Number(header.totalSummaryOffset));
-            const sum = ret.totalSummaryParser.parse(tail);
-            header.totalSummary = { ...sum, basesCovered: Number(sum.basesCovered) };
+        let totalSummary;
+        if (totalSummaryOffset) {
+            const b = buffer.subarray(Number(totalSummaryOffset));
+            let offset = 0;
+            const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+            const basesCovered = Number(dataView.getBigUint64(offset, le));
+            offset += 8;
+            const scoreMin = dataView.getFloat64(offset, le);
+            offset += 8;
+            const scoreMax = dataView.getFloat64(offset, le);
+            offset += 8;
+            const scoreSum = dataView.getFloat64(offset, le);
+            offset += 8;
+            const scoreSumSquares = dataView.getFloat64(offset, le);
+            offset += 8;
+            totalSummary = {
+                scoreMin,
+                scoreMax,
+                scoreSum,
+                scoreSumSquares,
+                basesCovered,
+            };
         }
-        return { ...header, isBigEndian };
+        else {
+            throw new Error('no stats');
+        }
+        return {
+            zoomLevels,
+            magic,
+            extHeaderOffset,
+            numZoomLevels,
+            fieldCount,
+            totalSummary,
+            definedFieldCount,
+            uncompressBufSize,
+            asOffset,
+            chromTreeOffset,
+            totalSummaryOffset,
+            unzoomedDataOffset,
+            unzoomedIndexOffset,
+            fileType,
+            version,
+            isBigEndian,
+            autoSql: asOffset
+                ? myToString(buffer.subarray(asOffset, buffer.indexOf(0, asOffset)))
+                : '',
+        };
     }
     _isBigEndian(buffer) {
         let ret = buffer.readInt32LE(0);
@@ -148,43 +161,50 @@ export class BBI {
     // todo: add progress if long running
     async _readChromTree(header, opts) {
         const isBE = header.isBigEndian;
-        const le = isBE ? 'big' : 'little';
+        const le = !isBE;
         const refsByNumber = [];
         const refsByName = {};
-        let unzoomedDataOffset = Number(header.unzoomedDataOffset);
-        const chromTreeOffset = Number(header.chromTreeOffset);
+        let unzoomedDataOffset = header.unzoomedDataOffset;
+        const chromTreeOffset = header.chromTreeOffset;
         while (unzoomedDataOffset % 4 !== 0) {
             unzoomedDataOffset += 1;
         }
         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(buffer);
-        const leafNodeParser = new Parser()
-            .endianess(le)
-            .string('key', { stripNull: true, length: keySize })
-            .uint32('refId')
-            .uint32('refSize')
-            .saveOffset('offset');
-        const nonleafNodeParser = new Parser()
-            .endianess(le)
-            .skip(keySize)
-            .uint64('childOffset')
-            .saveOffset('offset');
+        const b = buffer;
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        let offset = 0;
+        //    const magic = dataView.getUint32(offset, le)
+        offset += 4;
+        //   const blockSize = dataView.getUint32(offset, le)
+        offset += 4;
+        const keySize = dataView.getUint32(offset, le);
+        offset += 4;
+        //  const valSize = dataView.getUint32(offset, le)
+        offset += 4;
+        // const itemCount = dataView.getBigUint64(offset, le)
+        offset += 8;
         const rootNodeOffset = 32;
         const bptReadNode = async (currentOffset) => {
             let offset = currentOffset;
             if (offset >= buffer.length) {
                 throw new Error('reading beyond end of buffer');
             }
-            const ret = p.isLeafNode.parse(buffer.subarray(offset));
-            const { isLeafNode, cnt } = ret;
-            offset += ret.offset;
+            const isLeafNode = dataView.getUint8(offset);
+            offset += 2; //skip 1
+            const cnt = dataView.getUint16(offset, le);
+            offset += 2;
             if (isLeafNode) {
-                for (let n = 0; n < cnt; n += 1) {
-                    const leafRet = leafNodeParser.parse(buffer.subarray(offset));
-                    offset += leafRet.offset;
-                    const { key, refId, refSize } = leafRet;
+                for (let n = 0; n < cnt; n++) {
+                    const key = buffer
+                        .subarray(offset, offset + keySize)
+                        .toString()
+                        .replaceAll('\0', '');
+                    offset += keySize;
+                    const refId = dataView.getUint32(offset, le);
+                    offset += 4;
+                    const refSize = dataView.getUint32(offset, le);
+                    offset += 4;
                     const refRec = { name: key, id: refId, length: refSize };
                     refsByName[this.renameRefSeqs(key)] = refId;
                     refsByNumber[refId] = refRec;
@@ -193,10 +213,10 @@ export class BBI {
             else {
                 // parse index node
                 const nextNodes = [];
-                for (let n = 0; n < cnt; n += 1) {
-                    const nonleafRet = nonleafNodeParser.parse(buffer.subarray(offset));
-                    const { childOffset } = nonleafRet;
-                    offset += nonleafRet.offset;
+                for (let n = 0; n < cnt; n++) {
+                    offset += keySize;
+                    const childOffset = Number(dataView.getBigUint64(offset, le));
+                    offset += 8;
                     nextNodes.push(bptReadNode(Number(childOffset) - Number(chromTreeOffset)));
                 }
                 await Promise.all(nextNodes);

package/esm/bbi.js.map

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

@@ -1,4 +1,4 @@
-import AbortablePromiseCache from 'abortable-promise-cache';
+import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import { BBI, Feature, RequestOptions } from './bbi';
 interface Index {
     type: number;

package/esm/bigbed.js

@@ -1,9 +1,9 @@
 import { Buffer } from 'buffer';
-import { Parser } from 'binary-parser';
 import { Observable, merge, firstValueFrom } from 'rxjs';
 import { map, reduce } from 'rxjs/operators';
-import AbortablePromiseCache from 'abortable-promise-cache';
+import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import QuickLRU from 'quick-lru';
+// locals
 import { BBI } from './bbi';
 export function filterUndef(ts) {
     return ts.filter((t) => !!t);
@@ -28,43 +28,50 @@ export class BigBed extends BBI {
     }
     /*
      * parse the bigbed extraIndex fields
-     * @param abortSignal to abort operation
-     * @return a Promise for an array of Index data structure since there can be multiple extraIndexes in a bigbed, see bedToBigBed documentation
+     *
+     *
+     * @return a Promise for an array of Index data structure since there can be
+     * multiple extraIndexes in a bigbed, see bedToBigBed documentation
      */
     async _readIndices(opts) {
         const { extHeaderOffset, isBigEndian } = await this.getHeader(opts);
         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);
-        const { count, offset } = ret;
+        const le = !isBigEndian;
+        const b = data;
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        let offset = 0;
+        // const _size = dataView.getUint16(offset, le)
+        offset += 2;
+        const count = dataView.getUint16(offset, le);
+        offset += 2;
+        const dataOffset = Number(dataView.getBigUint64(offset, le));
+        offset += 8;
         // no extra index is defined if count==0
         if (count === 0) {
             return [];
         }
         const blocklen = 20;
         const len = blocklen * count;
-        const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, Number(offset));
-        const extParser = new Parser()
-            .endianess(le)
-            .int16('type')
-            .int16('fieldcount')
-            .uint64('offset')
-            .skip(4)
-            .int16('field');
+        const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, Number(dataOffset));
         const indices = [];
         for (let i = 0; i < count; i += 1) {
-            indices.push(extParser.parse(buffer.subarray(i * blocklen)));
+            const b = buffer.subarray(i * blocklen);
+            const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+            let offset = 0;
+            const type = dataView.getInt16(offset, le);
+            offset += 2;
+            const fieldcount = dataView.getInt16(offset, le);
+            offset += 2;
+            const dataOffset = Number(dataView.getBigUint64(offset, le));
+            offset += 8 + 4; //4 skip
+            const field = dataView.getInt16(offset, le);
+            indices.push({ type, fieldcount, offset: Number(dataOffset), field });
         }
         return indices;
     }
     /*
-     * perform a search in the bigbed extraIndex to find which blocks in the bigbed data to look for the
-     * actual feature data
+     * perform a search in the bigbed extraIndex to find which blocks in the
+     * bigbed data to look for the actual feature data
      *
      * @param name - the name to search for
      * @param opts - a SearchOptions argument with optional signal
@@ -77,52 +84,48 @@ export class BigBed extends BBI {
             return [];
         }
         const locs = indices.map(async (index) => {
-            const { offset, field } = index;
-            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(le)
-                .int32('magic')
-                .int32('blockSize')
-                .int32('keySize')
-                .int32('valSize')
-                .uint64('itemCount');
-            const { blockSize, keySize, valSize } = p.parse(data);
-            // console.log({blockSize,keySize,valSize})
-            const bpt = new Parser()
-                .endianess(le)
-                .int8('nodeType')
-                .skip(1)
-                .int16('cnt')
-                .choice({
-                tag: 'nodeType',
-                choices: {
-                    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')
-                            .uint32('reserved'),
-                    }),
-                },
-            });
+            const { offset: offset2, field } = index;
+            const { buffer: data } = await this.bbi.read(Buffer.alloc(32), 0, 32, offset2, opts);
+            const le = !isBigEndian;
+            const b = data;
+            const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+            let offset = 0;
+            // const _magic = dataView.getInt32(offset, le)
+            offset += 4;
+            const blockSize = dataView.getInt32(offset, le);
+            offset += 4;
+            const keySize = dataView.getInt32(offset, le);
+            offset += 4;
+            const valSize = dataView.getInt32(offset, le);
+            offset += 4;
+            // const _itemCount = Number(dataView.getBigUint64(offset, le))
+            offset += 8;
             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, val, opts);
-                const node = bpt.parse(buffer);
-                if (node.leafkeys) {
-                    let lastOffset;
-                    for (const { key, offset } of node.leafkeys) {
+                const b = buffer;
+                const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+                let offset = 0;
+                const nodeType = dataView.getInt8(offset);
+                offset += 2; //skip 1
+                const cnt = dataView.getInt16(offset, le);
+                offset += 2;
+                const keys = [];
+                if (nodeType === 0) {
+                    const leafkeys = [];
+                    for (let i = 0; i < cnt; i++) {
+                        const key = b
+                            .subarray(offset, offset + keySize)
+                            .toString()
+                            .replaceAll('\0', '');
+                        offset += keySize;
+                        const dataOffset = Number(dataView.getBigUint64(offset, le));
+                        offset += 8;
+                        leafkeys.push({ key, offset: dataOffset });
+                    }
+                    let lastOffset = 0;
+                    for (const { key, offset } of leafkeys) {
                         if (name.localeCompare(key) < 0 && lastOffset) {
                             return bptReadNode(lastOffset);
                         }
@@ -130,15 +133,31 @@ export class BigBed extends BBI {
                     }
                     return bptReadNode(lastOffset);
                 }
-                for (const n of node.keys) {
-                    if (n.key === name) {
-                        return { ...n, field };
+                else if (nodeType === 1) {
+                    for (let i = 0; i < cnt; i++) {
+                        const key = b
+                            .subarray(offset, offset + keySize)
+                            .toString()
+                            .replaceAll('\0', '');
+                        offset += keySize;
+                        const dataOffset = Number(dataView.getBigUint64(offset, le));
+                        offset += 8;
+                        const length = dataView.getUint32(offset, le);
+                        offset += 4;
+                        const reserved = dataView.getUint32(offset, le);
+                        offset += 4;
+                        keys.push({ key, offset: dataOffset, length, reserved });
+                    }
+                    for (const n of keys) {
+                        if (n.key === name) {
+                            return { ...n, field };
+                        }
                     }
+                    return undefined;
                 }
-                return undefined;
             };
             const rootNodeOffset = 32;
-            return bptReadNode(Number(offset) + rootNodeOffset);
+            return bptReadNode(offset2 + rootNodeOffset);
         });
         return filterUndef(await Promise.all(locs));
     }