@gmod/bbi 4.0.6 → 5.0.0

package/CHANGELOG.md

@@ -1,9 +1,14 @@
-## [4.0.6](https://github.com/GMOD/bbi-js/compare/v4.0.5...v4.0.6) (2024-07-23)
+# [5.0.0](https://github.com/GMOD/bbi-js/compare/v4.0.6...v5.0.0) (2024-08-09)
+
 
 
+## [4.0.6](https://github.com/GMOD/bbi-js/compare/v4.0.5...v4.0.6) (2024-07-23)
+
+- Use renamed abortable-promise-cache -> @gmod/abortable-promise-cache
 
 ## [4.0.5](https://github.com/GMOD/bbi-js/compare/v4.0.4...v4.0.5) (2024-06-19)
 
+- Improved linting
 
 
 ## [4.0.4](https://github.com/GMOD/bbi-js/compare/v4.0.3...v4.0.4) (2024-3-5)

package/dist/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/dist/bbi.js

@@ -11,74 +11,15 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BBI = void 0;
 const buffer_1 = require("buffer");
-const binary_parser_1 = require("binary-parser");
 const generic_filehandle_1 = require("generic-filehandle");
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 const block_view_1 = require("./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 binary_parser_1.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 binary_parser_1.Parser()
-            .endianess(le)
-            .uint32('reductionLevel')
-            .uint32('reserved')
-            .uint64('dataOffset')
-            .uint64('indexOffset'),
-    });
-    const totalSummaryParser = new binary_parser_1.Parser()
-        .endianess(le)
-        .uint64('basesCovered')
-        .doublele('scoreMin')
-        .doublele('scoreMax')
-        .doublele('scoreSum')
-        .doublele('scoreSumSquares');
-    const chromTreeParser = new binary_parser_1.Parser()
-        .endianess(le)
-        .uint32('magic')
-        .uint32('blockSize')
-        .uint32('keySize')
-        .uint32('valSize')
-        .uint64('itemCount');
-    const isLeafNode = new binary_parser_1.Parser()
-        .endianess(le)
-        .uint8('isLeafNode')
-        .skip(1)
-        .uint16('cnt')
-        .saveOffset('offset');
-    return {
-        chromTreeParser,
-        totalSummaryParser,
-        headerParser,
-        isLeafNode,
-    };
-}
 class BBI {
     getHeader(opts) {
         if (!this.headerP) {
@@ -90,7 +31,8 @@ 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
      *
@@ -124,30 +66,101 @@ class BBI {
     }
     _getMainHeader(opts_1) {
         return __awaiter(this, arguments, void 0, function* (opts, requestSize = 2000) {
+            const le = true;
             const { buffer } = yield this.bbi.read(buffer_1.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 = Object.assign(Object.assign({}, 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 Object.assign(Object.assign({}, 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) {
@@ -165,43 +178,50 @@ class BBI {
     _readChromTree(header, opts) {
         return __awaiter(this, void 0, void 0, function* () {
             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 } = yield this.bbi.read(buffer_1.Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts);
-            const p = getParsers(isBE);
-            const { keySize } = p.chromTreeParser.parse(buffer);
-            const leafNodeParser = new binary_parser_1.Parser()
-                .endianess(le)
-                .string('key', { stripNull: true, length: keySize })
-                .uint32('refId')
-                .uint32('refSize')
-                .saveOffset('offset');
-            const nonleafNodeParser = new binary_parser_1.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 = (currentOffset) => __awaiter(this, void 0, void 0, function* () {
                 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;
@@ -210,10 +230,10 @@ 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)));
                     }
                     yield Promise.all(nextNodes);

package/dist/bbi.js.map

@@ -1 +1 @@
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package/dist/bigbed.js

@@ -26,11 +26,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigBed = void 0;
 exports.filterUndef = filterUndef;
 const buffer_1 = require("buffer");
-const binary_parser_1 = require("binary-parser");
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
+// locals
 const bbi_1 = require("./bbi");
 function filterUndef(ts) {
     return ts.filter((t) => !!t);
@@ -57,45 +57,52 @@ class BigBed extends bbi_1.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
      */
     _readIndices(opts) {
         return __awaiter(this, void 0, void 0, function* () {
             const { extHeaderOffset, isBigEndian } = yield this.getHeader(opts);
             const { buffer: data } = yield this.bbi.read(buffer_1.Buffer.alloc(64), 0, 64, Number(extHeaderOffset));
-            const le = isBigEndian ? 'big' : 'little';
-            const ret = new binary_parser_1.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 } = yield this.bbi.read(buffer_1.Buffer.alloc(len), 0, len, Number(offset));
-            const extParser = new binary_parser_1.Parser()
-                .endianess(le)
-                .int16('type')
-                .int16('fieldcount')
-                .uint64('offset')
-                .skip(4)
-                .int16('field');
+            const { buffer } = yield this.bbi.read(buffer_1.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
@@ -109,52 +116,48 @@ class BigBed extends bbi_1.BBI {
                 return [];
             }
             const locs = indices.map((index) => __awaiter(this, void 0, void 0, function* () {
-                const { offset, field } = index;
-                const { buffer: data } = yield this.bbi.read(buffer_1.Buffer.alloc(32), 0, 32, Number(offset), opts);
-                const le = isBigEndian ? 'big' : 'little';
-                const p = new binary_parser_1.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 binary_parser_1.Parser()
-                    .endianess(le)
-                    .int8('nodeType')
-                    .skip(1)
-                    .int16('cnt')
-                    .choice({
-                    tag: 'nodeType',
-                    choices: {
-                        0: new binary_parser_1.Parser().array('leafkeys', {
-                            length: 'cnt',
-                            type: new binary_parser_1.Parser()
-                                .endianess(le)
-                                .string('key', { length: keySize, stripNull: true })
-                                .uint64('offset'),
-                        }),
-                        1: new binary_parser_1.Parser().array('keys', {
-                            length: 'cnt',
-                            type: new binary_parser_1.Parser()
-                                .endianess(le)
-                                .string('key', { length: keySize, stripNull: true })
-                                .uint64('offset')
-                                .uint32('length')
-                                .uint32('reserved'),
-                        }),
-                    },
-                });
+                const { offset: offset2, field } = index;
+                const { buffer: data } = yield this.bbi.read(buffer_1.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 = (nodeOffset) => __awaiter(this, void 0, void 0, function* () {
                     const val = Number(nodeOffset);
                     const len = 4 + blockSize * (keySize + valSize);
                     const { buffer } = yield this.bbi.read(buffer_1.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);
                             }
@@ -162,15 +165,31 @@ class BigBed extends bbi_1.BBI {
                         }
                         return bptReadNode(lastOffset);
                     }
-                    for (const n of node.keys) {
-                        if (n.key === name) {
-                            return Object.assign(Object.assign({}, 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 Object.assign(Object.assign({}, n), { field });
+                            }
                         }
+                        return undefined;
                     }
-                    return undefined;
                 });
                 const rootNodeOffset = 32;
-                return bptReadNode(Number(offset) + rootNodeOffset);
+                return bptReadNode(offset2 + rootNodeOffset);
             }));
             return filterUndef(yield Promise.all(locs));
         });