@gmod/bbi 4.0.6 → 5.0.1

package/dist/util.d.ts

@@ -2,22 +2,19 @@ export declare class AbortError extends Error {
     code: string;
     constructor(message: string);
 }
-export declare function groupBlocks(blocks: {
-    offset: bigint;
-    length: bigint;
-}[]): {
-    blocks: {
-        offset: bigint;
-        length: bigint;
-    }[];
-    length: bigint;
-    offset: bigint;
+interface Block {
+    offset: number;
+    length: number;
+}
+export declare function groupBlocks(blocks: Block[]): {
+    blocks: Block[];
+    length: number;
+    offset: number;
 }[];
 /**
- * Properly check if the given AbortSignal is aborted.
- * Per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
+ * Properly check if the given AbortSignal is aborted. Per the standard, if the
+ * signal reads as aborted, this function throws either a DOMException
+ * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
  *
  * For convenience, passing `undefined` is a no-op
  *
@@ -32,3 +29,4 @@ export declare function checkAbortSignal(signal?: AbortSignal): void;
  * @param {AbortSignal} signal
  */
 export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
+export {};

package/dist/util.js

@@ -23,18 +23,14 @@ exports.AbortError = AbortError;
 // sort blocks by file offset and
 // group blocks that are within 2KB of eachother
 function groupBlocks(blocks) {
-    blocks.sort((b0, b1) => Number(b0.offset) - Number(b1.offset));
+    blocks.sort((b0, b1) => b0.offset - b1.offset);
     const blockGroups = [];
     let lastBlock;
     let lastBlockEnd;
     for (const block of blocks) {
-        if (lastBlock &&
-            lastBlockEnd &&
-            Number(block.offset) - lastBlockEnd <= 2000) {
-            lastBlock.length = BigInt(Number(lastBlock.length) +
-                Number(block.length) -
-                lastBlockEnd +
-                Number(block.offset));
+        if (lastBlock && lastBlockEnd && block.offset - lastBlockEnd <= 2000) {
+            lastBlock.length =
+                lastBlock.length + block.length - lastBlockEnd + block.offset;
             lastBlock.blocks.push(block);
         }
         else {
@@ -44,15 +40,14 @@ function groupBlocks(blocks) {
                 offset: block.offset,
             }));
         }
-        lastBlockEnd = Number(lastBlock.offset) + Number(lastBlock.length);
+        lastBlockEnd = lastBlock.offset + lastBlock.length;
     }
     return blockGroups;
 }
 /**
- * Properly check if the given AbortSignal is aborted.
- * Per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
+ * Properly check if the given AbortSignal is aborted. Per the standard, if the
+ * signal reads as aborted, this function throws either a DOMException
+ * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
  *
  * For convenience, passing `undefined` is a no-op
  *
@@ -64,7 +59,6 @@ function checkAbortSignal(signal) {
         return;
     }
     if (signal.aborted) {
-        // console.log('bam aborted!')
         if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;AAeA,kCAwBC;AAYD,4CAcC;AAQD,0CAGC;AA5ED,MAAa,UAAW,SAAQ,KAAK;IAGnC,YAAmB,OAAe;QAChC,KAAK,CAAC,OAAO,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,GAAG,aAAa,CAAA;IAC3B,CAAC;CACF;AAPD,gCAOC;AAMD,iCAAiC;AACjC,gDAAgD;AAChD,SAAgB,WAAW,CAAC,MAAe;IACzC,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,CAAA;IAE9C,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,IAAI,SAAoD,CAAA;IACxD,IAAI,YAAgC,CAAA;IACpC,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,SAAS,IAAI,YAAY,IAAI,KAAK,CAAC,MAAM,GAAG,YAAY,IAAI,IAAI,EAAE,CAAC;YACrE,SAAS,CAAC,MAAM;gBACd,SAAS,CAAC,MAAM,GAAG,KAAK,CAAC,MAAM,GAAG,YAAY,GAAG,KAAK,CAAC,MAAM,CAAA;YAC/D,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC9B,CAAC;aAAM,CAAC;YACN,WAAW,CAAC,IAAI,CACd,CAAC,SAAS,GAAG;gBACX,MAAM,EAAE,CAAC,KAAK,CAAC;gBACf,MAAM,EAAE,KAAK,CAAC,MAAM;gBACpB,MAAM,EAAE,KAAK,CAAC,MAAM;aACrB,CAAC,CACH,CAAA;QACH,CAAC;QACD,YAAY,GAAG,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACpD,CAAC;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAED;;;;;;;;;GASG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA"}

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 +1,10 @@
 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) {
-    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 +16,8 @@ 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 +48,101 @@ 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
+                ? buffer.subarray(asOffset, buffer.indexOf(0, asOffset)).toString()
+                : '',
+        };
     }
     _isBigEndian(buffer) {
         let ret = buffer.readInt32LE(0);
@@ -148,43 +158,50 @@ 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 +210,10 @@ 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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