@gmod/bbi 5.0.1 → 6.0.0

package/CHANGELOG.md

@@ -1,3 +1,11 @@
+# [6.0.0](https://github.com/GMOD/bbi-js/compare/v5.0.2...v6.0.0) (2024-12-12)
+
+
+
+## [5.0.2](https://github.com/GMOD/bbi-js/compare/v5.0.1...v5.0.2) (2024-09-03)
+
+
+
 ## [5.0.1](https://github.com/GMOD/bbi-js/compare/v5.0.0...v5.0.1) (2024-08-09)
 
 

package/README.md

@@ -21,13 +21,13 @@ const file = new BigWig({
 })()
 ```
 
-If using remotely, you can use it in combination with generic-filehandle or your
-own implementation of something like generic-filehandle
-https://github.com/GMOD/generic-filehandle/
+If using remotely, you can use it in combination with generic-filehandle2 or
+your own implementation of something like generic-filehandle2
+https://github.com/GMOD/generic-filehandle2/
 
 ```typescript
 const { BigWig } = require('@gmod/bbi')
-const { RemoteFile } = require('generic-filehandle')
+const { RemoteFile } = require('generic-filehandle2')
 
 // if running in the browser or newer versions of node.js, RemoteFile will use
 // the the global fetch
@@ -57,7 +57,7 @@ Accepts an object containing either
 - url - path to a url
 - filehandle - a filehandle instance that you can implement as a custom class
   yourself. path and url are based on
-  https://www.npmjs.com/package/generic-filehandle but by implementing a class
+  https://www.npmjs.com/package/generic-filehandle2 but by implementing a class
   containing the Filehandle interface specified therein, you can pass it to this
   module
 

package/dist/bbi.d.ts

@@ -1,7 +1,7 @@
-import { GenericFilehandle } from 'generic-filehandle';
+import { GenericFilehandle } from 'generic-filehandle2';
 import { Observable } from 'rxjs';
 import { BlockView } from './block-view';
-interface ZoomLevel {
+export interface ZoomLevel {
     reductionLevel: number;
     reserved: number;
     dataOffset: number;
@@ -20,14 +20,14 @@ export interface Feature {
     uniqueId?: string;
     field?: number;
 }
-interface Statistics {
+export interface Statistics {
     scoreSum: number;
     basesCovered: number;
     scoreSumSquares: number;
     scoreMin: number;
     scoreMax: number;
 }
-interface RefInfo {
+export interface RefInfo {
     name: string;
     id: number;
     length: number;
@@ -48,7 +48,6 @@ export interface MainHeader {
     uncompressBufSize: number;
     chromTreeOffset: number;
     extHeaderOffset: number;
-    isBigEndian: boolean;
     fileType: string;
 }
 export interface Header extends MainHeader {
@@ -60,6 +59,10 @@ export interface RequestOptions {
     headers?: Record<string, string>;
     [key: string]: unknown;
 }
+export interface RequestOptions2 extends RequestOptions {
+    scale?: number;
+    basesPerSpan?: number;
+}
 export declare abstract class BBI {
     protected bbi: GenericFilehandle;
     private headerP?;
@@ -73,7 +76,6 @@ export declare abstract class BBI {
     });
     private _getHeader;
     private _getMainHeader;
-    private _isBigEndian;
     private _readChromTree;
     protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
     protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
@@ -81,17 +83,14 @@ export declare abstract class BBI {
      * Gets features from a BigWig file
      *
      * @param refName - The chromosome name
+     *
      * @param start - The start of a region
+     *
      * @param end - The end of a region
-     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+     *
+     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+     * or scale used to infer the zoomLevel to use
      */
-    getFeatureStream(refName: string, start: number, end: number, opts?: RequestOptions & {
-        scale?: number;
-        basesPerSpan?: number;
-    }): Promise<Observable<Feature[]>>;
-    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions & {
-        scale?: number;
-        basesPerSpan?: number;
-    }): Promise<Feature[]>;
+    getFeatureStream(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Observable<Feature[]>>;
+    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<Feature[]>;
 }
-export {};

package/dist/bbi.js

@@ -1,17 +1,7 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BBI = void 0;
-const buffer_1 = require("buffer");
-const generic_filehandle_1 = require("generic-filehandle");
+const generic_filehandle2_1 = require("generic-filehandle2");
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 const block_view_1 = require("./block-view");
@@ -20,7 +10,7 @@ const BIG_BED_MAGIC = -2021002517;
 class BBI {
     getHeader(opts) {
         if (!this.headerP) {
-            this.headerP = this._getHeader(opts).catch(e => {
+            this.headerP = this._getHeader(opts).catch((e) => {
                 this.headerP = undefined;
                 throw e;
             });
@@ -28,8 +18,7 @@ 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-filehandle2
      *
      * @param path - a Local file path as a string
      *
@@ -45,250 +34,236 @@ class BBI {
             this.bbi = filehandle;
         }
         else if (url) {
-            this.bbi = new generic_filehandle_1.RemoteFile(url);
+            this.bbi = new generic_filehandle2_1.RemoteFile(url);
         }
         else if (path) {
-            this.bbi = new generic_filehandle_1.LocalFile(path);
+            this.bbi = new generic_filehandle2_1.LocalFile(path);
         }
         else {
             throw new Error('no file given');
         }
     }
-    _getHeader(opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const header = yield this._getMainHeader(opts);
-            const chroms = yield this._readChromTree(header, opts);
-            return Object.assign(Object.assign({}, header), chroms);
-        });
+    async _getHeader(opts) {
+        const header = await this._getMainHeader(opts);
+        const chroms = await this._readChromTree(header, opts);
+        return {
+            ...header,
+            ...chroms,
+        };
     }
-    _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 b = buffer;
-            const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-            let offset = 0;
-            const magic = dataView.getInt32(offset, le);
+    async _getMainHeader(opts, requestSize = 2000) {
+        const b = await this.bbi.read(requestSize, 0, opts);
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        const r1 = dataView.getInt32(0, true);
+        if (r1 !== BIG_WIG_MAGIC && r1 !== BIG_BED_MAGIC) {
+            throw new Error('not a BigWig/BigBed file');
+        }
+        let offset = 0;
+        const magic = dataView.getInt32(offset, true);
+        offset += 4;
+        const version = dataView.getUint16(offset, true);
+        offset += 2;
+        const numZoomLevels = dataView.getUint16(offset, true);
+        offset += 2;
+        const chromTreeOffset = Number(dataView.getBigUint64(offset, true));
+        offset += 8;
+        const unzoomedDataOffset = Number(dataView.getBigUint64(offset, true));
+        offset += 8;
+        const unzoomedIndexOffset = Number(dataView.getBigUint64(offset, true));
+        offset += 8;
+        const fieldCount = dataView.getUint16(offset, true);
+        offset += 2;
+        const definedFieldCount = dataView.getUint16(offset, true);
+        offset += 2;
+        const asOffset = Number(dataView.getBigUint64(offset, true));
+        offset += 8;
+        const totalSummaryOffset = Number(dataView.getBigUint64(offset, true));
+        offset += 8;
+        const uncompressBufSize = dataView.getUint32(offset, true);
+        offset += 4;
+        const extHeaderOffset = Number(dataView.getBigUint64(offset, true));
+        offset += 8;
+        const zoomLevels = [];
+        for (let i = 0; i < numZoomLevels; i++) {
+            const reductionLevel = dataView.getUint32(offset, true);
             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));
+            const reserved = dataView.getUint32(offset, true);
+            offset += 4;
+            const dataOffset = Number(dataView.getBigUint64(offset, true));
             offset += 8;
-            const unzoomedDataOffset = Number(dataView.getBigUint64(offset, le));
+            const indexOffset = Number(dataView.getBigUint64(offset, true));
             offset += 8;
-            const unzoomedIndexOffset = Number(dataView.getBigUint64(offset, le));
+            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 (asOffset > requestSize || totalSummaryOffset > requestSize - 8 * 5) {
+            return this._getMainHeader(opts, requestSize * 2);
+        }
+        let totalSummary;
+        if (totalSummaryOffset) {
+            const b2 = b.subarray(Number(totalSummaryOffset));
+            let offset = 0;
+            const dataView = new DataView(b2.buffer, b2.byteOffset, b2.length);
+            const basesCovered = Number(dataView.getBigUint64(offset, true));
             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));
+            const scoreMin = dataView.getFloat64(offset, true);
             offset += 8;
-            const totalSummaryOffset = Number(dataView.getBigUint64(offset, le));
+            const scoreMax = dataView.getFloat64(offset, true);
             offset += 8;
-            const uncompressBufSize = dataView.getUint32(offset, le);
-            offset += 4;
-            const extHeaderOffset = Number(dataView.getBigUint64(offset, le));
+            const scoreSum = dataView.getFloat64(offset, true);
             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 (asOffset > requestSize || totalSummaryOffset > requestSize - 8 * 5) {
-                return this._getMainHeader(opts, requestSize * 2);
-            }
-            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,
-                };
-            }
-            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()
-                    : '',
+            const scoreSumSquares = dataView.getFloat64(offset, true);
+            offset += 8;
+            totalSummary = {
+                scoreMin,
+                scoreMax,
+                scoreSum,
+                scoreSumSquares,
+                basesCovered,
             };
-        });
-    }
-    _isBigEndian(buffer) {
-        let ret = buffer.readInt32LE(0);
-        if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
-            return false;
         }
-        ret = buffer.readInt32BE(0);
-        if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
-            return true;
+        else {
+            throw new Error('no stats');
         }
-        throw new Error('not a BigWig/BigBed file');
+        const decoder = new TextDecoder('utf8');
+        return {
+            zoomLevels,
+            magic,
+            extHeaderOffset,
+            numZoomLevels,
+            fieldCount,
+            totalSummary,
+            definedFieldCount,
+            uncompressBufSize,
+            asOffset,
+            chromTreeOffset,
+            totalSummaryOffset,
+            unzoomedDataOffset,
+            unzoomedIndexOffset,
+            fileType,
+            version,
+            autoSql: asOffset
+                ? decoder.decode(b.subarray(asOffset, b.indexOf(0, asOffset)))
+                : '',
+        };
     }
-    // todo: add progress if long running
-    _readChromTree(header, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const isBE = header.isBigEndian;
-            const le = !isBE;
-            const refsByNumber = [];
-            const refsByName = {};
-            let unzoomedDataOffset = header.unzoomedDataOffset;
-            const chromTreeOffset = header.chromTreeOffset;
-            while (unzoomedDataOffset % 4 !== 0) {
-                unzoomedDataOffset += 1;
+    async _readChromTree(header, opts) {
+        const refsByNumber = [];
+        const refsByName = {};
+        let unzoomedDataOffset = header.unzoomedDataOffset;
+        const chromTreeOffset = header.chromTreeOffset;
+        while (unzoomedDataOffset % 4 !== 0) {
+            unzoomedDataOffset += 1;
+        }
+        const off = unzoomedDataOffset - chromTreeOffset;
+        const b = await this.bbi.read(off, Number(chromTreeOffset), opts);
+        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        let offset = 0;
+        //    const magic = dataView.getUint32(offset, true)
+        offset += 4;
+        //   const blockSize = dataView.getUint32(offset, true)
+        offset += 4;
+        const keySize = dataView.getUint32(offset, true);
+        offset += 4;
+        //  const valSize = dataView.getUint32(offset, true)
+        offset += 4;
+        // const itemCount = dataView.getBigUint64(offset, true)
+        offset += 8;
+        const rootNodeOffset = 32;
+        const decoder = new TextDecoder('utf8');
+        const bptReadNode = async (currentOffset) => {
+            let offset = currentOffset;
+            if (offset >= b.length) {
+                throw new Error('reading beyond end of buffer');
             }
-            const off = unzoomedDataOffset - chromTreeOffset;
-            const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts);
-            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 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++) {
-                        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;
-                    }
+            const isLeafNode = dataView.getUint8(offset);
+            offset += 2; //skip 1
+            const cnt = dataView.getUint16(offset, true);
+            offset += 2;
+            if (isLeafNode) {
+                for (let n = 0; n < cnt; n++) {
+                    const key = decoder
+                        .decode(b.subarray(offset, offset + keySize))
+                        .replaceAll('\0', '');
+                    offset += keySize;
+                    const refId = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const refSize = dataView.getUint32(offset, true);
+                    offset += 4;
+                    refsByName[this.renameRefSeqs(key)] = refId;
+                    refsByNumber[refId] = {
+                        name: key,
+                        id: refId,
+                        length: refSize,
+                    };
                 }
-                else {
-                    // parse index node
-                    const nextNodes = [];
-                    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);
+            }
+            else {
+                // parse index node
+                const nextNodes = [];
+                for (let n = 0; n < cnt; n++) {
+                    offset += keySize;
+                    const childOffset = Number(dataView.getBigUint64(offset, true));
+                    offset += 8;
+                    nextNodes.push(bptReadNode(Number(childOffset) - Number(chromTreeOffset)));
                 }
-            });
-            yield bptReadNode(rootNodeOffset);
-            return {
-                refsByName,
-                refsByNumber,
-            };
-        });
+                await Promise.all(nextNodes);
+            }
+        };
+        await bptReadNode(rootNodeOffset);
+        return {
+            refsByName,
+            refsByNumber,
+        };
     }
     /*
      * fetches the "unzoomed" view of the bigwig data. this is the default for bigbed
      * @param abortSignal - a signal to optionally abort this operation
      */
-    getUnzoomedView(opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const { unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType, } = yield this.getHeader(opts);
-            return new block_view_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
-        });
+    async getUnzoomedView(opts) {
+        const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } = await this.getHeader(opts);
+        return new block_view_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize > 0, fileType);
     }
     /**
      * Gets features from a BigWig file
      *
      * @param refName - The chromosome name
+     *
      * @param start - The start of a region
+     *
      * @param end - The end of a region
-     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+     *
+     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+     * or scale used to infer the zoomLevel to use
      */
-    getFeatureStream(refName, start, end, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            yield this.getHeader(opts);
-            const chrName = this.renameRefSeqs(refName);
-            let view;
-            const { basesPerSpan, scale } = opts || {};
-            if (basesPerSpan) {
-                view = yield this.getView(1 / basesPerSpan, opts);
-            }
-            else if (scale) {
-                view = yield this.getView(scale, opts);
-            }
-            else {
-                view = yield this.getView(1, opts);
-            }
-            return new rxjs_1.Observable(observer => {
-                view
-                    .readWigData(chrName, start, end, observer, opts)
-                    .catch(e => observer.error(e));
+    async getFeatureStream(refName, start, end, opts) {
+        await this.getHeader(opts);
+        const chrName = this.renameRefSeqs(refName);
+        let view;
+        const { basesPerSpan, scale } = opts || {};
+        if (basesPerSpan) {
+            view = await this.getView(1 / basesPerSpan, opts);
+        }
+        else if (scale) {
+            view = await this.getView(scale, opts);
+        }
+        else {
+            view = await this.getView(1, opts);
+        }
+        return new rxjs_1.Observable(observer => {
+            view
+                .readWigData(chrName, start, end, observer, opts)
+                .catch((e) => {
+                observer.error(e);
             });
         });
     }
-    getFeatures(refName, start, end, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const ob = yield this.getFeatureStream(refName, start, end, opts);
-            const ret = yield (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
-            return ret.flat();
-        });
+    async getFeatures(refName, start, end, opts) {
+        const ob = await this.getFeatureStream(refName, start, end, opts);
+        const ret = await (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
+        return ret.flat();
     }
 }
 exports.BBI = BBI;